scholarly journals Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6643
Author(s):  
Guoling Chen ◽  
Chenqing Zheng ◽  
Nelson Wan ◽  
Daoqiang Liu ◽  
Vivian Wing Kan Fu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Haplotype Analysis ◽  
Genetic Relatedness ◽  
Wild Population ◽  
Critically Endangered ◽  
Assignment Test ◽  
Microsatellite Data ◽  
Wild Populations ◽  
Captive Populations ◽  
Mitochondrial Data

Background Captive populations permit research and conservation of endangered species in which these efforts are hardly implemented in wild populations. Thus, analysing genetic diversity and structure of captive populations offers unique opportunities. One example is the critically endangered Blue-crowned Laughingthrush, Garrulax courtoisi, which has only two known wild populations in Wuyuan, Jiangxi and Simao, Yunnan, China. We carried out the first conservation genetic study, in order to provide useful implications that allow for successful ex situ conservation and management of the Blue-crowned Laughingthrush. Methods Using the novel microsatellite markers developed by whole-genome sequencing, we genotyped two captive populations, from the Ocean Park Hong Kong, which are of unknown origin, and the Nanchang Zoo, which were introduced from the Wuyuan wild population since the year 2010–2011, respectively. 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 relatedness based on the microsatellite data with ML-Relate. Results Our results 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 weak population structuring between these two populations. The average pairwise relatedness coefficient was not significant, and their genetic relatedness was quantified. Discussion This study offers a genetic tool and consequently reveals a low level of genetic diversity within populations of a critically endangered bird species. Furthermore, our results indicate that we cannot exclude the probability that the origin of the Hong Kong captive population was the wild population from Wuyuan. These results provide valuable knowledge that can help improve conservation management and planning for both captive and wild Blue-crowned Laughingthrush populations.

scholarly journals Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites

2018 ◽  
Author(s):  
Guoling Chen ◽  
Chenqing Zheng ◽  
Nelson Wan ◽  
Daoqiang Liu ◽  
Vivian Wing Kan Fu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Haplotype Analysis ◽  
Critically Endangered ◽  
Assignment Test ◽  
Captive Population ◽  
Microsatellite Data ◽  
Population Assignment ◽  
Mitochondrial Data

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.

scholarly journals Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites

2018 ◽  
Author(s):  
Guoling Chen ◽  
Chenqing Zheng ◽  
Nelson Wan ◽  
Daoqiang Liu ◽  
Vivian Wing Kan Fu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Haplotype Analysis ◽  
Critically Endangered ◽  
Assignment Test ◽  
Captive Population ◽  
Microsatellite Data ◽  
Population Assignment ◽  
Mitochondrial Data

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.

scholarly journals Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites

2018 ◽  
Author(s):  
Guoling Chen ◽  
Chenqing Zheng ◽  
Nelson Wan ◽  
Daoqiang Liu ◽  
Vivian Wing Kan Fu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
Haplotype Analysis ◽  
Critically Endangered ◽  
Assignment Test ◽  
Captive Population ◽  
Microsatellite Data ◽  
Population Assignment ◽  
Mitochondrial Data

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.

scholarly journals Getting off to a good start? Genetic evaluation of the ex situ conservation project of the Critically Endangered Montseny brook newt (Calotriton arnoldi)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3447 ◽  
Author(s):  
Emilio Valbuena-Ureña ◽  
Anna Soler-Membrives ◽  
Sebastian Steinfartz ◽  
Mònica Alonso ◽  
Francesc Carbonell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Captive Breeding ◽  
Genetic Material ◽  
Morphological Differentiation ◽  
Critically Endangered ◽  
Ex Situ ◽  
Wild Populations ◽  
Breeding Programs ◽  
Captive Populations ◽  
In The Wild

Ex situ management strategies play an important role in the conservation of threatened species when the wild survival of the species cannot be ensured. Molecular markers have become an outstanding tool for the evaluation and management of captive breeding programs. Two main genetic objectives should be prioritized when planning breeding programs: the maintenance of maximum neutral genetic diversity, and to obtain “self-sustaining” captive populations. In this study, we use 24 microsatellite loci to analyze and evaluate the genetic representativity of the initial phases of the captive breeding program of the Montseny brook newt, Calotriton arnoldi, an Iberian endemic listed as Critically Endangered. The results show that the initial captive stock has 74–78% of the alleles present in the wild populations, and captures roughly 93–95% of their total genetic diversity as observed in a previous study on wild newts, although it does not reach the desired 97.5%. Moreover, the percentage of unrelatedness among individuals does not exceed 95%. Therefore, we conclude that the genetic diversity of the captive stock should be improved by incorporating genetic material from unrelated wild newts. In recognition of the previously described significant genetic and morphological differentiation between eastern and western wild populations of C. arnoldi, we suggest maintaining two distinct breeding lines, and we do not recommend outbreeding between these lines. Our comparisons of genetic diversity estimates between real and distinct sample-sized simulated populations corroborated that a minimum of 20 individuals are needed for each captive population, in order to match the level of genetic diversity present in the wild populations. Thus, the current initial stock should be reinforced by adding wild specimens. The captive stock and subsequent cohorts should be monitored in order to preserve genetic variation. In order to avoid genetic adaptation to captivity, occasionally incorporating previously genotyped individuals from the wild into the captive populations is recommended.

Genetic diversity maintained in comparison of captive-propagated and wild populations of Lampsilis fasciola and Ptychobranchus fasciolaris (Bivalvia: Unionidae)

2021 ◽  
Author(s):  
Nichelle M. VanTassel ◽  
Todd J. Morris ◽  
Christopher G. Wilson ◽  
David T Zanatta
Keyword(s):  
Genetic Diversity ◽  
Wild Population ◽  
Strong Support ◽  
Wild Populations ◽  
Effective Population ◽  
Brood Stock ◽  
Genetic Population ◽  
Captive Populations ◽  
Population Structure Analysis ◽  
Genetic Diversity And Structure

We compared the genetic diversity and structure between wild and captive-propagated freshwater mussels at risk in Canada, Lampsilis fasciola (Wavy-rayed Lampmussel, WRL) and Ptychobranchus fasciolaris (Kidneyshell, KS), using microsatellite generated genotypes. No significant differences were detected between wild and propagated WRL (from 12 mothers) or KS (from 7 mothers) based on genetic diversity metrics using Kruskal-Wallis tests. Effective population size (Ne) was estimated and there was considerable overlap in the estimated Ne between wild and captive populations of both species. Pairwise FST and Dest values among wild WRL, hatchery-raised WRL juveniles, and across different time periods (2008 to 2018) were generally low (FST = 0.007-0.043, Dest = 0.005-0.282). Pairwise FST and Dest for KS were not significant and low (0.012, 0.017). When comparing captive-reared offspring with the wild population, STRUCTURE analysis revealed strong support for a single genetic population. With at least 7 females contributing to brood stock, genetic diversity was maintained. Further research is needed to assess the male contribution to each glochidial brood, and the variability of genetic diversity in individual glochidial broods.

Genetic relatedness and cultivar identification in a valuable garden species, Hesperantha coccinea ( Schizostylis coccinea)

2009 ◽  
Vol 7 (03) ◽  
pp. 281-290
Author(s):  
Kirsten Wolff ◽  
Sabina Knees ◽  
Suzanne Cubey
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Dna Fingerprinting ◽  
Genetic Relatedness ◽  
Cultivar Identification ◽  
Wild Populations ◽  
Multilocus Genotypes ◽  
Expected Heterozygosity ◽  
Garden Plants ◽  
Garden Plant

DNA fingerprinting using microsatellites is a useful aid in cultivar identification, but has rarely been applied to garden plants. Eleven microsatellite markers were developed for the valuable garden plantHesperanthacoccinea(Schizostylis coccinea), and used to determine relatedness of accessions. Several accessions, described as separate cultivars, appeared to have identical genotypes. Among the 53 accessions tested, there were 34 unique multilocus genotypes. The level of polymorphism detected in the cultivars was high, with on average seven alleles per locus and an average expected heterozygosity of 0.72 across loci. It is clear from the genotypes that a large proportion of the cultivars are closely related to each other. The resulting markers can now be used to generate a complete database of all known cultivars of the species and to detect essentially derived cultivars. As an extension of this study, the markers identified here could also inform us about the genetic diversity in wild populations.

scholarly journals Genetic analysis and population structure of wild and cultivated wishbone flower (Torenia fournieri Lind.) lines related to specific floral color

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11702
Author(s):  
Shikai Guan ◽  
Qian Song ◽  
Jinye Zhou ◽  
Haixia Yan ◽  
Yuxiang Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Wild Population ◽  
Wild Populations ◽  
Torenia Fournieri ◽  
Similar Reduction ◽  
Floral Color ◽  
Hybrid Lines

Background The wishbone flower or Torenia fournieri Lind., an annual from tropical Indochina and southern China, is a popular ornamental plant, and many interspecific (T. fournieri × T. concolor) hybrid lines have been bred for the international market. The cultivated lines show a pattern of genetic similarity that correlates with floral color which informs on future breeding strategies. This study aimed to perform genetic analysis and population structure of cultivated hybrid lines comparing with closely related T. concolor wild populations. Methods We applied the retrotransposon based iPBS marker system for genotyping of a total of 136 accessions from 17 lines/populations of Torenia. These included 15 cultivated lines of three series: Duchess (A, B, C); Kauai (D, E, F, G, H, I, J); Little Kiss (K, L, M, N, P) and two wild T. concolor populations (Q and R). PCR products from each individual were applied to estimate the genetic diversity and differentiation between lines/populations. Results Genotyping results showed a pattern of genetic variation differentiating the 17 lines/populations characterized by their specific floral colors. The final PCoA analysis, phylogenetic tree construction, and Bayesian population structural bar plot all showed a clear subdivision of lines/populations analysed. The 15 cultivated hybrid lines and the wild population Q that collected from a small area showed the lowest genetic variability while the other wild population R which sampled from a larger area had the highest genetic variability. Discussion The extremely low genetic variability of 15 cultivated lines indicated that individual line has similar reduction in diversity/heterozygosity from a bottleneck event, and each retained a similar (but different from each other) content of the wild genetic diversity. The genetic variance for the two wild T. concolor populations could be due to our varied sampling methods. The two wild populations (Q, R) and the cultivated hybrid lines (I, K, M, N, P) are genetically more closely related, but strong positive correlations presented in cultivated lines A, C, E, M, and N. These results could be used to guide future Torenia breeding. Conclusions The genetic variation and population structure found in our study showed that cultivated hybrid lines had similar reduction in diversity/heterozygosity from a bottleneck event and each line retained a similar (but different from each other) content of the wild genetic diversity, especially when strong phenotypic selection of floral color overlaps. Generally, environmental factors could induce transposon activation and generate genetic variability which enabled the acceleration of the evolutionary process of wild Torenia species. Our study revealed that wild Torenia populations sampled from broad geographic region represent stronger species strength with outstanding genetic diversity, but selective breeding targeting a specific floral color decreased such genetic variability.

Testing the regional genetic representativeness of captive koala populations in South-East Queensland

2014 ◽  
Vol 41 (4) ◽  
pp. 277 ◽  
Author(s):  
Jennifer M. Seddon ◽  
Kristen E. Lee ◽  
Stephen D. Johnston ◽  
Vere N. Nicolson ◽  
Michael Pyne ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Microsatellite Loci ◽  
Ex Situ ◽  
Wild Populations ◽  
Phascolarctos Cinereus ◽  
Significant Differentiation ◽  
Captive Populations ◽  
Neutral Genetic Diversity ◽  
Leibler Divergence

Context Captive breeding for release back to the wild is an important component of ex situ conservation but requires genetic diversity that is representative of the wild population and has the ultimate goal of producing ecologically sustainable and resilient populations. However, defining and testing for representativeness of captive populations is difficult. Koalas (Phascolarctos cinereus) are bred for educational and tourism purposes in zoos and wildlife parks in South-East Queensland, but there are drastic declines evident in some wild koala populations in this region. Aim We compared genetic diversity at microsatellite loci and mitochondrial DNA in two captive koala populations with that of the local, wild koalas of South-East Queensland, determining the degree to which genetic diversity of neutral loci had been preserved and was represented in the captive populations. Key results The expected heterozygosity and the allelic richness was significantly greater in one captive colony than one wild South-East Queensland population. There was low but significant differentiation of the captive from wild populations using FST, with greater differentiation described by Jost’s Dest. In contrast, a newly introduced Kullback–Leibler divergence measure, which assesses similarity of allele frequencies, showed no significant divergence of colony and wild populations. The captive koalas lacked many of the mitochondrial haplotypes identified from South-East Queensland koalas and possessed seven other haplotypes. Conclusions Captive colonies of koalas have maintained levels of overall neutral genetic diversity similar to wild populations at microsatellite loci and low but significant differentiation likely resulted from drift and founder effects in small captive colonies or declining wild populations. Mitochondrial DNA suggests that captive founders were from a wider geographic source or that haplotypes have been lost locally. Implications Overall, tested captive koalas maintain sufficient microsatellite diversity to act as an in situ reservoir for neutral genetic diversity of regional populations.

scholarly journals Genetic diversity and population structure of founders from wildlife conservation management units and wild populations of critically endangered Dermatemys mawii

2019 ◽  
Vol 19 ◽  
pp. e00616 ◽  
Author(s):  
Manuel Ignacio Gallardo-Alvárez ◽  
Julia María Lesher-Gordillo ◽  
Salima Machkour-M’Rabet ◽  
Claudia Elena Zenteno-Ruiz ◽  
León David Olivera-Gómez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Wildlife Conservation ◽  
Conservation Management ◽  
Critically Endangered ◽  
Wild Populations ◽  
Management Units
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