Analysis of relatedness and determination of the source of founders in the captive bearded vulture, Gypaetus barbatus, population

Genetic relatedness among founders is a vitalparameter in the management of captivepopulations as kin structure can have asignificant effect on subsequent populationstructure. Methods for inferring relatednessfrom microsatellite markers have all beendeveloped for natural populations; theirapplicability to captive populations withunknown founder origins needs thereforetesting. We used information derived from 14microsatellites in 177 individuals and Quellerand Goodnight's approach, to estimaterelatedness in the captive bearded vulturepopulation and to test the assumption ofunrelated founders. Mean relatedness of knownparent–offspring, full-sib and half-sib pairswithin the captive population were in agreementwith theoretical distributions. Pairwiserelatedness values among the founders had amean of –0.051 (SE ± 0.007) and theirdistribution did only differ marginally fromthe one found in the natural Pyreneanpopulation. A maximum likelihood approach wasused to determine the likelihood of founderpairs to be as closely related as full-sibs orparent–offspring. These results were combinedwith data from 268 bp mitochondrial DNA controlregion sequences and studbook information. Wecould exclude a close relationship among themajority of the 36 successfully reproducingfounders. Our study therefore removesmanagement concerns about hidden problems ofinbreeding and inbreeding depression. Itdemonstrates the applicability of relatednessestimates based on microsatellite allelefrequency data even in captive populations.Furthermore, we verified studbook informationon the origin of two founders from thePyrenees, and show the value of assignmenttests based on microsatellites for deducingfounder origins and their important role infuture monitoring projects.     

The present Pyrenean population of bearded vulture (Gypaetus barbatus): Its genetic characteristics

The Pyrenean population of the endangered bearded vulture (Gypaetus barbatus) is the largest natural population in Europe. In this study, its current genetic variability was assessed using 110 animals of the recent population in order to know what the present situation. Sex identification by DNA methodology in the 110 bearded vultures, mitochondrial DNA (mtDNA) and eight microsatellite markers in 87 bearded vultures have been analysed. Our results for sex identification present a number of 49 males and 61 females; no significant differences for number of males and females in this population have been observed. mtDNA studies indicate that nucleotide and haplotype diversities and number of variable sites were low. Tajima's D test and Fu and Li's D* and F* tests suggest that mutations are selectively neutral and the population is expanding. A mean number of alleles per locus and a mean observed heterozygosity have been obtained by microsatellite analysis. FIS is not high, and inbreeding depression could be discarded in the near future. The results suggest that the Pyrenean population of bearded vultures have to be controlled in order to avoid the loss of genetic variability. This data should be taken into account when considering conservation plans for the species.     

Phylogeography, genetic structure and diversity in the endangered bearded vulture (Gypaetus barbatus, L) as revealed by mitochondrial DNA

Bearded vulture populations in the Western Palearctic have experienced a severe decline during the last two centuries that has led to the near extinction of the species in Europe. In this study we analyse the sequence variation at the mitochondrial control region throughout the species range to infer its recent evolutionary history and to evaluate the current genetic status of the species. This study became possible through the extensive use of museum specimens to study populations now extinct. Phylogenetic analysis revealed the existence of two divergent mitochondrial lineages, lineage A occurring mainly in Western European populations and lineage B in African, Eastern European and Central Asian populations. The relative frequencies of haplotypes belonging to each lineage in the different populations show a steep East-West clinal distribution with maximal mixture of the two lineages in the Alps and Greece populations. A genealogical signature for population growth was found for lineage B, but not for lineage A; futhermore the Clade B haplotypes in western populations and clade A haplo-types in eastern populations are recently derived, as revealed by their peripheral location in median-joining haplotype networks. This phylogeographical pattern suggests allopatric differentiation of the two lineages in separate Mediterranean and African or Asian glacial refugia, followed by range expansion from the latter leading to two secondary contact suture zones in Central Europe and North Africa. High levels of among-population differentiation were observed, although these were not correlated with geographical distance. Due to the marked genetic structure, extinction of Central European populations in the last century re-sulted in the loss of a major portion of the genetic diversity of the species. We also found direct evidence for the effect of drift altering the genetic composition of the remnant Pyrenean population after the demographic bottleneck of the last century. Our results argue for the management of the species as a single population, given the apparent ecological exchangeability of extant stocks, and support the ongoing reintroduction of mixed ancestry birds in the Alps and planned reintroductions in Southern Spain.     

Misleading population estimates: biases and consistency of visual surveys and matrix modelling in the endangered bearded vulture

Conservation strategies for long-lived vertebrates require accurate estimates of parameters relative to the populations' size, numbers of non-breeding individuals (the "cryptic" fraction of the population) and the age structure. Frequently, visual survey techniques are used to make these estimates but the accuracy of these approaches is questionable, mainly because of the existence of numerous potential biases. Here we compare data on population trends and age structure in a bearded vulture (Gypaetus barbatus) population from visual surveys performed at supplementary feeding stations with data derived from population matrix-modelling approximations. Our results suggest that visual surveys overestimate the number of immature (<2 years old) birds, whereas subadults (3-5 y.o.) and adults (>6 y.o.) were underestimated in comparison with the predictions of a population model using a stable-age distribution. In addition, we found that visual surveys did not provide conclusive information on true variations in the size of the focal population. Our results suggest that although long-term studies (i.e. population matrix modelling based on capture-recapture procedures) are a more time-consuming method, they provide more reliable and robust estimates of population parameters needed in designing and applying conservation strategies. The findings shown here are likely transferable to the management and conservation of other long-lived vertebrate populations that share similar life-history traits and ecological requirements.     

Population dynamics of the bearded vulture Gypaetus barbatus in southern Africa

The essential features of mortality and survivorship of bearded vultures Gypaetus barbatus in southern Africa were deduced from age class plumage characteristics. The population consisted of about 204 adult pairs within a breeding range of about 35,000 sq km. Pairs bred every year and produced, on average, about 0·9 young per pair per year. Young birds made up about 37% of the population, subadults 3·5% and adults 60%. About 182 fledged young were recruited to the population each year. The proportion of young birds in the population in different areas was inversely related to the breeding density of adult birds (range 24–47%). Young bird mortality over the four years to subadult age was 87%, the survival rate of adults was 94% and the mean lifespan of birds surviving to adulthood was 21·4 years. This study demonstrates the need to understand the relationship between adult breeding density and young bird numbers in different parts of their range to accurately deduce population dynamics characteristics.     

圈养小熊猫遗传多样性与种群遗传结构分析

小熊猫是亚洲特有的珍稀濒危动物,目前受到栖息地减少、片断化和人类活动干扰等威胁。中国圈养小熊猫已经有60 多年历史,约55 个机构曾经饲养过小熊猫,现今圈养数量有400 多只,评估小熊猫圈养种群的遗传多样性和遗传结构对科学维持圈养种群和保存遗传种质资源意义重大。本研究利用19 个微卫星座位,对中国境内11 个小熊猫圈养种群的116 只个体进行了遗传多样性评估及遗传结构分析。结果显示11 个种群都具有较高的遗传多样性,平均基因丰富度3.505 ± 1.033 (北京)至4.026 ± 1.219 (冕宁),期望杂合度0.631 ± 0.225(黄山)至0.782 ±0.171 (温岭)。其中福州和无锡种群极显著偏离Hardy-Weinberg 平衡。整个圈养群体内各个种群遗传分化系数为0.055,呈显著分化,表明11 个种群遗传分化水平较高。Bayesian 遗传聚类分析将11 个种群聚为三个遗传簇,与野生种群的遗传聚类结果一致。结论:小熊猫圈养种群与野生种群相比,同样具有较高的遗传多样性。因此,圈养小熊猫遗传管理的重点不再是引进野生个体充实圈养种群,应制订科学的繁殖计划,避免近交,从而维持圈养种群的遗传多样性。     

圈养大熊猫冷冻精液对其种群遗传多样性的作用

在过去34年的圈养大熊猫种群保护工作中,我们成功建立了全球最大的大熊猫精子库,目前已保存50只大熊猫个体总计7 000余支细管冷冻精液(冻精)。冷冻精液一方面可以使物种的遗传资源得到长久保存,另一方面可以通过人工授精的方式促进种群繁育。但是,圈养大熊猫冷冻精液对其种群遗传多样性的作用尚未有明确报道。本研究首先根据成都大熊猫繁育研究基地2000—2014年冷冻精液人工授精数据,对比分析了冻精人工授精个体和圈养种群的遗传多样性。结果显示,冻精人工授精个体遗传多样性均高于同年圈养种群的平均遗传多样性,表明在繁殖年份中冻精人工授精可以显著提高圈养大熊猫种群的遗传多样性。统计精子库中所有冻精个体的平均血缘系数并与圈养种群进行对比分析,探究冷冻精液对圈养种群遗传多样性的潜在作用。结果显示,精子库中有21只已死亡个体的精液,其中有66.67%的个体平均血缘系数低于圈养种群;有14只20岁以上个体的精液,其中有50.00%的个体平均血缘系数低于圈养种群;另有15只20岁以下个体的精液,其中有53.33%的个体平均血缘系数低于圈养种群,表明冷冻精液对圈养种群遗传多样性的保护具有重要价值。综上所述,冷冻精液不但有效保存了大熊猫遗传资源,而且在保护圈养种群遗传多样性方面具有积极的促进作用。     

Effective population size,genetic diversity,and coalescence time in subdivided populations

A formula for the effective population size for the finite island model of subdivided populations is derived. The formula indicates that the effective size can be substantially greater than the actual number of individuals in the entire population when the migration rate among subpopulations is small. It is shown that the mean nucleotide diversity, coalescence time, and heterozygosity for genes sampled from the entire population can be predicted fairly well from the theory for randomly mating populations if the effective population size for the finite island model is used.     

The number of breeders explains genetic connectivity in an endangered bird

Connectivity is central to ecology and evolution as it focuses on the movement of individuals or genes across landscapes. Genetic connectivity approaches aim to understand gene flow but often estimate it indirectly based on metrics of genetic differentiation, which can also be affected by other evolutionary forces such as genetic drift. Gene flow and genetic drift are driven by separate ecological mechanisms with potentially differing effects on genetic differentiation and interpretations of genetic connectivity. The ecological mechanisms contributing to gene flow and genetic drift are primarily effective dispersal, or movement followed by successful reproduction, and the number of breeders in a local population, N_b, respectively. Yet, rarely are these ecological mechanisms and genetic connectivity measured simultaneously across landscapes. We examine the roles of effective dispersal and N_b on genetic connectivity across the entire range of the endangered snail kite (Rostrhamus sociabilis plumbeus), between 2006–2015. We find that both N_b and effective dispersal are important predictors of genetic connectivity across this landscape, but that N_b has a 3 × stronger effect on genetic connectivity. Furthermore, N_b is positively correlated with heterozygosity and allelic richness within patches, suggesting a potentially important role of genetic drift, in addition to gene flow, on genetic connectivity. These results emphasize that conservation efforts should focus on not only between‐patch processes of movement but also within‐patch processes regarding habitat quality and local population size for increasing genetic connectivity.     

Plumage colour and feather structure of the bearded vulture (Gypaetus barbatus)

The rufous colouring on the feathers of the under parts of adult bearded vultures Gypaetus barbatus , studied by scanning electron microscopy, energy-dispersive X-ray microanalysis and X-ray diffraction analysis, is caused by an external deposit of iron oxide in the ferrihydrite state. Unstained feathers, e.g. in captive birds, are pure white. The feathers of young birds have similar coatings of iron oxide to those of adults, but because the feathers are pigmented pale to dark brown (dependent on age), the rusty colour is partly or totally obscured. The intensity of the colour in adult birds varies between individuals and within individuals with time; the more worn the feathers the more iron oxide they can hold. After heavy rainfall up to 30% of adult birds can become appreciably paler. Birds take about 6 days (range–9 days) to regain normal colouring. Iron oxide accumulates mainly in the axes of shafts and barbs, barbs and barbules and barbules and hamuli, and forms blob-like deposits at the ends of barbs and barbules on the outer layers of feathers. Iron oxide is probably acquired passively when bearded vultures come into contact with deposits in caves and on ledges on cliffs. The colour is then spread by preening. Iron oxide imparts camouflage to adult birds, but also reduces wear on the outer layer of feathers, makes feathers more rigid and probably helps control ectoparasites.     

Social heterosis and the maintenance of genetic diversity

Genetic diversity in species is often high in spite of directional selection or strong genetic drift. One resolution to this paradox may be through fitness benefits arising from interactions of genetically diverse individuals. Advantageous phenotypes that are impossible in single individuals (e.g. being simultaneously bold and shy) can be expressed by groups composed of genetically different individuals. Genetic diversity, therefore, can produce mutualistic benefits shared by all group members. We define this effect as 'social heterosis', and mathematically demonstrate maintenance of allelic diversity when diverse groups or neighbourhoods are more reproductively successful than homogenous ones. Through social heterosis, genetic diversity persists without: frequency dependence within groups, migration, balancing selection, genetic linkages, overdominance, antagonistic pleiotropy or nonrandom allele assortment. Social heterosis may also offer an alternative evolutionary pathway to cooperation that does not require clustering of related individuals, nepotistic favouritism towards kin, or overt reciprocity.     

Effects of parental number and duration of the breeding period on the effective population size and genetic diversity of a captive population of the endangered Tokyo bitterling Tanakia tanago (Teleostei: Cyprinidae)

The maintenance of genetic diversity is one of the chief concerns in the captive breeding of endangered species. Using microsatellite and mtDNA markers, we examined the effects of two key variables (parental number and duration of breeding period) on effective population size (N_e) and genetic diversity of offspring in an experimental breeding program for the endangered Tokyo bitterling, Tanakia tanago. Average heterozygosity and number of alleles of offspring estimated from microsatellite data increased with parental number in a breeding aquarium, and exhibited higher values for a long breeding period treatment (9 weeks) compared with a short breeding period (3 weeks). Haplotype diversity in mtDNA of offspring decreased with the reduction in parental number, and this tendency was greater for the short breeding period treatment. Genetic estimates of N_e obtained with two single‐sample estimation methods were consistently higher for the long breeding period treatment with the same number of parental fish. Average N_e/N ratios were ranged from 0.5 to 1.4, and were high especially in the long breeding period with small and medium parental number treatments. Our results suggest that the spawning intervals of females and alternative mating behaviors of males influence the effective size and genetic diversity of offspring in bitterling. To maintain the genetic diversity of captive T. tanago, we recommend that captive breeding programs should be conducted for a sufficiently long period with an optimal level of parental density, as well as using an adequate number of parents. Zoo Biol 31:656‐668, 2012. © 2011 Wiley Periodicals, Inc.     

Phylogeography of the endangered Otago skink, Oligosoma otagense: population structure, hybridisation and genetic diversity in captive populations

Climatic cooling and substantial tectonic activity since the late Miocene have had a pronounced influence on the evolutionary history of the fauna of New Zealand's South Island. However, many species have recently experienced dramatic range reductions due to habitat fragmentation and the introduction of mammalian predators and competitors. These anthropogenic impacts have been particularly severe in the tussock grasslands of the Otago region. The Otago skink (Oligosoma otagense), endemic to the region, is one of the most critically endangered vertebrates in New Zealand. We use mitochondrial DNA sequence data to investigate the evolutionary history of the Otago skink, examine its population genetic structure, and assess the level of genetic diversity in the individuals in the captive breeding program. Our data indicate that the Otago skink diverged from its closest relatives in the Miocene, consistent with the commencement of tectonic uplift of the Southern Alps. However, there is evidence for past introgression with the scree skink (O. waimatense) in the northern Otago-southern Canterbury region. The remnant populations in eastern Otago and western Otago are estimated to have diverged in the mid-Pliocene, with no haplotypes shared between these two regions. This divergence accounts for 95% of the genetic diversity in the species. Within both regions there is strong genetic structure among populations, although shared haplotypes are generally evident between adjacent localities. Although substantial genetic diversity is present in the captive population, all individuals originate from the eastern region and the majority had haplotypes that were not evident in the intensively managed populations at Macraes Flat. Our data indicate that eastern and western populations should continue to be regarded as separate management units. Knowledge of the genetic diversity of the breeding stock will act to inform the captive management of the Otago skink and contribute to a key recovery action for the species.     

Contemporary effective population size and predicted maintenance of genetic diversity in the endangered kea (Nestor notabilis)

Population size and the potential for maintenance of genetic diversity are critical information for the monitoring of species of conservation concern. However, direct estimates of population size are not always feasible, making indirect genetic approaches a valuable alternative. We estimated contemporary effective population size (N_e) in the endangered kea (Nestor notabilis) using three different methods. We then inferred the census size (N_C) using published N_e/N_C ratios and modelled the future maintenance of genetic diversity assuming a number of demographic parameters. Short-term N_e was small with a range-wide N_e?N_C was within the range of the current estimate (c. 1000–5000). Forward simulations showed low probability of retaining 90% of rare alleles without immigration. However, the probability of maintaining genetic diversity was high with immigration, juvenile survival of?≥?30%, and an initial sex ratio of c. 0.5–0.6. Despite the low N_e in kea, predator control and/or artificial immigration might be sufficient to maintain the present genetic diversity.     

Optimizing the genetic management of reintroduction projects: genetic population structure of the captive Northern Bald Ibis population

Many threatened species are bred in captivity for conservation purposes and some of these programmes aim at future reintroduction. The Northern Bald Ibis, Geronticus eremita, is a Critically Endangered bird species, with recently only one population remaining in the wild (Morocco, Souss Massa region). During the last two decades, two breeding programs for reintroduction have been started (in Austria and Spain). As the genetic constitution of the founding population can have strong effects on reintroduction success, we studied the genetic diversity of the two source populations for reintroduction (‘Waldrappteam’ and ‘Proyecto eremita’) as well as the European zoo population (all individuals held ex situ) by genotyping 642 individuals at 15 microsatellite loci. To test the hypothesis that the wild population in Morocco and the extinct wild population in the Middle East belong to different evolutionary significant units, we sequenced two mitochondrial DNA fragments. Our results show that the European zoo population is genetically highly structured, reflecting separate breeding lines. Genetic diversity was highest in the historic samples from the wild eastern population. DNA sequencing revealed only a single substitution distinguishing the wild eastern and wild western population. Contrary to that, the microsatellite analysis showed a clear differentiation between them. This suggests that genetic differentiation between the two populations is recent and does not confirm the existence of two evolutionary significant units. The European zoo population appears to be vital and suitable for reintroduction, but the management of the European zoo population and the two source populations for reintroductions can be optimized to reach a higher level of admixture.     

Development of eighteen tetranucleotide microsatellite markers in Tibetan Macaque (Macaca thibetana) and genetic diversity analysis of captive population

In this study, eighteen tetranucleotide microsatellite loci were isolated from AAAG-enriched and GATA-enriched libraries of the Tibetan macaque, Macaca thibetana. These loci were tested on 53 individuals of M. thibetana, and most loci were proved to be highly polymorphic. A total of 109 alleles were detected with an average of 6.06 alleles per locus. The PIC values of these loci ranged from 0.192 to 0.879, with an average of 0.624. The observed and expected heterozygosities ranged from 0.170 to 0.800 and from 0.217 to 0.898, with an average of 0.583 and 0.675, respectively. 5 loci significantly deviated from Hardy–Weinberg equilibrium (HWE). Significant linkage disequilibrium (LD) was found between 9 pairs of loci. The newly identified polymorphic markers would facilitate the study of M. thibetana on the population structure and genetic diversity.     

小熊猫圈养种群遗传多样性及其影响因子

利用寡核苷酸指纹探针ＬＺＦ－Ｉ检测了成都大熊猫繁育研究基地仿生态圈养场小熊猫种群全部２２只个体的ＤＮＡ指纹,检测结果表明其遗传多样性参数如下：⑴各体间ＤＡＮ指纹图的相似性为０．１７２;个体Ａ的指纹谱带在个体Ｂ中出现的概率为０．１８０６。⑵圈养种群的等位基因频率为０．０９４８,杂合率为９０．５２％,⑶种群中指名亚种亲本个体的引进是影响该种群遗传多样性的主要因子。