Genetic structure, habitat fragmentation and bottlenecks in Danish bank voles (Clethrionomys glareolus)

Tissue-samples from 161 bank voles (Clethrionomys glareolus) collected in three forests (five sampling localities) situated in eastern Jutland (Denmark) were analysed by nine microsatellite loci. The genetic diversity found within the populations was high (H_e=0.753–0.806).Bank voles have specific habitat requirements favouring woodlots, hedgerows and deciduous forests as their prime living area. Hence, a natural or human-induced fragmentation of the forest may cause a sub-structuring of the populations and thereby a restriction of dispersal among populations. The sub-structuring indicated by the observed significant genetic differentiation among the five geographically distinct localities (F_st =0.033, P<0.05) could either result from habitat fragmentation or a combination of home range behaviour and different tree composition in the forests. A road situated between two adjacent forests was not found to exert any barrier effect to the gene flow of bank voles. In one out of five localities investigated, genetic evidence for a recent bottleneck-like situation was found. Bank voles are known to exhibit sometimes huge density fluctuations not only from year to year but also from season to season. The bottleneck-like situation found could therefore be due to the low number of individuals during the low-density phase.     

The distinct effects of habitat fragmentation on population size

We sought to understand how the separation of habitats into spatially isolated fragments influences the abundance of organisms. Using a simple, deterministic model of population growth, we compared analytically exact solutions predicting abundance of consumers in two isolated patches with abundance of consumers in a single large patch where the carrying capacity of the large patch is the sum of the carrying capacities of the isolated ones. For the deterministic model, the effect of fragmentation was to slow the rate of population growth in the fragmented habitat relative to the intact one. We also analyzed a stochastic version of the model to examine the effect of fragmentation on population abundance when resources vary randomly in time. For the stochastic model, the effect of fragmentation was to reduce population abundance. We proved in closed-form, that for a non-equilibrium population exhibiting logistic population growth, fragmentation will reduce population size even when the total carrying capacity is not affected by fragmentation. We provide a theoretical basis for the prediction that habitat fragmentation amplifies the effect of habitat loss on the abundance of mobile organisms.     

Phylogenetic relationships among Boleosoma darter species (Percidae: Etheostoma)

Darters represent a species rich group of North American freshwater fishes studied in the context of their diverse morphology, behavior, and geographic distribution. We report the first molecular phylogenetic analyses of the Boleosoma darter clade that includes complete species sampling. We estimated the relationship among the species of Boleosoma using DNA sequence data from a mitochondrial (cytochrome b) and a nuclear gene (S7 ribosomal protein intron 1). Our analyses discovered that the two Boleosoma species with large geographic distributions (E. nigrum and E. olmstedi) do not form reciprocally monophyletic groups in either gene trees. Etheostoma susanae and E. perlongum were phylogenetically nested in E. nigrum and E. olmstedi, respectively. While analysis of the nuclear gene resulted in a phylogeny where E. longimanum and E. podostemone were sister species, the mitochondrial gene tree did not support this relationship. Etheostoma vitreum was phylogenetically nested within Boleosoma in the mitochondrial DNA and nuclear gene trees. Our analyses suggest that current concepts of species diversity underestimate phylogenetic diversity in Boleosoma and that Boleosoma species likely provide another example of the growing number of discovered instances of mitochondrial genome transfer between darter species.     

Genetic diversity and isolation in African Buffalo (Syncerus caffer)

We studied genetic diversity in 58 buffalo from the Kruger National Park (KNP) and Willem Pretorius Nature Reserve (WPNR). Thirty-three protein-encoding loci were resolved; three were polymorphic. Average heterozygosity (H) values did not differ substantially between adult and sub-adult animals from the KNP (2.65 and 2.89%, respectively), but were lower in animals from the isolated WPNR herd (H = 1.48% and only 3% polymorphic loci compared to 9.1%). Representative levels of genetic diversity exist in the large but disease-carrying herd, whereas the smaller disease-free herds available for translocations appear less polymorphic.     

京杭运河邵伯高邮段栖息地破碎化对狗獾种群数量分布的影响

栖息地破碎是生物多样性下降的主要原因之一。栖息地破碎引起的面积效应、隔离效应和边缘效应能影响动物种群的绝灭阈值、分布、多度、种间关系以及生态系统过程, 最终影响动物种群的数量分布。2006年10-11月和2007年10-11月, 利用全球定位系统(GPS)、地理信息系统(GIS)和样方法定量分析京杭运河邵伯至高邮段狗獾栖息地破碎化程度, 确定不同斑块的面积、斑块距离、斑块隔离度以及栖息地质量对斑块中狗獾数量分布的影响。结果表明, 各个斑块内狗獾的洞口数、粪堆数与该斑块的面积显著的正相关(r=0.961, P=0.039; r=0.999, P=0.023), 但与斑块距离、斑块隔离度无显著的相关性(P>0.05)。栖息地的质量也会影响狗獾的数量分布, 多元线性逐步回归分析表明, 人类干扰和与栖息地的郁闭性显著的影响狗獾的数量分布。以上结果说明, 京杭运河邵伯高邮段栖息地的破碎化程度对狗獾的数量分布还没有造成显著的直接影响, 但会间接降低栖息地的质量, 进而影响狗獾的生存。     

异叶泽兰的遗传多样性和居群历史动态研究

异叶泽兰属于菊科泽兰属,是该属分布海拔相对较高的植物,分布在青藏高原东部和横断山海拔1700～3000 m的地区.该文利用ycf6-psbM和rpl32-trnL两个叶绿体DNA(cpDNA)片段以及核DNA片段ITS(nITS)作为分子标记,研究了异叶泽兰的遗传多样性及其分布特征,探讨了其居群历史动态.结果表明:(1...     

The effect of habitat fragmentation on finescale population structure of wood frogs (Rana sylvatica)

We examined the impact of recent anthropogenic habitat fragmentation on the genetic structure of wood frog (Rana sylvatica) breeding sites in Wellington County of Ontario, Canada. In addition to geographic distance (average pairwise distance ~22 km, greatest distance ~50.22 km), four landscape features hypothesized to contribute to genetic differentiation between breeding sites were considered: road density, a major highway (highway 401), canopy cover, and watershed discontinuity. Analysis of data from 396 samples across nine breeding sites using eight microsatellite DNA loci, revealed a small degree of significant genetic structure between breeding sites. The presence of highway 401 and road density were correlated with small but statistically significant structure observed between several groups of sites. One outlier breeding site outside of Wellington County located within the city of Toronto, had significantly lower allelic richness and much larger population differentiation with the Wellington sites. Our data suggest that recent fragmentation has had an effect on wood frog population structure and also demonstrate the importance of dispersal for this species in maintaining levels of genetic diversity.     

A comparison of genetic structuring of Yellowcheek Darters (Etheostoma moorei) using AFLPs and allozymes

The goals of this study were to characterize the genetic structure of 6 populations of Etheostoma moorei (Yellowcheek Darter), endemic to the Little Red River watershed of central Arkansas, to estimate the levels of gene flow within isolated streams, and to compare AFLP genetic diversity and distance data to our previously published allozyme data. The Yellowcheek Darter is a candidate species for listing under the Endangered Species Act. This darter is found in previously connected headwater streams presently isolated and partially inundated downstream by Greers Ferry Reservoir. AFLP data for the Yellowcheek Darter was concordant with previous work utilizing allozymes (r_s = 0.682; p < 0.01), yet genetic differences among populations were greater in magnitude. Genetic diversity (polymorphism = 92.7; heterozygosity = 0.496) is higher for the Yellowcheek Darter than would be expected for a species in decline, and greater for AFLP versus allozyme data. Genetic structuring among streams was also more evident using AFLP data. Gene flow levels are indicative of a metapopulation structure within streams (F_ST = 0.003 − 0.010), with genetic structuring indicating distinct populations among streams.     

Genetic diversity in butterflies: Interactive effects of habitat fragmentation and climate-driven range expansion

Some species are expanding their ranges polewards during current climate warming. However, anthropogenic fragmentation of suitable habitat is affecting expansion rates and here we investigate interactions between range expansion, habitat fragmentation and genetic diversity. We examined three closely related Satyrinae butterflies, which differ in their habitat associations, from six sites along a transect in England from distribution core to expanding range margin. There was a significant decline in allozyme variation towards an expanding range margin in Pararge aegeria, which has the most restricted habitat availability, but not in Pyronia tithonus whose habitat is more widely available, or in a non-expanding 'control species' (Maniola jurtina). Moreover, data from another transect in Scotland indicated that declines in genetic diversity in P. aegeria were evident only on the transect in England, which had greater habitat fragmentation. Our results indicate that fragmentation of breeding habitats leads to more severe founder events during colonization, resulting in reduced diversity in marginal populations in more specialist species. The continued widespread loss of suitable habitats in the future may increase the likelihood of loss of genetic diversity in expanding species, which may affect whether or not species can adapt to future environmental change.     

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.     

Assessing habitat loss and fragmentation and their effects on population viability of forest specialist birds: Linking biogeographical and population approaches

Aim

Biogeographic approaches usually have been developed apart from population ecology, resulting in predictive models without key parameters needed to account for reproductive and behavioural limitations on dispersal. Our aim was to incorporate fully spatially explicit population traits into a classic species distribution model (SDM) using Geographic Information Systems (GIS), aiming at conservation purposes.

Location

Southern South America.

Methods

Our analysis incorporates the effects of habitat loss and fragmentation on population viability and therefore provides insights into how much spatially explicit population traits can improve the SDM prediction of habitable habitat. We utilized a well‐studied focal endemic bird of South American temperate rainforests (Scelorchilus rubecula). First, at a large scale, we assessed the historical extent habitat based on climate envelopes in an SDM. Second, we used a land cover change analysis at a regional scale to account for recent habitat loss and fragmentation. Third, we used empirically derived criteria to predict population responses to fragmented forest landscapes to identify actual losses of habitat and population. Then we selected three sites of high conservation value in southern Chile and applied our population model. Finally, we discuss the degree to which spatially explicit population traits can improve the SDM output without intervening in the modelling process itself.

Results

We found a historical habitat loss of 39.12% and an additional forest cover loss of 3.03% during 2000–2014; the latter occurred with a high degree of fragmentation, reducing the overall estimation of (1) carrying capacity by ?82.4%, ?33.1% and ?45.1% and (2) estimated number of pairs on viable populations by ?84.1%, ?33.0% and ?54.6% on the three selected sites.

Main conclusion

We conclude that our approach sharpened the SDM prediction on environmental suitability by 54.4%, adjusting the habitable area by adding population parameters through GIS, and allowing to incorporate other phenomena as fragmentation and habitat loss.

     

Genetic effects of habitat fragmentation in Viola pubescens (Violaceae), a perennial herb with chasmogamous and cleistogamous flowers

The reproductive biology of a plant species is important in the response of populations to habitat fragmentation, especially if plant-pollinator interactions are disrupted. The genetic effects of forest fragmentation were examined in the common understorey herb Viola pubescens, a species that produces self-pollinated cleistogamous (CL) flowers and potentially outcrossing chasmogamous (CH) flowers. Using allozymes, we measured genetic variation in different sized populations. These were located in woodlots of various sizes (0.5-40.5 ha) and distances from one another (0.3-46 km) within the agricultural landscape of central Ohio in the Midwestern United States. Changes in forest cover of each woodlot within the past 180 years were determined from historical sources and aerial photographs. Woodlot and population sizes were significantly and positively correlated with measures of genetic variation (A, P, HO and HE), with variation highest in populations in the largest woodlot population and lowest in the smallest woodlot population. Most large woodlots resulted from fluctuations in forest cover over the past 60 years, while smaller fragments remained the same size. Overall, populations in Crawford County were genetically differentiated from one another (theta = 0.34), but there was no relationship between genetic and geographical distance. Preliminary evidence for a single year indicated a high rate of outcrossing in most populations. Despite the CH/CL reproductive advantage and apparent outcrossing, populations of V. pubescens in small woodlots remain susceptible to potentially detrimental effects of fragmentation such as genetic drift and reduced levels of genetic variation.     

The population genetic consequences of habitat fragmentation for plants

Habitat fragmentation reduces the size and increases the spatial isolation of plant populations. Initial predictions have been that such changes will be accompanied by an erosion of genetic variation and increased interpopulation genetic divergence due to increased random genetic drift, elevated inbreeding and reduced gene flow. Results of recent empirical studies suggest that while genetic variation may decrease with reduced remnant population size, not all fragmentation events lead to genetic losses and different types of genetic variation (e.g. allozyme and quantitative variation) may respond differently. In some circumstances, fragmentation actually appears to increase gene flow among remnant populations, breaking down local genetic structure.     

Effects of habitat fragmentation and isolation on species richness: evidence from biogeographic patterns

Summary Habitat subdivision by geography or human activity may be an important determinant of regional species richness. Cumulative species-area relationships for vertebrates, land plants, and insects on island archipelagoes show that collections of small islands generally harbor more species than comparable areas composed of one or a few large islands. The effect of the degree of habitat subdivision in increasing species richness appears to increase with the distance from potential sources of colonists. Mountaintop biotas show no clear differences between species richness on large alpine areas and collections of smaller peaks. National park faunas generally have more species in collections of small parks than in the larger parks. In all cases where a consistent effect of subdivision is observed, the more subdivided collection of islands or isolates contains more species. To the degree that these data provide guidance for establishing nature reserves, they suggest that increasing the numbers of reserves may be an important component of conservation strategies.     

Genetic diversity and population structure of spottedtail goby (Synechogobius ommaturus) based on AFLP analysis

Larval dispersal may have an important impact on genetic structure of benthic fishes. To examine population genetic structure of spottedtail goby Synechogobius ommaturus, samples from five different locations of China and Kunsan population in Korea were analyzed by using amplified fragment length polymorphism (AFLP) technology. A total of 253 bands were identified from 91 individuals by 5 primer combinations and the percentage of polymorphic bands was 43.87%. The average gene diversity was 0.0794 ± 0.1470 and Shannon’s information index was 0.1279 ± 0.2138. The pairwise F_st values ranged from 0.022 to 0.201. The results of AMOVA analysis indicated that 90.54% of the genetic variation contained within populations and 9.46% occurred among populations. The gene flow estimates (Nm) demonstrated that different gene flow existed among populations from 0.994 to 11.114. No significant genealogical branches or clusters were recognized on the UPGMA tree. The results support the hypothesis that larval dispersal ability can be responsible for the genetic diversity and population structuring.     

Genetic consequence of restricted habitat and population decline in endangered Isoetes sinensis (Isoetaceae)

BACKGROUND AND AIMS: Isoetes sinensis (Isoeteaceae) is a critically endangered aquatic quillwort in eastern China. Rapid decline of extant population size and local population extinction have occurred in recent years and have raised great concerns among conservationists. METHODS: Amplified fragment length polymorphisms (AFLPs) were used to investigate the genetic variation and population structure of seven extant populations of the species. KEY RESULTS: Eight primer combinations produced a total of 343 unambiguous bands of which 210 (61.2 %) were polymorphic. Isoetes sinensis exhibited a high level of intra-population genetic diversity (H(E) = 0.118; hs = 0.147; I = 0.192; P = 35.2 %). The genetic variation within each of the populations was not positively correlated with their size, suggesting recent population decline, which is well in accordance with field data of demographic surveys. Moreover, a high degree of genetic differentiation (F(ST) = 0.535; G(ST) = 0.608; theta(B) = 0.607) was detected among populations and no correlation was found between geographical and genetic distance, suggesting that populations were in disequilibrium of migration-drift. Genetic drift played a more important role than gene flow in the current population genetic structure of I. sinensis because migration of I. sinensis is predominantly water-mediated and habitat range was highly influenced by environment changes. CONCLUSIONS: Genetic information obtained in the present study provides useful baseline data for formulating conservation strategies. Conservation management, including both reinforcement for in situ populations and ex situ conservation programmes should be carefully designed to avoid the potential risk of outbreeding depression by admixture of individuals from different regions. However, translocation within the same regional population should be considered as a measure of genetic enhancement to rehabilitate local populations. An ex situ conservation strategy for conserving all extant populations to maximize genomic representation of the species is also recommended.     

Influence of habitat fragmentation on population structure of red deer in Croatia

The genetic structure of red deer populations is under strong influence of human activities such as game management and habitat fragmentation. Using multilocus genotypes from 193 geo-referenced individuals, we evaluated the population genetic structure of three red deer populations in Croatia. The effect of habitat fragmentation on genetic structure was tested using Bayesian non-spatial and spatial clustering methods. Our results indicate levels of genetic diversity similar to the ones previously reported by other authors for stable and appropriately managed populations within all populations analyzed. The spatial clustering model was able to detect the effect of habitat fragmentation on population differentiation, supporting the use of spatially explicit methods in landscape genetics, and giving important guidelines for future road planning.     

A transient,positive effect of habitat fragmentation on insect population densities

We conducted an experimental landscape study to test the hypotheses that: (1) habitat removal results in short-term increases in population density in the remaining habitat patches (the crowding effect); (2) following habitat removal, density is higher in landscapes with more, smaller patches and more habitat edge (i.e., a higher level of habitat fragmentation per se) than in less fragmented landscapes, for the same total amount of habitat on the landscapes; (3) this positive effect of fragmentation per se on density is larger in landscapes with smaller inter-patch distances; and (4) these last two effects should be reduced or disappear over time following habitat removal. Our results did not support the first hypothesis, but they provided some support for the other three hypotheses, for two of the four Coccinellid species studied. As in other empirical studies of fragmentation per se on population density, the effects of fragmentation per se were weak and positive (when they did occur). This is the first study to document a transient effect of fragmentation per se on population density, and to show that this effect depends on inter-patch distances. We suggest that fragmentation per se increased the rate of immigration to patches, resulting in higher population densities in more fragmented landscapes.     

Genetic footprints of habitat fragmentation in the extant populations of Sinojackia (Styracaceae): implications for conservation

Sinojackia, a member of the family Styracaceae, is an endangered genus endemic to China. The number of populations and population size of Sinojackia have decreased sharply because of habitat fragmentation and destruction. We studied the genetic diversity of extant populations in two different cohorts (adult and seedling) using eight microsatellite markers to investigate the genetic footprints of habitat fragmentation in four recognized Sinojackia spp. and to develop appropriate conservation measures. Data on intrapopulational genetic diversity suggest that Sinojackia populations have maintained relatively high levels of genetic diversity and low levels of genetic differentiation despite severe fragmentation. The high genetic diversity may be explained by the outcrossing mating system and high longevity of Sinojackia spp. The amount of genetic variation is not associated with population size, which was also supported by bottleneck analysis. In the species studied, there was no significant difference in the genetic diversity between the two cohorts analysed. However, inbreeding increased from adult trees to seedling populations, suggesting that the higher proportion of biparental inbreeding in the recent generations of seedlings is the result of restricted current genetic flow caused by habitat fragmentation. Average seed set per population was not significantly correlated with either population size or genetic diversity. Conservation management should aim to monitor inbreeding and outbreeding depression carefully to ensure the in situ and ex situ conservation of Sinojackia spp. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ?? , ??–??.