Hybridization is increasingly recognized as a significant evolutionary process, in particular because it can lead to introgression of genes from one species to another. A striking pattern of ...discordance in the amount of introgression between mitochondrial and nuclear markers exists such that substantial mitochondrial introgression is often found in combination with no or little nuclear introgression. Multiple mechanisms have been proposed to explain this discordance, including positive selection for introgressing mitochondrial variants, several types of sex-biases, drift, negative selection against introgression in the nuclear genome, and spatial expansion. Most of these hypotheses are verbal, and have not been quantitatively evaluated so far. We use individualbased, multilocus, computer simulations of secondary contact under a wide range of demographic and genetic scenarios to evaluate the ability of the different mechanisms to produce discordant introgression. Sex-biases and spatial expansions fail to produce substantial mito-nuclear discordance. Drift and nuclear selection can produce strong discordance, but only under a limited range of conditions. In contrast, selection on the mitochondrial genome produces strong discordance, particularly when dispersal rates are low. However, commonly used statistical tests have little power to detect this selection. Altogether, these results dismiss several popular hypotheses, and provide support for adaptive mitochondrial introgression.
Climate is one of the main factors driving species distributions and global biodiversity patterns. Obtaining accurate predictions of species’ range shifts in response to ongoing climate change has ...thus become a key issue in ecology and conservation. Correlative species distribution models (cSDMs) have become a prominent tool to this aim in the last decade and have demonstrated good predictive abilities with current conditions, irrespective of the studied taxon. However, cSDMs rely on statistical association between species’ presence and environmental conditions and have rarely been challenged on their actual capacity to reflect causal relationships between species and climate. In this study, we question whether cSDMs can accurately identify if climate and species distributions are causally linked, a prerequisite for accurate prediction of range shift in relation to climate change. We compared the performance of cSDMs in predicting the distributions of 132 European terrestrial species, chosen randomly within five taxonomic groups (three vertebrate groups and two plant groups), and of 1,320 virtual species whose distribution is causally fully independent from climate. We found that (1) for real species, the performance of cSDMs varied principally with range size, rather than with taxonomic groups and (2) cSDMs did not predict the distributions of real species with a greater accuracy than the virtual ones. Our results unambiguously show that the high predictive power of cSDMs can be driven by spatial autocorrelation in climatic and distributional data and does not necessarily reflect causal relationships between climate and species distributions. Thus, high predictive performance of cSDMs does not ensure that they accurately depict the role of climate in shaping species distributions. Our findings therefore call for strong caution when using cSDMs to provide predictions on future range shifts in response to climate change.
Major histocompatibility complex (MHC) genes are crucial for the adaptive immune response of jawed vertebrates. Their variation, reaching extreme levels, is driven mainly by an arms race between ...hosts and pathogens. One hypothesised mechanism contributing to MHC polymorphism is adaptive introgression, the exchange of genetic variants between hybridising species favoured by selection, yet its effect on MHC variation is poorly understood. Detection of adaptive MHC introgression, though challenging, may be facilitated by the analysis of species complexes forming multiple hybrid zones. Here, we investigated MHC introgression in six hybrid zones formed by seven species of Podarcis lizards inhabiting the Iberian Peninsula. To differentiate adaptive introgression from neutral introgression, we compared the patterns of gene exchange in MHC and genome‐wide markers. We found elevated sharing of MHC alleles in the proximity of contact beyond the areas of detectable genome‐wide admixture in most hybrid zones and, in half of them, asymmetric MHC exchange. In general, the elevated MHC allele sharing between species pairs with abutting ranges compared to geographically isolated species pairs also supports the prevalence of introgression. Collectively, our results demonstrate widespread MHC introgression in the Iberian Podarcis complex and suggest its adaptiveness. Contrary to previous results from Triturus newts, we did not observe differences in the rate of introgression between MHC classes. Our work adds support to the emerging view of adaptive introgression as a key mechanism shaping MHC diversity. It also raises questions about the effect of elevated MHC variation and factors leading to the asymmetry of adaptive introgression.
In organisms reproducing sexually, speciation occurs when increasing divergence results in pre‐ or post‐zygotic reproductive isolation between lineages. Studies focusing on reproductive isolation ...origin in early stages of speciation are common and many rely on genomic scans to infer introgression providing limited information on the genomic architecture of reproductive isolation long‐term maintenance. This study analyses a natural hybrid zone between two species in a late stage of speciation. We used ddRADseq genotyping in the contact between Podarcis bocagei and P. carbonelli to examine admixture extent, analyse hybrid zone stability and assess genome‐wide variation in selection against introgression. We confirmed strong but incomplete reproductive isolation in a bimodal hybrid zone. New findings revealed population genetic structure within P. carbonelli in the contact zone; geographical and genomic clines analysis suggested strong selection against gene flow, but a relatively small proportion of the loci can introgress, mostly within the narrow contact zone. However, geographical clines revealed that a few introgressed loci show signs of potential positive selection, particularly into P. bocagei. Geographical clines also detected a signal of hybrid zone movement towards P. bocagei distribution. Genomic cline analysis revealed heterogeneous patterns of introgression among loci within the syntopy zone, but the majority maintain a strong association with the genomic background of origin. However, incongruences between both cline approaches were found, potentially driven by confounding effects on genomic clines. Last, an important role of the Z chromosome in reproductive isolation is suggested. Importantly, overall patterns of restricted introgression seem to result from numerous strong intrinsic barriers across the genome.
The interbreeding of individuals coming from genetically differentiated but incompletely isolated populations can lead to the formation of admixed populations, having important implications in ...ecology and evolution. In this simulation study, we evaluate how individual admixture proportions estimated by the software structure are quantitatively affected by different factors. Using various scenarios of admixture between two diverging populations, we found that unbalanced sampling from parental populations may seriously bias the inferred admixture proportions; moreover, proportionally large samples from the admixed population can also decrease the accuracy and precision of the inferences. As expected, weak differentiation between parental populations and drift after the admixture event strongly increase the biases caused by uneven sampling. We also show that admixture proportions are generally more biased when parental populations unequally contributed to the admixed population. Finally, with few exceptions, using a large number of markers reduces those biases, but using alternative priors for individual ancestry or the uncorrelated allele model only marginally affect the inference of admixture in most situations. We conclude that unbalanced sampling may cause important biases in the admixture proportions estimated by structure, especially when a small number of markers are used, and those biases can be worsened by the effect of drift and unequal genetic contribution of parental populations. Empirical studies should thus be careful with their sampling design and consider historical characteristics when using this software to estimate the ancestry of individuals from admixed populations.
Palearctic water frogs (genus Pelophylax) are an outstanding model in ecology and evolution, being widespread, speciose, either threatened or threatening to other species through biological ...invasions, and capable of siring hybrid offspring that escape the rules of sexual reproduction. Despite half a century of genetic research and hundreds of publications, the diversity, systematics and biogeography of Pelophylax still remain highly confusing, in no small part due to a lack of correspondence between studies. To provide a comprehensive overview, we gathered >13,000 sequences of barcoding genes from >1700 native and introduced localities and built multigene mitochondrial (~17 kb) and nuclear (~10 kb) phylogenies. We mapped all currently recognized taxa and their phylogeographic lineages (>40) to get a grasp on taxonomic issues, cyto‐nuclear discordances, the genetic makeup of hybridogenetic hybrids, and the origins of introduced populations. Competing hypotheses for the molecular calibration were evaluated through plausibility tests, implementing a new approach relying on predictions from the anuran speciation continuum. Based on our timetree, we propose a new biogeographic paradigm for the Palearctic since the Paleogene, notably by attributing a prominent role to the dynamics of the Paratethys, a vast paleo‐sea that extended over most of Europe. Furthermore, our results show that distinct marsh frog lineages from Eastern Europe, the Balkans, the Near East, and Central Asia (P. ridibundus ssp.) are naturally capable of inducing hybridogenesis with pool frogs (P. lessonae). We identified 14 alien lineages (mostly of P. ridibundus) over ~20 areas of invasions, especially in Western Europe, with genetic signatures disproportionally pointing to the Balkans and Anatolia as the regions of origins, in line with exporting records of the frog leg industry and the stocks of pet sellers. Pelophylax thus emerges as one of the most invasive amphibians worldwide, and deserves much higher conservation concern than currently given by the authorities fighting biological invasions.
By revisiting three decades of molecular data, we retraced the evolution and mapped the diversity of Pelophylax water frogs, a famous group of Eurasian amphibians. The results highlight the Paratethys Paleo‐sea as a major driver of diversification, implement a new timetree validation approach, emphasize the rare ability of lineages to hybridize despite substantial genomic divergence, and showcase the multiple origins of the exotic water frog populations extending all over Western Europe. Initially introduced via the frog leg industry, water frogs now represent one of the largest amphibian invasions worldwide.
Abstract
Dispersal has major impacts on population dynamics, population genetics and evolution, and also is critical for population management and conservation. Dispersal is frequently sex‐ and ...age‐specific, but current knowledge is strongly taxonomically biased toward birds and mammals.
Here, we provide estimates of dispersal in a threatened freshwater turtle species, the European pond turtle
Emys orbicularis
. Based on 15 years of capture‐mark‐recapture (CMR) monitoring and DNA samples from 194 individuals, we quantified both demographic and genetic dispersal between three sites separated by 1.5–3.5 km. We also investigated the effect of age and sex on dispersal.
Direct (CMR) and indirect (genetic) approaches provided consistent results, showing that the studied sites are connected with a flow of about one to three dozen migrants per generation. Dispersal was both age‐ and sex‐biased in this species, with frequent dispersal of adult males and a strong philopatry of juveniles (of both sexes) and adult females.
The network of canals and marshes allow effective dispersal to occur among the three study sites despite the relatively large distance separating them (≤3.5 km).
The strong philopatry of juveniles contrasts with the frequently higher dispersal rate in young birds and mammals and shows the relevance of investigating dispersal in various taxonomic groups. Our results provide useful information for the conservation of European pond turtle populations.
Aim
Global variation in animal colouration has inspired ecogeographical rules that suggest common patterns of recurrent adaptations to climate. However, little attention has been paid to the relative ...influence of the different climatic conditions encountered by species during their annual life cycle. We explored this question by testing whether breeding or non‐breeding climatic conditions most influence plumage colouration in gulls, a cosmopolitan group of birds with extensive variation in plumage darkness and seasonal migratory strategies.
Location
Global.
Time period
Contemporary.
Major taxa studied
All species and subspecies of gulls (Aves, Laridae).
Methods
We used literature data and digital images to assess two characteristics of plumage colouration in all 80 species and subspecies of gulls: the darkness of the mantle and the proportion of black on wingtips. For each species and subspecies, we collected data on migration distance and environmental variables across its breeding and non‐breeding range for both breeding and non‐breeding seasons. We performed a phylogenetic comparative analysis to quantify the relative influence of climatic conditions experienced during the breeding and non‐breeding season on plumage colouration.
Results
The climatic conditions encountered during the non‐breeding season explained interspecific variation in colouration better than the climate experienced during the breeding season. In accordance with hypotheses on the role of dark colouration in thermoregulation and feather protection, darker mantle colouration was positively correlated with insolation and negatively with air temperature. The proportion of black on wingtips was greater for long distance migrants wintering under insolated conditions than short distance migrants or residents occupying less insolated regions.
Main conclusions
In gulls, plumage colouration is predominantly shaped by selection experienced outside the breeding period, in accordance with the hypothesized photoprotective and thermoregulatory functions of avian plumage. This highlights the importance of taking into account seasonality and migration to understand global spatial patterns of avian colouration.
Island environments share distinctive characteristics that offer unique opportunities to investigate parallel evolution. Previous research has produced evidence of an island syndrome for ...morphological traits, life‐history strategies and ecological niches, but little is known about the response to insularity of other important traits such as animal signals. Here, we tested whether birds' plumage colouration is part of the island syndrome. We analysed with spectrophotometry the colouration of 116 species endemic to islands and their 116 closest mainland relatives. We found a pattern of reduced brightness and colour intensity for both sexes on islands. In addition, we found a decrease in the number of colour patches on islands that, in males, was associated with a decrease in the number of same‐family sympatric species. These results demonstrate a worldwide pattern of parallel colour changes on islands and suggest that a relaxation of selection on species recognition may be one of the mechanisms involved.
Coexistence with related species poses evolutionary challenges to which populations may react in diverse ways. When exposed to similar environments, sympatric populations of two species may adopt ...similar phenotypic trait values. However, selection may also favour trait divergence as a way to reduce competition for resources or mates. The characteristics of external body parts, such as coloration and external morphology, are involved to varying degrees in intraspecific signalling as well as in the adaptation to the environment and consequently may be diversely affected by interspecific interactions in sympatry. Here, we studied the effect of sympatry on various colour and morphological traits in males and females of two related newt species Lissotriton helveticus and L. vulgaris. Importantly, we did not only estimate how raw trait differences between species respond to sympatry, but also the marginal responses after controlling for environmental variation. We found that dorsal and caudal coloration converged in sympatry, likely reflecting their role in adaptation to local environments, especially concealment from predators. In contrast, aspects of male and female ventral coloration, which harbours sexual signals in both species, diverged in sympatry. This divergence may reduce opportunities for interspecific sexual interactions and the associated loss of energy, suggesting reproductive character displacement (RCD). Our study emphasizes the contrasting patterns of traits involved in different functions and calls for the need to consider this diversity in evolutionary studies.
In two European newts, coloured body parts used for sexual communication diverge where the species species coexist, but dorsal colour used for camouflage converge, tracking environmental conditions.
PDF
