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

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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High Genetic Diversity and Low Differentiation in Michelia shiluensis, an Endangered Magnolia Species in South China

Forests ◽

10.3390/f11040469 ◽

2020 ◽

Vol 11 (4) ◽

pp. 469 ◽

Cited By ~ 1

Author(s):

Yanwen Deng ◽

Tingting Liu ◽

Yuqing Xie ◽

Yaqing Wei ◽

Zicai Xie ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Human Disturbance ◽

Haplotype Diversity ◽

Conservation Strategy ◽

Ex Situ ◽

Conservation Strategies ◽

High Genetic Diversity ◽

Cpdna Markers

Research Highlights: This study is the first to examine the genetic diversity of Michelia shiluensis (Magnoliaceae). High genetic diversity and low differentiation were detected in this species. Based on these results, we discuss feasible protection measures to provide a basis for the conservation and utilization of M. shiluensis. Background and Objectives: Michelia shiluensis is distributed in Hainan and Guangdong province, China. Due to human disturbance, the population has decreased sharply, and there is thus an urgent need to evaluate genetic variation within this species in order to identify an optimal conservation strategy. Materials and Methods: In this study, we used eight nuclear single sequence repeat (nSSR) markers and two chloroplast DNA (cpDNA) markers to assess the genetic diversity, population structure, and dynamics of 78 samples collected from six populations. Results: The results showed that the average observed heterozygosity (Ho), expected heterozygosity (He), and percentage of polymorphic loci (PPL) from nSSR markers in each population of M. shiluensis were 0.686, 0.718, and 97.92%, respectively. For cpDNA markers, the overall haplotype diversity (Hd) was 0.674, and the nucleotide diversity was 0.220. Analysis of markers showed that the genetic variation between populations was much lower based on nSSR than on cpDNA (10.18% and 77.56%, respectively, based on an analysis of molecular variance (AMOVA)). Analysis of the population structure based on the two markers shows that one of the populations (DL) is very different from the other five. Conclusions: High genetic diversity and low population differentiation of M. shiluensis might be the result of rich ancestral genetic variation. The current decline in population may therefore be due to human disturbance rather than to inbreeding or genetic drift. Management and conservation strategies should focus on maintaining the genetic diversity in situ, and on the cultivation of seedlings ex-situ for transplanting back to their original habitat.

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The Tsushima leopard cat exhibits extremely low genetic diversity compared with the Korean Amur leopard cat: Implications for conservation

PeerJ ◽

10.7717/peerj.7297 ◽

2019 ◽

Vol 7 ◽

pp. e7297 ◽

Cited By ~ 1

Author(s):

Hideyuki Ito ◽

Miho Inoue-Murayama

Keyword(s):

Genetic Diversity ◽

Molecular Genetic ◽

Management Strategies ◽

Korean Population ◽

Ex Situ ◽

Genetic Management ◽

Founding Population ◽

Low Genetic Diversity ◽

Regional Population ◽

Leopard Cat

We examined genetic diversity of the wild Tsushima leopard cat—a regional population of the Amur leopard cat—using microsatellite markers. In addition, we compared genetic diversity of the Tsushima leopard cat with that of the Korean population of Amur leopard cat. Although bias should be considered when applying cross-species amplification, the Tsushima leopard cat showed a lower index of molecular genetic diversity than did the Korean population. These results were consistent with those obtained using other genetic markers, such as mitochondrial DNA and Y chromosome sequences. This low genetic diversity of the wild Tsushima leopard cat may be derived from the founding population. Furthermore, our results suggest that the captive populations held in Japanese zoos may show extremely low genetic diversity, leading to difficulties in genetic management of the Tsushima leopard cat. Moreover, the two regional populations were clearly separated using these marker sets. In the present study, we demonstrated that the genetic diversity of the Tsushima leopard cat is extremely low compared with that of the continental regional population. Importantly, the Japanese captive population for ex situ conservation was derived from a founding population with extremely low genetic diversity; hence, we assume that both the captive and wild populations showed extremely low genetic diversities. Our findings emphasize the need to develop carefully considered management strategies for genetic conservation.

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

PeerJ ◽

10.7717/peerj.3447 ◽

2017 ◽

Vol 5 ◽

pp. e3447 ◽

Cited By ~ 3

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.

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Effective population sizes and adaptive genetic variation in a captive bird population

PeerJ ◽

10.7717/peerj.5803 ◽

2018 ◽

Vol 6 ◽

pp. e5803 ◽

Cited By ~ 2

Author(s):

Giridhar Athrey ◽

Nikolas Faust ◽

Anne-Sophie Charlotte Hieke ◽

I. Lehr Brisbin

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Demographic History ◽

Ex Situ ◽

Adaptive Genetic Variation ◽

Effective Population ◽

B Locus ◽

Captive Populations ◽

Chain Of Custody ◽

Population Sizes

Captive populations are considered a key component of ex situ conservation programs. Research on multiple taxa has shown the differential success of maintaining demographic versus genetic stability and viability in captive populations. In typical captive populations, usually founded by few or related individuals, genetic diversity can be lost and inbreeding can accumulate rapidly, calling into question their ultimate utility for release into the wild. Furthermore, domestication selection for survival in captive conditions is another concern. Therefore, it is crucial to understand the dynamics of population sizes, particularly the effective population size, and genetic diversity at non-neutral and adaptive loci in captive populations. In this study, we assessed effective population sizes and genetic variation at both neutral microsatellite markers, as well as SNP variants from the MHC-B locus of a captive Red Junglefowl population. This population represents a rare instance of a population with a well-documented history in captivity, following a realistic scenario of chain-of-custody, unlike many captive lab populations. Our analyses, which included 27 individuals comprising the entirety of one captive population show very low neutral and adaptive genetic variation, as well as low effective sizes, which correspond with the known demographic history. Finally, our study also shows the divergent impacts of small effective size and inbreeding in captive populations on microsatellite versus adaptive genetic variation in the MHC-B locus. Our study provides insights into the difficulties of maintaining adaptive genetic variation in small captive populations.

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Effective population sizes and adaptive genetic variation in a captive bird population

10.1101/307728 ◽

2018 ◽

Author(s):

Giridhar Athrey ◽

Nikolas Faust ◽

Anne-Sophie Charlotte Hieke ◽

I. Lehr Brisbin

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Demographic History ◽

Ex Situ ◽

Adaptive Genetic Variation ◽

Effective Population ◽

B Locus ◽

Captive Populations ◽

Chain Of Custody ◽

Population Sizes

AbstractCaptive populations are considered a key component of ex situ conservation programs. Research on multiple taxa have shown the differential success of maintaining demographic versus genetic stability and viability in captive populations. In typical captive populations, usually founded by few or related individuals, genetic diversity can be lost and inbreeding can accumulate rapidly, calling into question their ultimate utility for release into the wild. Furthermore, domestication selection for survival in captive conditions is another concern. Therefore, it is crucial to understand the dynamics of population sizes, particularly the effective population size, and genetic diversity at non-neutral, at adaptive loci in captive populations.In this study, we assessed effective population sizes and genetic variation at both neutral microsatellite markers, as well as SNP variants from the MHC-B locus of a captive Red Junglefowl population. This population is represents a rare instance of a population with a well-documented history in captivity, following a realistic scenario of chain-of-custody, unlike captive lab populations. Our analysis, which included 27 individuals comprising the entirety of one captive population show very low neutral and adaptive genetic variation, as well as low effective sizes, which are surprising in spite of the known demographic history. Finally, our study also shows the divergent impacts of small effective size and inbreeding in captive populations on microsatellite versus adaptive genetic variation in the MHC-B locus. Our study provides insights into the difficulties of maintaining adaptive genetic variation in small captive populations.

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Conservation genetics of the threatened plant species Physaria filiformis (Missouri bladderpod) reveals strong genetic structure and a possible cryptic species

PLoS ONE ◽

10.1371/journal.pone.0247586 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0247586

Author(s):

Christine E. Edwards ◽

Brooke C. Tessier ◽

Joel F. Swift ◽

Burgund Bassüner ◽

Alexander G. Linan ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Structure ◽

Plant Species ◽

Genetic Drift ◽

Rare Species ◽

Ex Situ ◽

Ouachita Mountains ◽

Genetic Diversity And Structure ◽

Genetic Clusters

Understanding genetic diversity and structure in a rare species is critical for prioritizing both in situ and ex situ conservation efforts. One such rare species is Physaria filiformis (Brassicaceae), a threatened, winter annual plant species. The species has a naturally fragmented distribution, occupying three different soil types spread across four disjunct geographical locations in Missouri and Arkansas. The goals of this study were to understand: (1) whether factors associated with fragmentation and small population size (i.e., inbreeding, genetic drift or genetic bottlenecks) have reduced levels of genetic diversity, (2) how genetic variation is structured and which factors have influenced genetic structure, and (3) how much extant genetic variation of P. filiformis is currently publicly protected and the implications for the development of conservation strategies to protect its genetic diversity. Using 16 microsatellite markers, we genotyped individuals from 20 populations of P. filiformis from across its geographical range and one population of Physaria gracilis for comparison and analyzed genetic diversity and structure. Populations of P. filiformis showed comparable levels of genetic diversity to its congener, except a single population in northwest Arkansas showed evidence of a genetic bottleneck and two populations in the Ouachita Mountains of Arkansas showed lower genetic variation, consistent with genetic drift. Populations showed isolation by distance, indicating that migration is geographically limited, and analyses of genetic structure grouped individuals into seven geographically structured genetic clusters, with geographic location/spatial separation showing a strong influence on genetic structure. At least one population is protected for all genetic clusters except one in north-central Arkansas, which should therefore be prioritized for protection. Populations in the Ouachita Mountains were genetically divergent from the rest of P. filiformis; future morphological analyses are needed to identify whether it merits recognition as a new, extremely rare species.

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The genetic diversity and population structure of two endemic Amazonian quillwort (Isoetes L.) species

PeerJ ◽

10.7717/peerj.10274 ◽

2020 ◽

Vol 8 ◽

pp. e10274 ◽

Cited By ~ 1

Author(s):

Mirella Pupo Santos ◽

João V.S. Rabelo Araujo ◽

Arthur V. Sant’anna Lopes ◽

Julio Cesar Fiorio Vettorazzi ◽

Marcela Santana Bastos Boechat ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Geographical Location ◽

Inter Simple Sequence Repeat ◽

Shannon Index ◽

Conservation Strategies ◽

Amazon Forest ◽

Mass Extinctions ◽

Effective Conservation

Background Two endemic lycophyte species Isoetes cangae and Isoetes serracarajensis have been recently described in the State of Pará in the Amazon forest located in northern Brazil. Isoetes L. has survived through three mass extinctions. Plants are considered small-sized, heterosporous, and can display a great diversity of physiological adaptations to different environments. Thus, the current study aimed to estimate the genetic variation of the populations of I. cangae and I. serracarajensis to generate information about their different mechanisms for survival at the same geographical location that could point to different reproductive, adaptative and dispersal strategies and should be considered for effective conservation strategies. Methods The genetic diversity and population structure of I. cangae and I. serracarajensis were investigated using Inter Simple Sequence Repeat (ISSR) molecular markers. Total genomic DNA was isolated, and the genetic diversity parameters were calculated. Results The sixteen primers produced 115 reproducible bands, 87% of which were polymorphic. A high level of polymorphic loci (81.74% and 68.48%) and a high Shannon index (Sh = 0.376 and 0.289) were observed for I. cangae and I. serracarajensis, respectively. The coefficient of genetic differentiation between population areas (GST) showed a higher value in I. serracarajensis (0.5440). Gene flow was higher in I. cangae (1.715) and lower in I. serracarajensis populations (0.419). Overall, the results further show that I. serracarajensis and I. cangae are two species with considerable genetic variation and that these differences may reflect their habitats and modes of reproduction. These results should be considered in the development of effective conservation strategies for both species.

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Assessing the Psychological Priorities for Optimising Captive Asian Elephant (Elephas maximus) Welfare

Animals ◽

10.3390/ani10010039 ◽

2019 ◽

Vol 10 (1) ◽

pp. 39 ◽

Cited By ~ 3

Author(s):

Jake Stuart Veasey

Keyword(s):

Cognitive Processes ◽

Management Strategies ◽

Asian Elephant ◽

Evolutionary Significance ◽

Identification System ◽

Asian Elephants ◽

In Captivity ◽

In The Wild ◽

Human Care ◽

Species Specific

The welfare status of elephants under human care has been a contentious issue for two decades or more in numerous western countries. Much effort has gone into assessing the welfare of captive elephants at individual and population levels with little consensus having been achieved in relation to both the welfare requirements of captive elephants, or their absolute welfare status. A methodology capable of identifying the psychological priorities of elephants would greatly assist in both managing and assessing captive elephant welfare. Here, a Delphi-based Animal Welfare Priority Identification System© (APWIS©) is trialled to evaluate the reliability of the methodology and to determine the welfare significance of individual behaviours and cognitive processes for Asian elephants (Elaphus maximus). APWIS© examines the motivational characteristics, evolutionary significance and established welfare impacts of individual behaviours and cognitive processes of each species being assessed. The assessment carried out here indicates appetitive behaviours essential for survival in the wild, together species-specific social and cognitive opportunities are likely to be important to the welfare of Asian elephant in captivity. The output of this assessment, for the first time, provides comprehensive species-specific psychological/welfare priorities for Asian elephants that should be used to inform husbandry guidelines, habitat design and management strategies and can also provide a valuable reference tool for Asian elephant welfare assessment. The effective application of these insights could lead to substantive improvements in captive Asian elephant welfare.

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Strategies for conservation of germplasm in endemic redwoods in the face of climate change: a review

Plant Genetic Resources ◽

10.1017/s1479262111000153 ◽

2011 ◽

Vol 9 (3) ◽

pp. 411-422 ◽

Cited By ~ 5

Author(s):

M. R. Ahuja

Keyword(s):

Climate Change ◽

Genetic Diversity ◽

Conservation Strategy ◽

Ex Situ ◽

Conservation Strategies ◽

Phenotypic Traits ◽

Coast Redwood ◽

Giant Sequoia ◽

The Face

This study reviews the various conservation strategies applied to the four redwood species, namely coast redwood (Sequoia sempervirens), Sierra redwood or giant sequoia (Sequoiadendron giganteum), dawn redwood (Metasequoia glyptostroboides) and South American redwood or alerce (Fitzroya cupressoides), which are endemic in the USA, China and South America, respectively. All four redwood genera belong to the family Cupressaceae; they are monospecific, share a number of common phenotypic traits, including red wood, and are threatened in their native ranges due to human activity and a changing climate. Therefore, the management objective should be to conserve representative populations of the native species with as much genetic diversity as possible for their future survival. Those representative populations exhibiting relatively high levels of genetic diversity should be selected for germplasm preservation and monitored during the conservation phase by using molecular markers. In situ and ex situ strategies for the preservation of germplasm of the redwoods are discussed in this study. A holistic in situ gene conservation strategy calls for the regeneration of a large number of diverse redwood genotypes that exhibit adequate levels of neutral and adaptive genetic variability, by generative and vegetative methods for their preservation and maintenance in their endemic locations. At the same time, it would be desirable to conserve the redwoods in new ex situ reserves, away from their endemic locations with similar as well as different environmental conditions for testing their growth and survival capacities. In addition, other ex situ strategies involving biotechnological approaches for preservation of seeds, tissues, pollen and DNA in genebanks should also be fully exploited in the face of global climate change.

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Somewhat saved: a captive breeding programme for two endemic Christmas Island lizard species, now extinct in the wild

Oryx ◽

10.1017/s0030605316001071 ◽

2016 ◽

Vol 52 (1) ◽

pp. 171-174 ◽

Cited By ~ 8

Author(s):

Paul Andrew ◽

Hal Cogger ◽

Don Driscoll ◽

Samantha Flakus ◽

Peter Harlow ◽

...

Keyword(s):

Native Species ◽

Captive Breeding ◽

Biodiversity Loss ◽

Breeding Programme ◽

Lizard Species ◽

Christmas Island ◽

Captive Populations ◽

Captive Breeding Programme ◽

In Captivity ◽

In The Wild

AbstractAs with many islands, Christmas Island in the Indian Ocean has suffered severe biodiversity loss. Its terrestrial lizard fauna comprised five native species, of which four were endemic. These were abundant until at least the late 1970s, but four species declined rapidly thereafter and were last reported in the wild between 2009 and 2013. In response to the decline, a captive breeding programme was established in August 2009. This attempt came too late for the Christmas Island forest skink Emoia nativitatis, whose last known individual died in captivity in 2014, and for the non-endemic coastal skink Emoia atrocostata. However, two captive populations are now established for Lister's gecko Lepidodactylus listeri and the blue-tailed skink Cryptoblepharus egeriae. The conservation future for these two species is challenging: reintroduction will not be possible until the main threats are identified and controlled.

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