Genomic signatures of rapid local selection and introgression drive adaptive phylogeography in the European river skater.

Identifying where high genetic diversity is located across our planet and what factors affect the geographical patterns of genetic variation not only provides important insights into distributions of biodiversity but is also crucial for human health, animal and plant breeding and biodiversity conservation. Recent studies show that genetic diversity at nearly neutral genes decreases from the tropics to the poles in different taxa, mirroring the oldest recognized latitudinal gradient of species richness, yet functional genetic diversity has received little attention at such broad spatial or taxonomic scales. Here, we investigated latitudinal gradients in genetic diversity at a polymorphic exon 2 (MHC II DRB gene, 1515 sequences) of the major histocompatibility complex that confers resistance to parasites in 93 terrestrial mammal species at the global scale. We also estimated the effects of species traits, positive selection and anthropogenic biomes on genetic diversity. We found clear latitudinal gradients in genetic diversity and the presence of positive selection at exon 2. Absolute latitude, the presence of positive selection and body mass are important predictors of within‐species genetic diversity. A higher occurrence of positive selection, faster evolutionary speed or slower drift at low latitudes may shape the latitudinal gradient in the within‐species genetic diversity of the gene. Our results contribute to a greater understanding of how species traits, selection and drift geographically shape functional genetic diversity, broadening the generality of latitudinal biodiversity gradient. The results highlight the importance of conservation at low latitudes.

Recent studies explored whether the latitudinal diversity gradient extends to a latitudinal genetic diversity gradient. There is a knowledge gap concerning the genetic diversity distribution across marine invertebrates, and whether the latitudinal genetic diversity gradient results from congruent intraspecific trends. Here, we tested the hypotheses of the existence of a latitudinal mitochondrial genetic diversity gradient in marine decapods (crabs, hermit crabs, shrimps, lobsters) driven by environmental variables and that this gradient is the result of the accumulation of similar trends at the intraspecific level. We analyzed populational-level cytochrome oxidase subunit I sequence available for Tropical Western Atlantic species (1883 sequences, 23 species) to investigate the association between mitochondrial genetic diversity versus latitude, and genetic diversity versus six environmental variables (sea surface temperature, dissolved oxygen, chlorophyll-a, salinity, current velocity, pH). Intraspecific mitochondrial genetic diversity versus latitude analyses were also performed. Our findings indicate higher mitochondrial genetic diversity in lower latitudes (latitudinal genetic diversity gradient) driven by productivity and oxygen levels (only for nucleotide diversity). However, this trend is not caused by the accumulation of intraspecific patterns, which can be variable and species-specific. Our results indicate that different levels of biological organization can show discordant patterns and suggest caution when interpreting macroscale investigations.

Gradients of variation--or clines--have always intrigued biologists. Classically, they have been interpreted as the outcomes of antagonistic interactions between selection and gene flow. Alternatively, clines may also establish neutrally with isolation by distance (IBD) or secondary contact between previously isolated populations. The relative importance of natural selection and these two neutral processes in the establishment of clinal variation can be tested by comparing genetic differentiation at neutral genetic markers and at the studied trait. A third neutral process, surfing of a newly arisen mutation during the colonization of a new habitat, is more difficult to test. Here, we designed a spatially explicit approximate Bayesian computation (ABC) simulation framework to evaluate whether the strong cline in the genetically based reddish coloration observed in the European barn owl (Tyto alba) arose as a by-product of a range expansion or whether selection has to be invoked to explain this colour cline, for which we have previously ruled out the actions of IBD or secondary contact. Using ABC simulations and genetic data on 390 individuals from 20 locations genotyped at 22 microsatellites loci, we first determined how barn owls colonized Europe after the last glaciation. Using these results in new simulations on the evolution of the colour phenotype, and assuming various genetic architectures for the colour trait, we demonstrate that the observed colour cline cannot be due to the surfing of a neutral mutation. Taking advantage of spatially explicit ABC, which proved to be a powerful method to disentangle the respective roles of selection and drift in range expansions, we conclude that the formation of the colour cline observed in the barn owl must be due to natural selection.

Preface to the selected papers on modelling and control of metapopulation networks

Genetic diversity and metapopulation structure of the brown swimming crab (Callinectes bellicosus) along the coast of Sonora, Mexico: Implications for fisheries management

Recent phylogeographic work suggests the existence of latitudinal gradients in genetic diversity in northern Mexican plants, but very few studies have examined plants of the Chihuahuan Desert. Tidestromia lanuginosa is a morphologically variable annual species whose distribution includes the Chihuahuan Desert Region. Here we undertook phylogeographic analyses of chloroplast loci in this species to test whether genetic diversity and differentiation of Mexican populations of T. lanuginosa change along a latitudinal gradient and whether diversity is higher in Coahuila, consistent with ideas of lower plant community turnover during the Pleistocene. Haplotype network, maximum likelihood tree, and Bayesian phylogenetic haplotype were reconstructed, and genetic diversity was assessed among 26 populations. Barrier analysis was used to explore barriers to gene flow. Four major population groups were identified, corresponding with physiographic provinces in Mexico. Each population group displayed high levels of genetic structure, haplotype, and nucleotide diversity. Diversity was highest in southern populations across the species as a whole and among the Chihuahuan Desert populations. Tidestromia lanuginosa provides an important example of high phylogeographic and genetic diversity in plants of northern Mexico. Barriers to gene flow among the major population groups have most likely been due to a combination of orographic, climatic, and edaphic variables. The high genetic diversity of T. lanuginosa in southern and central Coahuila is consistent with the hypothesis of full-glacial refugia for arid-adapted plants in this area, and highlights the importance of this region as a center of diversity for the Chihuahuan Desert flora.

The green anole (Anolis carolinensis) is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of A. carolinensis using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of A. carolinensis evolutionary history in association with morphological, physiological, or reproductive biology studies among sampling localities and necessitate increased effort to resolve evolutionary relationships among natural populations. Here, we used anchored hybrid enrichment of hundreds of genetic markers across the genome of A. carolinensis and identified five strongly supported phylogeographic groups. Using multiple analyses, we produced a fully resolved species tree, investigated relative support for each lineage across all gene trees, and identified mito‐nuclear discordance when comparing our results to previous studies. We found fixed differences in only one clade—southern Florida restricted to the Everglades region—while most polymorphisms were shared between lineages. The southern Florida group likely diverged from other populations during the Pliocene, with all other diversification during the Pleistocene. Multiple lines of support, including phylogenetic relationships, a latitudinal gradient in genetic diversity, and relatively more stable long‐term population sizes in southern phylogeographic groups, indicate that diversification in A. carolinensis occurred northward from southern Florida.

Arnica montana is a clonal, self-incompatible herb of economic and intrinsic ecological value which is declining in large parts of its range. With the employment of microsatellite markers, we characterized the population structure and distribution of genetic diversity of 40 populations of A. montana sampled throughout Europe. We detected a clear geographical pattern of isolation and strong population structure, indicating limited gene flow. We also observed a negative latitudinal gradient in genetic diversity. Such patterns can be explained by paleo-historical colonization routes following the last glacial maximum, with regions characterized by higher genetic diversity corresponding to former glacial refugia. We recommend the implementation of conservation measures such as assisted gene flow in the populations characterized by low genetic diversity under consideration of the observed population structure. For the populations where high levels of genetic diversity are still retained, we recommend the maintenance of suitable habitat conditions. Our study emphasises the importance of conducting large-scale population genetic studies that consider postglacial recolonization history when planning active conservation measures such as assisted gene flow.

The level of genetic differentiation within and between evolutionary lineages of the common vole (Microtus arvalis) in Europe was examined by analyzing mitochondrial sequences from the control region (mtDNA) and 12 nuclear microsatellite loci (nucDNA) for 338 voles from 18 populations. The distribution of evolutionary lineages and the affinity of populations to lineages were determined with additional sequence data from the mitochondrial cytochrome b gene. Our analyses demonstrated very high levels of differentiation between populations (overall FST: mtDNA 70%; nucDNA 17%). The affinity of populations to evolutionary lineages was strongly reflected in mtDNA but not in nucDNA variation. Patterns of genetic structure for both markers visualized in synthetic genetic maps suggest a postglacial range expansion of the species into the Alps, as well as a potentially more ancient colonization from the northeast to the southwest of Europe. This expansion is supported by estimates for the divergence times between evolutionary lineages and within the western European lineage, which predate the last glacial maximum (LGM). Furthermore, all measures of genetic diversity within populations increased significantly with longitude and showed a trend toward increase with latitude. We conclude that the detected patterns are difficult to explain only by range expansions from separate LGM refugia close to the Mediterranean. This suggests that some M. arvalis populations persisted during the LGM in suitable habitat further north and that the gradients in genetic diversity may represent traces of a more ancient colonization of Europe by the species.

AimHow historical and contemporary eco‐evolutionary processes shape the patterns of genetic diversity and differentiation across species’ distribution range remains an open question with strong conservation implications. Focusing on the orange stony coral, Astroides calycularis, we (a) characterized the pattern of neutral genetic diversity across the distribution range; (b) gave insights into the underlying processes; and (c) discussed conservation implications with emphasis on a national park located on a hotspot of genetic diversity.LocationSouth Mediterranean Sea and Zembra National Park.MethodsWe combined new data from 12 microsatellites in 13 populations located in the Centre and in the Western Periphery of the distribution range with a published dataset including 16 populations from the Western and Eastern Peripheries. We analysed the relationship among parameters of genetic diversity (He, Ar(g)) and structure (population‐specific FST) and two measures of geographic peripherality. We compared two estimators of pairwise genetic structure (GST, DEST) across the distribution range. The evolutionary and demographic history of the populations following the Last Glacial Maximum was reconstructed using approximate Bayesian computations and maximum‐likelihood analyses. We inferred the contemporary connectivity among populations from Zembra National Park and with the neighbouring area of Cap Bon.ResultsWe demonstrate a decrease in genetic diversity and an increase in genetic differentiation from the Centre to the Eastern and Western Peripheries of the distribution range. Populations from Zembra show the highest genetic diversity reported in the species. We identified a spillover effect towards Cap Bon.Main conclusionsThe patterns of genetic diversity and differentiation are most likely explained by “the postglacial range expansion hypothesis” rather than the “central–peripheral hypothesis.” Enforcement of conservation measures should be considered to protect this genetic diversity pattern, in particular when considering the low effective population size inferred at many sites.

The level of genetic differentiation within and between evolutionary lineages of the common vole (Microtus arvalis) in Europe was examined by analyzing mitochondrial sequences from the control region (mtDNA) and 12 nuclear microsatellite loci (nucDNA) for 338 voles from 18 populations. The distribution of evolutionary lineages and the affinity of populations to lineages were determined with additional sequence data from the mitochondrial cytochrome b gene. Our analyses demonstrated very high levels of differentiation between populations (overall FST: mtDNA 70%; nucDNA 17%). The affinity of populations to evolutionary lineages was strongly reflected in mtDNA but not in nucDNA variation. Patterns of genetic structure for both markers visualized in synthetic genetic maps suggest a postglacial range expansion of the species into the Alps, as well as a potentially more ancient colonization from the northeast to the southwest of Europe. This expansion is supported by estimates for the divergence times between evolutionary lineages and within the western European lineage, which predate the last glacial maximum (LGM). Furthermore, all measures of genetic diversity within populations increased significantly with longitude and showed a trend toward increase with latitude. We conclude that the detected patterns are difficult to explain only by range expansions from separate LGM refugia close to the Mediterranean. This suggests that some M. arvalis populations persisted during the LGM in suitable habitat further north and that the gradients in genetic diversity may represent traces of a more ancient colonization of Europe by the species.

The stability and composition of communities are threatened with the intensifying of human impact on biodiversity. A crucial challenge of the next years will be to conserve biodiversity under climate changes. The factors that determine the distributions of species and the communities are of primary interest to the optimization of conservation actions. While studied for more than a century, the mechanisms underlying the Latitudinal Diversity Gradient (LDG) – one of the strongest biotic patterns on Earth – remain hotly debated. Contrasting patterns in different organism groups may help elucidate the underlying mechanisms. Here, we compare diversity patterns of vascular plants and bryophytes across Europe assessing not just species richness (SR), but also other aspects of diversity that may inform on the underlying assembly mechanisms, namely species turnover and nestedness. We applied species distributions and macroecological models to reconstruct vascular plants and bryophytes species richness (SR) across Europe. Coupled with species turnover and nestedness analyses, Lee’s L statistics and Procustes analyses. While vascular plants conform to the classical LDG, bryophytes exhibit markedly divergent latitudinal SR patterns, with higher richness in at high latitudes. Vascular plants have higher species turn-over at low latitudes and higher nestedness at high latitudes, in agreement with the tropical niche conservatism hypothesis as an explanation for the LDG. Contrary to LDG expectations, SR of bryophytes increase towards northern areas, with patterns of turnover and nestedness that suggest different origins for the southern and northern European bryophytes species pools.

Many arctic-alpine organisms have vast present-day ranges across Eurasia, but their history of refugial isolation, differentiation and postglacial expansion is poorly understood. The mountain avens, Dryas octopetala sensu lato, is a long-lived, wind-dispersed, diploid shrub forming one of the most important components of Eurasian tundras and heaths in terms of biomass. We address differentiation and migration history of the species with emphasis on the western and northern Eurasian parts of its distribution area, also including some East Greenlandic and North American populations (partly referred to as the closely related D. integrifolia M. Vahl). We analysed 459 plants from 52 populations for 155 amplified fragment length polymorphisms (AFLP) markers. The Eurasian plants were separated into two main groups, probably reflecting isolation and expansion from two major glacial refugia, situated south and east of the North European ice sheets, respectively. Virtually all of northwestern Europe as well as East Greenland have been colonized by the Southern lineage, whereas northwest Russia, the Tatra Mountains and the arctic archipelago of Svalbard have been colonized by the Eastern lineage. The data indicate a contact zone between the two lineages in northern Scandinavia and possibly in the Tatra Mountains. The two single populations analysed from the Caucasus and Altai Mountains were most closely related to the Eastern lineage but were strongly divergent from the remaining eastern populations, suggesting survival in separate refugia at least during the last glaciation. The North American populations grouped with those from East Greenland, irrespective of their taxonomic affiliation, but this may be caused by independent hybridization with D. integrifolia and therefore not reflect the true relationship between populations from these areas.

The Brazilian free-tailed bat (Tadarida brasiliensis) is a widely distributed Neotropical Molossidae species with significant ecological importance in pest control. Despite its broad range, the genetic diversity and population structure of South American populations remain poorly understood. This study assessed the genetic diversity, population structure, and demographic history of T. brasiliensis in southern Brazil (Capão do Leão) compared to available sequences from South, North, and Central American populations using COI and D-loop mitochondrial markers. Bayesian and coalescent-based analyses revealed deep divergence (~8.9 Mya) between northern and southern lineages, likely influenced by Andean uplift and Pleistocene climatic shifts. High genetic diversity was observed in southern populations, with distinct clades suggesting historical isolation. Population structure analyses confirmed significant differentiation between regions, with isolation-by-distance as a key driver. Demographic tests indicated post-glacial expansions (~0.5-0.12 Mya) in southern populations. These findings suggest that T. brasiliensis in South America comprises a single evolutionary lineage with complex demographic dynamics shaped by historical biogeographic barriers. The study highlights the need for further research on migratory connectivity and conservation strategies for this ecologically important species.

Hybridization frequently occurs in plant species. With repeated backcross, the introgression may influence evolutionary trajectories through the entry of foreign genes. However, the genetic admixture via hybridization events is often confused with the ancestral polymorphism, especially in closely related species that have experienced similar evolutionary events. In Taiwan, two independent-originated endemic snakebark maples have contrasted postglacial range expansion routes: northward and upward expansion in Acer caudatifolium and downward expansion in A. morrisonense. The range expansion causes the current parapatric distribution, increasing the possibility of introgression. This study elucidates how their genetic variation reflects introgression and historical demography. With 17 EST-SSR markers among the intensely sampled 657 individuals, we confirmed that the genetic admixture between species mainly was attributed to recent introgression instead of common ancestral polymorphism. The secondary contact scenario inferred by approximate Bayesian computation suggested that A. morrisonense received more genetic variations from A. caudatifolium. Introgression occurred in colonized Taiwan around the early Last Glacial Period. Furthermore, the demography of A. caudatifolium was more severely affected by introgression than A. morrisonense, especially in the wavefront populations with high altitude range expansion, implying an altitude-related adaptive introgression. In contrast, A. morrisonense exhibited ubiquitous introgression independent of postglacial expansion, suggesting that introgression in A. morrisonense was neutral. In terms of different genetic consequences, introgression had different demographic impacts on species with different altitude expansion directions even under the same climate-change conditions within an island.