@misc{dobzhansky1950evolution1,
    author = "Dobzhansky, T",
    title = "Evolution in the Tropics",
    year = "1950",
    howpublished = "American Scientist, v. 38, p. 208-221",
    note = "talkorigins\_source = {true}; raw\_reference = {Dobzhansky, T., 1950, Evolution in the Tropics: American Scientist, v. 38, p. 208-221.}"
}

@incollection{doi101016b9781483227344500176,
    author = "Zuckerkandl, Emile and Pauling, Linus",
    title = "Evolutionary Divergence and Convergence in Proteins",
    year = "1965",
    booktitle = "Elsevier eBooks",
    url = "https://doi.org/10.1016/b978-1-4832-2734-4.50017-6",
    doi = "10.1016/b978-1-4832-2734-4.50017-6",
    openalex = "W1534406401",
    references = "doi1043249781315081083"
}

@misc{kimura1968evolutionary2,
    author = "Kimura, M",
    title = "Evolutionary rate at the molecular level",
    year = "1968",
    howpublished = "Nature, v. 217, p. 624-626",
    note = "talkorigins\_source = {true}; raw\_reference = {Kimura, M., 1968, Evolutionary rate at the molecular level: Nature, v. 217, p. 624-626.}"
}

@article{doi1023072989767,
    author = "Baker, Herbert G.",
    title = "Evolution in the Tropics",
    year = "1970",
    journal = "Biotropica",
    abstract = "The substance of this article was delivered as the Presidential Address to the Society for the Study of Evolution, December 30, 1969, in Boston, Massachusetts. Attention is drawn to evolutionary studies in the tropics which appear to be advancing the subject significantly. Then, detailed attention is given to the possible evolutionary bases of the most striking biological characteristic of the tropics: the extraordinary floristic and faunistic diversity of tropical ecosystems. Because most contributions to the discussion of this topic have come from zoologists, the emphasis here is placed on botanical aspects. It is concluded that each of several potential explanations for the diversity may be valid and that a great need for the future is synthesis rather than arbitration between theories. THERE ARE MANY reasons why, as we come to the end of the 1960's, we should pay attention to what is happening in the study of evolution in the tropics. After many years of neglect, the tropics are getting more study by ecologists-and where the ecologists find their stimulation and their information there is also material for evolutionists, provided that we are still interested, as they are, in adaptation. Despite recent claims by molecular biologists (e.g., King and Jukes 1969, Wilson and Sarich 1969) for nonselective biochemical evolution, I believe that adaptation, maintained by natural selection, is still the cornerstone of the evolutionary edifice-and the tropics provide superb opportunities for studying multifarious examples of adaptation in action. Quite recently there have been important advances, with evolutionary significance, in several areas of tropical biology, and I should like to draw attention to some of them. For example, one of the most exciting developments in plant physiology in the last few years has been the demonstration that there are at least two biochemical pathways along which photosynthesis by flowering plants may proceed. The conventional or Calvin pathway (Calvin and Bassham 1962) involves phosphorylated chemical compounds with three carbon atoms while the more recently discovered pathway (Hatch and Slack 1966) involves four-carbon, dicarboxylic acids as early products of photosynthesis. Plants using the four-carbon pathway can fix carbon dioxide at rates up to twice that of those using the conventional mechanism, at least partly because they waste nothing in photorespiration. Correspondingly, their carbon dioxide compensation points (the level of CO2 in the atmosphere at which respiration just balances photosynthesis) are extremely low. Furthermore, they have peculiarities in the bundle sheaths of the leaves (Laetsch 1968) by which they may be recognized, as well as leaf structures which reduce gaseous exchange. Accumulation of carbon dioxide is facilitated under certain dark circumstances and, because C4 photosynthesis is not inhibited by accumulating oxygen during illumination (Olle Bjorkman, pers. comm.), their photosynthetic rates continue to increase as light intensities up to the maximum experienced in daylight are reached. Photosynthesis also continues even when dissolved carbon dioxide concentrations in the cells are reduced to low levels",
    url = "https://doi.org/10.2307/2989767",
    doi = "10.2307/2989767",
    openalex = "W2321539134"
}

@article{doi101126science1090005,
    author = "King, Mary‐Claire and Wilson, Allan C.",
    title = "Evolution at Two Levels in Humans and Chimpanzees",
    year = "1975",
    journal = "Science",
    url = "https://doi.org/10.1126/science.1090005",
    doi = "10.1126/science.1090005",
    openalex = "W2128969076",
    references = "doi101007bf00485780, doi101016002228367190324x, doi101016s002192581861823x, doi1010179781316276259010, doi101038224149a0, doi101073pnas581142, doi101073pnas6341088, doi101073pnas7183028, doi101093genetics701113, doi101126science15838051200, doi1023073001850, doi1043249781315081083, sarich1967immunological"
}

@article{doi101086283244,
    author = "Grime, J. P.",
    title = "Evidence for the Existence of Three Primary Strategies in Plants and Its Relevance to Ecological and Evolutionary Theory",
    year = "1977",
    journal = "The American Naturalist",
    abstract = "It is suggested that evolution in plants may be associated with the emergence of three primary strategies, each of which may be identified by reference to a number of characteristics including morphological features, resource allocation, phenology, and response to stress. The competitive strategy prevails in productive, relatively undisturbed vegetation, the stress-tolerant strategy is associated with continuously unproductive conditions, and the ruderal strategy is characteristic of severely disturbed but potentially productive habitats. A triangular model based upon the three strategies may be reconciled with the theory of r- and K-selection, provides an insight into the processes of vegetation succession and dominance, and appears to be capable of extension to fungi and to animals.",
    url = "https://doi.org/10.1086/283244",
    doi = "10.1086/283244",
    openalex = "W2055424972",
    references = "doi101038242344a0, doi101038250026a0, doi101086282454, doi101086282455, doi1015159781400881376, doi102307213332, doi1023072258728, doi10230725528056, doi1023073241344, doi105962bhltitle59991"
}

@article{doi101038scientificamerican117998,
    author = "Kimura, Motoo",
    title = "The Neutral Theory of Molecular Evolution",
    year = "1979",
    journal = "Scientific American",
    url = "https://doi.org/10.1038/scientificamerican1179-98",
    doi = "10.1038/scientificamerican1179-98",
    openalex = "W2045391589"
}

@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{doi101146annureves18110187000323,
    author = "Hillis, David M.",
    title = "MOLECULAR VERSUS MORPHOLOGICAL APPROACHES TO SYSTEMATICS",
    year = "1987",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes,...Read More",
    url = "https://doi.org/10.1146/annurev.es.18.110187.000323",
    doi = "10.1146/annurev.es.18.110187.000323",
    openalex = "W2100983857",
    references = "doi101017s0094837300005224, doi101038325031a0, doi101073pnas581142, doi101073pnas7641967, doi101093genetics762379, doi101093genetics893583, doi101093sysbio234536, doi101093sysbio33183, doi101111j155856461982tb05453x, doi1023072412685, doi1023072413259, doi1023072528001, doi1023072529912, doi104159harvard9780674865327, openalexw2032279931, openalexw3135630760"
}

@article{doi101086417338,
    author = "Hillis, David M. and Dixon, Michael T.",
    title = "Ribosomal DNA: Molecular Evolution and Phylogenetic Inference",
    year = "1991",
    journal = "The Quarterly Review of Biology",
    abstract = {Ribosomal DNA (rDNA) sequences have been aligned and compared in a number of living organisms, and this approach has provided a wealth of information about phylogenetic relationships. Studies of rDNA sequences have been used to infer phylogenetic history across a very broad spectrum, from studies among the basal lineages of life to relationships among closely related species and populations. The reasons for the systematic versatility of rDNA include the numerous rates of evolution among different regions of rDNA (both among and within genes), the presence of many copies of most rDNA sequences per genome, and the pattern of concerted evolution that occurs among repeated copies. These features facilitate the analysis of rDNA by direct RNA sequencing, DNA sequencing (either by cloning or amplification), and restriction enzyme methodologies. Constraints imposed by secondary structure of rRNA and concerted evolution need to be considered in phylogenetic analyses, but these constraints do not appear to impede seriously the usefulness of rDNA. An analysis of aligned sequences of the four nuclear and two mitochondrial rRNA genes identified regions of these genes that are likely to be useful to address phylogenetic problems over a wide range of levels of divergence. In general, the small subunit nuclear sequences appear to be best for elucidating Precambrian divergences, the large subunit nuclear sequences for Paleozoic and Mesozoic divergences, and the organellar sequences of both subunits for Cenozoic divergences. Primer sequences were designed for use in amplifying the entire nuclear rDNA array in 15 sections by use of the polymerase chain reaction; these "universal" primers complement previously described primers for the mitochondrial rRNA genes. Pairs of primers can be selected in conjunction with the analysis of divergence of the rRNA genes to address systematic problems throughout the hierarchy of life.},
    url = "https://doi.org/10.1086/417338",
    doi = "10.1086/417338",
    openalex = "W1969194381",
    references = "doi101073pnas74115088, doi101093nar20suppl2075, doi101126science202030, doi101126science2911720, doi101126science3277277, doi101146annureves18110187000323"
}

@book{doi101093oso97801985464120010001,
    author = "Harvey, Paul and Pagel, Mark",
    title = "The Comparative Method in Evolutionary Biology",
    year = "1991",
    abstract = "Abstract From Darwin onward, it has been second nature for evolutionary biologists to think comparatively because comparisons establish the generality of evolutionary phenomena. Do large genomes slow down development? What lifestyles select for large brains? Are extinction rates related to body size? These are all questions for the comparative method, and this book is about how such questions can be answered. The first chapter elaborates on suitable questions for the comparative approach and shows how it complements other approaches to problem-solving in evolution. The second chapter identifies the biological causes of similarity among closely related species for almost any observed character. The third chapter discusses methods for reconstructing phylogenetic trees and ancestral character states. The fourth chapter sets out to develop statistical tests that will determine whether different characters that exist in discrete states show evidence for correlated evolution. Chapter 5 turns to comparative analyses of continuously varying characters. Chapter 6 looks at allometry to exemplify the themes and methods discussed earlier, while the last chapter looks to future development of the comparative approach in both molecular and organismic biology.",
    url = "https://doi.org/10.1093/oso/9780198546412.001.0001",
    doi = "10.1093/oso/9780198546412.001.0001",
    openalex = "W4388245928"
}

@article{doi101093oxfordjournalsjhereda111190,
    author = "Hillis, David M. and Huelsenbeck, John P.",
    title = "Signal, Noise, and Reliability in Molecular Phylogenetic Analyses",
    year = "1992",
    journal = "Journal of Heredity",
    abstract = "DNA sequences and other molecular data compared among organisms may contain phylogenetic signal, or they may be randomized with respect to phylogenetic history. Some method is needed to distinguish phylogenetic signal from random noise to avoid analysis of data that have been randomized with respect to the historical relationships of the taxa being compared. We analyzed 8,000 random data matrices consisting of 10-500 binary or four-state characters and 5-25 taxa to study several options for detecting signal in systematic data bases. Analysis of random data often yields a single most-parsimonious tree, especially if the number of characters examined is large and the number of taxa examined is small (both often true in molecular studies). The most-parsimonious tree inferred from random data may also be considerably shorter than the second-best alternative. The distribution of tree lengths of all tree topologies (or a random sample thereof) provides a sensitive measure of phylogenetic signal: data matrices with phylogenetic signal produce tree-length distributions that are strongly skewed to the left, whereas those composed of random noise are closer to symmetrical. In simulations of phylogeny with varying rates of mutation (up to levels that produce random variation among taxa), the skewness of tree-length distributions is closely related to the success of parsimony in finding the true phylogeny. Tables of critical values of a skewness test statistic, g1, are provided for binary and four-state characters for 10-500 characters and 5-25 taxa. These tables can be used in a rapid and efficient test for significant structure in data matrices for phylogenetic analysis.",
    url = "https://doi.org/10.1093/oxfordjournals.jhered.a111190",
    doi = "10.1093/oxfordjournals.jhered.a111190",
    openalex = "W2270430976",
    references = "doi101146annureves18110187000323"
}

@article{doi1023072419070,
    author = "Doyle, Jeff J.",
    title = "Gene Trees and Species Trees: Molecular Systematics as One-Character Taxonomy",
    year = "1992",
    journal = "Systematic Botany",
    abstract = "Reconstruction of phylogenies from molecular data has become an important and increasingly common approach in systematics. The product of such studies is a gene tree, hypoth- esizing relationships among genes or genomes. This gene tree may be fundamentally incongruent with the true species phylogeny, due to various biological phenomena such as introgression, lineage sorting, or mistaken orthology. In such circumstances all of the gene tree characters defining the relationships of molecular taxa (haplotypes) may be necessarily correlated, and the gene or genome may behave as a single species tree character. In these circumstances robustness of the gene hypoth- esis is meaningless as a measure of confidence in the species phylogenetic hypothesis. Incongruence between a phylogenetic hypothesis based on numerous, presumably independent, non-molecular characters and a single gene tree should not be assumed to be due to noise in non-molecular data. As with other characters, a character phylogeny, in this case a gene tree, can be tested best by a parsimony analysis in which other characters are included. If independence of molecular characters is assumed, then each is an equivalent phylogenetic hypothesis, as is each non-molecular character, leading to the suggestion that direct combination is appropriate. Swamping becomes an issue when a large molecular data set may be behaving as a single character. To alleviate this problem, a gene tree may be treated as a single multistate character, either ordered or unordered, and included with non-molecular data to obtain a globally parsimonious result. An example is given using published molecular and non-molecular data from the Asteraceae.",
    url = "https://doi.org/10.2307/2419070",
    doi = "10.2307/2419070",
    openalex = "W2007270568",
    references = "doi101016b9780123987600500262, doi101093oxfordjournalsmolbeva040517, doi101093sysbio274401, doi1010970000505319941100000014, doi101111j155856461983tb05533x, doi101146annureves18110187000323, doi101146annureves18110187002421, doi1023072412448, doi1023072413039, doi107312nei92038"
}

@article{doi105860choice295104,
    title = "The comparative method in evolutionary biology",
    year = "1992",
    journal = "Choice Reviews Online",
    abstract = "The comparative method for studying adaptation why worry about phylogeny? reconstructing phylogenetic trees and ancestral character states comparative analysis of discrete data comparative analysis of continuous variables determining the form of comparative relationships.",
    url = "https://doi.org/10.5860/choice.29-5104",
    doi = "10.5860/choice.29-5104",
    openalex = "W1488393970"
}

@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"
}

@article{doi101098rstb19950087,
    author = "Nee, Sean and Holmes, Eddie C. and Rambaut, Andrew and Harvey, Paul",
    title = "Inferring population history from molecular phylogenies",
    year = "1995",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "Variable molecular sequences sampled from a population can be used to infer its dynamic history. Graphical methods are developed and applied to real data, illustrating ways of navigating through hypothesis space with two landmarks for reference: constant population size and exponentially growing population size.",
    url = "https://doi.org/10.1098/rstb.1995.0087",
    doi = "10.1098/rstb.1995.0087",
    openalex = "W1978546114"
}

@article{doi101007bf02338839,
    author = "Rannala, Bruce and Yang, Ziheng",
    title = "Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference",
    year = "1996",
    journal = "Journal of Molecular Evolution",
    url = "https://doi.org/10.1007/bf02338839",
    doi = "10.1007/bf02338839",
    openalex = "W2150783480",
    references = "doi101093oxfordjournalsmolbeva040259, doi101093sysbio422182, doi1023072992540"
}

@article{doi101146annurevecolsys271237,
    author = "Linhart, Yan B. and Grant, Michael C.",
    title = "EVOLUTIONARY SIGNIFICANCE OF LOCAL GENETIC DIFFERENTIATION IN PLANTS",
    year = "1996",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "▪ Abstract The study of natural plant populations has provided some of the strongest and most convincing cases of the operation of natural selection currently known, partly because of amenability to reciprocal transplant experiments, common garden work, and long-term in situ manipulation. Genetic differentiation among plant populations over small scales (a few cm to a few hundred cm) has been documented and is reviewed here, in herbaceous annuals and perennials, woody perennials, aquatics, terrestrials, narrow endemics, and widely distributed species. Character differentiation has been documented for most important features of plant structure and function. Examples are known for seed characters, leaf traits, phenology, physiological and biochemical activities, heavy metal tolerance, herbicide resistance, parasite resistance, competitive ability, organellar characters, breeding systems, and life history. Among the forces that have shaped these patterns of differentiation are toxic soils, fertilizers, mowing and grazing, soil moisture, temperature, light intensity, pollinating vectors, parasitism, gene flow, and natural dynamics. The breadth and depth of the evidence reviewed here strongly support the idea that natural selection is the principal force shaping genetic architecture in natural plant populations; that view needs to be more widely appreciated than it is at present.",
    url = "https://doi.org/10.1146/annurev.ecolsys.27.1.237",
    doi = "10.1146/annurev.ecolsys.27.1.237",
    openalex = "W2130703487",
    references = "doi101002j153721971987tb08586x, doi10100797814615694425, doi1010079781489930439, doi101016037811199090073z, doi101038scientificamerican117998, doi101111j155856461993tb01215x, doi101126science15739260, doi101146annureves06110175002011, doi101146annureves10110179001133, doi101146annureves15110184000433, doi101146annureves18110187000323, doi101146annureves19110188000551, doi101146annurevge25120191000245, doi1015159781400820108, doi1023072444338, doi104159harvard9780674865327, openalexw2080618944, openalexw2146778590"
}

@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{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"
}

@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"
}

@article{doi101146annurevecolsys36091704175539,
    author = "Goodwillie, Carol and Kalisz, Susan and Eckert, Christopher G.",
    title = "The Evolutionary Enigma of Mixed Mating Systems in Plants: Occurrence, Theoretical Explanations, and Empirical Evidence",
    year = "2005",
    journal = "Annual Review of Ecology Evolution and Systematics",
    abstract = "▪ Abstract Mixed mating, in which hermaphrodite plant species reproduce by both self- and cross-fertilization, presents a challenging problem for evolutionary biologists. Theory suggests that inbreeding depression, the main selective factor opposing the evolution of selfing, can be purged with self-fertilization, a process that is expected to yield pure strategies of either outcrossing or selfing. Here we present updated evidence suggesting that mixed mating systems are frequent in seed plants. We outline the floral and pollination mechanisms that can lead to intermediate outcrossing, review the theoretical models that address the stability of intermediate outcrossing, and examine relevant empirical evidence. A comparative analysis of estimated inbreeding coefficients and outcrossing rates suggests that mixed mating often evolves despite strong inbreeding depression. The adaptive significance of mixed mating has yet to be fully explained for any species. Recent theoretical and empirical work suggests that future progress will come from a better integration of studies of floral mechanisms, genetics, and ecology, and recognition of how selective pressures vary in space and time.",
    url = "https://doi.org/10.1146/annurev.ecolsys.36.091704.175539",
    doi = "10.1146/annurev.ecolsys.36.091704.175539",
    openalex = "W2127588110",
    references = "doi10100797814615694425, doi101111j109583122000tb01221x, doi101146annureves15110184000433, doi105860choice355054, doi105962bhltitle110800, openalexw2491318968"
}

@article{doi101093nargkm224,
    author = "Tárraga, Joaquín and Medina, Ignacio and Arbiza, Leonardo and Huerta‐Cepas, Jaime and Gabaldón, Toni and Dopazo, Joaquı́n and Dopazo, Hernán",
    title = "Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics",
    year = "2007",
    journal = "Nucleic Acids Research",
    abstract = "Phylemon is an online platform for phylogenetic and evolutionary analyses of molecular sequence data. It has been developed as a web server that integrates a suite of different tools selected among the most popular stand-alone programs in phylogenetic and evolutionary analysis. It has been conceived as a natural response to the increasing demand of data analysis of many experimental scientists wishing to add a molecular evolution and phylogenetics insight into their research. Tools included in Phylemon cover a wide yet selected range of programs: from the most basic for multiple sequence alignment to elaborate statistical methods of phylogenetic reconstruction including methods for evolutionary rates analyses and molecular adaptation. Phylemon has several features that differentiates it from other resources: (i) It offers an integrated environment that enables the direct concatenation of evolutionary analyses, the storage of results and handles required data format conversions, (ii) Once an outfile is produced, Phylemon suggests the next possible analyses, thus guiding the user and facilitating the integration of multi-step analyses, and (iii) users can define and save complete pipelines for specific phylogenetic analysis to be automatically used on many genes in subsequent sessions or multiple genes in a single session (phylogenomics). The Phylemon web server is available at http://phylemon.bioinfo.cipf.es.",
    url = "https://doi.org/10.1093/nar/gkm224",
    doi = "10.1093/nar/gkm224",
    openalex = "W2095319152"
}

@article{doi101186147121487214,
    author = "Drummond, Alexei J. and Rambaut, Andrew",
    title = "BEAST: Bayesian evolutionary analysis by sampling trees",
    year = "2007",
    journal = "BMC Evolutionary Biology",
    abstract = "BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis.",
    url = "https://doi.org/10.1186/1471-2148-7-214",
    doi = "10.1186/1471-2148-7-214",
    openalex = "W2110835349",
    references = "doi101007bf00160154, doi101007bf02101694, doi101007bf02101990, doi101016b9781483227344500176, doi101016s0169534703002167, doi10106311699114, doi101073pnas6341088, doi10108010635150290102456, doi101093bioinformatics178754, doi101093biomet57197, doi101093molbevmsi103, doi101093oxfordjournalsmolbeva003974, doi101093oxfordjournalsmolbeva025892, doi101093oxfordjournalsmolbeva040153, doi101126science1101074, doi101371journalpbio0040088, rambaut1998estimating"
}

@article{doi101038nrg2323,
    author = "Duffy, Siobain and Shackelton, Laura A. and Holmes, Edward C.",
    title = "Rates of evolutionary change in viruses: patterns and determinants",
    year = "2008",
    journal = "Nature Reviews Genetics",
    url = "https://doi.org/10.1038/nrg2323",
    doi = "10.1038/nrg2323",
    openalex = "W2020939898",
    references = "doi1010021521187820001222121057aidbies330co2w, doi101016s0169534703002167, doi101038nrg2146, doi101371journalpbio0040088"
}

@article{doi101111j15585646200800549x,
    author = "Edwards, Scott V.",
    title = "IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?",
    year = "2008",
    journal = "Evolution",
    abstract = {The advent and maturation of algorithms for estimating species trees-phylogenetic trees that allow gene tree heterogeneity and whose tips represent lineages, populations and species, as opposed to genes-represent an exciting confluence of phylogenetics, phylogeography, and population genetics, and ushers in a new generation of concepts and challenges for the molecular systematist. In this essay I argue that to better deal with the large multilocus datasets brought on by phylogenomics, and to better align the fields of phylogeography and phylogenetics, we should embrace the primacy of species trees, not only as a new and useful practical tool for systematics, but also as a long-standing conceptual goal of systematics that, largely due to the lack of appropriate computational tools, has been eclipsed in the past few decades. I suggest that phylogenies as gene trees are a "local optimum" for systematics, and review recent advances that will bring us to the broader optimum inherent in species trees. In addition to adopting new methods of phylogenetic analysis (and ideally reserving the term "phylogeny" for species trees rather than gene trees), the new paradigm suggests shifts in a number of practices, such as sampling data to maximize not only the number of accumulated sites but also the number of independently segregating genes; routinely using coalescent or other models in computer simulations to allow gene tree heterogeneity; and understanding better the role of concatenation in influencing topologies and confidence in phylogenies. By building on the foundation laid by concepts of gene trees and coalescent theory, and by taking cues from recent trends in multilocus phylogeography, molecular systematics stands to be enriched. Many of the challenges and lessons learned for estimating gene trees will carry over to the challenge of estimating species trees, although adopting the species tree paradigm will clarify many issues (such as the nature of polytomies and the star tree paradox), raise conceptually new challenges, or provide new answers to old questions.},
    url = "https://doi.org/10.1111/j.1558-5646.2008.00549.x",
    doi = "10.1111/j.1558-5646.2008.00549.x",
    openalex = "W2037654474",
    references = "doi101038nature04336, doi101038nature04789, doi101038nature06614, doi101073pnas0502030102, doi101073pnas0610699104, doi101086510633, doi101093sysbio3817, doi101111j155856461982tb05068x, doi101146annureves18110187000323, doi1023072419070, openalexw2611511275"
}

@article{doi101038ncomms2958,
    author = "Rabosky, Daniel L. and Santini, Francesco and Eastman, Jonathan M. and Smith, Stephen A. and Sidlauskas, Brian L. and Chang, Jonathan and Alfaro, Michael E.",
    title = "Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation",
    year = "2013",
    journal = "Nature Communications",
    url = "https://doi.org/10.1038/ncomms2958",
    doi = "10.1038/ncomms2958",
    openalex = "W2054715003",
    references = "doi10100797894010058529, doi101016jtree201204012, doi101017s009483730001280x, doi101023a1013311015886, doi10103714088000, doi101038248107a0, doi101038nature07893, doi101038nature10516, doi101038nrg2278, doi101073pnas0704088104, doi101086303327, doi101093bibbbn013, doi101093bioinformaticsbtl446, doi101093biomet824711, doi101093oxfordjournalsmolbeva003974, doi101093oxfordjournalsmolbeva025811, doi101111j155856461971tb01868x, doi101111j15585646201001026x, doi101146annurevecolsys281129, doi101146annurevecolsys291293, doi101186147121055113, doi1011861471214811275, doi1023072405671, doi105962bhltitle82303, doi107312simp93764"
}

@article{doi101371journalpcbi1003537,
    author = "Bouckaert, Remco and Heled, Joseph and Kühnert, Denise and Vaughan, Tim and Wu, Chieh‐Hsi and Xie, Dong and Suchard, Marc A. and Rambaut, Andrew and Drummond, Alexei J.",
    title = "BEAST 2: A Software Platform for Bayesian Evolutionary Analysis",
    year = "2014",
    journal = "PLoS Computational Biology",
    abstract = "We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.",
    url = "https://doi.org/10.1371/journal.pcbi.1003537",
    doi = "10.1371/journal.pcbi.1003537",
    openalex = "W2026062398",
    references = "doi101007bf01731581, doi101007bf01734359, doi101007bf02101694, doi101093molbevmsi103, doi101093molbevmsp274, doi101093molbevmss075, doi101093oxfordjournalsmolbeva040023, doi101186147121487214, doi101371journalpbio0040088, openalexw1593676244"
}

@article{doi101093nargkw408,
    author = "Ashkenazy, Haim and Abadi, Shiran and Martz, Eric and Chay, Ofer and Mayrose, Itay and Pupko, Tal and Ben‐Tal, Nir",
    title = "ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules",
    year = "2016",
    journal = "Nucleic Acids Research",
    abstract = "The degree of evolutionary conservation of an amino acid in a protein or a nucleic acid in DNA/RNA reflects a balance between its natural tendency to mutate and the overall need to retain the structural integrity and function of the macromolecule. The ConSurf web server (http://consurf.tau.ac.il), established over 15 years ago, analyses the evolutionary pattern of the amino/nucleic acids of the macromolecule to reveal regions that are important for structure and/or function. Starting from a query sequence or structure, the server automatically collects homologues, infers their multiple sequence alignment and reconstructs a phylogenetic tree that reflects their evolutionary relations. These data are then used, within a probabilistic framework, to estimate the evolutionary rates of each sequence position. Here we introduce several new features into ConSurf, including automatic selection of the best evolutionary model used to infer the rates, the ability to homology-model query proteins, prediction of the secondary structure of query RNA molecules from sequence, the ability to view the biological assembly of a query (in addition to the single chain), mapping of the conservation grades onto 2D RNA models and an advanced view of the phylogenetic tree that enables interactively rerunning ConSurf with the taxa of a sub-tree.",
    url = "https://doi.org/10.1093/nar/gkw408",
    doi = "10.1093/nar/gkw408",
    openalex = "W2376573086",
    references = "doi101006jmbi19909999, doi101006jmbi19931626, doi101007bf02498640, doi101016s0022283605803602, doi101038nmeth2109, doi101093bioinformaticsbtl158, doi101093bioinformaticsbts565, doi101093molbevmsn067, doi101093molbevmsr121, doi101093molbevmst010, doi101093nar281235, doi101093oxfordjournalsmolbeva040752, doi101109tac19741100705"
}

@article{doi101007s1322501804010,
    author = "Tedersoo, Leho and Sánchez‐Ramírez, Santiago and Kõljalg, Urmas and Bahram, Mohammad and Döring, Markus and Schigel, Dmitry and May, Tom W. and Ryberg, Martin and Abarenkov, Kessy",
    title = "High-level classification of the Fungi and a tool for evolutionary ecological analyses",
    year = "2018",
    journal = "Fungal Diversity",
    abstract = "High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum- and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomophthoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example of testing evolutionary ecological hypotheses based on a global soil fungal data set.",
    url = "https://doi.org/10.1007/s13225-018-0401-0",
    doi = "10.1007/s13225-018-0401-0",
    openalex = "W2803566787",
    references = "doi101073pnas1110633108, doi101146annurevmicro030117020324, doi101186s1286201708906"
}

@article{doi101093bioinformaticsbty633,
    author = "Paradis, Emmanuel and Schliep, Klaus",
    title = "ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R",
    year = "2018",
    journal = "Bioinformatics",
    abstract = "ape is distributed through the Comprehensive R Archive Network: http://cran.r-project.org/package=ape. Further information may be found at http://ape-package.ird.fr/.",
    url = "https://doi.org/10.1093/bioinformatics/bty633",
    doi = "10.1093/bioinformatics/bty633",
    openalex = "W2883251903",
    references = "doi1010079781461468684, doi101016jxcrm2020100098, doi101038nmeth3252, doi101093bioinformaticsbtg412, doi101093gigasciencegiaa060, doi10110120200210942748, doi101186147121059532, doi101186s12862020016316, doi1032614rmanuals, doi103389fmed202000161"
}

@article{doi101093molbevmsz189,
    author = "Darriba, Diego and Posada, David and Kozlov, Alexey M. and Stamatakis, Alexandros and Morel, Benoît and Flouri, Tomáš",
    title = "ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models",
    year = "2019",
    journal = "Molecular Biology and Evolution",
    abstract = "ModelTest-NG is a reimplementation from scratch of jModelTest and ProtTest, two popular tools for selecting the best-fit nucleotide and amino acid substitution models, respectively. ModelTest-NG is one to two orders of magnitude faster than jModelTest and ProtTest but equally accurate and introduces several new features, such as ascertainment bias correction, mixture, and free-rate models, or the automatic processing of single partitions. ModelTest-NG is available under a GNU GPL3 license at https://github.com/ddarriba/modeltest, last accessed September 2, 2019.",
    url = "https://doi.org/10.1093/molbev/msz189",
    doi = "10.1093/molbev/msz189",
    openalex = "W2969866109",
    references = "doi101038nmeth4285, doi101093molbevmsn083, doi101093sysbiosys029"
}

@article{doi101093molbevmsz197,
    author = "Pond, Sergei L. Kosakovsky and Poon, Art F. Y. and Velazquez, Ryan and Weaver, Steven and Hepler, N. Lance and Murrell, Ben and Shank, Stephen D. and Magalis, Brittany Rife and Bouvier, Dave and Nekrutenko, Anton and Wisotsky, Sadie R and Spielman, Stephanie J. and Frost, Simon D. W. and Muse, Spencer V.",
    title = "HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies",
    year = "2019",
    journal = "Molecular Biology and Evolution",
    abstract = "HYpothesis testing using PHYlogenies (HyPhy) is a scriptable, open-source package for fitting a broad range of evolutionary models to multiple sequence alignments, and for conducting subsequent parameter estimation and hypothesis testing, primarily in the maximum likelihood statistical framework. It has become a popular choice for characterizing various aspects of the evolutionary process: natural selection, evolutionary rates, recombination, and coevolution. The 2.5 release (available from www.hyphy.org) includes a completely re-engineered computational core and analysis library that introduces new classes of evolutionary models and statistical tests, delivers substantial performance and stability enhancements, improves usability, streamlines end-to-end analysis workflows, makes it easier to develop custom analyses, and is mostly backward compatible with previous HyPhy releases.",
    url = "https://doi.org/10.1093/molbev/msz197",
    doi = "10.1093/molbev/msz197",
    openalex = "W2970147901",
    references = "doi101371journalpcbi1006650"
}

@article{doi1011111755099813096,
    author = "Zhang, Dong and Gao, Fangluan and Jakovlić, Ivan and Zou, Hong and Zhang, Jin and Li, Wen X. and Wang, Gui T.",
    title = "PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies",
    year = "2019",
    journal = "Molecular Ecology Resources",
    abstract = "Multigene and genomic data sets have become commonplace in the field of phylogenetics, but many existing tools are not designed for such data sets, which often makes the analysis time-consuming and tedious. Here, we present PhyloSuite, a (cross-platform, open-source, stand-alone Python graphical user interface) user-friendly workflow desktop platform dedicated to streamlining molecular sequence data management and evolutionary phylogenetics studies. It uses a plugin-based system that integrates several phylogenetic and bioinformatic tools, thereby streamlining the entire procedure, from data acquisition to phylogenetic tree annotation (in combination with iTOL). It has the following features: (a) point-and-click and drag-and-drop graphical user interface; (b) a workplace to manage and organize molecular sequence data and results of analyses; (c) GenBank entry extraction and comparative statistics; and (d) a phylogenetic workflow with batch processing capability, comprising sequence alignment (mafft and macse), alignment optimization (trimAl, HmmCleaner and Gblocks), data set concatenation, best partitioning scheme and best evolutionary model selection (PartitionFinder and modelfinder), and phylogenetic inference (MrBayes and iq-tree). PhyloSuite is designed for both beginners and experienced researchers, allowing the former to quick-start their way into phylogenetic analysis, and the latter to conduct, store and manage their work in a streamlined way, and spend more time investigating scientific questions instead of wasting it on transferring files from one software program to another.",
    url = "https://doi.org/10.1111/1755-0998.13096",
    doi = "10.1111/1755-0998.13096",
    openalex = "W2979811825",
    references = "doi101016jtree200901009, doi101038nmeth4285, doi10108010635150701472164, doi101093bioinformaticsbtp348, doi101093bioinformaticsbts199, doi101093molbevmst010, doi101093sysbiosys029"
}

@article{doi101371journalpcbi1006650,
    author = "Bouckaert, Remco and Vaughan, Timothy G. and Barido‐Sottani, Joëlle and Duchêne, Sebastián and Fourment, Mathieu and Gavryushkina, Alexandra and Heled, Joseph and Jones, Graham and Kühnert, Denise and Maio, Nicola De and Matschiner, Michael and Mendes, Fábio K. and Müller, Nicola F. and Ogilvie, Huw A. and du Plessis, Louis and Popinga, Alex and Rambaut, Andrew and Rasmussen, David A. and Siveroni, Igor and Suchard, Marc A. and Wu, Chieh‐Hsi and Xie, Dong and Zhang, Chi and Stadler, Tanja and Drummond, Alexei J.",
    title = "BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis",
    year = "2019",
    journal = "PLoS Computational Biology",
    abstract = "Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.",
    url = "https://doi.org/10.1371/journal.pcbi.1006650",
    doi = "10.1371/journal.pcbi.1006650",
    openalex = "W2901954177",
    references = "doi101016jtree200901009, doi101038nature10231, doi101038nature13726, doi101073pnas1319091111, doi101073pnas89178322, doi101080106351501753462876, doi101093acprofoso97801985670280010001, doi101093genetics1551431, doi101093molbevmsp274, doi101093sysbiosyq085, doi101093sysbiosyr047, doi101093sysbiosyv080, doi101093vevey016, doi101098rspa19270118, doi101186147121487214, doi101186s1286201708906, doi1012019780429258411, doi101371journalpbio0040088, doi101371journalpcbi1003537"
}

@misc{esquerregheur2019old,
    author = "Esquerre Gheur, Damien",
    title = "Old World Serpents and New World Dragons: The Evolutionary Dynamics of Pythons and Liolaemid Lizards",
    year = "2019",
    publisher = "The Australian National University",
    abstract = "Since Darwin and Wallace, evolutionary biologists have been fascinated with the processes driving the evolution of biodiversity, species richness, ecology and morphology. Combining phylogenetic, geological, paleontological, ecological and climatic perspectives can shed light on evolutionary patterns at deep time scales to answer questions about the evolution of biodiversity. At the same time, looking at more shallow scales, where species are initially forming and diverging, can shed light on phylogeographic aspects of evolution. In this thesis I use two animal systems with comparable ages to understand evolutionary processes at both deep and shallow time-scales. Pythons (Pythonidae) are a diverse group of snakes distributed across the tropics and subtropics of the Old World. Their moderate species diversity (44 currently recognized species), is eclipsed by their remarkable morphological and ecological diversity. Liolaemid lizards (Liolaemidae), found in the southern portion of South America, also are diverse in their habitat use, reproductive mode and thermal niche, but are extremely species rich, with almost 300 currently recognized species. Both pythons and liolaemid lizards, based on different and common attributes, have been recognized as examples of an adaptive radiation. My research on pythons is summarized in the first three chapters. In Chapter 1, I use a phylogenomic dataset of over 300 loci and mitochondrial genomes, along with fossil calibrations, to reconstruct a time-calibrated species tree. Biogeographic reconstruction analyses reveal pythons likely originated in Asia, and only recently crossed Wallace’s line into Australo-Papua. Lineage and morphological diversification analyses show that once they crossed this line, pythons display a sudden burst of species, ecological and morphological diversity, consistent with ecological opportunity following colonization of a new environment with novel niches. In Chapter 2, I reconstruct ontogenetic allometric trajectories to illustrate changes in python head and body shape from juveniles to adults. I find that heterochrony (a dissociation of size, shape and age) is the initial developmental process responsible for pythons to diverge in morphology. Although this process involves shifting the rate and timing of development, it still requires that the direction of change along morphological space remain the same. However, I also find that at deeper evolutionary levels, the direction of shape change with size becomes evolvable, allowing pythons to explore more extreme phenotypes than previously available. Chapter 3 looks at phylogeographic patterns of one of the most iconic snakes in the world: the green tree pythons (Morelia viridis complex). Using a similar dataset as described above, but analysed in a species-delimitation and population structure framework, I identified deep phylogeographic structure within the group, and recognize two species, one of which comprises three subspecies. These taxa are highly cryptic, and the central cordillera of New Guinea likely played a key role in maintaining isolation between the lineages, allowing them to diverge. Chapter 4 switches the focus to the liolaemid lizards. I first sequenced mitochondrial loci for 40 species for which genetic data did not exist, and combined this with data from previous studies to build a time-calibrated tree with 258 terminal taxa, the most complete phylogenetic inference of the group to date. I tested multiple hypotheses on the diversification and evolutionary dynamics of liolaemids, all of which centered on the importance of the uplift of the Andes mountains in generating biodiversity. I find that most lineages originated in Andean regions before dispersing into surrounding biomes. Combined with findings that speciation rates are correlated with rising altitudes, I postulate the Andes acted as a species pump for the most diverse lizard group of South America. Moreover, using available data on distribution, thermal niche and reproductive mode (oviparity versus viviparity), I find that viviparity was the key factor in enabling liolamids to adapt to the high mountains of the Andes. Importantly, when lineages dispersed back into the lowlands, my results for Liolaemus, the most diverse genus in the family, suggest that several reversals back to oviparity must have occurred. This is one of the very few known cases where this reversal in reproductive mode has taken place. In Chapter 5 I focused on the Liolaemus (sensu stricto) subgenus, which is mostly distributed around the Andes between Chile and Argentina. Very rapid diversification events have rendered the phylogenetic relationships within this group extremely hard to resolve. I obtained tissues from almost 400 samples from the 87 described and 13 candidate species. I sequenced mitochondrial data using Sanger sequencing, and nuclear Single Nucleotide Polymorphisms (SNPs) using ddRADSeq, and used cutting edge phylogenetic reconstruction methods to resolve the evolutionary history of the group. I find very high levels of discordance between mitochondrial and nuclear data, suggesting extensive past introgression between lineages, highlighting single genetic markers and concatenation methods are of little use for resolving systematic relationships within the group. This is confirmed by the extensive reticulation events inferred by phylogenetic networks. Nevertheless, these results provide a huge step towards understanding the evolutionary patterns of Liolaemus in the context of the geological history of the Andes, and also help to improve a historically messy taxonomy, with the synonymy of many species and the likely species level status of many undescribed taxa. Finally, in Chapter 6, I explore the shallower evolutionary patterns of one of the most interesting groups of Liolaemus, the leopard lizards (Liolaemus leopardinus). Most species in this clade are found in the Andes mountains, but one is found in the isolated Costa cordillera. The mitochondrial genealogy suggests the taxon in the Costa mountains is sister to the rest, but the phylogenies estimated from thousands of independent SNPs instead suggest the pattern of all Andean species forming a clade is an artifact of past introgression. My molecular dating results suggest this group diverged during the Pleistocene, a period in time characterized by intermittent glacial and interglacial cycles. I suggest that past introgression occurred during glacial maxima, when taxa were forced down the mountains, enabling them to interbreed in the lowlands, followed by isolation in mountain tops during interglacial periods. I revise their taxonomy, sinking one species and describing another. My thesis highlights the importance of looking at different evolutionary timescales, geographic regions, and geohistorical processes to understand how biodiversity, is generated at all levels.",
    url = "https://openresearch-repository.anu.edu.au/handle/1885/165154",
    doi = "10.25911/5d778320337d4",
    openalex = "W2973085688"
}

@article{doi101016jympev2025108346,
    author = "Van Der Wal, Cara and Ahyong, Shane T and Adams, Maxim W D and Lo, Nathan and Ho, Simon Y W",
    title = "Total-evidence phylogenetic analysis resolves the evolutionary timescale of mantis shrimps (Stomatopoda) and provides insights into their molecular and morphological evolutionary rates.",
    year = "2025",
    journal = "Molecular phylogenetics and evolution",
    abstract = "The crustacean order Stomatopoda comprises approximately 500 species of mantis shrimps. These marine predators, common in tropical and subtropical waters, possess sophisticated visual systems and specialized hunting appendages. In this study, we infer the evolutionary relationships within Stomatopoda using a combined data set of 77 morphological characters, whole mitochondrial genomes, and three nuclear markers. Our data set includes representatives from all seven stomatopod superfamilies, including the first sequence data from Erythrosquilloidea. Using a Bayesian relaxed molecular clock with fossil-based calibration priors, we estimate that crown-group unipeltatan stomatopods appeared ∼ 143 (95 \% credible interval 199-98) million years ago in the Mesozoic. Additionally, our results support the hypothesis that specialized smashing and spearing appendages appeared early in the evolutionary history of Unipeltata. We found no evidence of a correlation between rates of morphological and molecular evolution across the phylogeny, but identified very high levels of among-lineage rate variation in the morphological characters. Our total-evidence analysis recovered evolutionary signals from both molecular and morphological data sets, demonstrating the merit in combining these sources of information for phylogenetic inference and evolutionary analysis.",
    url = "https://pubmed.ncbi.nlm.nih.gov/40194643/",
    doi = "10.1016/j.ympev.2025.108346",
    openalex = "W4409229529",
    pmid = "40194643",
    references = "doi101016jympev201208023, doi101080106351501753462876, doi101093molbevmsaa015, doi101093nargkh340, doi101093sysbiosys029, doi101093sysbiosyy032, doi101146annureves18110187000323, doi101186s1286201708906, doi101371journalpbio0040088, doi101371journalpcbi1006650"
}

@misc{doi10110120250720665814,
    author = "Estrada, Ernesto and Asar, Yasmin and Sauquet, Hervé and Ho, Simon Y. W.",
    title = "Unveiling the tempo of molecular and morphological evolution across the Tree of Life",
    year = "2025",
    booktitle = "bioRxiv (Cold Spring Harbor Laboratory)",
    abstract = "Abstract The evolution of Earth’s vast genetic and morphological diversity has been explained by an array of macroevolutionary models. At opposite ends of the spectrum lie two contrasting evolutionary models: phyletic gradualism and punctuated equilibria. Under a phyletic gradualism framework, evolutionary change accumulates along lineages and species are steadily transformed into new forms over time. In contrast, under punctuated equilibria, evolutionary change tends to occur in bursts at speciation events. Previous studies of molecular and morphological data have found varying levels of support for the two evolutionary models. We examined these models using comprehensive molecular and morphological data sets from 40 clades across the Tree of Life. Testing for associations between species richness and the amount of evolutionary change in sister clades, we find little evidence to support the punctuated equilibria model. However, we found high levels of among-lineage rate variation in molecular evolution and particularly morphological evolution. Our comparison of coding and non-coding genomic regions revealed contrasting patterns of among-lineage rate variation, without clear trends across taxa. Our study confirms that heterotachy is a dominant feature in macroevolution and that molecular and morphological evolution cannot simply be described by either a gradual or punctuated model.",
    url = "https://doi.org/10.1101/2025.07.20.665814",
    doi = "10.1101/2025.07.20.665814",
    openalex = "W4412527719",
    references = "doi101016jympev2025108346, doi101038nature10516, doi101038ncomms2958, doi101038nmeth4285, doi101073pnas0811087106, doi101093icb204653, doi101093molbevmsaa015, doi101093sysbio41118, doi101126science1084786, doi101126science1090005, doi104159harvard9780674865327"
}

@article{doi101111cla70024,
    author = "Zhao, Jing and Wang, Jia-Guan and Niu, Hong-Bin and Pan, Wei-Hao and Huang, Chuan-Jie and Liang, Zhen-Long and He, Zhao-Rong and Jiang, Li-Ju and Zhou, Xin-Mao",
    title = "Phylogeny and evolutionary history of subfamily Microsoroideae (Polypodiaceae): new insights from plastome and nuclear gene data.",
    year = "2026",
    journal = "Cladistics: the international journal of the Willi Hennig Society",
    abstract = "Subfamily Microsoroideae represent the third largest subfamily within Polypodiaceae. However, due to insufficient sampling, limited informative sites and considerable morphological diversification, the generic-level classification within Microsoroideae has been contentious. Furthermore, the origin and diversification history of this subfamily remain unclear. With the most extensive sampling to date, we provide a comprehensive and systematic elucidation of the evolutionary history of Microsoroideae. Our key findings include the following: (1) Microsoroideae can be divided into 5 superclades and 17 fully supported clades based on the plastome dataset, while nuclear gene dataset supports the division of Microsoroideae into 6 superclades and 19 monophyletic clades; (2) significant cytonuclear discordance and gene tree conflicts exist within Microsoroideae and can be explained by incomplete lineage sorting-particularly regarding the conflicting phylogenetic positions of Bosmania, and introgressive hybridization; (3) molecular dating consistently indicates that Microsoroideae originated in the early Eocene and began to diversify around the middle Eocene; (4) ancestral area reconstruction supports the Asian continent as both the origin and diversification centres of Microsoroideae; (5) paleoenvironmental changes, geological events and a series of dispersal and vicariance events are the primary drivers of the current distribution of Microsoroideae; (6) diversification rate analyses reveal that abrupt changes in the diversification rate of the maternal lineages of Microsoroideae are associated with the Middle Eocene Climatic Optimum; (7) nuclear gene data show that the diversification rate of the Lecanopteris clade is significantly higher than other clades, which is linked to its unique ant-associated traits; and (8) the diversification rates of Microsoroideae inferred from nuclear gene data exhibit different trends compared with those inferred from plastome data. This discrepancy may arise from frequent hybridization and polyploidization, which buffer environmental pressures. The findings not only have significant implications for the classification of Microsoroideae but also provide insights for the adaptive evolution of ferns.",
    url = "https://pubmed.ncbi.nlm.nih.gov/41480809/",
    doi = "10.1111/cla.70024",
    openalex = "W7117959445",
    pmid = "41480809",
    references = "doi101038nbt1883, doi101038nmeth4285, doi101093bioinformaticsbtg412, doi101093bioinformaticsbtp348, doi101093bioinformaticsbty191, doi101093bioinformaticsbty560, doi101093gigasciencegiab008, doi101093molbevmst010, doi101093molbevmsu300, doi101093sysbiosys029"
}