Speciation and secondary contact in a fossorial island endemic, the São Tomé caecilian

A period of isolation in allopatry typically precedes local adaptation and subsequent divergence among lineages. Alternatively, locally adapted phenotypes may arise and persist in the face of gene flow, resulting in strong correlations between ecologically-relevant phenotypic variation and corresponding environmental gradients. Quantifying genetic, ecological, and phenotypic divergence in such lineages can provide insights into the abiotic and biotic mechanisms that structure populations and drive the accumulation of phenotypic and taxonomic diversity. Low-vagility organisms whose distributions span ephemeral geographic barriers present the ideal evolutionary context within which to address these questions. Here, we combine genetic (mtDNA and genome-wide SNPs) and phenotypic data to investigate the divergence history of caecilians (Amphibia: Gymnophiona) endemic to the oceanic island of São Tomé in the Gulf of Guinea archipelago. Consistent with a previous mtDNA study, we find two phenotypically and genetically distinct lineages that occur along a north-to-south axis with extensive admixture in the centre of the island. Demographic modelling supports divergence in allopatry (~300 kya) followed by secondary contact (~95 kya). Consequently, in contrast to a morphological study that interpreted latitudinal phenotypic variation in these caecilians as a cline within a single widespread species, our analyses suggest a history of allopatric lineage divergence and subsequent hybridization that may have blurred species boundaries. We propose that late Pleistocene volcanic activity favoured allopatric divergence between these lineages with local adaptation to climate maintaining a stable hybrid zone in the centre of São Tomé Island. Our study joins a growing number of systems demonstrating lineage divergence on volcanic islands with stark environmental transitions across small geographic distances.

Species delimitation and digit number in a North African skink

Delimitation of species is an important and controversial area within evolutionary biology. Many species boundaries have been defined using morphological data. New genetic approaches now offer more objective evaluation and assessment of the reliability of morphological variation as an indicator that speciation has occurred. We examined geographic variation in morphology of the continuously distributed skink Chalcides mionecton from Morocco and used Bayesian analyses of nuclear and mitochondrial DNA (mtDNA) loci to examine: (i) their concordance with morphological patterns, (ii) support for species delimitation, (iii) timing of speciation, and (iv) levels of gene flow between species. Four digit individuals were found at sites between Cap Rhir (in the south) and the northern extreme of the range, whereas five-digit individuals were found in two disjunct areas: (i) south of Cap Rhir and (ii) the north of the range where they were often syntopic with four-digit individuals. The pattern of variation in generalized body dimensions was largely concordant with that in digit number, suggesting two general morphotypes. Bayesian analyses of population structure showed that individuals from sites south of Cap Rhir formed one genetic cluster, but that northern four- and five-digit individuals clustered together. Statistical support for delimitation of these genetic clusters into two species was provided by a recent Bayesian method. Phylogenetic-coalescent dating with external time calibrations indicates that speciation was relatively recent, with a 95% posterior interval of 0.46-2.66 mya. This postdates equivalent phylogenetic dating estimates of sequence divergence by approximately 1 Ma. Statistical analyses of a small number of independent loci provide important insights into the history of the speciation process in C. mionecton and support delimitation of populations into two species with distributions that are spatially discordant with patterns of morphological variation.

Genetic divergence is decoupled from ecological diversification in the Hawaiian Nesosydne planthoppers

Adaptive radiation involves ecological shifts coupled with isolation of gene pools. However, we know little about what drives the initial stages of divergence. We study a system in which ecological diversification is found within a chronologically well-defined geological matrix to provide insight into this enigmatic phase of radiation. We tested the hypothesis that a period of geographic isolation precedes ecological specialization in an adaptive radiation of host-specialized Hawaiian planthoppers. We examined population structure and history using mitochondrial and multiple independent microsatellite loci in a species whose geographic distribution on the island of Hawaii enabled us to observe the chronology of divergence in its very earliest stages. We found that genetic divergence is associated with geographic features but not different plant hosts and that divergence times are very recent and on the same timescales as the dynamic geology of the island. Our results suggest an important role for geography in the dynamics of the early stages of divergence.

The helminth community of the skink Chalcides sexlineatus from Gran Canaria (Canary Islands)

A survey of the gastrointestinal helminth communities of a population of Chalcides sexlineatus Steindachner, a small skink endemic to Gran Canaria island (Canary Archipelago, Spain), was conducted to determine the prevalence, abundance and species diversity of intestinal parasites in these reptiles. Only three parasite species were found, one cestode, Oochoristica agamae Baylis, 1919 and two nematodes, Parapharyngodon micipsae (Seurat, 1917) and Pharyngodonidae gen. sp. Helminth infracommunities of C. sexlineatus showed low values of abundance and species richness and diversity, being more similar to the helminth community of Tarentola boettgeri boettgeri (Steindachner) rather than those of Gallotia stehlini (Schenkel), both syntopic with the sampled host.

Does weather shape rodents? Climate related changes in morphology of two heteromyid species

Geographical variation in morphometric characters in heteromyid rodents has often correlated with climate gradients. Here, we used the long-term database of rodents trapped in the Sevilleta National Wildlife Refuge in New Mexico, USA to test whether significant annual changes in external morphometric characters are observed in a region with large variations in temperature and precipitation. We looked at the relationships between multiple temperature and precipitation variables and a number of morphological traits (body mass, body, tail, hind leg, and ear length) for two heteromyid rodents, Dipodomys merriami and Perognathus flavescens. Because these rodents can live multiple years in the wild, the climate variables for the year of the capture and the previous 2 years were included in the analyses. Using multiple linear regressions, we found that all of our morphometric traits, with the exception of tail length in D. merriami, had a significant relationship with one or more of the climate variables used. Our results demonstrate that effects of climate change on morphological traits occur over short periods, even in noninsular mammal populations. It is unclear, though, whether these changes are the result of morphological plasticity or natural selection.

Colonization history, ecological shifts and diversification in the evolution of endemic Galápagos weevils

Mitochondrial DNA sequence data were obtained for eight species of flightless Galapaganus endemic weevils and one winged close relative in order to study their colonization history and modes of diversification in the Galápagos Archipelago. Contrary to most other insular radiations, the phylogeny estimates we recovered for Galapaganus do not follow the progression rule of island biogeography. The penalized likelihood age estimates of colonization of the archipelago exceed the age of the emerged islands and underscore the potential role of now sunken seamounts for the early evolution of Galapaganus. The phylogeny proposes one intra-island origin for Galapaganus endemics, but monophyly tests suggest a larger contribution of in-situ speciation on older islands. Generalist habitat preferences were reconstructed as ancestral while shifts to highland habitats were reconstructed as having evolved independently on different islands. Magnitudes and patterns of diversification rate were found to differ between older and younger islands. Our analyses reveal that the colonization sequence of islands and timing of colonization of Galapaganus could be linked with the geological and volcanic history of the islands in a rather complex scenario. Even though most islands appear to have been colonized soon after their emergence, there are notable deviations from the pattern of sequential colonization expected under the progression rule when considering only the extant emerged islands. Patterns of diversification rate variation on older and younger islands correspond to the volcanic activity or remnants of such activity, while the pattern of independent evolution of restricted habitat preferences in different islands suggests that habitat shifts could also have contributed to species diversity in Galapaganus.

Radiation, multiple dispersal and parallelism in the skinks, Chalcides and Sphenops (Squamata: Scincidae), with comments on Scincus and Scincopus and the age of the Sahara Desert

Phylogenetic analysis using up to 1325 base pairs of mitochondrial DNA from 179 specimens and 30 species of Chalcides, Sphenops, Eumeces, Scincopus and Scincus indicates that Sphenops arose twice independently within Chalcides. It is consequently synonymized with that genus. Chalcides in this broader sense originated in Morocco, diversifying into four main clades about 10 Ma, after which some of its lineages dispersed widely to cover an area 40 times as large. Two separate lineages invaded the Canary Islands and at least five main lineages colonized southern Europe. At least five more spread across northern Africa, one extending into southwest Asia. Elongate bodies with reduced limbs have evolved at least four times in Chalcides, mesic 'grass-swimmers' being produced in one case and extensive adaptation to life in loose desert sand in two others. In clade, Chalcides striatus colonized SW Europe from NW Africa 2.6 Ma and C. chalcides mainland Italy 1.4 Ma, both invasions being across water, while C. c. vittatus reached Sardinia more recently, perhaps anthropogenically, and C. guentheri spread 1200km further east to Israel. C. minutus is a composite, with individuals from the type locality forming a long independent lineage and the remaining ones investigated being most closely related to C. mertensi. In the Northern clade, C. boulengeri and C. sepsoides spread east through sandy habitats north of the Sahara about 5 Ma, the latter reaching Egypt. C. bedriagai invaded Spain around the same time, perhaps during the Messinian period when the Mediterranean was dry, and shows considerable diversification. Although it is currently recognized as one species, the C. ocellatus clade exhibits as much phylogenetic depth as the other main clades of Chalcides, having at least six main lineages. These have independently invaded Malta and Sardinia from Tunisia and also southwest Arabia C. o. humilis appears to have spread over 4000 km through the Sahel, south of the Sahara quite recently, perhaps in the Pleistocene. In the Western clade of Chalcides, C. delislei appears to have dispersed in a similar way. There were also two invasions of the Canary Islands: one around 5 Ma by C. simonyi, and the other about 7 Ma by the ancestor of C. viridanus+C. sexlineatus. C. montanus was believed to be related to C. lanzai of the Northern clade, but in the mtDNA tree it is placed within C. polylepis of the Western clade, although this may possibly be an artifact of introgression. The Eumeces schneideri group, Scincopus and Scincus form a clade separate from Chalcides. Within this clade, the geographically disjunct E. schneideri group is paraphyletic. One of its members, E. algeriensis is the sister taxon to Scincopus, and Scincus may also be related to these taxa. The phylogeny suggests Scincopus entered desert conditions in Africa, up to 9.6 Ma and the same may have been true of Scincus up to 11.7 Ma. Scincus appears to have diversified and spread into Arabia around 6 Ma. Dates of origin and divergence of these skinks, desert Chalcides and other squamates agree with recent geological evidence that the Sahara is at least 5-7 My old. The subspecies Chalcides viridanus coeruleopunctatus is upgraded to the species level as C. coeruleopunctatus stat nov., on the basis of its large genetic divergence from C. v. viridanus.

Geological history and within-island diversity: a debris avalanche and the Tenerife lizard Gallotia galloti

Several processes have been described that could explain geographical variation and speciation within small islands, including fragmentation of populations through volcanic eruptions. Massive landslides, or debris avalanches, could cause similar effects. Here we analyse the potential impact of the 0.8 million-year-ago (Ma) Güimar valley debris avalanche on the phylogeography of the lizard Gallotia galloti on the Canary Island of Tenerife. Distributions of mitochondrial DNA lineages (based on cytochrome b sequences) were analysed on a 60-km southeastern coast transect centred on this area. Three main clades were detected, which can be divided into northern (one clade) and southern (two clades) groups that introgress across the valley. Maximum-likelihood estimates of migration rates (scaled for mutation rate) revealed highly asymmetric patterns, indicating that long-term gene flow into this region from both the northern and the southern populations greatly exceeded that in the opposite directions, consistent with recolonization of the area. The ancestral Tenerife node on the G. galloti tree is estimated at 0.80 Ma, matching closely with the geological estimate for the debris avalanche. Morphological variation (body dimensions and scalation) was also analysed and indicated a stepped cline in female scalation across the valley, although the patterns for male scalation and male and female body dimensions were not as clear. Together these findings provide support for the hypothesis that the debris avalanche has shaped the phylogeography of G. galloti and may even have been a primary cause of the within-island cladogenesis through population fragmentation and isolation. Current estimates of timing of island unification mean that the original hypothesis that within-island diversity is explained by the secondary contact of populations from the two ancient precursor islands of Teno and Anaga is less plausible for this and some other Tenerife species. Large-scale landslides have occurred on many volcanic islands, and so may have been instrumental in shaping within-island diversities.

Testing phylogeographic predictions on an active volcanic island: Brachyderes rugatus (Coleoptera: Curculionidae) on La Palma (Canary Islands)

Volcanic islands with well-characterized geological histories can provide ideal templates for generating and testing phylogeographic predictions. Many studies have sought to utilize these to investigate patterns of colonization and speciation within groups of closely related species across a number of islands. Here we focus attention within a single volcanic island with a well-characterized geological history to develop and test phylogeographic predictions. We develop phylogeographic predictions within the island of La Palma of the Canary Islands and test these using 69 haplotypes from 570 base pairs of mitochondrial DNA cytochrome oxidase II sequence data for 138 individuals of Brachyderes rugatus rugatus, a local endemic subspecies of curculionid beetle occurring throughout the island in the forests of Pinus canariensis. Although geological data do provide some explanatory power for the phylogeographic patterns found, our network-based analyses reveal a more complicated phylogeographic history than initial predictions generated from data on the geological history of the island. Reciprocal illumination of geological and phylogeographic history is also demonstrated with previous geological speculation gaining phylogeographic corroboration from our analyses.

The dynamics of genetic and morphological variation on volcanic islands

Oceanic archipelagos of volcanic origin have been important in the study of evolution because they provide repeated natural experiments allowing rigorous tests of evolutionary hypotheses. Ongoing volcanism on these islands may, however, affect the evolutionary diversification of species. Analysis of population structure and phylogeographic patterns in island populations can provide insight into evolutionary dynamics on volcanic islands. We analysed genetic and morphological variation in the gecko Tarentola boettgeri on the island of Gran Canaria and compared it with Tarentola delalandii on Tenerife, a neighbouring volcanic island of similar age but distinctly different geological past. Intraspecific divergence of mitochondrial haplotypes indicates long-term persistence of Tarentola on each island, with a phylogeographic signal left by older volcanic events. More recent volcanic eruptions (approximately 0.2 million years ago on Tenerife, approximately 2.2 million years ago on Gran Canaria) have left a signature of population expansion in the population genetic structure, the strength of which depends on the time since the last major volcanic eruption on each island. While these stochastic events have left traces in morphological variation in Tenerife, in Gran Canaria geographical variation was solely associated with environmental variables. This suggests that historically caused patterns in morphology may be overwritten by natural selection within 2 million years.

Phylogeography of the endangered darkling beetle species of Pimelia endemic to Gran Canaria (Canary Islands)

Phylogenetic and geographical nested clade analysis (NCA) methods were applied to mitochondrial DNA sequences of Pimelia darkling beetles (Coleoptera, Tenebrionidae) endemic to Gran Canaria, an island in the Canary archipelago. The three species P. granulicollis, P. estevezi and P. sparsa occur on the island, the latter with three recognized subspecies. Another species, P. fernandezlopezi (endemic to the island of La Gomera) is a close relative of P. granulicollis based on partial Cytochrome Oxidase I mtDNA sequences obtained in a previous study. Some of these beetles are endangered, so phylogeographical structure within species and populations can help to define conservation priorities. A total of about 700 bp of Cytochrome Oxidase II were examined in 18 populations and up to 75 individuals excluding outgroups. Among them, 22 haplotypes were exclusive to P. granulicollis and P. estevezi and 31 were from P. sparsa. Phylogenetic analysis points to the paraphyly of Gran Canarian Pimelia, as the La Gomera P. fernandezlopezi haplotypes are included in them, and reciprocal monophyly of two species groups: one constituted by P. granulicollis, P. estevezi and P. fernandezlopezi (subgenus Aphanaspis), and the other by P. sparsa'sensu lato'. The two species groups show a remarkably high mtDNA divergence. Within P. sparsa, different analyses all reveal a common result, i.e. conflict between current subspecific taxonomic designations and evolutionary units, while P. estevezi and P. fernandezlopezi are very close to P. granulicollis measured at the mtDNA level. Geographical NCA identifies several cases of nonrandom associations between haplotypes and geography that may be caused by allopatric fragmentation of populations with some cases of restriction of gene flow or range expansion. Analyses of molecular variance and geographical NCA allow definition of evolutionary units for conservation purposes in both species-groups and suggest scenarios in which vicariance caused by geological history of the island may have shaped the pattern of the mitochondrial genetic diversity of these beetles.

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

Ancient mitochondrial DNA sequences were used for investigating the evolution of an entire clade of extinct vertebrates, the endemic tortoises (Cylindraspis) of the Mascarene Islands in the Indian Ocean. Mitochondrial DNA corroborates morphological evidence that there were five species of tortoise with the following relationships: Cylindraspis triserrata ((Cylindraspis vosmaeri and Cylindraspis peltastes) (Cylindraspis inepta and Cylindraspis indica)). Phylogeny indicates that the ancestor of the group first colonized Mauritius where speciation produced C. triserrata and the ancestor of the other species including a second sympatric Mauritian form, C. inepta. A propagule derived from this lineage colonized Rodrigues 590 km to the east, where a second within-island speciation took place producing the sympatric C. vosmaeri and C. peltastes. A recent colonization of Réunion 150 km to the southwest produced C. indica. In the virtual absence of predators, the defensive features of the shells of Mascarene tortoises were largely dismantled, apparently in two stages. 'Saddlebacked' shells with high fronts evolved independently on all three islands. This and other features, such as a derived jaw structure and small body size, may be associated with niche differentiation in sympatric species and may represent a striking example of parallel differentiation in a large terrestrial vertebrate. The history of Mascarene tortoises contrasts with that of the Galápagos, where only a single species is present and surviving populations are genetically much more similar. However, they too show some reduction in anti-predator mechanisms and multiple development of populations with saddlebacked shells.

Population subdivision in marine environments: the contributions of biogeography, geographical distance and discontinuous habitat to genetic differentiation in a blennioid fish, Axoclinus nigricaudus

The relative importance of factors that may promote genetic differentiation in marine organisms is largely unknown. Here, contributions to population structure from a biogeographic boundary, geographical distance and the distribution of suitable habitat were investigated in Axoclinus nigricaudus, a small subtidal rock-reef fish, throughout its range in the Gulf of California. A 408-bp fragment of the mitochondrial control region was sequenced from 105 individuals. Variation was significantly partitioned between 28 of 36 possible combinations of population pairs. Phylogenetic analyses, hierarchical analyses of variance and a modified Mantel test substantiated a major break between two putative biogeographic regions. This genetic discontinuity coincides with an abrupt change in ecological characteristics, including temperature and salinity, but does not coincide with known oceanographic circulation patterns or any known historic barriers. There was an overall relationship of increasing genetic distance with increasing geographical distance between population pairs, in a manner consistent with isolation-by-distance. A significant habitat-by-geographical-distance interaction term indicated that, for a given geographical distance, populations separated by discontinuous habitat (sand) are more distinct genetically than are populations separated by continuous habitat (rock). In addition, populations separated by deep open waters were more genetically distinct than populations separated by continuous habitat (rock). These results indicate that levels of genetic differentiation among populations of A. nigricaudus cannot be explained by a single factor, but are due to the combined influences of biogeography, geographical distance and availability of suitable habitat.

Mitochondrial DNA, ecology and morphology: interpreting the phylogeography of the Nesotes (Coleoptera: Tenebrionidae) of Gran Canaria (Canary Islands)

The genus Nesotes (Coleoptera: Tenebrionidae) is represented in the Canary Islands by 19 endemic species, the majority of which are single island endemics. Nesotes conformis and N. fusculus are described on four and three islands, respectively, but each forms a paraphyletic assemblage between Gran Canaria and the other islands. The other described species for Gran Canaria are N. quadratus, N. lindbergi and N. piliger. Thirty-six individuals representing the five species on Gran Canaria have been sequenced for 675 bp of the mitochondrial DNA (mtDNA) cytochrome oxidase II gene. Neighbour-joining analysis of maximum likelihood distances resulted in five distinct mtDNA lineages for N. quadratus, two of which also include mitotypes of N. conformis. Each of the other three species is found on only one mtDNA lineage. We propose from the molecular data that differentiation in a widespread N. quadratus-type ancestor was followed by morphological adaptation to coastal, pine and laurel forest habitats.

Mitochondrial DNA control region diversity in the endangered blue chaffinch, Fringilla teydea

The blue chaffinch (Fringilla teydea) is found only on the two central Canary Islands of Gran Canaria and Tenerife, where it is restricted to pine forest habitat. It is reasonably abundant on the latter island but endangered on the former. Here, sequence variation was studied in a fragment spanning domains I and II of the mitochondrial DNA (mtDNA) control region. Phylogenetic analysis of all haplotypes with a F. coelebs outgroup indicated the two island populations were reciprocally monophyletic, supporting their individual conservation. Unlike in other species, most within-island haplotype diversity was due to mutations in the domain II region. Surprisingly, genetic diversity was greater in the smaller Gran Canarian population. We suggest that this is unlikely to be maintained under current population sizes although it may be mitigated by incorporating genetic information into the captive breeding programme.

Phylogeography and natural selection in the Tenerife gecko Tarentola delalandii: testing historical and adaptive hypotheses

Combining phylogeographic and matrix correspondence approaches in the analysis of geographical variation provides a fruitful approach to inferring the causes of molecular and morphological evolution within species. Here we present a study on the gecko Tarentola delalandii on the island of Tenerife, Canary Islands, which provides an outstanding model of an exceptionally high degree of phylogeographic differentiation in magnitude and pattern on a small spatial scale. We reconstruct the population history of T. delalandii using phylogeographic information, matrix correspondence tests and estimates of divergence times in conjunction with geological data. It appears that populations differentiated on three precursor islands and secondary contact followed the junction of these islands. The cytochrome b sequence appears to be evolving at least at approximately 1% per million years in this species. Matrix correspondence tests indicate that morphological character systems may reflect ecological selection regimes (colour pattern), history (body dimensions) or both (scalation). The results imply that natural selection can override a historical legacy, but also underline the potential relevance of molecular phylogenetic data for the interpretation of geographical variation in morphology.

Mitochondrial DNA evolution and population history of the Tenerife skink Chalcides viridanus

Recent studies of island lizards have suggested that historical vicariance as a result of volcanism may have played an important role in shaping patterns of within-island genetic diversity. The skink, Chalcides viridanus, shows variation in morphology within the volcanic island of Tenerife. Two mitochondrial DNA (mtDNA) fragments (from the 12S and 16S rRNA regions) were sequenced in individuals from 17 sites to evaluate the relationship between current phylogeography and the geological history of the island. Three main clades were detected. The two most basal clades were restricted to areas representing the ancient precursor islands of Teno and Anaga in the northwest and northeast of Tenerife, respectively. The third clade showed a widespread geographical distribution and provided evidence of a recent rapid expansion after a bottleneck. Within-island cladogenesis appears to have taken place during a recent period of volcanic activity and long after the ancient islands had been united by the eruptions that led to the formation of the Canadas edifice. Evidence of similar biogeographical histories are found in other species in the Canary archipelago, supporting the volcanism scenario as a potentially widespread cause of within-island differentiation in reptiles.