Rapidly declining fine-scale spatial genetic structure in female red deer

A growing literature now documents the presence of fine-scale genetic structure in wild vertebrate populations. Breeding population size, levels of dispersal and polygyny--all hypothesized to affect population genetic structure--are known to be influenced by ecological conditions experienced by populations. However the possibility of temporal or spatial variation in fine-scale genetic structure as a result of ecological change is rarely considered or explored. Here we investigate temporal variation in fine-scale genetic structure in a red deer population on the Isle or Rum, Scotland. We document extremely fine-scale spatial genetic structure (< 100 m) amongst females but not males across a 24-year study period during which resource competition has intensified and the population has reached habitat carrying capacity. Based on census data, adult deer were allocated to one of three subpopulations in each year of the study. Global F(ST) estimates for females generated using these subpopulations decreased over the study period, indicating a rapid decline in fine-scale genetic structure of the population. Global F(ST) estimates for males were not different from zero across the study period. Using census and genetic data, we illustrate that, as a consequence of a release from culling early in the study period, the number of breeding females has increased while levels of polygyny have decreased in this population. We found little evidence for increasing dispersal between subpopulations over time in either sex. We argue that both increasing female population size and decreasing polygyny could explain the decline in female population genetic structure.     

New interpretations of fine-scale spatial genetic structure

Recent methodological advances permit refined inferences of evolutionary processes from the fine-scale spatial genetic structure of plant populations. In this issue of Molecular Ecology, Born et al. (2008) exploit the full power of these methods by examining effects of ancient and recent landscape histories in an African rainforest tree species. The authors first detected admixture of distinct gene pools that may have formed in Pleistocene forest refuges. Then, comparing across six study populations in Gabon, the authors found similar patterns of fine-scale spatial genetic structure despite natural and anthropogenic variation in population density. The latter results suggest that enhanced gene dispersal may compensate for low population densities in fragmented landscapes.     

Unexpected population genetic structure of European roe deer in Poland: an invasion of the mtDNA genome from Siberian roe deer

Introgressive hybridization is a widespread evolutionary phenomenon which may lead to increased allelic variation at selective neutral loci and to transfer of fitness‐related traits to introgressed lineages. We inferred the population genetic structure of the European roe deer (Capreolus capreolus) in Poland from mitochondrial (CR and cyt b) and sex‐linked markers (ZFX, SRY, DBY4 and DBY8). Analyses of CR mtDNA sequences from 452 individuals indicated widespread introgression of Siberian roe deer (C. pygargus) mtDNA in the European roe deer genome, 2000 km from the current distribution range of C. pygargus. Introgressed individuals constituted 16.6% of the deer studied. Nearly 75% of them possessed haplotypes belonging to the group which arose 23 kyr ago and have not been detected within the natural range of Siberian roe deer, indicating that majority of present introgression has ancient origin. Unlike the mtDNA results, sex‐specific markers did not show signs of introgression. Species distribution modelling analyses suggested that C. pygargus could have extended its range as far west as Central Europe after last glacial maximum. The main hybridization event was probably associated with range expansion of the most abundant European roe deer lineage from western refugia and took place in Central Europe after the Younger Dryas (10.8–10.0 ka BP). Initially, introgressed mtDNA variants could have spread out on the wave of expansion through the mechanism of gene surfing, reaching high frequencies in European roe deer populations and leading to observed asymmetrical gene flow. Human‐mediated introductions of C. pygargus had minimal effect on the extent of mtDNA introgression.     

Population density and sex do not influence fine-scale natal dispersal in roe deer

It is commonly assumed that the propensity to disperse and the dispersal distance of mammals should increase with increasing density and be greater among males than among females. However, most empirical evidence, especially on large mammals, has focused on highly polygynous and dimorphic species displaying female-defence mating tactics. We tested these predictions on roe deer, a weakly polygynous species of large herbivore exhibiting a resource-defence mating tactic at a fine spatial scale. Using three long-term studies of populations that were subject to the experimental manipulation of size, we did not find any support for either prediction, whether in terms of dispersal probability or dispersal distance. Our findings of similar dispersal patterns in both sexes of roe deer suggest that the underlying cause of natal dispersal is not related to inbreeding avoidance in this species. The absence of positive density dependence in fine-scale dispersal behaviour suggests that roe deer natal dispersal is a pre-saturation process that is shaped by heterogeneities in habitat quality rather than by density per se.     

Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization

In the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immigration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad‐scale geographic origin assignment using nuclear markers to support law enforcement.     

Highly asymmetric fine-scale genetic structure between sexes of African striped mice and indication for condition dependent alternative male dispersal tactics

Sex-biased dispersal is observed in many taxa, but few studies have compared sex-biased dispersal among and within populations. We addressed the magnitude and habitat dependency of sex-biased dispersal in social African striped mice by separating group-related from population-related genetic variance to understand the contribution of each sex to deme structure. As dispersal over unoccupied habitat is likely to be more costly than dispersal within a population, we predicted that individuals leaving the natal population have a lower body condition, being inferior to heavier territorial individuals. Fine-scale genetic structure was detected in both sexes. Female relatedness decreased continuously from R = 0.21 at 25 m to zero at 500 m. Maximum male relatedness R = 0.05 was constant at distances between 25 and 75 m, becoming zero at 100 m. Genetic variance (F(ST) ) among seven locations was significantly higher in females than in males, while inbreeding estimates (F(IS) ) were significantly higher in males than in females. Assignment tests estimated significantly more migrants among males, while Bayesian clustering estimated only a single genetic unit cluster for males among the seven locations. The mean body mass of migrant males (44 g) was significantly lower than for males that remained resident and thus dispersed within their sub-population (48 g). Combined, the results showed habitat-independent male-biased dispersal and high female philopatry, and suggested that body condition was more important than kinship in male dispersal decisions. We suggest that locally inferior males are important for gene flow between sub-populations. Thus, males might follow alternative dispersal tactics.     

Fine-scale social and spatial genetic structure in Sitka black-tailed deer

The spatial extent of Sitka black-tailed deer (Odocoileus hemionus sitkensis) populations below the regional scale is relatively unknown, as is dispersal between populations. Here, we use noninvasive samples to genotype 221 Sitka black-tailed deer in three watersheds on Prince of Wales Island, Alaska, separated by a maximum of 44 km, using traditional and spatial genetic approaches. We find that despite geographic proximity, multiple lines of evidence suggest fine-scale genetic structure among the three study sites. The 2 most geographically distant watersheds differed significantly in genetic composition, suggesting an isolation-by-distance pattern. Within study sites, deer exhibited spatial genetic structure within a radius of 1,000 m. Based on a reduced sample of known-sex individuals, females exhibited positive spatial genetic structure within a radius of 500 m but males showed no structure. Moreover, females were more likely to be related to their 5 nearest female neighbors, regardless of distance, than were males. Evidence indicates dispersal by both sexes although it may be more common, or dispersal distances are greater, in males. Nonetheless, analysis of assignment indices and comparison of sex-specific correlograms found no evidence of sex-biased dispersal between watersheds. Patterns of spatial relatedness and connectivity suggest limited dispersal among Sitka black-tailed deer, creating genetic structure on a fine spatial scale, perhaps as small as the watershed.     

Limited seed dispersal shapes fine-scale spatial genetic structure in a Neotropical dioecious large-seeded palm

Seed and pollen dispersal contribute to gene flow and shape the genetic patterns of plants over fine spatial scales. We inferred fine-scale spatial genetic structure (FSGS) and estimated realized dispersal distances in Phytelephas aequatorialis, a Neotropical dioecious large-seeded palm. We aimed to explore how seed and pollen dispersal shape this genetic pattern in a focal population. For this purpose, we genotyped 138 seedlings and 99 adults with 20 newly developed microsatellite markers. We tested if rodent-mediated seed dispersal has a stronger influence than insect-mediated pollen dispersal in shaping FSGS. We also tested if pollen dispersal was influenced by the density of male palms around mother palms in order to further explore this ecological process in large-seeded plants. Rodent-mediated dispersal of these large seeds occurred mostly over short distances (mean 34.76 ± 34.06 m) while pollen dispersal distances were two times higher (mean 67.91 ± 38.29 m). The spatial extent of FSGS up to 35 m and the fact that seed dispersal did not increase the distance at which male alleles disperse suggest that spatially limited seed dispersal is the main factor shaping FSGS and contributes only marginally to gene flow within the population. Pollen dispersal distances depended on the density of male palms, decreasing when individuals show a clumped distribution and increasing when they are scattered. Our results show that limited seed dispersal mediated by rodents shapes FSGS in P. aequatorialis, while more extensive pollen dispersal accounts for a larger contribution to gene flow and may maintain high genetic diversity. Abstract in Spanish is available with online material.     

Nuclear and chloroplast genetic structure indicate fine-scale spatial dynamics in a neotropical tree population

Dicorynia guianensis is a canopy tree, endemic to the tropical rain forest of French Guiana. We compared generational and spatial genetic structure for maternally and biparentally inherited markers in two cohorts (adult and seedling) in order to infer processes shaping the distribution of genetic diversity. The study was conducted on a 40 ha study plot located at Paracou near Kourou, where 172 adults trees and 375 saplings were sampled. Aggregation of trees was therefore suggested at different distances, ranging from 100 to 400 m. There was a strong link between demographic and genetic spatial structures at small distances (less than 100 m) that is likely to be the consequence of restricted seed dispersal. Genetic differentiation was more pronounced between spatial aggregates than between cohorts. Despite the spatial differentiation, the species was able to maintain high levels of diversity for maternal genomes, suggesting rapid turnover of aggregates. Spatial autocorrelation was larger for chloroplast than nuclear markers indicating a strong asymmetry between pollen and seed flow. Fixation indices indicated a lower heterozygote deficiency for the adults, maybe because of gradual elimination of selfed trees. Genetic relatedness at lower distances was higher in adult trees than in saplings, as a result of generation overlapping in the adult cohort. Overall, our results confirm earlier biological knowledge about the dispersion mechanisms of the species, and lead to an enhanced role of spatial processes in the dynamics of genetic diversity of D. guianensis.     

High genetic diversity and contrasting fine-scale spatial genetic structure in four seasonally dry tropical forest tree species

In this study we compared population structure, genetic diversity and fine-scale spatial genetic structure (SGS) in four Bignoniaceae tree species, Handroanthus chrysotrichus, H. impetiginosus, Tabebuia roseoalba and H. serratifolius in a remnant of seasonally dry tropical forest in Central-West Brazil, based on polymorphisms at six microsatellite loci. All species, except T. roseoalba, presented the inverted ‘J’ population structure indicating recruitment of juveniles. Juveniles presented a clumped distribution suggesting limitation in dispersal or patchy distribution of suitable microhabitat for recruitment. All species showed high levels of polymorphism and genetic diversity but without a clear pattern of distribution among life stages. The SGS was significant for all species, except T. roseoalba, but the pattern and strength of the spatial genetic structure differed among species. Handroanthus serratifolius had stronger SGS with significant kinship until 77 m. For H. impetiginosus and H. chrysotrichus, kinship was significant just until 23 and 6 m, respectively. Despite the high genetic diversity, all species showed low number of adults and high fixation indices suggesting that habitat fragmentation and disturbance have been affecting these populations in Central-West Brazil.     

Analysis of spatial genetic structure in an expanding Pinus halepensis population reveals development of fine-scale genetic clustering over time

We analysed the change of spatial genetic structure (SGS) of reproductive individuals over time in an expanding Pinus halepensis population. To our knowledge, this is the first empirical study to analyse the temporal component of SGS by following the dynamics of successive cohorts of the same population over time, rather than analysing different age cohorts at a single time. SGS is influenced by various factors including restricted gene dispersal, microenvironmental selection, mating patterns and the spatial pattern of reproductive individuals. Several factors that affect SGS are expected to vary over time and as adult density increases. Using air photo analysis, tree-ring dating and molecular marker analysis we reconstructed the spread of reproductive individuals over 30 years beginning from five initial individuals. In the early stages, genotypes were distributed randomly in space. Over time and with increasing density, fine-scale (< 20 m) SGS developed and the magnitude of genetic clustering increased. The SGS was strongly affected by the initial spatial distribution and genetic variation of the founding individuals. The development of SGS may be explained by fine-scale environmental heterogeneity and possibly microenvironmental selection. Inbreeding and variation in reproductive success may have enhanced SGS magnitude over time.     

No genetic correlation between the sexes in mating frequency in the bean beetle, Callosobruchus chinensis

Female multiple mating, which is common in animals, may have evolved not in response to fitness advantages to females but as a genetic corollary to selection on males to mate frequently. This nonadaptive hypothesis assumes a genetic correlation between females and males in mating frequency, which has received a few empirical investigations. We tested this hypothesis by observing the correlated response in male mating frequency in the adzuki bean beetle, Callosobruchus chinensis to artificial selection on female propensity to remate. Compared to control females, females from lines selected for increased or decreased female propensity to remate had, respectively, higher or lower mating frequency measured by the number of mating within a given period. This indicates that female receptivity to remating is genetically correlated with female mating frequency, and thus the artificial selection for female propensity to remate influenced female mating frequency. In contrast, males from the selected lines that diverged in female mating frequency did not vary significantly in their mating frequency. These results indicate that there is no genetic correlation between the sexes in mating frequency in C. chinensis. This study shows that the reason why females in C. chinensis remate despite suffering fitness costs cannot be explained by indirect selection resulting from selection on males to mate multiple times.     

A heterogeneity test for fine-scale genetic structure

For organisms with limited vagility and/or occupying patchy habitats, we often encounter nonrandom patterns of genetic affinity over relatively small spatial scales, labelled fine-scale genetic structure. Both the extent and decay rate of that pattern can be expected to depend on numerous interesting demographic, ecological, historical, and mating system factors, and it would be useful to be able to compare different situations. There is, however, no heterogeneity test currently available for fine-scale genetic structure that would provide us with any guidance on whether the differences we encounter are statistically credible. Here, we develop a general nonparametric heterogeneity test, elaborating on standard autocorrelation methods for pairs of individuals. We first develop a 'pooled within-population' correlogram, where the distance classes (lags) can be defined as functions of distance. Using that pooled correlogram as our null-hypothesis reference frame, we then develop a heterogeneity test of the autocorrelations among different populations, lag-by-lag. From these single-lag tests, we construct an analogous test of heterogeneity for multilag correlograms. We illustrate with a pair of biological examples, one involving the Australian bush rat, the other involving toadshade trillium. The Australian bush rat has limited vagility, and sometimes occupies patchy habitat. We show that the autocorrelation pattern diverges somewhat between continuous and patchy habitat types. For toadshade trillium, clonal replication in Piedmont populations substantially increases autocorrelation for short lags, but clonal replication is less pronounced in mountain populations. Removal of clonal replicates reduces the autocorrelation for short lags and reverses the sign of the difference between mountain and Piedmont correlograms.     

Evolution of population genetic structure of the British roe deer by natural and anthropogenic processes (Capreolus capreolus)

Human influence typically impacts on natural populations of conservation interest. These interactions are varied and sometimes complex, and may be negative and unintended or associated with conservation and management strategy. Understanding the details of how these interactions influence and are influenced by natural evolutionary processes is essential to the development of effective conservation strategies. In this study, we investigate a species in Britain that has experienced both negative impact through overhunting in historical times and management efforts through culls and translocations. At the same time, there are regional populations that have been less affected by human influence. We use mtDNA and nuclear microsatellite DNA markers to investigate patterns of connectivity and diversity and find multiple insular populations in Britain that probably evolved within the Holocene (when the habitat was free of ice). We identify three concurrent processes. First, surviving indigenous populations show highly provincial patterns of philopatry, maintaining and generating population structure on a small geographic scale. Second, founder populations into habitat extirpated of native populations have expanded, but remained largely insular. Third, introductions into established populations generate some admixture. We discuss the implications for the evolution of diversity of the integration of natural processes with anthropogenic influences on population size and distribution.     

Life-history variation following habitat degradation associated with differing fine-scale spatial genetic structure in a rainforest cycad

Habitat degradation can result in drastic environmental changes potentially affecting the life-history of populations and aspects of the reproductive biology and the genetic structure within and among populations. Here, we explore how life-history differences between subpopulations from contrasting habitats may affect mating availability, which in turn will indirectly affect the strength of spatial genetic structure within populations of a tropical rainforest cycad (Zamia fairchildiana). Subpopulations exposed to higher light availability in degraded-forest habitats had male individuals that grew faster, reproduced earlier, and invested more in reproduction than in native-forest habitat subpopulations. These differences in life history resulted in degraded-habitat subpopulations showing a higher proportion of reproductive adults and greater mate availability in a reproductive season. Subpopulations in the degraded habitat showed weaker SGS, i.e., a smaller slope in the linear regression of genetic relatedness on linear distance. Environmentally induced changes in life history and subsequent changes in the strength of the SGS after habitat degradation may have important consequences for population viability and should be of concern in conservation.     

东北地区狍种群的遗传多样性研究

狍为我国重要的经济动物,并且是国家一级保护动物东北虎的主要猎物之一。因此,深入了解狍各地理单元内种群的遗传变异,可以为我们制定保护管理策略提供依据,进而使珍稀濒危物种得到有效的保护和管理。本文对88个不同狍个体(来自8个不同地点)的线粒体DNA控制区的部分序列进行了测定和群体分析,获得了463bp的片断,并检测到59个变异位点,占分析长度的7.84%,且这59个变异位点皆为碱基置换,未出现碱基插入或缺失的现象,定义了30种单倍型,核苷酸多样性平均值为0.02641,种群总体遗传多样性较高。从Tajima’sD和FuandLi’sD值的估算结果来看,这8个狍种群相对于中性进化的歧异度并没有明显的偏离(P0.1),没有明显的证据显示这8个狍种群间存在很强的平衡选择。30个单倍型整体上将东北狍种群分为3个亚群,分子变异分析表明3个亚群间基因流Nm均大于1,说明这3个狍亚群间存在着基因流。     

Microsatellites reveal fine-scale genetic structure in stream-living brown trout

Multilocus F _ST estimates revealed a pronounced genetic structure at six microsatellite loci in brown trout Salmo trutta in Nordre Finnvikelv, with at least three breeding units that remained stable over time. Significant differences in allele frequencies were found between five sections within a 3-km range, even when no physical barriers prevented fish from migrating between sections. It is argued that geological structures may rise to patterns resembling isolation by distance. Seemingly, the most important factor causing genetic differentiation in Nordre Finnvikelv is genetic drift in small populations that are geologically subdivided by a tributary and by impassable waterfalls. Some correlation between previous behavioural observations and genetic structures were found.