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1. Hidden in the DNA: How multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf‐litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae)

   https://doi.org/10.1111/jbi.13748  

   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 ( December 2019 , Journal of Biogeography)

   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.

   Central Amazonia, Brazil.

   Squamata; Gymnophthalmidae;Loxopholis osvaldoi.

   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).

   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.

   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.

    

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2. Regional drivers of diversification in the late Quaternary in a widely distributed generalist species, the common pheasant Phasianus colchicus

   https://doi.org/10.1111/jbi.13964  

   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 ( September 2020 , Journal of Biogeography)

   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.

   Asia.

   Common pheasantPhasianus colchicus.

   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.

   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.

   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.

    

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3. Discerning structure versus speciation in phylogeographic analysis of Seepage Salamanders ( Desmognathus aeneus ) using demography, environment, geography, and phenotype

   https://doi.org/10.1111/mec.17219  

   Pyron, R. Alexander ; Kakkera, Anvith ; Beamer, David A. ; O'Connell, Kyle A. ( November 2023 , Molecular Ecology)

   Numerous mechanisms can drive speciation, including isolation by adaptation, distance, and environment. These forces can promote genetic and phenotypic differentiation of local populations, the formation of phylogeographic lineages, and ultimately, completed speciation. However, conceptually similar mechanisms may also result in stabilizing rather than diversifying selection, leading to lineage integration and the long‐term persistence of population structure within genetically cohesive species. Processes that drive the formation and maintenance of geographic genetic diversity while facilitating high rates of migration and limiting phenotypic differentiation may thereby result in population genetic structure that is not accompanied by reproductive isolation. We suggest that this framework can be applied more broadly to address the classic dilemma of “structure” versus “species” when evaluating phylogeographic diversity, unifying population genetics, species delimitation, and the underlying study of speciation. We demonstrate one such instance in the Seepage Salamander (Desmognathus aeneus) from the southeastern United States. Recent studies estimated up to 6.3% mitochondrial divergence and four phylogenomic lineages with broad admixture across geographic hybrid zones, which could potentially represent distinct species supported by our species‐delimitation analyses. However, while limited dispersal promotes substantial isolation by distance, microhabitat specificity appears to yield stabilizing selection on a single, uniform, ecologically mediated phenotype. As a result, climatic cycles promote recurrent contact between lineages and repeated instances of high migration through time. Subsequent hybridization is apparently not counteracted by adaptive differentiation limiting introgression, leaving a single unified species with deeply divergent phylogeographic lineages that nonetheless do not appear to represent incipient species.

    

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4. Biogeographic barriers and historic climate shape the phylogeography and demography of the common gartersnake

   https://doi.org/10.1111/jbi.14709  

   Jones, II, Leonard N. ; Leaché, Adam D. ; Burbrink, Frank T. ( August 2023 , Journal of Biogeography)

   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.

   North America.

   Common gartersnake,Thamnophis sirtalis.

   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.

   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.

   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.

    

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5. Old divergence and restricted gene flow between torrent duck ( Merganetta armata ) subspecies in the Central and Southern Andes

   https://doi.org/10.1002/ece3.5538  

   Alza, Luis ; Lavretsky, Philip ; Peters, Jeffrey L. ; Cerón, Gerardo ; Smith, Matthew ; Kopuchian, Cecilia ; Astie, Andrea ; McCracken, Kevin G. ( August 2019 , Ecology and Evolution)

   To investigate the structure and rate of gene flow among populations of habitat‐specialized species to understand the ecological and evolutionary processes underpinning their population dynamics and historical demography, including speciation and extinction.

   Peruvian and Argentine Andes.

   Two subspecies of torrent duck (Merganetta armata).

   We sampled 156 individuals in Peru (M. a. leucogenis;Chillón River,n = 57 and Pachachaca River,n = 49) and Argentina (M. a. armata;Arroyo Grande River,n = 33 and Malargüe River,n = 17), and sequenced the mitochondrial DNA (mtDNA) control region to conduct coarse and fine‐scale demographic analyses of population structure. Additionally, to test for differences between subspecies, and across genetic markers with distinct inheritance patterns, a subset of individuals (Peru,n = 10 and Argentina,n = 9) was subjected to partial genome resequencing, obtaining 4,027 autosomal and 189 Z‐linked double‐digest restriction‐associated DNA sequences.

   Haplotype and nucleotide diversities were higher in Peru than Argentina across all markers. Peruvian and Argentine subspecies showed concordant species‐level differences (Φ_STmtDNA = 0.82; Φ_STautosomal = 0.30; Φ_STZ chromosome = 0.45), including no shared mtDNA haplotypes. Demographic parameters estimated for mtDNA using IM and IMa2 analyses, and for autosomal markers using∂a∂i(isolation‐with‐migration model), supported an old divergence (mtDNA = 600,000 years before present (ybp), 95% HPD range = 1.2 Mya to 200,000 ybp; and autosomal∂a∂i = 782,490 ybp), between the two subspecies, characteristic of deeply diverged lineages. The populations were well‐differentiated in Argentina but moderately differentiated in Peru, with low unidirectional gene flow in each country.

   We suggest that the South American Arid Diagonal was preexisting and remains a current phylogeographic barrier between the ranges of the two torrent duck subspecies, and the adult territoriality and breeding site fidelity to the rivers define their population structure.

    

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