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

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.

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Captive management and the maintenance of genetic diversity in a vulnerable marsupial, the greater bilby

Australian Mammalogy ◽

10.1071/am14009 ◽

2015 ◽

Vol 37 (2) ◽

pp. 170 ◽

Cited By ~ 6

Author(s):

Emily J. Miller ◽

Mark D. B. Eldridge ◽

Keith Morris ◽

Neil Thomas ◽

Catherine A. Herbert

Keyword(s):

Genetic Diversity ◽

Captive Breeding ◽

Natural Habitat ◽

Species Conservation ◽

Molecular Data ◽

Breeding Programs ◽

Captive Populations ◽

Genetic Impact ◽

Captive Breeding Programs

The endemic Australian greater bilby (Macrotis lagotis) is a vulnerable and iconic species. It has declined significantly due to habitat loss, as well as competition and predation from introduced species. Conservation measures include a National Recovery Plan that incorporates several captive breeding programs. Two of these programs were established within 12 months of one another (1997/98), with the same number and sex ratio of founding individuals, but executed different breeding strategies: (1) unmanipulated mating in semi–free range natural habitat versus (2) minimising mean kinship in large enclosures, with the supplementation of new individuals into both populations. This study evaluates the long-term genetic impact of these programs and examines the congruency between the pedigree studbook estimates of diversity and molecular data. Our data demonstrate that genetic diversity was maintained in both populations, with the supplementation of new individuals contributing to the gene pool. The studbook estimates of diversity and inbreeding are not consistent with the microsatellite data and should not solely be relied upon to evaluate the genetic health of captive populations. Our analyses suggest that captive breeding programs may not require costly and intensive management to effectively maintain long-term genetic diversity in a promiscuous species.

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Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d221036 ◽

2021 ◽

Vol 22 (10) ◽

Author(s):

Zulfahmi Zulfahmi ◽

Parjanto Parjanto ◽

Edi Purwanto ◽

Ahmad Yunus

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Genetic Differentiation ◽

Gene Diversity ◽

In Situ Conservation ◽

Genetic Material ◽

Ex Situ ◽

Breeding Programs ◽

The Mean

Abstract. Zulfahmi, Parjanto, Purwanto E, Yunus A. 2021. Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia. Biodiversitas 22: 4431-4439. Information on genetic variation within and among populations of Eurycoma apiculata plants is important to develop strategies for their conservation, sustainable use, and genetic improvement. To date, no information on genetic variation within and among populations of the E. apiculata has been reported. This study aims to assess genetic diversity within and among populations of E. apiculata based on RAPD markers, and to determine populations to collect E. apiculata genetic material for conservation and breeding programs. Young leaves of E. apiculata were collected from six natural populations. Fifteen RAPD primers were used to assess the genetic diversity of each population. The data obtained were analyzed with POPGEN and Arlequin software. The amplification results of 15 selected primers produced 3-16 loci with all primers 100% polymorphic. At the species level, the mean allele per locus (Na), number of effective alleles (Ne), percentage of polymorphic loci (PPL), Nei’s gene diversity index (He) and Shannon information index (I) were 2.000, 1.244, 100%, 0.167, and 0.286, respectively. At the population level, the mean values for Na, Ne, PPL, He and I were 1.393, 1.312, 39.27%, 0.119, and 0.186, respectively. The highest value of gene diversity within population (He) was found in the Lingga-1 population and the lowest value was found in the Rumbio population. The value of genetic differentiation among populations (GST) of E. apiculata is 0.284, consistent with the results of the AMOVA analysis which found that genetic variation among populations was 23.14%, indicates that the genetic variation of E. apiculata was more stored within populations than among populations. The gene flow (Nm) value of E. apiculata was 1.259 migrants per generation among populations. The Nm value of this species was high category, and could inhibit genetic differentiation among populations. The clustering of E. apiculata population based on the UPGMA dendrogram and PCA was inconsistent with its geographic distribution, reflecting the possibility that genes migration occurred between islands in the past. The main finding of this study was the genetic variation of the E. apiculata mostly stored within the population. Therefore, the population with the highest genetic diversity is a priority for in-situ conservation, and collection of E. apiculata genetic material for ex-situ conservation and breeding programs should be carried out minimum from Lingga-1 and Pokomo populations.

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

Wildlife Research ◽

10.1071/wr13103 ◽

2014 ◽

Vol 41 (4) ◽

pp. 277 ◽

Cited By ~ 6

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.

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Seedling Selection Using Molecular Approach for Ex Situ Conservation of Critically Endangered Tree Species (Vatica bantamensis (Hassk.) Benth. & Hook. ex Miq.) in Java, Indonesia

Tropical Conservation Science ◽

10.1177/1940082919849506 ◽

2019 ◽

Vol 12 ◽

pp. 194008291984950 ◽

Cited By ~ 1

Author(s):

Yayan Wahyu C. Kusuma ◽

Siti R. Ariati ◽

Rosniati A. Risna ◽

Chika Mitsuyuki ◽

Yoshihisa Suyama ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Plant Species ◽

Ex Situ Conservation ◽

Critically Endangered ◽

Ex Situ ◽

Genetic Diversity And Structure ◽

In The Wild ◽

Genetic Clusters ◽

Ex Situ Collection

Ex situ conservation is an important complementary strategy for in situ to conserve endangered plant species. However, the limited areas designated for ex situ conservation such as in botanic gardens have become a great challenge for conservation practitioners and scientists attempting to optimally conserve the genetic diversity of targeted plant species. Our study aimed to assess genetic diversity and structure of wild seedlings of Vatica bantamensis, an endemic and critically endangered dipterocarp from Java (Indonesia). We also estimated genetic differentiation between the wild seedlings and existing ex situ collection and evaluated the genetic diversity preserved in the ex situ collection. Our analysis, using 730 single-nucleotide polymorphisms loci, showed that wild seedlings exhibited higher genetic diversity than the ex situ collection (nucleotide diversity, µ = 0.26 and 0.16, respectively). Significant genetic differentiation was also detected ( FST = 0.32) between wild seedlings and ex situ collection. Furthermore, we found high kinship within the ex situ collection suggesting low genetic diversity since the founding collection. We also detected three distinct genetic clusters from all samples combined (analysis of molecular variance, ϕ = 0.48, p < .001), with two clusters present in the wild seedlings that were not represented in the ex situ collection. We recommend that supplementary collections from the two newly identified genetic clusters in the wild seedlings should be incorporated to increase genetic diversity in the ex situ collection. Furthermore, our study demonstrated that understanding the population genetics of targeted endangered species provides better results for ex situ conservation strategies.

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Genetic diversity, phylogenetic relationships and conservation of Edwards's Pheasant Lophura edwardsi

Bird Conservation International ◽

10.1017/s095927090000215x ◽

1998 ◽

Vol 8 (4) ◽

pp. 395-410 ◽

Cited By ~ 1

Author(s):

Alain Hennache ◽

Ettore Randi ◽

Vittorio Lucchini

Keyword(s):

Genetic Diversity ◽

Captive Breeding ◽

Nuclear Dna ◽

Genetic Research ◽

Ex Situ ◽

Historical Study ◽

Evolutionary Divergence ◽

Taxonomic Rank ◽

Mtdna Sequence ◽

In The Wild

SummaryAn historical study shows that the present day ex situ population of Edwards's Pheasant Lophura edwardsi, now numbering over 1,000 living specimens, originated in the 1920s from at least six different sources and c. 30 potential founders, including more males than females. Partial sequences, 820 nucleotides long, of the mitochondrial DNA (mtDNA) control-region were obtained in representatives of about half of 21 captive-reared bloodlines, identified from data in the revised International Studbook. All captive-reared birds had identical sequences. Sequences of mtDNA obtained from museum skins and samples of birds collected in the wild were slightly different from that representing the captivereared birds. The lack of mtDNA variability in the captive stock is probably due to the small number of founding females and genetic drift during c. 30 generations of captive breeding. Estimation of true extent of mtDNA sequence variability in historical and living wild Edwards's Pheasants awaits the procurement and analysis of more specimens. At least one bloodline of captive Edwards's Pheasant is polluted with exogenous genes resulting from past hybridization with Swinhoe's Pheasant L. sivinhoii. Edwards's Pheasant is more closely related to Vietnamese Pheasant L. hatinhensis and Imperial Pheasant L. imperialis than to several other taxa regarded as full species in the genus Lophura. However it is not yet possible to determine the extent of their evolutionary divergence and of their proper taxonomic rank. The initial results of this genetic research suggest that there should be efforts to (1) expand field sampling and genetic analyses of wild populations of Lophura species, (2) purge the captive stock of Edwards' Pheasant of all hybrids, (3) apply microsatellite analyses to estimate the level of genetic diversity in nuclear DNA.

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Genetic Diversity and Population Structure of Two Endangered Neotropical Parrots Inform In Situ and Ex Situ Conservation Strategies

Diversity ◽

10.3390/d13080386 ◽

2021 ◽

Vol 13 (8) ◽

pp. 386

Author(s):

Carlos I. Campos ◽

Melinda A. Martinez ◽

Daniel Acosta ◽

Jose A. Diaz-Luque ◽

Igor Berkunsky ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Management Strategies ◽

Ex Situ ◽

Conservation Strategies ◽

Genetic Management ◽

Captive Populations ◽

In Captivity ◽

In The Wild ◽

Genetic Signatures

A key aspect in the conservation of endangered populations is understanding patterns of genetic variation and structure, which can provide managers with critical information to support evidence-based status assessments and management strategies. This is especially important for species with small wild and larger captive populations, as found in many endangered parrots. We used genotypic data to assess genetic variation and structure in wild and captive populations of two endangered parrots, the blue-throated macaw, Ara glaucogularis, of Bolivia, and the thick-billed parrot, Rhynchopsitta pachyrhyncha, of Mexico. In the blue-throated macaw, we found evidence of weak genetic differentiation between wild northern and southern subpopulations, and between wild and captive populations. In the thick-billed parrot we found no signal of differentiation between the Madera and Tutuaca breeding colonies or between wild and captive populations. Similar levels of genetic diversity were detected in the wild and captive populations of both species, with private alleles detected in captivity in both, and in the wild in the thick-billed parrot. We found genetic signatures of a bottleneck in the northern blue-throated macaw subpopulation, but no such signal was identified in any other subpopulation of either species. Our results suggest both species could potentially benefit from reintroduction of genetic variation found in captivity, and emphasize the need for genetic management of captive populations.

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

PeerJ ◽

10.7717/peerj.6643 ◽

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.

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Microsatellite analysis reveals low genetic diversity in managed populations of the critically endangered gharial (Gavialis gangeticus) in India

Scientific Reports ◽

10.1038/s41598-021-85201-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Surya Prasad Sharma ◽

Mirza Ghazanfarullah Ghazi ◽

Suyash Katdare ◽

Niladri Dasgupta ◽

Samrat Mondol ◽

...

Keyword(s):

Genetic Diversity ◽

Indian Subcontinent ◽

Population Decline ◽

Mitochondrial Control Region ◽

Critically Endangered ◽

Term Survival ◽

Low Level ◽

Genetic Status ◽

In The Wild ◽

Gavialis Gangeticus

AbstractThe gharial (Gavialis gangeticus) is a critically endangered crocodylian, endemic to the Indian subcontinent. The species has experienced severe population decline during the twentieth century owing to habitat loss, poaching, and mortalities in passive fishing. Its extant populations have largely recovered through translocation programmes initiated in 1975. Understanding the genetic status of these populations is crucial for evaluating the effectiveness of the ongoing conservation efforts. This study assessed the genetic diversity, population structure, and evidence of genetic bottlenecks of the two managed populations inhabiting the Chambal and Girwa Rivers, which hold nearly 80% of the global gharial populations. We used seven polymorphic nuclear microsatellite loci and a 520 bp partial fragment of the mitochondrial control region (CR). The overall mean allelic richness (Ar) was 2.80 ± 0.40, and the observed (Ho) and expected (He) heterozygosities were 0.40 ± 0.05 and 0.39 ± 0.05, respectively. We observed low levels of genetic differentiation between populations (FST = 0.039, P < 0.05; G’ST = 0.058, P < 0.05 Jost’s D = 0.016, P < 0.05). The bottleneck analysis using the M ratio (Chambal = 0.31 ± 0.06; Girwa = 0.41 ± 0.12) suggested the presence of a genetic bottleneck in both populations. The mitochondrial CR also showed a low level of variation, with two haplotypes observed in the Girwa population. This study highlights the low level of genetic diversity in the two largest managed gharial populations in the wild. Hence, it is recommended to assess the genetic status of extant wild and captive gharial populations for planning future translocation programmes to ensure long-term survival in the wild.

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Conservation biology of the critically endangered salamander, Paradactylodon persicus gorganensis (Clergue-Gazeau & Thorn, 1979) (Amphibia: Hynobiidae) in northeastern Iran

Animal Biology ◽

10.1163/15707563-bja10057 ◽

2021 ◽

pp. 1-12

Author(s):

Seyyed Saeed Hosseinian Yousefkhani

Keyword(s):

High Elevation ◽

Quality Parameters ◽

Critically Endangered ◽

Ex Situ ◽

Conservation Action ◽

Agriculture Industry ◽

Negative Effect ◽

In The Wild ◽

Future Viability ◽

Anthropogenic Threats

Abstract Paradactylodon persicus gorganensis is a critically endangered salamander found in northeastern Iran which faces increasing major anthropogenic threats such as agriculture, industry and mining. The aim of the current study is to identify key environmental variables associated with the species’ presence. Also, measuring and comparing the water quality parameters in habitats where P. p. gorganensis is present and absent are the other aims of the study. The results indicate that high pH and dissolved oxygen values have a negative effect on the species’ presence, while its presence was strongly correlated with low mean water temperatures. The species’ range in response to the climate change will shift to the south and east, where areas of high elevation occur, because the species favors cold habitats. This study indicates that it will be particularly important to evaluate the whole range where P. p. gorganensis exists when preparing conservation action plans. It is recommended that ex-situ conservation programs are incorporated into conservation planning for the species, because the number of individuals in the wild is so low and their future viability is fragile.

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Population genetics and conservation of the critically endangered Clematis acerifolia (Ranunculaceae)

Canadian Journal of Botany ◽

10.1139/b05-097 ◽

2005 ◽

Vol 83 (10) ◽

pp. 1248-1256 ◽

Cited By ~ 5

Author(s):

J. López-Pujol ◽

F.-M. Zhang ◽

S. Ge

Keyword(s):

Genetic Diversity ◽

Population Genetic ◽

Critically Endangered ◽

Ex Situ ◽

Genetic Structuring ◽

Long Term Storage ◽

Hardy Weinberg Equilibrium ◽

Term Storage

Allozyme electrophoresis was used to evaluate the levels of genetic diversity and population genetic structure of the critically endangered Clematis acerifolia Maximowicz (Ranunculaceae), a narrow endemic species in China. On the basis of variation at 19 putative loci in nine populations covering the entire distribution of this species, low values of genetic diversity were detected (P = 20.5%, A = 1.27, and He = 0.072). A significant deficiency of heterozygotes was found in all populations. Most loci showed deviations from the Hardy–Weinberg equilibrium, probably as a result of population genetic structuring. The high genetic divergence among populations (FST = 0.273) can be interpreted as an effect of the extinction of local populations and genetic drift within extant populations, and has probably been enhanced by habitat fragmentation in recent decades. Threats to this species are mainly anthropogenic (road works, construction of holiday resorts, and extraction activities), although stochastic risks cannot be ignored. Therefore, to preserve extant genetic variation of C. acerifolia, in situ strategies, such as the preservation of its habitat or at least the most diverse populations, and ex situ measures, such as the collection and long-term storage of seeds, should be adopted.

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