Ancient mitochondrial DNA and morphology elucidate an extinct island radiation of Indian Ocean giant tortoises (Cylindraspis)

Reappraising the evolutionary history of the largest known gecko, the presumably extinct Hoplodactylus delcourti, via high-throughput sequencing of archival DNA

Hoplodactylus delcourti is a presumably extinct species of diplodactylid gecko known only from a single specimen of unknown provenance. It is by far the largest known gekkotan, approximately 50% longer than the next largest-known species. It has been considered a member of the New Zealand endemic genus Hoplodactylus based on external morphological features including shared toe pad structure. We obtained DNA from a bone sample of the only known specimen to generate high-throughput sequence data suitable for phylogenetic analysis of its evolutionary history. Complementary sequence data were obtained from a broad sample of diplodactylid geckos. Our results indicate that the species is not most closely related to extant Hoplodactylus or any other New Zealand gecko. Instead, it is a member of a clade whose living species are endemic to New Caledonia. Phylogenetic comparative analyses indicate that the New Caledonian diplodactylid clade has evolved significantly more disparate body sizes than either the Australian or New Zealand clades. Toe pad structure has changed repeatedly across diplodactylids, including multiple times in the New Caledonia clade, partially explaining the convergence in form between H. delcourti and New Zealand Hoplodactylus. Based on the phylogenetic results, we place H. delcourti in a new genus.

Ancient DNA elucidates the lost world of western Indian Ocean giant tortoises and reveals a new extinct species from Madagascar

Before humans arrived, giant tortoises occurred on many western Indian Ocean islands. We combined ancient DNA, phylogenetic, ancestral range, and molecular clock analyses with radiocarbon and paleogeographic evidence to decipher their diversity and biogeography. Using a mitogenomic time tree, we propose that the ancestor of the extinct Mascarene tortoises spread from Africa in the Eocene to now-sunken islands northeast of Madagascar. From these islands, the Mascarenes were repeatedly colonized. Another out-of-Africa dispersal (latest Eocene/Oligocene) produced on Madagascar giant, large, and small tortoise species. Two giant and one large species disappeared c. 1000 to 600 years ago, the latter described here as new to science using nuclear and mitochondrial DNA. From Madagascar, the Granitic Seychelles were colonized (Early Pliocene) and from there, repeatedly Aldabra (Late Pleistocene). The Granitic Seychelles populations were eradicated and later reintroduced from Aldabra. Our results underline that integrating ancient DNA data into a multi-evidence framework substantially enhances the knowledge of the past diversity of island faunas.

Mitochondrial DNA and Distribution Modelling Evidenced the Lost Genetic Diversity and Wild-Residence of Star Tortoise, Geochelone elegans (Testudines: Testudinidae) in India

The Indian star tortoise (Geochelone elegans) is a massively traded animal in South Asia. To mitigate this risk, the conservation agencies recommended guidelines to safeguard this charismatic species in nature. We adopted mitochondrial DNA-based investigation and performed species distribution modeling of G. elegans throughout its distribution range in the Indian subcontinent. The genetic analyses revealed weak genetic landscape shape interpolations, low intraspecific distances (0% to 1.5%) with mixed haplotype diversity, and a single molecular operational taxonomic unit (MOTU) in the cytochrome b gene dataset. The star tortoise, G. elegans, and its sister species Geochelone platynota showed a monophyletic clustering in the Bayesian (BA) phylogeny. We also attempt to understand the habitat suitability and quality of G. elegans in its distribution range. Our results suggest that, out of the extant area, only 56,495 km² (9.90%) is suitable for this species, with regions of highest suitability in Sri Lanka. Comparative habitat quality estimation suggests the patch shape complexity and habitat fragmentation are greater in the western and southern ranges of India, which have been greatly influenced by an increased level of urbanization and agriculture practices. We have also provided a retrospect on the potential threat to G. elegans related to the wildlife trade on the regional and international spectrum. Our results detected multiple trading hubs and junctions overlying within the suitable ranges which need special attention in the vicinity. The present study calls for a proper conservation strategy to combat the fragmented distribution and explicitly recommends intensive genetic screening of founder individuals or isolated adult colonies, implementing scientific breeding, and subsequent wild release to restore the lost genetic diversity of star tortoises.

Ancestral transoceanic colonization and recent population reduction in a nonannual killifish from the Seychelles archipelago

Whether freshwater fish colonize remote islands following tectonic or transoceanic dispersal remains an evolutionary puzzle. Integrating dating of known tectonic events with phylogenomics and current species distribution, we find that killifish species distribution is not explained by species dispersal by tectonic drift only. Investigating the colonization of a nonannual killifish (golden panchax, Pachypanchax playfairii) on the Seychelle islands, we found genetic support for transoceanic dispersal and experimentally discovered an adaptation to complete tolerance to seawater. At the macroevolutionary scale, despite their long-lasting isolation, nonannual golden panchax show stronger genome-wide purifying selection than annual killifishes from continental Africa. However, progressive decline in effective population size over a more recent timescale has probably led to the segregation of slightly deleterious mutations across golden panchax populations, which represents a potential threat for species preservation in the long term.

On the origin of giant seeds: the macroevolution of the double coconut (Lodoicea maldivica) and its relatives (Borasseae, Arecaceae)

Seed size shapes plant evolution and ecosystems, and may be driven by plant size and architecture, dispersers, habitat and insularity. How these factors influence the evolution of giant seeds is unclear, as are the rate of evolution and the biogeographical consequences of giant seeds. We generated DNA and seed size data for the palm tribe Borasseae (Arecaceae) and its relatives, which show a wide diversity in seed size and include the double coconut (Lodoicea maldivica), the largest seed in the world. We inferred their phylogeny, dispersal history and rates of change in seed size, and evaluated the possible influence of plant size, inflorescence branching, habitat and insularity on these changes. Large seeds were involved in 10 oceanic dispersals. Following theoretical predictions, we found that: taller plants with fewer-branched inflorescences produced larger seeds; seed size tended to evolve faster on islands (except Madagascar); and seeds of shade-loving Borasseae tended to be larger. Plant size and inflorescence branching may constrain seed size in Borasseae and their relatives. The possible roles of insularity, habitat and dispersers are difficult to disentangle. Evolutionary contingencies better explain the gigantism of the double coconut than unusually high rates of seed size increase.

Origin, extinction and ancient DNA of a new fossil insular viper: molecular clues of overseas immigration

Viperinae is a subfamily of viperid snakes whose fossil record in the Mediterranean islands is, until now, restricted to 12 palaeontological deposits on seven islands. Revision of the material excavated 30 years ago from the Middle/Late Pleistocene–Holocene deposit of Es Pouàs [Eivissa (= Ibiza), Balearic Islands, western Mediterranean] revealed about 6000 bones of a small-sized viper across different stratigraphic levels. Its morphological characteristics are different enough to known species of Vipera to warrant the description of a new species, but the nearly complete mitochondrial genome obtained from this snake based on a sample dated to 16 130 ± 45 bp, suggested it belonged to a new insular population of Lataste’s viper (Vipera latastei), Vipera latastei ebusitana subsp. nov. Phylogenetic analysis indicates that the dispersal of the ancestors of V. l. ebusitana to Eivissa, most probably from a north-east Iberian population, occurred via overwater colonization < 1.5 Mya, well after the Messinian Salinity Crisis (5.97–5.32 Mya) when land bridges allowed terrestrial colonization of the Balearic Islands by mainland faunas. The morphological differences between V. l. ebusitana and the Iberian populations suggest that it is a new dwarf taxon resulting from insular evolutionary processes, becoming extinct shortly after the first human arrival to this island about 4000 years ago.

Ancient mitogenomics clarifies radiation of extinct Mascarene giant tortoises (Cylindraspis spp.)

The five extinct giant tortoises of the genus Cylindraspis belong to the most iconic species of the enigmatic fauna of the Mascarene Islands that went largely extinct after the discovery of the islands. To resolve the phylogeny and biogeography of Cylindraspis, we analysed a data set of 45 mitogenomes that includes all lineages of extant tortoises and eight near-complete sequences of all Mascarene species extracted from historic and subfossil material. Cylindraspis is an ancient lineage that diverged as early as the late Eocene. Diversification of Cylindraspis commenced in the mid-Oligocene, long before the formation of the Mascarene Islands. This rejects any notion suggesting that the group either arrived from nearby or distant continents over the course of the last millions of years or had even been translocated to the islands by humans. Instead, Cylindraspis likely originated on now submerged islands of the Réunion Hotspot and utilized these to island hop to reach the Mascarenes. The final diversification took place both before and after the arrival on the Mascarenes. With Cylindraspis a deeply divergent clade of tortoises became extinct that evolved long before the dodo or the Rodrigues solitaire, two other charismatic species of the lost Mascarene fauna.

Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoise Chelonoidis alburyorum

Ancient DNA of extinct species from the Pleistocene and Holocene has provided valuable evolutionary insights. However, these are largely restricted to mammals and high latitudes because DNA preservation in warm climates is typically poor. In the tropics and subtropics, non-avian reptiles constitute a significant part of the fauna and little is known about the genetics of the many extinct reptiles from tropical islands. We have reconstructed the near-complete mitochondrial genome of an extinct giant tortoise from the Bahamas (Chelonoidis alburyorum) using an approximately 1 000-year-old humerus from a water-filled sinkhole (blue hole) on Great Abaco Island. Phylogenetic and molecular clock analyses place this extinct species as closely related to Galápagos (C. niger complex) and Chaco tortoises (C. chilensis), and provide evidence for repeated overseas dispersal in this tortoise group. The ancestors of extant Chelonoidis species arrived in South America from Africa only after the opening of the Atlantic Ocean and dispersed from there to the Caribbean and the Galápagos Islands. Our results also suggest that the anoxic, thermally buffered environment of blue holes may enhance DNA preservation, and thus are opening a window for better understanding evolution and population history of extinct tropical species, which would likely still exist without human impact.

Single origin of the Mascarene stick insects: ancient radiation on sunken islands?

BACKGROUND

The study of islands as model systems plays a key role in understanding many evolutionary processes. Knowledge of the historical events leading to present-day island communities is pivotal for exploring fundamental mechanisms of speciation and adaptation. The remote Mascarene archipelago (Mauritius, Réunion, Rodrigues), considered to be the product of an age-progressive trend of north-to-south volcanic activity in the Indian Ocean, hosts a remarkably diverse, endemic and threatened concentration of flora and fauna that has traditionally been considered to be biogeographically related to Madagascar and Africa. To explore the evolutionary diversity of the Mascarene stick insects (Phasmatodea), we constructed a global phylogeny from approximately 2.4 kb of mitochondrial and nuclear sequence data of more than 120 species representing all major phasmatodean lineages.

RESULTS

Based on the obtained time-calibrated molecular tree we demonstrate that the current phasmid community of the Mascarene archipelago, which consists of members of four presumably unrelated traditional subfamilies, is the result of a single ancient dispersal event from Australasia and started radiating between 16-29 million years ago, significantly predating the age of Mauritius (8-10 million years).

CONCLUSIONS

We propose that the Mascarene stick insects diversified on landmasses now eroded away, presumably to the north of Mauritius. In consequence, ancient islands have probably persisted in the Indian Ocean until the emergence of Mauritius and not only served as stepping stones for colonisation events during sea-level lowstands, but as long-lasting cradles of evolution. These ancient landmasses most likely allowed for adaptive speciation and served as significant sources of diversity that contributed to the biomes of the Mascarene archipelago and the megadiverse Madagascar.

One extinct turtle species less: Pelusios seychellensis is not extinct, it never existed

Pelusios seychellensis is thought to be a freshwater turtle species endemic to the island of Mahé, Seychelles. There are only three museum specimens from the late 19(th) century known. The species has been never found again, despite intensive searches on Mahé. Therefore, P. seychellensis has been declared as "Extinct" by the IUCN and is the sole putatively extinct freshwater turtle species. Using DNA sequences of three mitochondrial genes of the historical type specimen and phylogenetic analyses including all other species of the genus, we provide evidence that the description of P. seychellensis was erroneously based on a widely distributed West African species, P. castaneus. Consequently, we synonymize the two species and delete P. seychellensis from the list of extinct chelonian species and from the faunal list of the Seychelles.

The determinants of the molecular substitution process in turtles

Neutral rates of molecular evolution vary across species, and this variation has been shown to be related to biological traits. One of the first patterns to be observed in vertebrates has been an inverse relationship between body mass (BM) and substitution rates. The effects of three major life-history traits (LHT) that covary with BM - metabolic rate, generation time and longevity (LON) - have been invoked to explain this relationship. However, most of the theoretical and empirical evidence supporting this relationship comes from endothermic vertebrates, that is, mammals and birds, in which the environmental conditions, especially temperature, do not have a direct impact on cellular and molecular biology. We analysed the variations in mitochondrial and nuclear rates of synonymous substitution across 224 turtle species and examined their correlation with two LHT (LON and BM) and two environmental variables [latitude (LAT) and habitat]. Our analyses indicate that in turtles, neutral rates of molecular evolution are hardly correlated with LON or BM. Rather, both the mitochondrial and nuclear substitution rates are significantly correlated with LAT - faster evolution in the tropics - and especially so for aquatic species. These results question the generality of the relationships reported in mammals and birds and suggest that environmental factors might be the strongest determinants of the mutation rate in ectotherms.

In and out of Madagascar: dispersal to peripheral islands, insular speciation and diversification of Indian Ocean daisy trees (Psiadia, Asteraceae)

Madagascar is surrounded by archipelagos varying widely in origin, age and structure. Although small and geologically young, these archipelagos have accumulated disproportionate numbers of unique lineages in comparison to Madagascar, highlighting the role of waif-dispersal and rapid in situ diversification processes in generating endemic biodiversity. We reconstruct the evolutionary and biogeographical history of the genus Psiadia (Asteraceae), a plant genus with near equal numbers of species in Madagascar and surrounding islands. Analyzing patterns and processes of diversification, we explain species accumulation on peripheral islands and aim to offer new insights on the origin and potential causes for diversification in the Madagascar and Indian Ocean Islands biodiversity hotspot. Our results provide support for an African origin of the group, with strong support for non-monophyly. Colonization of the Mascarenes took place by two evolutionary distinct lineages from Madagascar, via two independent dispersal events, each unique for their spatial and temporal properties. Significant shifts in diversification rate followed regional expansion, resulting in co-occurring and phenotypically convergent species on high-elevation volcanic slopes. Like other endemic island lineages, Psiadia have been highly successful in dispersing to and radiating on isolated oceanic islands, typified by high habitat diversity and dynamic ecosystems fuelled by continued geological activity. Results stress the important biogeographical role for Rodrigues in serving as an outlying stepping stone from which regional colonization took place. We discuss how isolated volcanic islands contribute to regional diversity by generating substantial numbers of endemic species on short temporal scales. Factors pertaining to the mode and tempo of archipelago formation and its geographical isolation strongly govern evolutionary pathways available for species diversification, and the potential for successful diversification of dispersed lineages, therefore, appears highly dependent on the timing of arrival, as habitat and resource properties change dramatically over the course of oceanic island evolution.

The evolution of island gigantism and body size variation in tortoises and turtles

Extant chelonians (turtles and tortoises) span almost four orders of magnitude of body size, including the startling examples of gigantism seen in the tortoises of the Galapagos and Seychelles islands. However, the evolutionary determinants of size diversity in chelonians are poorly understood. We present a comparative analysis of body size evolution in turtles and tortoises within a phylogenetic framework. Our results reveal a pronounced relationship between habitat and optimal body size in chelonians. We found strong evidence for separate, larger optimal body sizes for sea turtles and island tortoises, the latter showing support for the rule of island gigantism in non-mammalian amniotes. Optimal sizes for freshwater and mainland terrestrial turtles are similar and smaller, although the range of body size variation in these forms is qualitatively greater. The greater number of potential niches in freshwater and terrestrial environments may mean that body size relationships are more complicated in these habitats.

Study of the carapace shape and growth in two Galápagos tortoise lineages

Galápagos tortoises possess two main shell forms, domed and saddleback, that correlate with the biogeographic history of this species group. However, the lack of description of morphological shell variation within and among populations has prevented the understanding of the contribution of evolutionary forces and the potential role of ontogeny in shaping morphological shell differences. Here, we analyze two lineages of Galápagos tortoises inhabiting Santa Cruz Island by applying geometric morphometrics in combination with a photogrammetry 3D reconstruction method on a set of tortoises of different ages (from juvenile to adult). The aim of this study is to describe morphological features on the carapace that could be used for taxonomic recognition by taking into account confounding factors, such as the morphological changes occurring during growth. Our results indicate that despite the shared similarities of growth patterns and of morphological changes observed during growth, the two lineages and the different sexes can be distinguished on the basis of distinct carapace features. Lineages differ by the shape of the vertebral (especially concerning their width) and pleural scutes, with one lineage having a more compressed carapace shape, whereas the other possesses a carapace that is more elongated and expanded toward the sides as well as an higher positioning of the first vertebral scute. Furthermore, females have a more elongated and wider carapace shape than males. Finally, carapace shape changes with growth, with vertebral scutes becoming narrower and pleural scutes becoming larger during late ontogeny.

Species identification using the cytochrome b gene of commercial turtle shells

Turtle shells and their gelled products are familiar in some countries as foods, tonics and medicines. These shells may come from endangered and protected species, requiring the identification of the species present to enforce national and international legislation. We report on the design of five combinations of primer pairs for the identification of turtle shells and shell fragments used as ornaments, food products and medicines. The types of samples used are those encountered frequently and will typically contain highly degraded DNA. The success rate for species identification using the test described is dependent upon the choice of primer sets used and the length of the expected amplification product. Gelled products were simulated by the process of decoction for up to 12 h, after which all the turtle species could be identified from the liquid samples. This study establishes a method for the identification of commercial turtle shells and illustrates a simulated case using gelled products.

A dated phylogeny of the palm tribe Chamaedoreeae supports Eocene dispersal between Africa, North and South America

The palm tribe Chamaedoreeae reaches its higher diversity in Central America, however, its distribution ranges from the north eastern part of Mexico to Bolivia with a disjunction to the Mascarene Islands in the Indian Ocean. The disjunct distribution of Chamaedoreeae is generally considered a result of Gondwana vicariance and extinction from Africa and/or Madagascar. However, latitudinal migrations and their role in shaping the distribution of this tribe in the Americas have been largely overlooked. In this study we used seven plastid and two nuclear DNA regions to investigate the phylogenetic relationships and biogeography of the Chamaedoreeae. The resulting phylogeny fully resolved the generic relationships within the tribe. The exact area of origin of the tribe remains uncertain, but dating analyses indicated an initial diversification of the Chamaedoreeae during the Early Eocene, followed by long distance dispersion to the Mascarene Islands in the late Miocene. The radiation of Hyophorbe could have taking place on islands in the Indian Ocean now submerged, but its former presence in Africa or Madagascar cannot be ruled out. At least two independent migrations between North and South America predating the rise of the Panama isthmus need to be postulated to explain the distribution of Chamaedoreeae, one during the Middle Eocene and a second during the Miocene. Whereas the traditional interpretation of distribution of Chamaedoreeae species assumes a west Gondwana origin of the group, the findings presented in this paper make it equally possible to interpret the group as a primarily boreotropical element.

A molecular phylogeny of tortoises (Testudines: Testudinidae) based on mitochondrial and nuclear genes

Although tortoises of the family Testudinidae represent a familiar and widely distributed group of turtles, their phylogenetic relationships have remained contentious. In this study, we included 32 testudinid species (all genera and subgenera, and all species of Geochelone, representing 65% of the total familial species diversity), and both mitochondrial (12S rRNA, 16S rRNA, and cytb) and nuclear (Cmos and Rag2) DNA data with a total of 3387 aligned characters. Using diverse phylogenetic methods (Maximum Parsimony, Maximum Likelihood, and Bayesian Analysis) congruent support is found for a well-resolved phylogeny. The most basal testudinid lineage includes a novel sister relationship between Asian Manouria and North American Gopherus. In addition, this phylogeny supports two other major testudinid clades: Indotestudo+Malacochersus+Testudo; and a diverse clade including Pyxis, Aldabrachelys, Homopus, Chersina, Psammobates, Kinixys, and Geochelone. However, we find Geochelone rampantly polyphyletic, with species distributed in at least four independent clades. Biogeographic analysis based on this phylogeny is consistent with an Asian origin for the family (as supported by the fossil record), but rejects the long-standing hypothesis of South American tortoises originating in North America. By contrast, and of special significance, our results support Africa as the ancestral continental area for all testudinids except Manouria and Gopherus. Based on our systematic findings, we also propose modifications concerning Testudinidae taxonomy.

Species identification of Kachuga tecta using the cytochrome b gene

A DNA technique has been established for the identification to species level of tortoises. The test on the shell of the animal was used to identify samples from the species Kachuga tecta. A total of 100 tortoise shell specimens collected from the National Council of Agriculture (COA), Taiwan, were used in this study. Primer pairs were designed to amplify partial DNA fragments of cytochrome b within the mitochondrial genome. The DNA data showed that among the 100 samples, there were four distinct haplotype DNA sequences, within which there were a total of 90 variable sites. Between haplotypes I and II, there was only 1 nucleotide difference at position 228. Between haplotypes I and III, 65 nucleotide differences were observed; haplotypes I and IV, 62 nucleotide differences; and haplotypes III and IV, 56 nucleotide differences were observed. There were 66 and 63 nucleotide differences between haplotypes II and III and haplotypes II and IV respectively. All four haplotypes were compared with the DNA sequences held at the GenBank and EMBL databases. The most similar species were K. tecta (haplotype I and II), Morenia ocellata (haplotype III) and Geoclemys hamiltonii (haplotype IV), and their respective mtDNA similarities were 99.5%, 99.3%, 89.9% and 99.5%. However, as haplotype III was only 89.9% homologous with M. ocellata, it would seem that this haplotype shows only a limited relationship with a similar species registered currently in these databases. The method established by this study is an additional method for the identification of samples protected under Convention International Trade in Endangered Species (CITES) and will improve the work for the preservation of the endangered species.

Using ancient and recent DNA to explore relationships of extinct and endangered Leiolopisma skinks (Reptilia: Scincidae) in the Mascarene islands

Phylogenetic analysis, using 1455 bp of recent mtDNA (cytochrome b 714 bp, 12S rRNA 376 bp) and nuclear (c-mos 365 bp) sequence from 42 species and 33 genera of Scincidae, confirms Leiolopisma telfairii, now confined to Round island off Mauritius, is a member of the mainly Australasian Eugongylus group of the Lygosominae. Ancient mtDNA (cytochrome b 307 bp, 12S rRNA 376 bp) was also extracted from subfossils of two other Mascarene taxa that are now extinct: the giant L. mauritiana from Mauritius and Leiolopisma sp., known only from fragmentary remains from Réunion. Sequence divergences of 4.2-5.7% show that all three forms were distinct and form a clade. There is restricted evidence that L. mauritiana and L. sp. from Réunion were sister species. Monophyly and relationships suggest Leiolopisma arose from a single transmarine invasion of the oceanic Mascarene islands from Australasia, 5600-7000 km away. This origin is similar to that of Cryptoblepharus skinks and Nactus geckos in the archipelago but contrasts with Phelsuma day geckos, which appear to have arrived from Madagascar where Mascarene Cylindraspis tortoises may also have originated. Diversification of the known species of Leiolopisma occurred from about 2.3-3.4 Mya, probably beginning on Mauritius with later invasion of Réunion. The initial coloniser may have had a relatively large body-size, but L. mauritiana is likely to have become gigantic within the Mascarenes. Other relationships supported by this investigation include the following. Scincines: Pamelaescincus+Janetaescincus, and Androngo (Amphiglossus, Paracontias). Lygosomines: Sphenomorphus group--(Sphenomorphus, Lipinia (Ctenotus, Anomalopus (Eulamprus and Gnypetoscincus))): Egernia group--Egernia (Cyclodomorphus, Tiliqua); Eugongylus group--(Oligosoma, Bassiana. (Lampropholis (Niveoscincus, Carlia))).

Reconstructing an island radiation using ancient and recent DNA: the extinct and living day geckos (Phelsuma) of the Mascarene islands

Mitochondrial (12SrRNA and cyt b, 1086 bp) and nuclear (c-mos, 374 bp) DNA sequences were used to investigate relationships and biogeography of 24 living and extinct taxa of Phelsuma geckos. Monophyly of Phelsuma and sister relationship to the SW African Rhoptropella is corroborated. Phelsuma originated on Madagascar and made multiple long-distance invasions of oceanic islands including the Mascarenes, Aldabra, Comores, Seychelles, Andamans, and perhaps Pemba. The Mascarenes were probably colonised once, about 4.2-5.1Ma, and here Phelsuma rosagularis and Phelsuma inexpectata are newly recognised as species, as are three lineages of Phelsuma cepediana. Mascarene relationships are: Phelsuma edwardnewtoni, Phelsuma gigas (Phelsuma guentheri ((((P. cepediana A (P. cepediana B, C)) P. rosagularis) Phelsuma borbonica) ((Phelsuma ornata, P. inexpectata) Phelsuma guimbeaui))). The two recently extinct species, P. edwardnewtoni and the giant secondarily nocturnal Phelsuma gigas, differentiated on Rodrigues while on Mauritius the large nocturnal P. guentheri separated from a small diurnal form that radiated into six species, a likely result of volcanic activity. Two small-bodied lineages from Mauritius invaded the more recent island of Réunion producing two more species. Outside the Mascarenes, two mainly Madagascan assemblages are substantiated: Phelsuma serraticauda (Phelsuma lineata, Phelsuma laticauda, Phelsuma quadriocellata); (Phelsuma m. kochi (Phelsuma m. grandis, Phelsuma abboti)) (Phelsuma astriata, Phelsuma sundbergi). Their relationships to the Mascarene clade, and to Phelsuma mutabilis, Phelsuma standingi and Phelsuma andamanensis are unresolved.

Paleobiogeography: The Relevance of Fossils to Biogeography

▪ Abstract  Paleobiogeography has advanced as a discipline owing to the increasing utilization of a phylogenetic approach to the study of biogeographic patterns. Coupled with this, there has been an increasing interdigitation of paleontology with molecular systematics because of the development of techniques to analyze ancient DNA and because of the use of sophisticated methods to utilize molecules to date evolutionary divergence events. One pervasive pattern emerging from several paleontological and molecular analyses of paleobiogeographic patterns is the recognition that repeated episodes of range expansion or geo-dispersal occur congruently in several different lineages, just as congruent patterns of vicariance also occur in independent lineages. The development of new analytical methods based on a modified version of Brooks Parsimony Analysis makes it possible to analyze both geo-dispersal and vicariance in a phylogenetic context, suggesting that biogeography as a discipline should focus on the analysis of a variety of congruent phenomena, not just vicariance. The important role that extinction plays in influencing apparent biogeographic patterns among modern and fossil groups suggests that this is another area ripe for new methodological developments.

Was there a second adaptive radiation of giant tortoises in the Indian Ocean? Using mitochondrial DNA to investigate speciation and biogeography of Aldabrachelys (Reptilia, Testudinidae)

A radiation of five species of giant tortoises (Cylindraspis) existed in the southwest Indian Ocean, on the Mascarene islands, and another (of Aldabrachelys) has been postulated on small islands north of Madagascar, from where at least eight nominal species have been named and up to five have been recently recognized. Of 37 specimens of Madagascan and small-island Aldabrachelys investigated by us, 23 yielded significant portions of a 428-base-pair (bp) fragment of mitochondrial (cytochrome b and tRNA-Glu), including type material of seven nominal species (A. arnoldi, A. dussumieri, A. hololissa, A. daudinii, A. sumierei, A. ponderosa and A. gouffei). These and nearly all the remaining specimens, including 15 additional captive individuals sequenced previously, show little variation. Thirty-three exhibit no differences and the remainder diverge by only 1-4 bp (0.23-0.93%). This contrasts with more widely accepted tortoise species which show much greater inter- and intraspecific differences. The non-Madagascan material examined may therefore only represent a single species and all specimens may come from Aldabra where the common haplotype is known to occur. The present study provides no evidence against the Madagascan origin for Aldabra tortoises suggested by a previous molecular phylogenetic analysis, the direction of marine currents and phylogeography of other reptiles in the area. Ancient mitochondrial DNA from the extinct subfossil A. grandidieri of Madagascar differs at 25 sites (5.8%) from all other Aldabrachelys samples examined here.

Are the native giant tortoises from the Seychelles really extinct? A genetic perspective based on mtDNA and microsatellite data

The extinction of the giant tortoises of the Seychelles Archipelago has long been suspected but is not beyond doubt. A recent morphological study of the giant tortoises of the western Indian Ocean concluded that specimens of two native Seychelles species survive in captivity today alongside giant tortoises of Aldabra, which are numerous in zoos as well as in the wild. This claim has been controversial because some of the morphological characters used to identify these species, several measures of carapace morphology, are reputed to be quite sensitive to captive conditions. Nonetheless, the potential survival of giant tortoise species previously thought extinct presents an exciting scenario for conservation. We used mitochondrial DNA sequences and nuclear microsatellites to examine the validity of the rediscovered species of Seychelles giant tortoises. Our results indicate that the morphotypes suspected to represent Seychelles species do not show levels of variation and genetic structuring consistent with long periods of reproductive isolation. We found no variation in the mitochondrial control region among 55 individuals examined and no genetic structuring in eight microsatellite loci, pointing to the survival of just a single lineage of Indian Ocean tortoises.

The evolutionary origin of Indian Ocean tortoises (Dipsochelys)

Today, the only surviving wild population of giant tortoises in the Indian Ocean occurs on the island of Aldabra. However, giant tortoises once inhabited islands throughout the western Indian Ocean. Madagascar, Africa, and India have all been suggested as possible sources of colonization for these islands. To address the origin of Indian Ocean tortoises (Dipsochelys, formerly Geochelone gigantea), we sequenced the 12S, 16S, and cyt b genes of the mitochondrial DNA. Our phylogenetic analysis shows Dipsochelys to be embedded within the Malagasy lineage, providing evidence that Indian Ocean giant tortoises are derived from a common Malagasy ancestor. This result points to Madagascar as the source of colonization for western Indian Ocean islands by giant tortoises. Tortoises are known to survive long oceanic voyages by floating with ocean currents, and thus, currents flowing northward towards the Aldabra archipelago from the east coast of Madagascar would have provided means for the colonization of western Indian Ocean islands. Additionally, we found an accelerated rate of sequence evolution in the two Malagasy Pyxis species examined. This finding supports previous theories that shorter generation time and smaller body size are related to an increase in mitochondrial DNA substitution rate in vertebrates.