Spatial and demographic population genetic structure in Catasetum viridiflavum across a human-disturbed habitat

Spatial and temporal genetic structures were examined across sites on islands and mainland (continuous forest) populations of an epiphytic orchid, Catasetum viridiflavum, using 17 polymorphic allozyme loci. I tested whether patches on islands or at mainland sites comprised small local populations or a large population. Low among population differentiation was observed across the landscape suggesting that the species-specific pollinator and tiny wind-dispersed seeds maintain interconnections among distant patches. Temporal genetic structure among stage classes, and among breeding individuals are important components of the maintenance of genetic variation in this orchid. The natural history of this species including small breeding populations, probable high frequency of mating among relatives, and the high rates of seed movement among sites contribute to the high FIS. These data show that physically isolated patches in this epiphytic orchid comprise a single larger genetic population, which is independent of the physical distances among sites. Although quite different in ecological and life history characteristics, the genetic structure of this orchid demonstrates a pattern similar to temperate and tropical trees in fragmented landscapes.     

Fine-scale population genetic structure in a fission-fusion society

Nonrandom patterns of mating and dispersal create fine-scale genetic structure in natural populations — especially of social mammals — with important evolutionary and conservation genetic consequences. Such structure is well-characterized for typical mammalian societies; that is, societies where social group composition is stable, dispersal is male-biased, and males form permanent breeding associations in just one or a few social groups over the course of their lives. However, genetic structure is not well understood for social mammals that differ from this pattern, including elephants. In elephant societies, social groups fission and fuse, and males never form permanent breeding associations with female groups. Here, we combine 33 years of behavioural observations with genetic information for 545 African elephants ( Loxodonta africana ), to investigate how mating and dispersal behaviours structure genetic variation between social groups and across age classes. We found that, like most social mammals, female matrilocality in elephants creates co-ancestry within core social groups and significant genetic differentiation between groups (Φ_ST = 0.058). However, unlike typical social mammals, male elephants do not bias reproduction towards a limited subset of social groups, and instead breed randomly across the population. As a result, reproductively dominant males mediate gene flow between core groups, which creates cohorts of similar-aged paternal relatives across the population. Because poaching tends to eliminate the oldest elephants from populations, illegal hunting and poaching are likely to erode fine-scale genetic structure. We discuss our results and their evolutionary and conservation genetic implications in the context of other social mammals.     

Fine-scale spatial genetic structure in mixed oak stands with different levels of hybridization

Oaks are model species for the study of natural introgressive hybridization. High interfertility among oak taxa might result in collective evolution, through transpecific spread of advantageous alleles, challenging the standard concept of species. Nine highly polymorphic microsatellite (nuSSR) loci were analysed in three mixed oak populations of Quercus pyrenaica and Quercus petraea (Montejo, Somosierra and Robregordo) with different density and hybridization rates. Both leaf morphology and molecular markers were used to assess individual admixture rates. Insights about the relative effect of density and hybridization rates on fine-scale spatial genetic structure (SGS) were obtained from autocorrelograms and Sp statistics. Differences in SGS among populations were higher than between species. These differences cannot be attributed solely to census densities but also relate to other factors, such as the spatial configuration of the population. Hybridization was an important factor shaping within-population spatial genetic structure, and an interspecific component of SGS was found in Somosierra. Indirect estimates of historical gene flow in Montejo were compared with actual values of gene dispersal assessed by parentage analysis in a former study. Similar values were found for current and historical gene flow in both species, which might reflect demographical stability.     

Fine-scale spatial genetic structure and gene flow in a small, fragmented population of Sinojackia rehderiana (Styracaceae), an endangered tree species endemic to China

Populations of Sinojackia rehderiana are highly threatened and have small and scattered distribution due to habitat fragmentation and human activities. Understanding changes in genetic diversity, the fine-scale spatial genetic structure (SGS) at different life stages and gene flow of S. rehderiana is critical for developing successful conservation strategies for fragmented populations of this endangered species. In this study, 208 adults, 114 juveniles and 136 seedlings in a 50 × 100-m transect within an old-growth forest were mapped and genotyped using eight microsatellite makers to investigate the genetic diversity and SGS of this species. No significant differences in genetic diversity among different life-history stages were found. However, a significant heterozygote deficiency in adults and seedlings may result from substantial biparental inbreeding. Significant fine-scale spatial structure was found in different life-history stages within 19 m, suggesting that seed dispersal mainly occurred near a mother tree. Both historical and contemporary estimates of gene flow (13.06 and 16.77 m) indicated short-distance gene dispersal in isolated populations of S. rehderiana. The consistent spatial structure revealed in different life stages is most likely the result of limited gene flow. Our results have important implications for conservation of extant populations of S. rehderiana. Measures for promoting pollen flow should be taken for in situ conservation. The presence of a SGS in fragmented populations implies that seeds for ex situ conservation should be collected from trees at least 19-m apart to reduce genetic similarity between neighbouring individuals.     

Fine-scale genetic structure and dispersal in cooperatively breeding apostlebirds

In cooperatively breeding species, restricted dispersal of offspring leads to clustering of closely related individuals, increasing the potential both for indirect genetic benefits and inbreeding costs. In apostlebirds (Struthidea cinerea), philopatry by both sexes results in the formation of large (up to 17 birds), predominantly sedentary breeding groups that remain stable throughout the year. We examined patterns of relatedness and fine-scale genetic structure within a population of apostlebirds using six polymorphic microsatellite loci. We found evidence of fine-scale genetic structure within the study population that is consistent with behavioural observations of short-distance dispersal, natal philopatry by both sexes and restricted movement of breeding groups between seasons. Global F(ST) values among breeding groups were significantly positive, and the average level of pairwise relatedness was significantly higher for individuals within groups than between groups. For individuals from different breeding groups, geographical distance was negatively correlated with pairwise relatedness and positively correlated with pairwise F(ST). However, when each sex was examined separately, this pattern was significant only among males, suggesting that females may disperse over longer distances. We discuss the potential for kin selection to influence the evolution and maintenance of cooperative breeding in apostlebirds. Our results demonstrate that spatial genetic structural analysis offers a useful alternative to field observations in examining dispersal patterns of cooperative breeders.     

Fine-scale population genetic structure and sex-biased dispersal in the smooth snake (Coronella austriaca) in southern England

Human-induced alteration of natural habitats has the potential to impact on the genetic structuring of remnant populations at multiple spatial scales. Species from higher trophic levels, such as snakes, are expected to be particularly susceptible to land-use changes. We examined fine-scale population structure and looked for evidence of sex-biased dispersal in smooth snakes (Coronella austriaca), sampled from 10 heathland localities situated within a managed coniferous forest in Dorset, United Kingdom. Despite the limited distances between heathland areas (maximum <6 km), there was a small but significant structuring of populations based on eight microsatellite loci. This followed an isolation-by-distance model using both straight line and 'biological' distances between sampling sites, suggesting C. austriaca's low vagility as the causal factor, rather than closed canopy conifer forest exerting an effect as a barrier to dispersal. Within population comparisons of male and female snakes showed evidence for sex-biased dispersal, with three of four analyses finding significantly higher dispersal in males than in females. We suggest that the fine-scale spatial genetic structuring and sex-biased dispersal have important implications for the conservation of C. austriaca, and highlight the value of heathland areas within commercial conifer plantations with regards to their future management.     

Population genetic structure and dispersal across a fragmented landscape in cerulean warblers (<Emphasis Type="Italic">Dendroica cerulea</Emphasis>)

Cerulean warblers (Dendroica cerulea) have experienced significant declines across their breeding range and presently exist in disjunct populations, largely because of extensive loss and fragmentation of their breeding and wintering habitat. Despite this overall decline, a recent north-eastern expansion of the breeding range has been proposed, and some researchers have suggested that the eastern Ontario population may be acting as a source population maintaining sink populations elsewhere. However, little is known about either the geographic distribution of genetic variation or dispersal in these birds. We assayed variation in five microsatellite loci and a 366 base-pair fragment of the mitochondrial control region among 154 cerulean warblers from five populations throughout the breeding range. No evidence of population genetic structure was found. Assignment tests suggested that six individuals were either inter-population migrants or descendants of recent migrants. The lack of population genetic structure is probably due to a combination of historical association and contemporary dispersal. Population decline does not appear to have reduced genetic variation yet. Overall results suggest that cerulean warblers from Ontario, Illinois, Arkansas and Tennessee should be considered a single genetic management unit for conservation.     

Unexpected persistence on habitat islands: genetic signatures reveal dispersal of a eucalypt-dependent marsupial through a hostile pine matrix

Several factors contribute to the extinction of populations in fragmented habitat but key ones include habitat loss and disruptions to connectivity. Aspects of the ecology of greater gliders (Petauroides volans), along with observations of their response to native forest clearance at a site in southeastern Australia, lead to the prediction in the 1960s that the species would not persist in the replacement exotic pine plantation. However, 35 years later, the species was observed in many remnant native vegetation patches retained within the plantation boundary, albeit at a lower occupancy rate than at matched continuous forest control sites. To determine the role of patch connectivity in persistence of P. volans in remnants, we employed 12 microsatellite markers to genotype individuals from 11 remnants, three contemporary nearby continuous native eucalypt forest sites and a sample collected during native vegetation clearance at the site in the 1960s. Patch samples retained substantially more genetic diversity than expected under an isolation model, suggesting that patches have experienced some immigration. Five putative patch immigrants--two from sampled sites 1- and 7-km distant, and three from unresolved or unsampled localities--were identified via genetic parentage and population assignment analyses. Patch populations displayed varying levels of admixture in Bayesian genetic structure analyses, with the oldest and most geographically isolated ones showing the least admixture, suggesting they have experienced relatively little immigration. Evidence of at least some immigration into patches may explain why P. volans has persisted contrary to expectation in heavily fragmented habitat.     

Fine-scale genetic structure of life history stages in the food-deceptive orchid Orchis purpurea

In natural plant populations, fine-scale spatial genetic structure can result from limited gene flow, selection pressures or historical events, but the role of each factor is in general hard to discern. One way to investigate the origination of spatial genetic structure within a plant population consists of comparing spatial genetic structure among different life history stages. In this study, spatial genetic structure of the food-deceptive orchid Orchis purpurea was determined across life history stages in two populations that were regenerating after many years of population decline. Based on demographic analyses (2001-2004), we distinguished between recruits and adult plants. For both sites, there was no difference in the proportion of polymorphic loci and expected heterozygosity between life history stages. However, spatial autocorrelation analyses showed that spatial genetic structure increased in magnitude with life history stage. Weak or no spatial genetic structure was observed for recruits, whereas adult plants showed a pattern that is consistent with that found in other species with a predominantly outcrossing mating system. The observed differences between seedlings and adults are probably a consequence of changes in management of the two study sites and associated demographic changes in both populations. Our results illustrate that recurrent population crashes and recovery may strongly affect genetic diversity and fine-scale spatial genetic structure of plant populations.     

Significant genetic boundaries and spatial dynamics of giant pandas occupying fragmented habitat across southwest China

Understanding population history and genetic structure are key drivers of ecological research. Here, we studied two highly fragmented and isolated populations (Xiaoxiangling and Daxiangling) of giant pandas (Ailuropoda melanoleuca) at the extreme southwestern edge of their distribution. This area also contains the Dadu River, national road 108 and various human infrastructure and development, providing an ideal region in which we can identify the effects of different barriers on animal movements. We used partial mitochondrial control region (mtDNA) and nine microsatellite loci (nuclear DNA) data derived from 192 faecal and one blood sample collected from the wild. We found 136 genotypes corresponding to 53 unique multilocus genotypes and eight unique control region haplotypes (653 bp). Significant genetic boundaries correlated spatially with the Dadu River (K = 2). We estimate that a major divergence took place between these populations 26,000 years bp, at around the similar time the rock surface of valley bottom formed in Dadu River. The national road has resulted in further recent population differentiation (Pairwise F(S) on mtDNA and nuclear DNA) so that in effect, four smaller sub-populations now exist. Promisingly, we identified two possible first-generation migrants and their migration paths, and recommended the immediate construction of a number of corridors. Fortunately, the Chinese government has accepted our advice and is now planning corridor construction.     

Male-biased dispersal in a tropical Australian snake (Stegonotus cucullatus, Colubridae)

Sex-based differences in dispersal distances can affect critical population parameters such as inbreeding rates and the spatial scale of local adaptation. Males tend to disperse further than females in mammals, whereas the reverse is true for birds; too few reptiles have been studied to reveal generalities for that group. Although reptiles are most diverse and abundant in the tropics, few tropical reptiles have been studied in this respect. We combine data from a long-term (10-year) mark–recapture study with genetic information (based on nine microsatellite markers) on slatey-grey snakes ( Stegonotus cucullatus , Colubridae) in the Australian wet-dry tropics. Males attain larger body sizes than females, and both genetic and mark–recapture data show that males also disperse further than females. Recapture records show that hatchling males dispersed away from their release points whereas hatchling females did not, and adult males moved further than adult females. In the genetic analysis, males contributed less to overall F _ST and relatedness than did females ( F _STm = 0.0025, F _STf = 0.0275, P  < 0.001; r _m = 0.0053; r _f = 0.0550; P  < 0.001). Spatial autocorrelation analyses within the largest population revealed a similar pattern, with spatial structuring stronger for females than males. Overall, our genetic analyses not only supported the mark–recapture data, but also extended our insights by revealing occasional long-distance dispersal not detected by the mark–recapture study.     

Landscape, habitat characteristics and the genetic population structure of two caddisflies

1. In a region of south‐eastern England, we investigated the hierarchical genetic structure of populations of two stream‐dwelling caddisflies (Trichoptera: Polycentropodidae) with contrasting distributions: Plectrocnemia conspersa inhabits numerous small, patchily distributed seeps and streams, while the confamilial Polycentropus flavomaculatus is found in fewer but larger streams and rivers. We also contrasted the genetic structure of P. conspersa in the lowland south‐east with that in an upland region in the north west. 2. Microsatellite genotypes were obtained from samples of both species taken from a ‘core area’ and at sites 15, 40 and 100 km from this core (two regions for P. conspersa, totalling 45 sites and 1405 larvae; one region for P. flavomaculatus, totalling 10 sites and 269 larvae). 3. The genetic structure of P. conspersa differed in the two regions. In the upland north‐west, significant genetic differentiation was observed at a spatial scale of around 40 km from the core, while there was no structure in the lowland south‐east up to around 100 km. Areas of high altitude did not appear directly to reduce gene flow, whereas other potential landscape barriers, including particular geological formations, large urban areas and the sea had a pronounced effect. 4. Weak genetic differentiation in P. conspersa across large distances, particularly in the lowland south‐east, suggests that it disperses strongly, facilitating gene flow within and between catchments. Conversely, for P. flavomaculatus we found strong genetic differentiation between almost all sites, suggesting that dispersal is much more limited. 5. Greater dispersal in the patchily distributed P. conspersa than in P. flavomaculatus, which occupies larger and presumably more persistent habitats, could be a general feature of other similarly distributed aquatic insects. While higher relief is potentially a partial barrier to dispersal, P. conspersamust have effective gene flow through such apparently inhospitable terrain, perhaps attributable to dispersal between neighbouring small and ephemeral populations. Indeed, its exploitation of headwaters and seeps requires the ability to disperse between such sites. Apparently it cannot, however, overcome more continuous barriers, consisting of large tracts of landscape with few habitable larval sites. Such landscapes, including those created by humans, may have a stronger effect on population connectivity and colonization in the longer term.     

Microsatellite analysis of demographic genetic structure in fragmented populations of the tropical tree Symphonia globulifera

We developed genetic markers for three microsatellite loci in the tropical tree Symphonia globulifera and used them to examine the demographic genetic consequences of forest fragmentation. High levels of genetic variation were revealed in samples of adults, saplings, and seedlings. The more-variable loci exhibited less stability in allelic composition across sites and stages. The number of alleles per hectare (ha) of forest was similar when continuous forest plots were compared to plots from fragmented forest for all three stages. This pattern also held for the number of unique multilocus adult and sapling genotypes, but the number of unique seedling genotypes per ha of fragmented forest greatly exceeded expectations based on continuous forest data, probably due to the concentration of seeds into remnant forest patches by foraging bats. Significant inbreeding and genetic differentiation were most often associated with the fragmented forest and the seedlings. Finally, principal component analysis reaffirmed that a bottleneck, acting in concert with pre-existing genetic structure in the adults, had led to enhanced and rapid divergence in the seedlings following deforestation, a result that is of central interest for landscape management.     

Rolling stones and stable homes: social structure,habitat diversity and population genetics of the Hawaiian spinner dolphin (Stenella longirostris)

Spinner dolphins (Stenella longirostris) exhibit different social behaviours at two regions in the Hawaiian Archipelago: off the high volcanic islands in the SE archipelago they form dynamic groups with ever‐changing membership, but in the low carbonate atolls in the NW archipelago they form long‐term stable groups. To determine whether these environmental and social differences influence population genetic structure, we surveyed spinner dolphins throughout the Hawaiian Archipelago with mtDNA control region sequences and 10 microsatellite loci (n = 505). F‐statistics, Bayesian cluster analyses, and assignment tests revealed population genetic separations between most islands, with less genetic structuring among the NW atolls than among the SE high islands. The populations with the most stable social structure (Midway and Kure Atolls) have the highest gene flow between populations (mtDNA Φ_ST < 0.001, P = 0.357; microsatellite F_ST = ?0.001; P = 0.597), and a population with dynamic groups and fluid social structure (the Kona Coast of the island of Hawai’i) has the lowest gene flow (mtDNA 0.042 < Φ_ST < 0.236, P < 0.05; microsatellite 0.016 < F_ST < 0.040, P < 0.001). We suggest that gene flow, dispersal, and social structure are influenced by the availability of habitat and resources at each island. Genetic comparisons to a South Pacific location (n = 16) indicate that Hawaiian populations are genetically depauperate and isolated from other Pacific locations (mtDNA 0.216 < F_ST < 0.643, P < 0.001; microsatellite 0.058 < F_ST < 0.090, P < 0.001); this isolation may also influence social and genetic structure within Hawai’i. Our results illustrate that genetic and social structure are flexible traits that can vary between even closely‐related populations.     

Fine-scale genetic structuring in a natural population of European wild rabbits (Oryctolagus cuniculus)

The genetic structure of a free-living tagged population of European wild rabbits (Oryctolagus cuniculus) was investigated for two consecutive years (1990 and 1991) using 10 polymorphic microsatellite loci. A specific social behaviour, the formation of stable breeding groups, influenced the genetic structure of the population. These breeding groups were shown to constitute genetically differentiated units with low levels of gene flow between them. The average relatedness among members of a social group was higher than within the population as a whole. As a result of female philopatry coupled with male-biased natal dispersal, the relatedness of females was higher than that of males, both within social groups and in the whole population. Furthermore, the average relatedness of females within groups was twice the relatedness of females between groups. This study reveals marked fine-scale, intrapopulation genetic structure, which is attributable to the social behaviour of the European wild rabbit.     

Historical habitat connectivity affects current genetic structure in a grassland species

Many recent studies have explored the effects of present and past landscape structure on species distribution and diversity. However, we know little about the effects of past landscape structure on distribution of genetic diversity within and between populations of a single species. Here we describe the relationship between present and past landscape structure (landscape connectivity and habitat size estimated from historical maps) and current genetic structure in a perennial herb, Succisa pratensis. We used allozymes as co‐dominant markers to estimate genetic diversity and deviation from Hardy–Weinberg equilibrium in 31 populations distributed within a 5 km² agricultural landscape. The results showed that current genetic diversity of populations was related to habitat suitability, habitat age, habitat size and habitat connectivity in the past. The effects of habitat age and past connectivity on genetic diversity were in most cases also significant after taking the current landscape structure into account. Moreover, current genetic similarity between populations was affected by past connectivity after accounting for current landscape structure. In both cases, the oldest time layer (1850) was the most informative. Most populations showed heterozygote excess, indicating disequilibrium due to recent gene flow or selection against homozygotes. These results suggest that habitat age and past connectivity are important determinants of distribution of genetic diversity between populations at a scale of a few kilometres. Landscape history may significantly contribute to our understanding of distribution of current genetic structure within species and the genetic structure may be used to better understand landscape history, even at a small scale.     

Low genetic variability, female-biased dispersal and high movement rates in an urban population of Eurasian badgers Meles meles

1. Urban and rural populations of animals can differ in their behaviour, both in order to meet their ecological requirements and due to the constraints imposed by different environments. The study of urban populations can therefore offer useful insights into the behavioural flexibility of a species as a whole, as well as indicating how the species in question adapts to a specifically urban environment. 2. The genetic structure of a population can provide information about social structure and movement patterns that is difficult to obtain by other means. Using non-invasively collected hair samples, we estimated the population size of Eurasian badgers Meles meles in the city of Brighton, England, and calculated population-specific parameters of genetic variability and sex-specific rates of outbreeding and dispersal. 3. Population density was high in the context of badger densities reported throughout their range. This was due to a high density of social groups rather than large numbers of individuals per group. 4. The allelic richness of the population was low compared with other British populations. However, the rate of extra-group paternity and the relatively frequent (mainly temporary) intergroup movements suggest that, on a local scale, the population was outbred. Although members of both sexes visited other groups, there was a trend for more females to make intergroup movements. 5. The results reveal that urban badgers can achieve high densities and suggest that while some population parameters are similar between urban and rural populations, the frequency of intergroup movements is higher among urban badgers. In a wider context, these results demonstrate the ability of non-invasive genetic sampling to provide information about the population density, social structure and behaviour of urban wildlife.     

Decreased relatedness between male prickly forest skinks(<Emphasis Type=BoldItalic>Gnypetoscincus queenslandiae</Emphasis>) in habitat fragments

In species with low levels of dispersal the chance of closely related individuals breeding may be a potential problem; sex-biased dispersal is a mechanism that may decrease the possibility of cosanguineous mating. Fragmentation of the habitat in which a species lives may affect mechanisms such as sex-biased dispersal, which may in turn exacerbate more direct effects of fragmentation such as decreasing population size that may lead to inbreeding depression. Relatedness statistics calculated using microsatellite DNA data showed that rainforest fragmentation has had an effect on the patterns of dispersal in the prickly forest skink (Gnypetoscincus queenslandiae), a rainforest endemic of the Wet Tropics of north eastern Australia. A lower level of relatedness was found in fragments compared to continuous forest sites due to a significantly lower level of pairwise relatedness between males in rainforest fragments. The pattern of genetic relatedness between sexes indicates the presence of male-biased dispersal in this species, with a stronger pattern detected in populations in rainforest fragments. Male prickly forest skinks may have to move further in fragmented habitat in order to find mates or suitable habitat logs.     

Spatial genetic structure of a small rodent in a heterogeneous landscape

Gene flow in natural populations may be strongly influenced by landscape features. The integration of landscape characteristics in population genetic studies may thus improve our understanding of population functioning. In this study, we investigated the population genetic structure and gene flow pattern for the common vole, Microtus arvalis, in a heterogeneous landscape characterised by strong spatial and temporal variation. The studied area is an intensive agricultural zone of approximately 500 km² crossed by a motorway. We used individual-based Bayesian methods to define the number of population units and their spatial borders without prior delimitation of such units. Unexpectedly, we determined a single genetic unit that covered the entire area studied. In particular, the motorway considered as a likely barrier to dispersal was not associated with any spatial genetic discontinuity. Using computer simulations, we demonstrated that recent anthropogenic barriers to effective dispersal are difficult to detect through analysis of genetic variation for species with large effective population sizes. We observed a slight, but significant, pattern of isolation by distance over the whole study site. Spatial autocorrelation analyses detected genetic structuring on a local scale, most probably due to the social organisation of the study species. Overall, our analysis suggests intense small-scale dispersal associated with a large effective population size. High dispersal rates may be imposed by the strong spatio-temporal heterogeneity of habitat quality, which characterises intensive agroecosystems.