Geographic isolation

@book{simpson1980splendid1,
    author = "Simpson, G. G",
    title = "Splendid Isolation",
    year = "1980",
    publisher = "The Curious History of South American Mammals: New Haven, Connecticut, Ylae University Press",
    note = "talkorigins\_source = {true}; raw\_reference = {Simpson, G. G., 1980, Splendid Isolation: The Curious History of South American Mammals: New Haven, Connecticut, Ylae University Press.}"
}

It is shown that for allele frequency data a useful measure of the extent of gene flow between a pair of populations is M∘=(1/FST-1)/4, which is the estimated level of gene flow in an island model at equilibrium. For DNA sequence data, the same formula can be used if F ST is replaced by N ST. In a population with restricted dispersal, analytic theory shows that there is a simple relationship between M̂ and geographic distance in both equilibrium and non-equilibrium populations and that this relationship is approximately independent of mutation rate when the mutation rate is small. Simulation results show that with reasonable sample sizes, isolation by distance can indeed be detected and that, at least in some cases, non-equilibrium patterns can be distinguished. This approach to analyzing isolation by distance is used for two allozyme data sets, one from gulls and one from pocket gophers.

@article{doi101111j155856461993tb01215x,
    author = "Slatkin, Montgomery",
    title = "ISOLATION BY DISTANCE IN EQUILIBRIUM AND NON-EQUILIBRIUM POPULATIONS",
    year = "1993",
    journal = "Evolution",
    abstract = "It is shown that for allele frequency data a useful measure of the extent of gene flow between a pair of populations is M∘=(1/FST-1)/4, which is the estimated level of gene flow in an island model at equilibrium. For DNA sequence data, the same formula can be used if F ST is replaced by N ST. In a population with restricted dispersal, analytic theory shows that there is a simple relationship between M̂ and geographic distance in both equilibrium and non-equilibrium populations and that this relationship is approximately independent of mutation rate when the mutation rate is small. Simulation results show that with reasonable sample sizes, isolation by distance can indeed be detected and that, at least in some cases, non-equilibrium patterns can be distinguished. This approach to analyzing isolation by distance is used for two allozyme data sets, one from gulls and one from pocket gophers.",
    url = "https://doi.org/10.1111/j.1558-5646.1993.tb01215.x",
    doi = "10.1111/j.1558-5646.1993.tb01215.x",
    openalex = "W1974744321",
    references = "doi101086282771, doi101093genetics1053767"
}

We formalize the use of allele frequency and geographic information for the construction of gene trees at the intraspecific level and extend the concept of evolutionary parsimony to molecular variance parsimony. The central principle is to consider a particular gene tree as a variable to be optimized in the estimation of a given population statistic. We propose three population statistics that are related to variance components and that are explicit functions of phylogenetic information. The methodology is applied in the context of minimum spanning trees (MSTs) and human mitochondrial DNA restriction data, but could be extended to accommodate other tree-making procedures, as well as other data types. We pursue optimal trees by heuristic optimization over a search space of more than 1.29 billion MSTs. This very large number of equally parsimonious trees underlines the lack of resolution of conventional parsimony procedures. This lack of resolution is highlighted by the observation that equally parsimonious trees yield very different estimates of population genetic diversity and genetic structure, as shown by null distributions of the population statistics, obtained by evaluation of 10,000 random MSTs. We propose a non-parametric test for the similarity between any two trees, based on the distribution of a weighted coevolutionary correlation. The ability to test for tree relatedness leads to the definition of a class of solutions instead of a single solution. Members of the class share virtually all of the critical internal structure of the tree but differ in the placement of singleton branch tips.

@article{doi101093genetics1361343,
    author = "Excoffier, Laurent and Smouse, Peter E.",
    title = "Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony.",
    year = "1994",
    journal = "Genetics",
    abstract = "We formalize the use of allele frequency and geographic information for the construction of gene trees at the intraspecific level and extend the concept of evolutionary parsimony to molecular variance parsimony. The central principle is to consider a particular gene tree as a variable to be optimized in the estimation of a given population statistic. We propose three population statistics that are related to variance components and that are explicit functions of phylogenetic information. The methodology is applied in the context of minimum spanning trees (MSTs) and human mitochondrial DNA restriction data, but could be extended to accommodate other tree-making procedures, as well as other data types. We pursue optimal trees by heuristic optimization over a search space of more than 1.29 billion MSTs. This very large number of equally parsimonious trees underlines the lack of resolution of conventional parsimony procedures. This lack of resolution is highlighted by the observation that equally parsimonious trees yield very different estimates of population genetic diversity and genetic structure, as shown by null distributions of the population statistics, obtained by evaluation of 10,000 random MSTs. We propose a non-parametric test for the similarity between any two trees, based on the distribution of a weighted coevolutionary correlation. The ability to test for tree relatedness leads to the definition of a class of solutions instead of a single solution. Members of the class share virtually all of the critical internal structure of the tree but differ in the placement of singleton branch tips.",
    url = "https://doi.org/10.1093/genetics/136.1.343",
    doi = "10.1093/genetics/136.1.343",
    openalex = "W2287087292"
}

Population densities of terrestrial animals tend to be higher and less variable near the center versus along the periphery of a species' geographic range. If extinctions are tied to local population dynamics, geographic ranges of endangered species should collapse inward, with remnant populations persisting near the center of a species' historic range. Geographic-Information-System analysis of range collapse in nonvolant, terrestrial mammals reveals, however, that extant populations of 23 of 31 species were located along the periphery, not the center, of their historic range. In addition, range collapse appears to be independent of fragment area and has a directional bias from east to west. Persistence of endangered populations also appears to be greater on islands than on continents. These results contradict conventional wisdom in biogeography and macroecology and have important implications for conserving biodiversity. Because of their relative isolation from central populations and from a suite of anthropogenic disturbances, islands and other sites along the periphery of a species' historic range represent critical refugia for many endangered species.

@article{doi1023071382345,
    author = "Lomolino, Mark V. and Channell, Rob",
    title = "Splendid Isolation: Patterns of Geographic Range Collapse in Endangered Mammals",
    year = "1995",
    journal = "Journal of Mammalogy",
    abstract = "Population densities of terrestrial animals tend to be higher and less variable near the center versus along the periphery of a species' geographic range. If extinctions are tied to local population dynamics, geographic ranges of endangered species should collapse inward, with remnant populations persisting near the center of a species' historic range. Geographic-Information-System analysis of range collapse in nonvolant, terrestrial mammals reveals, however, that extant populations of 23 of 31 species were located along the periphery, not the center, of their historic range. In addition, range collapse appears to be independent of fragment area and has a directional bias from east to west. Persistence of endangered populations also appears to be greater on islands than on continents. These results contradict conventional wisdom in biogeography and macroecology and have important implications for conserving biodiversity. Because of their relative isolation from central populations and from a suite of anthropogenic disturbances, islands and other sites along the periphery of a species' historic range represent critical refugia for many endangered species.",
    url = "https://doi.org/10.2307/1382345",
    doi = "10.2307/1382345",
    openalex = "W2043208989",
    references = "doi101016000632078690025x, doi101016000632079291047v, doi1010160169534794902488, doi101126science21545381351, doi101126science2454917477, doi1015159781400881376, doi1023071935620, doi1023072259626, doi105860choice290892, doi105962bhltitle44956"
}

@article{lomolino1995splendid,
    author = "Lomolino, M. V. and Channell, R.",
    title = "Splendid Isolation: Patterns of Geographic Range Collapse in Endangered Mammals",
    year = "1995",
    journal = "Journal of Mammalogy",
    url = "https://doi.org/10.2307/1382345",
    doi = "10.2307/1382345",
    number = "2",
    pages = "335-347",
    volume = "76"
}

▪ Abstract Comparative, quantitative biogeographic studies are revealing empirical patterns of interspecific variation in the sizes, shapes, boundaries, and internal structures of geographic ranges; these patterns promise to contribute to understanding the historical and ecological processes that influence the distributions of species. This review focuses on characteristics of ranges that appear to reflect the influences of environmental limiting factors and dispersal. Among organisms as a whole, range size varies by more than 12 orders of magnitude. Within genera, families, orders, and classes of plants and animals, range size often varies by several orders of magnitude, and this variation is associated with variation in body size, population density, dispersal mode, latitude, elevation, and depth (in marine systems). The shapes of ranges and the dynamic changes in range boundaries reflect the interacting influences of limiting environmental conditions (niche variables) and dispersal/extinction dynamics. These processes also presumably account for most of the internal structure of ranges: the spatial patterns and orders-of-magnitude of variation in the abundance of species among sites within their ranges. The results of this kind of “ecological biogeography”need to be integrated with the results of phylogenetic and paleoenvironmental approaches to “historical biogeography”so we can better understand the processes that have determined the geographic distributions of organisms.

@article{doi101146annurevecolsys271597,
    author = "Brown, James H. and Stevens, George C. and Kaufman, Dawn M.",
    title = "THE GEOGRAPHIC RANGE: Size, Shape, Boundaries, and Internal Structure",
    year = "1996",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "▪ Abstract Comparative, quantitative biogeographic studies are revealing empirical patterns of interspecific variation in the sizes, shapes, boundaries, and internal structures of geographic ranges; these patterns promise to contribute to understanding the historical and ecological processes that influence the distributions of species. This review focuses on characteristics of ranges that appear to reflect the influences of environmental limiting factors and dispersal. Among organisms as a whole, range size varies by more than 12 orders of magnitude. Within genera, families, orders, and classes of plants and animals, range size often varies by several orders of magnitude, and this variation is associated with variation in body size, population density, dispersal mode, latitude, elevation, and depth (in marine systems). The shapes of ranges and the dynamic changes in range boundaries reflect the interacting influences of limiting environmental conditions (niche variables) and dispersal/extinction dynamics. These processes also presumably account for most of the internal structure of ranges: the spatial patterns and orders-of-magnitude of variation in the abundance of species among sites within their ranges. The results of this kind of “ecological biogeography”need to be integrated with the results of phylogenetic and paleoenvironmental approaches to “historical biogeography”so we can better understand the processes that have determined the geographic distributions of organisms.",
    url = "https://doi.org/10.1146/annurev.ecolsys.27.1.597",
    doi = "10.1146/annurev.ecolsys.27.1.597",
    openalex = "W2170505236",
    references = "doi10103823876, doi10106312995555, doi101086284267, doi101086284880, doi101086284913, doi101093aesa492190, doi101111j1469185x1983tb00380x, doi101126science24348951145, doi1023071382345, doi1023071933500, doi1023071940431, doi1023072259626, doi1023073544021, doi1023073669094, jablonski1983larval, lomolino1995splendid, openalexw1500291103, openalexw1989371375"
}

Abstract No species occurs everywhere. Indeed, the majority are absent from most places, and where they do occur they are usually quite rare. Gaston discusses the structure of these distributions - the structure of the geographic ranges of species. Gaston is particularly concerned with the factors that determine the limits to a species’ geographic range, how the sizes of those ranges vary, and patterns in that variation. Also considered are the distribution of individuals amongst those sites where a species does occur and what determines that distribution, and some of the practical implications of all these. Both in a pure and applied context, ecologists need a broader perspective on their subject matter than has historically prevailed. This book provides one such perspective. A must have book for any researchers and graduate students studying macroecology, biogeography and conservation biology.

@book{doi101093oso97801985264070010001,
    author = "Gaston, Kevin J.",
    title = "The Structure and Dynamics of Geographic Ranges",
    year = "2003",
    abstract = "Abstract No species occurs everywhere. Indeed, the majority are absent from most places, and where they do occur they are usually quite rare. Gaston discusses the structure of these distributions - the structure of the geographic ranges of species. Gaston is particularly concerned with the factors that determine the limits to a species’ geographic range, how the sizes of those ranges vary, and patterns in that variation. Also considered are the distribution of individuals amongst those sites where a species does occur and what determines that distribution, and some of the practical implications of all these. Both in a pure and applied context, ecologists need a broader perspective on their subject matter than has historically prevailed. This book provides one such perspective. A must have book for any researchers and graduate students studying macroecology, biogeography and conservation biology.",
    url = "https://doi.org/10.1093/oso/9780198526407.001.0001",
    doi = "10.1093/oso/9780198526407.001.0001",
    openalex = "W1593262638"
}

Rabies virus exists in dogs on Sri Lanka as a single, minimally divergent lineage only distantly related to other rabies virus lineages in Asia. Stable, geographically isolated virus populations are susceptible to local extinction. A fully implemented rabies-control campaign could make Sri Lanka the first Asian country in >30 years to become free of rabies virus.

@article{doi103201eid0903020545,
    author = "Nanayakkara, Susilakanthi and Smith, Jean S and Rupprecht, Charles E",
    title = "Rabies in Sri Lanka: splendid isolation.",
    year = "2003",
    journal = "Emerging infectious diseases",
    abstract = "Rabies virus exists in dogs on Sri Lanka as a single, minimally divergent lineage only distantly related to other rabies virus lineages in Asia. Stable, geographically isolated virus populations are susceptible to local extinction. A fully implemented rabies-control campaign could make Sri Lanka the first Asian country in >30 years to become free of rabies virus.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC2958551/",
    doi = "10.3201/eid0903.020545",
    openalex = "W2013489903",
    pmcid = "PMC2958551",
    pmid = "12643834",
    references = "doi101006viro19951285, doi101056nejm199101243240401, doi101093infdis1662296, doi101093nar1462671, doi101128jvi7517809681042001, doi103201eid0803010330, doi10758900903558362231, openalexw19217140, openalexw4302065358"
}

In a previous paper In their study, Greenberg et al. used targeted gene replacement to construct lines having different alleles of the desaturase-2 (desat2) locus-a gene involved in synthesis of cuticular hydrocarbons. They found that different alleles had different effects on flies' responses to cold and starvation stress: carriers of the African and Caribbean allele (ds2 Z) consistently had less cold resistance and greater starvation resistance than carriers of the Cosmopolitan allele (ds2 M). Because there was earlier evidence for sexual isolation between carriers of different desat2 alleles (African females homozygous for ds2 Z discriminate against non-African males homozygous for ds2 M; Fang et al. 2002), possibly because different cuticular hydrocarbons act as mating cues,

@article{doi101111j001438202006tb01143x,
    author = "Coyne, Jerry A. and Elwyn, Susannah",
    title = "DESATURASE‐2, ENVIRONMENTAL ADAPTATION, AND SEXUAL ISOLATION IN DROSOPHILA MELANOGASTER",
    year = "2006",
    journal = "Evolution",
    abstract = "In a previous paper In their study, Greenberg et al. used targeted gene replacement to construct lines having different alleles of the desaturase-2 (desat2) locus-a gene involved in synthesis of cuticular hydrocarbons. They found that different alleles had different effects on flies' responses to cold and starvation stress: carriers of the African and Caribbean allele (ds2 Z) consistently had less cold resistance and greater starvation resistance than carriers of the Cosmopolitan allele (ds2 M). Because there was earlier evidence for sexual isolation between carriers of different desat2 alleles (African females homozygous for ds2 Z discriminate against non-African males homozygous for ds2 M; Fang et al. 2002), possibly because different cuticular hydrocarbons act as mating cues,",
    url = "https://doi.org/10.1111/j.0014-3820.2006.tb01143.x",
    doi = "10.1111/j.0014-3820.2006.tb01143.x",
    openalex = "W4236671098",
    references = "doi101086428388, doi101093genetics1622781, doi101111j001438202006tb01106x, doi101111j001438202006tb01142x, doi101126science1090432"
}

In historical biogeography, model-based inference methods for reconstructing the evolution of geographic ranges on phylogenetic trees are poorly developed relative to the diversity of analogous methods available for inferring character evolution. We attempt to rectify this deficiency by constructing a dispersal-extinction-cladogenesis (DEC) model for geographic range evolution that specifies instantaneous transition rates between discrete states (ranges) along phylogenetic branches and apply it to estimating likelihoods of ancestral states (range inheritance scenarios) at cladogenesis events. Unlike an earlier version of this approach, the present model allows for an analytical solution to probabilities of range transitions as a function of time, enabling free parameters in the model, rates of dispersal, and local extinction to be estimated by maximum likelihood. Simulation results indicate that accurate parameter estimates may be difficult to obtain in practice but also show that ancestral range inheritance scenarios nevertheless can be correctly recovered with high success if rates of range evolution are low relative to the rate of cladogenesis. We apply the DEC model to a previously published, exemplary case study of island biogeography involving Hawaiian endemic angiosperms in Psychotria (Rubiaceae), showing how the DEC model can be iteratively refined from inspecting inferences of range evolution and also how geological constraints involving times of island origin may be imposed on the likelihood function. The DEC model is sufficiently similar to character models that it might serve as a gateway through which many existing comparative methods for characters could be imported into the realm of historical biogeography; moreover, it might also inspire the conceptual expansion of character models toward inclusion of evolutionary change as directly coincident, either as cause or consequence, with cladogenesis events. The DEC model is thus an incremental advance that highlights considerable potential in the nascent field of model-based historical biogeographic inference.

@article{doi10108010635150701883881,
    author = "Ree, Richard H. and Smith, Stephen A.",
    title = "Maximum Likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction, and Cladogenesis",
    year = "2008",
    journal = "Systematic Biology",
    abstract = "In historical biogeography, model-based inference methods for reconstructing the evolution of geographic ranges on phylogenetic trees are poorly developed relative to the diversity of analogous methods available for inferring character evolution. We attempt to rectify this deficiency by constructing a dispersal-extinction-cladogenesis (DEC) model for geographic range evolution that specifies instantaneous transition rates between discrete states (ranges) along phylogenetic branches and apply it to estimating likelihoods of ancestral states (range inheritance scenarios) at cladogenesis events. Unlike an earlier version of this approach, the present model allows for an analytical solution to probabilities of range transitions as a function of time, enabling free parameters in the model, rates of dispersal, and local extinction to be estimated by maximum likelihood. Simulation results indicate that accurate parameter estimates may be difficult to obtain in practice but also show that ancestral range inheritance scenarios nevertheless can be correctly recovered with high success if rates of range evolution are low relative to the rate of cladogenesis. We apply the DEC model to a previously published, exemplary case study of island biogeography involving Hawaiian endemic angiosperms in Psychotria (Rubiaceae), showing how the DEC model can be iteratively refined from inspecting inferences of range evolution and also how geological constraints involving times of island origin may be imposed on the likelihood function. The DEC model is sufficiently similar to character models that it might serve as a gateway through which many existing comparative methods for characters could be imported into the realm of historical biogeography; moreover, it might also inspire the conceptual expansion of character models toward inclusion of evolutionary change as directly coincident, either as cause or consequence, with cladogenesis events. The DEC model is thus an incremental advance that highlights considerable potential in the nascent field of model-based historical biogeographic inference.",
    url = "https://doi.org/10.1080/10635150701883881",
    doi = "10.1080/10635150701883881",
    openalex = "W2101095863",
    references = "doi101007bf01734359, doi10108010635150390192780, doi10108010635150490522232, doi10108010635150701607033, doi101080106351599260184, doi101086503444, doi101093sysbio461195, doi101098rspb19940006, doi101111j001438202005tb00940x, doi101111j155856461997tb05095x"
}

The phylogeographic structure of the widely distributed arid and semi‐arid Australian splendid fairy‐wren Malurus splendens was investigated by using variation in plumage characters and mitochondrial DNA (mtDNA). We examined sequences of the mtDNA ND2 gene and used spectrophotometry to quantify chromatic variation in plumage in order to test the current morphology‐based intraspecific taxonomy of M. splendens and to discriminate between hypotheses invoking allopatric and parapatric processes in the origin of diversity in the complex. Genetic diversity of M. splendens fell into three divergent geographically structured clades. One represents populations ascribed to the western subspecies M. s. splendens, the other populations of central M. s. musgravi and the third all eastern populations currently ascribed to M. s. emmottorum and M. s. melanotus. Plumage patterns clearly differentiate M. s. splendens and M. s. musgravi, and spectrophotometry identified a step‐wise transition in spectra between M. s. melanotus and M. s. emmottorum. Congruence of patterns of phenotypic and genetic variation among western, central and eastern populations of M. splendens strongly suggests that these populations have diverged in allopatry on either side of historical biogeographic barriers in this region. Decoupled patterns of phenotypic and genetic diversity suggest that the divergence of M. s. melanotus and M. s. emmottorum may have occurred without periods of isolation perhaps in response to differences in local environmental conditions, or alternatively, mtDNA and plumage may have different rates of evolution. Critically, we encountered issues with the placement of the root of the M. splendens complex. The root was placed within the subspecies M. s. splendens separating its northern and southern populations and rendering the subspecies paraphyletic.

@article{doi101111j1600048x200804383x,
    author = "Kearns, Anna M. and Joseph, Leo and Edwards, Scott V. and Double, Michael C.",
    title = "Inferring the phylogeography and evolutionary history of the splendid fairy‐wren Malurus splendens from mitochondrial DNA and spectrophotometry",
    year = "2008",
    journal = "Journal of Avian Biology",
    abstract = "The phylogeographic structure of the widely distributed arid and semi‐arid Australian splendid fairy‐wren Malurus splendens was investigated by using variation in plumage characters and mitochondrial DNA (mtDNA). We examined sequences of the mtDNA ND2 gene and used spectrophotometry to quantify chromatic variation in plumage in order to test the current morphology‐based intraspecific taxonomy of M. splendens and to discriminate between hypotheses invoking allopatric and parapatric processes in the origin of diversity in the complex. Genetic diversity of M. splendens fell into three divergent geographically structured clades. One represents populations ascribed to the western subspecies M. s. splendens, the other populations of central M. s. musgravi and the third all eastern populations currently ascribed to M. s. emmottorum and M. s. melanotus. Plumage patterns clearly differentiate M. s. splendens and M. s. musgravi, and spectrophotometry identified a step‐wise transition in spectra between M. s. melanotus and M. s. emmottorum. Congruence of patterns of phenotypic and genetic variation among western, central and eastern populations of M. splendens strongly suggests that these populations have diverged in allopatry on either side of historical biogeographic barriers in this region. Decoupled patterns of phenotypic and genetic diversity suggest that the divergence of M. s. melanotus and M. s. emmottorum may have occurred without periods of isolation perhaps in response to differences in local environmental conditions, or alternatively, mtDNA and plumage may have different rates of evolution. Critically, we encountered issues with the placement of the root of the M. splendens complex. The root was placed within the subspecies M. s. splendens separating its northern and southern populations and rendering the subspecies paraphyletic.",
    url = "https://doi.org/10.1111/j.1600-048x.2008.04383.x",
    doi = "10.1111/j.1600-048x.2008.04383.x",
    openalex = "W2079869095",
    references = "doi101046j1365294x200001020x, doi101093bioinformatics149817, doi101093bioinformatics178754, doi101093bioinformaticsbtg359, doi101093genetics1233585, doi101093genetics1472915, doi101093oxfordjournalsmolbeva026201, doi1013851592591922365, doi105860choice392183, openalexw2994240441"
}

Understanding of the determinants of species' geographic range limits remains poorly integrated. In part, this is because of the diversity of perspectives on the issue, and because empirical studies have lagged substantially behind developments in theory. Here, I provide a broad overview, drawing together many of the disparate threads, considering, in turn, how influences on the terms of a simple single-population equation can determine range limits. There is theoretical and empirical evidence for systematic changes towards range limits under some circumstances in each of the demographic parameters. However, under other circumstances, no such changes may take place in particular parameters, or they may occur in a different direction, with limitation still occurring. This suggests that (i) little about range limitation can categorically be inferred from many empirical studies, which document change in only one demographic parameter, (ii) there is a need for studies that document variation in all of the parameters, and (iii) in agreement with theoretical evidence that range limits can be formed in the presence or absence of hard boundaries, environmental gradients or biotic interactions, there may be few general patterns as to the determinants of these limits, with most claimed generalities at least having many exceptions.

@article{doi101098rspb20081480,
    author = "Gaston, Kevin J.",
    title = "Geographic range limits: achieving synthesis",
    year = "2009",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "Understanding of the determinants of species' geographic range limits remains poorly integrated. In part, this is because of the diversity of perspectives on the issue, and because empirical studies have lagged substantially behind developments in theory. Here, I provide a broad overview, drawing together many of the disparate threads, considering, in turn, how influences on the terms of a simple single-population equation can determine range limits. There is theoretical and empirical evidence for systematic changes towards range limits under some circumstances in each of the demographic parameters. However, under other circumstances, no such changes may take place in particular parameters, or they may occur in a different direction, with limitation still occurring. This suggests that (i) little about range limitation can categorically be inferred from many empirical studies, which document change in only one demographic parameter, (ii) there is a need for studies that document variation in all of the parameters, and (iii) in agreement with theoretical evidence that range limits can be formed in the presence or absence of hard boundaries, environmental gradients or biotic interactions, there may be few general patterns as to the determinants of these limits, with most claimed generalities at least having many exceptions.",
    url = "https://doi.org/10.1098/rspb.2008.1480",
    doi = "10.1098/rspb.2008.1480",
    openalex = "W2147134797",
    references = "doi101046j14610248200200297x, openalexw2151235472"
}

Splendid alfonsino Beryx splendens is a commercial species in several countries, but is not currently exploited in New Caledonia. Information on species biology and genetics can influence the development of fisheries and assist in their management, but the genetic structuring and diversity of B. splendens populations remain largely unknown. To improve knowledge of genetic parameters, we used mitochondrial DNA sequences to conduct a comparative study of populations from throughout the world. Fragments of 815 bp of cytochrome b gene were sequenced and used to interpret the species history. We analyzed 204 individuals representing 14 geographical populations worldwide. A special focus was put on populations from New Caledonia. Analysis of variation between sequences, based on pairwise F statistics and AMOVA, demonstrated a population subdivision between the Atlantic and Indo-Pacific Oceans (Fst = 0.11-0.32; P < 0.05). Minimum-spanning network analysis revealed a mainly star-shaped pattern, with two lineages that may represent population expansion following a bottleneck/founder event and/or suggest colonization by migratory events over large distances. Our observations demonstrated that the species seems to follow the oceanic currents. Analysis of the nucleotide sequences revealed 122 variable sites, which defined numerous haplotypes, some associated with particular geographical regions. These data suggest an extremely high intra-specific genetic diversity, even at small scales. Focusing on the New Caledonia area, statistical analysis did not reveal sub-structuring among samples, suggesting again that at least a fraction of individuals migrate. No significant isolation by distance pattern was observed in this species (R = -0.22; P = 0.79) among seamount populations in the EEZ.

@article{doi101007s107090129628y,
    author = "Lévy-Hartmann, Lauriana and Roussel, Valérie and Letourneur, Yves and Sellos, Daniel Y",
    title = "Global and New Caledonian patterns of population genetic variation in the deep-sea splendid alfonsino, Beryx splendens, inferred from mtDNA.",
    year = "2011",
    journal = "Genetica",
    abstract = "Splendid alfonsino Beryx splendens is a commercial species in several countries, but is not currently exploited in New Caledonia. Information on species biology and genetics can influence the development of fisheries and assist in their management, but the genetic structuring and diversity of B. splendens populations remain largely unknown. To improve knowledge of genetic parameters, we used mitochondrial DNA sequences to conduct a comparative study of populations from throughout the world. Fragments of 815 bp of cytochrome b gene were sequenced and used to interpret the species history. We analyzed 204 individuals representing 14 geographical populations worldwide. A special focus was put on populations from New Caledonia. Analysis of variation between sequences, based on pairwise F statistics and AMOVA, demonstrated a population subdivision between the Atlantic and Indo-Pacific Oceans (Fst = 0.11-0.32; P < 0.05). Minimum-spanning network analysis revealed a mainly star-shaped pattern, with two lineages that may represent population expansion following a bottleneck/founder event and/or suggest colonization by migratory events over large distances. Our observations demonstrated that the species seems to follow the oceanic currents. Analysis of the nucleotide sequences revealed 122 variable sites, which defined numerous haplotypes, some associated with particular geographical regions. These data suggest an extremely high intra-specific genetic diversity, even at small scales. Focusing on the New Caledonia area, statistical analysis did not reveal sub-structuring among samples, suggesting again that at least a fraction of individuals migrate. No significant isolation by distance pattern was observed in this species (R = -0.22; P = 0.79) among seamount populations in the EEZ.",
    url = "https://pubmed.ncbi.nlm.nih.gov/22527688/",
    doi = "10.1007/s10709-012-9628-y",
    openalex = "W2002501489",
    pmid = "22527688",
    references = "doi101093bioinformatics124357, doi101093genetics1233585, doi101093genetics1312479, doi101093genetics1472915, doi101093molbevmsm092, doi101093oxfordjournalsmolbeva026036, doi101111jbi14281, doi107312nei92038, openalexw2119799171, openalexw3199943451"
}

Understanding landscape processes driving patterns of population genetic differentiation and diversity has been a long-standing focus of ecology and evolutionary biology. Gene flow may be reduced by historical, ecological or geographic factors, resulting in patterns of isolation by distance (IBD) or isolation by environment (IBE). Although IBE has been found in many natural systems, most studies investigating patterns of IBD and IBE in nature have used anonymous neutral genetic markers, precluding inference of selection mechanisms or identification of genes potentially under selection. Using landscape genomics, the simultaneous study of genomic and ecological landscapes, we investigated the processes driving population genetic patterns of White-breasted Nuthatches (Sitta carolinensis) in sky islands (montane forest habitat islands) of the Madrean Archipelago. Using more than 4000 single nucleotide polymorphisms and multiple tests to investigate the relationship between genetic differentiation and geographic or ecological distance, we identified IBE, and a lack of IBD, among sky island populations of S. carolinensis. Using three tests to identify selection, we found 79 loci putatively under selection; of these, seven matched CDS regions in the Zebra Finch. The loci under selection were highly associated with climate extremes (maximum temperature of warmest month and minimum precipitation of driest month). These results provide evidence for IBE - disentangled from IBD - in sky island vertebrates and identify potential adaptive genetic variation.

@article{doi101111mec13258,
    author = "Manthey, Joseph D. and Moyle, Robert G.",
    title = "Isolation by environment in White‐breasted Nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach",
    year = "2015",
    journal = "Molecular Ecology",
    abstract = "Understanding landscape processes driving patterns of population genetic differentiation and diversity has been a long-standing focus of ecology and evolutionary biology. Gene flow may be reduced by historical, ecological or geographic factors, resulting in patterns of isolation by distance (IBD) or isolation by environment (IBE). Although IBE has been found in many natural systems, most studies investigating patterns of IBD and IBE in nature have used anonymous neutral genetic markers, precluding inference of selection mechanisms or identification of genes potentially under selection. Using landscape genomics, the simultaneous study of genomic and ecological landscapes, we investigated the processes driving population genetic patterns of White-breasted Nuthatches (Sitta carolinensis) in sky islands (montane forest habitat islands) of the Madrean Archipelago. Using more than 4000 single nucleotide polymorphisms and multiple tests to investigate the relationship between genetic differentiation and geographic or ecological distance, we identified IBE, and a lack of IBD, among sky island populations of S. carolinensis. Using three tests to identify selection, we found 79 loci putatively under selection; of these, seven matched CDS regions in the Zebra Finch. The loci under selection were highly associated with climate extremes (maximum temperature of warmest month and minimum precipitation of driest month). These results provide evidence for IBE - disentangled from IBD - in sky island vertebrates and identify potential adaptive genetic variation.",
    url = "https://doi.org/10.1111/mec.13258",
    doi = "10.1111/mec.13258",
    openalex = "W2139226491",
    references = "doi101111evo12107"
}

FIGURE 1. Geographic distribution map of Myrceugenia (Myrtaceae). Collections date from 1816 to 2023 (12,233 herbarium records from 35 herbaria).

@misc{proença2024figure,
    author = "Proença, Carolyn Elinore Barnes and Vieira, Fábio Christiano Speck and Sano, Paulo Takeo and Villarroel, Daniel",
    title = "FIGURE 1 in In splendid isolation: a new cloud forest species expands the distribution of Myrceugenia (Myrtaceae) into Las Yungas and adds a new genus to the flora of Bolivia",
    year = "2024",
    publisher = "Zenodo",
    abstract = "FIGURE 1. Geographic distribution map of Myrceugenia (Myrtaceae). Collections date from 1816 to 2023 (12,233 herbarium records from 35 herbaria).",
    url = "https://zenodo.org/doi/10.5281/zenodo.14520890",
    doi = "10.5281/zenodo.14520890"
}