Multilocus genotypes from Charles Darwin's finches: biodiversity lost since the voyage of the Beagle

Genetic analysis of museum specimens offers a direct window into a past that can predate the loss of extinct forms. We genotyped 18 Galápagos finches collected by Charles Darwin and companions during the voyage of the Beagle in 1835, and 22 specimens collected in 1901. Our goals were to determine if significant genetic diversity has been lost since the Beagle voyage and to determine the genetic source of specimens for which the collection locale was not recorded. Using ‘ancient’ DNA techniques, we quantified variation at 14 autosomal microsatellite loci. Assignment tests showed several museum specimens genetically matched recently field-sampled birds from their island of origin. Some were misclassified or were difficult to classify. Darwin''s exceptionally large ground finches (Geospiza magnirostris) from Floreana and San Cristóbal were genetically distinct from several other currently existing populations. Sharp-beaked ground finches (Geospiza difficilis) from Floreana and Isabela were also genetically distinct. These four populations are currently extinct, yet they were more genetically distinct from congeners than many other species of Darwin''s finches are from each other. We conclude that a significant amount of the finch biodiversity observed and collected by Darwin has been lost since the voyage of the Beagle.     

Urban living influences the nesting success of Darwin’s finches in the Galápagos Islands

Urbanization is expanding worldwide with major consequences for organisms. Anthropogenic factors can reduce the fitness of animals but may have benefits, such as consistent human food availability. Understanding anthropogenic trade‐offs is critical in environments with variable levels of natural food availability, such as the Galápagos Islands, an area of rapid urbanization. For example, during dry years, the reproductive success of bird species, such as Darwin''s finches, is low because reduced precipitation impacts food availability. Urban areas provide supplemental human food to finches, which could improve their reproductive success during years with low natural food availability. However, urban finches might face trade‐offs, such as the incorporation of anthropogenic debris (e.g., string, plastic) into their nests, which may increase mortality. In our study, we determined the effect of urbanization on the nesting success of small ground finches (Geospiza fuliginosa; a species of Darwin''s finch) during a dry year on San Cristóbal Island. We quantified nest building, egg laying and hatching, and fledging in an urban and nonurban area and characterized the anthropogenic debris in nests. We also documented mortalities including nest trash‐related deaths and whether anthropogenic materials directly led to entanglement‐ or ingestion‐related nest mortalities. Overall, urban finches built more nests, laid more eggs, and produced more fledglings than nonurban finches. However, every nest in the urban area contained anthropogenic material, which resulted in 18% nestling mortality while nonurban nests had no anthropogenic debris. Our study showed that urban living has trade‐offs: urban birds have overall higher nesting success during a dry year than nonurban birds, but urban birds can suffer mortality from anthropogenic‐related nest‐materials. These results suggest that despite potential costs, finches benefit overall from urban living and urbanization may buffer the effects of limited resource availability in the Galápagos Islands.     

Increasing prevalence of avian poxvirus in Darwin's finches and its effect on male pairing success

Island populations harbour a comparatively species-poor pathogen community, often resulting in naïve host species that experience compromised immunity when faced with novel diseases. Over 95% of the Galápagos avifauna have survived 400 years of human settlement, yet currently face threats due to introduced diseases such as avian poxvirus. On Hawaii, declining populations of birds and even some extinctions have been attributed to avian poxvirus, and hence, identifying the prevalence and fitness costs of avian poxvirus on the Galápagos is a conservation priority. Surveys of avian poxvirus in Darwin's finches on Santa Cruz Island between 2000 and 2004 found a 33% annual increase in the prevalence of pox lesions in ground finches. Comparisons of pox prevalence on three islands (Santa Cruz, Floreana, and Isabela) were made in 2004, which indicated significant variation in pox prevalence across islands (Isabela>Santa Cruz>Floreana). Darwin's finch species were found to be differentially affected by poxvirus, with a higher prevalence in ground finches than in tree finches. There was a significant effect of habitat, even within species, with higher prevalence in the lowlands than highlands. Pox prevalence was not correlated with sex or body condition. However, male small ground finches Geospiza fuliginosa with evidence of pox were less likely to have a mate (16.6% paired) compared with males without pox (77% paired), indicating fitness costs associated with poxvirus infection.     

Increasing prevalence of avian poxvirus in Darwin's finches and its effect on male pairing success

Island populations harbour a comparatively species‐poor pathogen community, often resulting in naïve host species that experience compromised immunity when faced with novel diseases. Over 95% of the Galápagos avifauna have survived 400 years of human settlement, yet currently face threats due to introduced diseases such as avian poxvirus. On Hawaii, declining populations of birds and even some extinctions have been attributed to avian poxvirus, and hence, identifying the prevalence and fitness costs of avian poxvirus on the Galápagos is a conservation priority. Surveys of avian poxvirus in Darwin's finches on Santa Cruz Island between 2000 and 2004 found a 33% annual increase in the prevalence of pox lesions in ground finches. Comparisons of pox prevalence on three islands (Santa Cruz, Floreana, and Isabela) were made in 2004, which indicated significant variation in pox prevalence across islands (Isabela>Santa Cruz>Floreana). Darwin's finch species were found to be differentially affected by poxvirus, with a higher prevalence in ground finches than in tree finches. There was a significant effect of habitat, even within species, with higher prevalence in the lowlands than highlands. Pox prevalence was not correlated with sex or body condition. However, male small ground finches Geospiza fuliginosa with evidence of pox were less likely to have a mate (16.6% paired) compared with males without pox (77% paired), indicating fitness costs associated with poxvirus infection.     

Evidence for regular ongoing introductions of mosquito disease vectors into the Galápagos Islands

Wildlife on isolated oceanic islands is highly susceptible to the introduction of pathogens. The recent establishment in the Galápagos Islands of the mosquito Culex quinquefasciatus, a vector for diseases such as avian malaria and West Nile fever, is considered a serious risk factor for the archipelago''s endemic fauna. Here we present evidence from the monitoring of aeroplanes and genetic analysis that C. quinquefasciatus is regularly introduced via aircraft into the Galápagos Archipelago. Genetic population structure and admixture analysis demonstrates that these mosquitoes breed with, and integrate successfully into, already-established populations of C. quinquefasciatus in the Galápagos, and that there is ongoing movement of mosquitoes between islands. Tourist cruise boats and inter-island boat services are the most likely mechanism for transporting Culex mosquitoes between islands. Such anthropogenic mosquito movements increase the risk of the introduction of mosquito-borne diseases novel to Galápagos and their subsequent widespread dissemination across the archipelago. Failure to implement and maintain measures to prevent the human-assisted transport of mosquitoes to and among the islands could have catastrophic consequences for the endemic wildlife of Galápagos.     

Biogeography of Parasitic Nematode Communities in the Galápagos Giant Tortoise: Implications for Conservation Management

The Galápagos giant tortoise is an icon of the unique, endemic biodiversity of Galápagos, but little is known of its parasitic fauna. We assessed the diversity of parasitic nematode communities and their spatial distributions within four wild tortoise populations comprising three species across three Galápagos islands, and consider their implication for Galápagos tortoise conservation programmes. Coprological examinations revealed nematode eggs to be common, with more than 80% of tortoises infected within each wild population. Faecal samples from tortoises within captive breeding centres on Santa Cruz, Isabela and San Cristobal islands also were examined. Five different nematode egg types were identified: oxyuroid, ascarid, trichurid and two types of strongyle. Sequencing of the 18S small-subunit ribosomal RNA gene from adult nematodes passed with faeces identified novel sequences indicative of rhabditid and ascaridid species. In the wild, the composition of nematode communities varied according to tortoise species, which co-varied with island, but nematode diversity and abundance were reduced or altered in captive-reared animals. Evolutionary and ecological factors are likely responsible for the variation in nematode distributions in the wild. This possible species/island-parasite co-evolution has not been considered previously for Galápagos tortoises. We recommend that conservation efforts, such as the current Galápagos tortoise captive breeding/rearing and release programme, be managed with respect to parasite biogeography and host-parasite co-evolutionary processes in addition to the biogeography of the host.     

Effects of age,sex, and ENSO phase on foraging and flight performance in Nazca boobies

Age‐related changes in survival and reproduction are common in seabirds; however, the underlying causes remain elusive. A lack of experience for young individuals, and a decline in foraging performance for old birds, could underlie age‐related variation in reproduction because reproductive success is connected closely to provisioning offspring. For seabirds, flapping flight during foraging trips is physiologically costly; inexperience or senescent decline in performance of this demanding activity might cap delivery of food to the nest, providing a proximate explanation for poor breeding success in young and old age, respectively. We evaluated the hypothesis that young and old Nazca boobies (Sula granti), a Galápagos seabird, demonstrate deficits in foraging outcomes and flight performance. We tagged incubating male and female adults across the life span with both accelerometer and GPS loggers during the incubation periods of two breeding seasons (years), during the 2015 El Niño and the following weak La Niña. We tested the ability of age, sex, and environment to explain variation in foraging outcomes (e.g., mass gained) and flight variables (e.g., wingbeat frequency). Consistent with senescence, old birds gained less mass while foraging than middle‐aged individuals, a marginal effect, and achieved a slower airspeed late in a foraging trip. Contrary to expectations, young birds showed no deficit in foraging outcomes or flight performance, except for airspeed (contingent on environment). Young birds flew slower than middle‐aged birds in 2015, but faster than middle‐aged birds in 2016. Wingbeat frequency, flap–glide ratio, and body displacement (approximating wingbeat strength) failed to predict airspeed and were unaffected by age. Sex influenced nearly all aspects of performance. Environment affected flight performance and foraging outcomes. Boobies'' foraging outcomes were better during the extreme 2015 El Niño than during the 2016 weak La Niña, a surprising result given the negative effects tropical seabirds often experience during extreme El Niños.     

Review Oribatid mites of the Galápagos Islands – faunistics, ecology and speciation

The results from investigations on oribatid mites of the Galápagos archipelago during 10 years are presented. Samples were taken on all larger and most smaller islands of the archipelago, as well as in all vegetation zones and some special habitats such as grass or cactus litter and fumaroles. A total of 202 oribatid species belonging to 64 families were encountered; among them 81 species are new to science. The Oribatida occur from the littoral zone to the summit of the volcanoes. Diversity and abundance increases from the arid to the moister zones at higher elevations. Most species prefer moist habitats at medium to higher elevations of the islands, in some parts reaching remarkably high abundances (in the Scalesia zone of Santa Cruz approximately 18 000 individuals m–2). The species richness of an island depends on the altitude and number of available habitats rather than the area of the island. Many oribatid species on the Galápagos Islands have a wide biogeographical distribution. The majority originate from the Central and South American mainland, but several Pacific and even Holarctic elements were also found. In comparison with the species composition of the adjacent mainland, the oribatid mite fauna of the Galápagos Islands can be regarded as disharmonic. Sea surface transportation has been proved at least between the islands, which also applies to oribatid species living at higher elevations. Long distance dispersal can be assumed to be mainly hydrochorous. The oribatid fauna of the littoral and arid vegetation zones is presented in detail. Some species even inhabit such extreme habitats as warm fern litter in fumaroles or hot volcanic soils. Others were mainly found in or near agricultural areas, suggesting human introduction. Striking distribution patterns within the archipelago are discussed. The distribution of endemic forms in the genera Aeroppia, Scapheremaeus, Scheloribates and Cultrobates indicates both speciation on different islands, as well as speciation on the same island by occupying different habitats.     

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 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.Subject terms: Phylogenetics, Population genetics     

Stress physiology as a predictor of survival in Galapagos marine iguanas

Although glucocorticoid hormones are considered important physiological regulators for surviving adverse environmental stimuli (stressors), evidence for such a role is sparse and usually extrapolated from glucocorticoid effects under laboratory, short-term and/or non-emergency conditions. Galápagos marine iguanas (Amblyrhynchus cristatus) provide an excellent model for determining the ultimate function of a glucocorticoid response because susceptibility to starvation induced by El Niño conditions is essentially their only major natural stressor. In a prospective study, we captured 98 adult male marine iguanas and assessed four major components of their glucocorticoid response: baseline corticosterone titres; corticosterone responses to acute stressors (capture and handling); the maximal capacity to secrete corticosterone (via adrenocorticotropin injection); and the ability to terminate corticosterone responses (negative feedback). Several months after collecting initial measurements, weak El Niño conditions affected the Galápagos and 23 iguanas died. The dead iguanas were typified by a reduced efficacy of negative feedback (i.e. poorer post-stress suppression of corticosterone release) compared with surviving iguanas. We found no prior differences between dead and alive iguanas in baseline corticosterone concentrations, responses to acute stressors, nor in capacity to respond. These data suggest that a greater ability to terminate a stress response conferred a survival advantage during starvation.     

Ecoimmunity in Darwin's Finches: Invasive Parasites Trigger Acquired Immunity in the Medium Ground Finch (Geospiza fortis)

Background

Invasive parasites are a major threat to island populations of animals. Darwin''s finches of the Galápagos Islands are under attack by introduced pox virus (Poxvirus avium) and nest flies (Philornis downsi). We developed assays for parasite-specific antibody responses in Darwin''s finches (Geospiza fortis), to test for relationships between adaptive immune responses to novel parasites and spatial-temporal variation in the occurrence of parasite pressure among G. fortis populations.

Methodology/Principal Findings

We developed enzyme-linked immunosorbent assays (ELISAs) for the presence of antibodies in the serum of Darwin''s finches specific to pox virus or Philornis proteins. We compared antibody levels between bird populations with and without evidence of pox infection (visible lesions), and among birds sampled before nesting (prior to nest-fly exposure) versus during nesting (with fly exposure). Birds from the Pox-positive population had higher levels of pox-binding antibodies. Philornis-binding antibody levels were higher in birds sampled during nesting. Female birds, which occupy the nest, had higher Philornis-binding antibody levels than males. The study was limited by an inability to confirm pox exposure independent of obvious lesions. However, the lasting effects of pox infection (e.g., scarring and lost digits) were expected to be reliable indicators of prior pox infection.

Conclusions/Significance

This is the first demonstration, to our knowledge, of parasite-specific antibody responses to multiple classes of parasites in a wild population of birds. Darwin''s finches initiated acquired immune responses to novel parasites. Our study has vital implications for invasion biology and ecological immunology. The adaptive immune response of Darwin''s finches may help combat the negative effects of parasitism. Alternatively, the physiological cost of mounting such a response could outweigh any benefits, accelerating population decline. Tests of the fitness implications of parasite-specific immune responses in Darwin''s finches are urgently needed.     

Conspecific versus heterospecific gene exchange between populations of Darwin's finches

This study addresses the extent and consequences of gene exchange between populations of Darwin''s finches. Four species of ground finches (Geospiza) inhabit the small island of Daphne Major in the centre of the Galápagos archipelago. We undertook a study of microsatellite DNA variation at 16 loci in order to quantify gene flow within species owing to immigration and between species owing to hybridization. A combination of pedigrees of observed breeders and assignments of individuals to populations by the program Structure enabled us to determine the frequency of gene exchange and the island of origin of immigrants in some cases. The relatively large populations of Geospiza fortis and G. scandens receive conspecific immigrants at a rate of less than one per generation. They exchange genes more frequently by rare but repeated hybridization. Effects of heterospecific gene flow from hybridization are not counteracted by lower fitness of the offspring. As a result, the standing genetic variation of the two main resident populations on Daphne Major is enhanced to a greater extent by introgressive hybridization than through breeding with conspecific immigrants. Immigrant G. fuliginosa also breeds with G. fortis. Conspecific immigration was highest in the fourth species, G. magnirostris. This species is much larger than the other three and perhaps for this reason it has not bred with any of them. The source island of most immigrants is probably the neighbouring island of Santa Cruz. Evolutionary change may be inhibited in G. magnirostris by continuing gene flow, but enhanced in G. fortis and G. scandens by introgressive hybridization.     

Differentiation with drift: a spatio-temporal genetic analysis of Galápagos mockingbird populations (Mimus spp.)

Small and isolated island populations provide ideal systems to study the effects of limited population size, genetic drift and gene flow on genetic diversity. We assessed genetic diversity within and differentiation among 19 mockingbird populations on 15 Galápagos islands, covering all four endemic species, using 16 microsatellite loci. We tested for signs of drift and gene flow, and used historic specimens to assess genetic change over the last century and to estimate effective population sizes. Within-population genetic diversity and effective population sizes varied substantially among island populations and correlated strongly with island size, suggesting that island size serves as a good predictor for effective population size. Genetic differentiation among populations was pronounced and increased with geographical distance. A century of genetic drift did not change genetic diversity on an archipelago-wide scale, but genetic drift led to loss of genetic diversity in small populations, especially in one of the two remaining populations of the endangered Floreana mockingbird. Unlike in other Galápagos bird species such as the Darwin''s finches, gene flow among mockingbird populations was low. The clear pattern of genetically distinct populations reflects the effects of genetic drift and suggests that Galápagos mockingbirds are evolving in relative isolation.     

Pollination patterns and plant breeding systems in the Galápagos: a review

Background

Despite the importance of the Galápagos Islands for the development of central concepts in ecology and evolution, the understanding of many ecological processes in this archipelago is still very basic. One such process is pollination, which provides an important service to both plants and their pollinators. The rather modest level of knowledge on this subject has so far limited our predictive power on the consequences of the increasing threat of introduced plants and pollinators to this unique archipelago.

Scope

As a first step toward building a unified view of the state of pollination in the Galápagos, a thorough literature search was conducted on the breeding systems of the archipelago''s flora and compiled all documented flower–visitor interactions. Based on 38 studies from the last 100 years, we retrieved 329 unique interactions between 123 flowering plant species (50 endemics, 39 non-endemic natives, 26 introduced and eight of unknown origin) from 41 families and 120 animal species from 13 orders. We discuss the emergent patterns and identify promising research avenues in the field.

Conclusions

Although breeding systems are known for <20 % of the flora, most species in our database were self-compatible. Moreover, the incidence of autogamy among endemics, non-endemic natives and alien species did not differ significantly, being high in all groups, which suggests that a poor pollinator fauna does not represent a constraint to the integration of new plant species into the native communities. Most interactions detected (approx. 90 %) come from a single island (most of them from Santa Cruz). Hymenopterans (mainly the endemic carpenter bee Xylocopa darwinii and ants), followed by lepidopterans, were the most important flower visitors. Dipterans were much more important flower visitors in the humid zone than in the dry zone. Bird and lizard pollination has been occasionally reported in the dry zone. Strong biases were detected in the sampling effort dedicated to different islands, time of day, focal plants and functional groups of visitors. Thus, the existing patterns need to be confronted with new and less biased data. The implementation of a community-level approach could greatly increase our understanding of pollination on the islands and our ability to predict the consequences of plant invasions for the natural ecosystems of the Galápagos.     

Characterization of canarypox-like viruses infecting endemic birds in the Galápagos Islands

The presence of avian pox in endemic birds in the Galápagos Islands has led to concern that the health of these birds may be threatened by avipoxvirus introduction by domestic birds. We describe here a simple polymerase chain reaction-based method for identification and discrimination of avipoxvirus strains similar to the fowlpox or canarypox viruses. This method, in conjunction with DNA sequencing of two polymerase chain reaction-amplified loci totaling about 800 bp, was used to identify two avipoxvirus strains, Gal1 and Gal2, in pox lesions from yellow warblers (Dendroica petechia), finches (Geospiza spp.), and Galápagos mockingbirds (Nesomimus parvulus) from the inhabited islands of Santa Cruz and Isabela. Both strains were found in all three passerine taxa, and sequences from both strains were less than 5% different from each other and from canarypox virus. In contrast, chickens in Galápagos were infected with a virus that appears to be identical in sequence to the characterized fowlpox virus and about 30% different from the canarypox/Galápagos group viruses in the regions sequenced. These results indicate the presence of canarypox-like viruses in endemic passerine birds that are distinct from the fowlpox virus infecting chickens on Galápagos. Alignment of the sequence of a 5.9-kb region of the genome revealed that sequence identities among Gal1, Gal2, and canarypox viruses were clustered in discrete regions. This indicates that recombination between poxvirus strains in combination with mutation led to the canarypox-like viruses that are now prevalent in the Galápagos.     

A phylogeny of Darwin's finches based on microsatellite DNA length variation

Allele length variation at 16 microsatellite loci was used to estimate the phylogeny of 13 out of the 14 species of Darwin''s finches. The resulting topology was similar to previous phylogenies based on morphological and allozyme variation. An unexpected result was that genetic divergence among Galápagos Island populations of the warbler finch (Certhidea olivacea) predates the radiation of all other Darwin''s finches. This deep split is surprising in view of the relatively weak morphological differentiation among Certhidea populations and supports the hypothesis that the ancestor of all Darwin''s finches was phenotypically similar to Certhidea. The results also resolve a biogeographical problem: the Cocos Island finch evolved after the Galápagos finch radiation was under way, supporting the hypothesis that this distant island was colonized from the Galápagos Islands. Monophyletic relationships are supported for both major groups, the ground finches (Geospiza) and the tree finches (Camarhynchus and Cactospiza), although the vegetarian finch (Platyspiza crassirostris) appears to have diverged prior to the separation of ground and tree finches. These results demonstrate the use of microsatellites for reconstructing phylogenies of closely related species and interpreting their evolutionary and biogeographic histories.     

Historical Isolation of the Galápagos Carpenter Bee (Xylocopa darwini) despite Strong Flight Capability and Ecological Amplitude

Colonization across the Galápagos Islands by the carpenter bee (Xylocopa darwini) was reconstructed based on distribution of mitochondrial haplotypes (cytochrome oxidase II (COII) sequences) and haplotype lineages. A total of 12 haplotypes were found in 118 individuals of X. darwini. Distributional, phylogenetic and phylogeographic analyses suggest early colonization of most islands followed by historical isolation in two main groups: eastern and central-western islands. Evidence of recurrent inter-island colonization of haplotypes is largely lacking, despite strong flight capability and ecological amplitude of the species. Recent palaeogeographic data suggest that several of the current islands were connected in the past and thus the isolation pattern may have been even more pronounced. A contrast analysis was also carried out on 10 animal groups of the Galápagos Islands, and on haplotype colonization of seven animal and plant species from several oceanic archipelagos (the Galápagos, Azores, Canary Islands). New colonization metrics on the number of potential vs. inferred colonization events revealed that the Galápagos carpenter bee shows one of the most significant examples of geographic isolation.     

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

Background

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.

Methodology/Findings

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.

Significance

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.     

Divergence with gene flow as facilitated by ecological differences: within-island variation in Darwin's finches

Divergence and speciation can sometimes proceed in the face of, and even be enhanced by, ongoing gene flow. We here study divergence with gene flow in Darwin''s finches, focusing on the role of ecological/adaptive differences in maintaining/promoting divergence and reproductive isolation. To this end, we survey allelic variation at 10 microsatellite loci for 989 medium ground finches (Geospiza fortis) on Santa Cruz Island, Galápagos. We find only small genetic differences among G. fortis from different sites. We instead find noteworthy genetic differences associated with beak. Moreover, G. fortis at the site with the greatest divergence in beak size also showed the greatest divergence at neutral markers; i.e. the lowest gene flow. Finally, morphological and genetic differentiation between the G. fortis beak-size morphs was intermediate to that between G. fortis and its smaller (Geospiza fuliginosa) and larger (Geospiza magnirostris) congeners. We conclude that ecological differences associated with beak size (i.e. foraging) influence patterns of gene flow within G. fortis on a single island, providing additional support for ecological speciation in the face of gene flow. Patterns of genetic similarity within and between species also suggest that interspecific hybridization might contribute to the formation of beak-size morphs within G. fortis.