On the roles of landscape heterogeneity and environmental variation in determining population genomic structure in a dendritic system

Dispersal and natural selection are key evolutionary processes shaping the distribution of phenotypic and genetic diversity. For species inhabiting complex spatial environments however, it is unclear how the balance between gene flow and selection may be influenced by landscape heterogeneity and environmental variation. Here, we evaluated the effects of dendritic landscape structure and the selective forces of hydroclimatic variation on population genomic parameters for the Murray River rainbowfish, Melanotaenia fluviatilis across the Murray–Darling Basin, Australia. We genotyped 249 rainbowfish at 17,503 high‐quality SNP loci and integrated these with models of network connectivity and high‐resolution environmental data within a riverscape genomics framework. We tested competing models of gene flow before using multivariate genotype–environment association (GEA) analysis to test for signals of adaptive divergence associated with hydroclimatic variation. Patterns of neutral genetic variation were consistent with expectations based on the stream hierarchy model and M. fluviatilis’ moderate dispersal ability. Models incorporating dendritic network structure suggested that landscape heterogeneity is a more important factor determining connectivity and gene flow than waterway distance. Extending these results, we also introduce a novel approach to controlling for the unique effects of dendritic network structure in GEA analyses of populations of aquatic species. We identified 146 candidate loci potentially underlying a polygenic adaptive response to seasonal fluctuations in stream flow and variation in the relative timing of temperature and precipitation extremes. Our findings underscore an emerging predominant role for seasonal variation in hydroclimatic conditions driving local adaptation and are relevant for informing proactive conservation management.     

Phylogenetic analysis of Aphanius from the endorheic Kor River Basin in the Zagros Mountains,South‐western Iran (Teleostei: Cyprinodontiformes: Cyprinodontidae)

Morphologically similar populations of Aphanius that are currently considered as A. sophiae inhabit the endorheic Kor River Basin in the Zagros Mountains. Using genetic analysis based on mtDNA (cytochrome b), combined with examination of morphology (morphometry, meristics, otoliths), we discovered that what is thought to be A. sophiae is actually two distinct species, one of which is described as A. shirini sp. n. The males of the new species can be distinguished from those of all other Iranian inland Aphanius species by having only 7–10 clearly defined white flank bars, which is the lowest number of flank bars among the Iranian inland Aphanius species. Both males and females differ from all other Iranian inland Aphanius species by having a significantly longer caudal peduncle and a smaller dorsal fin depth. Based on the PhyML and Bayesian likelihood trees, A. shirini is sister to A. vladykovi from the Karoun Basin in the Zagros Mountains. Our results indicate that an ancient exorheic Kor River Basin existed in the Late Miocene and Pliocene. The close phylogenetic relationship between A. shirini and A. vladykovi suggests that the pre‐Pliocene drainage in the ancient Kor River Basin was directed to the north‐west (to the Karoun Basin), and not to the south‐east as in the present‐day Kor Basin. Both A. shirini and A. vladykovi represent the highest altitude records for Aphanius. We conclude that the splits of A. shirini and A. vladykovi can be linked to tectonic events in the Middle to Late Miocene, which created the highest altitudes (>3000 m) in the Zagros Mountains, and led to isolation of populations. The present‐day endorheic Kor Basin is known to have formed in the Late Pleistocene or Early Holocene, and the ‘young’ age of A. sophiae is clearly related to this history. Our results contribute to elucidate the link between geological history and the present‐day species diversity in the tectonically still active Zagros Mountains of Iran.     

Landscape genetics and spatial pattern of phenotypic variation of Eristalis tenax across Europe

A study of population connectivity of the migratory insect species, such as dronefly Eristalis tenax (Diptera, Syrphidae), has an essential importance in understanding the relative influence of the evolutionary forces and environmental features that interact in the spatial distribution of molecular and morphological diversity. However, specific study aiming to understand spatial genetic structure of dronefly populations and its migratory potential is lacking. Hence, we studied a spatial pattern of genetic and phenotypic variation of seven European populations of E. tenax incorporating landscape genetic methods using allozyme data, wing size and shape and abdominal colour pattern. Based on the observed lack of genotypic structuring, we suggested that there has been sufficient long‐distance gene flow to effectively homogenize population structuring at a broader geographical scale. Wing shape similarity among populations and an overlap of abdominal colour variation showed no clear clustering related to geography, which is in congruence with genetic data. However, genetic (F_ST values) and phenotypic (wing size) data and landscape genetics indicated subdivision between the Balkan populations (four Serbian samples) and populations from Central (Germany and Switzerland) and Northern (Finland) Europe. These findings indicated a potential connection between the Central and Northern Europe supporting the Central European origin of the flies caught in Finland. Thus, by performing spatial analysis and combining genetic–morphological approach, we shed light on the movement pattern in complex landscapes and thus provided the necessary guidelines to a broad‐scale analysis of this widespread generalist pollinator.     

Genomic data reveal deep genetic structure but no support for current taxonomic designation in a grasshopper species complex

Taxonomy has traditionally relied on morphological and ecological traits to interpret and classify biological diversity. Over the last decade, technological advances and conceptual developments in the field of molecular ecology and systematics have eased the generation of genomic data and changed the paradigm of biodiversity analysis. Here we illustrate how traditional taxonomy has led to species designations that are supported neither by high throughput sequencing data nor by the quantitative integration of genomic information with other sources of evidence. Specifically, we focus on Omocestus antigai and Omocestus navasi, two montane grasshoppers from the Pyrenean region that were originally described based on quantitative phenotypic differences and distinct habitat associations (alpine vs. Mediterranean‐montane habitats). To validate current taxonomic designations, test species boundaries, and understand the factors that have contributed to genetic divergence, we obtained phenotypic (geometric morphometrics) and genome‐wide SNP data (ddRADSeq) from populations covering the entire known distribution of the two taxa. Coalescent‐based phylogenetic reconstructions, integrative Bayesian model‐based species delimitation, and landscape genetic analyses revealed that populations assigned to the two taxa show a spatial distribution of genetic variation that do not match with current taxonomic designations and is incompatible with ecological/environmental speciation. Our results support little phenotypic variation among populations and a marked genetic structure that is mostly explained by geographic distances and limited population connectivity across the abrupt landscapes characterizing the study region. Overall, this study highlights the importance of integrative approaches to identify taxonomic units and elucidate the evolutionary history of species.     

Predicting the effects of climate change on population connectivity and genetic diversity of an imperiled freshwater mussel,Cumberlandia monodonta (Bivalvia: Margaritiferidae), in riverine systems

In the face of global climate change, organisms may respond to temperature increases by shifting their ranges poleward or to higher altitudes. However, the direction of range shifts in riverine systems is less clear. Because rivers are dendritic networks, there is only one dispersal route from any given location to another. Thus, range shifts are only possible if branches are connected by suitable habitat, and stream‐dwelling organisms can disperse through these branches. We used Cumberlandia monodonta (Bivalvia: Unionoida: Margaritiferidae) as a model species to investigate the effects of climate change on population connectivity because a majority of contemporary populations are panmictic. We combined ecological niche models (ENMs) with population genetic simulations to investigate the effects of climate change on population connectivity and genetic diversity of C. monodonta. The ENMs were constructed using bioclimatic and landscape data to project shifts in suitable habitat under future climate scenarios. We then used forward‐time simulations to project potential changes in genetic diversity and population connectivity based on these range shifts. ENM results under current conditions indicated long stretches of highly suitable habitat in rivers where C. monodonta persists; populations in the upper Mississippi River remain connected by suitable habitat that does not impede gene flow. Future climate scenarios projected northward and headwater‐ward range contraction and drastic declines in habitat suitability for most extant populations throughout the Mississippi River Basin. Simulations indicated that climate change would greatly reduce genetic diversity and connectivity across populations. Results suggest that a single, large population of C. monodonta will become further fragmented into smaller populations, each of which will be isolated and begin to differentiate genetically. Because C. monodonta is a widely distributed species and purely aquatic, our results suggest that persistence and connectivity of stream‐dwelling organisms will be significantly altered in response to future climate change.     

Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics

Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population‐specific and pairwise F_ST) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate‐related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and F_ST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin‐wide to the metapopulation scale). Sensitivity analysis (leave‐one‐population‐out) revealed consistent relationships between climate variables and F_ST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.     

Toxicity and population structure of the Rough‐Skinned Newt (Taricha granulosa) outside the range of an arms race with resistant predators

Species interactions, and their fitness consequences, vary across the geographic range of a coevolutionary relationship. This spatial heterogeneity in reciprocal selection is predicted to generate a geographic mosaic of local adaptation, wherein coevolutionary traits are phenotypically variable from one location to the next. Under this framework, allopatric populations should lack variation in coevolutionary traits due to the absence of reciprocal selection. We examine phenotypic variation in tetrodotoxin (TTX) toxicity of the Rough‐Skinned Newt (Taricha granulosa) in regions of allopatry with its TTX‐resistant predator, the Common Garter Snake (Thamnophis sirtalis). In sympatry, geographic patterns of phenotypic exaggeration in toxicity and toxin‐resistance are closely correlated in prey and predator, implying that reciprocal selection drives phenotypic variation in coevolutionary traits. Therefore, in allopatry with TTX‐resistant predators, we expect to find uniformly low levels of newt toxicity. We characterized TTX toxicity in northwestern North America, including the Alaskan panhandle where Ta. granulosa occur in allopatry with Th. sirtalis. First, we used microsatellite markers to estimate population genetic structure and determine if any phenotypic variation in toxicity might be explained by historical divergence. We found northern populations of Ta. granulosa generally lacked population structure in a pattern consistent with northern range expansion after the Pleistocene. Next, we chose a cluster of sites in Alaska, which uniformly lacked genetic divergence, to test for phenotypic divergence in toxicity. As predicted, overall levels of newt toxicity were low; however, we also detected unexpected among‐ and within‐population variation in toxicity. Most notably, a small number of individuals contained large doses of TTX that rival means of toxic populations in sympatry with Th. sirtalis. Phenotypic variation in toxicity, despite limited neutral genetic divergence, suggests that factors other than reciprocal selection with Th. sirtalis likely contribute to geographic patterns of toxicity in Ta. granulosa.     

Contrasting geographic patterns of genetic variation for molecular markers vs. phenotypic traits in the energy grass Miscanthus sinensis

Species and hybrids of Miscanthus are a promising energy crop, but their outcrossing mating systems and perennial life cycles are serious challenges for breeding programs. One approach to accelerating the domestication of Miscanthus is to harness the tremendous genetic variation that is present within this genus using phenotypic data from extensive field trials, high‐density genotyping and sequencing technologies, and rapidly developing statistical methods of relating phenotype to genotype. The success of this approach, however, hinges on detailed knowledge about the population genetic structure of the germplasm used in the breeding program. We therefore used data for 120 single‐nucleotide polymorphism and 52 simple sequence repeat markers to depict patterns of putatively neutral population structure among 244 Miscanthus genotypes grown in a field trial near Aberystwyth (UK) and delineate a population of 145 M . sinensis genotypes that will be used for association mapping and genomic selection. Comparative multivariate analyses of molecular marker and phenotypic data for 17 traits related to phenology, morphology/biomass, and cell wall composition revealed significant geographic patterns in this population. A longitudinal cline accounted for a substantial proportion of molecular marker variation (R² = 0.60, P = 3.4 × 10^?15). In contrast, genetic variation for phenotypic traits tended to follow latitudinal and altitudinal gradients, with several traits appearing to have been affected by divergent selection (i.e., Q_ST >> F_ST). These contrasting geographic trends are unusual relative to other plants and provide opportunities for powerful studies of phenotype–genotype associations and the evolutionary history of M. sinensis.     

Natural rewilding of the Great Basin: Genetic consequences of recolonization by black bears (Ursus americanus)

Aim

In the mid‐20th century, many populations of large‐bodied mammals experienced declines throughout North America. Fortunately, within the last several decades, some have begun to rebound and even recolonize extirpated portions of their native range, including black bears (Ursus americanus) in the montane areas of the western Great Basin. In this study, we examine genetic variation in source and recolonized areas to better understand the genetic consequences of recolonization.

Location

Western Great Basin, USA.

Methods

Using multiple loci, we characterized genetic variation among source and recently recolonized areas occupied by black bears, tested for population structure and applied approximate Bayesian computation to test competing hypotheses of demographic history. We assessed signals of gene flow using expectations of genetic consequences derived from alternative modes of recolonization (bottleneck, metapopulation, island model) and tested for significant signals of genetic bottlenecks in areas recently recolonized by black bears.

Results

As anticipated from field survey data and hypothesized expectations, genetic variation of western Great Basin black bears retain an overall signature of demographic decline followed by recent rebound. Furthermore, results reveal that bears in the recolonized range are minimally differentiated from the source area, but newly established subpopulations have lower effective population sizes and reduced allelic diversity. Nevertheless, recolonized areas fail to show a significant signal of a genetic bottleneck. Moreover, bears occupying recolonized areas experience asymmetric gene flow, yielding strong support for a model of genetic connectivity that is best described as a metapopulation.

Main Conclusion

This study presents one of the few empirical examples of genetic consequences of natural recolonization in large‐bodied mammals. Furthermore, these results have implications for understanding the complexities associated with the genetic consequences of recent and ongoing recolonization and highlight the need to develop management strategies uniquely tailored to support connectivity between source and recolonized areas.

     

Phenotypic diversification and island evolution of pipistrelle bats (Pipistrellus pipistrellus group) in the Mediterranean region inferred from geometric morphometrics and molecular phylogenetics

Aim The Mediterranean Basin is a centre of radiation for numerous species groups. To increase our understanding of the mechanisms underlying speciation and radiation events in this region, we assessed the phenotypic variability within the Pipistrellus pipistrellus–pygmaeus–hanaki species complex. Although bats form the second largest mammalian order, studies of insular evolution in this group are scarce. We approached this problem from a microevolutionary perspective and tested for the recurrence of the insular syndrome. Location The Mediterranean Basin, with a special focus on isolated populations from Corsica, the Maghreb, Cyprus, Cyrenaica and Crete. Methods Phenotypic variability was assessed by cranial morphometrics using the coordinates of 41 3D landmarks and associated geometric‐morphometric methods. We analysed 125 specimens representing all of the lineages in the species complex. Differences between taxa and between insular and continental populations in cranial size, shape, form and allometries were tested using analyses of variance and visualized using boxplots and canonical variate analysis. Relationships between molecular data from a previous study (cytochrome b sequences) and morphometric data were tested with co‐inertia analyses (RV test) and multivariate regressions. Results The three species were relatively well differentiated in cranial size and shape, and each species showed a significant amount of inter‐population variability. Comparisons of pairs of insular versus continental populations revealed heterogeneities in cranial patterns among island phenotypes, suggesting no recurrent insular syndrome. Molecular and phenotypic traits were correlated, except for molecular and lateral cranium shape. Main conclusions The Pipistrellus pipistrellus – pygmaeus – hanaki species complex exhibits phenotypic variability as a result of the fragmentation of its distribution (especially on islands), its phylogenetic and phylogeographic history and, most probably, other evolutionary factors that were not investigated in this study. We found no recurrent pattern of evolution on islands, indicating that site‐specific factors play a prevailing role on Mediterranean islands. The correlation between molecular and phenotypic data is incomplete, suggesting that factors other than phylogenetic relationships, potentially connected with feeding ecology, have played a role in shaping cranial morphology in this species complex.     

PHENOTYPIC VARIATION AND GENOTYPIC DIVERSITY IN A PLANKTONIC POPULATION OF THE TOXIGENIC MARINE DINOFLAGELLATE ALEXANDRIUM TAMARENSE (DINOPHYCEAE)1

Multiple clonal isolates from a geographic population of Alexandrium tamarense (M. Lebour) Balech from the North Sea exhibited high genotypic and phenotypic variation. Genetic heterogeneity was such that no clonal lineage was repeatedly sampled according to genotypic markers specified by amplified fragment length polymorphism (AFLP) and microsatellites. Subsampling of genotypic data from both markers showed that ordination of individuals by pair‐wise genetic dissimilarity indices was more reliable by AFLP (482 biallelic loci) than by microsatellites (18 loci). However, resulting patterns of pair‐wise genetic similarities from both markers were significantly correlated (Mantel test P < 0.005). The composition of neurotoxins associated with paralytic shellfish poisoning (PSP) was also highly diverse among these isolates and allowed clustering of toxin phenotypes based on prevalence of individual toxins. Correlation analysis of pair‐wise relatedness of individual clones according to PSP‐toxin profiles and both genotypic characters failed to yield close associations. The expression of allelochemical properties against the cryptophyte Rhodomonas salina (Wis?ouch) D. R. A. Hill et Wetherbee and the predatory dinoflagellate Oxyrrhis marina Dujard. manifested population‐wide variation of responses in the target species, from no visible effect to complete lysis of target cells. Whereas the high genotypic variation indicates high potential for adaptability of the population, we interpret the wide phenotypic variation as evidence for lack of strong selective pressure on respective phenotypic traits at the time the population was sampled. Population markers as applied here may elucidate the ecological significance of respective traits when followed under variable environmental conditions, thereby revealing how variation is maintained within populations.     

Shell morphology and color of the subtidal whelk Buccinum undatum exhibit fine‐scaled spatial patterns

Geographical patterns in morphology can be the result of divergence among populations due to neutral or selective changes and/or phenotypic plasticity in response to different environments. Marine gastropods are ideal subjects on which to explore these patterns, by virtue of the remarkable intraspecific variation in life‐history traits and morphology often observed across relatively small spatial scales. The ubiquitous N‐Atlantic common whelk (Buccinum undatum) is well known for spatial variation in life‐history traits and morphology. Previous studies on genetic population structure have revealed that it exhibits significant differentiation across geographic distances. Within Breiðafjörður Bay, a large and shallow bay in W‐Iceland, genetic differentiation was demonstrated between whelks from sites separated by just 20 km. Here, we extended our previous studies on the common whelk in Breiðafjörður Bay by quantifying phenotypic variation in shell morphology and color throughout the Bay. We sought to test whether trait differentiation is dependent on geographic distance and/or environmental variability. Whelk in Breiðafjörður Bay displayed fine‐scale patterns of spatial variation in shape, thickness, and color diversity. Differentiation increased with increasing distance between populations, indicating that population connectivity is limited. Both shape and color varied along a gradient from the inner part of the bay in the east to the outer part in the west. Whelk shells in the innermost part of Breiðafjörður Bay were thick with an elongate shell, round aperture, and low color diversity, whereas in the outer part of the bay the shells were thinner, rounder, with a more elongate aperture and richer color diversity. Significant site‐specific difference in shell traits of the common whelk in correlation with environmental variables indicates the presence of local ecotypes and limited demographic connectivity.     

Migratory behaviour shapes spatial genetic structure of cyprinid fishes within the Lake Malawi catchment

• Genetic differences among freshwater fish populations are dependent on life‐history characteristics of the species, including the range of adult dispersal and the extent of homing to natal breeding grounds. However, the effects of variation in such characteristics on population genetic connectivity are rarely studied comparatively among closely related species.
• We studied population genetic structure within three congeneric cyprinid species from the Lake Malawi catchment that differ substantially in life‐history traits and conservation status, using a combination of microsatellite and mitochondrial DNA markers. Mpasa (Opsaridium microlepis) is a large (70 cm total length) migratory species that spawns in rivers, but as an adult is exclusively known from the main lake body. Sanjika (Opsaridium microcephalum), is a medium size (30 cm total length) species that exists in lake breeding, river‐lake migratory and apparently landlocked populations. Dwarf sanjika (Opsaridium tweddleorum) is a small non‐migratory species (15 cm total length) that persists in small tributaries surrounding the main lake and adjoining rivers.
• The results revealed striking differences among the three species in spatial genetic structuring. The river‐lake migratory mpasa showed only weak yet significant population genetic structure within the main Lake Malawi catchment, suggesting that there is no strong natal homing. The habitat‐generalist sanjika showed only weak spatial genetic differentiation at microsatellite loci within the Lake Malawi catchment, but moderate structure in mitochondrial DNA, potentially reflecting male‐biased dispersal. The river‐restricted dwarf sanjika showed strong genetic structure in both microsatellite and mitochondrial DNA, suggesting strictly limited dispersal at both adult and juvenile stages.
• We conclude that contrasting migration life histories have resulted in dramatically different patterns of population genetic structure among these congeneric species. The observed patterns demonstrate how divergent life‐history evolution may strongly influence broader patterns of population genetic connectivity in freshwater fish, with consequences for management and conservation. Specifically the results suggesting gene flow among Lake Malawi populations of mpasa, an IUCN red‐listed ‘Endangered’ species endemic to the lake catchment, imply that conservation initiatives operating at both local and catchment scales are needed to reverse local population decline.

     

Morphological and genetic differentiation in populations of the dispersal‐limited coco de mer (Lodoicea maldivica): implications for management and conservation

Aims Developing plant conservation strategies requires knowledge of ecological and genetic processes underlying population dynamics. We aimed to quantify morphological and genetic differentiation among remnant populations of the iconic coco‐de‐mer palm Lodoicea maldivica. We hypothesized that limited gene flow among widely spaced populations would result in high genetic variation and large phenotypic differences among populations. Location Islands of Praslin and Curieuse (CU), Seychelles, Indian Ocean. Methods We conducted an extensive population survey and recorded morphological parameters for 447 Lodoicea in the main populations at Vallée de Mai (VM) and Fond Ferdinand (FF) on Praslin, and on CU. We collected leaf material from 180 trees in these populations for DNA genotyping using amplified fragment length polymorphisms. Results A total of 16,766 Lodoicea trees were recorded in the three populations (72.6% of Lodoicea on both islands). Lodoicea trees at VM and FF showed similar morphology, but differed in most parameters from those at CU, which were shorter, grew more slowly and produced fewer seeds. Mean overall genetic diversity was 0.337, and percentage of polymorphic loci was 91.1. Genetic diversity of the CU population was lower than that at VM and FF. There was weak genetic differentiation between CU and Praslin populations, but 99% of all genetic diversity was within populations. Main conclusions Trees on CU differed in growth and morphology from those of the two Praslin populations. These phenotypic differences, however, were not mirrored in the genetic structure of the populations. All populations were relatively genetically diverse with remarkably little differentiation among populations. This suggests that the capacity of Lodoicea to dominate across a range of habitats may be because of high phenotypic plasticity. High genetic connectivity may be maintained through long‐distance wind pollination. Given the uncertainty about the extent of underlying adaptive variation, we recommend that restoration projects avoid transferring seeds between island populations.     

Biogeography and evolution of the Holarctic zooplankton genus Leptodora (Crustacea: Branchiopoda: Haplopoda)

Aim To reconstruct the phylogeographic history of the Holarctic carnivorous genus Leptodora (Crustacea: Cladocera: Haplopoda). Location We studied the DNA of between one and five specimens each from 28 populations distributed across the Holarctic, but with emphasis on Eurasia. Methods We sequenced a mitochondrial (cytochrome c oxidase subunit I) and a nuclear (elongation factor‐1α) gene, and combined this molecular information with geological and palaeoclimatological data. Haplotype networks and phylogenetic trees were constructed using a Bayesian and maximum likelihood approach. A molecular clock was applied. Results Leptodora consists of three clades (Leptodora kindtii in Europe, Leptodora richardi in China and Japan, and Leptodora sp. in North America), with insular subclades in Japan and in the eastern Mediterranean. The North American clade was not studied in detail. Leptodora richardi is the more thermophilic of the three. It extends from the Tropic of Cancer in the south to the Heilong Basin in the north. The western European L. kindtii is more cold‐water adapted than the eastern Mediterranean subclade. ‘West European’ and ‘Chinese’ clades are broadly separated by a hybrid zone in Siberia and European Russia as far west as the Volga. These hybrids have the mitochondrial DNA of L. kindtii, the nuclear DNA of L. richardi and the low‐temperature preference of L. kindtii, and may have formed as recently as the Holocene hypsithermal. A pure L. kindtii population in the Upper Irtysh catchment, east of the Dzungarian Gates, has been sequestered in endorheic Lake Wulungu, Xinjiang, since the mid‐Pleistocene. Main conclusions Application of a molecular clock places the most recent common ancestor of the North American, East Asian and European populations in the mid‐Miocene. The North American taxon is still living in isolation, while the Eurasian taxa, separated by the Alpine folding, made contact again in the Pleistocene, when the cold‐stenothermic L. kindtii repeatedly moved eastwards across Siberia and back. The population in Xinjiang is a relict of an early wave coming from western Europe: it crossed the Dzungarian Gates during a humid mid‐Pleistocene event, probably corresponding to the Apsheron transgression in the Caspian Basin. Later aridity isolated it there, and it started accumulating private haplotypes. The Holocene Euro‐Siberian hybrid zone may eventually engulf all European populations.     

Cross‐scale effects of structural and functional connectivity in pond networks on amphibian distribution in agricultural landscapes

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Integrative approaches to guide conservation decisions: Using genomics to define conservation units and functional corridors

Climate change and increasing habitat loss greatly impact species survival, requiring range shifts, phenotypic plasticity and/or evolutionary change for long‐term persistence, which may not readily occur unaided in threatened species. Therefore, defining conservation actions requires a detailed assessment of evolutionary factors. Existing genetic diversity needs to be thoroughly evaluated and spatially mapped to define conservation units (CUs) in an evolutionary context, and we address that here. We also propose a multidisciplinary approach to determine corridors and functional connectivity between CUs by including genetic diversity in the modelling while controlling for isolation by distance and phylogeographic history. We evaluate our approach on a Near Threatened Iberian endemic rodent by analysing genotyping‐by‐sequencing (GBS) genomic data from 107 Cabrera voles (Microtus cabrerae), screening the entire species distribution to define categories of CUs and their connectivity: We defined six management units (MUs) which can be grouped into four evolutionarily significant units (ESUs) and three (putatively) adaptive units (AUs). We demonstrate that the three different categories of CU can be objectively defined using genomic data, and their characteristics and connectivity can inform conservation decision‐making. In particular, we show that connectivity of the Cabrera vole is very limited in eastern Iberia and that the pre‐Pyrenean and part of the Betic geographic nuclei contribute the most to the species genetic diversity. We argue that a multidisciplinary framework for CU definition is essential and that this framework needs a strong evolutionary basis.     

High‐resolution genetic analysis reveals extensive gene flow within the jellyfish Pelagia noctiluca (Scyphozoa) in the North Atlantic and Mediterranean Sea

Despite the importance of gelatinous zooplankton as components of marine ecosystems, both ecologically and socio‐economically, relatively little information is known about population persistence or connectivity in jellyfish. In the present study, we employed a combination of nuclear microsatellite markers and sequence data from the mitochondrial cytochrome oxidase I (COI) gene to determine levels and patterns of population genetic structuring in the holoplanktonic jellyfish Pelagia noctiluca across the northeast Atlantic Ocean and Mediterranean Sea. Our results indicate a high degree of connectivity in P. noctiluca, with little evidence of geographical structuring of genetic variation. A small but significant differentiation of Atlantic Ocean and Mediterranean stocks was detected based on the microsatellite data, but no evidence of differentiation was observed with the mtDNA, probably due to the higher power of the microsatellites to detect low levels of genetic structuring. Two clearly distinct groups of genotypes were observed within the mtDNA COI, which probably diverged in the early Pleistocene, but with no evidence of geographical structuring. Palaeodistribution modelling of P. noctiluca at the Last Glacial Maximum (LGM; c. 21 Kya) indicated large areas of suitable habitat south of the species’ current‐day distribution, with little reduction in area. The congruent evidence for minimal genetic differentiation from the nuclear microsatellites and the mtDNA, coupled with the results of the palaeodistribution modelling, supports the idea of long‐term population stability and connectivity, thus providing key insights into the population dynamics and demography of this important species.     

Fine‐scale habitat preferences influence within‐river population connectivity: a case‐study using two sympatric New Zealand Galaxias fish species

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