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DNA from the Past Informs Ex Situ Conservation for the Future: An “Extinct” Species of Galápagos Tortoise Identified in Captivity

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Michael A Russello
Michael A Russello
Michael A Russello
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Nikos Poulakakis at University of Crete
Nikos Poulakakis
James P. Gibbs at SUNY College of Environmental Science and Forestry
James P. Gibbs
Washington Tapia at Biodiversa Consultores
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Abstract and Figures

Although not unusual to find captive relicts of species lost in the wild, rarely are presumed extinct species rediscovered outside of their native range. A recent study detected living descendents of an extinct Galápagos tortoise species (Chelonoidis elephantopus) once endemic to Floreana Island on the neighboring island of Isabela. This finding adds to the growing cryptic diversity detected among these species in the wild. There also exists a large number of Galápagos tortoises in captivity of ambiguous origin. The recently accumulated population-level haplotypic and genotypic data now available for C. elephantopus add a critical reference population to the existing database of 11 extant species for investigating the origin of captive individuals of unknown ancestry. We reanalyzed mitochondrial DNA control region haplotypes and microsatellite genotypes of 156 captive individuals using an expanded reference database that included all extant Galápagos tortoise species as well as the extinct species from Floreana. Nine individuals (six females and three males) exhibited strong signatures of Floreana ancestry and a high probability of assignment to C. elephantopus as detected by Bayesian assignment and clustering analyses of empirical and simulated data. One male with high assignment probability to C. elephantopus based on microsatellite genotypic data also possessed a "Floreana-like" mitochondrial DNA haplotype. Historical DNA analysis of museum specimens has provided critical spatial and temporal components to ecological, evolutionary, taxonomic and conservation-related research, but rarely has it informed ex situ species recovery efforts. Here, the availability of population-level genotypic data from the extinct C. elephantopus enabled the identification of nine Galápagos tortoise individuals of substantial conservation value that were previously misassigned to extant species of varying conservation status. As all captive individuals of C. elephantopus ancestry currently reside at a centralized breeding facility on Santa Cruz, these findings permit breeding efforts to commence in support of the reestablishment of this extinct species to its native range.
Distribution of giant tortoises throughout the Galá pagos archipelago. Island names are capitalized; shaded islands indicate presence of extant tortoise populations (species names italicized). Populations are indicated by geographical name (e.g., Vó lcan Wolf) and associated sampling site (e.g., PBL, PBR). Triangles represent volcanoes on Isabela Island and circles indicate additional sampling locations. Figure modified from Russello et al. [5]. doi:10.1371/journal.pone.0008683.g001
Distribution of giant tortoises throughout the Galá pagos archipelago. Island names are capitalized; shaded islands indicate presence of extant tortoise populations (species names italicized). Populations are indicated by geographical name (e.g., Vó lcan Wolf) and associated sampling site (e.g., PBL, PBR). Triangles represent volcanoes on Isabela Island and circles indicate additional sampling locations. Figure modified from Russello et al. [5]. doi:10.1371/journal.pone.0008683.g001
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. Captive Galápagos tortoises of unknown origin with signatures of Floreana ancestry.
. Captive Galápagos tortoises of unknown origin with signatures of Floreana ancestry.
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Patterns of Floreana mixed ancestry as revealed by genotype simulations and Bayesian clustering analyses. STRUCTURE triangle plot revealing clustering patterns of individuals of Floreana mixed ancestry with simulated parental and F1 genotypes for all possible pairwise comparisons involving Puerto Bravo (PBR), Floreana (FLO) and Españ ola (ESP) populations. For display purposes, only simulated parental and F1 distributions are shown. Colors according to embedded legend. doi:10.1371/journal.pone.0008683.g002
Patterns of Floreana mixed ancestry as revealed by genotype simulations and Bayesian clustering analyses. STRUCTURE triangle plot revealing clustering patterns of individuals of Floreana mixed ancestry with simulated parental and F1 genotypes for all possible pairwise comparisons involving Puerto Bravo (PBR), Floreana (FLO) and Españ ola (ESP) populations. For display purposes, only simulated parental and F1 distributions are shown. Colors according to embedded legend. doi:10.1371/journal.pone.0008683.g002
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Relatedness structure of captive individuals of Floreana mixed ancestry. Distribution of observed Lynch and Ritland's [36] relatedness values calculated for CDRS individuals of detected Floreana ancestry ( N ) overlaid upon those calculated from 1000 simulated unrelated (#), half-sibling (h), full-sibling (g), and parent-offspring (e) dyads. doi:10.1371/journal.pone.0008683.g003
Relatedness structure of captive individuals of Floreana mixed ancestry. Distribution of observed Lynch and Ritland's [36] relatedness values calculated for CDRS individuals of detected Floreana ancestry ( N ) overlaid upon those calculated from 1000 simulated unrelated (#), half-sibling (h), full-sibling (g), and parent-offspring (e) dyads. doi:10.1371/journal.pone.0008683.g003
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Island names are capitalized; shaded islands indicate presence of extant tortoise populations (species names italicized). Populations are indicated by geographical name (e.g., Vólcan Wolf) and associated sampling site (e.g., PBL, PBR). Triangles represent volcanoes on Isabela Island and circles indicate additional sampling locations. Figure modified from Russello et al. [5].
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Island names are capitalized; shaded islands indicate presence of extant tortoise populations (species names italicized). Populations are indicated by geographical name (e.g., Vólcan Wolf) and associated sampling site (e.g., PBL, PBR). Triangles represent volcanoes on Isabela Island and circles indicate additional sampling locations. Figure modified from Russello et al. [5].
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DNA from the Past Informs Ex Situ Conservation for the Future: An “Extinct” Species of Galápagos Tortoise Identified in Captivi
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Supplementary resource (1)

Table S1
Data
January 2010
Michael A. Russello · Nikos Poulakakis · James P. Gibbs · Washington Tapia · Adalgisa Caccone
... It was suggested from mtDNA and microsatellite data that some C. nigra individuals are of "hybrid origin", i.e., F1 from "purebred" parents or backcrosses (e.g. Garrick, Benavides, Russello, Hyseni, et al., 2014;Russello, Poulakakis, et al., 2010). Among the four individuals of our sample for which microsatellite data are available, two were consistently assigned to the same population by the three methods used by Russello, Poulakakis, et al. (2010), whereas two obtained conflicting assignments. ...
... Garrick, Benavides, Russello, Hyseni, et al., 2014;Russello, Poulakakis, et al., 2010). Among the four individuals of our sample for which microsatellite data are available, two were consistently assigned to the same population by the three methods used by Russello, Poulakakis, et al. (2010), whereas two obtained conflicting assignments. Russello, Poulakakis, et al. (2010) Figure 1 -Each filled circle corresponds to a single species of animals in which the transcriptome of at least four individuals was sequenced (Perry et al., 2012;Romiguier, Gayral, et al., 2014). ...
... Among the four individuals of our sample for which microsatellite data are available, two were consistently assigned to the same population by the three methods used by Russello, Poulakakis, et al. (2010), whereas two obtained conflicting assignments. Russello, Poulakakis, et al. (2010) Figure 1 -Each filled circle corresponds to a single species of animals in which the transcriptome of at least four individuals was sequenced (Perry et al., 2012;Romiguier, Gayral, et al., 2014). Harvest ant Messor barbarus was excluded due to its highly specific mating system (Romiguier, Fournier, et al., 2017). ...
Lacking conservation genomics in the giant Galápagos tortoise
Article
Full-text available
  • Nov 2021
Conservation policy in the giant Galpagos tortoise, an iconic endangered animal, has been assisted by genetic markers for 15 years: a dozen loci have been used to delineate thirteen (sub)species, between which hybridization is prevented. Here, comparative reanalysis of a previously published NGS data set reveals a conflict with traditional markers. Genetic diversity and population substructure in the giant Galpagos tortoise are found to be particularly low, questioning the genetic relevance of current conservation practices. Further examination of giant Galapagos tortoise population genomics is critically needed.
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... These hybrids live among the endemic C. becki population on Volcano Wolf, Isabela Island (Garrick et al. 2012;Poulakakis et al. 2008). Their initial hybridization is thought to have happened within the last 200 years and had been human mediated, as there is no natural dispersal route between islands, but ships' logbooks detail the collection and depositing of tortoises between islands (Pritchard 1996 (Miller et al. 2018;Russello et al. 2010). The breeders were housed in a single corral with mating occurring at random. ...
... During the nesting season the corrals are checked daily for new nests, with the eggs removed and taken to be artificially incubated. from the 20 breeders in V1 were collected from the brachial vein of the front leg(Miller et al. 2017;Russello et al. 2010). Small tissue biopsies were obtained from the 98 successfully hatched offspring (20 hatched 2017/2018, 43 hatched 2018/2019, 35 hatched 2019/2020) and stored at ambient temperature in Longmire Lysis buffer (Longmire et al. 1997) until arrival in the lab, after which they were stored at 4 °C. ...
Temporal Monitoring of the Floreana Island Galapagos Giant Tortoise Captive Breeding Program
Article
  • Jul 2022
Captive breeding programs benefit from genetic analyses that identify relatedness between individuals, assign parentage to offspring, and track levels of genetic diversity. Monitoring these parameters across breeding cycles is critical to the success of a captive breeding program as it allows conservation managers to iteratively evaluate and adjust program structure. However, in practice, genetic tracking of breeding outcomes is rarely conducted. Here, we examined the first three offspring cohorts (2017–2020) of the genetically-informed captive breeding program for the Floreana Island Galapagos giant tortoise, Chelonoidis niger. This captive breeding program is unique as the Floreana tortoise has been extinct since the 1800s, but its genome persists, in part, in the form of living hybrids with the extant Volcano Wolf tortoise, Chelonoidis becki. Breeding over the study period took place at the Galapagos National Park Directorate breeding facility in four corrals, each containing three females and two males. Using 17 microsatellite markers, we were able to assign parentage to 94 of the 98 offspring produced over the study period. We observe that despite the addition of more founders since the pilot breeding program, the effective population size remains low, and changes to the arrangements of breeding corrals may be necessary to encourage more equal reproductive output from the males. This study demonstrates the value of hybrids for species restoration and the importance of continually reassessing the outcomes of captive breeding.
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... Another surprise was revealed during a reanalysis of 156 captive tortoises in Galapagos using the expanded database that included historical specimens: nine exhibited a strong genetic signature of Floreana tortoise ancestry (Russello et al. 2010). Based on this discovery, a pilot breeding program using the admixed tortoises with partial Floreana tortoise ancestry already in captivity was initiated; it ran from 2011 to 2014 and produced 130 offspring (Miller et al. 2018). ...
... These assessments also indicated that the amount of C. niger genome representation in a restored population could be increased by targeted management actions, but only by a moderate amount. Although some have suggested full recovery of the C. niger genome through backcrossing (e.g., Russello et al. 2010), this option is largely excluded by the biology of tortoises themselves (extreme generation time) and the likelihood of inbreeding depression caused by backcrossing ). In addition, such a program would result in the production of hundreds of offspring that, based on the goal of achieving a population identical to the extinct species, could not be released into the wild. ...
Floreana and Pinta Islands: Restoring tortoise populations through lost lineage recovery
Chapter
  • Jan 2021
The giant tortoise species of Floreana (Chelonoidis niger) and Pinta (C. abingdonii) Islands are extinct. Efforts to restore tortoise populations on both islands prioritize ecosystem and island restoration through the return of giant tortoises and their role as ecological engineers. This chapter describes the landscape and history of Pinta and Floreana Islands, including the exploitation and eventual extinction of their saddleback tortoise species and the arrival, impact, control, and eradication of introduced mammals. The chapter describes the discovery of tortoises with mixed ancestry on Wolf Volcano on northern Isabela Island, including some with Floreana tortoise ancestry and fewer with Pinta tortoise ancestry. This discovery jump-started efforts to restore tortoise populations on both islands with tortoises with partial ancestry of the extinct species. The chapter ends with a discussion of island restoration through the replacement of extinct tortoise species using lost lineages, including planning efforts to ensure rapid population growth and genetic diversity.
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... Analysis of genetic data in modern populations has proven to be a powerful tool for reconstructing crucial aspects of the evolutionary history of threatened species, thus informing conservation management (Willerslev and Cooper 2005, Rohland and Hofreiter 2007, Leonard 2008, Gangloff et al. 2012a. Similarly, the analysis of ancient DNA (aDNA) is valued as a means to compare past and present levels of genetic variation Lambert 2008, Shepherd et al. 2012), identify the ranges of morphologically indistinct taxa (Russello et al. 2010, Steeves et al. 2010, Robertson et al. 2011, Spurgin et al. 2014) and provide accurate species delineation (Boessenkool et al. 2009). Such data are valuable for conservation managers seeking diagnostic tools to accurately assign conservation status and provide guidance for the restoration of species that have undergone extreme range declines (Hofkin et al. 2003, Valentine et al. 2007, Russello et al. 2010. ...
... Similarly, the analysis of ancient DNA (aDNA) is valued as a means to compare past and present levels of genetic variation Lambert 2008, Shepherd et al. 2012), identify the ranges of morphologically indistinct taxa (Russello et al. 2010, Steeves et al. 2010, Robertson et al. 2011, Spurgin et al. 2014) and provide accurate species delineation (Boessenkool et al. 2009). Such data are valuable for conservation managers seeking diagnostic tools to accurately assign conservation status and provide guidance for the restoration of species that have undergone extreme range declines (Hofkin et al. 2003, Valentine et al. 2007, Russello et al. 2010. ...
Comprehensive evidence for subspecies designations in Cook's Petrel Pterodroma cookii with implications for conservation management
Article
Full-text available
  • Oct 2020
Cook’s Petrel Pterodroma cookii is an endemic New Zealand seabird that has experienced a large range decline since the arrival of humans and now only breeds on two offshore islands (Te Hauturu-o-Toi/Little Barrier Island and Whenua Hou/Codfish Island) at the extreme ends of its former distribution. Morphological, behavioural, and mitochondrial cytochrome oxidase 1 (CO1) sequence data led a previous study to recognise the two extant populations as distinct conservation management units. Here, we further examine the genetic relationship between the extant popula- tions using two nuclear introns (β-fibint7 and PAX). Using one mitochondrial locus (CO1), we also investigate the past distribution of a single nucleotide polymorphism (SNP) that differentiates the modern populations using bone and museum skins sourced from within its former range across New Zealand’s North and South Islands. We found significant population genetic structure between the two extant Cook’s Petrel populations for one of the two nuclear introns (β-fibint7). The mitochondrial DNA CO1 analysis indicated that the SNP variant found in the Codfish Island population was formerly widely distributed across both the North and South Islands, whereas the Little Barrier Island variant was detected only in North Island samples. We argue that these combined data support the recognition of the extant populations as different subspecies. Previous names for these taxa exist, thus Cook’s Petrel from Little Barrier Island becomes Pterodroma cookii cookii and Cook’s Petrel from Codfish Island becomes P. c. orientalis. Furthermore, we suggest that both genetic and non-genetic data should be taken into consideration when planning future mainland translocations. Namely, any translocations on the South Island should be sourced from Codfish Island and future translocations on the North Island should continue to be sourced from Little Barrier Island only.
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... We also attempted to genotype the historical individuals at 12 microsatellite loci that have been successfully employed in previous studies of Galapagos giant tortoise museum samples using published protocols (Russello et al. 2007;Poulakakis et al. 2008;Russello et al. 2010), but in this case, they did not yield reliable genotypes. ...
A new lineage of Galapagos giant tortoises identified from museum samples
Article
Full-text available
  • Feb 2022
  • HEREDITY
The Galapagos Archipelago is recognized as a natural laboratory for studying evolutionary processes. San Cristóbal was one of the first islands colonized by tortoises, which radiated from there across the archipelago to inhabit 10 islands. Here, we sequenced the mitochondrial control region from six historical giant tortoises from San Cristóbal (five long deceased individuals found in a cave and one found alive during an expedition in 1906) and discovered that the five from the cave are from a clade that is distinct among known Galapagos giant tortoises but closely related to the species from Española and Pinta Islands. The haplotype of the individual collected alive in 1906 is in the same clade as the haplotype in the contemporary population. To search for traces of a second lineage in the contemporary population on San Cristóbal, we closely examined the population by sequencing the mitochondrial control region for 129 individuals and genotyping 70 of these for both 21 microsatellite loci and >12,000 genome-wide single nucleotide polymorphisms [SNPs]. Only a single mitochondrial haplotype was found, with no evidence to suggest substructure based on the nuclear markers. Given the geographic and temporal proximity of the two deeply divergent mitochondrial lineages in the historical samples, they were likely sympatric, raising the possibility that the lineages coexisted. Without the museum samples, this important discovery of an additional lineage of Galapagos giant tortoise would not have been possible, underscoring the value of such collections and providing insights into the early evolution of this iconic radiation.
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... There is a wealth of existing information about the geological history of the Galapagos archipelago that has provided important context for reconstructing colonization and divergence processes in this group (e.g., Geist et al., 2014;Grehan, 2001;Poulakakis et al., 2012Poulakakis et al., , 2020, as has information on the recent human-mediated impacts that have shaped contemporary tortoise populations (Pritchard, 1996). Population genetic and phylogenetic studies of this system have progressed over the last two decades (reviewed in Caccone, 2021), benefiting from increasingly comprehensive geographic and genetic sampling, and advances in the number and type of available genetic markers, from sequencing a handful of genes and genotyping microsatellites (Caccone et al., 1999Ciofi et al., 2002Ciofi et al., , 2006Edwards et al., 2013Edwards et al., , 2014Garrick et al., 2012;Russello et al., 2007Russello et al., , 2010, to reduced-representation sequencing (Gaughran et al., 2018;Miller et al., 2018), full mitochondrial genome sequencing Poulakakis et al., 2020) and publication of a reference genome (Quesada et al., 2019). Thus, our understanding of the differentiation among, and levels of diversity within the species has been built up over time, with each generation of genetic technology providing additional data and insights (see "Study System" in Materials and methods for a brief summary). ...
Demographic history and patterns of molecular evolution from whole genome sequencing in the radiation of Galapagos giant tortoises
Article
Full-text available
Whole genome sequencing provides deep insights into the evolutionary history of a species, including patterns of diversity, signals of selection, and historical demography. When applied to closely related taxa with a wealth of background knowledge, population genomics provides a comparative context for interpreting population genetic summary statistics and comparing empirical results with the expectations of population genetic theory. The Galapagos giant tortoises (Chelonoidis spp.), an iconic rapid and recent radiation, offer such an opportunity. Here, we sequenced whole genomes from three individuals of the 12 extant lineages of Galapagos giant tortoise and estimate diversity measures and reconstruct changes in coalescent rate over time. We also compare the number of derived alleles in each lineage to infer how synonymous and nonsynonymous mutation accumulation rates correlate with population size and life history traits. Remarkably, we find that patterns of molecular evolution are similar within individuals of the same lineage, but can differ significantly among lineages, reinforcing the evolutionary distinctiveness of the Galapagos giant tortoise species. Notably, differences in mutation accumulation among lineages do not align with simple population genetic predictions, suggesting that the drivers of purifying selection are more complex than is currently appreciated. By integrating results from earlier population genetic and phylogeographic studies with new findings from the analysis of whole genomes, we provide the most in‐depth insights to date on the evolution of Galapagos giant tortoises, and identify discrepancies between expectation from population genetic theory and empirical data that warrant further scrutiny.
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... DNA was extracted from 150 blood samples using Qiagen blood and tissue extraction kits. These samples included the 144 saddle-backed individuals mentioned above along with six individuals already housed at the Galápagos National Park Breeding Center on Santa Cruz Island that were previously identified to have Floreana ancestry 35 . All samples were sequenced at ~700 bp of the mitochondrial DNA control and were genotyped at 12 dinucleotide microsatellites, using previously developed protocols (detailed procedures in Supplementary Methods). ...
Identification of Genetically Important Individuals of the Rediscovered Floreana Galápagos Giant Tortoise ( Chelonoidis elephantopus ) Provide Founders for Species Restoration Program
Preprint
Full-text available
  • Aug 2017
Species are being lost at an unprecedented rate due to human-driven environmental changes. The cases in which species declared extinct can be revived are rare. However, here we report that a remote volcano in the Galápagos Islands hosts many giant tortoises with high ancestry from a species previously declared as extinct: Chelonoidis elephantopus or the Floreana tortoise. Of 150 individuals with distinctive morphology sampled from the volcano, genetic analyses revealed that 65 had C. elephantopus ancestry and thirty-two were translocated from the volcano’s slopes to a captive breeding center. A genetically informed captive breeding program now being initiated will, over the next decades, return C. elephantopu s tortoises to Floreana Island to serve as engineers of the island’s ecosystems. Ironically, it was the haphazard translocations by mariners killing tortoises for food centuries ago that created the unique opportunity to revive this “lost” species today.
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Identifying key monitoring areas for tree insect pest risks in China under climate change
Article
  • Oct 2024
  • J ECON ENTOMOL
Climate change can exacerbate pest population growth, posing significant threats to ecosystem functions and services, social development, and food security. Risk assessment is a valuable tool for effective pest management that identifies potential pest expansion and ecosystem dispersal patterns. We applied a habitat suitability model coupled with priority protection planning software to determine key monitoring areas (KMA) for tree insect pest risks under climate change and used forest ecoregions and nature reserves to assess the ecological risk of insect pest invasion. Finally, we collated the prevention and control measures for reducing future pest invasions. The KMA for tree insect pests in our current and future climate is mainly concentrated in eastern and southern China. However, with climate change, the KMA gradually expands from southeastern to northeastern China. In the current and future climate scenarios, ecoregions requiring high monitoring levels were restricted to the eastern and southern coastal areas of China, and nature reserves requiring the highest monitoring levels were mainly distributed in southeastern China. Tree insect pest invasion assessment using ecoregions and nature reserves identified that future climates increase the risk of pest invasions in forest ecoregions and nature reserves, especially in northeastern China. The increased risk and severity of tree insect pest invasions require implementing monitoring and preventative measures in these areas. We effectively assessed the pest invasion risks using forest ecoregions and nature reserves under climate change. Our assessments suggest that monitoring and early prevention should focus on southeastern and northeastern China.
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Evolution and phylogenetics
Chapter
  • Jan 2021
This chapter describes the insights resulting from 25 years of research on the evolutionary history, phylogeny, and phylogeography of Galapagos giant tortoises. A hypothesis is presented that describes when and how tortoises arrived in Galapagos, identifies the tortoises’ closest living relatives, and outlines how tortoises colonized the different islands and volcanoes. Insights based on genetic data help explain the dynamics of Galapagos giant tortoise populations and impacts of natural events and human activities on current patterns and levels of genetic diversity in many of the species. Together this information on tortoise evolution and phylogenetics has provided critical guidance for tortoise conservation programs, particularly for priority setting and captive breeding and repopulation programs.
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The Galapagos: Island home of giant tortoises
Chapter
  • Jan 2021
Galapagos is at once inspiring and disheartening, given its complex history of discovery, exploration, overexploitation, colonization, extinctions, conservation challenges, and successes. Galapagos giant tortoises are central to each of these phases and developments. While suffering overexploitation and species loss, Galapagos tortoises are also the focus of dedicated, innovative efforts to restore these imperiled species and the ecosystems they inhabit. All told, Galapagos, and its tortoises, provide a microcosm of life on Earth, and the roles that humans play.
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Backcrossing as a species restoration technique
Article
Full-text available
  • Mar 2023
  • ZOO BIOL
An investigation was conducted on the phenotypic results of mouse hybridization and seven generations of backcrossing, observing reciprocal F1 hybrids and backcrosses of Mus spretus and a laboratory strain of Mus domesticus C57BL/6J. F1 hybrids, backcrosses, and pure control specimens were measured for 6 body characteristics, 4 pelage coloration characteristics, 14 behaviors, and reproduction as reflected in litter size. Backcrossing was pursued for seven generations to FBC7 (i.e., "Backcross 7" or seven generations from commencement of backcrossing from an F1 hybrid female) where species restoration is mathematically calculated to be at 99.7%. Except for a minority of FBC7 M. spretus specimens failing to conform completely to one pelage characteristic, FBC7 specimens were indistinguishable from controls both subjectively and in all areas of measurement. The M. spretus backcross line was followed generation by generation and was largely conforming to controls by FBC4 at latest. The same effect was observed in the reciprocal M. domesticus backcross line. Fertility was negatively affected in F1 hybrids but restored or improved in backcross generations. Discussion is offered on hybridization and backcrossing as it occurs in nature and how it has been used or could be used as an additional ex situ tool in wildlife conservation efforts. It is concluded that conservation-oriented backcrossing is a practical species/subspecies restoration technique and has the potential to make genetic rescue feasible with minimal gene flow at the binomial level. Backcrossing is most applicable in closely monitored ex situ settings (1) where only one sex remains of a given taxon; and (2) where inbreeding depression seriously threatens a remnant taxon's ability to recover, and the only gene flow option is from another distinct species.
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ESTIMATING RELATEDNESS USING GENETIC MARKERS
Article
  • Mar 1989
  • EVOLUTION
A new method is described for estimating genetic relatedness from genetic markers such as protein polymorphisms. It is based on Grafen's (1985) relatedness coefficient and is most easily interpreted in terms of identity by descent rather than as a genetic regression. It has several advantages over methods currently in use: it eliminates a downward bias for small sample sizes; it improves estimation of relatedness for subsets of population samples; and it allows estimation of relatedness for a single group or for a single pair of individuals. Individual estimates of relatedness tend to be highly variable but, in aggregate, can still be very useful as data for nonparametric tests. Such tests allow testing for differences in relatedness between two samples or for correlating individual relatedness values with another variable.
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Genetics and conservation on Islands: The Galaápagos giant tortoise as a case study
Chapter
  • Jan 2015
INTRODUCTION The study of intraspecific genetic variation has demonstrated a vast potential to reconstruct phylogeographic patterns, infer historical demographic processes and define levels of gene flow of conservation relevance (Avise 2004). Evolutionary and demographic studies, along with evidence of current genetic and ecological diversity can, in fact, describe levels of population distinctiveness and direct management initiatives of importance to the retention of intraspecific genetic variability and the long-term fitness of endangered species (Fraser and Bernatchez 2001). Population divergence and taxonomy Molecular genetics is a particularly valuable tool for the study of island systems where different selective pressures and dispersal ability of endemic species can hamper clear patterns of morphological and ecological diversification for populations of taxonomic importance. In the Galápagos giant tortoise Geochelone nigra (or G. elephantopus: see Zug 1997), the taxonomy first proposed by Van Denburgh (1914) has been somewhat controversial. Taxon designation was originally based on two main tortoise morphologies and their variants: a large, dome morphotype with rounded carapace and short limbs, and a smaller saddlebacked form with a highly elevated anterior part of the carapace, longer neck and limbs, and thinner shell. Five saddlebacked subspecies were described, on the islands of Española (hoodensis), San Cristóbal (chatamensis), Pinzón (ephippium), Fernandina (phantastica) and Pinta (abingdoni). Domed tortoises were instead reported from Santa Cruz (porteri), Rábida (wallacei) and in Isabela on Volcan Darwin (microphyes), Volcan Alcedo (vandenburghi), Sierra Negra (guntheri) and Cerro Azul (vicina). Tortoises from Santiago (darwini) are of intermediate morphology. Similarly, heterogeneous morphotypes, assigned to the becki subspecies, were described on Volcan Wolf, in northern Isabela. For the majority of island populations recent genetic analysis validated the proposed taxonomy, while for others new patterns were recovered which were inconsistent with previous morphologically based nomenclature (Caccone et al. 2002; Beheregaray et al. 2003a; Russello et al. 2005; Ciofi et al. 2006).
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Mus booduga. In: IUCN 2012. IUCN Red List of Threatened Species. Version 2012.2. .
Article
  • Jun 2008
Red List Category & Criteria: Least Concern ver 3.1 Year Published: 2008 Date Assessed: 2008-06-30 Assessor(s): Aplin, K., Molur, S. & Nameer, P.O. Reviewer(s): Amori, G. (Small Nonvolant Mammal Red List Authority) & Cox, N. (Global Mammal Assessment Team)
View
Estimating Relatedness Using Genetic Markers
Article
  • Mar 1989
A new method is described for estimating genetic relatedness from genetic markers such as protein polymorphisms. It is based on Grafen's (1985) relatedness coefficient and is most easily interpreted in terms of identity by descent rather than as a genetic regression. It has several advantages over methods currently in use: it eliminates a downward bias for small sample sizes; it improves estimation of relatedness for subsets of population samples; and it allows estimation of relatedness for a single group or for a single pair of individuals. Individual estimates of relatedness tend to be highly variable but, in aggregate, can still be very useful as data for nonparametric tests. Such tests allow testing for differences in relatedness between two samples or for correlating individual relatedness values with another variable.
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Phylogeography and history of Galápagos tortoises
Article
  • May 2007
  • EVOLUTION
— We examined the phylogeography and history of giant Galàpagos tortoise populations based on mito-chondrial DNA sequence data from 161 individuals from 21 sampling sites representing the 11 currently recognized extant taxa. Molecular clock and geological considerations indicate a founding of the monophyletic Galàpagos lineage around 2–3 million years ago, which would allow for all the diversification to have occurred on extant islands. Founding events generally occurred from geologically older to younger islands with some islands colonized more than once. Six of the 11 named taxa can be associated with monophyletic maternal lineages. One, Geochelone porteri on Santa Cruz Island, consists of two distinct populations connected by the deepest node in the archipelago-wide phylogeny, whereas tortoises in northwest Santa Cruz are closely related to those on adjacent Pinzón Island. Volcan Wolf, the northernmost volcano of Isabela Island, consists of both a unique set of maternal lineages and recent migrants from other islands, indicating multiple colonizations possibly due to human transport or multiple colonization and partial elimination through competition. These genetic findings are consistent with the mixed morphology of tortoises on this volcano. No clear genetic differentiation between two taxa on the two southernmost volcanoes of Isabela was evident. Extinction of crucial populations by human activities confounds whether domed versus saddleback carapaces of different populations are mono- or polyphyletic. Our findings revealed a complex phylogeography and history for this tortoise radiation within an insular environment and have implications for efforts to conserve these endangered biological treasures.
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Lineage identification of Galápagos tortoises in captivity worldwide
Article
Ex situ conservation strategies may be substantially informed by genetic data, and yet only recently have such approaches been used to facilitate captive population management of endangered species. The Galápagos tortoise Geochelone nigra is an endangered species that has benefited greatly from the application of molecular and population genetic data, but remains vulnerable throughout its range. The geographic and evolutionary origins of 98 tortoises in private collections and zoos on three continents were identified using mitochondrial DNA (mtDNA) control region sequences and multi-locus microsatellite genotype data relative to a large database of representative samplings from all extant populations, including historical population allele frequency data for the Geochelone nigra abingdoni taxon on Pinta by way of museum specimens. All but six individuals had mtDNA haplotypes previously sampled, with the novel haplotypes identified as most closely related to robust populations on the islands of Santa Cruz and Isabela. Multi-locus genotypic assignments corroborated the results obtained from the mtDNA analyses, with 83.7% of individuals consistently assigned to the same locality by both datasets. Overall, the majority of captive unknowns sampled were assigned to the La Caseta Geochelone nigra porteri population, with no fewer than six individuals of hybrid origin detected. Although a purported Pinta individual was revealed to be of Pinzón ancestry, the two females currently housed with Lonesome George exhibited haplotypic and genotypic signatures that indicate that they are among the most appropriate matches for captive breeding. More generally, molecular approaches continue to represent important tools for assessing conservation value, minimizing hybridization and guiding management programs for preserving the distinctiveness of G. nigra taxa in captivity.
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Evolutionary divergence of giant tortoises in Galapagos
Article
  • Jan 1984
  • BIOL J LINN SOC
The giant tortoises in the Galapagos Archipelago diverge considerably in size, and in shape and other carapace characteristics. The saddleback morphotype is known only from insular faunas lacking large terrestrial predators (i.e. Galapagos and Mauritius) and in Galapagos is associated with xeric habitats where vertical feeding range and vertical reach in agonistic encounters are adaptive. The large domed morphotype is associated with relatively cool, mesic habitats where intraspecific competition for food and other resources may be less intense than in xeric habitats. Other external characteristics that differ between tortoise populations are also correlated with ecological variation. Tortoises have radiated into a mosaic of ecological conditions in the Galapagos but critical data are lacking on the role of genetic and environmental controls on phenotypic variation. Morphological divergence in tortoises is potentially a better indicator of present ecological conditions than of evolutionary relationships.
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