Low genetic diversity and high genetic divergence caused by inbreeding and geographical isolation in the populations of endangered species Loropetalum subcordatum (Hamamelidaceae) endemic to China

Loropetalum subcordatum (Hamamelidaceae) is one of the most endangered angiosperm species in China. It is narrowly distributed in a few localities in the evergreen broadleaved forest of southern China. Up to now only a few dozen remnant individuals have been found in the four extant populations. In this project, we studied its genetic diversity and population genetic structure using the high resolution molecular marker of amplified fragment length polymorphism. In total, 47 individuals from all the four populations (including all individuals in three populations) were analyzed. Comparably low genetic diversity within populations was revealed and significantly high genetic differentiation among the populations was detected. Four independent groups were identified which corresponded with their geographical ranges. Autogamy is considered to be the major factor contributing to the low genetic variation and high genetic divergence within this species. In addition, small population size, restricted distribution range, geographical isolation and limited seed dispersal may also contribute to the low genetic diversity and high population genetic differentiation. Clonal reproduction was inferred to occur in the two island populations. Suggestions for conservation strategies are provided to preserve the genetic resources of this species.     

Phylogeography and genetic effects of habitat fragmentation on endangered Taxus yunnanensis in southwest China as revealed by microsatellite data

It is not known how the profoundly complex topography and habitat heterogeneity generated by the uplift of the Qinghai‐Tibetan Plateau (QTP) during the late Tertiary affected population genetic structure of endangered Taxus yunnanensis. In addition, the effects of habitat fragmentation due to anthropogenic disturbance on genetic diversity and population differentiation of this species have not been studied. T. yunnanensis is an ancient tree/shrub mainly distributed in southwest China. Recently, the species has suffered a sharp decline due to excessive logging for its famous anticancer metabolite taxol, resulting in smaller and more isolated populations. To understand the phylogeography and genetic consequences of habitat fragmentation of this endangered species, using 11 polymorphic microsatellites, we genotyped 288 individuals from 14 populations from a range‐wide sampling in China. Our results suggest that two different population groups that were once isolated have persisted in situ during glacial periods in both areas, and have not merged since. Habitat fragmentation has led to significant genetic bottlenecks, high inbreeding and population divergence in this species. The two different population groups of T. yunnanensis could be attributed to restricted gene flow caused through isolation by geographical barriers and by habitat heterogeneity during uplift of the QTP, or the existence of two separate glacial refugia during the Pleistocene. In situ and ex situ conservation of the two Evolutionarily Significant Units (ESUs), artificial gene flow between populations and a comprehensive understanding of the pollination system in this endangered species are suggested from this study.     

Landscape scale genetic effects of habitat fragmentation on a high gene flow species: Speyeria idalia (Nymphalidae)

Detection of the genetic effects of recent habitat fragmentation in natural populations can be a difficult task, especially for high gene flow species. Previous analyses of mitochondrial DNA data from across the current range of Speyeria idalia indicated that the species exhibited high levels of gene flow among populations, with the exception of an isolated population in the eastern portion of its range. However, some populations are found on isolated habitat patches, which were recently separated from one another by large expanses of uninhabitable terrain, in the form of row crop agriculture. The goal of this study was to compare levels of genetic differentiation and diversity among populations found in relatively continuous habitat to populations in both recently and historically isolated habitat. Four microsatellite loci were used to genotype over 300 individuals from five populations in continuous habitat, five populations in recently fragmented habitat, and one historically isolated population. Results from the historically isolated population were concordant with previous analyses and suggest significant differentiation. Also, microsatellite data were consistent with the genetic effects of habitat fragmentation for the recently isolated populations, in the form of increased differentiation and decreased genetic diversity when compared to nonfragmented populations. These results suggest that given the appropriate control populations, microsatellite markers can be used to detect the effects of recent habitat fragmentation in natural populations, even at a large geographical scale in high gene flow species.     

Population genetic effects of urban habitat fragmentation in the perennial herb Viola pubescens (Violaceae) using ISSR markers

BACKGROUND AND AIMS: Fragmentation of natural habitats can negatively impact plant populations by leading to reduced genetic variation and increased genetic distance as populations become geographically and genetically isolated from one another. To test whether such detrimental effects occur within an urban landscape, the genetic structure of six populations of the perennial herb Viola pubescens was characterized in the metropolitan area of Greater Cincinnati in southwestern Ohio, USA. METHODS: Using three inter-simple sequence repeat (ISSR) markers, 51 loci amplified across all urban populations. For reference, four previously examined agricultural populations in central/northern Ohio and a geographically distant population in Michigan were also included in the analysis. KEY RESULTS: Urban populations retained high levels of genetic variation (percentage of polymorphic loci, P(p) = 80.7 %) with similar genetic distances among populations and an absence of unique alleles. Geographic and genetic distances were correlated with one another, and all populations grouped according to region. Individuals from urban populations clustered together and away from individuals from agricultural populations and from the Michigan population in a principle coordinates analysis. Hierarchical analysis of molecular variance (AMOVA) revealed that most of the genetic variability was partitioned within populations (69.1 %) and among groups (22.2 %) of southwestern Ohio, central/northern Ohio and Michigan groups. Mean F(st) was 0.308, indicating substantial population differentiation. CONCLUSIONS: It is concluded that urban fragmentation does not appear to impede gene flow in V. pubescens in southwestern Ohio. These results are consistent with life history traits of this species and the possibility of high insect abundance in urban habitats due to diverse floral resources and nesting sites. Combined with the cleistogamous breeding system of this species, pollinator availability in the urban matrix may buffer populations against detrimental effects of habitat fragmentation, at least in larger forest fragments. Consequently, it may be inappropriate to generalize about genetic effects of fragmentation across landscapes or even across plant species with different pollination systems.     

景观遗传学原理及其在生境片断化遗传效应研究中的应用

景观遗传学是近年来在景观生态学和种群遗传学之间形成的一个交叉领域,强调景观的组成、空间构型和环境梯度对基因流、种群遗传空间结构和局域种群适应的影响。景观遗传学尚未成为一门独立的学科,其理论基础主要来自分子遗传学、种群生物学和景观生态学。现代分子遗传标记技术、遥感和GIS支持下的景观分析和空间统计方法的综合运用是景观遗传学主要研究途径。系统介绍了景观遗传学的基础概念,关键科学问题,基本理论框架,及其与相邻研究领域的关系,综述了景观遗传学最为关注的现实课题——景观碎裂化的种群遗传效应的研究进展,主要涉及生境片断化的遗传效应、不同属性的物种响应、以及生境片断化过程的选择作用等方面。通过采取一种跨尺度的视角,景观遗传学研究显著深化了关于景观碎裂化对生物多样性影响的理解。     

Genetic effects of habitat fragmentation and population isolation on Etheostoma raneyi (Percidae)

The use of genetic methods to quantify the effects of anthropogenic habitat fragmentation on population structure has become increasingly common. However, in today’s highly fragmented habitats, researchers have sometimes concluded that populations are currently genetically isolated due to habitat fragmentation without testing the possibility that populations were genetically isolated before European settlement. Etheostoma raneyi is a benthic headwater fish restricted to river drainages in northern Mississippi, USA, that has a suite of adaptive traits that correlate with poor dispersal ability. Aquatic habitat within this area has been extensively modified, primarily by flood-control projects, and populations in headwater streams have possibly become genetically isolated from one another. We used microsatellite markers to quantify genetic structure as well as contemporary and historical gene flow across the range of the species. Results indicated that genetically distinct populations exist in each headwater stream analyzed, current gene flow rates are lower than historical rates, most genetic variation is partitioned among populations, and populations in the Yocona River drainage show lower levels of genetic diversity than populations in the Tallahatchie River drainage and other Etheostoma species. All populations have negative F_IS scores, of which roughly half are significant relative to Hardy–Weinberg expectations, perhaps due to small population sizes. We conclude that anthropogenic habitat alteration and fragmentation has had a profoundly negative impact on the species by isolating E. raneyi within headwater stream reaches. Further research is needed to inform conservation strategies, but populations in the Yocona River drainage are in dire need of management action. Carefully planned human-mediated dispersal and habitat restoration should be explored as management options across the range of the species.     

Assessing the genetic consequences of habitat fragmentation on the federally threatened cheat mountain salamander (Plethodon nettingi): a comparative,multi-locus approach

Comparative population genetic studies of closely related taxa provide a powerful framework for evaluating if and to what degree a species of conservation concern has been negatively impacted by factors such as habitat fragmentation, decreased population connectivity, inbreeding and genetic drift. In this study, we take advantage of a paired sampling strategy to compare the population genetics of the geographically restricted, federally threatened Cheat Mountain salamander (Plethodon nettingi) to those of its partially sympatric, but much more widely distributed congener, the red-backed salamander (P. cinereus), where the two species overlap in the Appalachian mountains of West Virginia. Mitochondrial DNA haplotype and nucleotide diversity were lower in P. nettingi, as were a variety of metrics of nuclear genetic diversity estimated from microsatellite data. Population differentiation and structuring were greater in P. nettingi, suggesting reduced gene flow following fragmentation. Significant inbreeding and evidence of recent population bottlenecks were also seen in P. nettingi and estimated population sizes were smaller. Estimates of contemporary gene flow, as measured through kinship, also showed more restricted gene flow in P. nettingi. Overall, our comparative study provides strong evidence that the small and highly fragmented nature of its geographic distribution has resulted in a suite of negative genetic consequences for the federally threatened Cheat Mountain salamander. Management efforts aimed at enhancing the genetic health and long-term viability of this species should focus on increasing population connectivity through establishment of forest habitat corridors where possible and exploring the potential merits of translocations.

     

Temporal and spatial analyses disclose consequences of habitat fragmentation on the genetic diversity in capercaillie (Tetrao urogallus)

As a result of habitat fragmentation, the capercaillie ( Tetrao urogallus ) population in the Black Forest mountain range in southwestern Germany has declined rapidly during the last decades and now persists in patchy isolated fragments. To study the effects of fragmentation, we quantified dispersal patterns by genotyping 213 individuals in four subpopulations. We used a landscape genetics approach to analyse individual genetic variation, and despite overall low genetic structure, we found strong indications for a major boundary separating the northern part of the Black Forest area from the other subpopulations. Males and females display different gene flow patterns across the landscape. Females tend to disperse across longer distances than do males. We additionally studied the effects of the population decline on genetic diversity during the last hundred years. Although the population has dramatically declined from over 4000 to 250 males over a few decades, genetic diversity was not affected in the same way. We found two haplotypes that were present only in historic samples but microsatellite markers revealed no significant reduction in genetic diversity. Among historic samples, genetic differentiation was very low, indicating that the current genetic structure is caused by recent habitat fragmentation. We argue that inferences about reduced genetic diversity are drawn cautiously and recommend sampling over different temporal scales.     

Effect of habitat fragmentation on levels and patterns of genetic diversity in natural populations of the peat moss Polytrichum commune

Peat bogs represent unique ecosystems that are under particular threat from fragmentation due to peat harvesting, with only 38% of the original peatland in Europe remaining intact and unaffected by peat cutting, drainage and silviculture. In this study, we have used microsatellite markers to determine levels and patterns of genetic diversity in both cut and uncut natural populations of the peat moss Polytrichum commune. Overall diversity levels suggest that there is more genetic variation present than had previously been assumed for bryophytes. Despite this, diversity values from completely cut bogs were found to be lower than those from uncut peatlands (average 0.729 versus 0.880). In addition, the genetic diversity was more highly structured in the cut populations, further suggesting that genetic drift is already affecting genetic diversity in peat bogs subjected to fragmentation.     

Dispersal, habitat differences, and comparative phylogeography of Southeast Asian seahorses (Syngnathidae: Hippocampus)

Four distinct phylogeographical patterns across Southeast Asia were observed for four species of seahorse (genus Hippocampus) with differing ecologies. For all species, genetic differentiation (based on cytochrome b sequence comparisons) was significantly associated with sample site (Phi(ST) = 0.190-0.810, P < 0.0001) and with geographical distance (Mantel's r = 0.37-0.59, P < 0.019). Geographic locations of genetic breaks were inconsistent across species in 7/10 comparisons, although some similarities across species were also observed. The two shallow-water species (Hippocampus barbouri and Hippocampus kuda) have colonized the Sunda Shelf to a lesser degree than the two deeper-water species (Hippocampus spinosissimus and Hippocampus trimaculatus). In all species the presence of geographically restricted haplotypes in the Philippines could indicate past population fragmentation and/or long-distance colonization. A nested clade analysis (NCA) revealed that long-distance colonization and/or fragmentation were likely the dominant forces that structure populations of the two shallow-water species, whereas range expansion and restricted dispersal with isolation by distance were proportionally more important in the history of the two deeper-water species. H. trimaculatus has the most widespread haplotypes [average clade distance (D(c)) of nonsingleton haplotypes = 1169 km], indicating potentially high dispersal capabilities, whereas H. barbouri has the least widespread haplotypes (average D(c) = 67 km) indicating potentially lower dispersal capabilities. Pleistocene separation of marine basins and postglacial flooding of the Sunda Shelf are extrinsic factors likely to have contributed to the phylogeographical structure observed, whereas differences among the species appear to reflect their individual ecologies.     

Compounding effects of habitat fragmentation and predation on bird nests

Habitat fragmentation and invasive species are two of the greatest threats to species diversity worldwide. This is particularly relevant for oceanic islands with vulnerable endemics. Here, we examine how habitat fragmentation influences nest predation by Rattus spp. on cup‐nesting birds in Samoan forests. We determined models for predicting predation rates by Rattus on artificial nests at two scales: (i) the position of the bird's nest within the landscape (e.g. proximity to mixed crop plantations, distance to forest edge); and (ii) the microhabitat in the immediate vicinity of the nest (e.g. nest height, ground cover, slope). Nest cameras showed only one mammal predator, the black rat (Rattus rattus), predating artificial nests. The optimal model predicting nest predation rates by black rats included a landscape variable, proximity to plantations and a local nest site variable, the percentage of low (<15 cm) ground cover surrounding the nest tree. Predation rates were 22 ± 13% higher for nests in forest edges near mixed crop plantations than in edges without plantations. In contrast, predation rates did not vary significantly between edge habitat where the matrix did not contain plantations, and interior forest sites (>1 km from the edge). As ground cover reduced, nest predation rates increased. Waxtags containing either coconut or peanut butter were used as a second method for assessing nest predation. The rates at which these were chewed followed patterns similar to the predation of the artificial nests. Rural development in Samoa will increase the proportion of forest edge near plantations. Our results suggest that this will increase the proportion of forest birds that experience nest predation from black rats. Further research is required to determine if rat control is needed to maintain even interior forest sites populations of predator‐sensitive bird species on South Pacific islands.     

Passerine Pollination of Rhodoleia championii (Hamamelidaceae) in Subtropical China

The pollination ecology and breeding system of the Hamamelidaceae tree species Rhodoleia championii were studied in an evergreen broad-leaved forest in Nankunshan National Forest in Guangdong Province in China. Rhodoleia championii produces lipid-rich pollen grains and dilute nectar (averaging 0.7 mL/d and 9% sugar), with nectar production peaking before 0800 h; the species is self-incompatible and does not set seed asexually. Seven species of nectar-foraging birds visited the inflorescences, with the most common visitors being Japanese white-eyes (Zosterops japonicus, Zosteropidae) and fork-tailed sunbirds (Aethopyga christinae, Nectariniidae). Bumblebees and honeybees played limited roles as pollinators. As documented by fossils from Europe, the Rhodoleia stem lineage dates back at least to the Paleocene. Bird pollination, however, is unlikely to have evolved before the Oligocene when sunbirds arrived in Europe, and pollination by Z. japonicus cannot be much older than 250,000 million years ago, when Z. japonicus diverged from its closest relative.     

The impact of habitat loss and fragmentation on genetic drift and fixation time

In this study, a simple genetic model is integrated with an established method from landscape ecology to investigate the effect of habitat geometry and availability on genetic drift. Previous ecological modelling has identified a sharp threshold in habitat availability for species' persistence, beyond which the species rapidly becomes extinct. This study demonstrates the existence of a similar threshold for fixation time of selectively neutral genotypes by genetic drift, the location of which is determined by habitat shape and spatial correlation of habitat loss. Time to fixation is greater for habitats if they are long and thin rather than square. Despite reductions in population size due to habitat loss, fixation time remains relatively constant until a pre-threshold value, beyond which there is often a substantial increase in time to fixation. Further habitat loss results in the percolation threshold being reached and beyond this point the time to fixation decreases very rapidly. This study reveals a complex relationship between habitat availability, habitat geometry and the process of genetic drift. Possible implications of our results for conservation are discussed. Further work is required to improve our understanding of the interaction between evolutionary, ecological and landscape processes.     

Effects of habitat fragmentation, population size and demographic history on genetic diversity: the Cross River gorilla in a comparative context

In small and fragmented populations, genetic diversity may be reduced owing to increased levels of drift and inbreeding. This reduced diversity is often associated with decreased fitness and a higher threat of extinction. However, it is difficult to determine when a population has low diversity except in a comparative context. We assessed genetic variability in the critically endangered Cross River gorilla (Gorilla gorilla diehli), a small and fragmented population, using 11 autosomal microsatellite loci. We show that levels of diversity in the Cross River population are not evenly distributed across the three genetically identified subpopulations, and that one centrally located subpopulation has higher levels of variability than the others. All measures of genetic variability in the Cross River population were comparable to those of the similarly small mountain gorilla (G. beringei beringei) populations (Bwindi and Virunga). However, for some measures both the Cross River and mountain gorilla populations show lower levels of diversity than a sample from a large, continuous western gorilla population (Mondika, G. gorilla gorilla). Finally, we tested for the genetic signature of a bottleneck in each of the four populations. Only Cross River showed strong evidence of a reduction in population size, suggesting that the reduction in size of this population was more recent or abrupt than in the two mountain gorilla populations. These results emphasize the need for maintaining connectivity in fragmented populations and highlight the importance of allowing small populations to expand.     

桂林岩溶石山檵木种群空间格局及其关联性

种群的空间分布格局及其关联性反映了种群演替方式和对环境因子的适应策略,对植被的恢复与重建、生物多样性保护等具有重要的意义和价值.为了解桂林岩溶石山檵木种群的空间分布格局及其关联性,在对其进行群落调查的基础上,采用点格局方法,以Ripley K函数为基础,运用其衍生的成对相关函数和Ripley L函数对檵木种群的空间分布格局以及不同径级之间关联性进行分析.结果表明:檵木种群的径级结构呈倒“J”型分布,小径级个体占较大比例,种群自然更新状况良好,属增长型种群;檵木种群3个径级的个体在小尺度上呈聚集分布,但随着空间尺度的增大,聚集强度逐渐减弱,趋向随机分布;檵木种群3个不同径级的个体间在小尺度下均呈现无关联,随着尺度增大,不同径级个体的空间关联性呈现正关联或负关联;檵木种群个体间径级差异越大,它们的空间关联性越弱,甚至可能逐渐转变为负关联.本研究结果有助于了解桂林岩溶石山檵木种群在生长发育过程中的生态策略和物种共存的尺度依赖性特征及其形成机制,从而为岩溶石山森林植被的恢复与重建、保护和经营管理提供参考.     

Predation on artificial ground nests in relation to forest fragmentation, agricultural land and habitat structure

The impacts of forest fragmentation agricultural land and habitat structure on depredation of artificial ground nests were studied in the cultivated area in central Finland and in the forest dominated area in Finnish Lapland The overall predation rate did not differ between the regions The overall predation rate was also independent of landscape characteristics forest patch size and the distance to patch edge However, nest predation was clearly affected by the agricultural land since the robbing rate in forest edges was higher near farmlands than further away This effect was caused by avian predators which proportional importance in predation was higher in the agricultural landscape than in the forest landscape In both regions, depredation correlated positively with high numbers of pine and spruce This can be mainly explained by the preference of predators over coniferous forest habitat as a living or hunting area     

The effect of habitat fragmentation on dispersal patterns, mating behavior, and genetic variation in a pika (Ochotona princeps) metapopulation

 Habitat fragmentation is becoming increasingly common, yet, the effect of habitat spatial structure on population dynamics remains undetermined for most species. Populations of a single species found in fragmented and nonfragmented habitat present a rare opportunity to examine the effect of habitat spatial structure on population dynamics. This study investigates the impact of highly fragmented habitat on dispersal patterns, mating behavior, and genetic variation in a pika (Ochotona princeps) population with a mainland-island spatial structure. Juvenile dispersal patterns in fragmented habitat revealed that individuals tended to disperse to neighboring habitat patches. However, within-patch band-sharing scores from multilocus DNA fingerprints did not differ from what would be expected if individuals were assorting randomly among habitat patches each year. Multiple, short-distance dispersal targets for juveniles and occasional long-distance dispersal events suggest that habitat fragmentation on this scale has not resulted in restricted dispersal and a genetically subdivided population. Although pikas tended to mate with the closest available partner, DNA fingerprinting band-sharing scores between mated pairs were consistent with a random mating hypothesis. Random mating in this population appears to be an incidental effect of dispersal in a fragmented habitat. This pattern is distinct from that found in nonfragmented habitat (large talus patches) where mating was non-random and consistent with mating between individuals of intermediate relatedness. DNA fingerprinting data revealed within-species variation in the mating habits of the pika directly attributable to habitat spatial structure. Received: 4 November 1996 / Accepted: 30 June 1997     

Effects of current and historic habitat fragmentation on the genetic structure of the sand goby Pomatoschistus minutus (Osteichthys,Gobiidae)

Habitat fragmentation is a major force that will influence the evolution of a species and its distribution range. Pomatoschistus minutus, the sand goby, has a North Atlantic–Mediterranean distribution and shows various level of habitat fragmentation along its geographic repartition. The use of mitochondrial sequences of the cytochrome b (cyt b) gene and two co‐dominant sets of nuclear markers (introns and microsatellites) allowed us to describe the relationships between P. minutus populations belonging to several different geographical regions of Europe and to assess the structure of populations inhabiting the Golfe du Lion, along the French Mediterranean coast. The present study confirms that the taxon located in the Adriatic Sea (Venice) should be considered as a distinct species, separated approximately 1.75 Mya. The comparison of P. minutus between the Atlantic and western Mediterranean coasts using polymorphic co‐dominant markers revealed that they belong to two demographically independent units, and thus could be considered as well as distinct species, more recently separated (0.3 Mya). The Pleistocene glaciations seem therefore to have played an important role in the diversification of this complex. Finally, at a regional scale in the Golfe du Lion, P. minutus appears to form a single huge homogeneous population. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 175–198.