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Journal articles on the topic 'Phylogeography'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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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 i

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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 (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 ha

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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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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 (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 retic

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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 (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 idio

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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 (2006): 1851–65. http://dx.doi.org/10.1111/j.1365-2699.2006.01574.x.

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Lavery, Tyrone H., Lucas H. DeCicco, Karen V. Olson, Piokera S. Holland, and Robert G. Moyle. "Phylogeography of Solomon Islands blossom bats reflects oceanic divides and Pleistocene connections." Journal of Biogeography 50, no. 5 (2023): 920–31. https://doi.org/10.5281/zenodo.14818151.

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(Uploaded by Plazi for the Bat Literature Project) Aim: Periodic lowering of sea levels and formation of land bridges can reshape phylogeographic patterns of insular biotas. Using archipelago-wide sampling, we aimed to test if phylogeography of an old-endemic bat lineage reflected Pleistocene land bridges.

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Bowen, Brian W., Michelle R. Gaither, Joseph D. DiBattista, et al. "Comparative phylogeography of the ocean planet." Proceedings of the National Academy of Sciences 113, no. 29 (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 di

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9

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

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10

Urbaniak, Jacek, and Paweł Kwiatkowski. "Plant Taxonomy, Systematics and Phylogeography." Plants 13, no. 19 (2024): 2670. http://dx.doi.org/10.3390/plants13192670.

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Plant taxonomy and phylogeny deal with very important problems related to the genetic diversity of populations found in different geographical regions, trying to present the variability of these populations but also to explain their origin. For this reason, such studies examining the conditioned diversity of plant populations were the subject of this Special Issue (SI) of the journal Plants. This SI contains ten original articles and one review article concerning phylogeography and related sciences, i.e., biogeography, taxonomy, and systematics, as well as the genetic variability that lies at

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11

Peter Linder, H. "Phylogeography." Journal of Biogeography 44, no. 2 (2017): 243–44. http://dx.doi.org/10.1111/jbi.12958.

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12

Venton, Danielle. "Phylogeography." Proceedings of the National Academy of Sciences 110, no. 11 (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 (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 (2000): 384–85. http://dx.doi.org/10.1016/s0169-5347(00)01901-7.

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15

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 (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 d

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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 (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

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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.

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Bagley, Justin C., and Jerald B. Johnson. "Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas." Biological Reviews 89, no. 4 (2014): 767–90. https://doi.org/10.5281/zenodo.13463730.

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(Uploaded by Plazi for the Bat Literature Project) Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeography studies and their contribution to understanding the origins, assembly, and diversification of the LCA biota against the backdrop of regional geologic and climatic history, and previous biogeographical inquiry. Studies to date reveal that phylogeographical signal within taxa of differing distributions reflects a d

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Bagley, Justin C., and Jerald B. Johnson. "Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas." Biological Reviews 89, no. 4 (2014): 767–90. https://doi.org/10.5281/zenodo.13463730.

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(Uploaded by Plazi for the Bat Literature Project) Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeography studies and their contribution to understanding the origins, assembly, and diversification of the LCA biota against the backdrop of regional geologic and climatic history, and previous biogeographical inquiry. Studies to date reveal that phylogeographical signal within taxa of differing distributions reflects a d

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Bagley, Justin C., and Jerald B. Johnson. "Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas." Biological Reviews 89, no. 4 (2014): 767–90. https://doi.org/10.5281/zenodo.13463730.

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(Uploaded by Plazi for the Bat Literature Project) Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeography studies and their contribution to understanding the origins, assembly, and diversification of the LCA biota against the backdrop of regional geologic and climatic history, and previous biogeographical inquiry. Studies to date reveal that phylogeographical signal within taxa of differing distributions reflects a d

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Bagley, Justin C., and Jerald B. Johnson. "Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas." Biological Reviews 89, no. 4 (2014): 767–90. https://doi.org/10.5281/zenodo.13463730.

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(Uploaded by Plazi for the Bat Literature Project) Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeography studies and their contribution to understanding the origins, assembly, and diversification of the LCA biota against the backdrop of regional geologic and climatic history, and previous biogeographical inquiry. Studies to date reveal that phylogeographical signal within taxa of differing distributions reflects a d

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Bagley, Justin C., and Jerald B. Johnson. "Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas." Biological Reviews 89, no. 4 (2014): 767–90. https://doi.org/10.5281/zenodo.13463730.

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(Uploaded by Plazi for the Bat Literature Project) Lower Central America (LCA) provides a geologically complex and dynamic, richly biodiverse model for studying the recent assembly and diversification of a Neotropical biota. Here, we review the growing literature of LCA phylogeography studies and their contribution to understanding the origins, assembly, and diversification of the LCA biota against the backdrop of regional geologic and climatic history, and previous biogeographical inquiry. Studies to date reveal that phylogeographical signal within taxa of differing distributions reflects a d

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23

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 phylogeograph

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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 (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

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Knowles, L. Lacey. "Statistical Phylogeography." Annual Review of Ecology, Evolution, and Systematics 40, no. 1 (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 (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 (2002): 2623–35. http://dx.doi.org/10.1046/j.1365-294x.2002.01410.x.

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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 (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

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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 m

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Harcourt, Alexander H. "Human phylogeography and diversity." Proceedings of the National Academy of Sciences 113, no. 29 (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

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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 Nort

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Carpenter, Kent E., Paul H. Barber, Eric D. Crandall, 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

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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 province

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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 phyloge

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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 (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

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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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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 (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 f

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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 (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 gen

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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 bein

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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. https://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 bein

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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 (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

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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. Sear

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Shaw, A. Jonathan, Stuart F. McDaniel, Olaf Werner, and Rosa M. Ros. "Phylogeography and Phylodemography." Bryologist 105, no. 3 (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 (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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MARGOS, GABRIELE, SANTIAGO CASTILLO-RAMÍREZ, and ANNE GATEWOOD HOEN. "Phylogeography of Lyme borreliosis-group spirochetes and methicillin-resistantStaphylococcus aureus." Parasitology 139, no. 14 (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 phylogeograph

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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

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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 (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

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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 (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, At

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Kalkauskas, Antanas, Umberto Perron, Yuxuan Sun, et al. "Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk." PLOS Computational Biology 17, no. 1 (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 r

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