Latitudinal divergence in a widespread amphibian: Contrasting patterns of neutral and adaptive genomic variation

Abstract

Stochastic effects from demographic processes and selection are expected to shape the distribution of genetic variation in spatially heterogeneous environments. As the amount of genetic variation is central for long-term persistence of populations, understanding how these processes affect variation over large-scale geographical gradients is pivotal. We investigated the distribution of neutral and putatively adaptive genetic variation, and reconstructed demographic history in the moor frog (Rana arvalis) using 136 individuals from 15 populations along a 1,700-km latitudinal gradient from northern Germany to northern Sweden. Using double digest restriction-site associated DNA sequencing we obtained 27,590 single nucleotide polymorphisms (SNPs), and identified differentiation outliers and SNPs associated with growing season length. The populations grouped into a southern and a northern cluster, representing two phylogeographical lineages from different post-glacial colonization routes. Hybrid index estimation and demographic model selection showed strong support for a southern and northern lineage and evidence of gene flow between regions located on each side of a contact zone. However, patterns of past gene flow over the contact zone differed between neutral and putatively adaptive SNPs. While neutral nucleotide diversity was higher along the southern than the northern part of the gradient, nucleotide diversity in differentiation outliers showed the opposite pattern, suggesting differences in the relative strength of selection and drift along the gradient. Variation associated with growing season length decreased with latitude along the southern part of the gradient, but not along the northern part where variation was lower, suggesting stronger climate-mediated selection in the north. Outlier SNPs included loci involved in immunity and developmental processes. K E Y W O R D S adaptive divergence, amphibians, divergent selection, genetic drift, range expansion, small populations 1 | INTRODUC TI ON Species with wide geographical distributions are powerful model systems for investigating how selection and neutral processes shape genetic and phenotypic variation across heterogeneousenvironments, which may be affected by both contemporary processes as well as the demographic history of populations. However, disentangling the relative role of these processes along spatial gradients is challenging because environmental, genetic and phenotypic variation often co-vary in the same direction. When dispersal

Ecological Factors Generally Not Altitude Related Played Main Roles in Driving Potential Adaptive Evolution at Elevational Range Margin Populations of Taiwan Incense Cedar (Calocedrus formosana)

“…However, central populations can also be vulnerable in the face of global climate change (Bennett et al, 2015). Our results of finding high frequency outlier loci at high-and low-elevations ( Figure 4A) are in consistent with findings of evolutionary adaptation occur in leading-and trailing-edge populations of species shifting their ranges because of warming (Ackerly, 2003;Hampe and Petit, 2005;Thuiller et al, 2008;Chen et al, 2014;Rödin-Mörch et al, 2019). Additionally, outlier loci beginning to accumulate their frequencies at different elevations were also observed, suggestive of an ongoing process of outliers accumulating frequencies as selective pressures persist at local scales.…”

Contrasting signatures of introgression in North American box turtle (Terrapenespp.) contact zones

“…Diminishing sequencing costs coupled with an upsurge in genomic annotations have facilitated extensive application of this reverse-ecology approach within a variety of ecological contexts. Examples include inference of adaptive divergence in seasonal growth and variability in immune responses (Rödin-Mörch et al 2019), biodiversity response to environmental gradients (temperature, Keller & Seehausen 2012; altitudinal, Guo et al 2016; elevational, Waterhouse et al 2018; Teske et al 2019), and an increased capacity to examine contemporary effects, such as that of anthropogenic modulation of reproductive boundaries (Garroway et al 2010; Taylor et al 2014; Grabenstein & Taylor 2018). A result is an increased resolution with which to gauge how environmental and climatic shifts over both geologic and contemporary timescales shift species distributions and alter pre-existing adaptive gradients (Rosenzweig et al 2008; Taylor et al 2015; Ryan et al 2018).…”

Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans

“…R. arvalis shows a different pattern of dual postglacial colonization from south and north to Scandinavia, the contact zone being situated in central northern Sweden [39,40]. Populations at the northern edge are smaller, more fragmented and isolated relative to populations at the core of the distribution range [41][42][43]. As a consequence of decreasing effective population size at range margins, many species show lower genetic variation at the edge of their distribution range in concordance with the central-marginal hypothesis [44].…”

“…The Mature Peptide domain displayed 12 out of 14 and five out of five, for Temporin-Brevinin and Palustrin respectively, of the positively selected sites within the hypervariable region. Ten sites (3,21,40,43,44,47,49,50,51,56) out of 14 in Temporin-Brevinin group were identified by at least two (See figure on previous page.) Fig.…”

“…These results were mainly explained by a complex pattern of varying levels of drift and selection along the latitudinal gradient which is influenced by colonization history of the species [40,47]. Both in R. temporaria and R. arvalis the highest genetic variation both in neutral and adaptive allele frequencies is found in the southernmost regions of the latitudinal gradient [43,48,49].…”