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 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.

scholarly journals Rejection of a serial founder effects model of genetic and linguistic coevolution

2012 ◽  
Vol 279 (1736) ◽  
pp. 2281-2288 ◽  
Author(s):  
Keith Hunley ◽  
Claire Bowern ◽  
Meghan Healy
Keyword(s):  
Genetic Diversity ◽  
Negative Correlation ◽  
Microsatellite Loci ◽  
Population Genetic ◽  
Evolutionary Process ◽  
Founder Effects ◽  
Genetic Studies ◽  
Neutral Genetic Diversity ◽  
Genetic Pattern ◽  
Autosomal Microsatellite Loci

Recent genetic studies attribute the negative correlation between population genetic diversity and distance from Africa to a serial founder effects (SFE) evolutionary process. A recent linguistic study concluded that a similar decay in phoneme inventories in human languages was also the product of the SFE process. However, the SFE process makes additional predictions for patterns of neutral genetic diversity, both within and between groups, that have not yet been tested on phonemic data. In this study, we describe these predictions and test them on linguistic and genetic samples. The linguistic sample consists of 725 widespread languages, which together contain 908 distinct phonemes. The genetic sample consists of 614 autosomal microsatellite loci in 100 widespread populations. All aspects of the genetic pattern are consistent with the predictions of SFE. In contrast, most of the predictions of SFE are violated for the phonemic data. We show that phoneme inventories provide information about recent contacts between languages. However, because phonemes change rapidly, they cannot provide information about more ancient evolutionary processes.

scholarly journals Demographic and genetic factors in the recovery or demise ofex situpopulations following a severe bottleneck in fifteen species of Hawaiian tree snails

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1406 ◽  
Author(s):  
Melissa R. Price ◽  
David Sischo ◽  
Mark-Anthony Pascua ◽  
Michael G. Hadfield
Keyword(s):  
Life History Traits ◽  
Human Impacts ◽  
Ex Situ ◽  
Wild Populations ◽  
Captive Populations ◽  
Introduced Predators ◽  
In Captivity ◽  
Term Data

Wild populations of endangered Hawaiian tree snails have declined precipitously over the last century due to introduced predators and other human impacts. Life history traits, such as very low fecundity (<5 offspring per year across taxa) and maturity at approximately four years of age have made recovery difficult. Conservation efforts such asin situpredator-free enclosures may increase survival to maturity by protecting offspring from predation, but no long-term data existed prior to this study demonstrating the demographic and genetic parameters necessary to maintain populations within those enclosures. We evaluated over 20 years of evidence for the dynamics of survival and extinction in captiveex situpopulations of Hawaiian tree snails established from wild-collected individuals. From 1991 to 2006, small numbers of snails (<15) from fifteen species were collected from the wild to initiate captive-reared populations as a hedge against extinction. This small number of founders resulted in a severe bottleneck in each of the captive-reared populations. We identified key demographic parameters that predicted population recovery from this bottleneck. Species with captive populations that produced between two and four offspring per adult per year and had 20–50% of those offspring survive to maturity recovered to numbers above 100 individuals, and maintained viable populations following a decline that occurred between 2009 and 2014. Those populations that had less than two offspring per adult per year and less than 20% survival to maturity did not reach 100 individuals in captivity, and many of these populations died out during the recent decline. We suggest that small reductions in fitness may contribute to extirpation in taxa with inherently low fecundity, by keeping populations below a threshold number essential to long-term recovery. Futureex situpopulations should be founded with no less than 15 adults, and maintained in conditions closely approximating the temperature and humidity of source locations to optimize fitness. Permanent translocations of wild populations for conservation purposes will be more likely to succeed with greater than 100 adults, and should be limited to locations with a similar climate to source locations.

scholarly journals Genetic diversity of wild and cultivated Coffea canephora in northeastern DR Congo and the implications for conservation.

2021 ◽  
Author(s):  
Samuel Vanden Abeele ◽  
Steven B. Janssens ◽  
Justin Asimonyio Anio ◽  
Yves Bawin ◽  
Jonas Depecker ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Coffea Canephora ◽  
Congo Basin ◽  
Ex Situ ◽  
Gene Pools ◽  
Wild Populations ◽  
Genetic Composition ◽  
Robusta Coffee ◽  
Republic Of The Congo

Premise: Many cultivated coffee varieties descend from Coffea canephora, commonly known as Robusta coffee. The Congo Basin has a century long history of Robusta coffee cultivation and breeding, and is hypothesized to be the region of origin of many of the cultivated Robusta varieties. Since little is known about the genetic composition of C. canephora in this region, we assessed the genetic diversity of wild and cultivated C. canephora shrubs in the Democratic Republic of the Congo. Methods: Using 18 microsatellite markers, we studied the genetic composition of wild and backyard-grown C. canephora shrubs in the Tshopo and Ituri provinces, and from the INERA Yangambi Coffee Collection. We assessed genetic clustering patterns, genetic diversity, and genetic differentiation between populations. Key results: Genetic differentiation was relatively strong between wild and cultivated C. canephora shrubs, and both gene pools harbored multiple unique alleles. Strong genetic differentiation was also observed between wild populations. The level of genetic diversity in wild populations was similar to that of the INERA Yangambi Coffee Collection, but local wild genotypes were mostly missing from that collection. Shrubs grown in the backyards were genetically similar to the breeding material from INERA Yangambi. Conclusions: Most C. canephora that is grown in local backyards originated from INERA breeding programs, while a few shrubs were obtained directly from surrounding forests. The INERA Yangambi Coffee Collection could benefit from an enrichment with local wild genotypes, to increase the genetic resources available for breeding purposes, as well as to support ex situ conservation.

scholarly journals The endangered Dama dama mesopotamica Brooke, 1875: genetic variability, allelic loss and hybridization signals

2012 ◽  
Vol 81 (4) ◽  
pp. 223-233 ◽  
Author(s):  
José L. Fernández-García
Keyword(s):  
Microsatellite Loci ◽  
Allelic Richness ◽  
Fallow Deer ◽  
Ex Situ ◽  
Allelic Loss ◽  
Dama Dama ◽  
Captive Populations ◽  
Dama Mesopotamica ◽  
High Conservation ◽  
The 19Th Century

The Persian fallow deer (Dama dama mesopotamica) formerly widespread in the Middle East was described scientifically at the end of the 19th century and considered extinct ever since. In 1956 it was rediscovered in south-western Iran. As a result, several countries have undertaken actions to reintroduce this subspecies in its native territory. In 2007 the Christian Oswald Foundation, in close cooperation with Iranian institutions, launched plans of in situ and ex situ breeding actions, with its centre in the German Von Opel Zoo and with cooperative Mediterranean partner countries as Israel, to support conservation efforts under scientific control. We performed genetic studies to study the suspected hybridization with European fallow deer (Dama dama dama) and a commitment to preserve pureblood populations. We used a set of microsatellite loci to examine genetic variation and recent hybridization with the European fallow deer. All microsatellite loci used were polymorphic, but some were monomorphic within subspecies. The allelic richness was similar in both subspecies but the ‘private allelic richness’ was reduced to a half in the Persian fallow deer, signalling allelic loss due to genetic drift and inbreeding. Moreover, we showed the presence of two discrete groups representing the two subspecies, with no signs of admixture or hybridization. Furthermore, Persian fallow deer studied here belong to two pre-defined genetics groups: the wild and the (more genetically impoverished) captive populations of Persian fallow deer. Finally, the Persian fallow deer deserves a high conservation priority, both in the Iranian stock and in the captive populations, so as to avoid hybridization.

Low genetic diversity and inbreeding depression in Queensland Koalas

1993 ◽  
Vol 20 (2) ◽  
pp. 177 ◽  
Author(s):  
JMW Wilmer ◽  
A Melzer ◽  
F Carrick ◽  
C Moritz
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Inbreeding Depression ◽  
Natural Populations ◽  
Small Population ◽  
Phascolarctos Cinereus ◽  
Low Genetic Diversity ◽  
History Of ◽  
Biased Sex Ratio ◽  
Two Populations

The amount of genetic variation in two natural populations of Queensland koalas (Phascolarctos cinereus adustus) was assessed by analysis of mitochondrial DNA. Levels and any adverse effects of inbreeding (inbreeding depression) were estimated from the pedigree of a well-characterised captive colony. Genetic diversity of mitochondrial DNA was found to be exceedingly low both within and between the two populations, but the variation detected was found to be strongly structured geographically. Inbreeding levels in the captive colony were moderate to high yet the only apparent evidence of inbreeding depression was a male-biased sex ratio. There was no evidence for decreased juvenile survivorship or growth rate with inbreeding. Because of the limited data it would be premature to conclude that koalas are relatively resistant to the effects of inbreeding. However, we suggest the hypothesis that koalas have a history of small population size, resulting in reduced susceptibility to inbreeding depression.

scholarly journals Selection of optimal spawning pairs to maintain genetic variation among captive populations of Acipenseridae based on the polymorphism of microsatellite loci

2016 ◽  
Vol 24 (2) ◽  
pp. 77-84 ◽  
Author(s):  
Dariusz Kaczmarczyk
Keyword(s):  
Genetic Variation ◽  
Computer Program ◽  
Microsatellite Loci ◽  
Fish Farm ◽  
Actual Data ◽  
Wild Populations ◽  
Captive Populations ◽  
In Captivity ◽  
Theoretical Paper ◽  
Selection Of

Abstract The American paddlefish, Polyodon spathula (Walbaum), is an endangered acipenserid fish. Its wild populations are supplemented with stocking material that is obtained by conducting artificial spawning in aquaculture conditions. When fish are bred in captivity, it is important to select breeding pairs that will produce the most genetically diverse progeny, since this permits maintaining the fitness of wild populations. Breeding pairs of land animals are selected successfully based on the polymorphism of their microsatellite loci. This theoretical paper asks how to adapt this technique to fish so that American paddlefish spawners can be paired with the aim of producing restocking material in aquaculture that maintains genetic variation. To test our calculating techniques, we used actual data on the polymorphism of the microsatellites from paddlefish broodstock at the Pogorze fish farm (Poland). The data enabled us to do calculations that showed which spawner pairs would create the most genetically diverse offspring and how to assemble sets of spawning pairs that would be best for maintaining genetic variation. The method presented in this paper can be used for breeding fish in aquaculture to help conserve species. It could also be used in a computer program which would automate calculations and present them in easy-to-read tables and graphs.

scholarly journals Genetic diversity and population structure of Amorphophallus albus, a plant species with extremely small populations (PSESP) endemic to dry-hot valley of Jinsha River

2020 ◽  
Author(s):  
Rong Tang ◽  
Erxi Liu ◽  
Yazhou Zhang ◽  
Johann Schinnerl ◽  
Weibang Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Plant Species ◽  
Ex Situ ◽  
Small Populations ◽  
Wild Populations ◽  
Jinsha River ◽  
High Genetic Diversity ◽  
Cultivated Populations

Abstract Background: Amorphophallus albus P. Y. Liu & J. F. Chen (Araceae) is a plant species with extremely small populations (PSESP) and an important economic crop endemic to dry-hot valleys along the Jinsha River. In order to gain information for sustaining the development and conservation of A. albus, we studied the genetic diversity and population structure of this species using microsatellite markers (SSR). In this study, we analysed 364 individuals belonging to 24 populations, including four wild populations and three ex-situ cultivated populations, collected in the provinces Yunnan, Sichuan and Hubei. Results: The population genetic analyses indicated that A. albus possesses moderate genetic diversity with the percentage of polymorphic loci (PPL) from 69.23% to 100%, an expected heterozygosity (He) of 0.504 and an average Shannon's Information Index (I) 0.912. Analysis of molecular variance (AMOVA) indicated that most of the variance (71%) resided within populations and the estimated gene flow (Nm) was 0.61. The results of UPGMA cluster tree, STRUCTURE analyses together with the Mantel test (R2 = 0.352, P < 0.01) indicated that geographically closely located populations are clustered together with some exceptions. Conclusions: Our results showed that A. albus still possesses moderate genetic variation in most of the studied populations, and for now, most cultivated populations were naturally distributed but still some reintroduction exists. For sustaining the present genetic variation, some protections measures are necessary for the wild populations and also for the cultivated ones with high genetic diversity.

Genetic Diversity and Demographic History of an Upper Hill Dipterocarp (Shorea platyclados): Implications for Conservation

2019 ◽  
Vol 110 (7) ◽  
pp. 844-856 ◽  
Author(s):  
Chin-Hong Ng ◽  
Soon-Leong Lee ◽  
Lee-Hong Tnah ◽  
Kevin K S Ng ◽  
Chai-Ting Lee ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci ◽  
Gene Diversity ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Population History ◽  
Conservation Strategy ◽  
Ex Situ ◽  
History Of ◽  
Shorea Platyclados

Abstract Southeast Asian rainforests at upper hill elevations are increasingly vulnerable to degradation because most lowland forest areas have been converted to different land uses. As such, understanding the genetics of upper hill species is becoming more crucial for their future management and conservation. Shorea platyclados is an important, widespread upper hill dipterocarp in Malaysia. To elucidate the genetic structure of S. platyclados and ultimately provide guidelines for a conservation strategy for this species, we carried out a comprehensive study of the genetic diversity and demographic history of S. platyclados. Twenty-seven populations of S. platyclados across its range in Malaysia were genotyped at 15 polymorphic microsatellite loci and sequenced at seven noncoding chloroplast DNA (cpDNA) regions. A total of 303 alleles were derived from the microsatellite loci, and 29 haplotypes were identified based on 2892 bp of concatenated cpDNA sequences. The populations showed moderately high genetic diversity (mean HE = 0.680 for microsatellite gene diversity and HT = 0.650 for total haplotype diversity) and low genetic differentiation (FST = 0.060). Bayesian clustering divided the studied populations into two groups corresponding to western and eastern Malaysia. Bottleneck analysis did not detect any recent bottleneck events. Extended Bayesian skyline analyses showed a model of constant size for the past population history of this species. Based on our findings, priority areas for in situ and ex situ conservation and a minimum population size are recommended for the sustainable utilization of S. platyclados.

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