The evolution of phylogeographic data sets

Garrick, Ryan C.; Bonatelli, Isabel A. S.; Hyseni, Chaz; Morales, Ariadna E.; Pelletier, Tara A.; Perez, Manolo F.; Rice, Edwin; Satler, Jordan D.; Symula, Rebecca E.; Thomé, Maria Tereza C.; Carstens, Bryan C.

doi:10.1111/mec.13108

Cited by 124 publications

(119 citation statements)

References 66 publications

(58 reference statements)

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“…Phylogeography is a prolific discipline, with nearly 40 000 investigations published to date (Web of Science search of 'phylogeograph*' in title, abstract or keywords, 6 January 2016) on species collected from more than 4.8 Â 10 6 localities [69]. These studies represent a tremendous resource for the rspb.royalsocietypublishing.org Proc.…”

Section: Results and Discussion (A) General Overviewmentioning

confidence: 99%

Identifying cryptic diversity with predictive phylogeography

et al. 2016

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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 ecosystemlevel 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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Section: Results and Discussion (A) General Overviewmentioning

confidence: 99%

Identifying cryptic diversity with predictive phylogeography

et al. 2016

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“…The drawbacks of using mitochondrial DNA (mtDNA) as the sole marker of genetic variation among and within populations are now widely acknowledged 11–13 , to the extent that a comparative approach using both mitochondrial and nuclear genetic data is becoming customary in phylogeographic investigations 14 . At the same time, however, after more than three decades when most phylogeographic studies adopted a single-marker approach (since 15 ), there is now a huge amount of mtDNA data which needs to be complemented, in order to reach reliable conclusions about the evolutionary history and current genetic structure of populations.…”

Section: Introductionmentioning

confidence: 99%

Hybridization and extensive mitochondrial introgression among fire salamanders in peninsular Italy

Bisconti

Porretta

Arduino

et al. 2018

Sci Rep

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Discordance between mitochondrial and nuclear patterns of population genetic structure is providing key insights into the eco-evolutionary dynamics between and within species, and their assessment is highly relevant to biodiversity monitoring practices based on DNA barcoding approaches. Here, we investigate the population genetic structure of the fire salamander Salamandra salamandra in peninsular Italy. Both mitochondrial and nuclear markers clearly identified two main population groups. However, nuclear and mitochondrial zones of geographic transition between groups were located 600 km from one another. Recent population declines in central Italy partially erased the genetic imprints of past hybridization dynamics. However, the overall pattern of genetic variation, together with morphological and fossil data, suggest that a rampant mitochondrial introgression triggered the observed mitonuclear discordance, following a post-glacial secondary contact between lineages. Our results clearly show the major role played by reticulate evolution in shaping the structure of Salamandra salamandra populations and, together with similar findings in other regions of the species’ range, contribute to identify the fire salamander as a particularly intriguing case to investigate the complexity of mechanisms triggering patterns of mitonuclear discordance in animals.

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“…Phylogeography has progressed rapidly in the last three decades, with new genetic markers (7,8), analytical techniques (9), and synergies with landscape ecology and population genetics (10)(11)(12). Combined, these advances have revealed previously unrecognized genetic variation and its spatial and environmental correlates; however, phenotypic variation in those same diverging lineages has not received the same attention.…”

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confidence: 99%

Phenotypes in phylogeography: Species’ traits, environmental variation, and vertebrate diversification

Zamudio

Bell

Mason

2016

Proc. Natl. Acad. Sci. U.S.A.

189

173

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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.phylogeography | phenotype | function | trait | concordance P hylogeography, as originally defined, focused on processes governing the spatial distribution of genealogical lineages within species (1). One of the strengths of the field at its inception was formalizing conceptual links among heredity (processes at the level of individual pedigrees), divergence at the population level, and phylogenetic relationships among species (1). This analytical framework bridged microevolutionary processes acting within populations and macroevolutionary patterns at larger spatial and temporal scales. From the earliest applications, empirical phylogeographic studies described spatial patterns of genetic diversity and inferred underlying mechanisms, thus contributing to the explanatory and predictive power of the field (2). If most species show phylogeographic structure caused by landscape features that impede gene flow, then the geographic distribution of divergent lineages should coincide among species that coinhabit those landscapes. Further, phylogeographic breaks or contact zones should arise as lineages diverge allopatrically or come into secondary contact after divergence, respectively. This explicit prediction (1) resulted in a search for shared geographic patterns in genetic structure among species and the birth of comparative phylogeography (3, 4). Now, with thousands of taxon-specific phylogeographic studies published and synthesized in comparative studies (5, 6), we have learned a tremendous amount about the geography of genetic structure both within and among species.Phylogeogra...

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The evolution of phylogeographic data sets

Cited by 124 publications

References 66 publications

Identifying cryptic diversity with predictive phylogeography

Identifying cryptic diversity with predictive phylogeography

Hybridization and extensive mitochondrial introgression among fire salamanders in peninsular Italy

Phenotypes in phylogeography: Species’ traits, environmental variation, and vertebrate diversification

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