1
|
Çilingir FG, A'Bear L, Hansen D, Davis LR, Bunbury N, Ozgul A, Croll D, Grossen C. Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population. Gigascience 2022; 11:giac090. [PMID: 36251273 PMCID: PMC9553416 DOI: 10.1093/gigascience/giac090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/22/2022] [Accepted: 09/12/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two giant tortoise species left in the world. The species is endemic to Aldabra Atoll in Seychelles and is listed as Vulnerable on the International Union for Conservation of Nature Red List (v2.3) due to its limited distribution and threats posed by climate change. Genomic resources for A. gigantea are lacking, hampering conservation efforts for both wild and ex situpopulations. A high-quality genome would also open avenues to investigate the genetic basis of the species' exceptionally long life span. FINDINGS We produced the first chromosome-level de novo genome assembly of A. gigantea using PacBio High-Fidelity sequencing and high-throughput chromosome conformation capture. We produced a 2.37-Gbp assembly with a scaffold N50 of 148.6 Mbp and a resolution into 26 chromosomes. RNA sequencing-assisted gene model prediction identified 23,953 protein-coding genes and 1.1 Gbp of repetitive sequences. Synteny analyses among turtle genomes revealed high levels of chromosomal collinearity even among distantly related taxa. To assess the utility of the high-quality assembly for species conservation, we performed a low-coverage resequencing of 30 individuals from wild populations and two zoo individuals. Our genome-wide population structure analyses detected genetic population structure in the wild and identified the most likely origin of the zoo-housed individuals. We further identified putatively deleterious mutations to be monitored. CONCLUSIONS We establish a high-quality chromosome-level reference genome for A. gigantea and one of the most complete turtle genomes available. We show that low-coverage whole-genome resequencing, for which alignment to the reference genome is a necessity, is a powerful tool to assess the population structure of the wild population and reveal the geographic origins of ex situ individuals relevant for genetic diversity management and rewilding efforts.
Collapse
Affiliation(s)
- F Gözde Çilingir
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
| | - Luke A'Bear
- Seychelles Islands Foundation, Victoria, Republic of Seychelles
| | - Dennis Hansen
- Zoological Museum, University of Zurich, Zurich 8006, Switzerland
- Indian Ocean Tortoise Alliance, Ile Cerf, Victoria, Republic of Seychelles
| | | | - Nancy Bunbury
- Seychelles Islands Foundation, Victoria, Republic of Seychelles
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Arpat Ozgul
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
| | - Daniel Croll
- Institute of Biology, University of Neuchâtel, Neuchâtel 2000, Switzerland
| | - Christine Grossen
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
| |
Collapse
|
2
|
Çilingir FG, Hansen D, Bunbury N, Postma E, Baxter R, Turnbull L, Ozgul A, Grossen C. Low-coverage reduced representation sequencing reveals subtle within-island genetic structure in Aldabra giant tortoises. Ecol Evol 2022; 12:e8739. [PMID: 35342600 PMCID: PMC8931707 DOI: 10.1002/ece3.8739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 02/01/2023] Open
Abstract
Aldabrachelys gigantea (Aldabra giant tortoise) is one of only two giant tortoise species left in the world and survives as a single wild population of over 100,000 individuals on Aldabra Atoll, Seychelles. Despite this large current population size, the species faces an uncertain future because of its extremely restricted distribution range and high vulnerability to the projected consequences of climate change. Captive-bred A. gigantea are increasingly used in rewilding programs across the region, where they are introduced to replace extinct giant tortoises in an attempt to functionally resurrect degraded island ecosystems. However, there has been little consideration of the current levels of genetic variation and differentiation within and among the islands on Aldabra. As previous microsatellite studies were inconclusive, we combined low-coverage and double-digest restriction-associated DNA (ddRAD) sequencing to analyze samples from 33 tortoises (11 from each main island). Using 5426 variant sites within the tortoise genome, we detected patterns of within-island population structure, but no differentiation between the islands. These unexpected results highlight the importance of using genome-wide genetic markers to capture higher-resolution genetic structure to inform future management plans, even in a seemingly panmictic population. We show that low-coverage ddRAD sequencing provides an affordable alternative approach to conservation genomic projects of non-model species with large genomes.
Collapse
Affiliation(s)
- F. Gözde Çilingir
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Dennis Hansen
- Zoological MuseumUniversity of ZurichZurichSwitzerland
- Indian Ocean Tortoise AllianceVictoriaSeychelles
| | - Nancy Bunbury
- Seychelles Islands FoundationVictoriaSeychelles
- Centre for Ecology and ConservationCollege of Life and Environmental SciencesUniversity of ExeterPenrynUK
| | - Erik Postma
- Centre for Ecology and ConservationCollege of Life and Environmental SciencesUniversity of ExeterPenrynUK
| | | | | | - Arpat Ozgul
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Christine Grossen
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| |
Collapse
|
3
|
Lemoine RT, Svenning J. Nativeness is not binary ‐ a graduated terminology for native and non‐native species in the Anthropocene. Restor Ecol 2022. [DOI: 10.1111/rec.13636] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Rhys Taylor Lemoine
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE) & Section for Ecoinformatics and Biodiversity, Department of Biology Aarhus University, Ny Munkegade 114 DK‐8000 Aarhus C Denmark
| | - Jens‐Christian Svenning
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE) & Section for Ecoinformatics and Biodiversity, Department of Biology Aarhus University, Ny Munkegade 114 DK‐8000 Aarhus C Denmark
| |
Collapse
|
4
|
Abstract
AbstractThe Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two remaining giant tortoise species worldwide. Captive-bred A. gigantea are being used in rewilding projects in the Western Indian Ocean to functionally replace the extinct endemic giant tortoise species and restore degraded island ecosystems. Furthermore, large-scale translocations may become necessary as rising sea levels threaten the only wild population on the low-lying Aldabra Atoll. Critical management decisions would be greatly facilitated by insights on the genetic structure of breeding populations. We used a double-digest restriction-associated DNA sequencing (ddRAD-seq) approach to identify single nucleotide polymorphisms (SNP) among the wild population and two additional captive populations of A. gigantea. A total of 1674 unlinked, putatively neutral genome-wide SNPs were identified. The values of expected heterozygosity ranged from 0.33 to 0.5, whereas the minor allele frequency ranged from 0.20 to 0.5. These novel SNP markers will serve as useful tools for informing the conservation of A. gigantea.
Collapse
|
5
|
Falcón W, Hansen DM. Island rewilding with giant tortoises in an era of climate change. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2017.0442. [PMID: 30348869 DOI: 10.1098/rstb.2017.0442] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2018] [Indexed: 12/28/2022] Open
Abstract
Replacing recently extinct endemic giant tortoises with extant, functional analogues provide the perhaps best examples of island rewilding to date. Yet, an efficient future application of this conservation action is challenging in an era of climate change. We here present and discuss a conceptual framework that can serve as a roadmap for the study and application of tortoise rewilding in an uncertain future. We focus on three main ecological functions mediated by giant tortoises, namely herbivory, seed dispersal and nutrient cycling, and discuss how climate change is likely to impact these. We then propose and discuss mitigation strategies such as artificial constructed shade sites and water holes that can help drive and maintain the ecosystem functions provided by the tortoises on a landscape scale. The application of the framework and the mitigation strategies are illustrated with examples from both wild and rewilded populations of the Aldabra giant tortoise, Aldabrachelys gigantea, in the Western Indian Ocean.This article is part of the theme issue 'Trophic rewilding: consequences for ecosystems under global change'.
Collapse
Affiliation(s)
- Wilfredo Falcón
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland.,Bureau of Research and Conservation of Habitats and Biodiversity, Department of Natural and Environmental Resources, PO Box 366147, San Juan, PR 00936, USA
| | - Dennis M Hansen
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland .,Zoological Museum, University of Zurich, Karl-Schmid-Strasse 4, Zurich 8006, Switzerland
| |
Collapse
|
6
|
Island biodiversity conservation needs palaeoecology. Nat Ecol Evol 2017; 1:181. [PMID: 28812590 DOI: 10.1038/s41559-017-0181] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 05/05/2017] [Indexed: 11/09/2022]
Abstract
The discovery and colonization of islands by humans has invariably resulted in their widespread ecological transformation. The small and isolated populations of many island taxa, and their evolution in the absence of humans and their introduced taxa, mean that they are particularly vulnerable to human activities. Consequently, even the most degraded islands are a focus for restoration, eradication, and monitoring programmes to protect the remaining endemic and/or relict populations. Here, we build a framework that incorporates an assessment of the degree of change from multiple baseline reference periods using long-term ecological data. The use of multiple reference points may provide information on both the variability of natural systems and responses to successive waves of cultural transformation of island ecosystems, involving, for example, the alteration of fire and grazing regimes and the introduction of non-native species. We provide exemplification of how such approaches can provide valuable information for biodiversity conservation managers of island ecosystems.
Collapse
|
7
|
McCauley DJ, Hardesty‐Moore M, Halpern BS, Young HS. A mammoth undertaking: harnessing insight from functional ecology to shape de‐extinction priority setting. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12728] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Douglas J. McCauley
- Department of Ecology, Evolution, and Marine Biology University of California Santa Barbara CA93106 USA
| | - Molly Hardesty‐Moore
- Department of Ecology, Evolution, and Marine Biology University of California Santa Barbara CA93106 USA
| | - Benjamin S. Halpern
- Bren School of Environmental Science & Management University of California Santa Barbara CA93106 USA
- National Center for Ecological Analysis and Synthesis University of California 735 State St. Suite 300 Santa Barbara CA93101 USA
- Imperial College London Silwood Park Campus Buckhurst Rd AscotSL57PY UK
| | - Hillary S. Young
- Department of Ecology, Evolution, and Marine Biology University of California Santa Barbara CA93106 USA
| |
Collapse
|
8
|
Traveset A, Fernández-Palacios JM, Kueffer C, Bellingham PJ, Morden C, Drake DR. Introduction to the Special Issue: Advances in island plant biology since Sherwin Carlquist's Island Biology. AOB PLANTS 2015; 8:plv148. [PMID: 26722109 PMCID: PMC4740358 DOI: 10.1093/aobpla/plv148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 12/08/2015] [Indexed: 05/17/2023]
Abstract
Sherwin Carlquist's seminal publications-in particular his classic Island Biology, published in 1974-formulated hypotheses specific to island biology that remain valuable today. This special issue brings together some of the most interesting contributions presented at the First Island Biology Symposium hosted in Honolulu on 7-11 July 2014. We compiled a total of 18 contributions that present data from multiple archipelagos across the world and from different disciplines within the plant sciences. In this introductory paper, we first provide a short overview of Carlquist's life and work and then summarize the main findings of the collated papers. A first group of papers deals with issues to which Carlquist notably contributed: long-distance dispersal, adaptive radiation and plant reproductive biology. The findings of such studies demonstrate the extent to which the field has advanced thanks to (i) the increasing availability and richness of island data, covering many taxonomic groups and islands; (ii) new information from the geosciences, phylogenetics and palaeoecology, which allows us a more realistic understanding of the geological and biological development of islands and their biotas; and (iii) the new theoretical and methodological advances that allow us to assess patterns of abundance, diversity and distribution of island biota over large spatial scales. Most other papers in the issue cover a range of topics related to plant conservation on islands, such as causes and consequences of mutualistic disruptions (due to pollinator or disperser losses, introduction of alien predators, etc.). Island biologists are increasingly considering reintroducing ecologically important species to suitable habitats within their historic range and to neighbouring islands with depauperate communities of vertebrate seed dispersers, and an instructive example is given here. Finally, contributions on ecological networks demonstrate the usefulness of this methodological tool to advancing conservation management and better predicting the consequences of disturbances on species and interactions in the fragile insular ecosystems.
Collapse
Affiliation(s)
- Anna Traveset
- Mediterranean Institute for Advanced Studies (CSIC-UIB), C/Miquel Marqués 21, 07190 Esporles, Mallorca, Balearic Islands, Spain
| | - José María Fernández-Palacios
- Island Ecology and Biogeography Research Group, Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, La Laguna 38206, Tenerife, Spain
| | - Christoph Kueffer
- Institute of Integrative Biology, ETH Zurich, Universitätstrasse 16, CH-8092 Zurich, Switzerland
| | | | - Clifford Morden
- Department of Botany, University of Hawai'i at Mānoa, 3190 Maile Way, Honolulu, HI 96822, USA
| | - Donald R Drake
- Department of Botany, University of Hawai'i at Mānoa, 3190 Maile Way, Honolulu, HI 96822, USA
| |
Collapse
|