Abstract Background Disentangling the drivers of genetic differentiation is one of the cornerstones in evolution. This is because genetic diversity, and the way in which it is partitioned within and among populations across space, is an important asset for the ability of populations to adapt and persist in changing environments. We tested three major hypotheses accounting for genetic differentiation—isolation-by-distance (IBD), isolation-by-environment (IBE) and isolation-by-resistance (IBR)—in the annual plant Arabidopsis thaliana across the Iberian Peninsula, the region with the largest genomic diversity. To that end, we sampled, genotyped with genome-wide SNPs, and analyzed 1772 individuals from 278 populations distributed across the Iberian Peninsula. Results IBD, and to a lesser extent IBE, were the most important drivers of genetic differentiation in A. thaliana . In other words, dispersal limitation, genetic drift, and to a lesser extent local adaptation to environmental gradients, accounted for the within- and among-population distribution of genetic diversity. Analyses applied to the four Iberian genetic clusters, which represent the joint outcome of the long demographic and adaptive history of the species in the region, showed similar results except for one cluster, in which IBR (a function of landscape heterogeneity) was the most important driver of genetic differentiation. Using spatial hierarchical Bayesian models, we found that precipitation seasonality and topsoil pH chiefly accounted for the geographic distribution of genetic diversity in Iberian A. thaliana . Conclusions Overall, the interplay between the influence of precipitation seasonality on genetic diversity and the effect of restricted dispersal and genetic drift on genetic differentiation emerges as the major forces underlying the evolutionary trajectory of Iberian A. thaliana .
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Neo‐sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks ( Eremophila alpestris )
Genetic structure and phenotypic variation among populations are affected by both geographic distance and environmental variation across species' distributions. Understanding the relative contributions of isolation by distance (IBD) and isolation by environment (IBE) is important for elucidating population dynamics across habitats and ecological gradients. In this study, we compared phenotypic and genetic variation among Horned Lark (
- NSF-PAR ID:
- 10446295
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Molecular Ecology
- Volume:
- 31
- Issue:
- 6
- ISSN:
- 0962-1083
- Page Range / eLocation ID:
- p. 1783-1799
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Aim Intraspecific genetic variation is key for adaptation and survival in changing environments and is known to be influenced by many factors, including population size, dispersal and life‐history traits. We investigated genetic variation within Neotropical amphibian species to provide insights into how natural history traits, phylogenetic relatedness, climatic and geographic characteristics can explain intraspecific genetic diversity.
Location Neotropics.
Taxon Amphibians.
Methods We assembled data sets using open‐access databases for natural history traits, genetic sequences, phylogenetic trees, climatic and geographic data. For each species, we calculated overall nucleotide diversity (
π ) and tested for isolation by distance (IBD) and isolation by environment (IBE). We then identified predictors ofπ , IBD and IBE using random forest (RF) regression or RF classification. We also fitted phylogenetic generalized linear mixed models (PGLMMs) to predictπ , IBD and IBE.Results We compiled 4052 mitochondrial DNA sequences from 256 amphibian species (230 frogs and 26 salamanders), georeferencing 2477 sequences from 176 species that were not linked to occurrence data. RF regressions and PGLMMs were congruent in identifying range size and precipitation (
σ ) as the most important predictors ofπ , influencing it positively. RF classification and PGLMMs identified minimum elevation as an important predictor of IBD; most species without IBD tended to occur at higher elevations. Maximum latitude and precipitation (σ ) were the best predictors of IBE, and most species without IBE occur at lower latitudes and in areas with more variable precipitation.Main Conclusions This study identified predictors of genetic variation in Neotropical amphibians using both machine learning and phylogenetic methods. This approach was valuable to determine which predictors were congruent between methods. We found that species with small ranges or living in zones with less variable precipitation tended to have low genetic diversity. We also showed that Western Mesoamerica, Andes and Atlantic Forest biogeographic units harbour high diversity across many species that should be prioritized for protection. These results could play a key role in the development of conservation strategies for Neotropical amphibians.
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Abstract Aim Phylogenetic diversification is a precursor to speciation, but the underlying patterns and processes are not well‐studied in lichens. Here we investigate what factors drive diversification in two tropical, morphologically similar macrolichens that occupy a similar range but differ in altitudinal and habitat preferences, testing for isolation by distance (IBD), environment (IBE), and fragmentation (IBF).
Location Neotropics, Hawaii, Macaronesia.
Taxon Sticta andina ,S. scabrosa (Peltigeraceae).Methods We analysed 395 specimens from 135 localities, using the fungal ITS barcoding marker to assess phylogenetic diversification, through maximum likelihood tree reconstruction, TCS haplotype networks, and Tajima's D. Mantel tests were employed to detect structure in genetic vs. geographic, environmental, and fragmentation distances. Habitat preferences were quantitatively assessed by statistical analysis of locality‐based BIOclim variables.
Results Sticta andina exhibited high phenotypic variation and reticulate phylogenetic diversity across its range, whereas the phenotypically uniformS. scabrosa contained two main haplotypes, one unique to Hawaii.Sticta andina is restricted to well‐preserved andine forests and paramos, naturally fragmented habitats due to disruptive topology, whereasS. scabrosa thrives in lowland to lower montane zones in exposed or disturbed microsites, representing a continuous habitat.Sticta scabrosa showed IBD only across its full range (separating the Hawaiian population) but not within continental Central and South America, there exhibiting a negative Tajima's D.Sticta andina did not exhibit IBD but IBE at continental level and IBF in the northern Andes.Main conclusions Autecology, particularly preference for either low or high altitudes, indirectly drives phylogenetic diversification. Low diversification in the low altitude species,
S. scabrosa , can be attributed to rapid expansion and effective gene flow across a more or less continuous niche due to disturbance tolerance. In contract, high diversification in the high altitude species,S. andina , can be explained by niche differentiation (IBE) and fragmentation (IBF) caused by the Andean uplift. -
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Abstract The integration of ecological niche modelling into phylogeographic analyses has allowed for the identification and testing of potential refugia under a hypothesis‐based framework, where the expected patterns of higher genetic diversity in refugial populations and evidence of range expansion of nonrefugial populations are corroborated with empirical data. In this study, we focus on a montane‐restricted cryophilic harvestman,
Sclerobunus robustus , distributed throughout the heterogeneous Southern Rocky Mountains and Intermontane Plateau of southwestern North America. We identified hypothetical refugia using ecological niche models (ENMs) across three time periods, corroborated these refugia with population genetic methods using double‐digest RAD‐seq data and conducted population‐level phylogenetic and divergence dating analyses. ENMs identify two large temporally persistent regions in the mid‐latitude highlands. Genetic patterns support these two hypothesized refugia with higher genetic diversity within refugial populations and evidence for range expansion in populations found outside hypothesized refugia. Phylogenetic analyses identify five to six genetically divergent, geographically cohesive clades ofS. robustus . Divergence dating analyses suggest that these separate refugia date to the Pliocene and that divergence between clades pre‐dates the late Pleistocene glacial cycles, while diversification within clades was likely driven by these cycles. Population genetic analyses reveal effects of both isolation by distance (IBD) and isolation by environment (IBE), with IBD more important in the continuous mountainous portion of the distribution, while IBE was stronger in the populations inhabiting the isolated sky islands of the south. Using model‐based coalescent approaches, we find support for postdivergence migration between clades from separate refugia. -
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Premise Industrialization and human activities have elevated temperatures and caused novel precipitation patterns, altering soil moisture and nutrient availability. Predicting evolutionary responses to climate change requires information on the agents of selection that drive local adaptation and influence resource acquisition and allocation. Here, we examined the contribution of nutrient and drought stress to local adaptation, and we tested whether trade‐offs across fitness components constrain or facilitate adaptation under resource stress.
Methods We exposed 35 families of
Boechera stricta (Brassicaceae) to three levels of water and two levels of nutrient supply in a factorial design in the greenhouse. We sourced maternal families from a broad elevational gradient (2499–3530 m a.s.l.), representing disparate soil moisture and nutrient availability.Results Concordant with local adaptation, maternal families from arid, low‐elevation populations had enhanced fecundity under severe drought over those from more mesic, high‐elevation sites. Furthermore, fitness trade‐offs between growth and reproductive success depended on the environmental context. Under high, but not low, nutrient levels, we found a negative phenotypic relationship between the probability of reproduction and growth rate. Similarly, a negative phenotypic association only emerged between fecundity and growth under severe drought stress, not the benign water treatment levels, indicating that stressful resource environments alter the direction of trait correlations. Genetic covariances were broadly concordant with these phenotypic patterns.
Conclusions Despite high heritabilities in all fitness components across treatments, trade‐offs between growth and reproduction could constrain adaptation to increasing drought stress and novel nutrient levels.
