Dataset Information

Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise.

ABSTRACT: Population genetic theory related to the consequences of rapid population decline is well-developed, but there are very few empirical studies where sampling was conducted before and after a known bottleneck event. Such knowledge is of particular importance for species restoration, given links between genetic diversity and the probability of long-term persistence. To directly evaluate the relationship between current genetic diversity and past demographic events, we collected genome-wide single nucleotide polymorphism data from prebottleneck historical (c.1906) and postbottleneck contemporary (c.2014) samples of Pinzón giant tortoises (Chelonoidis duncanensis; n = 25 and 149 individuals, respectively) endemic to a single island in the Galapagos. Pinzón giant tortoises had a historically large population size that was reduced to just 150-200 individuals in the mid 20th century. Since then, Pinzón's tortoise population has recovered through an ex situ head-start programme in which eggs or pre-emergent individuals were collected from natural nests on the island, reared ex situ in captivity until they were 4-5 years old and subsequently repatriated. We found that the extent and distribution of genetic variation in the historical and contemporary samples were very similar, with the latter group not exhibiting the characteristic genetic patterns of recent population decline. No population structure was detected either spatially or temporally. We estimated an effective population size (N e) of 58 (95% CI = 50-69) for the postbottleneck population; no prebottleneck N e point estimate was attainable (95% CI = 39-infinity) likely due to the sample size being lower than the true N e. Overall, the historical sample provided a valuable benchmark for evaluating the head-start captive breeding programme, revealing high retention of genetic variation and no skew in representation despite the documented bottleneck event. Moreover, this work demonstrates the effectiveness of head-starting in rescuing the Pinzón giant tortoise from almost certain extinction.

SUBMITTER: Jensen EL

PROVIDER: S-EPMC6231475 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise.

Jensen Evelyn L EL Edwards Danielle L DL Garrick Ryan C RC Miller Joshua M JM Gibbs James P JP Cayot Linda J LJ Tapia Washington W Caccone Adalgisa A Russello Michael A MA

Evolutionary applications 20180813 10

Population genetic theory related to the consequences of rapid population decline is well-developed, but there are very few empirical studies where sampling was conducted before and after a known bottleneck event. Such knowledge is of particular importance for species restoration, given links between genetic diversity and the probability of long-term persistence. To directly evaluate the relationship between current genetic diversity and past demographic events, we collected genome-wide single n ...[more]

PMID: 30459831

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Project description:Restoration of extirpated species via captive breeding has typically relied on population viability as the primary criterion for evaluating success. This criterion is inadequate when species reintroduction is undertaken to restore ecological functions and interactions. Herein we report on the demographic and ecological outcomes of a five-decade-long population restoration program for a critically endangered species of "ecosystem engineer": the endemic Española giant Galapagos tortoise (Chelonoidis hoodensis). Our analysis of complementary datasets on tortoise demography and movement, tortoise-plant interactions and Española Island's vegetation history indicated that the repatriated tortoise population is secure from a strictly demographic perspective: about half of tortoises released on the island since 1975 were still alive in 2007, in situ reproduction is now significant, and future extinction risk is low with or without continued repatriation. Declining survival rates, somatic growth rates, and body condition of repatriates suggests, however, that resources for continued population growth are increasingly limited. Soil stable carbon isotope analyses indicated a pronounced shift toward woody plants in the recent history of the island's plant community, likely a legacy of changes in competitive relations between woody and herbaceous plants induced by now-eradicated feral goats and prolonged absence of tortoises. Woody plants are of concern because they block tortoise movement and hinder recruitment of cactus--a critical resource for tortoises. Tortoises restrict themselves to remnant cactus patches and areas of low woody plant density in the center of the island despite an apparent capacity to colonize a far greater range, likely because of a lack of cactus elsewhere on the island. We conclude that ecosystem-level criteria for success of species reintroduction efforts take much longer to achieve than population-level criteria; moreover, reinstatement of endangered species as fully functioning ecosystem engineers may often require large-scale habitat restoration efforts in concert with population restoration.

Project description:The conservation of biodiverse areas around the world has contributed to the protection and recovery of endangered species. This has been the case for 11 species of Galapagos giant tortoises (Chelonoidis spp.) that today are successfully maintained over six islands: Española, Santiago, Pinzon, Isabela, San Cristobal and Santa Cruz. A favourable state of conservation will depend however on future development in the islands. In Santa Cruz Island the development of the agricultural areas has encroached on the migratory routes of the southwestern species C. porteri and may be an emergent conflict for tortoise conservation. We investigated the social and ecological inter-linkages using two methods framed under a participatory rural appraisal (PRA) approach: semi-structured interviews and questionnaires to study farmers' perceptions and attitudinal factors regarding giant tortoises; as well as the associated socio-economic impacts of the conflict. Moreover, we coupled the PRA approach with an ecological assessment of giant tortoises' population density by performing transect counts during the two yearly phases of giant tortoises' migration to the lowlands (January to June) and back to the highlands (July to December). Our results indicate that farmers reporting damage and cultivating crops have higher odds of taking actions (fencing and physical actions) towards giant tortoises; regardless of having (or not) a negative perception towards the species. The economic losses for crops and fences averaged 2.8 USD/m2 and 13USD/m, respectively, and provide an initial step to further analyse and characterise the direct and indirect damage costs. Finally, we estimated a density of 76 and 185 individuals of giant tortoises per km2 in the rural area for the lowland and highland migratory phases, respectively. Our approach provides grounded scientific social and ecological information to effectively inform and aid managers, policy and decision makers in the selection of adequate social and ecological criteria to implement the best available options in the resolution of this emergent conservation conflict.

Project description:Long-term population history can influence the genetic effects of recent bottlenecks. Therefore, for threatened or endangered species, an understanding of the past is relevant when formulating conservation strategies. Levels of variation at neutral markers have been useful for estimating local effective population sizes (N e ) and inferring whether population sizes increased or decreased over time. Furthermore, analyses of genotypic, allelic frequency, and phylogenetic information can potentially be used to separate historical from recent demographic changes. For 15 populations of Galápagos giant tortoises (Chelonoidis sp.), we used 12 microsatellite loci and DNA sequences from the mitochondrial control region and a nuclear intron, to reconstruct demographic history on shallow (past ?100 generations, ?2500 years) and deep (pre-Holocene, >10 thousand years ago) timescales. At the deep timescale, three populations showed strong signals of growth, but with different magnitudes and timing, indicating different underlying causes. Furthermore, estimated historical N e of populations across the archipelago showed no correlation with island age or size, underscoring the complexity of predicting demographic history a priori. At the shallow timescale, all populations carried some signature of a genetic bottleneck, and for 12 populations, point estimates of contemporary N e were very small (i.e., < 50). On the basis of the comparison of these genetic estimates with published census size data, N e generally represented ?0.16 of the census size. However, the variance in this ratio across populations was considerable. Overall, our data suggest that idiosyncratic and geographically localized forces shaped the demographic history of tortoise populations. Furthermore, from a conservation perspective, the separation of demographic events occurring on shallow versus deep timescales permits the identification of naturally rare versus newly rare populations; this distinction should facilitate prioritization of management action.

Dataset Information

Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise.

Publications

Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise.

Similar Datasets

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