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Journal articles on the topic 'Phylogeography'
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1
Domínguez-Domínguez, D., and E. Vázquez– Domínguez. "Filogeografía: aplicaciones en taxonomía y conservación." Animal Biodiversity and Conservation 32, no. 1 (2009): 59–70. http://dx.doi.org/10.32800/abc.2009.32.0059.
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Phylogeography: applications in taxonomy and conservation. Phylogeography is defined as the discipline that studies the principles and processes that determine the geographical distribution of genealogical lineages. Two of the study areas where phylogeographic approaches are used more and more frequently are taxonomy and conservation. In this review we first present a general description of phylogeography and then discuss how research in taxonomy and conservation has been addressed when using phylogeographic approaches, emphasising in particular the limitations that need to be considered. We include relevant examples of studies with animals in order to help readers acquire the sense and scope of such applications and select the appropriate study design to meet these objectives.
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Zamudio, Kelly R., Rayna C. Bell, and Nicholas A. Mason. "Phenotypes in phylogeography: Species’ traits, environmental variation, and vertebrate diversification." Proceedings of the National Academy of Sciences 113, no. 29 (July 18, 2016): 8041–48. http://dx.doi.org/10.1073/pnas.1602237113.
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Almost 30 y ago, the field of intraspecific phylogeography laid the foundation for spatially explicit and genealogically informed studies of population divergence. With new methods and markers, the focus in phylogeography shifted to previously unrecognized geographic genetic variation, thus reducing the attention paid to phenotypic variation in those same diverging lineages. Although phenotypic differences among lineages once provided the main data for studies of evolutionary change, the mechanisms shaping phenotypic differentiation and their integration with intraspecific genetic structure have been underexplored in phylogeographic studies. However, phenotypes are targets of selection and play important roles in species performance, recognition, and diversification. Here, we focus on three questions. First, how can phenotypes elucidate mechanisms underlying concordant or idiosyncratic responses of vertebrate species evolving in shared landscapes? Second, what mechanisms underlie the concordance or discordance of phenotypic and phylogeographic differentiation? Third, how can phylogeography contribute to our understanding of functional phenotypic evolution? We demonstrate that the integration of phenotypic data extends the reach of phylogeography to explain the origin and maintenance of biodiversity. Finally, we stress the importance of natural history collections as sources of high-quality phenotypic data that span temporal and spatial axes.
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Edwards, Scott V., Sally Potter, C. Jonathan Schmitt, Jason G. Bragg, and Craig Moritz. "Reticulation, divergence, and the phylogeography–phylogenetics continuum." Proceedings of the National Academy of Sciences 113, no. 29 (July 18, 2016): 8025–32. http://dx.doi.org/10.1073/pnas.1601066113.
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Phylogeography, and its extensions into comparative phylogeography, have their roots in the layering of gene trees across geography, a paradigm that was greatly facilitated by the nonrecombining, fast evolution provided by animal mtDNA. As phylogeography moves into the era of next-generation sequencing, the specter of reticulation at several levels—within loci and genomes in the form of recombination and across populations and species in the form of introgression—has raised its head with a prominence even greater than glimpsed during the nuclear gene PCR era. Here we explore the theme of reticulation in comparative phylogeography, speciation analysis, and phylogenomics, and ask how the centrality of gene trees has fared in the next-generation era. To frame these issues, we first provide a snapshot of multilocus phylogeographic studies across the Carpentarian Barrier, a prominent biogeographic barrier dividing faunas spanning the monsoon tropics in northern Australia. We find that divergence across this barrier is evident in most species, but is heterogeneous in time and demographic history, often reflecting the taxonomic distinctness of lineages spanning it. We then discuss a variety of forces generating reticulate patterns in phylogeography, including introgression, contact zones, and the potential selection-driven outliers on next-generation molecular markers. We emphasize the continued need for demographic models incorporating reticulation at the level of genomes and populations, and conclude that gene trees, whether explicit or implicit, should continue to play a role in the future of phylogeography.
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Temirbayeva, K. "Biogeography and phylogeography." Journal of Geography and Environmental Management 44, no. 1 (2017): 64–67. http://dx.doi.org/10.26577/jgem.2017.1.349.
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Papadopoulou, Anna, and L. Lacey Knowles. "Toward a paradigm shift in comparative phylogeography driven by trait-based hypotheses." Proceedings of the National Academy of Sciences 113, no. 29 (July 18, 2016): 8018–24. http://dx.doi.org/10.1073/pnas.1601069113.
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For three decades, comparative phylogeography has conceptually and methodologically relied on the concordance criterion for providing insights into the historical/biogeographic processes driving population genetic structure and divergence. Here we discuss how this emphasis, and the corresponding lack of methods for extracting information about biotic/intrinsic contributions to patterns of genetic variation, may bias our general understanding of the factors driving genetic structure. Specifically, this emphasis has promoted a tendency to attribute discordant phylogeographic patterns to the idiosyncracies of history, as well as an adherence to generic null expectations of concordance with reduced predictive power. We advocate that it is time for a paradigm shift in comparative phylogeography, especially given the limited utility of the concordance criterion as genomic data provide ever-increasing levels of resolution. Instead of adhering to the concordance-discordance dichotomy, comparative phylogeography needs to emphasize the contribution of taxon-specific traits that will determine whether concordance is a meaningful criterion for evaluating hypotheses or may predict discordant phylogeographic structure. Through reference to some case studies we illustrate how refined hypotheses based on taxon-specific traits can provide improved predictive frameworks to forecast species responses to climatic change or biogeographic barriers while gaining unique insights about the taxa themselves and their interactions with their environment. We outline a potential avenue toward a synthetic comparative phylogeographic paradigm that includes addressing some important conceptual and methodological challenges related to study design and application of model-based approaches for evaluating support of trait-based hypotheses under the proposed paradigm.
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Bowen, Brian W., Michelle R. Gaither, Joseph D. DiBattista, Matthew Iacchei, Kimberly R. Andrews, W. Stewart Grant, Robert J. Toonen, and John C. Briggs. "Comparative phylogeography of the ocean planet." Proceedings of the National Academy of Sciences 113, no. 29 (July 18, 2016): 7962–69. http://dx.doi.org/10.1073/pnas.1602404113.
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Understanding how geography, oceanography, and climate have ultimately shaped marine biodiversity requires aligning the distributions of genetic diversity across multiple taxa. Here, we examine phylogeographic partitions in the sea against a backdrop of biogeographic provinces defined by taxonomy, endemism, and species composition. The taxonomic identities used to define biogeographic provinces are routinely accompanied by diagnostic genetic differences between sister species, indicating interspecific concordance between biogeography and phylogeography. In cases where individual species are distributed across two or more biogeographic provinces, shifts in genotype frequencies often align with biogeographic boundaries, providing intraspecific concordance between biogeography and phylogeography. Here, we provide examples of comparative phylogeography from (i) tropical seas that host the highest marine biodiversity, (ii) temperate seas with high productivity but volatile coastlines, (iii) migratory marine fauna, and (iv) plankton that are the most abundant eukaryotes on earth. Tropical and temperate zones both show impacts of glacial cycles, the former primarily through changing sea levels, and the latter through coastal habitat disruption. The general concordance between biogeography and phylogeography indicates that the population-level genetic divergences observed between provinces are a starting point for macroevolutionary divergences between species. However, isolation between provinces does not account for all marine biodiversity; the remainder arises through alternative pathways, such as ecological speciation and parapatric (semiisolated) divergences within provinces and biodiversity hotspots.
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Kidd, David M., and Michael G. Ritchie. "Phylogeographic information systems: putting the geography into phylogeography." Journal of Biogeography 33, no. 11 (November 2006): 1851–65. http://dx.doi.org/10.1111/j.1365-2699.2006.01574.x.
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Byrne, M. "Phylogeography provides an evolutionary context for the conservation of a diverse and ancient flora." Australian Journal of Botany 55, no. 3 (2007): 316. http://dx.doi.org/10.1071/bt06072.
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Phylogeography can inform conservation strategies through assessment of genetic diversity that incorporates an evolutionary perspective, and allows evaluation within a geographical context, thus providing integration with other biogeographical information. Comparative phylogeography can identify significant historical processes that have had major influences on the biota and provides a historical context for understanding current species distributions. The phylogeographic patterns in the flora of south-western Australia are reviewed. Concordant patterns of lineage divergence in three unrelated taxa from separate families with widespread distributions indicate a common response to major historical processes involved in Pleistocene climatic fluctuations. Identification of highly divergent haplotypes in some species indicates areas that may represent refugia during times of climatic instability. Analysis of phylogeographic patterns in the flora of south-western Australia has revealed the influence of historical climate change in promoting high phylogenetic diversity within species that is comparable to the high species diversity that is well known in the Western Australian flora. Knowledge of historical influences and species responses provides an evolutionary context for conservation management strategies that facilitate the continued action of dynamic evolutionary processes.
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PAUČULOVÁ, LENKA, MAROŠ DZURINKA, MARTINA ŠEMELÁKOVÁ, ALEXANDER CSANÁDY, and ĽUBOMÍR PANIGAJ. "Phylogeography, genetic structure and wing pattern variation of Erebia pronoe (Esper, 1780) (Lepidoptera: Nymphalidae) in Europe." Zootaxa 4441, no. 2 (June 27, 2018): 279. http://dx.doi.org/10.11646/zootaxa.4441.2.5.
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The distribution of genetic diversity within Erebia pronoe (Esper, 1780) populations in relation to biogeographic ranges is essential for understanding the processes of evolution, speciation and phylogeography in this species. A certain degree of genetic variability was expected because of the species’ linkage solely to calcareous soils. These ideas were focused on the water ringlet E. pronoe, a European endemic montane butterfly distributed over a narrow area of mountains, with its occurrence dependent on nutrient plants. Therefore, the origin, occurrence, phylogeography and variability are described in defined mountain localities in Europe in the light of glaciation events that occurred during the Quaternary (Pleistocene) period. The species’ phylogeography is based on a combination of two mitochondrial genes (COI, CR) and morphology (wing morphometry). The study comprised samples from the Western Carpathians, Pyrenees, Alps, South-Eastern Carpathians (Romania) and Southern Limestone Alps (Slovenia). Moreover, the species’ remarkable phylogeographic structure was observed, including four morphologic lineages and divergent genetic lineages. These lineages cover the Carpathian Mountains as well as the Western European mountains (Spanish populations) with no apparent gene flow between most regions, even across distances of only hundreds of kilometres.
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Peter Linder, H. "Phylogeography." Journal of Biogeography 44, no. 2 (January 25, 2017): 243–44. http://dx.doi.org/10.1111/jbi.12958.
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Venton, Danielle. "Phylogeography." Proceedings of the National Academy of Sciences 110, no. 11 (March 12, 2013): 4158. http://dx.doi.org/10.1073/pnas.1302993110.
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Emerson, Brent C., and Godfrey M. Hewitt. "Phylogeography." Current Biology 15, no. 10 (May 2005): R367—R371. http://dx.doi.org/10.1016/j.cub.2005.05.016.
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Rieseberg, Loren H. "Phylogeography." Trends in Ecology & Evolution 15, no. 9 (September 2000): 384–85. http://dx.doi.org/10.1016/s0169-5347(00)01901-7.
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Zink, Robert M., Ann E. Kessen, Theresa V. Line, and Rachelle C. Blackwell-Rago. "Comparative Phylogeography of Some Aridland Bird Species." Condor 103, no. 1 (February 1, 2001): 1–10. http://dx.doi.org/10.1093/condor/103.1.1.
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Abstract We compared mitochondrial DNA sequences for six species distributed across the aridlands of North America to document phylogeographic patterns and assess levels of congruence. The Curve-billed Thrasher (Toxostoma curvirostre) and Canyon Towhee (Pipilo fuscus) show genetic divisions between the Sonoran and Chihuahuan Deserts, whereas the Cactus Wren (Campylorhynchus brunneicapillus), Black-tailed Gnatcatcher (Polioptila melanura), and Verdin (Auriparus flaviceps) do not. Most likely, species without phylogeographic structure only recently colonized their entire current range. Therefore, although these species are today part of a widespread avifauna, species' distributions were historically different from today. In Baja California, the Cactus Wren and the Verdin show phylogeographic breaks at 28°–30°N, consistent with a division previously described in the LeConte's Thrasher (Toxostoma lecontei) and in some members of the herpetofauna. These genetic divisions were likely caused by isolation resulting from a mid-peninsular seaway that existed one million years ago. Hence, these species appear to have been broadly sympatric for at least one million years. In contrast, the California Gnatcatcher (Polioptila californica) lacks such a phylogeographic division, and apparently only recently expanded into the northern part of its current range. Thus, not all species in Baja California have had similar histories, although further sampling might reveal a general pattern. Comparative phylogeography therefore provides an indirect method of evaluating the long-term stability of faunas via assessment of levels of phylogeographic congruence, and can show whether particular species are likely to have had a long period of co-association.
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Colgan, D. J., and P. da Costa. "The mitochondrial DNA haplotypes of snails of the estuarine hydrobiid genus Tatea cross species and biogeographic boundaries." Marine and Freshwater Research 60, no. 8 (2009): 861. http://dx.doi.org/10.1071/mf08200.
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Investigations of estuarine taxa can provide a perspective on phylogeography that complements studies of marine littoral organisms. For example, reductions in gene flow between populations and increased genetic structuring would be expected in estuarine species. The substantial amount of information about marine species and the habitat diversity along long latitudinal spans makes south-eastern Australia an excellent potential location for comparing marine and estuarine taxa. To investigate this potential, we studied the phylogeography of the two species in the estuarine gastropod genus Tatea. These have extensive and broadly overlapping distributions that encompass known marine phylogeographic boundaries. Against expectation, both Tatea species showed a remarkable lack of geographic and inter-specific variability in mitochondrial 12S rRNA (107 specimens) and cytochrome c oxidase subunit I (39) DNA sequences. No major phylogeographic discontinuities were revealed in either species and there was minimal haplotype divergence between them for either 12S rRNA or COI. The patterns of mitochondrial DNA variation discovered in Tatea may be due to a recent selective sweep or range expansion from a population in which there was little variability. Both possibilities are complicated by having to explain the similarity of the patterns in the two species.
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McCafferty, S. Shawn, Andrew Martin, and Eldredge Bermingham. "Phylogeographic Diversity of the Lower Central American Cichlid Andinoacara coeruleopunctatus (Cichlidae)." International Journal of Evolutionary Biology 2012 (September 12, 2012): 1–12. http://dx.doi.org/10.1155/2012/780169.
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It is well appreciated that historical and ecological processes are important determinates of freshwater biogeographic assemblages. Phylogeography can potentially lend important insights into the relative contribution of historical processes in biogeography. However, the extent that phylogeography reflects historical patterns of drainage connection may depend in large part on the dispersal capability of the species. Here, we test the hypothesis that due to their relatively greater dispersal capabilities, the neotropical cichlid species Andinoacara coeruleopunctatus will display a phylogeographic pattern that differs from previously described biogeographic assemblages in this important region. Based on an analysis of 318 individuals using mtDNA ATPase 6/8 sequence and restriction fragment length polymorphism data, we found eight distinct clades that are closely associated with biogeographic patterns. The branching patterns among the clades and a Bayesian clock analysis suggest a relatively rapid colonization and diversification among drainages in the emergent Isthmus of Panama followed by the coalescing of some drainages due to historical connections. We also present evidence for extensive cross-cordillera sharing of clades in central Panama and the Canal region. Our results suggest that contemporary phylogeographic patterns and diversification in Lower Central American fishes reflect an interaction of historical drainage connections, dispersal, and demographic processes.
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Taniguchi, Shoji, Johanna Bertl, Andreas Futschik, Hirohisa Kishino, and Toshio Okazaki. "Waves Out of the Korean Peninsula and Inter- and Intra-Species Replacements in Freshwater Fishes in Japan." Genes 12, no. 2 (February 21, 2021): 303. http://dx.doi.org/10.3390/genes12020303.
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The Japanese archipelago is located at the periphery of the continent of Asia. Rivers in the Japanese archipelago, separated from the continent of Asia by about 17 Ma, have experienced an intermittent exchange of freshwater fish taxa through a narrow land bridge generated by lowered sea level. As the Korean Peninsula and Japanese archipelago were not covered by an ice sheet during glacial periods, phylogeographical analyses in this region can trace the history of biota that were, for a long time, beyond the last glacial maximum. In this study, we analyzed the phylogeography of four freshwater fish taxa, Hemibarbus longirostris, dark chub Nipponocypris temminckii, Tanakia ssp. and Carassius ssp., whose distributions include both the Korean Peninsula and Western Japan. We found for each taxon that a small component of diverse Korean clades of freshwater fishes migrated in waves into the Japanese archipelago to form the current phylogeographic structure of biota. The replacements of indigenous populations by succeeding migrants may have also influenced the phylogeography.
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Neureiter, Nico, Peter Ranacher, Rik van Gijn, Balthasar Bickel, and Robert Weibel. "Can Bayesian phylogeography reconstruct migrations and expansions in linguistic evolution?" Royal Society Open Science 8, no. 1 (January 13, 2021): 201079. http://dx.doi.org/10.1098/rsos.201079.
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Bayesian phylogeography has been used in historical linguistics to reconstruct homelands and expansions of language families, but the reliability of these reconstructions has remained unclear. We contribute to this discussion with a simulation study where we distinguish two types of spatial processes: migration , where populations or languages leave one place for another, and expansion , where populations or languages gradually expand their territory. We simulate migration and expansion in two scenarios with varying degrees of spatial directional trends and evaluate the performance of state-of-the-art phylogeographic methods. Our results show that these methods fail to reconstruct migrations, but work surprisingly well on expansions, even under severe directional trends. We demonstrate that migrations and expansions have typical phylogenetic and spatial patterns, which in the one case inhibit and in the other facilitate phylogeographic reconstruction. Furthermore, we propose descriptive statistics to identify whether a real sample of languages, their relationship and spatial distribution, better fits a migration or an expansion scenario. Bringing together the results of the simulation study and theoretical arguments, we make recommendations for assessing the adequacy of phylogeographic models to reconstruct the spatial evolution of languages.
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Byrne, M., and M. Hankinson. "Testing the variability of chloroplast sequences for plant phylogeography." Australian Journal of Botany 60, no. 7 (2012): 569. http://dx.doi.org/10.1071/bt12146.
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Phylogeography in plants is hampered by lack of DNA-sequence regions that detect sufficient variation in intra-specific lineages to reveal historical patterns. We tested 13 putatively highly variable non-coding chloroplast regions in six species complexes, from four different angiosperm families, where phylogeographic patterns have previously been identified using restriction fragment length polymorphism analysis of the chloroplast genome. All regions tested amplified in most of the species. The intergenic spacer regions trnQ–rps16, trnS–trnG, psbA–trnH, psbD–trnT and ndhC–trnV were the five most promising regions for phylogeographic analysis in terms of variability, and petB and rpl16 were variable, given the utility of being amplified in a single reaction. The trnQ–rps16 and psbA–trnH intergenic spacer regions and the rpl16 D4-loop intron showed variation between known lineages in all species. The psbA–trnH intergenic spacer that has been suggested as a suitable barcoding gene for plants, generally showed a level of variation similar to that in other variable regions in the species investigated here, suggesting that some caution is required in the use of this region for barcoding applications. The present analysis identified a set of seven chloroplast regions that are a useful basis for informed selection of sequences for assessment of phylogeographic structure in plants.
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Knowles, L. Lacey. "Statistical Phylogeography." Annual Review of Ecology, Evolution, and Systematics 40, no. 1 (December 2009): 593–612. http://dx.doi.org/10.1146/annurev.ecolsys.38.091206.095702.
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Knowles, L. Lacey, and Wayne P. Maddison. "Statistical phylogeography." Molecular Ecology 11, no. 12 (December 2002): 2623–35. http://dx.doi.org/10.1046/j.1365-294x.2002.01637.x.
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Knowles, L. Lacey, and Wayne P. Maddison. "Statistical Phylogeography." Molecular Ecology 11, no. 12 (December 2002): 2623–35. http://dx.doi.org/10.1046/j.1365-294x.2002.01410.x.
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Harcourt, Alexander H. "Human phylogeography and diversity." Proceedings of the National Academy of Sciences 113, no. 29 (July 18, 2016): 8072–78. http://dx.doi.org/10.1073/pnas.1601068113.
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Homo sapiens phylogeography begins with the species’ origin nearly 200 kya in Africa. First signs of the species outside Africa (in Arabia) are from 125 kya. Earliest dates elsewhere are now 100 kya in China, 45 kya in Australia and southern Europe (maybe even 60 kya in Australia), 32 kya in northeast Siberia, and maybe 20 kya in the Americas. Humans reached arctic regions and oceanic islands last—arctic North America about 5 kya, mid- and eastern Pacific islands about 2–1 kya, and New Zealand about 700 y ago. Initial routes along coasts seem the most likely given abundant and easily harvested shellfish there as indicated by huge ancient oyster shell middens on all continents. Nevertheless, the effect of geographic barriers—mountains and oceans—is clear. The phylogeographic pattern of diasporas from several single origins—northeast Africa to Eurasia, southeast Eurasia to Australia, and northeast Siberia to the Americas—allows the equivalent of a repeat experiment on the relation between geography and phylogenetic and cultural diversity. On all continents, cultural diversity is high in productive low latitudes, presumably because such regions can support populations of sustainable size in a small area, therefore allowing a high density of cultures. Of course, other factors operate. South America has an unusually low density of cultures in its tropical latitudes. A likely factor is the phylogeographic movement of peoples from the Old World bringing novel and hence, lethal diseases to the New World, a foretaste, perhaps, of present day global transport of tropical diseases.
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Perera, Ana, D. James Harris, Daniele Salvi, Miguel Carretero, and Marco Bologna. "Preliminary survey on genetic variation within the Pygmy Algyroides, Algyroides fitzingeri, across Corsica and Sardinia." Amphibia-Reptilia 32, no. 2 (2011): 281–86. http://dx.doi.org/10.1163/017353711x556989.
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AbstractAlgyroides fitzingeri is a Corso-Sardinian endemic lizard belonging to a relictual genus within the Lacertini radiation. In recent phylogeographic studies of Corso-Sardinian endemic lizards incongruent patterns are emerging. We investigated the mitochondrial genetic variation of A. fitzingeri across Corsica and Sardinia to obtain a preliminary portrait of its phylogeographic history. This species showed some polymorphism, but with low genetic differentiation between populations, that probably originated during the Pleistocene. Corsican populations are closely related to those from North Sardinia and are likely to have originated from them, given the higher diversity and deeper phylogeographic structure observed in Sardinia than in Corsica. While the phylogeographic structure of A. fitzingeri in Corsica is surprisingly shallow when compared with other co-distributed lizards, in Sardinia a common pattern apparently emerges. Further research is needed to confirm the hypotheses here presented and to provide a conclusive assessment of the phylogeography of this species.
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Carpenter, Kent E., Paul H. Barber, Eric D. Crandall, Ma Carmen A. Ablan-Lagman, Ambariyanto, Gusti Ngurah Mahardika, B. Mabel Manjaji-Matsumoto, et al. "Comparative Phylogeography of the Coral Triangle and Implications for Marine Management." Journal of Marine Biology 2011 (2011): 1–14. http://dx.doi.org/10.1155/2011/396982.
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Extreme concentration of marine biodiversity and exploitation of marine resources in the Coral Triangle pose challenges to biogeographers and resource managers. Comparative phylogeography provides a powerful tool to test biogeographic hypotheses evoked to explain species richness in the Coral Triangle. It can also be used to delineate management units for marine resources. After about a decade of phylogeographical studies, patterns for the Coral Triangle are emerging. Broad connectivity in some species support the notion that larvae have maintained gene flow among distant populations for long periods. Other phylogeographic patterns suggest vicariant events resulting from Pleistocene sea level fluctuations, which have, at least occasionally, resulted in speciation. Divergence dates ranging back to the Miocene suggest that changing land configurations may have precipitated an explosion of species diversification. A synthesis of the marine phylogeographic studies reveals repeated patterns that corroborate hypothesized biogeographic processes and suggest improved management schemes for marine resources.
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Colgan, D. J. "Marine and estuarine phylogeography of the coasts of south-eastern Australia." Marine and Freshwater Research 67, no. 11 (2016): 1597. http://dx.doi.org/10.1071/mf15106.
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Understanding a region’s phylogeography is essential for an evolutionary perspective on its biological conservation. This review examines the phylogeographic structures in south-eastern Australia that have been revealed by mitochondrial DNA sequencing and other genetic techniques and examines whether they can be explained by known factors. The review covers species that occur in the intertidal zone or, even infrequently, in the shallow subtidal zone. The coasts most frequently associated with phylogeographic structure are the boundaries between the Peronian and Maugean biogeographical provinces in southern New South Wales and the Maugean and Flindersian provinces in South Australia, the areas in Victoria and north-eastern Tasmania separated by the Bassian Isthmus at glacial maxima, long sandy stretches without rocky intertidal habitat on the Ninety Mile Beach in Victoria and the Younghusband Peninsula–Coorong in South Australia, southern Tasmania and Bass Strait, which acts as a barrier for littoral species.
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Hung, Chih-Ming, Sergei V. Drovetski, and Robert M. Zink. "Matching loci surveyed to questions asked in phylogeography." Proceedings of the Royal Society B: Biological Sciences 283, no. 1826 (March 16, 2016): 20152340. http://dx.doi.org/10.1098/rspb.2015.2340.
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Although mitochondrial DNA (mtDNA) has long been used for assessing genetic variation within and between populations, its workhorse role in phylogeography has been criticized owing to its single-locus nature. The only choice for testing mtDNA results is to survey nuclear loci, which brings into contrast the difference in locus effective size and coalescence times. Thus, it remains unclear how erroneous mtDNA-based estimates of species history might be, especially for evolutionary events in the recent past. To test the robustness of mtDNA and nuclear sequences in phylogeography, we provide one of the largest paired comparisons of summary statistics and demographic parameters estimated from mitochondrial, five Z-linked and 10 autosomal genes of 30 avian species co-distributed in the Caucasus and Europe. The results suggest that mtDNA is robust in estimating inter-population divergence but not in intra-population diversity, which is sensitive to population size change. Here, we provide empirical evidence showing that mtDNA was more likely to detect population divergence than any other single locus owing to its smaller N e and thus faster coalescent time. Therefore, at least in birds, numerous studies that have based their inferences of phylogeographic patterns solely on mtDNA should not be readily dismissed.
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Bouckaert, Remco. "Phylogeography by diffusion on a sphere: whole world phylogeography." PeerJ 4 (September 6, 2016): e2406. http://dx.doi.org/10.7717/peerj.2406.
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BackgroundTechniques for reconstructing geographical history along a phylogeny can answer many questions of interest about the geographical origins of species. Bayesian models based on the assumption that taxa move through a diffusion process have found many applications. However, these methods rely on diffusion processes on a plane, and do not take the spherical nature of our planet in account. Performing an analysis that covers the whole world thus does not take in account the distortions caused by projections like the Mercator projection.ResultsIn this paper, we introduce a Bayesian phylogeographical method based on diffusion on a sphere. When the area where taxa are sampled from is small, a sphere can be approximated by a plane and the model results in the same inferences as with models using diffusion on a plane. For taxa sampled from the whole world, we obtain substantial differences. We present an efficient algorithm for performing inference in a Markov Chain Monte Carlo (MCMC) algorithm, and show applications to small and large samples areas. We compare results between planar and spherical diffusion in a simulation study and apply the method by inferring the origin of Hepatitis B based on sequences sampled from Eurasia and Africa.ConclusionsWe describe a framework for performing phylogeographical inference, which is suitable when the distortion introduced by map projections is large, but works well on a smaller scale as well. The framework allows sampling tips from regions, which is useful when the exact sample location is unknown, and placing prior information on locations of clades in the tree. The method is implemented in the GEO_SPHERE package in BEAST 2, which is open source licensed under LGPL and allows joint tree and geography inference under a wide range of models.
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Espíndola, Anahí, Megan Ruffley, Megan L. Smith, Bryan C. Carstens, David C. Tank, and Jack Sullivan. "Identifying cryptic diversity with predictive phylogeography." Proceedings of the Royal Society B: Biological Sciences 283, no. 1841 (October 26, 2016): 20161529. http://dx.doi.org/10.1098/rspb.2016.1529.
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Identifying units of biological diversity is a major goal of organismal biology. An increasing literature has focused on the importance of cryptic diversity, defined as the presence of deeply diverged lineages within a single species. While most discoveries of cryptic lineages proceed on a taxon-by-taxon basis, rapid assessments of biodiversity are needed to inform conservation policy and decision-making. Here, we introduce a predictive framework for phylogeography that allows rapidly identifying cryptic diversity. Our approach proceeds by collecting environmental, taxonomic and genetic data from codistributed taxa with known phylogeographic histories. We define these taxa as a reference set, and categorize them as either harbouring or lacking cryptic diversity. We then build a random forest classifier that allows us to predict which other taxa endemic to the same biome are likely to contain cryptic diversity. We apply this framework to data from two sets of disjunct ecosystems known to harbour taxa with cryptic diversity: the mesic temperate forests of the Pacific Northwest of North America and the arid lands of Southwestern North America. The predictive approach presented here is accurate, with prediction accuracies placed between 65% and 98.79% depending of the ecosystem. This seems to indicate that our method can be successfully used to address ecosystem-level questions about cryptic diversity. Further, our application for the prediction of the cryptic/non-cryptic nature of unknown species is easily applicable and provides results that agree with recent discoveries from those systems. Our results demonstrate that the transition of phylogeography from a descriptive to a predictive discipline is possible and effective.
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Sork, Victoria L., Paul F. Gugger, Jin-Ming Chen, and Silke Werth. "Evolutionary lessons from California plant phylogeography." Proceedings of the National Academy of Sciences 113, no. 29 (July 18, 2016): 8064–71. http://dx.doi.org/10.1073/pnas.1602675113.
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Phylogeography documents the spatial distribution of genetic lineages that result from demographic processes, such as population expansion, population contraction, and gene movement, shaped by climate fluctuations and the physical landscape. Because most phylogeographic studies have used neutral markers, the role of selection may have been undervalued. In this paper, we contend that plants provide a useful evolutionary lesson about the impact of selection on spatial patterns of neutral genetic variation, when the environment affects which individuals can colonize new sites, and on adaptive genetic variation, when environmental heterogeneity creates divergence at specific loci underlying local adaptation. Specifically, we discuss five characteristics found in plants that intensify the impact of selection: sessile growth form, high reproductive output, leptokurtic dispersal, isolation by environment, and the potential to evolve longevity. Collectively, these traits exacerbate the impact of environment on movement between populations and local selection pressures—both of which influence phylogeographic structure. We illustrate how these unique traits shape these processes with case studies of the California endemic oak, Quercus lobata, and the western North American lichen, Ramalina menziesii. Obviously, the lessons we learn from plant traits are not unique to plants, but they highlight the need for future animal, plant, and microbe studies to incorporate its impact. Modern tools that generate genome-wide sequence data are now allowing us to decipher how evolutionary processes affect the spatial distribution of different kinds of genes and also to better model future spatial distribution of species in response to climate change.
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Fritz, Uwe, Krystal A. Tolley, Melita Vamberger, and Flora Ihlow. "Phylogeny and phylogeography of chelonians from sub-Saharan Africa—A review of current knowledge in tribute to Margaretha D. Hofmeyr." Vertebrate Zoology 72 (October 24, 2022): 951–69. http://dx.doi.org/10.3897/vz.72.e95681.
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Species-level phylogeny and especially phylogeography of African chelonians is a comparatively under-studied field of research. We review the current knowledge of phylogeny and phylogeography, highlight congruence of spatial phylogeographic patterns amongst chelonians and other taxa and suggest future research directions to address gaps in knowledge. Our review shows that phylogeographic and phylogenetic investigations have led to unexpected findings. For example, for Pelomedusa, a putatively wide-ranging monotypic terrapin genus, cryptic diversity was revealed, with more than ten species being uncovered. The formerly recognized tortoise genus Homopus sensu lato was found to be paraphyletic with respect to Chersina. To resolve this situation, Homopus was restricted to the four-toed species H. areolatus and H. femoralis and the genus Chersobius was resurrected for the five-toed species C. boulengeri, C. signatus, and C. solus. Three previously recognized taxa were shown to be invalid, viz. the putatively extinct terrapin species Pelusios seychellensis and the tortoise subspecies Chersobius signatus cafer and Stigmochelys pardalis babcocki. Together with taxonomy, the knowledge of phylogeographic structuring sets a solid foundation for conservation measures and allows the identification of Management and Conservation Units. However, the current legislation, in particular the enforcement of the Nagoya Protocol under the Convention of Biological Diversity (CBD), has largely halted research on widely distributed taxa and turned the well-intended concept of Access and Benefit Sharing into a major impediment for conservation and research. The current situation leads for many species to a continued usage of outdated and incorrect taxonomic classifications resulting in an error cascade of conservation decisions. This is counterproductive to the aims of the CBD, that is, the protection of biodiversity. Sequencing historical DNA from museum specimens using aDNA approaches could be a short-term approach to mitigate, but not solve, this impediment.
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Sukhanova, L. V., V. V. Smirnov, N. S. Smirnova-Zalumi, T. V. Belomestnykh, and S. V. Kirilchik. "Molecular Phylogeography of Lake Baikal Coregonid Fishes." Advances in Limnology 63 (April 2, 2012): 261–83. http://dx.doi.org/10.1127/advlim/63/2012/261.
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Jenkins, Tom L., Rita Castilho, and Jamie R. Stevens. "Meta-analysis of northeast Atlantic marine taxa shows contrasting phylogeographic patterns following post-LGM expansions." PeerJ 6 (September 28, 2018): e5684. http://dx.doi.org/10.7717/peerj.5684.
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Background Comparative phylogeography enables the study of historical and evolutionary processes that have contributed to shaping patterns of contemporary genetic diversity across co-distributed species. In this study, we explored genetic structure and historical demography in a range of coastal marine species across the northeast Atlantic to assess whether there are commonalities in phylogeographic patterns across taxa and to evaluate whether the timings of population expansions were linked to the Last Glacial Maximum (LGM). Methods A literature search was conducted using Web of Science. Search terms were chosen to maximise the inclusion of articles reporting on population structure and phylogeography from the northeast Atlantic; titles and abstracts were screened to identify suitable articles within the scope of this study. Given the proven utility of mtDNA in comparative phylogeography and the availability of these data in the public domain, a meta-analysis was conducted using published mtDNA gene sequences. A standardised methodology was implemented to ensure that the genealogy and demographic history of all mtDNA datasets were reanalysed in a consistent and directly comparable manner. Results Mitochondrial DNA datasets were built for 21 species. The meta-analysis revealed significant population differentiation in 16 species and four main types of haplotype network were found, with haplotypes in some species unique to specific geographical locations. A signal of rapid expansion was detected in 16 species, whereas five species showed evidence of a stable population size. Corrected mutation rates indicated that the majority of expansions were estimated to have occurred after the earliest estimate for the LGM (∼26.5 Kyr), while few expansions were estimated to have pre-dated the LGM. Conclusion This study suggests that post-LGM expansion appeared to be common in a range of marine taxa, supporting the concept of rapid expansions after the LGM as the ice sheets started to retreat. However, despite the commonality of expansion patterns in many of these taxa, phylogeographic patterns appear to differ in the species included in this study. This suggests that species-specific evolutionary processes, as well as historical events, have likely influenced the distribution of genetic diversity of marine taxa in the northeast Atlantic.
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MARGOS, GABRIELE, SANTIAGO CASTILLO-RAMÍREZ, and ANNE GATEWOOD HOEN. "Phylogeography of Lyme borreliosis-group spirochetes and methicillin-resistantStaphylococcus aureus." Parasitology 139, no. 14 (May 23, 2012): 1952–65. http://dx.doi.org/10.1017/s0031182012000741.
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SUMMARYMultilocus sequence typing (MLST) and multilocus sequence analysis (MLSA) have revolutionized understanding the global epidemiology of many medically relevant bacteria utilizing a number, mostly seven, of housekeeping genes. A more recent introduction, single nucleotide polymorphisms (SNPs), constitutes an even more powerful tool for bacterial typing, population genetic studies and phylogeography. The introduction of massive parallel sequencing has made genome re-sequencing and SNP discovery more economical for investigations of microbial organisms. In this paper we review phylogeographic studies on Lyme borreliosis (LB)-group spirochetes and methicillin-resistantStaphylococcus aureus(MRSA). Members of the LB-group spirochetes are tick-transmitted zoonotic bacteria that have many hosts and differ in their degree of host specialism, constituting a highly complex system. MRSA is a directly transmitted pathogen that may be acquired by contact with infected people, animals or MRSA-contaminated objects. For the LB-group spirochetes, MLSA has proved a powerful tool for species assignment and phylogeographic investigations while forS. aureus, genome-wide SNP data have been used to study the very short-term evolution of two important MRSA lineages, ST239 and ST225. These data are detailed in this review.
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Bobo-Pinilla, Javier, Esteban Salmerón-Sánchez, Antonio J. Mendoza-Fernández, Juan F. Mota, and Julio Peñas. "Conservation and Phylogeography of Plants: From the Mediterranean to the Rest of the World." Diversity 14, no. 2 (January 24, 2022): 78. http://dx.doi.org/10.3390/d14020078.
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During the last decades, phylogeography has transformed the ways to analyze and understand plant diversity and biogeography. The repeated and increasingly detailed articles made from DNA data with phylogeographical procedures and algorithms have revolutionized biodiversity research, particularly on biodiversity conservation. This paper presents a systematic literature review of the different ways in which phylogeography has been applied to plants in Mediterranean-type ecosystems (MTEs), especially to rare, threatened, and endemic plants. Studies ranged from basic research to how phylogeography is actually contributing to management conservation of Mediterranean plants. Finally, new and future phylogeography perspectives with integrative scientific arguments and conceptual bases applied to plant conservation biology are discussed.
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Shaw, A. Jonathan, Stuart F. McDaniel, Olaf Werner, and Rosa M. Ros. "Phylogeography and Phylodemography." Bryologist 105, no. 3 (September 2002): 373–83. http://dx.doi.org/10.1639/0007-2745(2002)105[0373:pap]2.0.co;2.
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Signorovitch, Ana Y., Stephen L. Dellaporta, and Leo W. Buss. "Caribbean Placozoan Phylogeography." Biological Bulletin 211, no. 2 (October 2006): 149–56. http://dx.doi.org/10.2307/4134589.
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Cirkovic, V., G. Stamenkovic, M. Siljic, A. Gligic, and M. Stanojevic. "Tula virus phylogeography." International Journal of Infectious Diseases 79 (February 2019): 121. http://dx.doi.org/10.1016/j.ijid.2018.11.297.
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Joseph, L., and C. Moritz. "Mitochondrial-Dna Phylogeography of Birds in Eastern Australian Rain-Forests - First Fragments." Australian Journal of Zoology 42, no. 3 (1994): 385. http://dx.doi.org/10.1071/zo9940385.
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We studied the historical biogeography of eastern Australian rainforests, in particular whether Plio-Pleistocene rainforest refugia existed, through phylogeography of mitochondrial DNA (mtDNA) in seven bird species. Restriction fragment length polymorphisms in four species endemic to northeastern Queensland rainforests showed that within-species differentiation was concordantly structured in two of these (grey-headed robin, Poecilodryas albispecularis, and chowchilla, Orthonyx spaldingii) but not in the others (Australian fernwern, Oreoscopus gutturalis, and Atherton scrubwren, Sericornis keri). Between two more geographically widespread species not confined to rainforests (yellow-throated scrubwren, S. citreogularis, and large-billed scrubwren, S. magnirostris), phylogeographic patterns in north-eastern Queensland were not structured; in the same two species, however, mtDNA diversity was clearly apportioned between south-eastern and north-eastern Queensland, so showing phylogeographic congruence at that geographic scale. A seventh species (white-browed scrubwren, S. frontalis), a wide-ranging habitat-generalist, showed no phylogeographic structure at any geographical scale. The refuge hypothesis is supported in that the location of the genetic break in the grey-headed robin and the chowchilla is identical to that previously reported for mammals and skinks. However, the lack of complete congruence across all endemic species suggests that species with broadly similar current ecologies were not affected in the same way. Evolutionary histories that are more complex and idiosyncratic than previously thought are implicated rather than outright rejection of the refuge hypothesis.
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Ma, Cong, Metin Balaban, Jingxian Liu, Siqi Chen, Li Ding, and Benjamin J. Raphael. "Abstract 1205: Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics." Cancer Research 84, no. 6_Supplement (March 22, 2024): 1205. http://dx.doi.org/10.1158/1538-7445.am2024-1205.
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Abstract Tumors evolve through the acquisition of somatic mutations over time and across space. While the temporal aspects of tumor evolution can be inferred by applying phylogenetic techniques to bulk or single-cell DNA sequencing data, the spatial aspects of tumor evolution remain understudied. Spatially resolved transcriptomics (SRT) measures gene expression at thousands of spatial locations in a tumor, but does not directly measure genetic aberrations. Thus, SRT data has not yet been fully utilized for tumor evolution studies. We introduce CalicoST, an algorithm that simultaneously infers allele-specific copy number aberrations (CNAs) and derives a phylogeographic model of tumor evolution from SRT data. By modeling CNA-induced perturbations in both gene expression and allele frequencies, CalicoST identifies important types of CNAs - including copy-neutral loss of heterozygosity (CNLOH) and mirrored subclonal CNAs - that are invisible to total copy number analysis. On SRT data from nine patients from the Human Tumor Atlas Network (HTAN), CalicoST achieves an average accuracy of 86%, approximately 21% higher than existing methods. On two of these patients with multiple adjacent slices, CalicoST reconstructs a tumor phylogeography that describes the spread of cancerous clones in three-dimensional space. CalicoST analysis of multiple SRT slices from a cancerous prostate organ reveals five spatially coherent clones, with mirrored subclonal CNAs distinguishing clones on the two sides of the prostate, and a bifurcating phylogeography in both genetic and physical space that suggests a polyclonal cancer. Citation Format: Cong Ma, Metin Balaban, Jingxian Liu, Siqi Chen, Li Ding, Benjamin J. Raphael. Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1205.
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Coimbra, Raphael T. F., Rafael F. Magalhães, Priscila Lemes, Flávia R. Miranda, and Fabrício R. Santos. "Integrative Phylogeography Reveals Conservation Priorities for the Giant Anteater Myrmecophaga tridactyla in Brazil." Diversity 14, no. 7 (July 5, 2022): 542. http://dx.doi.org/10.3390/d14070542.
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The giant anteater (Myrmecophaga tridactyla) is a strictly myrmecophagous xenarthran species that ranges from Honduras to northern Argentina, occupying various habitats, from grassland and floodplains to forests. According to the IUCN, it is a vulnerable species mainly threatened by poaching, habitat loss and fragmentation, and road kills. Here, we investigate the phylogeography, distribution, ecology, and historical demography of Brazilian populations of the giant anteater. We analysed two mitochondrial (mtDNA) and three nuclear (nDNA) markers in 106 individuals from the Cerrado, Pantanal, Atlantic Forest, and Amazon Forest biomes through analyses of population structure and demography, phylogeography, and ecological niche modelling. Two divergent mtDNA clusters were found, one in the Amazon (AM) and another in the Cerrado, Pantanal, and Atlantic Forest biomes (CEPTAF). At the population level, CEPTAF presented higher mtDNA haplotype richness than AM and a unidirectional mtDNA gene flow was identified from AM to CEPTAF, which could be linked to more favourable habitat conditions for the species in Cerrado and Pantanal. Paleodemographic reconstructions with mtDNA and nDNA data indicate a large population expansion of the species starting at the end of the Pleistocene. Finally, the integrative phylogeographic analyses of giant anteater populations reinforce the importance of the Brazilian Cerrado as a priority biome for the species’ conservation.
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Kalkauskas, Antanas, Umberto Perron, Yuxuan Sun, Nick Goldman, Guy Baele, Stephane Guindon, and Nicola De Maio. "Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk." PLOS Computational Biology 17, no. 1 (January 6, 2021): e1008561. http://dx.doi.org/10.1371/journal.pcbi.1008561.
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Phylogeographic inference allows reconstruction of past geographical spread of pathogens or living organisms by integrating genetic and geographic data. A popular model in continuous phylogeography—with location data provided in the form of latitude and longitude coordinates—describes spread as a Brownian motion (Brownian Motion Phylogeography, BMP) in continuous space and time, akin to similar models of continuous trait evolution. Here, we show that reconstructions using this model can be strongly affected by sampling biases, such as the lack of sampling from certain areas. As an attempt to reduce the effects of sampling bias on BMP, we consider the addition of sequence-free samples from under-sampled areas. While this approach alleviates the effects of sampling bias, in most scenarios this will not be a viable option due to the need for prior knowledge of an outbreak’s spatial distribution. We therefore consider an alternative model, the spatial Λ-Fleming-Viot process (ΛFV), which has recently gained popularity in population genetics. Despite the ΛFV’s robustness to sampling biases, we find that the different assumptions of the ΛFV and BMP models result in different applicabilities, with the ΛFV being more appropriate for scenarios of endemic spread, and BMP being more appropriate for recent outbreaks or colonizations.
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Trichas, Apostolos, Maria Smirli, Anna Papadopoulou, Ioannis Anastasiou, Bekir Keskin, and Nikos Poulakakis. "Dispersal versus vicariance in the Aegean: combining molecular and morphological phylogenies of eastern Mediterranean Dendarus (Coleoptera: Tenebrionidae) sheds new light on the phylogeography of the Aegean area." Zoological Journal of the Linnean Society 190, no. 3 (April 13, 2020): 824–43. http://dx.doi.org/10.1093/zoolinnean/zlaa022.
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Abstract The Aegean archipelago, as an ‘evolutionary laboratory of nature’, is an ideal model for research in phylogeography. In this area, the darkling beetles of the genus Dendarus (distributed from Morocco to the Caucasus) exhibit a high level of diversity with 36 species, 27 of which are island endemics. However, their taxonomy is complex and unstable, having undergone continuous revision to address extensive morphological and ecological plasticity. Here, we examine the phylogenetic relationships of 23 species from Greece and Turkey, using mitochondrial and nuclear DNA sequences and 61 morphological characters, to unveil their phylogeny in the Aegean. This helps to clarify phylogeographic scenarios and historical processes that shaped the observed patterns. The analyses reveal 13 distinct lineages with several para- and polyphyletic cases that correspond to three major phylogroups [south/south-east Aegean (D. foraminosus complex, D. rhodius, D. sporadicus, D. wettsteini); central to north Aegean, Turkey and mainland Greece (D. crenulatus, D. moesiacus group, D. sinuatus complex, D. stygius) and mainland Greece (D. messenius, D. paganettii)], indicating the need for further taxonomic re-evaluation. Lineage topology and phylogeography suggest a spatial and temporal sequence of geographic isolation, following either a vicariant or a dispersal model coincident with major palaeogeographic separations in the Aegean.
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MORGAN, E. R., E. L. CLARE, R. JEFFERIES, and J. R. STEVENS. "Parasite epidemiology in a changing world: can molecular phylogeography help us tell the wood from the trees?" Parasitology 139, no. 14 (August 24, 2012): 1924–38. http://dx.doi.org/10.1017/s0031182012001060.
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SUMMARYMolecular phylogeography has revolutionised our ability to infer past biogeographic events from cross-sectional data on current parasite populations. In ecological parasitology, this approach has been used to address fundamental questions concerning host-parasite co-evolution and geographic patterns of spread, and has raised many technical issues and problems of interpretation. For applied parasitologists, the added complexity inherent in adding population genetic structure to perceived parasite distributions can sometimes seem to cloud rather than clarify approaches to control. In this paper, we use case studies firstly to illustrate the potential extent of cryptic diversity in parasite and parasitoid populations, secondly to consider how anthropogenic influences including movement of domestic animals affect the geographic distribution and host associations of parasite genotypes, and thirdly to explore the applied relevance of these processes to parasites of socio-economic importance. The contribution of phylogeographic approaches to deeper understanding of parasite biology in these cases is assessed. Thus, molecular data on the emerging parasites Angiostrongylus vasorum in dogs and wild canids, and the myiasis-causing flies Lucilia spp. in sheep and Cochliomyia hominovorax in humans, lead to clear implications for control efforts to limit global spread. Broader applications of molecular phylogeography to understanding parasite distributions in an era of rapid global change are also discussed.
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Shelley, James J., Bruno O. David, Christine E. Thacker, Andy S. Hicks, Matt G. Jarvis, and Peter J. Unmack. "Phylogeography of the Cran’s bully Gobiomorphus basalis (Gobiiformes: Eleotridae) and an analysis of species boundaries within the New Zealand radiation of Gobiomorphus." Biological Journal of the Linnean Society 130, no. 2 (May 15, 2020): 365–81. http://dx.doi.org/10.1093/biolinnean/blaa052.
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Abstract New Zealand has a complex recent history of climatic and tectonic change that has left variable signatures in the geographic distribution and genetic structure of the region’s flora and fauna. To identify concordant patterns, a broad range of taxa must be examined and compared. In New Zealand’s North Island, a consensus is forming as to the dominant biogeographic barriers in the region although obligate freshwater taxa have not been considered in this framework. We use single-nucleotide polymorphisms to investigate phylogeography in the widespread obligate freshwater fish Gobiomorphus basalis on the North Island. Phylogeographic patterns within G. basalis reveal biogeographic disjunctions that are in some ways consistent and in other ways at odds with established patterns, providing insight into the processes that have shaped the islands’ biogeography. We also use phylogeography to delineate species boundaries within the entire New Zealand radiation of Gobiomorphus and find that it contains several morphologically cryptic species. We resolve two clades within G. basalis that correspond to areas north and south of the Taupo Volcanic Zone. We confirm the distinctiveness of Gobiomorphus alpinus relative to Gobiomorphus cotidianus, as well as the presence of two lineages within Gobiomorphus breviceps that were previously identified based on mitochondrial data.
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Banker, Sarah E., Alan R. Lemmon, Alyssa Bigelow Hassinger, Mysia Dye, Sean D. Holland, Michelle L. Kortyna, Oscar E. Ospina, Hannah Ralicki, and Emily Moriarty Lemmon. "Hierarchical Hybrid Enrichment: Multitiered Genomic Data Collection Across Evolutionary Scales, With Application to Chorus Frogs (Pseudacris)." Systematic Biology 69, no. 4 (December 30, 2019): 756–73. http://dx.doi.org/10.1093/sysbio/syz074.
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Abstract Determining the optimal targets of genomic subsampling for phylogenomics, phylogeography, and population genomics remains a challenge for evolutionary biologists. Of the available methods for subsampling the genome, hybrid enrichment (sequence capture) has become one of the primary means of data collection for systematics, due to the flexibility and cost efficiency of this approach. Despite the utility of this method, information is lacking as to what genomic targets are most appropriate for addressing questions at different evolutionary scales. In this study, first, we compare the benefits of target loci developed for deep- and shallow scales by comparing these loci at each of three taxonomic levels: within a genus (phylogenetics), within a species (phylogeography), and within a hybrid zone (population genomics). Specifically, we target evolutionarily conserved loci that are appropriate for deeper phylogenetic scales and more rapidly evolving loci that are informative for phylogeographic and population genomic scales. Second, we assess the efficacy of targeting multiple-locus sets for different taxonomic levels in the same hybrid enrichment reaction, an approach we term hierarchical hybrid enrichment. Third, we apply this approach to the North American chorus frog genus Pseudacris to answer key evolutionary questions across taxonomic and temporal scales. We demonstrate that in this system the type of genomic target that produces the most resolved gene trees differs depending on the taxonomic level, although the potential for error is substantially lower for the deep-scale loci at all levels. We successfully recover data for the two different locus sets with high efficiency. Using hierarchical data targeting deep and shallow levels: we 1) resolve the phylogeny of the genus Pseudacris and introduce a novel visual and hypothesis testing method that uses nodal heat maps to examine the robustness of branch support values to the removal of sites and loci; 2) estimate the phylogeographic history of Pseudacris feriarum, which reveals up to five independent invasions leading to sympatry with congener Pseudacris nigrita to form replicated reinforcement contact zones with ongoing gene flow into sympatry; and 3) quantify with high confidence the frequency of hybridization in one of these zones between P. feriarum and P. nigrita, which is lower than microsatellite-based estimates. We find that the hierarchical hybrid enrichment approach offers an efficient, multitiered data collection method for simultaneously addressing questions spanning multiple evolutionary scales. [Anchored hybrid enrichment; heat map; hybridization; phylogenetics; phylogeography; population genomics; reinforcement; reproductive character displacement.]
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Byrne, M., and B. Hines. "Phylogeographical analysis of cpDNA variation in Eucalyptus loxophleba (Myrtaceae)." Australian Journal of Botany 52, no. 4 (2004): 459. http://dx.doi.org/10.1071/bt03117.
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Comparative phylogeography can reveal significant historical events that have had common influences on species with similar distributions. Phylogeographic analyses of eucalypts should provide insight into the influence of historical processes, since eucalypts are a dominant component of the Australian flora. However, use of chloroplast DNA in eucalypts is complicated by sharing of haplotypes among species, which has been attributed to hybridisation and introgression, although these patterns could also be accounted for by incomplete lineage sorting of ancestral polymorphism. Phylogeographic patterns in the cp genome of E. loxophleba Benth., a widespread species throughout southern Western Australia, were investigated by using RFLP analysis. The chloroplast diversity was structured into two geographically distinct lineages and nested clade analysis inferred historical fragmentation as the major influence on the phylogeographic pattern. The divergence between the lineages and their geographic distributions were similar to geographically discrete divergent lineages that have been identified in two other unrelated species from different families in southern Western Australia. Congruence of phylogeographic patterns in the three species provides evidence to support the hypothesis of significant influence of climatic instability during the Pleistocene caused by cyclic contraction and expansion of the mesic and arid zones.
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Rocha-Méndez, Alberto, Luis A. Sánchez-González, Enrique Arbeláez-Cortés, and Adolfo G. Navarro-Sigüenza. "Phylogeography indicates incomplete genetic divergence among phenotypically differentiated montane forest populations of Atlapetes albinucha (Aves, Passerellidae)." ZooKeys 809 (December 19, 2018): 125–48. http://dx.doi.org/10.3897/zookeys.809.28743.
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The White-naped Brushfinch (Atlapetesalbinucha) comprises up to eight allopatric subspecies mainly identified by the color of the underparts (gray vs. yellow belly). Yellow and gray bellied forms were long considered two different species (A.albinuchaandA.gutturalis), but they are presently considered as one polytypic species. Previous studies in the genusAtlapeteshave shown that the phylogeny, based on molecular data, is not congruent with characters such as coloration, ecology, or distributional patterns. The phylogeography ofA.albinuchawas analyzed using two mitochondrial DNA regions from samples including 24 different localities throughout montane areas from eastern Mexico to Colombia. Phylogeographic analyses using Bayesian inference, maximum likelihood and haplotype network revealed incomplete geographic structure. The genetic diversity pattern is congruent with a recent process of expansion, which is also supported by Ecological Niche Models (ENM) constructed for the species and projected into three past scenarios. Overall, the results revealed an incomplete genetic divergence among populations ofA.albinuchain spite of the species’ ample range, which contrasts with previous results of phylogeographic patterns in other Neotropical montane forest bird species, suggesting idiosyncratic evolutionary histories for different taxa throughout the region.
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Alexander, Matthew P., and Kevin J. Burns. "Intraspecific Phylogeography and Adaptive Divergence in the White-Headed Woodpecker." Condor 108, no. 3 (August 1, 2006): 489–508. http://dx.doi.org/10.1093/condor/108.3.489.
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AbstractThis study uses mitochondrial DNA (mtDNA) to examine the phylogeography of the White-headed Woodpecker (Picoides albolarvatus), one of the least-studied woodpeckers in North America. A mismatch distribution and calculation of Tajima's D indicate that the overall phylogeographic history of the species is characterized by a recent range expansion that probably occurred after the start of the Pleistocene. In addition, a nested clade phylogeographic analysis indicates that additional processes such as allopatric fragmentation and restricted gene flow have influenced the evolutionary history of this species. Traditionally, the White-headed Woodpecker has been split into two subspecies whose distributions meet in the northern part of the Transverse Ranges in California. The two subspecies differ morphologically, with the southern subspecies having a larger bill in proportion to its body size than the northern subspecies. Geographical variation in mtDNA is concordant with a division at the Transverse Ranges that corresponds to the morphological variation seen between the two subspecies. An analysis of molecular variance indicates that 27% of the genetic variation results from differences between the northern and southern subspecies. Furthermore, birds in the northern part of the range differ from those in the southern part of the range by at least one base substitution. These results agree with the hypothesis that the larger bill of the southern subspecies is the result of recent local adaptation to feeding on the large cones of Coulter pines (Pinus coulteri).
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Gyuranecz, Miklós, Dawn N. Birdsell, Wolf Splettstoesser, Erik Seibold, Stephen M. Beckstrom-Sternberg, László Makrai, László Fodor, et al. "Phylogeography ofFrancisella tularensissubsp.holarctica, Europe." Emerging Infectious Diseases 18, no. 2 (February 2012): 290–93. http://dx.doi.org/10.3201/eid1802.111305.
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