Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites
- Published
- Accepted
- Subject Areas
- Conservation Biology, Evolutionary Studies, Genetics, Zoology
- Keywords
- Conservation genetics, Garrulax, genetic diversity, genetic relatedness, zoo, Critically Endangered, Captive population, microsatellites, next-generation sequencing
- Copyright
- © 2018 Chen et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2018. Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites. PeerJ Preprints 6:e27038v2 https://doi.org/10.7287/peerj.preprints.27038v2
Abstract
Background. Understanding genetic diversity and population structure is critically important for the conservation and management of endangered species. These factors are particularly relevant for species with small populations and/or restricted ranges, such as the critically endangered Blue-crowned Laughingthrush, Garrulax courtoisi, which has only two wild populations left in Wuyuan, Jiangxi and Simao, Yunnan, China.
Methods. In this study, novel microsatellites markers were developed using whole-genome sequencing of the target species. We genotyped 14 and nine individuals from the Oceanic Park of Hong Kong, which are of unknown origin, and the Nanchang Zoo, which were introduced from the wild Wuyuan population, respectively, using the novel microsatellite markers. The genetic diversity of captive Blue-crowned Laughingthrush populations was estimated based on genetic polymorphisms revealed by a new microsatellite data set and mitochondrial sequences.Then, we characterised the population structure using STRUCTURE, principal coordinates analysis, population assignment test using the microsatellite data, and haplotype analysis of mitochondrial data. Additionally, we quantified genetic relatednessbased on the microsatellite data with ML-Relate.
Results. This is the first study to describe this novel set of 12 microsatellite markers for Blue-crowned Laughingthrush. Our results based on the microsatellite dataset and mitochondrial sequences showed equally low levels of genetic diversity of the two captive Blue-crowned Laughingthrush populations. The population structure analysis, population assignment test using the microsatellite data, and haplotype analysis of the mitochondrial data showed some population structuring between these two populations. The average pairwise relatedness coefficient was not significant, and their genetic relatedness was quantified.
Discussion. This study provided a genetic tool which allowed the first estimate of captive population genetic diversity and relatedness for a critically endangered bird species. Furthermore, our results indicate that we cannot exclude the possibility that the origin of the Hong Kong captive population was the wild Wuyuan population. These results provide valuable knowledge that can help improve conservation management and planning for both captive and wild Blue-crowned Laughingthrush populations.
Author Comment
We have carefully considered and addressed all comments and suggestions from the two reviewers. You can find the reviewers’comments interspersed with our responses to these below in red colour.（please see the attachment of Rebuttal letter in the PeerJ website）Since both reviewers addressed concerns about the validity of the findings, we reorganized the introduction and discussion in order to avoid over-interpration of the results. Due to the limitation of samples, we tried to focus on dicussing on the main aspects out of results. Moreover, we attempted to proposed hypothesis in prior base on current knowledge (and gaps) of the study species.
Supplemental Information
Sample voucher numbers and sequence GenBank accession numbers of two captive Blue-crowned Laughingthrush (Garrulax courtoisi) populations used in this article. (OPHK= Ocean Park, Hong Kong, SYS=Sun Yat-sen University)
Pairwise genetic relatedness among analysed pairs of Blue-crowned Laughingthrush individuals
Genetic kinship between each pair of individuals that has the highest likelihood at lower diagonal (PO = Parent / Offspring; FS = Full siblings; HS = Half siblings; U = Unrelated), and the pairwise relatedness based on the Queller and Goodnight estimator (RQG) are provided for each pair of individuals at upper diagonal. Table S2a. indicate OPHK population of Blue-crowned Laughingthrush, and Table S2b. indicate NCZ population of Blue-crowned Laughingthrush. (OPHK: Ocean Park Hong Kong, NCZ: Nanchang Zoo).
Raw Data 2. Genotype of the 12 microsatellite loci in a sample set of two captive Blue-crowned Laughingthrush populations
Raw Data. Abbreviations indicate different Blue-crowned Laughingthrush populations (OPHK: Ocean Park Hong Kong, NCZ: Nanchang Zoo).
Analysis of statistical power to detect significant differentiation based on the 12 microsatellite markers used in this study
Datasets with eight predefined levels of population differentiation (FST values of 0.001, 0.0025, 0.005, 0.01, 0.02, 0.05, 0.075) were generated using POWSIM. Statistical power was defined as the proportion of times the null hypothesis of equal allele frequencies across populations was rejected using a chi-square test or a Fisher’s exact test.
