Title: Biogeographic barriers and historic climate shape the phylogeography and demography of the common gartersnake
AbstractAim
Current distributions of widespread North American (NA) species have been shaped by Pleistocene glacial cycles, latitudinal temperature gradients, sharp longitudinal habitat transitions and the vicariant effects of major mountain and river systems that subdivide the continent. Within these transcontinental species, genetic diversity patterns might not conform to established biogeographic breaks compared to more spatially restricted taxa due to intrinsic differences or spatiotemporal differences. In this study, we highlight the effects of these extrinsic variables on genetic structuring by investigating the phylogeographic history of a widespread generalist squamate found throughout NA.
Location
North America.
Taxon
Common gartersnake,Thamnophis sirtalis.
Methods
We evaluate the effects of major river basins and the forest‐grassland transition into the Interior Plains on genetic structure patterns using phylogenetic, spatially informed population structure and demographic analyses of single nucleotide polymorphism data and address range expansion history with ecological niche modelling using locality and historic climate data.
Results
We identify four phylogeographic lineages with varying degrees of connectivity between them. We find discordant population structure patterns between sex‐linked and autosomal loci with respect to the relationship between the central NA lineage relative to coastal lineages. We find support for southeast Pleistocene refugia where recent secondary contact occurred during the Last Glacial Maximum and evidence for both northern and southern refugia in western NA.
Main Conclusion
Our results provide strong evidence for a Pliocene origin forT. sirtalisin central‐southeastern NA preceding its rapid expansion across the continent prior to middle Pleistocene climate‐mediated lineage formation. We implicate major riverine networks within the Mississippi watershed in likely repeated westward expansion events across the Interior Plains. Finally, we corroborate prior conclusions that phenotypic differences between subspecies do not reflect shared evolutionary history and note that the degree of separation between inferred lineages warrants further investigation before any taxonomic revisions are proposed.
Duvernell, David D.; Westhafer, Eric; Schaefer, Jacob F.(
, Journal of Biogeography)
AbstractAim
We used genome‐scale sampling to assess the phylogeography of a group of topminnows in theFundulus notatusspecies complex. Two of the species have undergone extensive range expansions resulting in broadly overlapping distributions, and sympatry within drainages has provided opportunities for hybridization and introgression. We assessed the timing and pattern of range expansion in the context of late Pleistocene–Holocene drainage events and evaluated the evidence for introgressive hybridization between species.
Location
Central and southern United States including drainages of the Gulf of Mexico Coastal Plain and portions of the Mississippi River drainage in and around the Central Highlands.
We sampled members of theF. notatusspecies complex throughout their respective ranges, including numerous drainage systems where species co‐occur. We collected genome‐wide single nucleotide polymorphisms (SNPs) using the genotype‐by‐sequencing (GBS) method and subjected data to population genetic analyses to infer the population histories of both species, including explicit tests for admixture and introgression. The methods employed includedSTRUCTURE, principal coordinates analysis, TreeMix and approximate Bayesian computation.
Results
Genetic data are presented for 749 individuals sampled from 14F. notatus, 20F. olivaceusand 2F. euryzonuspopulations. Members of the species complex differed in phylogeographic structure, withF. notatusexhibiting geographic clusters corresponding to Pleistocene coastal drainages andF. olivaceuscomparatively lacking in phylogeographic structure. Evidence for interspecific introgression varied by drainage.
Main conclusions
Populations ofF. notatusandF. olivaceusexhibited contrasting patterns of lineage diversity among coastal drainages, indicating interspecific differences in their Pleistocene southern refugia. Phylogeographic patterns in both species indicated that range expansions into the northern limits of contemporary distributions coincided with and continued subsequent to the Last Glacial Maximum. There was evidence of introgression between species in some, but not all drainages where the species co‐occur, in a pattern that is correlated with previous estimates of hybridization rates.
Cassidy, Ellen R.; Galbreath, Kurt E.; Smyser, ed., Timothy(
, Journal of Mammalogy)
Abstract
Across eastern North America, glacial cycles of the Pleistocene drove episodic latitudinal range shifts by temperate species. Isolation of populations within low-latitude refugia during glacial maxima was enhanced by physiographic barriers, leading to patterns of phylogeographic differentiation that are shared across diverse taxa. Postglacial population expansion created opportunities for differentiated lineages to come into contact, with various potential population-genetic outcomes. Northern short-tailed shrews (Blarina brevicauda) exhibit three mitochondrial phylogroups that probably originated via glacial-age range restriction and isolation. We investigate the history of postglacial expansion and interlineage contact between historically isolated regional populations of B. brevicauda. Morphological differences between skulls of shrews representing a Western lineage and those representing Central and Eastern lineages are consistent with past subspecies delineations. However, we demonstrate broad range overlap between neighboring phylogroups across the Upper Peninsula and Lower Peninsula in Michigan. Further, incongruence between phylogroup association and morphology among individuals in Upper Peninsula populations suggests that genetic admixture between shrews representing the Western and Central groups has occurred in the past and may be ongoing. We show that across most cranial measurements, shrews within the contact zone are morphologically most similar to the Central group regardless of mitochondrial identity, but one measurement in these contact zone shrews (depth of skull) is more similar to that seen in the Western group. These results suggest that hybridization between historically isolated populations has resulted in the origin of a novel skull phenotype that is proportionally deeper, narrower, and shorter than those seen in core Western and Central populations.
Marques-Souza, Sergio; Machado Pellegrino, Katia C.; Oliveira Brunes, Tuliana; Carnaval, Ana Carolina; Pacheco Damasceno, Roberta; Lima de Oliveira Borges, Manoela; Candia Gallardo, Carlos; Rodrigues, Miguel Trefaut(
, Journal of Biogeography)
AbstractAim
To investigate the cryptic diversity and diversification timing in the putatively low‐dispersal Amazonian leaf‐litter lizardLoxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation.
Location
Central Amazonia, Brazil.
Taxon
Squamata; Gymnophthalmidae;Loxopholis osvaldoi.
Methods
We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through phylogenetic and coalescent analyses. A species tree and divergence dates of lineages were inferred with *BEAST, employing multiple DNA substitution rates. The potential genetic impacts of geographical distance among localities, the environment and the position of localities in relation to main rivers were tested by redundancy analysis (RDA).
Results
We detected 11 independently evolving and largely divergent intraspecific lineages. Lineage distribution patterns are complex and do not match any conspicuous barrier to gene flow, except for the Amazon River. Most lineages appear to have originated in the lower Miocene and Pliocene, in disagreement with the Pleistocene refuge hypothesis. IBD, IBE and rivers appear to have acted in concert establishing and maintaining genetic structure. However, when controlling for other explanatory variables, IBD explains significantly more variation than rivers, IBE or historical factors.
Main Conclusions
Our results strongly suggest thatL.osvaldoiis a species complex. Future taxonomic work should use an integrative approach to explore whether morphological variation is present and congruent with the genetic data. While the use of a sensitive dating analysis allowed us to better describe the diversification history ofL.osvaldoi, the lack of a spatial model of Neogene river dynamics prevents the test of specific, more informative river barrier hypotheses. The data suggest that nonlinear correlation analyses (e.g. RDA) should be preferred to detect factors that affect phylogeographic patterns in the Amazon, instead of linear multiple regressions (e.g. Mantel tests). Given the high level of cryptic diversity detected within this and other Amazonian species, we caution against hypothesis tests based solely on the distribution of nominal taxa, which can provide a rather incomplete view of the processes behind Amazonian diversity.
Liu, Simin; Liu, Yang; Jelen, Edouard; Alibadian, Mansour; Yao, Cheng‐Te; Li, Xintong; Kayvanfar, Nasrin; Wang, Yutao; Vahidi, Farhad S. M.; Han, Jian‐Lin; et al(
, Journal of Biogeography)
AbstractAim
Pleistocene climate and associated environmental changes have influenced phylogeographic patterns of many species. These not only depend on a species’ life history but also vary regionally. Consequently, populations of widespread species that occur in several biomes might display different evolutionary trajectories. We aimed to identify regional drivers of diversification in the common pheasant, a widely distributed ecological generalist.
Location
Asia.
Taxon
Common pheasantPhasianus colchicus.
Methods
Using a comprehensive geographical sampling of 204 individuals from the species’ entire range genotyped at seven nuclear and two mitochondrial loci, we reconstructed spatio‐temporal diversification and demographic history of the common pheasant. We applied Bayesian phylogenetic inference to describe phylogeographic structure, generated a species tree and inferred demographic history within and migration between lineages. Moreover, to establish a taxonomic framework, we conducted a species delimitation analysis.
Results
The common pheasant diversified during the Late Pleistocene into eight distinct lineages. It originated at the edge of the Qinghai–Tibetan plateau and spread to East and Central Asia. Only the widely distributed lowland lineage of East Asia displayed recent range expansion. Greater phylogeographic structure was identified elsewhere, with lineages showing no sign of recent demographic changes. One lineage in south‐central China is the result of long‐term isolation within a climatically stable but topographically complex region. In lineages from arid Central Asia and China, range expansions were impeded by repeated population fragmentation during dry glacial periods and by recent aridification.
Main conclusions
Spatio‐temporal phylogeographic frameworks of widespread taxa such as the common pheasant provide valuable opportunities to identify divergent drivers of regional diversification. Our results suggest that diversification and population histories in the eight distinct evolutionary lineages were shaped by regionally variable effects of past climate and associated environmental changes. The evolutionary history of the common pheasant is best reflected by its being split into three species.
Leaché, Adam D.; Portik, Daniel M.; Rivera, Danielle; Rödel, Mark‐Oliver; Penner, Johannes; Gvoždík, Václav; Greenbaum, Eli; Jongsma, Gregory F. M.; Ofori‐Boateng, Caleb; Burger, Marius; et al(
, Journal of Biogeography)
AbstractAim
Species with wide distributions spanning the African Guinean and Congolian rain forests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rain forest species, the African foam‐nest treefrogChiromantis rufescens.
Location
Guinean and Congolian rain forests, West and Central Africa.
Taxon
Chiromantis rufescens.
Methods
We collected mitochondrial DNA (mtDNA) and single‐nucleotide polymorphism (SNP) data for 130 samples ofC. rufescens. After estimating population structure and inferring species trees using coalescent methods, we tested demographic models to evaluate alternative population divergence histories that varied with respect to gene flow, population size change and periods of isolation and secondary contact. Species distribution models were used to identify the regions of climatic stability that could have served as forest refugia since the last interglacial.
Results
Population structure withinC. rufescensresembles the major biogeographic regions of the Guinean and Congolian forests. Coalescent‐based phylogenetic analyses provide strong support for an early divergence between the western Upper Guinean forest and the remaining populations. Demographic inferences support diversification models with gene flow and population size changes even in cases where contemporary populations are currently allopatric, which provides support for forest refugia and barrier models. Species distribution models suggest that forest refugia were available for each of the populations throughout the Pleistocene.
Main conclusions
Considering historical demography is essential for understanding population diversification, especially in complex landscapes such as those found in the Guineo–Congolian forest. Population demographic inferences help connect the patterns of genetic variation to diversification model predictions. The diversification history ofC. rufescenswas shaped by a variety of processes, including vicariance from river barriers, forest fragmentation and adaptive evolution along environmental gradients.
Jones, II, Leonard N., Leaché, Adam D., and Burbrink, Frank T. Biogeographic barriers and historic climate shape the phylogeography and demography of the common gartersnake. Journal of Biogeography 50.12 Web. doi:10.1111/jbi.14709.
Jones, II, Leonard N., Leaché, Adam D., & Burbrink, Frank T. Biogeographic barriers and historic climate shape the phylogeography and demography of the common gartersnake. Journal of Biogeography, 50 (12). https://doi.org/10.1111/jbi.14709
Jones, II, Leonard N., Leaché, Adam D., and Burbrink, Frank T.
"Biogeographic barriers and historic climate shape the phylogeography and demography of the common gartersnake". Journal of Biogeography 50 (12). Country unknown/Code not available: Wiley-Blackwell. https://doi.org/10.1111/jbi.14709.https://par.nsf.gov/biblio/10460711.
@article{osti_10460711,
place = {Country unknown/Code not available},
title = {Biogeographic barriers and historic climate shape the phylogeography and demography of the common gartersnake},
url = {https://par.nsf.gov/biblio/10460711},
DOI = {10.1111/jbi.14709},
abstractNote = {Abstract AimCurrent distributions of widespread North American (NA) species have been shaped by Pleistocene glacial cycles, latitudinal temperature gradients, sharp longitudinal habitat transitions and the vicariant effects of major mountain and river systems that subdivide the continent. Within these transcontinental species, genetic diversity patterns might not conform to established biogeographic breaks compared to more spatially restricted taxa due to intrinsic differences or spatiotemporal differences. In this study, we highlight the effects of these extrinsic variables on genetic structuring by investigating the phylogeographic history of a widespread generalist squamate found throughout NA. LocationNorth America. TaxonCommon gartersnake,Thamnophis sirtalis. MethodsWe evaluate the effects of major river basins and the forest‐grassland transition into the Interior Plains on genetic structure patterns using phylogenetic, spatially informed population structure and demographic analyses of single nucleotide polymorphism data and address range expansion history with ecological niche modelling using locality and historic climate data. ResultsWe identify four phylogeographic lineages with varying degrees of connectivity between them. We find discordant population structure patterns between sex‐linked and autosomal loci with respect to the relationship between the central NA lineage relative to coastal lineages. We find support for southeast Pleistocene refugia where recent secondary contact occurred during the Last Glacial Maximum and evidence for both northern and southern refugia in western NA. Main ConclusionOur results provide strong evidence for a Pliocene origin forT. sirtalisin central‐southeastern NA preceding its rapid expansion across the continent prior to middle Pleistocene climate‐mediated lineage formation. We implicate major riverine networks within the Mississippi watershed in likely repeated westward expansion events across the Interior Plains. Finally, we corroborate prior conclusions that phenotypic differences between subspecies do not reflect shared evolutionary history and note that the degree of separation between inferred lineages warrants further investigation before any taxonomic revisions are proposed.},
journal = {Journal of Biogeography},
volume = {50},
number = {12},
publisher = {Wiley-Blackwell},
author = {Jones, II, Leonard N. and Leaché, Adam D. and Burbrink, Frank T.},
}
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