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Fig. 2 in A new lineage of Galapagos giant tortoises identified from museum samples

Fig. 2 Statistical parsimony haplotype network of the mitochondrial control region (668 bp) for 129 contemporary individuals from San Cristóbal and six historical specimens collected in 1906, as well as 28 representative haplotypes from the other species of Galapagos giant tortoise. The name of the island where each species occurs is labeled with capital letters, with current taxonomy in italics. Haplotypes are represented as black circles on the network, the size of the circle is proportional to the frequency of the haplotype in the analysis. Open circles represent unsampled, hypothesized haplotypes, and hash marks indicate a single mutational change. Reticulations reflect uncertainty in relationships, or homoplasy.

Fig. 4 Barplots depicting K in A new lineage of Galapagos giant tortoises identified from museum samples

Fig. 4 Barplots depicting K = 2 for the STRUCTURE analysis using the SNP (12 192 loci) and microsatellite (21 loci) genotypes for the contemporary San Cristóbal population (n = 64). Each bar represents an individual and the proportion of the bar that is each color represents the membership of that individual to the two clusters. The order of individuals is the same in both plots, black boxes around bars highlight individuals with a greater than 0.4 discrepancy in assignment proportions between the analyses.

Fig. 3 in A new lineage of Galapagos giant tortoises identified from museum samples

Fig. 3 Bayesian Inference maximum clade credibility cladogram showing relationships among the San Cristóbal historical samples from the cave and collected alive in 1906, and a reference dataset of 93 Galapagos giant tortoise haplotypes and three outgroups based on the mitochondrial control region (alignment length 718 bp), estimated using BEAST with a strict clock and Birth Death tree. The numbers on the branches are the posterior probability support values. § indicates the C. chathamensis type specimen. The name of the island where each clade is found is in capitals, with current taxonomy in italics.

Fig. 1 in A new lineage of Galapagos giant tortoises identified from museum samples

Fig. 1 Map of the Galapagos Archipelago, indicating the locations of each Chelonoidis species, with San Cristóbal Island enlarged in the inset map. Island names are in capital letters. The approximate location of the cave where the bones were found in 1906 is marked, as is the approximate location where CAS 8133 was collected alive and the region of Punta Pitt.

opencc-zeroAug 2022View details →

Microsatellite genotypes for temporal monitoring of the Floreana Island Galapagos Giant Tortoise captive breeding program

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.

opencc-zeroMay 2023View details →

Raw data from: Environmental variation structures reproduction and recruitment in long-lived mega-herbivores: Galapagos Giant Tortoises

Understanding drivers of vital rates is important for testing life history theory, predicting population dynamics, and guiding conservation. Migratory, long-lived animals are important to life history theory because they present an extreme among trade-offs in vital rates: delayed maturity, low fecundity, variable recruitment rates, and long generation times. Understanding how vital rates respond to environmental variation has been elusive for such species because of difficulties in studying wide-ranging animals over extended periods. Populations that live on elevation gradients can provide tractable study systems because considerable environmental change occurs over small geographic distances. Galapagos tortoises are an iconic example; they are long-lived, migrate seasonally, face multiple anthropogenic threats, and have cryptic early life history stages for which vital rates are unknown. From 2012–2021, we studied the reproductive ecology of two species of Galapagos tortoises along elevation gradients that coincided with substantial change in climate and vegetation productivity. Specifically, we 1) measured physical and reproductive condition of adult females, 2) tracked the movements of 33 adult females using GPS telemetry, and re-located them seasonally to measure condition, 3) recorded nest temperatures, clutch characteristics, and egg survival from 107 nests, and 4) used radio telemetry to re-locate 104 hatchlings to monitor growth, survival, and movements. We also monitored temperature, rainfall, and primary productivity from field and remotely sensed data along the elevation gradient. Adult females were either elevational migrants or year-round lowland residents. Migrants had higher body condition than residents, and body condition was positively correlated with fecundity. Nests occurred in the hottest, driest part of the tortoise's range, between 6–165m elevation. Clutch size increased with elevation, egg survival declined, and hatchling survival and growth were highest at intermediate elevations. Hatchlings dispersed rapidly between 100–750 m from their nests before becoming sedentary in ranges <0.05 ha. Environmental variability mediated by elevation influenced adult fecundity and juvenile recruitment. Predicted future climates will profoundly impact the relationships between elevation and vital rates of Galapagos tortoises and other species living on elevation gradients. Resilience will be maximized by ensuring connectivity of foraging and reproductive areas within current and possible future elevational ranges of these species.

publicNov 2024View details →

Whole-genome sequencing confirms multiple species of Galapagos giant tortoises

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publicAug 2022View details →

Microsatellite genotypes for temporal monitoring of the Floreana Island Galapagos Giant Tortoise captive breeding program

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publicMay 2025View details →

Synteny enabled upgrade of the Galapagos giant tortoise genome improves inferences of runs of homozygosity

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publicMay 2023View details →

Raw data from: Environmental variation structures reproduction and recruitment in long-lived mega-herbivores: Galapagos Giant Tortoises

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opencc-zeroDec 2017View details →

Data from: Genetic pedigree analysis of the pilot breeding program for the rediscovered Galapagos giant tortoise from Floreana island

An aim of many captive breeding programs is to increase population sizes for reintroduction and establishment of self-sustaining wild populations. Genetic analyses play a critical role in these programs: monitoring genetic variation, identifying the origin of individuals, and assigning parentage to track family sizes. Here we use genetic pedigree analyses to examine three seasons of a pilot breeding program for the Floreana island Galapagos giant tortoise, C. niger, that had been declared extinct for ~150 years until individuals with mixed ancestry were recently discovered. We determined that eight of nine founding individuals were assigned parentage to at least one of 130 offspring produced, though there was considerable reproductive skew. In addition, we observed that genetic diversity of the progeny was lower than that of the founders. Despite the observed reproductive skew, we did not see evidence for assortative mating based on relatedness, but there was a trend towards reduced fitness when more related individuals bred. Finally, we found that the majority of progeny had ancestry assigned to the Floreana species (mean±SE = 0.51±0.02), though individual estimates varied. The success of these pilot seasons bodes well for a larger breeding program to help restore the previously extinct tortoise from Floreana island. Future efforts should continue to monitor for reproductive skew and assortative mating in order to maintain allelic diversity. We would also recommend forming smaller breeding groups and rotating individuals among them to prevent long-term reproductive skew among pairs.

opencc-zeroDec 2017View details →

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

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 pre-bottleneck historical (c.1906) and post-bottleneck 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 program 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 was 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 (Ne) of 58 (95% CI = 50-69) for the post-bottleneck population; no pre-bottleneck Ne point estimate was attainable (95% CI = 39-infinity) likely due to the sample size being lower than the true Ne. Overall, the historical sample provided a valuable benchmark for evaluating the head-start captive breeding program, 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.

Fig 5 in Description of a New Galapagos Giant Tortoise Species (Chelonoidis; Testudines: Testudinidae) from Cerro Fatal on Santa Cruz Island

Fig 5. Frequency distribution of genetic distances between different Galapagos giant tortoise species (A: microsatellite DNA, B: mitochondrial DNA). For each histogram, a dark gray column indicates where the observed genetic distance between the Cerro Fatal and Reserva tortoises falls. Left: Microsatellite genetic distances calculated from purebred individuals in the reference measured using FST (top) or RST (below). Right: DNA sequence genetic distances based on mtDNA haplotypes from purebred individuals in the reference database, measured using uncorrected p-distances (top), or maximum likelihood (ML)-corrected distances (below).

Fig 2 in Description of a New Galapagos Giant Tortoise Species (Chelonoidis; Testudines: Testudinidae) from Cerro Fatal on Santa Cruz Island

Fig 2. (A) Bayesian Inference (BI) tree reconstructed from the dataset including all unique mtDNA control region haplotypes previously sampled from extant and extinct species as well as the three museum specimens of giant Galapagos tortoises analyzed in this study. Numbers on branches indicate posterior probabilities. Only the nodal support values for the major lineages are presented. Red and green colors identify museum samples analyzed in the present and previous studies, respectively. (B) Haplotype network showing matrilineal diversity recovered from 70 sequences of C. porteri from Reserva, 51 sequences of the lineage from Cerro Fatal, and 2 sequences of C. chathamensis from San Cristóbal Island. Twenty-five inferred mutations separate the haplogroups of Chelonoidis sp. nov. from Cerro Fatal from the ones from C. porteri from Reserva.

Fig 1 in Description of a New Galapagos Giant Tortoise Species (Chelonoidis; Testudines: Testudinidae) from Cerro Fatal on Santa Cruz Island

Fig 1. Geographic distribution of the two known lineages of giant tortoises on Santa Cruz Island: Chelonoidis porteri (Reserva) and Chelonoidis sp. nov. (Cerro Fatal) (indicated in dark gray). Light gray area connecting the distribution areas of the two species indicates agricultural land. Modified from Russello et al. [11].

Fig 6. A-E in Description of a New Galapagos Giant Tortoise Species (Chelonoidis; Testudines: Testudinidae) from Cerro Fatal on Santa Cruz Island

Fig 6. A-E. The skull of the museum specimen UWZS 32700, holotype for Chelonoidis sp. nov. from Cerro Fatal in Santa Cruz (A: dorsal, B: ventral, C: occipital, D: frontal and E: lateral view).

Fig 4 in Description of a New Galapagos Giant Tortoise Species (Chelonoidis; Testudines: Testudinidae) from Cerro Fatal on Santa Cruz Island

Fig 4. Genetic membership from Bayesian assignment tests in STRUCTURE for the three museum individuals, relative to the genotypic database representing the Cerro Fatal (black) and Reserva (white) giant tortoise populations. Each bar represents an individual and the proportional color of each bar represents the percentage membership (i.e., Q-value) in each of the reference clusters. Museum individuals include the C. porteri holotype (#) and the two Cerro Fatal specimens tested as putative candidates for the Chelonoidis sp. nov. holotype (*).

Fig 3 in Description of a New Galapagos Giant Tortoise Species (Chelonoidis; Testudines: Testudinidae) from Cerro Fatal on Santa Cruz Island

Fig 3. Polymorphic sites between Chelonoidis sp. nov. (Cerro Fatal—Santa Cruz), C. chathamensis (San Cristóbal), and C. porteri (Reserva— Santa Cruz). The position of diagnostic locations is relative to the Genbank record AY956622 for porCF1 from Cerro Fatal. - = gap position and K = G/T polymorphism.

opencc-zeroDec 2021View details →

Data from: A new lineage of Galapagos giant tortoises identified from museum samples

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 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]. The dataset archived here consists of a VCF file of the SNPs genotyped through ddRAD and a structure file of the 21 microsatellites with the genotypes for the same 64 individuals in each. Only a single mitochondrial haplotype was found, with no evidence to suggest substructure based on the nuclear markers.