Sun skink landscape genomics: assessing the roles of micro‐evolutionary processes in shaping genetic and phenotypic diversity across a heterogeneous and fragmented landscape

Barley, Anthony J.; Monnahan, Patrick J.; Thomson, Robert C.; Grismer, L. Lee; Brown, Rafe M.

doi:10.1111/mec.13151

Cited by 36 publications

(30 citation statements)

References 107 publications

(182 reference statements)

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“…As such, ancestral populations can subdivide and accumulate genetic differences without morphological divergence, generating "cryptic" lineages or species (69). Philippine sun skinks, for example, exhibit deep phylogenetic splits concordant with geography but show little to no morphological variation among lineages (70). Similar patterns in black salamanders (71), plainbacked thrushes (72), and field voles (73) indicate that cryptic lineages are prevalent among vertebrates.…”

Section: Geographically Dispersed Phenotypes Without Phylogeographicmentioning

confidence: 62%

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

Zamudio

Bell

Mason

2016

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

203

175

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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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Section: Geographically Dispersed Phenotypes Without Phylogeographicmentioning

confidence: 62%

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

Zamudio

Bell

Mason

2016

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

203

175

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“…Ideally, well‐studied systems would eventually pair landscape genetic inferences with studies of phenotypic traits and, ultimately, adaptive markers (Barrett & Hoekstra ; Barley et al . ). On this front, there are important approaches being developed using genomic data with many markers to identify genetic variation that is strongly correlated with environment variation across landscapes (e.g.…”

Section: Avoiding the Pitfalls And Advancing The Conceptual Frameworkmentioning

confidence: 97%

Navigating the pitfalls and promise of landscape genetics

et al. 2016

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The field of landscape genetics has been evolving rapidly since its emergence in the early 2000s. New applications, techniques and criticisms of techniques appear like clockwork with each new journal issue. The developments are an encouraging, and at times bewildering, sign of progress in an exciting new field of study. However, we suggest that the rapid expansion of landscape genetics has belied important flaws in the development of the field, and we add an air of caution to this breakneck pace of expansion. Specifically, landscape genetic studies often lose sight of the fundamental principles and complex consequences of gene flow, instead favouring simplistic interpretations and broad inferences not necessarily warranted by the data. Here, we describe common pitfalls that characterize such studies, and provide practical guidance to improve landscape genetic investigation, with careful consideration of inferential limits, scale, replication, and the ecological and evolutionary context of spatial genetic patterns. Ultimately, the utility of landscape genetics will depend on translating the relationship between gene flow and landscape features into an understanding of long‐term population outcomes. We hope the perspective presented here will steer landscape genetics down a more scientifically sound and productive path, garnering a field that is as informative in the future as it is popular now.

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“…Eutropis macropthalma ) and Eutropis rudis (Barley et al 2014), this species (Fig. 54) clearly possesses the dispersal capacity to overcome marine barriers to colonization and yet, at a much finer scale, has been shown to possess the genomic signature of habitat fragmentation in the Philippines (Barley et al 2015). A truly widespread species, Eutropis multifasciata does not qualify for any elevated level of threat and must be considered “Least Concern” (DD; IUCN 2016).…”

Section: Species Accountsmentioning

confidence: 99%

The amphibians and reptiles of Mindanao Island, southern Philippines, II: the herpetofauna of northeast Mindanao and adjacent islands

Sanguila¹,

Cobb²,

Siler³

et al. 2016

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We summarize all available amphibian and reptile species distribution data from the northeast Mindanao faunal region, including small islands associated with this subcenter of endemic vertebrate biodiversity. Together with all publicly available historical information from biodiversity repositories, we present new data from several major herpetological surveys, including recently conducted inventories on four major mountains of northeast Mindanao, and adjacent islands of Camiguin Sur, Dinagat, and Siargao. We present species accounts for all taxa, comment on unresolved taxonomic problems, and provide revisions to outdated IUCN conservation status assessments in cases where our new data significantly alter earlier classification status summaries. Together, our comprehensive analysis of this fauna suggests that the greater Mindanao faunal region possesses distinct subcenters of amphibian and reptile species diversity, and that until this area is revisited and its fauna and actually studied, with on-the-ground field work including targeted surveys of species distributions coupled to the study their natural history, our understanding of the diversity and conservation status of southern Philippine herpetological fauna will remain incomplete. Nevertheless, the northeast Mindanao geographical area (Caraga Region) appears to have the highest herpetological species diversity (at least 126 species) of any comparably-sized Philippine faunal subregion.

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Sun skink landscape genomics: assessing the roles of micro‐evolutionary processes in shaping genetic and phenotypic diversity across a heterogeneous and fragmented landscape

Cited by 36 publications

References 107 publications

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

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

Navigating the pitfalls and promise of landscape genetics

The amphibians and reptiles of Mindanao Island, southern Philippines, II: the herpetofauna of northeast Mindanao and adjacent islands

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