Background:Diet analysis is essential to understanding the functional role of large bird species in food webs.Mor-phological analysis of regurgitated bird pellet contents is time intensive and may underestimate biodiv...Background:Diet analysis is essential to understanding the functional role of large bird species in food webs.Mor-phological analysis of regurgitated bird pellet contents is time intensive and may underestimate biodiversity.DNA metabarcoding has the ability to circumvent these issues,but has yet to be done.Methods:We present a pilot study using DNA metabarcoding of MT-RNR1 and MT-CO1 markers to determine the species of origin and prey of 45 pellets collected in Qinghai and Gansu Provinces,China.Results:We detected four raptor species[Eurasian Eagle Owl(Bubo bubo),Saker Falcon(Falco cherrug),Steppe Eagle(Aquila nipalensis),and Upland Buzzard(Buteo hemilasius)]and 11 unique prey species across 10 families and 4 classes.Mammals were the greatest detected prey class with Plateau Pika(Ochotona curzoniae)being the most frequent.Observed Shannon’s and Simpson’s diversity for Upland Buzzard were 1.089 and 0.479,respectively,while expected values were 1.312±0.266 and 0.485±0.086.For Eurasian Eagle Owl,observed values were 1.202 and 0.565,while expected values were 1.502±0.340 and 0.580±0.114.Interspecific dietary niche partitioning between the two spe-cies was not detected.Conclusions:Our results demonstrate successful use of DNA metabarcoding for understanding diet via a novel noninvasive sample type to identify common and uncommon species.More work is needed to understand how raptor diets vary locally,and the mechanisms that enable exploitation of similar dietary resources.This approach has wide ranging applicability to other birds of prey,and demonstrates the power of using DNA metabarcoding to study species noninvasively.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
基金funded by the National Key Technology R&D Program of China(2019YFA0607103)Snow Leopard Conservancy(G1900014,G2000019)+2 种基金Cleveland Metroparks Zoo(G1800082)Panthera Corporation and The Andrew Sabin Family Foundation(G1900011,G2000017)Welfare Project of the National Scientific Research Institution(CAFYBB2019ZE003).
文摘Background:Diet analysis is essential to understanding the functional role of large bird species in food webs.Mor-phological analysis of regurgitated bird pellet contents is time intensive and may underestimate biodiversity.DNA metabarcoding has the ability to circumvent these issues,but has yet to be done.Methods:We present a pilot study using DNA metabarcoding of MT-RNR1 and MT-CO1 markers to determine the species of origin and prey of 45 pellets collected in Qinghai and Gansu Provinces,China.Results:We detected four raptor species[Eurasian Eagle Owl(Bubo bubo),Saker Falcon(Falco cherrug),Steppe Eagle(Aquila nipalensis),and Upland Buzzard(Buteo hemilasius)]and 11 unique prey species across 10 families and 4 classes.Mammals were the greatest detected prey class with Plateau Pika(Ochotona curzoniae)being the most frequent.Observed Shannon’s and Simpson’s diversity for Upland Buzzard were 1.089 and 0.479,respectively,while expected values were 1.312±0.266 and 0.485±0.086.For Eurasian Eagle Owl,observed values were 1.202 and 0.565,while expected values were 1.502±0.340 and 0.580±0.114.Interspecific dietary niche partitioning between the two spe-cies was not detected.Conclusions:Our results demonstrate successful use of DNA metabarcoding for understanding diet via a novel noninvasive sample type to identify common and uncommon species.More work is needed to understand how raptor diets vary locally,and the mechanisms that enable exploitation of similar dietary resources.This approach has wide ranging applicability to other birds of prey,and demonstrates the power of using DNA metabarcoding to study species noninvasively.
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.
