The microsatellite analysis of DNA plays an important role in studying the population genetics such as population structure, genetic variability and diversity, phylogenetic relationships of wild population of endanger...The microsatellite analysis of DNA plays an important role in studying the population genetics such as population structure, genetic variability and diversity, phylogenetic relationships of wild population of endangered species. The main aim of this study was the estimation of ten microsatellite markers variability in the F. cherrug and F. peregrinus populations. We investigated genetic diversity and structure of populations by using non-invasive genetic identification of individuals to characterize populations of raptors living in the captivity and wild in the Czech Republic during the breeding seasons 2009 and 2010. Within Falco cherrug, significant moderate genetic differentiation （FsT） was observed between Falco cherrug wild and captive. This means that there could be a little differentiation between the wild and the captive populations caused by Falco cherrug subspecies origin or hybridization in the captivity. The absence of significant genetic differentiation between Falco peregrinus wild and captive may be caused by the influence of reintroduction the captive populations in the past. Whereas one breeding population ofFalco peregrinus （Kokorinsko2 2010） was clustered by UPGMA dendrogram into the individual group, we assumed this population like independent, maybe not influenced by other groups. Moreover, a larger sample size would be necessary to confirm the hypothesis.展开更多
Accurate individual identification is required to estimate survival rates in avian populations.For endangered species,non-invasive methods of obtaining individual identification,such as using molted feathers as a sour...Accurate individual identification is required to estimate survival rates in avian populations.For endangered species,non-invasive methods of obtaining individual identification,such as using molted feathers as a source of DNA for microsatellite markers,are preferred because of less disturbance,easy sample preparation and high efficiency.With the availability of many avian genomes,a few pipelines isolating genome-wide microsatellites have been published,but it is still a challenge to isolate microsatellites from the reference genome efficiently.Here,we have developed an integrated tool comprising a bioinformatic pipeline and experimental procedures for microsatellite isolation and validation based on the reference genome.We have identified over 95000 microsatellite loci and established a system comprising 10 highly polymorphic markers(PIC value:0.49–0.93,mean:0.79)for an endangered species,saker falcon(Falco cherrug).These markers(except 1)were successfully amplified in 126 molted feathers,exhibiting high amplification success rates(83.9–99.7%),high quality index(0.90–0.97)and low allelic dropout rates(1–9.5%).To further assess the efficiency of this marker system in a population study,we identified individual sakers using these molted feathers(adult)and 146 plucked feathers(offspring).The use of parent and offspring samples enabled us to infer the genotype of missing samples(N=28),and all adult genotypes were used to ascertain that breeding turnover is a useful proxy for survival estimation in sakers.Our study presents a cost-effective tool for microsatellite isolation based on publicly available reference genomes and demonstrates the power of this tool in estimating key parameters of avian population dynamics.展开更多
文摘The microsatellite analysis of DNA plays an important role in studying the population genetics such as population structure, genetic variability and diversity, phylogenetic relationships of wild population of endangered species. The main aim of this study was the estimation of ten microsatellite markers variability in the F. cherrug and F. peregrinus populations. We investigated genetic diversity and structure of populations by using non-invasive genetic identification of individuals to characterize populations of raptors living in the captivity and wild in the Czech Republic during the breeding seasons 2009 and 2010. Within Falco cherrug, significant moderate genetic differentiation （FsT） was observed between Falco cherrug wild and captive. This means that there could be a little differentiation between the wild and the captive populations caused by Falco cherrug subspecies origin or hybridization in the captivity. The absence of significant genetic differentiation between Falco peregrinus wild and captive may be caused by the influence of reintroduction the captive populations in the past. Whereas one breeding population ofFalco peregrinus （Kokorinsko2 2010） was clustered by UPGMA dendrogram into the individual group, we assumed this population like independent, maybe not influenced by other groups. Moreover, a larger sample size would be necessary to confirm the hypothesis.
基金Stipend and research expenses of Xian Hou were provided by the National Key Program of Research and Development,Ministry of Science and Technology,China(2016YFC0503200)the National Natural Science Foundation of China(Nos.31522052 and 31471993)+1 种基金This project was funded by the Environment Agency of Abu DhabiThe fieldwork was partially supported by the Science and Technology Service Network Initiative of Chinese Academy of Sciences(KFJ_STSZDTP-013-1).
文摘Accurate individual identification is required to estimate survival rates in avian populations.For endangered species,non-invasive methods of obtaining individual identification,such as using molted feathers as a source of DNA for microsatellite markers,are preferred because of less disturbance,easy sample preparation and high efficiency.With the availability of many avian genomes,a few pipelines isolating genome-wide microsatellites have been published,but it is still a challenge to isolate microsatellites from the reference genome efficiently.Here,we have developed an integrated tool comprising a bioinformatic pipeline and experimental procedures for microsatellite isolation and validation based on the reference genome.We have identified over 95000 microsatellite loci and established a system comprising 10 highly polymorphic markers(PIC value:0.49–0.93,mean:0.79)for an endangered species,saker falcon(Falco cherrug).These markers(except 1)were successfully amplified in 126 molted feathers,exhibiting high amplification success rates(83.9–99.7%),high quality index(0.90–0.97)and low allelic dropout rates(1–9.5%).To further assess the efficiency of this marker system in a population study,we identified individual sakers using these molted feathers(adult)and 146 plucked feathers(offspring).The use of parent and offspring samples enabled us to infer the genotype of missing samples(N=28),and all adult genotypes were used to ascertain that breeding turnover is a useful proxy for survival estimation in sakers.Our study presents a cost-effective tool for microsatellite isolation based on publicly available reference genomes and demonstrates the power of this tool in estimating key parameters of avian population dynamics.
