The roles of allopatric fragmentation and niche divergence in intraspecific lineage diversification in the common midwife toad (Alytes obstetricans)

Abstract

Aim: Understanding the roles of allopatric fragmentation and niche divergence in intraspecific lineage diversification is central to our comprehension of how new species arise and evolve. Here we integrate an extensive multilocus dataset with species distribution models to address these topics in genetically differentiated population lineages of the common midwife toad (Alytes obstetricans).Location: Iberian Peninsula, Western Europe. Methods:We genotyped 965 individuals from 142 localities at 12 microsatellite loci to finely delineate the ranges of population lineages in A. obstetricans. We then built ecological niche-based models for each lineage and tested for niche overlap, equivalency and similarity based on PCA-env analyses. We also investigated the relationship between genetic and environmental distances across lineages. Results:We recovered seven differentiated genetic clusters, with mostly different (sometimes nonoverlapping) niches. However, niches are not more divergent than expected given the largely allopatric ranges of population lineages. We found no significant isolation by environment within lineages, with genetic distances mostly explained by geographical distances.Main conclusions: Allopatric fragmentation in A. obstetricans resulted in (sometimes highly) different niches in intraspecific population lineages. Within lineages, isolation by distance is the major driver of patterns of genetic variation. Our study highlights the importance of incorporating intraspecific genetic structure into species distribution models to explore spatial patterns of genetic diversity in terms of their underlying processes. K E Y W O R D Sdiversification, ecological niche-based modelling, intraspecific lineage, microsatellites, niche conservatism, niche divergence

Are glacial refugia hotspots of speciation and cytonuclear discordances? Answers from the genomic phylogeography of Spanish common frogs

“…In R. temporaria , future surveys should focus on T3, another enigmatic mtDNA lineage restricted to a single valley (Benasque) in the Central Pyrenees (Vences et al, ). Diverged but ephemeral mtDNAs also persist in other Iberian taxa, e.g., the Pyrenean haplogroup E of Alytes obstetricans (Maia‐Carvalho et al, ). Hence, the maintenance of ghost mitochondrial lineages can create mirages of cryptic species (Hinojosa et al, ), but at the same time mitochondrial capture and replacement may conceal genuine evolutionary divergences (Dufresnes, Mazepa, et al, ).…”

“…In R. temporaria, future surveys should focus on T3, another enigmatic mtDNA lineage restricted to a single valley (Benasque) in the Central Pyrenees . Diverged but ephemeral mtDNAs also persist in other Iberian taxa, e.g., the Pyrenean haplogroup E of Alytes obstetricans (Maia-Carvalho et al, 2018).…”

Evaluating surrogates of genetic diversity for conservation planning

“…Despite this, several studies from which we obtained data noted congruence between the spatial patterns of microsatellite genetic diversity and hypotheses of geographic range expansion (Pereira et al 2018), postglacial recolonization patterns (Sequeira et al 2008;Ferchaud et al 2015), and climatic refugia (Gutiérrez-Rodríguez et al 2017a). Additionally, they found strong similarities between the spatial patterns of genetic diversity revealed by microsatellite markers and mitochondrial DNA (Sequeira et al 2008;Gonçalves et al 2009;Gutiérrez-Rodríguez et al 2017a;Maia-Carvalho et al 2018).…”

“…Geographic and resistance distances were not highly effective surrogates for representing broad-scale genetic diversity in most of our studied species. Within our study species, distant populations can have more similar genetic characteristics than nearby populations depending on the genetic lineage to which they belong (e.g., Gonçalves et al 2009;Maia-Carvalho et al 2018;Valbuena-Ureña et al 2018), admixed populations can exhibit distinct combinations of genetic characteristics (Sequeira et al 2008;Gonçalves et al 2009;Pereira et al 2018), and-particularly for amphibian species with limited dispersal abilities-populations can exhibit fine-scale subdivision within genetic lineages (Sequeira et al 2008;Pereira et al 2018;Valbuena-Ureña et al 2018). As a consequence-despite statistically significant patterns of isolation by distance and resistance-our prioritizations based on geographic and resistance distances often missed genetically distinct groups of populations.…”

“…Our study area encompassed the Iberian Peninsula. We compiled nuclear microsatellite genotype and sampling site data-encompassing most of each species' geographic range-for 7 amphibian and 3 reptilian species from previous studies (Table 1) (Sequeira et al 2008;Gonçalves et al 2009;Remón et al 2013;Dias et al 2015;Ferchaud et al 2015;Gutiérrez-Rodríguez et al 2017a, 2017bMaia-Carvalho et al 2018;Pereira et al 2018;Valbuena-Ureña et al 2018) (Supporting Information). These species are endemic-or very nearly endemicto the Iberian Peninsula and have different environmental affinities, with Mediterranean or Eurosiberian-Atlantic distributions.…”