Phylogeographic history and gene flow among giant Galápagos tortoises on southern Isabela Island

Volcanic islands represent excellent models with which to study the effect of vicariance on colonization and dispersal, particularly when the evolution of genetic diversity mirrors the sequence of geological events that led to island formation. Phylogeographic inference, however, can be particularly challenging for recent dispersal events within islands, where the antagonistic effects of land bridge formation and vicariance can affect movements of organisms with limited dispersal ability. We investigated levels of genetic divergence and recovered signatures of dispersal events for 631 Galápagos giant tortoises across the volcanoes of Sierra Negra and Cerro Azul on the island of Isabela. These volcanoes are among the most recent formations in the Galápagos (<0.7 million years), and previous studies based on genetic and morphological data could not recover a consistent pattern of lineage sorting. We integrated nested clade analysis of mitochondrial DNA control region sequences, to infer historical patterns of colonization, and a novel Bayesian multilocus genotyping method for recovering evidence of recent migration across volcanoes using eleven microsatellite loci. These genetic studies illuminate taxonomic distinctions as well as provide guidance to possible repatriation programs aimed at countering the rapid population declines of these spectacular animals.     

Phylogeography and history of giant Galápagos tortoises

Abstract.— 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.     

Microsatellite analysis of genetic divergence among populations of giant Galápagos tortoises

Giant Galápagos tortoises represent an interesting model for the study of patterns of genetic divergence and adaptive differentiation related to island colonization events. Recent mitochondrial DNA work elucidated the evolutionary history of the species and helped to clarify aspects of nomenclature. We used 10 microsatellite loci to assess levels of genetic divergence among and within island populations. In particular, we described the genetic structure of tortoises on the island of Isabela, where discrimination of different taxa is still subject of debate. Individual island populations were all genetically distinct. The island of Santa Cruz harboured two distinct populations. On Isabela, populations of Volcan Wolf, Darwin and Alcedo were significantly different from each other. On the other hand, Volcan Wolf showed allelic similarity with the island of Santiago. On Southern Isabela, lower genetic divergence was found between Northeast Sierra Negra and Volcan Alcedo, while patterns of gene flow were recorded among tortoises of Cerro Azul and Southeast Sierra Negra. These tortoises have endured heavy exploitation during the last three centuries and recently attracted much concern due to the current number of stochastic and deterministic threats to extant populations. Our study complements previous investigation based on mtDNA diversity and provides further information that may help devising tortoise management plans.     

On vegetation recovery,goats and giant tortoises on Pinta Island,Galápagos,Ecuador

Data on vegetational changes on Pinta Island, Galápagos, collected during the period 1970–1988, show that feral goats have had a destructive impact on the vegetation. Stands of Scalesia baurii ssp. hopkinsii (Asteraceae) and Opuntia galapageia var. galapageia (Cactaceae) were close to a complete collapse, while stands of Bursera graveolens (Burseraceae) apparently were able to persist for a longer time. After the elimination of large numbers of goats, Scalesia, Opuntia and Bursera were recovering rapidly, but the patterns of regeneration differed in accordance with differences in longevity, growth and seedling establishment.It is suggested that the absence of herbivores (the Pinta subspecies of giant tortoise is practically extinct, and feral goats were finally eradicated in 1990) in the long term may lead to decreased diversity in the vegetation of Pinta. As a management experiment aimed at conserving the biological diversity of Pinta, it is proposed to reintroduce giant tortoises to the island, preceded and accompanied by a careful long-term monitoring of vegetational changes.Contribution No. 486 of the Charles Darwin Foundation for the Galápagos Isles.     

Genetic divergence, phylogeography and conservation units of giant tortoises from Santa Cruz and Pinzón, Galápagos Islands

Island radiations can offer challenging systemsfor the implementation of conservation policiesbecause descendent populations may exhibitdifferent levels of adaptive divergence,reproductive isolation, and phylogeneticdistinctiveness. This seems particularly truefor the endangered Galápagos gianttortoises (Geochelone nigra), whichcomprise a lineage that radiated rapidly andconcomitantly with the evolution of thearchipelago. We used mitochondrial DNAsequences and microsatellite markers toinvestigate the genetic structure, and toreconstruct genealogical relationships and thehistory of population colonization of gianttortoises from the Islands of Santa Cruz andPinzón, including samples of a basal taxonfrom the Island of San Cristóbal.Populations displayed marked geneticdivergence, contrasting demographic histories,and deep phylogeographic structure. The patternof diversification among populations wasconsistent with geological and biogeographichistory, and to some extent, with adaptive andmorphological divergence. Results stronglyindicate the presence of a minimum of fourconservation units with long-standingevolutionary separation: two in Santa Cruz, onein Pinzón, and one in San Cristóbal. Wepropose that these findings be effectivelyintegrated with other existing data by theappropriate environmental agencies to evaluatecurrent conservation efforts and implement newstrategies aimed at protecting the integrityand diversity of giant tortoise populations.     

Genetic analysis of a successful repatriation programme: giant Galápagos tortoises

As natural populations of endangered species dwindle to precarious levels, remaining members are sometimes brought into captivity, allowed to breed and their offspring returned to the natural habitat. One goal of such repatriation programmes is to retain as much of the genetic variation of the species as possible. A taxon of giant Galápagos tortoises on the island of Espa?ola has been the subject of a captive breeding-repatriation programme for 33 years. Core breeders, consisting of 12 females and three males, have produced more than 1200 offspring that have been released on Espa?ola where in situ reproduction has recently been observed. Using microsatellite DNA markers, we have determined the maternity and paternity of 132 repatriated offspring. Contributions of the breeders are highly skewed. This has led to a further loss of genetic variation that is detrimental to the long-term survival of the population. Modifications to the breeding programme could alleviate this problem.     

Fruit and pedicel characters derived from Galápagos Tomatoes’

By relatively simple breeding procedures, seven different modifications of fruit and pedicel have been successfully transferred from wild tomatoes of the Galápagos Islands to large-fruited cultivars. Some of these traits, the majority of which are simply inherited, may have horticultural value. Such introgression from the wild forms is expedited by the remarkable freedom from barriers at any stage of the breeding processes.     

Unravelling the peculiarities of island life: vicariance, dispersal and the diversification of the extinct and extant giant Galápagos tortoises

In isolated oceanic islands, colonization patterns are often interpreted as resulting from dispersal rather than vicariant events. Such inferences may not be appropriate when island associations change over time and new islands do not form in a simple linear trend. Further complexity in the phylogeography of ocean islands arises when dealing with endangered taxa as extinctions, uncertainty on the number of evolutionary ‘units’, and human activities can obscure the progression of colonization events. Here, we address these issues through a reconstruction of the evolutionary history of giant Galápagos tortoises, integrating DNA data from extinct and extant species with information on recent human activities and newly available geological data. Our results show that only three of the five extinct or nearly extinct species should be considered independent evolutionary units. Dispersal from mainland South America started at approximately 3.2 Ma after the emergence of the two oldest islands of San Cristobal and Española. Dispersal from older to younger islands began approximately 1.74 Ma and was followed by multiple colonizations from different sources within the archipelago. Vicariant events, spurred by island formation, coalescence, and separation, contributed to lineage diversifications on Pinzón and Floreana dating from 1.26 and 0.85 Ma. This work provides an example of how to reconstruct the history of endangered taxa in spite of extinctions and human‐mediated dispersal events and highlights the need to take into account both vicariance and dispersal when dealing with organisms from islands whose associations are not simply explained by a linear emergence model.     

A hitchhikers guide to the Galápagos: co-phylogeography of Galápagos mockingbirds and their parasites

Background

Parasites are evolutionary hitchhikers whose phylogenies often track the evolutionary history of their hosts. Incongruence in the evolutionary history of closely associated lineages can be explained through a variety of possible events including host switching and host independent speciation. However, in recently diverged lineages stochastic population processes, such as retention of ancestral polymorphism or secondary contact, can also explain discordant genealogies, even in fully co-speciating taxa. The relatively simple biogeographic arrangement of the Galápagos archipelago, compared with mainland biomes, provides a framework to identify stochastic and evolutionary informative components of genealogic data in these recently diverged organisms.

Results

Mitochondrial DNA sequences were obtained for four species of Galápagos mockingbirds and three sympatric species of ectoparasites - two louse and one mite species. These data were complemented with nuclear EF1α sequences in selected samples of parasites and with information from microsatellite loci in the mockingbirds. Mitochondrial sequence data revealed differences in population genetic diversity between all taxa and varying degrees of topological congruence between host and parasite lineages. A very low level of genetic variability and lack of congruence was found in one of the louse parasites, which was excluded from subsequent joint analysis of mitochondrial data. The reconciled multi-species tree obtained from the analysis is congruent with both the nuclear data and the geological history of the islands.

Conclusions

The gene genealogies of Galápagos mockingbirds and two of their ectoparasites show strong phylogeographic correlations, with instances of incongruence mostly explained by ancestral genetic polymorphism. A third parasite genealogy shows low levels of genetic diversity and little evidence of co-phylogeny with their hosts. These differences can mostly be explained by variation in life-history characteristics, primarily host specificity and dispersal capabilities. We show that pooling genetic data from organisms living in close ecological association reveals a more accurate phylogeographic history for these taxa. Our results have implications for the conservation and taxonomy of Galápagos mockingbirds and their parasites.     

Co-phylogeography and comparative population genetics of the threatened Galápagos hawk and three ectoparasite species: ecology shapes population histories within parasite communities

Comparative microevolutionary studies of multiple parasites occurring on a single host species can help shed light on the processes underlying parasite diversification. We compared the phylogeographical histories, population genetic structures and population divergence times of three co-distributed and phylogenetically independent ectoparasitic insect species, including an amblyceran and an ischnoceran louse (Insecta: Phthiraptera), a hippoboscid fly (Insecta: Diptera) and their endemic avian host in the Galápagos Islands. The Galápagos hawk (Aves: Falconiformes: Buteo galapagoensis) is a recently arrived endemic lineage in the Galápagos Islands and its island populations are diverging evolutionarily. Each parasite species differed in relative dispersal ability and distribution within the host populations, which allowed us to make predictions about their degree of population genetic structure and whether they tracked host gene flow and colonization history among islands. To control for DNA region in comparisons across these phylogenetically distant taxa, we sequenced ~1 kb of homologous mitochondrial DNA from samples collected from all island populations of the host. Remarkably, the host was invariant across mitochondrial regions that were comparatively variable in each of the parasite species, to degrees consistent with differences in their natural histories. Differences in these natural history traits were predictably correlated with the evolutionary trajectories of each parasite species, including rates of interisland gene flow and tracking of hosts by parasites. Congruence between the population structures of the ischnoceran louse and the host suggests that the ischnoceran may yield insight into the cryptic evolutionary history of its endangered host, potentially aiding in its conservation management.     

The Galápagos Islands: biogeographic patterns and geology

In the traditional biogeographic model, the Galápagos Islands appeared a few million years ago in a sea where no other islands existed and were colonized from areas outside the region. However, recent work has shown that the Galápagos hotspot is 139 million years old (Early Cretaceous), and so groups are likely to have survived at the hotspot by dispersal of populations onto new islands from older ones. This process of metapopulation dynamics means that species can persist indefinitely in an oceanic region, as long as new islands are being produced. Metapopulations can also undergo vicariance into two metapopulations, for example at active island arcs that are rifted by transform faults. We reviewed the geographic relationships of Galápagos groups and found 10 biogeographic patterns that are shared by at least two groups. Each of the patterns coincides spatially with a major tectonic structure; these structures include: the East Pacific Rise; west Pacific and American subduction zones; large igneous plateaus in the Pacific; Alisitos terrane (Baja California), Guerrero terrane (western Mexico); rifting of North and South America; formation of the Caribbean Plateau by the Galápagos hotspot, and its eastward movement; accretion of Galápagos hotspot tracks; Andean uplift; and displacement on the Romeral fault system. All these geological features were active in the Cretaceous, suggesting that geological change at that time caused vicariance in widespread ancestors. The present distributions are explicable if ancestors survived as metapopulations occupying both the Galápagos hotspot and other regions before differentiating, more or less in situ.     

Extreme difference in rate of mitochondrial and nuclear DNA evolution in a large ectotherm, Galápagos tortoises

We sequenced approximately 4.5 kb of mtDNA from 161 individuals representing 11 named taxa of giant Galápagos tortoises (Geochelone nigra) and about 4 kb of non-coding nuclear DNA from fewer individuals of these same 11 taxa. In comparing mtDNA and nucDNA divergences, only silent substitutions (introns, ITS, mtDNA control region, and synonymous substitutions in coding sequences) were considered. mtDNA divergence was about 30 times greater than that for nucDNA. This rate discrepancy for mtDNA and nucDNA is the greatest yet documented and is particularly surprising for large ectothermic animals that are thought to have relatively low rates of mtDNA evolution. This observation may be due to the somewhat unusual reproductive biology and biogeographic history of these organisms. The implication is that the ratio of effective population size of nucDNA/mtDNA is much greater than the usually assumed four. The nearly neutral theory of molecular evolution predicts this would lead to a greater difference between rates of evolution.     

Endocrine-reproductive-immune interactions in female and male Galápagos marine iguanas

Endocrine-immune interactions are variable across species and contexts making it difficult to discern consistent patterns. There is a paucity of data in non-model systems making these relationships even more nebulous, particularly in reptiles. In the present study, we have completed a more comprehensive test of the relationship among steroid hormones and ecologically relevant immune measures. We tested the relationship between baseline and stress-induced levels of sex and adrenal steroid hormones and standard ecoimmunological metrics in both female and male Galápagos marine iguanas (Amblyrhynchus cristatus). We found significant associations between adrenal activity and immunity, whereby females that mounted greater corticosterone responses to stress had lower basal and stress-induced immunity (i.e., bactericidal ability). Males showed the opposite relationship, suggesting sex-specific immunomodulatory actions of corticosterone. In both sexes, we observed a stress-induced increase in corticosterone, and in females a stress-induced increase in bactericidal ability. Consistent with other taxa, we also found that baseline corticosterone and testosterone in males was inversely related to baseline bactericidal ability. However, in females, we found a positive relationship between both testosterone and progesterone and bactericidal ability. Multivariate analysis did not discern any further endocrine-immune relationships, suggesting that interactions between adrenal, sex steroid hormones, and the immune system may not be direct and instead may be responding to other common stimuli, (i.e., reproductive status, energy). Taken together, these data illustrate significant endocrine-immune interactions that are highly dependent on sex and the stress state of the animal.     

Steroid hormones and aggression in female Galápagos marine iguanas

We studied steroid hormone patterns and aggression during breeding in female Galápagos marine iguanas (Amblyrhynchus cristatus). Females display vigorously towards courting males after copulating (female-male aggression), as well as fight for and defend nest sites against other females (female-female aggression). To understand the neuroendocrine basis of this aggressive behavior, we examined changes in testosterone (T), estradiol (E₂), corticosterone (CORT), and progesterone (P₄) during the mating and nesting periods, and then measured levels in nesting females captured during aggressive interactions. Testosterone reached maximal levels during the mating stage when female-male aggression was most common, and increased slightly, but significantly, during the nesting stage when female-female aggression was most common. However, fighting females had significantly lower T, but higher E₂ and P₄, than non-fighting females. It remains unclear whether these changes in hormone levels during aggressive interactions are a cause or a consequence of a change in behavior. Our results support the “challenge hypothesis”, but suggest that E₂ and/or P₄ may increase in response to aggressive challenges in females just as T does in males. Females may be rapidly aromatizing T to elevate circulating levels of E₂ during aggressive interactions. This hypothesis could explain why non-fighting females had slightly elevated baseline T, but extremely low E₂, during stages when aggressive interactions were most common. Although P₄ increased rapidly during aggressive encounters, it is unclear whether it acts directly to affect behavior, or indirectly via conversion to E₂. The rapid production and conversion of E₂ and P₄ may be an important mechanism underlying female aggression in vertebrates.     

Ecological drift and local exposures drive enteric bacterial community differences within species of Galápagos iguanas

Diet strongly influences the intestinal microbial communities through species sorting. Alternatively, these communicates may differ because of chance variation in local microbial exposures or species losses among allopatric host populations (i.e. ecological drift). We investigated how these forces shape enteric communities of Galápagos marine and land iguanas. Geographically proximate populations shared more similar communities within a host ecotype, suggesting a role for ecological drift during host colonization of the islands. Additionally, evidence of taxa sharing between proximate heterospecific host populations suggests that contemporary local exposures also influence the gut community assembly. While selective forces such as host-bacterial interactions or dietary differences are dominant drivers of intestinal community differences among hosts, historical and contemporary processes of ecological drift may lead to differences in bacterial composition within a host species. Whether such differences in community structure translate into geographic variation in benefits derived from these intimate microbial communities remains to be explored.