Isolation by resistance explains genetic diversity in the<i>Arremon</i>brushfinches of northern Mesoamerica

Moreno-Contreras, Israel; Llanes‐Quevedo, Alexander; Sánchez‐González, Luis A.; Arizmendi, Marı́a del Coro; Navarro‐Sigüenza, Adolfo G.

doi:10.1111/mec.16948

Cited by 3 publications

(2 citation statements)

References 157 publications

(251 reference statements)

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“…Resistance distance calculations in IBR often utilize data related to species traits or habitats ( Thomas et al 2015 ; Weber et al 2017 ). One common method is to calculate resistance distance based on niche model predictions, since gene flow between populations can be limited by suitable habitats ( Myers et al 2019 ; Zhang et al 2020 ; Shu et al 2022 ; Moreno-Contreras et al 2023 ). In IBE and IBR analyses, based on L. lutea 's elevational distribution range and preference for evergreen broadleaved forest and woodland, we considered 2 other variables in addition to the bioclimatic factors, namely altitude and land cover.…”

Section: Discussionmentioning

confidence: 99%

“…Mantel test is one of the most popular approaches to evaluate spatial processes driving population structure ( Diniz-Filho et al 2013 ; Zhang et al 2020 ), but it has been frequently critiqued because results were inconsistent with expectations and there were issues with type I (false-positive) and type II (false-negative) error rates ( Legendre et al 2015 ; Somers and Jackson 2022 ). Therefore, we used MLPE and MRDM to determine which model better explains genetic variation in L. lutea ( Moreno-Contreras et al 2023 ).…”

Section: Discussionmentioning

confidence: 99%

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Landscape Heterogeneity Explains the Genetic Differentiation of a Forest Bird across the Sino-Himalayan Mountains

Jiao,

Wu,

Zhang

et al. 2024

Molecular Biology and Evolution

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Mountains are the world’s most important centers of biodiversity. The Sino-Himalayan Mountains (SHM) are global biodiversity hotspot due to their extremely high species richness and endemicity. Ample research investigated the impact of the Qinghai-Tibet Plateau uplift and Quaternary glaciations in driving species diversification in plants and animals across the SHM. However, little is known about the role of landscape heterogeneity and other environmental features in driving diversification in this region. We utilized whole genomes and phenotypic data in combination with landscape genetic approaches to investigate population structure, demography, and genetic diversity in a forest songbird species native to the SHM, the Red-billed Leiothrix (Leiothrix lutea). We identified five phylogeographic clades, including one in the East of China, one in Yunnan, and three in Tibet, roughly consistent with differences in song and plumage coloration but incongruent with traditional subspecies boundaries. Isolation-by-resistance model best explained population differentiation within L. lutea, with extensive secondary contact after allopatric isolation leading to admixture among clades. Ecological niche modeling indicated relative stability in the extent of suitable distribution areas of the species across Quaternary glacial cycles. Our results underscore the importance of mountains in the diversification of this species, given that most of the distinct genetic clades are concentrated in a relatively small area in the SHM region, while a single shallow clade populates vast lower-lying areas to the east. This study highlights the crucial role of landscape heterogeneity in promoting differentiation and provides a deep genomic perspective on the mechanisms through which diversity hotspots form.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Landscape Heterogeneity Explains the Genetic Differentiation of a Forest Bird across the Sino-Himalayan Mountains

Jiao,

Wu,

Zhang

et al. 2024

Molecular Biology and Evolution

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

Pyron,

Kakkera,

Beamer

et al. 2023

Molecular Ecology

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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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Considerable genetic diversity and structure despite narrow endemism and limited ecological specialization in the Hayden's ringlet, Coenonympha haydenii

Springer,

Gompert

2024

Molecular Ecology

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Understanding the processes that underlie the development of population genetic structure is central to the study of evolution. Patterns of genetic structure, in turn, can reveal signatures of isolation by distance (IBD), barriers to gene flow, or even the genesis of speciation. However, it is unclear how severe range restriction might impact the processes that dominate the development of genetic structure. In narrow endemic species, is population structure likely to be adaptive in nature, or rather the result of genetic drift? In this study, we investigated patterns of genetic diversity and structure in the narrow endemic Hayden's ringlet butterfly. Specifically, we asked to what degree genetic structure in the Hayden's ringlet can be explained by IBD, isolation by resistance (IBR) (in the form of geographic or ecological barriers to migration between populations), and isolation by environment (in the form of differences in host plant availability and preference). We employed a genotyping‐by‐sequencing (GBS) approach coupled with host preference assays, Bayesian modelling, and population genomic analyses to answer these questions. Our results suggest that despite their restricted range, levels of genetic diversity in the Hayden's ringlet are comparable to those seen in more widespread butterfly species. Hayden's ringlets showed a strong preference for feeding on grasses relative to sedges, but neither larval preference nor potential host availability at sampling sites correlated with genetic structure. We conclude that geography, in the form of IBR and simple IBD, was the major driver of contemporary patterns of differentiation in this narrow endemic species.

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Isolation by resistance explains genetic diversity in theArremonbrushfinches of northern Mesoamerica

Abstract: Evolutionary theory suggests that genetic differentiation between and within natural populations is the result of neutral (e.g., gene flow) and adaptive (e.g., natural selection) processes (Mayr, 1963;

Cited by 3 publications

References 157 publications

Landscape Heterogeneity Explains the Genetic Differentiation of a Forest Bird across the Sino-Himalayan Mountains

Landscape Heterogeneity Explains the Genetic Differentiation of a Forest Bird across the Sino-Himalayan Mountains

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

Considerable genetic diversity and structure despite narrow endemism and limited ecological specialization in the Hayden's ringlet, Coenonympha haydenii

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