Evolutionary time

@article{doi101007bf00137351,
    author = "Gould, Stephen Jay",
    title = "Dollo on Dollo's law: Irreversibility and the status of evolutionary laws",
    year = "1970",
    journal = "Journal of the History of Biology",
    url = "https://doi.org/10.1007/bf00137351",
    doi = "10.1007/bf00137351",
    openalex = "W1971035778"
}

@article{openalexw2145250129,
    author = "Valen, Leigh Van",
    title = "A NEW EVOLUTIONARY LAW.",
    year = "1973",
    journal = "Medical Entomology and Zoology",
    openalex = "W2145250129"
}

Rarefaction analysis of extinctions in the Late Permian indicates that as many as 96 percent of all marine species may have died out, thus forcing the marine biosphere to pass through a small bottleneck. With such severity of extinction, chance elimination of certain biologic groups would have been probable. Some of the changes in biologic composition observed at the Permo-Triassic boundary may be explained as an evolutionary founder effect that followed the bottleneck.

@article{doi101126science2064415217,
    author = "Raup, David M.",
    title = "Size of the Permo-Triassic Bottleneck and Its Evolutionary Implications",
    year = "1979",
    journal = "Science",
    abstract = "Rarefaction analysis of extinctions in the Late Permian indicates that as many as 96 percent of all marine species may have died out, thus forcing the marine biosphere to pass through a small bottleneck. With such severity of extinction, chance elimination of certain biologic groups would have been probable. Some of the changes in biologic composition observed at the Permo-Triassic boundary may be explained as an evolutionary founder effect that followed the bottleneck.",
    url = "https://doi.org/10.1126/science.206.4415.217",
    doi = "10.1126/science.206.4415.217",
    openalex = "W2067885793",
    references = "doi101017s0094837300002633, doi101017s0094837300004917, doi101017s0094837300005972, doi101017s0094837300006539, doi101086282541, doi101086282781, doi101098rstb19250002, doi101126science17740541065, doi101126science2034379458, doi1023071934145, doi105281zenodo16226412, valentine1978a"
}

@article{doi101007bf01734359,
    author = "Felsenstein, Joseph",
    title = "Evolutionary trees from DNA sequences: A maximum likelihood approach",
    year = "1981",
    journal = "Journal of Molecular Evolution",
    url = "https://doi.org/10.1007/bf01734359",
    doi = "10.1007/bf01734359",
    openalex = "W2102424972",
    references = "doi101007bf01659159, doi101007bf01797451, doi101093sysbio223240, doi101093sysbio274401, doi101111j155856461965tb01722x, doi101111j251761611977tb01600x, doi101126science1553760279, doi101159000152448, doi1023072412810, doi1023072412923, openalexw2341059552, openalexw3141390961"
}

@article{doi1023074581,
    author = "Ormond, Rupert and Krebs, J. R. and Davies, Nigel",
    title = "Behavioural Ecology: An Evolutionary Approach",
    year = "1983",
    journal = "Journal of Animal Ecology",
    url = "https://doi.org/10.2307/4581",
    doi = "10.2307/4581",
    openalex = "W2315288864"
}

@article{crossref1987asymmetry,
    title = "Asymmetry of lineages and the direction of evolutionary time",
    year = "1987",
    journal = "Deep Sea Research Part B. Oceanographic Literature Review",
    url = "https://doi.org/10.1016/0198-0254(87)96146-2",
    doi = "10.1016/0198-0254(87)96146-2",
    number = "12",
    openalex = "W4233080495",
    pages = "1077",
    volume = "34"
}

Evolutionary time has a characteristic direction as demonstrated by the asymmetry of clade diversity diagrams in large statistical samples. Evolutionary groups generally concentrate diversity during their early histories, producing a preponderance of bottom-heavy clades among those that arise early in the history of a larger group. This pattern holds across taxonomic levels and across differences in anatomy and ecology (marine invertebrates, terrestrial mammals). The quantitative study of directionality in life's history (replacing vague, untestable, and culturally laden notions of "progress") should receive more attention from paleobiologists.

@article{doi101126science23648071437,
    author = "Gould, S J and Gilinsky, N L and German, R Z",
    title = "Asymmetry of lineages and the direction of evolutionary time.",
    year = "1987",
    journal = "Science (New York, N.Y.)",
    abstract = {Evolutionary time has a characteristic direction as demonstrated by the asymmetry of clade diversity diagrams in large statistical samples. Evolutionary groups generally concentrate diversity during their early histories, producing a preponderance of bottom-heavy clades among those that arise early in the history of a larger group. This pattern holds across taxonomic levels and across differences in anatomy and ecology (marine invertebrates, terrestrial mammals). The quantitative study of directionality in life's history (replacing vague, untestable, and culturally laden notions of "progress") should receive more attention from paleobiologists.},
    url = "https://pubmed.ncbi.nlm.nih.gov/17793231/",
    doi = "10.1126/science.236.4807.1437",
    openalex = "W1986740993",
    pmid = "17793231",
    references = "doi101017s009483730000508x, doi101017s0094837300008186, doi101038293435a0, doi101086627905, doi101093sysbio233305, doi101126science2064415217, doi1023072412538, doi1023072694382, openalexw2754161204, openalexw659460302"
}

Evolutionary time has a characteristic direction as demonstrated by the asymmetry of clade diversity diagrams in large statistical samples. Evolutionary groups generally concentrate diversity during their early histories, producing a preponderance of bottom-heavy clades among those that arise early in the history of a larger group. This pattern holds across taxonomic levels and across differences in anatomy and ecology (marine invertebrates, terrestrial mammals). The quantitative study of directionality in life's history (replacing vague, untestable, and culturally laden notions of "progress") should receive more attention from paleobiologists.

@article{gould1987asymmetry,
    author = "Gould, Stephen Jay and Gilinsky, Norman L. and German, Rebecca Z.",
    title = "Asymmetry of Lineages and the Direction of Evolutionary Time",
    year = "1987",
    journal = "Science",
    abstract = {Evolutionary time has a characteristic direction as demonstrated by the asymmetry of clade diversity diagrams in large statistical samples. Evolutionary groups generally concentrate diversity during their early histories, producing a preponderance of bottom-heavy clades among those that arise early in the history of a larger group. This pattern holds across taxonomic levels and across differences in anatomy and ecology (marine invertebrates, terrestrial mammals). The quantitative study of directionality in life's history (replacing vague, untestable, and culturally laden notions of "progress") should receive more attention from paleobiologists.},
    url = "https://doi.org/10.1126/science.236.4807.1437",
    doi = "10.1126/science.236.4807.1437",
    number = "4807",
    openalex = "W1986740993",
    pages = "1437-1441",
    volume = "236",
    references = "doi101017s009483730000508x, doi101017s0094837300008022, doi101017s0094837300008186, doi101038293435a0, doi101086627905, doi101093sysbio233305, doi101126science2064415217, doi1023072412538, doi1023072694382, openalexw2754161204, openalexw659460302"
}

@misc{gould1987asymmetry1,
    author = "Gould, S. J. and Gilinsky, N. L. and German, R. Z",
    title = "Asymmetry of lineages and the directions of evolutionary time",
    year = "1987",
    howpublished = "Science, v. 236, p. 1437-1441",
    note = "talkorigins\_source = {true}; raw\_reference = {Gould, S. J., Gilinsky, N. L., and German, R. Z., 1987, Asymmetry of lineages and the directions of evolutionary time: Science, v. 236, p. 1437-1441.}"
}

Part 1 Natural selection and life histories: evolutionary models in behavioural ecology evolution of life histories human behavioural ecology. Part 2 Exploitation of resources: decision-making competition for resources interactions between predators and prey. Part 3 Sexual selection and reproductive strategies: sexual selection parental investment mating systems. Part 4 Co-operation and conflict: co-operative breeding in birds and mammals conflict and co-operation in insects communication.

@article{doi1023075530,
    author = "Adams, Jonathan and Krebs, J. R. and Davies, N. B.",
    title = "Behavioural Ecology: An Evolutionary Approach",
    year = "1992",
    journal = "Journal of Animal Ecology",
    abstract = "Part 1 Natural selection and life histories: evolutionary models in behavioural ecology evolution of life histories human behavioural ecology. Part 2 Exploitation of resources: decision-making competition for resources interactions between predators and prey. Part 3 Sexual selection and reproductive strategies: sexual selection parental investment mating systems. Part 4 Co-operation and conflict: co-operative breeding in birds and mammals conflict and co-operation in insects communication.",
    url = "https://doi.org/10.2307/5530",
    doi = "10.2307/5530",
    openalex = "W2136284908"
}

Disparity is a measure of the range or significance of morphology in a given sample of organisms, as opposed to diversity, which is expressed in terms of the number (and sometimes ranking) of taxa. At present there is no agreed definition of disparity, much less any consensus on how to measure it. Two possible categories of metric are considered here, one independent of any hypothesis of relationship (phenetics), the other constrained within an evolutionary framework (cladistics). The Early Cambrian radiation was clearly a period of significant morphologic and taxonomic diversification. However, we question the interpretation of its first generation products as numerous body plans at the highest level. Four phenetic and two cladistic measures have been used to compare disparity among Cambrian arthropods with that in the living fauna. Phenetic methods assessing character-state variability and the amount of morphological attribute space occupied yield similar results for Cambrian and Recent arthropods. Assessments of disparity within a taxonomic framework rely on the identification of particular characters that delineate higher level body plans. This requires a phylogenetic interpretation, a cladistic investigation of hierarchical structure in the data. Both sets of arthropods fall within the same major clades, and within this cladistic framework the amount of character-state evolution in the two groups is comparable. None of these methods identifies markedly greater disparity among the Cambrian compared with the Recent taxa. Although measures of disparity are applied here to a consideration of the Cambrian radiation, the metrics clearly have a much wider potential for estimating macroevolutionary trends independently from existing taxonomic frameworks. Geometric morphometry is ideal for measuring morphological variety at lower taxonomic levels, but it requires the recognition of homologous landmarks in all the forms under comparison, or the identification of entire homologous structures. Conventional phenetics has much wider application as it can operate on data coded as discrete homologous character states (this facility is also a requirement of cladistics), which are a more appropriate basis for comparing disparity in markedly dissimilar forms.

@article{doi101017s009483730001263x,
    author = "Wills, Matthew A. and Briggs, Derek E. G. and Fortey, Richard A.",
    title = "Disparity as an evolutionary index: a comparison of Cambrian and Recent arthropods",
    year = "1994",
    journal = "Paleobiology",
    abstract = "Disparity is a measure of the range or significance of morphology in a given sample of organisms, as opposed to diversity, which is expressed in terms of the number (and sometimes ranking) of taxa. At present there is no agreed definition of disparity, much less any consensus on how to measure it. Two possible categories of metric are considered here, one independent of any hypothesis of relationship (phenetics), the other constrained within an evolutionary framework (cladistics). The Early Cambrian radiation was clearly a period of significant morphologic and taxonomic diversification. However, we question the interpretation of its first generation products as numerous body plans at the highest level. Four phenetic and two cladistic measures have been used to compare disparity among Cambrian arthropods with that in the living fauna. Phenetic methods assessing character-state variability and the amount of morphological attribute space occupied yield similar results for Cambrian and Recent arthropods. Assessments of disparity within a taxonomic framework rely on the identification of particular characters that delineate higher level body plans. This requires a phylogenetic interpretation, a cladistic investigation of hierarchical structure in the data. Both sets of arthropods fall within the same major clades, and within this cladistic framework the amount of character-state evolution in the two groups is comparable. None of these methods identifies markedly greater disparity among the Cambrian compared with the Recent taxa. Although measures of disparity are applied here to a consideration of the Cambrian radiation, the metrics clearly have a much wider potential for estimating macroevolutionary trends independently from existing taxonomic frameworks. Geometric morphometry is ideal for measuring morphological variety at lower taxonomic levels, but it requires the recognition of homologous landmarks in all the forms under comparison, or the identification of entire homologous structures. Conventional phenetics has much wider application as it can operate on data coded as discrete homologous character states (this facility is also a requirement of cladistics), which are a more appropriate basis for comparing disparity in markedly dissimilar forms.",
    url = "https://doi.org/10.1017/s009483730001263x",
    doi = "10.1017/s009483730001263x",
    openalex = "W2131955742",
    references = "crossref1977chapter, doi101007bf02289565, doi101007bf02289630, doi101007bf02289694, doi101017s0094837300015864, doi101093biomet5334325, doi101098rstb19810007, doi101098rstb19830020, doi101098rstb19850005, doi101111j155856461982tb05453x, doi10113719781611970319, doi101144gsjgs14940631, doi1023072288218, doi1023072346439, doi103133ofr81743, doi105281zenodo16435756, doi105860choice273873, openalexw2754161204, openalexw2944885317"
}

Phylogenies reconstructed from contemporary taxa do not contain information about lineages that have gone extinct. We derive probability models for such phylogenies, allowing real data to be compared with specified null models of evolution, and lineage birth and death rates to be estimated.

@article{doi101098rstb19940068,
    author = "Nee, Sean and May, Robert M. and Harvey, Paul",
    title = "The reconstructed evolutionary process",
    year = "1994",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "Phylogenies reconstructed from contemporary taxa do not contain information about lineages that have gone extinct. We derive probability models for such phylogenies, allowing real data to be compared with specified null models of evolution, and lineage birth and death rates to be estimated.",
    url = "https://doi.org/10.1098/rstb.1994.0068",
    doi = "10.1098/rstb.1994.0068",
    openalex = "W2154552181",
    references = "doi101086627905"
}

Large-scale evolutionary trends may result from driving forces or from passive diffusion in bounded spaces. Such trends are persistent directional changes in higher taxa spanning significant periods of geological time; examples include the frequently cited long-term trends in size, complexity, and fitness in life as a whole, as well as trends in lesser supraspecific taxa and trends in space. In a driven trend, the distribution mean increases on account of a force (which may manifest itself as a bias in the direction of change) that acts on lineages throughout the space in which diversification occurs. In a passive system, no pervasive force or bias exists, but the mean increases because change in one direction is blocked by a boundary, or other inhomogeneity, in some limited region of the space. Two tests have been used to distinguish these trend mechanisms: (1) the test based on the behavior of the minimum; and (2) the ancestor-descendant test, based on comparisons in a random sample of ancestor-descendant pairs that lie far from any possible lower bound. For skewed distributions, a third test is introduced here: (3) the subclade test, based on the mean skewness of a sample of subclades drawn from the tail of a terminal distribution. With certain restrictions, a system is driven if the minimum increases, if increases significantly outnumber decreases among ancestor-descendant pairs, and if the mean skew of subclades is significantly positive. A passive mechanism is more difficult to demonstrate but is the more likely mechanism if decreases outnumber increases and if the mean skew of subclades is negative. Unlike the other tests, the subclade test requires no detailed phylogeny or paleontological time series, but only terminal (e.g., modern) distributions. Monte Carlo simulations of the diversification of a clade are used to show how the subclade test works. In the empirical cases examined, the three tests gave concordant results, suggesting first, that they work, and second, that the passive and driven mechanisms may correspond to natural categories of causes of large-scale trends.

@article{doi101111j155856461994tb02211x,
    author = "McShea, Daniel W.",
    title = "MECHANISMS OF LARGE-SCALE EVOLUTIONARY TRENDS",
    year = "1994",
    journal = "Evolution",
    abstract = "Large-scale evolutionary trends may result from driving forces or from passive diffusion in bounded spaces. Such trends are persistent directional changes in higher taxa spanning significant periods of geological time; examples include the frequently cited long-term trends in size, complexity, and fitness in life as a whole, as well as trends in lesser supraspecific taxa and trends in space. In a driven trend, the distribution mean increases on account of a force (which may manifest itself as a bias in the direction of change) that acts on lineages throughout the space in which diversification occurs. In a passive system, no pervasive force or bias exists, but the mean increases because change in one direction is blocked by a boundary, or other inhomogeneity, in some limited region of the space. Two tests have been used to distinguish these trend mechanisms: (1) the test based on the behavior of the minimum; and (2) the ancestor-descendant test, based on comparisons in a random sample of ancestor-descendant pairs that lie far from any possible lower bound. For skewed distributions, a third test is introduced here: (3) the subclade test, based on the mean skewness of a sample of subclades drawn from the tail of a terminal distribution. With certain restrictions, a system is driven if the minimum increases, if increases significantly outnumber decreases among ancestor-descendant pairs, and if the mean skew of subclades is significantly positive. A passive mechanism is more difficult to demonstrate but is the more likely mechanism if decreases outnumber increases and if the mean skew of subclades is negative. Unlike the other tests, the subclade test requires no detailed phylogeny or paleontological time series, but only terminal (e.g., modern) distributions. Monte Carlo simulations of the diversification of a clade are used to show how the subclade test works. In the empirical cases examined, the three tests gave concordant results, suggesting first, that they work, and second, that the passive and driven mechanisms may correspond to natural categories of causes of large-scale trends.",
    url = "https://doi.org/10.1111/j.1558-5646.1994.tb02211.x",
    doi = "10.1111/j.1558-5646.1994.tb02211.x",
    openalex = "W1992960291",
    references = "doi101007bf00132234, doi101017s0022336000059126, doi101038365748a0, doi101111j109583121992tb00630x, doi1023072412538, doi1023073514444"
}

The hypothesis of escalation states that enemies-competitors, predators, and dangerous prey-are the most important agents of natural selection among individual organisms, and that enemy-related adaptation and responses brought about long-term evolutionary trends in the morphology, behavior, and distribution of organisms over the course of the Phanerozoic. In contrast to this top-down view of the role of organisms in determining the directions of evolution, the hypothesis of coevolution holds that two interacting species or groups of species change in response to each other. I review and evaluate these hypotheses in the light of criticisms about the existence of evolutionary trends and the role of interactions of species in evolution. Models describing the evolutionary effects organisms have on each other have been based largely on population dynamics and on cost-benefit analyses of the net outcome of interactions between species. Yet, the hypotheses of escalation and coevolution are statements about the nature, frequency, causes, and role of selection. Although these models have provided valuable insights and have forced some modifications in the hypotheses of escalation, studies seeking to distinguish between escalation and coevolution will require empirical observations and cost-benefit evaluations of the discrete events of interaction that collectively constitute organism-caused selection.

@article{doi101146annureves25110194001251,
    author = "Vermeij, Geerat J.",
    title = "THE EVOLUTIONARY INTERACTION AMONG SPECIES: Selection, Escalation, and Coevolution",
    year = "1994",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "The hypothesis of escalation states that enemies-competitors, predators, and dangerous prey-are the most important agents of natural selection among individual organisms, and that enemy-related adaptation and responses brought about long-term evolutionary trends in the morphology, behavior, and distribution of organisms over the course of the Phanerozoic. In contrast to this top-down view of the role of organisms in determining the directions of evolution, the hypothesis of coevolution holds that two interacting species or groups of species change in response to each other. I review and evaluate these hypotheses in the light of criticisms about the existence of evolutionary trends and the role of interactions of species in evolution. Models describing the evolutionary effects organisms have on each other have been based largely on population dynamics and on cost-benefit analyses of the net outcome of interactions between species. Yet, the hypotheses of escalation and coevolution are statements about the nature, frequency, causes, and role of selection. Although these models have provided valuable insights and have forced some modifications in the hypotheses of escalation, studies seeking to distinguish between escalation and coevolution will require empirical observations and cost-benefit evaluations of the discrete events of interaction that collectively constitute organism-caused selection.",
    url = "https://doi.org/10.1146/annurev.es.25.110194.001251",
    doi = "10.1146/annurev.es.25.110194.001251",
    openalex = "W2112937332",
    references = "doi101017s0022336000059126, doi101017s0094837300011350, doi101017s0094837300012793, doi101017s0094837300013920, doi101111j155856461959tb03005x"
}

@article{doi101038374227a0,
    author = "Szathmáry, Eörs and Smith, John Maynard",
    title = "The major evolutionary transitions",
    year = "1995",
    journal = "Nature",
    url = "https://doi.org/10.1038/374227a0",
    doi = "10.1038/374227a0",
    openalex = "W2058598267",
    references = "doi10100797836427811004, doi101007bf00450633, doi101007bf00623322, doi1010160022519364900384, doi101016s0022519389801699, doi101017s0140525x00081061, doi101038371215a0, doi101111j155856461995tb04464x, doi101128mr5244524841988, doi1015159781400820108, doi1015159781400858712, doi1023072063069, doi1023072576242, doi107312rens91062, openalexw2624262714"
}

Inferences about macroevolutionary processes have traditionally depended solely on the fossil record, but such inferences can be strengthened by also considering the shapes of the phylogenetic trees that link extant taxa. The realization that phylogenies reflect macroevolutionary processes has led to a growing literature of theoretical and comparative studies of tree shape. Two aspects of tree shape are particularly important: tree balance and the distribution of branch lenghts. We examine and evaluate recent developments in and connections between these two aspects, and suggest directions for future research. Studies of tree shape promise useful and powerful tests of macroevolutionary hypotheses. With appropriate further research, tree shape may help us detect mass extinctions and adaptive radiations, measure continuos variation in speciation and extinction rates, and associate changes in these rates with ecological or biogeographical causes. The usefulness of tree shape extends well beyond the study of macroevolution. We discuss applications to other areas of biology, including coevolution, phylogenetic inference, population biology, and developmental biology.

@article{doi101086419657,
    author = "Mooers, Arne Ø. and Heard, Stephen B.",
    title = "Inferring Evolutionary Process from Phylogenetic Tree Shape",
    year = "1997",
    journal = "The Quarterly Review of Biology",
    abstract = "Inferences about macroevolutionary processes have traditionally depended solely on the fossil record, but such inferences can be strengthened by also considering the shapes of the phylogenetic trees that link extant taxa. The realization that phylogenies reflect macroevolutionary processes has led to a growing literature of theoretical and comparative studies of tree shape. Two aspects of tree shape are particularly important: tree balance and the distribution of branch lenghts. We examine and evaluate recent developments in and connections between these two aspects, and suggest directions for future research. Studies of tree shape promise useful and powerful tests of macroevolutionary hypotheses. With appropriate further research, tree shape may help us detect mass extinctions and adaptive radiations, measure continuos variation in speciation and extinction rates, and associate changes in these rates with ecological or biogeographical causes. The usefulness of tree shape extends well beyond the study of macroevolution. We discuss applications to other areas of biology, including coevolution, phylogenetic inference, population biology, and developmental biology.",
    url = "https://doi.org/10.1086/419657",
    doi = "10.1086/419657",
    openalex = "W2117055771",
    references = "doi101017s009483730000508x, doi10108010292389509380518, doi101098rspb19960088, doi101126science22246281123, doi10129879780300237856, doi1023072412808"
}

A new method for estimating divergence times when evolutionary rates are variable across lineages is proposed. The method, called nonparametric rate smoothing (NPRS), relies on minimization of ancestor-descendant local rate changes and is motivated by the likelihood that evolutionary rates are autocorrelated in time. Fossil information pertaining to minimum and/or maximum ages of nodes in a phylogeny is incorporated into the algorithms by constrained optimization techniques. The accuracy of NPRS was examined by comparison to a clock-based maximum-likelihood method in computer simulations. NPRS provides more accurate estimates of divergence times when (1) sequence lengths are sufficiently long, (2) rates are truly nonclocklike, and (3) rates are moderately to highly autocorrelated in time. The algorithms were applied to estimate divergence times in seed plants based on data from the chloroplast rbcL gene. Both constrained and unconstrained NPRS methods tended to produce divergence time estimates more consistent with paleobotanical evidence than did clock-based estimates.

@article{doi101093oxfordjournalsmolbeva025731,
    author = "Sanderson, Michael J.",
    title = "A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy",
    year = "1997",
    journal = "Molecular Biology and Evolution",
    abstract = "A new method for estimating divergence times when evolutionary rates are variable across lineages is proposed. The method, called nonparametric rate smoothing (NPRS), relies on minimization of ancestor-descendant local rate changes and is motivated by the likelihood that evolutionary rates are autocorrelated in time. Fossil information pertaining to minimum and/or maximum ages of nodes in a phylogeny is incorporated into the algorithms by constrained optimization techniques. The accuracy of NPRS was examined by comparison to a clock-based maximum-likelihood method in computer simulations. NPRS provides more accurate estimates of divergence times when (1) sequence lengths are sufficiently long, (2) rates are truly nonclocklike, and (3) rates are moderately to highly autocorrelated in time. The algorithms were applied to estimate divergence times in seed plants based on data from the chloroplast rbcL gene. Both constrained and unconstrained NPRS methods tended to produce divergence time estimates more consistent with paleobotanical evidence than did clock-based estimates.",
    url = "https://doi.org/10.1093/oxfordjournals.molbev.a025731",
    doi = "10.1093/oxfordjournals.molbev.a025731",
    openalex = "W1964575260",
    references = "doi101007bf01797451, doi101126science2715248470, doi10113000917613198311503tdonag20co2"
}

@article{doi105860choice344488,
    title = "Evolutionary paleobiology",
    year = "1997",
    journal = "Choice Reviews Online",
    url = "https://doi.org/10.5860/choice.34-4488",
    doi = "10.5860/choice.34-4488",
    openalex = "W4249025931"
}

Phylogenies reconstructed from gene sequences can be used to investigate the tempo and mode of species diversification. Here we develop and use new statistical methods to infer past patterns of speciation and extinction from molecular phylogenies. Specifically, we test the null hypothesis that per-lineage speciation and extinction rates have remained constant through time. Rejection of this hypothesis may provide evidence for evolutionary events such as adaptive radiations or key adaptations. In contrast to previous approaches, our methods are robust to incomplete taxon sampling and are conservative with respect to extinction. Using simulation we investigate, first, the adverse effects of failing to take incomplete sampling into account and, second, the power and reliability of our tests. When applied to published phylogenies our tests suggest that, in some cases, speciation rates have decreased through time.

@article{doi101098rspb20001278,
    author = "Pybus, Oliver G. and Harvey, Paul",
    title = "Testing macro–evolutionary models using incomplete molecular phylogenies",
    year = "2000",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "Phylogenies reconstructed from gene sequences can be used to investigate the tempo and mode of species diversification. Here we develop and use new statistical methods to infer past patterns of speciation and extinction from molecular phylogenies. Specifically, we test the null hypothesis that per-lineage speciation and extinction rates have remained constant through time. Rejection of this hypothesis may provide evidence for evolutionary events such as adaptive radiations or key adaptations. In contrast to previous approaches, our methods are robust to incomplete taxon sampling and are conservative with respect to extinction. Using simulation we investigate, first, the adverse effects of failing to take incomplete sampling into account and, second, the power and reliability of our tests. When applied to published phylogenies our tests suggest that, in some cases, speciation rates have decreased through time.",
    url = "https://doi.org/10.1098/rspb.2000.1278",
    doi = "10.1098/rspb.2000.1278",
    openalex = "W2118610143",
    references = "doi101086627905"
}

Gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, but it is unclear how often gene duplicates arise and how frequently they evolve new functions. Observations from the genomic databases for several eukaryotic species suggest that duplicate genes arise at a very high rate, on average 0.01 per gene per million years. Most duplicated genes experience a brief period of relaxed selection early in their history, with a moderate fraction of them evolving in an effectively neutral manner during this period. However, the vast majority of gene duplicates are silenced within a few million years, with the few survivors subsequently experiencing strong purifying selection. Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species.

@article{doi101126science29054941151,
    author = "Lynch, Michael and Conery, John S.",
    title = "The Evolutionary Fate and Consequences of Duplicate Genes",
    year = "2000",
    journal = "Science",
    abstract = "Gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, but it is unclear how often gene duplicates arise and how frequently they evolve new functions. Observations from the genomic databases for several eukaryotic species suggest that duplicate genes arise at a very high rate, on average 0.01 per gene per million years. Most duplicated genes experience a brief period of relaxed selection early in their history, with a moderate fraction of them evolving in an effectively neutral manner during this period. However, the vast majority of gene duplicates are silenced within a few million years, with the few survivors subsequently experiencing strong purifying selection. Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species.",
    url = "https://doi.org/10.1126/science.290.5494.1151",
    doi = "10.1126/science.290.5494.1151",
    openalex = "W2019591778",
    references = "doi101023a1006392424384, doi101038387489a0, doi101046j14390388200200356x, doi101093genetics15141531, doi101093genetics1541459, doi101093nar25173389, doi101098rspb19940058, doi101126science28253941711, doi101126science28754612204, doi101242dev1994supplement125, doi1023072412932"
}

@book{doi102307jctvjsf433,
    author = "Gould, Stephen Jay",
    title = "The Structure of Evolutionary Theory",
    year = "2002",
    booktitle = "Harvard University Press eBooks",
    url = "https://doi.org/10.2307/j.ctvjsf433",
    doi = "10.2307/j.ctvjsf433",
    openalex = "W4300925890"
}

* *1. Defining and Revising the Structure of Evolutionary Theory * Part I: The History of Darwinian Logic and Debate *2. The Essence of Darwinism and the Basis of Modern Orthodoxy: An Exegesis of the Origin of Species *3. Seeds of Hierarchy *4. Internalism and Laws of Form: Pre-Darwinian Alternatives to Functionalism *5. The Fruitful Facets of Galton's Polyhedron: Channels and Saltations in Post-Darwinian Formalism *6. Pattern and Progress on the Geological Stage *7. The Modern Synthesis as a Limited Consensus * Part II: Towards a Revised and Expanded Evolutionary Theory *8. Species as Individuals in the Hierarchical Theory of Selection *9. Punctuated Equilibrium and the Validation of Macroevolutionary Theory *10. The Integration of Constraint and Adaptation (Structure and Function) in Ontogeny and Phylogeny: Historical Constraints and the Evolution of Development *11. The Integration of Constraint and Adaptation (Structure and Function) in Ontogeny and Phylogeny: Structural Constraints, Spandrels, and the Centrality of Exaptation in Macroevolution *12. Tiers of Time and Trials of Extrapolationism, With an Epilog on the Interaction of General Theory and Contingent History * Bibliography * Index

@article{doi105860choice396411,
    author = "Gould, Stephen Jay",
    title = "The structure of evolutionary theory",
    year = "2002",
    journal = "Choice Reviews Online",
    abstract = "* *1. Defining and Revising the Structure of Evolutionary Theory * Part I: The History of Darwinian Logic and Debate *2. The Essence of Darwinism and the Basis of Modern Orthodoxy: An Exegesis of the Origin of Species *3. Seeds of Hierarchy *4. Internalism and Laws of Form: Pre-Darwinian Alternatives to Functionalism *5. The Fruitful Facets of Galton's Polyhedron: Channels and Saltations in Post-Darwinian Formalism *6. Pattern and Progress on the Geological Stage *7. The Modern Synthesis as a Limited Consensus * Part II: Towards a Revised and Expanded Evolutionary Theory *8. Species as Individuals in the Hierarchical Theory of Selection *9. Punctuated Equilibrium and the Validation of Macroevolutionary Theory *10. The Integration of Constraint and Adaptation (Structure and Function) in Ontogeny and Phylogeny: Historical Constraints and the Evolution of Development *11. The Integration of Constraint and Adaptation (Structure and Function) in Ontogeny and Phylogeny: Structural Constraints, Spandrels, and the Centrality of Exaptation in Macroevolution *12. Tiers of Time and Trials of Extrapolationism, With an Epilog on the Interaction of General Theory and Contingent History * Bibliography * Index",
    url = "https://doi.org/10.5860/choice.39-6411",
    doi = "10.5860/choice.39-6411",
    openalex = "W1539968307"
}

Identification of general properties of evolutionary radiations has been hindered by the lack of a general statistical and phylogenetic approach applicable across diverse taxa. We present a comparative analytical framework for examining phylogenetic patterns of diversification and morphological disparity with data from four iguanian-lizard taxa that exhibit substantially different patterns of evolution. Taxa whose diversification occurred disproportionately early in their evolutionary history partition more of their morphological disparity among, rather than within, subclades. This inverse relationship between timing of diversification and morphological disparity within subclades may be a general feature that transcends the historically contingent properties of different evolutionary radiations.

@article{doi101126science1084786,
    author = "Harmon, Luke J. and Schulte, James A. and Larson, Allan and Losos, Jonathan B.",
    title = "Tempo and Mode of Evolutionary Radiation in Iguanian Lizards",
    year = "2003",
    journal = "Science",
    abstract = "Identification of general properties of evolutionary radiations has been hindered by the lack of a general statistical and phylogenetic approach applicable across diverse taxa. We present a comparative analytical framework for examining phylogenetic patterns of diversification and morphological disparity with data from four iguanian-lizard taxa that exhibit substantially different patterns of evolution. Taxa whose diversification occurred disproportionately early in their evolutionary history partition more of their morphological disparity among, rather than within, subclades. This inverse relationship between timing of diversification and morphological disparity within subclades may be a general feature that transcends the historically contingent properties of different evolutionary radiations.",
    url = "https://doi.org/10.1126/science.1084786",
    doi = "10.1126/science.1084786",
    openalex = "W2002820714",
    references = "doi101017s0094837300015864, doi101111j109583121996tb01693x, doi101146annurevecolsys281129"
}

@incollection{doi101007978366206278418,
    author = "Bown, Paul R. and Lees, Jackie A. and Young, J. R.",
    title = "Calcareous nannoplankton evolution and diversity through time",
    year = "2004",
    url = "https://doi.org/10.1007/978-3-662-06278-4\_18",
    doi = "10.1007/978-3-662-06278-4\_18",
    openalex = "W138655657",
    references = "doi1010079789401149020, doi1010160011747167900654, doi1010160012825273900925, doi1010160031018291900753, doi101016s0012825200000374, doi101017cbo9780511628948, doi101017s0094837300013178, doi1010292001pa000623, doi101093oso97801985491780010001, doi101093oxfordjournalsmolbeva026092, doi101126science1059412, doi101126science23547931156, doi101126science23648071437, doi101130spe332, doi101144gsjgs15420265, doi102110pec95040129, doi1023073515466, doi102687999013, gould1987asymmetry"
}

@article{doi101016jphysrep200704004,
    author = "Szabó, György and Fáth, Gábor",
    title = "Evolutionary games on graphs",
    year = "2007",
    journal = "Physics Reports",
    url = "https://doi.org/10.1016/j.physrep.2007.04.004",
    doi = "10.1016/j.physrep.2007.04.004",
    openalex = "W1992195122",
    references = "doi1010160022519364900384, doi1010160022519364900396, doi101017cbo9780511806292, doi101038246015a0, doi10103830918, doi101038366223a0, doi101038nature00823, doi101038nature03607, doi101090mbk12132, doi101098rspa19270118, doi101103revmodphys65851, doi101103revmodphys7447, doi10111911934457, doi10111911986710, doi101126science16238591243, doi101126science2865439509, doi101126science7466396, doi1011370129022, doi101137s003614450342480, doi1015159780691213255, doi1015159780691213255004, doi1023072256497, doi1023072341823, doi102307257983, doi102307jctvjghw98, doi105962bhltitle27468, openalexw2040525210, openalexw2624262714"
}

@article{doi101016jtree200702010,
    author = "Després, Laurence and David, Jean‐Philippe and Gallet, Christiane",
    title = "The evolutionary ecology of insect resistance to plant chemicals",
    year = "2007",
    journal = "Trends in Ecology \& Evolution",
    url = "https://doi.org/10.1016/j.tree.2007.02.010",
    doi = "10.1016/j.tree.2007.02.010",
    openalex = "W2029436323",
    references = "doi101016s0378111900005333, doi101111j13652583200400529x, doi101146annurevento47091201145121"
}

@article{doi101016jtree200707009,
    author = "Rankin, Daniel J. and Bargum, Katja and Kokko, Hanna",
    title = "The tragedy of the commons in evolutionary biology",
    year = "2007",
    journal = "Trends in Ecology \& Evolution",
    url = "https://doi.org/10.1016/j.tree.2007.07.009",
    doi = "10.1016/j.tree.2007.07.009",
    openalex = "W2116738092",
    references = "doi101093acprofoso97801992679720010001"
}

This open source software is written entirely in the R language and is freely available through the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/.

@article{doi101093bioinformaticsbtm538,
    author = "Harmon, Luke J. and Weir, Jason T. and Brock, Chad D. and Glor, Richard E. and Challenger, Wendell",
    title = "GEIGER: investigating evolutionary radiations",
    year = "2007",
    journal = "Bioinformatics",
    abstract = "This open source software is written entirely in the R language and is freely available through the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/.",
    url = "https://doi.org/10.1093/bioinformatics/btm538",
    doi = "10.1093/bioinformatics/btm538",
    openalex = "W2117368100",
    references = "doi10103844766, doi101093oso97801985052350010001, doi101111j001438202001tb00826x"
}

Size-selective harvesting, where the large individuals of a particular species are preferentially taken, is common in both marine and terrestrial habitats. Preferential removal of larger individuals of a species has been shown to have a negative effect on its demography, life history and ecology, and empirical studies are increasingly documenting such impacts. But determining whether the observed changes represent evolutionary response or phenotypic plasticity remains a challenge. In addition, the problem is not recognized in most management plans for fish and marine invertebrates that still mandate a minimum size restriction. We use examples from both aquatic and terrestrial habitats to illustrate some of the biological consequences of size-selective harvesting and discuss possible future directions of research as well as changes in management policy needed to mitigate its negative biological impacts.

@article{doi101111j1365294x200703522x,
    author = "Fenberg, Phillip B. and Roy, Kaustuv",
    title = "Ecological and evolutionary consequences of size‐selective harvesting: how much do we know?",
    year = "2007",
    journal = "Molecular Ecology",
    abstract = "Size-selective harvesting, where the large individuals of a particular species are preferentially taken, is common in both marine and terrestrial habitats. Preferential removal of larger individuals of a species has been shown to have a negative effect on its demography, life history and ecology, and empirical studies are increasingly documenting such impacts. But determining whether the observed changes represent evolutionary response or phenotypic plasticity remains a challenge. In addition, the problem is not recognized in most management plans for fish and marine invertebrates that still mandate a minimum size restriction. We use examples from both aquatic and terrestrial habitats to illustrate some of the biological consequences of size-selective harvesting and discuss possible future directions of research as well as changes in management policy needed to mitigate its negative biological impacts.",
    url = "https://doi.org/10.1111/j.1365-294x.2007.03522.x",
    doi = "10.1111/j.1365-294x.2007.03522.x",
    openalex = "W2139419519",
    references = "doi101017s0022336000059126"
}

@article{doi101111j15585646200700129x,
    author = "Hunt, G.",
    title = "EVOLUTIONARY DIVERGENCE IN DIRECTIONS OF HIGH PHENOTYPIC VARIANCE IN THE OSTRACODE GENUS POSEIDONAMICUS",
    year = "2007",
    journal = "Evolution; international journal of organic evolution",
    url = "https://www.semanticscholar.org/paper/c8853205cef50626a90157a4927cf06a4364dc04",
    doi = "10.1111/j.1558-5646.2007.00129.x",
    is_oa = "true",
    number = "7",
    pages = "1560-1576",
    semanticscholar_citation_count = "120",
    semanticscholar_id = "c8853205cef50626a90157a4927cf06a4364dc04",
    volume = "61"
}

Evolution may be dominated by biotic factors, as in the Red Queen model, or abiotic factors, as in the Court Jester model, or a mixture of both. The two models appear to operate predominantly over different geographic and temporal scales: Competition, predation, and other biotic factors shape ecosystems locally and over short time spans, but extrinsic factors such as climate and oceanographic and tectonic events shape larger-scale patterns regionally and globally, and through thousands and millions of years. Paleobiological studies suggest that species diversity is driven largely by abiotic factors such as climate, landscape, or food supply, and comparative phylogenetic approaches offer new insights into clade dynamics.

@article{doi101126science1157719,
    author = "Benton, Michael J.",
    title = "The Red Queen and the Court Jester: Species Diversity and the Role of Biotic and Abiotic Factors Through Time",
    year = "2009",
    journal = "Science",
    abstract = "Evolution may be dominated by biotic factors, as in the Red Queen model, or abiotic factors, as in the Court Jester model, or a mixture of both. The two models appear to operate predominantly over different geographic and temporal scales: Competition, predation, and other biotic factors shape ecosystems locally and over short time spans, but extrinsic factors such as climate and oceanographic and tectonic events shape larger-scale patterns regionally and globally, and through thousands and millions of years. Paleobiological studies suggest that species diversity is driven largely by abiotic factors such as climate, landscape, or food supply, and comparative phylogenetic approaches offer new insights into clade dynamics.",
    url = "https://doi.org/10.1126/science.1157719",
    doi = "10.1126/science.1157719",
    openalex = "W2092302011",
    references = "doi101017s0094837300008186, doi101073pnas092150999, doi101098rspb20080715, doi101111j14754983200600611x, doi101111j14754983200600612x, doi101111j15585646200800317x, doi101126science1130880, doi101126science1156963, doi101126science1161833, doi101126science7701342, doi1016710272463420010210172dteotr20co2"
}

Closely related organisms usually occupy similar ecological niches, leading to intense competition and even extinction. Such competition also can promote rapid phenotypic evolution and ecological divergence. This process may end with the stable occupation of distinct niches or, alternatively, may entail repeated bouts of evolution. Here we examine two Escherichia coli lineages, called L and S, that coexisted for more than 30,000 generations after diverging from a common ancestor. Both lineages underwent sustained phenotypic evolution based on global transcription and resource utilization profiles, with L seeming to encroach over time on the catabolic profile of S. Reciprocal invasion experiments with L and S clones from the same or different generations revealed evolutionary changes in their interaction, including an asymmetry that confirmed the encroachment by L on the niche of the S lineage. In general, L and S clones from the same generation showed negative frequency-dependent effects, consistent with stable coexistence. However, L clones could invade S clones from both earlier and later generations, whereas S clones could invade only L clones from earlier generations. In this system, the long-term coexistence of competing lineages evidently depended on successive rounds of evolution, rather than on initial divergence followed by a static equilibrium.

@article{doi101073pnas1207091109,
    author = "Gac, Mickael Le and Plucain, Jessica and Hindré, T. and Lenski, R. and Schneider, D.",
    title = "Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with Escherichia coli",
    year = "2012",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Closely related organisms usually occupy similar ecological niches, leading to intense competition and even extinction. Such competition also can promote rapid phenotypic evolution and ecological divergence. This process may end with the stable occupation of distinct niches or, alternatively, may entail repeated bouts of evolution. Here we examine two Escherichia coli lineages, called L and S, that coexisted for more than 30,000 generations after diverging from a common ancestor. Both lineages underwent sustained phenotypic evolution based on global transcription and resource utilization profiles, with L seeming to encroach over time on the catabolic profile of S. Reciprocal invasion experiments with L and S clones from the same or different generations revealed evolutionary changes in their interaction, including an asymmetry that confirmed the encroachment by L on the niche of the S lineage. In general, L and S clones from the same generation showed negative frequency-dependent effects, consistent with stable coexistence. However, L clones could invade S clones from both earlier and later generations, whereas S clones could invade only L clones from earlier generations. In this system, the long-term coexistence of competing lineages evidently depended on successive rounds of evolution, rather than on initial divergence followed by a static equilibrium.",
    url = "https://www.pnas.org/content/pnas/109/24/9487.full.pdf",
    doi = "10.1073/pnas.1207091109",
    is_oa = "true",
    number = "24",
    pages = "9487-9492",
    semanticscholar_citation_count = "122",
    semanticscholar_id = "68d9f3e134c3433c12e2a64df3ee190fa3543955",
    volume = "109"
}

The impressive body of work on the major evolutionary transitions in the last 20 y calls for a reconstruction of the theory although a 2D account (evolution of informational systems and transitions in individuality) remains. Significant advances include the concept of fraternal and egalitarian transitions (lower-level units like and unlike, respectively). Multilevel selection, first without, then with, the collectives in focus is an important explanatory mechanism. Transitions are decomposed into phases of origin, maintenance, and transformation (i.e., further evolution) of the higher level units, which helps reduce the number of transitions in the revised list by two so that it is less top-heavy. After the transition, units show strong cooperation and very limited realized conflict. The origins of cells, the emergence of the genetic code and translation, the evolution of the eukaryotic cell, multicellularity, and the origin of human groups with language are reconsidered in some detail in the light of new data and considerations. Arguments are given why sex is not in the revised list as a separate transition. Some of the transitions can be recursive (e.g., plastids, multicellularity) or limited (transitions that share the usual features of major transitions without a massive phylogenetic impact, such as the micro- and macronuclei in ciliates). During transitions, new units of reproduction emerge, and establishment of such units requires high fidelity of reproduction (as opposed to mere replication).

@article{doi101073pnas1421398112,
    author = "Szathmáry, Eörs",
    title = "Toward major evolutionary transitions theory 2.0",
    year = "2015",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "The impressive body of work on the major evolutionary transitions in the last 20 y calls for a reconstruction of the theory although a 2D account (evolution of informational systems and transitions in individuality) remains. Significant advances include the concept of fraternal and egalitarian transitions (lower-level units like and unlike, respectively). Multilevel selection, first without, then with, the collectives in focus is an important explanatory mechanism. Transitions are decomposed into phases of origin, maintenance, and transformation (i.e., further evolution) of the higher level units, which helps reduce the number of transitions in the revised list by two so that it is less top-heavy. After the transition, units show strong cooperation and very limited realized conflict. The origins of cells, the emergence of the genetic code and translation, the evolution of the eukaryotic cell, multicellularity, and the origin of human groups with language are reconsidered in some detail in the light of new data and considerations. Arguments are given why sex is not in the revised list as a separate transition. Some of the transitions can be recursive (e.g., plastids, multicellularity) or limited (transitions that share the usual features of major transitions without a massive phylogenetic impact, such as the micro- and macronuclei in ciliates). During transitions, new units of reproduction emerge, and establishment of such units requires high fidelity of reproduction (as opposed to mere replication).",
    url = "https://doi.org/10.1073/pnas.1421398112",
    doi = "10.1073/pnas.1421398112",
    openalex = "W2158225543",
    references = "doi101002anie201204968, doi101002sici1520660219981127aidinbi430co26, doi101038280445a0, doi101093acprofosobl97801995520470010001, doi101098rstb20090095, doi1011861745615071, nunney1985group"
}

The evolution of life on earth has been driven by a small number of major evolutionary transitions. These transitions have been characterized by individuals that could previously replicate independently, cooperating to form a new, more complex life form. For example, archaea and eubacteria formed eukaryotic cells, and cells formed multicellular organisms. However, not all cooperative groups are en route to major transitions. How can we explain why major evolutionary transitions have or haven't taken place on different branches of the tree of life? We break down major transitions into two steps: the formation of a cooperative group and the transformation of that group into an integrated entity. We show how these steps require cooperation, division of labor, communication, mutual dependence, and negligible within-group conflict. We find that certain ecological conditions and the ways in which groups form have played recurrent roles in driving multiple transitions. In contrast, we find that other factors have played relatively minor roles at many key points, such as within-group kin discrimination and mechanisms to actively repress competition. More generally, by identifying the small number of factors that have driven major transitions, we provide a simpler and more unified description of how life on earth has evolved.

@article{doi101073pnas1421402112,
    author = "West, Stuart A. and Fisher, Roberta M. and Gardner, Andy and Kiers, E. Toby",
    title = "Major evolutionary transitions in individuality",
    year = "2015",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "The evolution of life on earth has been driven by a small number of major evolutionary transitions. These transitions have been characterized by individuals that could previously replicate independently, cooperating to form a new, more complex life form. For example, archaea and eubacteria formed eukaryotic cells, and cells formed multicellular organisms. However, not all cooperative groups are en route to major transitions. How can we explain why major evolutionary transitions have or haven't taken place on different branches of the tree of life? We break down major transitions into two steps: the formation of a cooperative group and the transformation of that group into an integrated entity. We show how these steps require cooperation, division of labor, communication, mutual dependence, and negligible within-group conflict. We find that certain ecological conditions and the ways in which groups form have played recurrent roles in driving multiple transitions. In contrast, we find that other factors have played relatively minor roles at many key points, such as within-group kin discrimination and mechanisms to actively repress competition. More generally, by identifying the small number of factors that have driven major transitions, we provide a simpler and more unified description of how life on earth has evolved.",
    url = "https://doi.org/10.1073/pnas.1421402112",
    doi = "10.1073/pnas.1421402112",
    openalex = "W2160332754",
    references = "doi101098rstb20090095, doi101111j14209101200801681x, doi101146annurevecolsys36102403114735"
}

The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks.

@article{doi101126scienceaaa4788,
    author = "Kapheim, Karen M. and Pan, Hailin and Li, Cai and Salzberg, Steven L. and Puiu, Daniela and Magoč, Tanja and Robertson, Hugh M. and Hudson, Matthew E. and Venkat, Aarti and Fischman, Brielle J. and Hernández, Álvaro González and Yandell, Mark and Ence, Daniel and Holt, Carson and Yocum, George D. and Kemp, William P. and Bosch, Jordi and Waterhouse, Robert M. and Zdobnov, Evgeny M. and Stolle, Eckart and Kraus, Frank Bernhard and Helbing, Sophie and Moritz, Robin F. A. and Glastad, Karl M. and Hunt, Brendan G. and Goodisman, Michael A. D. and Hauser, Frank and Grimmelikhuijzen, Cornelis J.P. and Pinheiro, Daniel Guariz and Nunes, Francis Morais Franco and Soares, Michelle Prioli Miranda and Tanaka, Erica D. and Simões, Zilá Luz Paulino and Hartfelder, Klaus and Evans, Jay D. and Barribeau, Seth M. and Johnson, Reed M. and Massey, Jonathan H. and Southey, Bruce R. and Hasselmann, Martin and Hamacher, Daniel and Biewer, Matthias and Kent, Clement F. and Zayed, Amro and Blatti, Charles and Sinha, Saurabh and Johnston, J. Spencer and Hanrahan, Shawn J. and Kocher, Sarah D. and Wang, Jun and Robinson, Gene E. and Zhang, Guojie",
    title = "Genomic signatures of evolutionary transitions from solitary to group living",
    year = "2015",
    journal = "Science",
    abstract = "The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks.",
    url = "https://doi.org/10.1126/science.aaa4788",
    doi = "10.1126/science.aaa4788",
    openalex = "W1592395964",
    references = "doi101016jbbapap201006012"
}

@article{doi101007s1053901695422,
    author = "Doolittle, W. Ford and Booth, Austin",
    title = "It’s the song, not the singer: an exploration of holobiosis and evolutionary theory",
    year = "2016",
    journal = "Biology \& Philosophy",
    url = "https://doi.org/10.1007/s10539-016-9542-2",
    doi = "10.1007/s10539-016-9542-2",
    openalex = "W2530941327",
    references = "doi101093acprofosobl97801995520470010001"
}

@article{doi101007s1169201693890,
    author = "Gontier, Nathalie",
    title = "Guest-Editorial Introduction: Converging Evolutionary Patterns in Life and Culture",
    year = "2016",
    journal = "Evolutionary Biology",
    url = "https://doi.org/10.1007/s11692-016-9389-0",
    doi = "10.1007/s11692-016-9389-0",
    openalex = "W2531608350",
    references = "doi10100797833191504517"
}

Discrete character-taxon matrices are increasingly being used in an attempt to understand the pattern and tempo of morphological evolution; however, methodological sophistication and bespoke software implementations have lagged behind. In the present study, an attempt is made to provide a state-of-the-art description of methodologies and introduce a new R package (Claddis) for performing foundational disparity (morphologic diversity) and rate calculations. Simulations using its core functions show that: (1) of the two most commonly used distance metrics (Generalized Euclidean Distance and Gower's Coefficient), the latter tends to carry forward more of the true signal; (2) a novel distance metric may improve signal retention further; (3) this signal retention may come at the cost of pruning incomplete taxa from the data set; and (4) the utility of bivariate plots of ordination spaces are undermined by their frequently extremely low variances. By contrast, challenges to estimating morphologic tempo are presented qualitatively, such as how trees are time-scaled and changes are counted. Both disparity and rates deserve better time series approaches that could unlock new macroevolutionary analyses. However, these challenges need not be fatal, and several potential future solutions and directions are suggested.

@article{doi101111bij12746,
    author = "Lloyd, Graeme T.",
    title = "Estimating morphological diversity and tempo with discrete character-taxon matrices: implementation, challenges, progress, and future directions",
    year = "2016",
    journal = "Biological Journal of the Linnean Society",
    abstract = "Discrete character-taxon matrices are increasingly being used in an attempt to understand the pattern and tempo of morphological evolution; however, methodological sophistication and bespoke software implementations have lagged behind. In the present study, an attempt is made to provide a state-of-the-art description of methodologies and introduce a new R package (Claddis) for performing foundational disparity (morphologic diversity) and rate calculations. Simulations using its core functions show that: (1) of the two most commonly used distance metrics (Generalized Euclidean Distance and Gower's Coefficient), the latter tends to carry forward more of the true signal; (2) a novel distance metric may improve signal retention further; (3) this signal retention may come at the cost of pruning incomplete taxa from the data set; and (4) the utility of bivariate plots of ordination spaces are undermined by their frequently extremely low variances. By contrast, challenges to estimating morphologic tempo are presented qualitatively, such as how trees are time-scaled and changes are counted. Both disparity and rates deserve better time series approaches that could unlock new macroevolutionary analyses. However, these challenges need not be fatal, and several potential future solutions and directions are suggested.",
    url = "https://doi.org/10.1111/bij.12746",
    doi = "10.1111/bij.12746",
    openalex = "W2280099985",
    references = "doi101016jcub201408034, doi101073pnas1302642110, doi101093bioinformaticsbtg412, doi101093biomet5234591, doi101093sysbio204406, doi101111brv12038, doi101111j10960031200800217x, doi101111j10963642200900571x, doi101111j2041210x201100169x, doi101111j2041210x201200223x, doi101111j251761611995tb02031x, doi101111pala12142, doi101126science1252243, doi101371journalpcbi1003537, doi101666009483731999251mditer20co2, doi1018637jssv022i04, doi1023072412116, doi102992014590582006371pon20co2, openalexw3217097258, openalexw586972754"
}

Flatfish cranial asymmetry represents one of the most remarkable morphological innovations among vertebrates, and has fueled vigorous debate on the manner and rate at which strikingly divergent phenotypes evolve. A surprising result of many recent molecular phylogenetic studies is the lack of support for flatfish monophyly, where increasingly larger DNA datasets of up to 23 loci have either yielded a weakly supported flatfish clade or indicated the group is polyphyletic. Lack of resolution for flatfish relationships has been attributed to analytical limitations for dealing with processes such as nucleotide non-stationarity and incomplete lineage sorting (ILS). We tackle this phylogenetic problem using a sequence dataset comprising more than 1,000 ultraconserved DNA element (UCE) loci covering 45 carangimorphs, the broader clade containing flatfishes and several other specialized lineages such as remoras, billfishes, and archerfishes. We present a phylogeny based on UCE loci that unequivocally supports flatfish monophyly and a single origin of asymmetry. We document similar levels of discordance among UCE loci as in previous, smaller molecular datasets. However, relationships among flatfishes and carangimorphs recovered from multilocus concatenated and species tree analyses of our data are robust to the analytical framework applied and size of data matrix used. By integrating the UCE data with a rich fossil record, we find that the most distinctive carangimorph bodyplans arose rapidly during the Paleogene (66.0–23.03 Ma). Flatfish asymmetry, for example, likely evolved over an interval of no more than 2.97 million years. The longstanding uncertainty in phylogenetic hypotheses for flatfishes and their carangimorph relatives highlights the limitations of smaller molecular datasets when applied to successive, rapid divergences. Here, we recovered significant support for flatfish monophyly and relationships among carangimorphs through analysis of over 1,000 UCE loci. The resulting time-calibrated phylogeny points to phenotypic divergence early within carangimorph history that broadly matches with the predictions of adaptive models of lineage diversification.

@article{doi101186s128620160786x,
    author = "Harrington, R. and Faircloth, B. and Eytan, R. and Smith, W. and Near, T. and Alfaro, M. and Friedman, M.",
    title = "Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye",
    year = "2016",
    journal = "BMC Evolutionary Biology",
    abstract = "Flatfish cranial asymmetry represents one of the most remarkable morphological innovations among vertebrates, and has fueled vigorous debate on the manner and rate at which strikingly divergent phenotypes evolve. A surprising result of many recent molecular phylogenetic studies is the lack of support for flatfish monophyly, where increasingly larger DNA datasets of up to 23 loci have either yielded a weakly supported flatfish clade or indicated the group is polyphyletic. Lack of resolution for flatfish relationships has been attributed to analytical limitations for dealing with processes such as nucleotide non-stationarity and incomplete lineage sorting (ILS). We tackle this phylogenetic problem using a sequence dataset comprising more than 1,000 ultraconserved DNA element (UCE) loci covering 45 carangimorphs, the broader clade containing flatfishes and several other specialized lineages such as remoras, billfishes, and archerfishes. We present a phylogeny based on UCE loci that unequivocally supports flatfish monophyly and a single origin of asymmetry. We document similar levels of discordance among UCE loci as in previous, smaller molecular datasets. However, relationships among flatfishes and carangimorphs recovered from multilocus concatenated and species tree analyses of our data are robust to the analytical framework applied and size of data matrix used. By integrating the UCE data with a rich fossil record, we find that the most distinctive carangimorph bodyplans arose rapidly during the Paleogene (66.0–23.03 Ma). Flatfish asymmetry, for example, likely evolved over an interval of no more than 2.97 million years. The longstanding uncertainty in phylogenetic hypotheses for flatfishes and their carangimorph relatives highlights the limitations of smaller molecular datasets when applied to successive, rapid divergences. Here, we recovered significant support for flatfish monophyly and relationships among carangimorphs through analysis of over 1,000 UCE loci. The resulting time-calibrated phylogeny points to phenotypic divergence early within carangimorph history that broadly matches with the predictions of adaptive models of lineage diversification.",
    url = "https://bmcevolbiol.biomedcentral.com/track/pdf/10.1186/s12862-016-0786-x",
    doi = "10.1186/s12862-016-0786-x",
    is_oa = "true",
    number = "1",
    semanticscholar_citation_count = "98",
    semanticscholar_id = "fba689bc183f88acbc28c2115005a9f0f2ed9dc8",
    volume = "16"
}

@article{doi101038nature21074,
    author = "Cooney, Christopher R. and Bright, Jen A. and Capp, Elliot J. R. and Chira, Angela M. and Hughes, Emma C. and Moody, Christopher J. and Nouri, L. O. and Varley, Zoë K. and Thomas, Gavin H.",
    title = "Mega-evolutionary dynamics of the adaptive radiation of birds",
    year = "2017",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature21074",
    doi = "10.1038/nature21074",
    openalex = "W2585565608",
    references = "doi10100703064746897, doi101016c20100662092, doi101016jcub201508003, doi101038nature10516, doi101038nature11631, doi101038nature15697, doi101073pnas1302642110, doi101093molbevmss075, doi1011112041210x12035, doi101111j2041210x201100169x, doi101126science1157704, doi101126science1160662, doi1018637jssv033i02, doi105860choice485062"
}

@incollection{doi101007978331972478230,
    author = "Gontier, Nathalie",
    title = "On How Epistemology and Ontology Converge Through Evolution: The Applied Evolutionary Epistemological Approach",
    year = "2018",
    booktitle = "˜The œfrontiers collection",
    url = "https://doi.org/10.1007/978-3-319-72478-2\_30",
    doi = "10.1007/978-3-319-72478-2\_30",
    openalex = "W2789395182",
    references = "doi10100797833191504517"
}

Fishes are characterized by their capacity to occupy all aquatic environments and by their amazing range of size and morphology. While it is known that habitat influenced the diversity dynamics of fish clades, studies on environmental colonization events through the evolutionary history of ray‐finned fishes have yielded conflicting results as to the origin of modern clades and preferential directions of shifts. The effects of habitat over morphological evolution such as body size remain poorly known in vertebrates. However, body size evolution is more frequently addressed in terms of variation through time and numerous studies have demonstrated that successive taxa within a clade tend to increase in size through time (Cope's or Depéret's rule). We use phylogenetic comparative methods on a genus‐level actinopterygian super‐tree based on extant and fossil data covering the Late Jurassic‐Paleogene interval. Results indicate marine ancestry for freshwater lineages and a dominance of colonizations from marine clades towards other habitats. Similar trends in environment occupancy among different ray‐finned clades are explored. Three main trends affecting non‐closely‐related clades are recognized: (i) the freshwater invaders, (ii) the predominantly marine dwellers and (iii) the environmentally labile fishes. Habitat effects on body size evolution are not statistically supported, but most actinopterygian subclades originate from small‐sized ancestors and tend to increase in size in the course of their evolutionary history. This trend is clear for lineages restricted for long periods of time in the same environments, either marine or freshwater, but it is not observed in environmentally labile fish lineages.

@article{doi101111faf12275,
    author = "Guinot, G. and Cavin, L.",
    title = "Body size evolution and habitat colonization across 100 million years (Late Jurassic–Paleocene) of the actinopterygian evolutionary history",
    year = "2018",
    journal = "Fish and Fisheries",
    abstract = "Fishes are characterized by their capacity to occupy all aquatic environments and by their amazing range of size and morphology. While it is known that habitat influenced the diversity dynamics of fish clades, studies on environmental colonization events through the evolutionary history of ray‐finned fishes have yielded conflicting results as to the origin of modern clades and preferential directions of shifts. The effects of habitat over morphological evolution such as body size remain poorly known in vertebrates. However, body size evolution is more frequently addressed in terms of variation through time and numerous studies have demonstrated that successive taxa within a clade tend to increase in size through time (Cope's or Depéret's rule). We use phylogenetic comparative methods on a genus‐level actinopterygian super‐tree based on extant and fossil data covering the Late Jurassic‐Paleogene interval. Results indicate marine ancestry for freshwater lineages and a dominance of colonizations from marine clades towards other habitats. Similar trends in environment occupancy among different ray‐finned clades are explored. Three main trends affecting non‐closely‐related clades are recognized: (i) the freshwater invaders, (ii) the predominantly marine dwellers and (iii) the environmentally labile fishes. Habitat effects on body size evolution are not statistically supported, but most actinopterygian subclades originate from small‐sized ancestors and tend to increase in size in the course of their evolutionary history. This trend is clear for lineages restricted for long periods of time in the same environments, either marine or freshwater, but it is not observed in environmentally labile fish lineages.",
    url = "https://www.semanticscholar.org/paper/005f86cb8dbee4ff06a35ddfc3afbb73f9104c5e",
    doi = "10.1111/FAF.12275",
    is_oa = "true",
    number = "4",
    pages = "577-597",
    semanticscholar_citation_count = "24",
    semanticscholar_id = "005f86cb8dbee4ff06a35ddfc3afbb73f9104c5e",
    volume = "19"
}

Biological evolution is a fact-but the many conflicting theories of evolution remain controversial even today. When Adaptation and Natural Selection was first published in 1966, it struck a powerful blow against those who argued for the concept of group selection-the idea that evolution acts to select entire species rather than individuals. Williams's famous work in favor of simple Darwinism over group selection has become a classic of science literature, valued for its thorough and convincing argument and its relevance to many fields outside of biology. Now with a new foreword by Richard Dawkins, Adaptation and Natural Selection is an essential text for understanding the nature of scientific debate

@book{doi1015159780691185507,
    author = "Williams, George C.",
    title = "Adaptation and Natural Selection: A Critique of Some Current Evolutionary Thought",
    year = "2018",
    abstract = "Biological evolution is a fact-but the many conflicting theories of evolution remain controversial even today. When Adaptation and Natural Selection was first published in 1966, it struck a powerful blow against those who argued for the concept of group selection-the idea that evolution acts to select entire species rather than individuals. Williams's famous work in favor of simple Darwinism over group selection has become a classic of science literature, valued for its thorough and convincing argument and its relevance to many fields outside of biology. Now with a new foreword by Richard Dawkins, Adaptation and Natural Selection is an essential text for understanding the nature of scientific debate",
    url = "https://doi.org/10.1515/9780691185507",
    doi = "10.1515/9780691185507",
    openalex = "W1480083809"
}

Butterflies and moths (Lepidoptera) are one of the major superradiations of insects, comprising nearly 160,000 described extant species. As herbivores, pollinators, and prey, Lepidoptera play a fundamental role in almost every terrestrial ecosystem. Lepidoptera are also indicators of environmental change and serve as models for research on mimicry and genetics. They have been central to the development of coevolutionary hypotheses, such as butterflies with flowering plants and moths’ evolutionary arms race with echolocating bats. However, these hypotheses have not been rigorously tested, because a robust lepidopteran phylogeny and timing of evolutionary novelties are lacking. To address these issues, we inferred a comprehensive phylogeny of Lepidoptera, using the largest dataset assembled for the order (2,098 orthologous protein-coding genes from transcriptomes of 186 species, representing nearly all superfamilies), and dated it with carefully evaluated synapomorphy-based fossils. The oldest members of the Lepidoptera crown group appeared in the Late Carboniferous (∼300 Ma) and fed on nonvascular land plants. Lepidoptera evolved the tube-like proboscis in the Middle Triassic (∼241 Ma), which allowed them to acquire nectar from flowering plants. This morphological innovation, along with other traits, likely promoted the extraordinary diversification of superfamily-level lepidopteran crown groups. The ancestor of butterflies was likely nocturnal, and our results indicate that butterflies became day-flying in the Late Cretaceous (∼98 Ma). Moth hearing organs arose multiple times before the evolutionary arms race between moths and bats, perhaps initially detecting a wide range of sound frequencies before being co-opted to specifically detect bat sonar. Our study provides an essential framework for future comparative studies on butterfly and moth evolution.

@article{doi101073pnas1907847116,
    author = "Kawahara, Akito Y. and Plotkin, David and Espeland, Marianne and Meusemann, Karen and Toussaint, Emmanuel F. A. and Donath, Alexander and Gimnich, France and Frandsen, Paul B. and Zwick, Andreas and dos Reis, Mario and Barber, Jesse R. and Peters, Ralph S. and Liu, Shanlin and Zhou, Xin and Mayer, Christoph and Podsiadłowski, Lars and Storer, Caroline and Yack, Jayne E. and Misof, Bernhard and Breinholt, Jesse W.",
    title = "Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths",
    year = "2019",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Butterflies and moths (Lepidoptera) are one of the major superradiations of insects, comprising nearly 160,000 described extant species. As herbivores, pollinators, and prey, Lepidoptera play a fundamental role in almost every terrestrial ecosystem. Lepidoptera are also indicators of environmental change and serve as models for research on mimicry and genetics. They have been central to the development of coevolutionary hypotheses, such as butterflies with flowering plants and moths’ evolutionary arms race with echolocating bats. However, these hypotheses have not been rigorously tested, because a robust lepidopteran phylogeny and timing of evolutionary novelties are lacking. To address these issues, we inferred a comprehensive phylogeny of Lepidoptera, using the largest dataset assembled for the order (2,098 orthologous protein-coding genes from transcriptomes of 186 species, representing nearly all superfamilies), and dated it with carefully evaluated synapomorphy-based fossils. The oldest members of the Lepidoptera crown group appeared in the Late Carboniferous (∼300 Ma) and fed on nonvascular land plants. Lepidoptera evolved the tube-like proboscis in the Middle Triassic (∼241 Ma), which allowed them to acquire nectar from flowering plants. This morphological innovation, along with other traits, likely promoted the extraordinary diversification of superfamily-level lepidopteran crown groups. The ancestor of butterflies was likely nocturnal, and our results indicate that butterflies became day-flying in the Late Cretaceous (∼98 Ma). Moth hearing organs arose multiple times before the evolutionary arms race between moths and bats, perhaps initially detecting a wide range of sound frequencies before being co-opted to specifically detect bat sonar. Our study provides an essential framework for future comparative studies on butterfly and moth evolution.",
    url = "https://doi.org/10.1073/pnas.1907847116",
    doi = "10.1073/pnas.1907847116",
    openalex = "W2982062771",
    references = "doi101073pnas1213621109, doi101093bioinformaticsbtu033, doi101093molbevmsm088, doi101093molbevmst010, doi101093molbevmsu300, doi101093molbevmsw260, doi101093molbevmsx281, doi101093nargkl315, doi101093sysbiosyq010, doi101098rspb20120683, doi101111evo12681, doi101111j155856461964tb01674x, doi101111j2041210x201100169x, doi101186s128590182129y"
}

The comparative method has long been a fundamental exploratory tool in evolutionary biology, but this venerable approach was revolutionized in 1985, when Felsenstein published "Phylogenies and the Comparative Method" in The American Naturalist. This article forced comparative biologists to start thinking phylogenetically when conducting statistical analyses of correlated trait evolution rather than simply applying conventional statistical methods that ignore evolutionary relationships. It did so by introducing a novel analytical method (phylogenetically "independent contrasts") that required a phylogenetic topology with branch lengths and that assumed a Brownian motion model of trait evolution. Independent contrasts enabled comparative biologists to avoid the statistical dilemma of nonindependence of species values, arising from shared ancestry, but came at the cost of needing a detailed phylogeny and of accepting a specific model of character change. Nevertheless, this article not only revitalized comparative biology but even encouraged studies aimed at estimating phylogenies. Felsenstein's characteristically lucid and concise statement of the problem (illustrated with powerful graphics), coupled with an oncoming flood of new molecular data and techniques for estimating phylogenies, led Felsenstein's 1985 article to become the second most cited article in the history of this journal. Here we present a personal review of comparative biology before, during, and after Joe's article. For historical context, we append a perspective written by Joe himself that describes how his article evolved, unedited transcripts of reviews of his submitted manuscript, and a guide to some nontrivial calculations. These additional materials help emphasize that the process of science does not always occur gradually or predictably.

@article{doi101086703055,
    author = "Huey, Raymond B. and Garland, Theodore and Turelli, Michael",
    title = "Revisiting a Key Innovation in Evolutionary Biology: Felsenstein’s “Phylogenies and the Comparative Method”",
    year = "2019",
    journal = "The American Naturalist",
    abstract = {The comparative method has long been a fundamental exploratory tool in evolutionary biology, but this venerable approach was revolutionized in 1985, when Felsenstein published "Phylogenies and the Comparative Method" in The American Naturalist. This article forced comparative biologists to start thinking phylogenetically when conducting statistical analyses of correlated trait evolution rather than simply applying conventional statistical methods that ignore evolutionary relationships. It did so by introducing a novel analytical method (phylogenetically "independent contrasts") that required a phylogenetic topology with branch lengths and that assumed a Brownian motion model of trait evolution. Independent contrasts enabled comparative biologists to avoid the statistical dilemma of nonindependence of species values, arising from shared ancestry, but came at the cost of needing a detailed phylogeny and of accepting a specific model of character change. Nevertheless, this article not only revitalized comparative biology but even encouraged studies aimed at estimating phylogenies. Felsenstein's characteristically lucid and concise statement of the problem (illustrated with powerful graphics), coupled with an oncoming flood of new molecular data and techniques for estimating phylogenies, led Felsenstein's 1985 article to become the second most cited article in the history of this journal. Here we present a personal review of comparative biology before, during, and after Joe's article. For historical context, we append a perspective written by Joe himself that describes how his article evolved, unedited transcripts of reviews of his submitted manuscript, and a guide to some nontrivial calculations. These additional materials help emphasize that the process of science does not always occur gradually or predictably.},
    url = "https://doi.org/10.1086/703055",
    doi = "10.1086/703055",
    openalex = "W2933507162",
    references = "doi101073pnas0704088104, doi101086660020, doi101086physzool67430163866, doi101093sysbiosyy031, doi101242jeb01745"
}

The ongoing SARS-CoV-2 evolution process has generated several variants due to its continuous mutations, making pandemics more critical. The present study illustrates SARS-CoV-2 evolution and its emerging mutations in five directions. First, the significant mutations in the genome and S-glycoprotein were analyzed in different variants. Three linear models were developed with the regression line to depict the mutational load for S-glycoprotein, total genome excluding S-glycoprotein, and whole genome. Second, the continent-wide evolution of SARS-CoV-2 and its variants with their clades and divergence were evaluated. It showed the region-wise evolution of the SARS-CoV-2 variants and their clustering event. The major clades for each variant were identified. One example is clade 21K, a major clade of the Omicron variant. Third, lineage dynamics and comparison between SARS-CoV-2 lineages across different countries are also illustrated, demonstrating dominant variants in various countries over time. Fourth, gene-wise mutation patterns and genetic variability of SARS-CoV-2 variants across various countries are illustrated. High mutation patterns were found in the ORF10, ORF6, S, and low mutation pattern E genes. Finally, emerging AA point mutations (T478K, L452R, N501Y, S477N, E484A, Q498R, and Y505H), their frequencies, and country-wise occurrence were identified, and the highest event of two mutations (T478K and L452R) was observed.

@article{doi101007s1135702200619y,
    author = "Chakraborty, C. and Bhattacharya, M. and Sharma, A. R. and Dhama, K. and Lee, Sang-Soo",
    title = "Continent-wide evolutionary trends of emerging SARS-CoV-2 variants: dynamic profiles from Alpha to Omicron",
    year = "2022",
    journal = "GeroScience",
    abstract = "The ongoing SARS-CoV-2 evolution process has generated several variants due to its continuous mutations, making pandemics more critical. The present study illustrates SARS-CoV-2 evolution and its emerging mutations in five directions. First, the significant mutations in the genome and S-glycoprotein were analyzed in different variants. Three linear models were developed with the regression line to depict the mutational load for S-glycoprotein, total genome excluding S-glycoprotein, and whole genome. Second, the continent-wide evolution of SARS-CoV-2 and its variants with their clades and divergence were evaluated. It showed the region-wise evolution of the SARS-CoV-2 variants and their clustering event. The major clades for each variant were identified. One example is clade 21K, a major clade of the Omicron variant. Third, lineage dynamics and comparison between SARS-CoV-2 lineages across different countries are also illustrated, demonstrating dominant variants in various countries over time. Fourth, gene-wise mutation patterns and genetic variability of SARS-CoV-2 variants across various countries are illustrated. High mutation patterns were found in the ORF10, ORF6, S, and low mutation pattern E genes. Finally, emerging AA point mutations (T478K, L452R, N501Y, S477N, E484A, Q498R, and Y505H), their frequencies, and country-wise occurrence were identified, and the highest event of two mutations (T478K and L452R) was observed.",
    url = "https://link.springer.com/content/pdf/10.1007/s11357-022-00619-y.pdf",
    doi = "10.1007/s11357-022-00619-y",
    is_oa = "true",
    number = "5",
    pages = "2371-2392",
    semanticscholar_citation_count = "20",
    semanticscholar_id = "f62bf77d9714996231c7d496e675ce974c075ed9",
    volume = "44"
}

Background Body size is a fundamental organismal trait. However, as body size and ecological contexts change across developmental time, evolutionary divergence may cause unexpected patterns of body size diversity among developmental stages. This may be particularly evident in polyphenic developmental stages specialized for dispersal. The dauer larva is such a stage in nematodes, and Caenorhabditis species disperse by traveling on invertebrate carriers. Here, we describe the morphology of a stress-resistant, dauer-like larval stage of the nematode Caenorhabditis inopinata , whose adults can grow to be nearly twice as long as its close relative, the model organism C. elegans . Results We find that a dauer-like, stress-resistant larval stage in two isolates of C. inopinata is on average 13% shorter and 30% wider than the dauer larvae of C. elegans , despite its much longer adult stage. Additionally, many C. inopinata dauer-like larvae were ensheathed, a possible novelty in this lineage reminiscent of the infective juveniles of parasitic nematodes. Variation in dauer-like larva formation frequency among twenty-four wild isolates of C. inopinata was also observed, although frequencies were low across all isolates (< 2%), with many isolates unable to produce dauer-like larvae under conventional laboratory conditions. Conclusion Most Caenorhabditis species thrive on rotting plants and disperse on snails, slugs, or isopods (among others) whereas C. inopinata is ecologically divergent and thrives in fresh Ficus septica figs and disperses on their pollinating wasps. While there is some unknown factor of the fig environment that promotes elongated body size in C. inopinata adults, the small size or unique life history of its fig wasp carrier may be driving the divergent morphology of its stress-resistant larval stages. Further characterization of the behavior, development, and morphology of this stage will refine connections to homologous developmental stages in other species and determine whether ecological divergence across multiple developmental stages can promote unexpected and opposing changes in body size dimensions within a single species.

@article{doi101186s4085002200131y,
    author = "Hammerschmith, Eric W. and Woodruff, Gavin C. and Moser, K. A. and Johnson, E. and Phillips, P.",
    title = "Opposing directions of stage-specific body shape change in a close relative of C. elegans",
    year = "2022",
    journal = "BMC Zoology",
    abstract = "Background Body size is a fundamental organismal trait. However, as body size and ecological contexts change across developmental time, evolutionary divergence may cause unexpected patterns of body size diversity among developmental stages. This may be particularly evident in polyphenic developmental stages specialized for dispersal. The dauer larva is such a stage in nematodes, and Caenorhabditis species disperse by traveling on invertebrate carriers. Here, we describe the morphology of a stress-resistant, dauer-like larval stage of the nematode Caenorhabditis inopinata , whose adults can grow to be nearly twice as long as its close relative, the model organism C. elegans . Results We find that a dauer-like, stress-resistant larval stage in two isolates of C. inopinata is on average 13\% shorter and 30\% wider than the dauer larvae of C. elegans , despite its much longer adult stage. Additionally, many C. inopinata dauer-like larvae were ensheathed, a possible novelty in this lineage reminiscent of the infective juveniles of parasitic nematodes. Variation in dauer-like larva formation frequency among twenty-four wild isolates of C. inopinata was also observed, although frequencies were low across all isolates (< 2\%), with many isolates unable to produce dauer-like larvae under conventional laboratory conditions. Conclusion Most Caenorhabditis species thrive on rotting plants and disperse on snails, slugs, or isopods (among others) whereas C. inopinata is ecologically divergent and thrives in fresh Ficus septica figs and disperses on their pollinating wasps. While there is some unknown factor of the fig environment that promotes elongated body size in C. inopinata adults, the small size or unique life history of its fig wasp carrier may be driving the divergent morphology of its stress-resistant larval stages. Further characterization of the behavior, development, and morphology of this stage will refine connections to homologous developmental stages in other species and determine whether ecological divergence across multiple developmental stages can promote unexpected and opposing changes in body size dimensions within a single species.",
    url = "https://bmczool.biomedcentral.com/counter/pdf/10.1186/s40850-022-00131-y",
    doi = "10.1186/s40850-022-00131-y",
    is_oa = "true",
    number = "1",
    semanticscholar_citation_count = "7",
    semanticscholar_id = "1eb76294990b2d1b0f44719510233df8e545e375",
    volume = "7"
}

Polyploidisation often results in genome rearrangements that may involve changes in both the single-copy sequences and the repetitive genome fraction. In this study, we performed a comprehensive comparative analysis of repetitive DNA, with a particular focus on ribosomal DNA (rDNA), in Brachypodium hybridum (2n = 4x = 30, subgenome composition DDSS), an allotetraploid resulting from a natural cross between two diploid species that resemble the modern B. distachyon (2n = 10; DD) and B. stacei (2n = 20; SS). Taking advantage of the recurrent origin of B. hybridum, we investigated two genotypes, Bhyb26 and ABR113, differing markedly in their evolutionary age (1.4 and 0.14 Mya, respectively) and which resulted from opposite cross directions. To identify the origin of rDNA loci we employed cytogenetic and molecular methods (FISH, gCAPS and Southern hybridisation), phylogenetic and genomic approaches. Unlike the general maintenance of doubled gene dosage in B. hybridum, the rRNA genes showed a remarkable tendency towards diploidisation at both locus and unit levels. While the partial elimination of 35S rDNA units occurred in the younger ABR113 lineage, unidirectional elimination of the entire locus was observed in the older Bhyb26 lineage. Additionally, a novel 5S rDNA family was amplified in Bhyb26 replacing the parental units. The 35S and 5S rDNA units were preferentially eliminated from the S- and D-subgenome, respectively. Thus, in the more ancient B. hybridum lineage, Bhyb26, 5S and 35S rRNA genes are likely expressed from different subgenomes, highlighting the complexity of polyploid regulatory networks. Comparative analyses between two B. hybridum lineages of distinct evolutionary ages revealed that although the recent lineage ABR113 exhibited an additive pattern of rDNA loci distribution, the ancient lineage Bhyb26 demonstrated a pronounced tendency toward diploidisation manifested by the reduction in the number of both 35S and 5S loci. In conclusion, the age of the allopolyploid appears to be a decisive factor in rDNA turnover in B. hybridum.

@article{doi101186s12870024056585,
    author = "Trunova, Dana and Borowska-Zuchowska, Natalia and Mykhailyk, Serhii and Xia, Kai and Zhu, Yuanbin and Sancho, R. and Rojek-Jelonek, Magdalena and Garcia, Sònia and Wang, Kai and Catalán, P. and Kovařík, A. and Hasterok, R. and Kolano, B.",
    title = "Does time matter? Intraspecific diversity of ribosomal RNA genes in lineages of the allopolyploid model grass Brachypodium hybridum with different evolutionary ages",
    year = "2024",
    journal = "BMC Plant Biology",
    abstract = "Polyploidisation often results in genome rearrangements that may involve changes in both the single-copy sequences and the repetitive genome fraction. In this study, we performed a comprehensive comparative analysis of repetitive DNA, with a particular focus on ribosomal DNA (rDNA), in Brachypodium hybridum (2n = 4x = 30, subgenome composition DDSS), an allotetraploid resulting from a natural cross between two diploid species that resemble the modern B. distachyon (2n = 10; DD) and B. stacei (2n = 20; SS). Taking advantage of the recurrent origin of B. hybridum, we investigated two genotypes, Bhyb26 and ABR113, differing markedly in their evolutionary age (1.4 and 0.14 Mya, respectively) and which resulted from opposite cross directions. To identify the origin of rDNA loci we employed cytogenetic and molecular methods (FISH, gCAPS and Southern hybridisation), phylogenetic and genomic approaches. Unlike the general maintenance of doubled gene dosage in B. hybridum, the rRNA genes showed a remarkable tendency towards diploidisation at both locus and unit levels. While the partial elimination of 35S rDNA units occurred in the younger ABR113 lineage, unidirectional elimination of the entire locus was observed in the older Bhyb26 lineage. Additionally, a novel 5S rDNA family was amplified in Bhyb26 replacing the parental units. The 35S and 5S rDNA units were preferentially eliminated from the S- and D-subgenome, respectively. Thus, in the more ancient B. hybridum lineage, Bhyb26, 5S and 35S rRNA genes are likely expressed from different subgenomes, highlighting the complexity of polyploid regulatory networks. Comparative analyses between two B. hybridum lineages of distinct evolutionary ages revealed that although the recent lineage ABR113 exhibited an additive pattern of rDNA loci distribution, the ancient lineage Bhyb26 demonstrated a pronounced tendency toward diploidisation manifested by the reduction in the number of both 35S and 5S loci. In conclusion, the age of the allopolyploid appears to be a decisive factor in rDNA turnover in B. hybridum.",
    url = "https://www.semanticscholar.org/paper/b95986016ac0c4eb4a396a651d4e936a3475cb83",
    doi = "10.1186/s12870-024-05658-5",
    is_oa = "true",
    number = "1",
    semanticscholar_citation_count = "5",
    semanticscholar_id = "b95986016ac0c4eb4a396a651d4e936a3475cb83",
    volume = "24"
}

The evolution of multicellular organisms involves the emergence of cellular collectives that eventually become units of selection in their own right. The process can be facilitated by ecological conditions that impose heritable variance in fitness on nascent collectives with long-term persistence depending on capacity of competing lineages to transition reliably between soma- and germ-like stages of proto-life cycles. Prior work with experimental bacterial populations showed rapid increases in collective-level fitness with capacity to switch between life cycle phases being a particular focus of selection. Here we report experiments in which the most successful lineage from the earlier study was further propagated for 10 life cycle generations under regimes that required different investment in the somalike phase. To explore the adaptive significance of switching, a control was included in which reliable transitioning between life cycle phases was abolished. The switch proved central to maintenance of fitness. Moreover, in a non-switch treatment, where solutions to producing a robust and enduring soma-phase were required, evolution of mutL -dependent switching emerged de novo. A newly developed computational pipeline (colgen) was used to display the moment-by-moment evolutionary dynamics of lineages providing rare visual evidence of the roles of chance, history and selection. Colgen, underpinned by a Bayesian model, was further used to propagate hundreds of mutations back through temporal genealogical series, predict lineages and time points corresponding to changes of likely adaptive significance, and in one instance, via a combination of targeted sequencing, genetics and analyses of fitness consequences, adaptive significance of a single mutation was demonstrated. Overall, our results shed light on the mechanisms by which collectives adapt to new selective challenges and demonstrate the value of genealogy-centered approaches for investigating the dynamics of lineage-level selection.

@misc{doulcier2024evolutionary,
    author = "Doulcier, Guilhem and Remigi, Philippe and Rexin, Daniel and Rainey, Paul B.",
    title = "Evolutionary dynamics of nascent multicellular lineages",
    year = "2024",
    abstract = "The evolution of multicellular organisms involves the emergence of cellular collectives that eventually become units of selection in their own right. The process can be facilitated by ecological conditions that impose heritable variance in fitness on nascent collectives with long-term persistence depending on capacity of competing lineages to transition reliably between soma- and germ-like stages of proto-life cycles. Prior work with experimental bacterial populations showed rapid increases in collective-level fitness with capacity to switch between life cycle phases being a particular focus of selection. Here we report experiments in which the most successful lineage from the earlier study was further propagated for 10 life cycle generations under regimes that required different investment in the somalike phase. To explore the adaptive significance of switching, a control was included in which reliable transitioning between life cycle phases was abolished. The switch proved central to maintenance of fitness. Moreover, in a non-switch treatment, where solutions to producing a robust and enduring soma-phase were required, evolution of mutL -dependent switching emerged de novo. A newly developed computational pipeline (colgen) was used to display the moment-by-moment evolutionary dynamics of lineages providing rare visual evidence of the roles of chance, history and selection. Colgen, underpinned by a Bayesian model, was further used to propagate hundreds of mutations back through temporal genealogical series, predict lineages and time points corresponding to changes of likely adaptive significance, and in one instance, via a combination of targeted sequencing, genetics and analyses of fitness consequences, adaptive significance of a single mutation was demonstrated. Overall, our results shed light on the mechanisms by which collectives adapt to new selective challenges and demonstrate the value of genealogy-centered approaches for investigating the dynamics of lineage-level selection.",
    url = "https://doi.org/10.1101/2024.05.10.593459",
    doi = "10.1101/2024.05.10.593459",
    openalex = "W4396894299",
    references = "doi101002sici1520660219981127aidinbi430co26, doi101007978149390554612, doi101016jtree201206001, doi101038nature01906, doi101086410450, doi101093acprofoso97801992679720010001, doi101093acprofosobl97801995520470010001, doi10110120240501592015, doi101111j251761611977tb01600x, doi101126science16238591243, doi101146annurevecolsys36102403114735"
}

Macroautophagy (hereafter referred to as autophagy) requires the coordinated action of approximately 20 autophagy-related (ATG) genes. Duplication of ATG genes has had a major impact on the evolution of the autophagy pathway among major lineages. One duplication hotspot is in vertebrates. However, the exact duplication timing, post-duplication evolutionary divergence patterns, and its relation to functional differences among paralogs have not been investigated in detail. Here, we demonstrate that most ATG genes were likely duplicated by whole-genome duplication events near the root of vertebrates. We compared the sequence and gene expression divergence between paralogs and categorized the evolutionary fates (i.e., how ancestral function is divided between paralogs). Within the paralog pairs that evolved most asymmetrically, namely BECN, WIPI (WIPI1 and WIPI2), and ATG16, one paralog likely retained the ancestral function, allowing the other to evolve under less constraint. While no obvious asymmetry was observed between ATG9A and ATG9B in non-mammalian vertebrates, ATG9B experienced marked sequence divergence and expression level reduction in mammals, suggesting a shift in balance. Expression patterns among the ULK-1 (ULK1 and ULK2), GABARAP (GABARAP and GABARAPL1), and LC3 (LC3A and LC3B) pairs were more consistent with hypofunctionalization/dosage sharing, such that ancestral function depends on both paralogs. We also demonstrate that both ULK1 and ULK2 can support autophagy, whereas only BECN1, but not BECN2, has autophagic function and discuss the relationship between autophagic function and evolutionary divergence between paralogs. The present detailed analysis of ATG gene duplication in vertebrates provides a critical time-line for interpreting functional differentiation between homologs.

@article{doi1010801554862720262618126,
    author = "Zhang, Sidi and Koyama-Honda, Ikuko and Hiratsuka, Daiki and Mizushima, Noboru",
    title = "ATG gene duplication in vertebrates: evolutionary divergence and its functional implications",
    year = "2025",
    journal = "Autophagy",
    abstract = "Macroautophagy (hereafter referred to as autophagy) requires the coordinated action of approximately 20 autophagy-related (ATG) genes. Duplication of ATG genes has had a major impact on the evolution of the autophagy pathway among major lineages. One duplication hotspot is in vertebrates. However, the exact duplication timing, post-duplication evolutionary divergence patterns, and its relation to functional differences among paralogs have not been investigated in detail. Here, we demonstrate that most ATG genes were likely duplicated by whole-genome duplication events near the root of vertebrates. We compared the sequence and gene expression divergence between paralogs and categorized the evolutionary fates (i.e., how ancestral function is divided between paralogs). Within the paralog pairs that evolved most asymmetrically, namely BECN, WIPI (WIPI1 and WIPI2), and ATG16, one paralog likely retained the ancestral function, allowing the other to evolve under less constraint. While no obvious asymmetry was observed between ATG9A and ATG9B in non-mammalian vertebrates, ATG9B experienced marked sequence divergence and expression level reduction in mammals, suggesting a shift in balance. Expression patterns among the ULK-1 (ULK1 and ULK2), GABARAP (GABARAP and GABARAPL1), and LC3 (LC3A and LC3B) pairs were more consistent with hypofunctionalization/dosage sharing, such that ancestral function depends on both paralogs. We also demonstrate that both ULK1 and ULK2 can support autophagy, whereas only BECN1, but not BECN2, has autophagic function and discuss the relationship between autophagic function and evolutionary divergence between paralogs. The present detailed analysis of ATG gene duplication in vertebrates provides a critical time-line for interpreting functional differentiation between homologs.",
    url = "https://www.semanticscholar.org/paper/ac9b5caabcec7c3bf03c1957d27ee572d67cdaf0",
    doi = "10.1080/15548627.2026.2618126",
    is_oa = "true",
    number = "4",
    pages = "648-665",
    semanticscholar_id = "ac9b5caabcec7c3bf03c1957d27ee572d67cdaf0",
    volume = "22"
}

-dependent switching emerged de novo. A newly developed computational pipeline (colgen) was used to display the moment-by-moment evolutionary dynamics of lineages, providing rare visual evidence of the roles of chance, history and selection. Colgen, underpinned by a Bayesian model, was further used to propagate hundreds of mutations back through temporal genealogical series, predict lineages and time points corresponding to changes of likely adaptive significance, and in one instance, via a combination of targeted sequencing, genetics and analyses of fitness consequences, the adaptive significance of a single mutation was demonstrated. Overall, our results shed light on the mechanisms by which collectives adapt to new selective challenges and demonstrate the value of genealogy-centred approaches for investigating the dynamics of lineage-level selection.

@article{doi101098rspb20241195,
    author = "Doulcier, Guilhem and Remigi, Philippe and Rexin, Daniel and Rainey, Paul B.",
    title = "Evolutionary dynamics of nascent multicellular lineages",
    year = "2025",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "-dependent switching emerged de novo. A newly developed computational pipeline (colgen) was used to display the moment-by-moment evolutionary dynamics of lineages, providing rare visual evidence of the roles of chance, history and selection. Colgen, underpinned by a Bayesian model, was further used to propagate hundreds of mutations back through temporal genealogical series, predict lineages and time points corresponding to changes of likely adaptive significance, and in one instance, via a combination of targeted sequencing, genetics and analyses of fitness consequences, the adaptive significance of a single mutation was demonstrated. Overall, our results shed light on the mechanisms by which collectives adapt to new selective challenges and demonstrate the value of genealogy-centred approaches for investigating the dynamics of lineage-level selection.",
    url = "https://doi.org/10.1098/rspb.2024.1195",
    doi = "10.1098/rspb.2024.1195",
    openalex = "W4409912837",
    references = "doi101007978149390554612, doi101016jtree201206001, doi101093acprofoso97801992679720010001, doi101093acprofosobl97801995520470010001, doi101098rspb20241195, doi101111j155856461988tb02518x, doi101126science16238591243, doi101126scienceadr2756, doi101146annurevecolsys36102403114735, doi1023072410462, doulcier2024evolutionary, openalexw1511986666"
}

, representative of archaic and contemporary infections, to study the impact of deep historical differences shaped by decades of adaptation in varying antibiotic and host pressures. We evaluated these effects by comparing immediate and adaptive responses to the last-resort antibiotic, tigecycline (TGC). The strains demonstrated divergent transcriptional responses, suggesting that baseline transcript levels may dictate global responses to antibiotics. Experimental evolution in TGC revealed clear differences in population dynamics, with hard sweeps in populations founded by one strain and no mutations reaching fixation in the other strain. AMR was acquired through predictable mechanisms of increased efflux and drug target modification; however, efflux targets were dictated by strain background. Genetic adaptation may outweigh historic differences in transcriptional networks, as evolved populations no longer show transcriptomic signatures of drug response. Importantly, fitness-resistance trade-offs were only observed in lineages evolved from the archaic strain, while the contemporary reference isolate suffered no fitness defects. This suggests that decades of adaptation to antibiotics resulted in pre-existing compensatory mechanisms in the more contemporary isolate, an important example of a beneficial effect of historical contingencies.

@article{doi101099mic0001570,
    author = "Rokes, Alecia B. and Santos-López, Alfonso and Cooper, Vaughn S.",
    title = "History shapes regulatory and evolutionary responses to tigecycline in two reference strains of Acinetobacter baumannii",
    year = "2025",
    journal = "Microbiology",
    abstract = ", representative of archaic and contemporary infections, to study the impact of deep historical differences shaped by decades of adaptation in varying antibiotic and host pressures. We evaluated these effects by comparing immediate and adaptive responses to the last-resort antibiotic, tigecycline (TGC). The strains demonstrated divergent transcriptional responses, suggesting that baseline transcript levels may dictate global responses to antibiotics. Experimental evolution in TGC revealed clear differences in population dynamics, with hard sweeps in populations founded by one strain and no mutations reaching fixation in the other strain. AMR was acquired through predictable mechanisms of increased efflux and drug target modification; however, efflux targets were dictated by strain background. Genetic adaptation may outweigh historic differences in transcriptional networks, as evolved populations no longer show transcriptomic signatures of drug response. Importantly, fitness-resistance trade-offs were only observed in lineages evolved from the archaic strain, while the contemporary reference isolate suffered no fitness defects. This suggests that decades of adaptation to antibiotics resulted in pre-existing compensatory mechanisms in the more contemporary isolate, an important example of a beneficial effect of historical contingencies.",
    url = "https://doi.org/10.1099/mic.0.001570",
    doi = "10.1099/mic.0.001570",
    openalex = "W4411147558",
    references = "doi101126scienceadr2756"
}

To reside in marine habitats, marine fishes must actively eliminate the excess Na+ and Cl- they acquire from their environment. These ions are passively absorbed across body surfaces and through the ingestion of seawater (SW), which is necessary to maintain water balance. Salt secretion occurs through the actions of mitochondrion-rich 'SW-type ionocytes' in the gills or other specialized salt-secreting organs. For nearly 50 years, the SW-type ionocyte model proposed by Patricio Silva and colleagues has proven remarkably enduring. The Silva model guided researchers toward identifying key molecular components of SW-type ionocytes, such as cystic fibrosis transmembrane conductance regulator 1 (Cftr1), Na+/K+/2Cl- cotransporter 1 (Nkcc1) and the inwardly rectifying K+ channel (Kir). However, emerging findings indicate that alternative molecular mechanisms may complement, or in some cases, operate in lieu of those included in the Silva model. In this Commentary, we argue that it is time to critically evaluate whether ionocyte-based strategies for salt secretion are more diverse than currently recognized. We highlight recent developments regarding the operation of Cftr-independent ionocytes in lamprey, the emerging role of anoctamin 1 (Ano1) in lamprey and bony fishes, and various 'new' pathways for Cl- and K+ to enter and exit ionocytes. Additionally, we propose future research directions for identifying novel salt-secretory mechanisms in various lineages of marine fishes. We conclude this Commentary by presenting three hypotheses for the divergence of ionocyte-mediated salt secretion in marine fishes and outlining a conceptual framework for considering the evolutionary homology of salt-secreting ionocytes across vertebrates.

@article{doi101242jeb251075,
    author = "Shaughnessy, C. and Breves, Jason P.",
    title = "Salt-secreting ionocytes in marine fishes: new dimensions and evolutionary implications of a fundamental model.",
    year = "2025",
    journal = "The Journal of experimental biology",
    abstract = "To reside in marine habitats, marine fishes must actively eliminate the excess Na+ and Cl- they acquire from their environment. These ions are passively absorbed across body surfaces and through the ingestion of seawater (SW), which is necessary to maintain water balance. Salt secretion occurs through the actions of mitochondrion-rich 'SW-type ionocytes' in the gills or other specialized salt-secreting organs. For nearly 50 years, the SW-type ionocyte model proposed by Patricio Silva and colleagues has proven remarkably enduring. The Silva model guided researchers toward identifying key molecular components of SW-type ionocytes, such as cystic fibrosis transmembrane conductance regulator 1 (Cftr1), Na+/K+/2Cl- cotransporter 1 (Nkcc1) and the inwardly rectifying K+ channel (Kir). However, emerging findings indicate that alternative molecular mechanisms may complement, or in some cases, operate in lieu of those included in the Silva model. In this Commentary, we argue that it is time to critically evaluate whether ionocyte-based strategies for salt secretion are more diverse than currently recognized. We highlight recent developments regarding the operation of Cftr-independent ionocytes in lamprey, the emerging role of anoctamin 1 (Ano1) in lamprey and bony fishes, and various 'new' pathways for Cl- and K+ to enter and exit ionocytes. Additionally, we propose future research directions for identifying novel salt-secretory mechanisms in various lineages of marine fishes. We conclude this Commentary by presenting three hypotheses for the divergence of ionocyte-mediated salt secretion in marine fishes and outlining a conceptual framework for considering the evolutionary homology of salt-secreting ionocytes across vertebrates.",
    url = "https://www.semanticscholar.org/paper/5f9e689d82d3e0d9a60e4cd75793dd1f26ce3b7e",
    doi = "10.1242/jeb.251075",
    is_oa = "true",
    number = "21",
    semanticscholar_citation_count = "1",
    semanticscholar_id = "5f9e689d82d3e0d9a60e4cd75793dd1f26ce3b7e",
    volume = "228"
}