Spatial genetic analysis of the grass snake,Natrix natrix (Squamata: Colubridae), in an intensively used agricultural landscape

Both the conversion of natural habitats to farmland and efforts at increasing the yield of existing crops contribute to a decline in biodiversity. As a consequence of land conversion, specialised species are restricted to remnants of original habitat patches, which are frequently isolated. This may lead to a genetic differentiation of the subpopulations. We used seven microsatellite markers to examine the genetic population structure of the grass snake, Natrix natrix (Linnaeus, 1758), sampled in remnants of pristine habitat embedded in an intensively used agricultural landscape in north‐western Switzerland. The study area, a former wetland, has been drained and gradually converted into an agricultural plain in the last century, reducing the pristine habitat to approximately 1% of the entire area. The grass snake feeds almost entirely on amphibians, and is therefore associated with wetlands. In Central Europe, the species shows severe decline, most probably as a result of wetland drainage and decrease of amphibian populations. We found no genetically distinct grass snake populations in the study area covering 90 km². This implies that there is an exchange of individuals between small remnants of original habitat. Thus, gene flow may prevent any genetic differentiation of subpopulations distributed over a relatively large area. Our results show that a specialized snake species can persist in an intensively used agricultural landscape, provided that suitable habitat patches are interconnected. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 51–58.     

Fine‐scale patterns of genetic divergence within and between morphologically variable subspecies of the sea urchin Heliocidaris erythrogramma (Echinometridae)

The spatial scale over which genetic divergences occur between populations and the extent that they are paralleled by morphological differences can vary greatly among marine species. In the present study, we use a hierarchical spatial design to investigate genetic structure in Heliocidaris erythrogramma occurring on near shore limestone reefs in Western Australia. These reefs are inhabited by two distinct subspecies: the thick‐spined Heliocidaris erythrogramma armigera and the thin‐spined Heliocidaris erythrogramma erythrogramma, each of which also have distinct colour patterns. In addition to pronounced morphological variation, H. erythrogramma exhibits a relatively short (3–4 days) planktonic phase before settlement and metamorphosis, which limits their capacity for dispersal. We used microsatellite markers to determine whether patterns of genetic structure were influenced more by morphological or life history limitations to dispersal. Both individual and population‐level analyses found significant genetic differentiation between subspecies, which was independent of geographical distance. Genetic diversity was considerably lower within H. e. erythrogramma than within H. e. armigera and genetic divergence was four‐fold greater between subspecies than among populations within subspecies. This pattern was consistent even at fine spatial scales (< 5 km). We did detect some evidence of gene flow between the subspecies; however, it appears to be highly restricted. Within subspecies, genetic structure was more clearly driven by dispersal capacity, although weak patterns of isolation‐by‐distance suggest that there may be other factors limiting gene exchange between populations. Our results show that spatial patterns of genetic structure in Western Australian H. erythrogramma is influenced by a range of factors but is primarily correlated with the distribution of morphologically distinct subspecies. This suggests the presence of reproductive barriers to gene exchange between them and demonstrates that morphological variation can be a good predictor of genetic divergence. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 578–592.     

Genetic and phenotypic differences between thistle populations in response to habitat and weed management practices

Rapid evolutionary change is increasingly being recognized as commonplace, but the evolutionary consequences for species and ecosystems under human‐induced selection regimes have not been explored in detail, although many species occur in such environments. In a common garden experiment and with amplified fragment length polymorphism markers, we examined whether genetic differentiation has taken place between spatially intermixed populations of creeping thistles Cirsium arvense (Asteraceae) collected from a natural habitat (maritime shores), a semi‐natural habitat (road verges) and arable fields under two management regimes: conventional and organic farming. Populations of C. arvense have altered genetically and locally adapted their growth patterns with changed land use. Although plants from different habitats showed similar total biomass production, shoot and root production was higher for maritime populations, suggesting selection for increased competitive ability. Competitive ability then declined in the order semi‐natural, conventional farms and organic farms. Thistles in arable fields may be more selected for tolerance against disturbances from herbicides and mechanical weed control. In addition, early shoot sprouting and genetic analysis showed differentiation between plants originating from conventional farms and farms that were converted to organic 9–30 years ago, suggesting some adaptation to altered crop cultivation practices. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 797–807.     

Geographical and morphological variation within and between colour phases in Coris julis (L. 1758), a protogynous marine fish

The possible differences between sexes in patterns of morphological variation in geographical space have been explored only in gonochorist freshwater species. We explored patterns of body shape variation in geographical space in a marine sequential hermaphrodite species, Coris julis (L. 1758), analyzing variation both within and between colour phases, through the use of geometric morphometrics and spatially‐explicit statistical analyses. We also tested for the association of body shape with two environmental variables: temperature and chlorophyll a concentration, as obtained from time‐series of satellite‐derived data. Both colour phases showed a significant morphological variation in geographical space and patterns of variation divergent between phases. Although the morphological variation was qualitatively similar, individuals in the initial colour phase showed a more marked variation than individuals in the terminal phase. Body shape showed a weak but significant correlation with environmental variables, which was more pronounced in primary specimens. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 148–162.     

Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas)

Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies aiming to evaluate the genetic health of the exploited populations. The present study is based on a set of ten nuclear markers amplified in 331 individuals from ten different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially‐overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and instead showed a large and stable historical effective size. This result could be accounted for by specific life‐history traits (reproduction and longevity) and the limitations of molecular markers in covering recent timescales for nontemporal samples. The findings of the present study emphasize the need to integrate information on effective population sizes and life‐history parameters when evaluating population connectivity levels from genetic data. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 407–418.     

Genetic diversity in Atlantic Forest trees: fragmentation effects on Astronium graveolens (Anacardiaceae) and Metrodorea nigra (Rutaceae), species with distinct seed dispersal strategies

We explore the genetic structure and variability in autochorous Metrodorea nigra (Rutaceae) and anemochorous Astronium graveolens (Anacardiaceae), two species affected by deforestation in the Atlantic Forest of Brazil. The effects of deforestation and the depletion of the habitat within the remaining patches of forest are evaluated by comparing the variability between saplings and adults of each of these two species. The results indicate that the depletion of forest land and the deteriorating condition of the remaining fragments of forest may reduce the level of endogamous breeding in wind‐dispersed species. In autochorous species, the fragmentation of forest land has less notable effects on genetic attributes, but pollen flow could be decreased as a result of the reduced number of insects flying between the forest remnants. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164 , 326–336.     

Microhabitat preferences drive phylogeographic disparities in two Australian funnel web spiders

Comparative phylogeography is underpinned by the assumption that sympatrically‐distributed taxa will have experienced similar environmental histories, resulting in broadly congruent spatial structuring of phylogenetic lineages, particularly if they inhabit similar niches. However, divergent local conditions, specifically those related to microhabitat, may produce significantly divergent systematic signatures of demographic histories. In the present study, we compare the phylogenetic and population genetic spatial patterns displayed by two species of niche‐separated (but sympatrically distributed) Australian funnel web spiders (Mygalomorphae: Hexathelidae). We demonstrate that an apparently minor disparity in habitat niche has led to divergent experiences of a common environmental history in the saproxylic Hadronyche cerberea and the ground‐burrowing Atrax sutherlandi. Furthermore, we take a crucial first step in documenting the molecular systematics of a group that has traditionally suffered from a dearth of research interest. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 805–819.     

Phylogeography and population structure of European sea bass in the north‐east Atlantic

The European sea bass Dicentrarchus labrax represents a historically and commercially valuable species in the north‐east Atlantic, although the demographic history and the patterns of geographical structure of the species in the north‐east Atlantic remain poorly understood. The present study investigates the population genetic structure of sea bass in north‐western European waters, employing different genetic markers [a portion of the mitochondrial (mt)DNA control region and 13 nuclear microsatellites] aiming to unravel demographic history and population connectivity. The results obtained show a previously unrecognized pattern of population divergence at mtDNA, with three strikingly different lineages identified. Extant sea bass populations, including the Mediterranean lineage, derive from an Atlantic ancestor. A much increased number of nuclear microsatellite loci (comparatively to previous studies) still fail to detect biologically meaningful patterns of spatial genetic structuring in the North Atlantic. Past Pleistocene glacial and interglacial events and some degree of female philopatry might be at the basis of the current geographical separation of the Atlantic lineages that has been identified. Signatures of sudden demographic expansions are more evident in the most recent mitochondrial lineages, and their slight, yet significant, geographical segregation leads to the hypothesis that present‐day spawning grounds for European sea bass may still to some extent be linked to their most recent glacial refugia. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 364–377.     

Panmixia on a continental scale in a widely distributed colonial waterbird

Many highly mobile species, such as migratory birds, can move and disperse over long distances, yet exhibit high levels of population genetic structuring. Although movement capabilities may enable dispersal, gene flow may be restricted by behavioural constraints such as philopatry. In the present study, we examined patterns of genetic differentiation across the range of a highly mobile, colonial waterbird. American white pelicans (Pelecanus erythrorhynchos) breed across continental North America and are currently experiencing a range expansion, especially on the eastern range limit. To assess patterns of genetic structuring, we sampled 333 individuals from 19 colonies across their North American range. The use of ten variable microsatellite markers revealed high levels of allelic richness with no population differentiation. Both Bayesian and frequentist approaches to examining genetic structuring revealed a single panmictic population. We found no evidence of genetic structuring across the Continental Divide or between migratory and non‐migratory colonies. The lack of any genetic structure across the range indicates that, unlike other waterbirds with similar life‐history characteristics, extensive gene flow and presumably low philopatry appear to preclude genetic differentiation. The lack of population genetic structure in American white pelicans provides an example of range‐wide panmixia, a rare phenomenon in any terrestrial species. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 583–592.     

Range limits,large‐scale biogeographic variation,and localized evolutionary dynamics in a polymorphic damselfly

Studies of heritable colour polymorphisms allow investigators to track the genetic dynamics of natural populations. By comparing polymorphic populations over large geographic areas and across generations, issues about both morph stability and evolutionary dynamics can be addressed, increasing our understanding of the potential mechanisms maintaining genetic polymorphisms. In the present study, we investigated population morph frequencies in a sex‐limited heritable colour polymorphic damselfly (Ischnura elegans, Vander Linden), with three discrete female morphs. We compared the frequencies of these three female morphs in 120 different populations from ten European countries at differing latitudes and longitudes. There were pronounced differences in morph frequencies both across the entire European biogeographic range, as well as at a smaller scale within regions. We also found considerable between‐population variation at the local scale within regions, particularly at the edges of the range of this species. We discuss these findings in the context of recent models of adaptive population divergence along the range of a species. This polymorphism is thus highly dynamic, with stable morph frequencies at the core of the species range but fluctuating morph dynamics at the range limits. We finish with a discussion of how local interactions and climatic factors can be expected to have a strong influence on the biogeographic patterns in this species and other sexually selected polymorphisms. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 775–785.     

The birth of an endemic species flock: demographic history of the Bellamya group (Gastropoda,Viviparidae) in Lake Malawi

Changes in habitat stability may significantly shape evolutionary patterns and processes in ancient lakes. In the present study, we use a hierarchical combination of molecular phylogenetic and coalescent approaches to investigate the evolutionary history of the endemic species of the gastropod genus Bellamya in the African rift‐lake Malawi. By integrating our findings with reported palaeontological and palaeolimnological data, we demonstrate that all but one evolutionary lineage of the Pliocene Bellamya fauna in Lake Malawi became extinct. Coalescent analyses indicate that the modern radiation underwent both a sudden demographic and a spatial expansion after a genetic bottleneck. We argue that a reflooding of the lake after severe Pleistocene low stands offers a straightforward explanation for this pattern and may have triggered speciation processes in the modern endemic Bellamya radiation in Lake Malawi. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 130–143.     

Colour plasticity and background matching in a threespine stickleback species pair

Examining differences in colour plasticity between closely‐related species in relation to the heterogeneity of background colours found in their respective habitats may offer important insight into how cryptic colour change evolves in natural populations. In the present study, we examined whether nonbreeding dorsal body coloration has diverged between sympatric species of stickleback along with changes in habitat‐specific background colours. The small, limnetic species primarily occupies the pelagic zone and the large, benthic species inhabits the littoral zone. We placed benthic and limnetic sticklebacks against extremes of habitat background colours and measured their degree of background matching and colour plasticity. Benthics matched the littoral background colour more closely than did the limnetics, although there was no difference between species in their resemblance to the pelagic background colour. Benthics were able to resemble both background colours by exhibiting greater directional colour plasticity in their dorsal body coloration than limnetics, which may be an adaptive response to the greater spectral heterogeneity of the littoral zone. The present study highlights how habitat‐specific spectral characteristics may shape cryptic coloration differences between stickleback species. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 902–914.     

Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in South‐East Asia

Tropical rainforests in South‐East Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag‐based simple sequence repeats and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the south‐western part of Borneo, genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28–0.09 million years before present and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.     

Conservation genetics of the rare Iberian endemic Cheirolophus uliginosus (Asteraceae)

Cheirolophus uliginosus is a rare species, endemic to the south‐western Iberian Peninsula, and listed as a characteristic taxon from the temperate Atlantic wet heaths, a priority habitat for conservation by the European Union. The conservation status of this species in most of its distribution area is poorly known, but, in recent times, some populations have disappeared and there has been a reduction in the number of individuals in others. In this context, we analysed the effects of population size on genetic diversity, revealing that genetic erosion and inbreeding depression could be having a significant impact on smaller populations. Furthermore, we studied the patterns of genetic structure and variability at the species level, finding a strikingly low within‐population diversity and high among‐population genetic differentiation. Finally, the genetic structure analyses suggested a long and complex phylogeographical history of C. uliginosus in the region, in agreement with the climate relict status proposed for this species. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 157–171.     

A cryptic genetic boundary in remnant populations of a long‐lived,bird‐pollinated shrub Banksia sphaerocarpa var. caesia (Proteaceae)

Plant species often exhibit genetic structure at multiple spatial scales. Detection of this structure may depend on the sampling strategy used. We intensively sampled a common, naturally patchy Banksia species within a 200 km² region, in order to assess patterns of genetic diversity and structure at multiple spatial scales. In total, 1321 adult shrubs from 37 geographical populations were genotyped using eight highly polymorphic microsatellite markers developed for the species. Genetic structure was detected at three spatial scales. First, we identified a stark and unexpected division of the landscape into two genetic subregions, one to the north‐east and one to the south‐west of the sampling grid. This differentiation was based on sudden, highly structured differences in common allele frequencies, the cause of which is unknown but that may relate to physical and reproductive barriers to gene flow, localised selection, and/or historical processes. Second, we observed genetic differentiation of populations within these subregions, reflecting previously described patterns of restricted pollen flow in this species. Finally, fine‐scale genetic structure, although weak, was observed within some of the populations (mean S_P = 0.01837). When feasible, intensive sampling may uncover cryptic patterns of genetic structure that would otherwise be overlooked when sampling at broader spatial scales. Further studies using a similar sampling strategy may reveal this type of discontinuity to be a feature of other south‐western Australian taxa and has implications for our understanding of evolution in this landscape as well as conservation into the future. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 241–255.     

Long‐term ‘islands’ in the landscape: low gene flow,effective population size and genetic divergence in the shrub Hakea oldfieldii (Proteaceae)

The genetic structure of disjunct populations is determined by founding genetic properties, demographic processes, gene flow, drift and local selection. We aim to identify the genetic consequences of natural population disjunction at regional and local scales in Hakea oldfieldii using nuclear and plastid markers to investigate long‐term effective population sizes and gene flow, and patterns of diversity and divergence, among populations. Regional divergence was significant as shown by a consistent pattern in principal coordinates, neighbor‐joining and Bayesian analyses, but divergence at the local level was also significant with localized distribution of plastid haplotypes and populations clustering separately in Bayesian analyses. Historical, recent and first‐generation gene flow was low, suggesting that recent habitat fragmentation has not reduced gene migration significantly. Genetic bottlenecks were detected in three populations. Long‐term effective population size was significantly correlated with the number of alleles/locus and observed heterozygosity, but not with census population size, suggesting that the loss of diversity is associated with long‐term changes rather than recent fragmentation. Inbreeding coefficients were significant in only three populations, suggesting that the loss of diversity is linked to drift and bottlenecks associated with demographic processes (local extinction by fires) rather than inbreeding. Historical disjunction as a result of specific ecological requirements, contraction of habitats following drying during the Pleistocene, low gene flow and changes in population size are likely to have been important forces driving divergence through isolation by distance and drift. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 319–334.     

Mimetic colour pattern evolution in the highly polymorphic Bombus trifasciatus (Hymenoptera: Apidae) species complex and its comimics

Müllerian mimetic systems have uncovered some of the dynamic processes by which natural selection can drive the radiation of convergent and divergent phenotypes. We examined evolution involving Müllerian mimicry in bumble bees by documenting the distribution and evolution of colour patterns amongst three colour‐polymorphic lineages –Bombus trifasciatus Smith, Bombus haemorrhoidalis Smith, and Bombus breviceps Smith – that mimic each other across ～14 colour groups in South‐East Asia. Using mitochondrial DNA sequence data, we estimated relationships within each lineage to infer the processes that gave rise to the colour diversity and develop hypotheses on species recognition. We expanded on our assessment of species delineation in the B. trifasciatus lineage using three nuclear gene fragments and morphometrics. Comparison of colour patterns amongst georeferenced specimens showed considerable variation in the degree and geographical range of mimicry amongst mimicry groups. Phylogenetic estimates show high rates of colour pattern evolution, with colour variation often exceeding variation within the fast‐evolving mitochondrial genes. The molecular data, and to some degree the morphometric data, support unique histories for several taxa recognized previously within the B. trifasciatus lineage, which may include several species. Early vicariant events within the B. trifasciatus lineage are likely to have occurred ～2.2 Mya in the mountains of south‐west China. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 805–826.     

Dispersal and habitat fidelity of bog and forest growth forms of Hawaiian Metrosideros (Myrtaceae)

The Hawaiian endemic Metrosideros polymorpha is known for its high levels of morphological diversity and localized adaptation to a range of habitats. At the ecotone between bogs and forests, individuals exhibiting morphological extremes can be found within a few metres of each other. The objective of this study was to examine the genetic diversity and structure of morphologically distinct neighbouring populations of M. polymorpha, growing in bogs and adjacent forests across multiple islands. We explored these relationships using the molecular technique of inter‐simple sequence repeats (ISSRs). The majority (90.79%) of genetic variation was found within populations, 8.53% of the differentiation among populations can be attributed to differences between microhabitat types within islands and very little of the genetic differentiation is explained by the differences among islands (0.68%). These high levels of genetic homogeneity across populations could be the result of extensive gene flow and/or recent isolation of populations. We introduce a nearest genetic neighbour (NGN) analysis to examine detailed relationships of dispersal within and among populations by habitat and island. Using this approach, we provide evidence for habitat fidelity within bog populations and a positive correlation between island age and the proportion of same‐island NGNs. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 162 , 558–571.     

Defining the colour pattern phenotype in bumble bees (Bombus): a new model for evo devo

Few insects exhibit the striking colour pattern radiation found in bumble bees (Bombus), which have diversified globally into a wide range of colours and patterns. Their potent sting is often advertised by conspicuous bands of contrasting colour commonly mimicked by scores of harmless (Batesian mimics) and noxious species (Müllerian co‐mimics). Despite extensive documentation of colour pattern diversification, next to nothing is known about the genetic regulation of pattern formation in bumble bees, hindering progress toward a more general model of the evolution of colour pattern mimicry. A critical first step in understanding the colour pattern genotype is an unambiguous understanding of the phenotype under selection, which has not been objectively defined in bumble bees. Here, we quantitatively define the principal colour pattern elements that comprise the phenotype array across all species. Matrix analysis of meticulously scored colour patterns of ～95% of described species indicates there are 12 discrete primary ‘ground plan’ elements in common among all species, many of which correspond to segmentation patterning. Additional secondary elements characterize individual species and geographical variants. The boundaries of these elements appear to correspond to expression patterns of Hox genes in Drosophila and Apis but also suggest novel post‐Hox specialization of abdominal patterning. Our findings provide the first foundation for exploring candidate genes regulating adaptive pattern variation in bumble bees and broaden the framework for understanding common genetic mechanisms of pattern evolution in insects. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 384–404.