Parallel gigantism and complex colonization patterns in the Cape Verde scincid lizards Mabuya and Macroscincus (Reptilia: Scincidae) revealed by mitochondrial DNA sequences

Smaller islands, bigger appetites: evolutionary strategies of insular endemic skinks

Competitive dietary and morphological divergence among co-occurring species are fundamental aspects of ecological communities, particularly on islands. Cabo Verde (~570 km west of continental Africa) hosts several endemic reptiles descended from common ancestors, with sympatric species exhibiting wide morphological variation and competing for limited resources. To explore the mechanisms of resource partitioning between coexisting species, DNA metabarcoding was used to compare the diets of large and small skinks, Chioninia vaillantii and Chioninia delalandii, in sympatric and allopatric contexts on Fogo Island and in a more competitive context on the small and resource-poor Cima Islet. The morphological variation of all populations was also examined to test the character displacement hypothesis and to compare the effect of different competitive scenarios. Results showed significant differences in diet and linear measurements between species and populations. The two sympatric populations of C. delalandii on Fogo and Cima showed similar changes in head morphology compared to the allopatric population, supporting character displacement. The effect of higher competitive pressure on Cima was evidenced by the increased morphological and dietary variation observed. This study demonstrates how sister species develop dietary adaptations/morphologies to maintain stable coexistence, especially in highly competitive scenarios, providing useful insights for effective conservation strategies.

Swimming through the sands of the Sahara and Arabian deserts: Phylogeny of sandfish skinks (Scincidae, Scincus) reveals a recent and rapid diversification

Large parts of the Sahara Desert and Arabia are covered by sand seas and sand dunes, which are inhabited by specialized animal communities. For example, many lizards have developed adaptations to life in loose sand, including sand-swimming behavior. The best-known sand swimmers of the Saharo-Arabia are the sandfish skinks (genus Scincus). Although there are currently only four Scincus species recognized, their phylogenetic relationships have not yet been addressed in detail. We use eight genetic markers (three mitochondrial, five nuclear) and a complete sampling of species to infer the relationships within the genus. We employ multiple phylogenetic approaches to reconstruct the evolutionary history of these skinks and to assess the level of reticulation at the onset of their radiation. Our results indicate the presence of five strongly supported species-level lineages, four represented by the currently recognized species and the fifth by S. scincus conirostris, which does not form a clade with S. scincus. Based on these results we elevate the Iranian and northern Arabian S. conirostris to the species level. The two Saharan species, S. albifasciatus and S. scincus, are sister in all analyses. Deeper relationships within the genus, however, remained largely unresolved despite the extensive genetic data set. This basal polytomy, together with the fact that we detected no sign of hybridization in the history of the genus, indicates that the diversification of the five Scincus species was rapid, burst-like, and not followed by secondary hybridization events. Divergence time estimations show a Middle Pliocene crown radiation of the genus (3.3 Mya). We hypothesize that the aridification of the Saharo-Arabia that began in the Late Miocene triggered the initial diversification of Scincus, and that the subsequent expansion of sand deserts enabled their dispersal over the large Saharan and Arabian range. We discuss the evolution of body form in sand swimming lizards and ponder how Scincus retained their fully limbed morphology despite being sand swimmers that are typically limbless.

Phylogeography and invasion history of Aedes aegypti, the Dengue and Zika mosquito vector in Cape Verde islands (West Africa)

Aedes-borne arboviruses have spread globally with outbreaks of vast impact on human populations and health systems. The West African archipelago of Cape Verde had its first outbreak of Dengue in 2009, at the time the largest recorded in Africa, and was one of the few African countries affected by the Zika virus epidemic. Aedes aegypti was the mosquito vector involved in both outbreaks. We performed a phylogeographic and population genetics study of A. aegypti in Cape Verde in order to infer the geographic origin and evolutionary history of this mosquito. These results are discussed with respect to the implications for vector control and prevention of future outbreaks. Mosquitoes captured before and after the Dengue outbreak on the islands of Santiago, Brava, and Fogo were analyzed with two mitochondrial genes COI and ND4, 14 microsatellite loci and five kdr mutations. Genetic variability was comparable to other African populations. Our results suggest that A. aegypti invaded Cape Verde at the beginning of the Holocene from West Africa. Given the historic importance of Cape Verde in the transatlantic trade of the 16th-17th centuries, a possible contribution to the genetic pool of the founding populations in the New World cannot be fully discarded. However, contemporary gene flow with the Americas is likely to be infrequent. No kdr mutations associated with pyrethroid resistance were detected. The implications for vector control and prevention of future outbreaks are discussed.

Modeling directional spatio-temporal processes in island biogeography

A key challenge in island biogeography is to quantity the role of dispersal in shaping biodiversity patterns among the islands of a given archipelago. Here, we propose such a framework. Dispersal within oceanic archipelagos may be conceptualized as a spatio‐temporal process dependent on: (1) the spatial distribution of islands, because the probability of successful dispersal is inversely related to the spatial distance between islands and (2) the chronological sequence of island formation that determines the directional asymmetry of dispersal (hypothesized to be predominantly from older to younger islands). From these premises, directional network models may be constructed, representing putative connections among islands. These models may be translated to eigenfunctions in order to be incorporated into statistical analysis. The framework was tested with 12 datasets from the Hawaii, Azores, and Canaries. The explanatory power of directional network models for explaining species composition patterns, assessed by the Jaccard dissimilarity index, was compared with simpler time‐isolation models. The amount of variation explained by the network models ranged from 5.5% (for Coleoptera in Hawaii) to 60.2% (for Pteridophytes in Canary Islands). In relation to the four studied taxa, the variation explained by network models was higher for Pteridophytes in the three archipelagos. By the contrary, small fractions of explained variation were observed for Coleoptera (5.5%) and Araneae (8.6%) in Hawaii. Time‐isolation models were, in general, not statistical significant and explained less variation than the equivalent directional network models for all the datasets. Directional network models provide a way for evaluating the spatio‐temporal signature of species dispersal. The method allows building scenarios against which hypotheses about dispersal within archipelagos may be tested. The new framework may help to uncover the pathways via which species have colonized the islands of a given archipelago and to understand the origins of insular biodiversity.

Review of the distribution and conservation status of the terrestrial reptiles of the Cape Verde Islands

Cape Verde has a higher number of reptile taxa and endemics than any of the five archipelagos in the Macaronesian region. Mapping the precise distributions and assessing the conservation status of reptiles is the first step towards effective conservation. Presence/absence and abundance data were gathered from extensive fieldwork and post-1980 literature. Evaluation of conservation status was considered at specific and subspecific levels, following IUCN Red List criteria and using RAMAS. Fieldwork confirmed the occurrence of 34 of 37 previously recorded taxa (31 native, three exotic). One taxon continues to be considered Extinct. Three broad distribution and rarity patterns were identified: widespread and abundant taxa occurring on ≥ 2 islands/islets, widespread or abundant taxa restricted to one island, and rare or limited range taxa occurring on small areas of islands or islets. More than a third of taxa have areas of occupancy < 20 km2 and extents of occurrence < 100 km2. Geckos are rarer than skinks because of their high habitat specialization, with 58% occurring on only one island/islet. About half of all taxa are potentially threatened, twice the proportion of those in the Canary Islands, a difference that could be explained by the smaller area and greater aridity of the Cape Verde islands. The criterion used for most threat categorizations is geographical range, and the most pervasive threats are natural disasters, intrinsic factors of the species and introduced species. The importance of applying conservation status at the subspecific level to island endemics is emphasized. Several conservation measures are proposed, including optimized design of protected areas.

Hybridization and population structure of the Culex pipiens complex in the islands of Macaronesia

The Culex pipiens complex includes two widespread mosquito vector species, Cx. pipiens and Cx. quinquefasciatus. The distribution of these species varies in latitude, with the former being present in temperate regions and the latter in tropical and subtropical regions. However, their distribution range overlaps in certain areas and interspecific hybridization has been documented. Genetic introgression between these species may have epidemiological repercussions for West Nile virus (WNV) transmission. Bayesian clustering analysis based on multilocus genotypes of 12 microsatellites was used to determine levels of hybridization between these two species in Macaronesian islands, the only contact zone described in West Africa. The distribution of the two species reflects both the islands' biogeography and historical aspects of human colonization. Madeira Island displayed a homogenous population of Cx. pipiens, whereas Cape Verde showed a more intriguing scenario with extensive hybridization. In the islands of Brava and Santiago, only Cx. quinquefasciatus was found, while in Fogo and Maio high hybrid rates (∼40%) between the two species were detected. Within the admixed populations, second-generation hybrids (∼50%) were identified suggesting a lack of isolation mechanisms. The observed levels of hybridization may locally potentiate the transmission to humans of zoonotic arboviruses such as WNV.

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.

Phylogeographic inferences from the mtDNA variation of the three-toed skink,Chalcides chalcides (Reptilia: Scincidae)

Genetic diversity was analyzed in Chalcides chalcides populations from peninsular Italy, Sardinia, Sicily and Tunisia by sequencing 400 bp at the 5' end of the mitochondrial gene encoding cytochrome b (cyt b) and by restriction fragment length polymorphism (RFLP) analysis of two mitochondrial DNA segments (ND-1/2 and ND-3/4). The results of the phylogenetic analysis highlighted the presence of three main clades corresponding with three of the four main geographical areas (Tunisia, Sicily and the Italian peninsula), while Sardinia proved to be closely related to Tunisian haplotypes suggesting a colonization of this island from North Africa by human agency in historical times. On the contrary, the splitting times estimated on the basis of cyt b sequence data seem to indicate a more ancient colonization of Sicily and the Italian Peninsula, as a consequence of tectonic and climatic events that affected the Mediterranean Basin during the Pleistocene. Finally, the analysis of the genetic variability of C. chalcides populations showed a remarkable genetic homogeneity in Italian populations when compared to the Tunisian ones. This condition could be explained by a rapid post-glacial expansion from refugial populations that implied serial bottlenecking with progressive loss of haplotypes, resulting in a low genetic diversity in the populations inhabiting the more recently colonized areas.

Phylogenetic relationships of Hemidactylus geckos from the Gulf of Guinea islands: patterns of natural colonizations and anthropogenic introductions estimated from mitochondrial and nuclear DNA sequences

Mitochondrial DNA (12S rRNA, 16S rRNA, and cytochrome b) sequences and nuclear sequences (C-mos and alpha-Enolase) were analyzed within all known Hemidactylus species from all three volcanic islands in the Gulf of Guinea that have never been connected to the continent. These comprise both endemic and widespread species. Our aim was to determine if the widespread species was introduced anthropogenically, to determine the number of distinct genetic lineages within the islands, and to determine if the endemic forms constituted a monophyletic group. Our results suggest that a previously undescribed species on São Tomé is the sister taxon to Hemidactylus newtoni, endemic to Annobon. Genetic variation between populations of Hemidactylus greefii from São Tomé and Principe is very high based on mtDNA sequences, but the forms cannot be distinguished using the nuclear DNA sequences. Hemidactylus mabouia appears to have been anthropogenically introduced to all three islands. The island endemics do not form a monophyletic group, suggesting multiple independent colonizations of the islands.

Phylogeography of the false smooth snakes, Macroprotodon (Serpentes, Colubridae): mitochondrial DNA sequences show European populations arrived recently from Northwest Africa

Mitochondrial DNA (1075 bp: cytochrome b, 300 bp; 12S rRNA, 393 bp; and 16S rRNA, 382 bp) corroborates the monophyly of the genus Macroprotodon and of the species M. mauritanicus, M. abubakeri, and M. brevis. The subspecies M. brevis ibericus is also monophyletic. The mtDNA tree presented here indicates that M. cucullatus consists of at least two separate units and may possibly represent a primitive morphology rather than a species in its own right. However, this hypothesis is tentative since it is only reflects the history of a single evolutionary unit (mtDNA). A definitive understanding of the evolution of M. cucullatus will not be possible until informative nuclear markers are added to the mitochondrial data. Macroprotodon appears to have originated in the Maghreb region of NW Africa and speciated there around 4-5.5 million years ago around the end of the Miocene period, after which its three main lineages may each have expanded north into more mesic conditions. The group also spread eastwards into coastal areas of Libya quite recently and on to Egypt and Israel. Later still, M. b. ibericus from extreme north Morocco reached the Iberian Peninsula, and M. mauritanicus from Tunisia or Algeria colonised the Balearic Islands of Menorca and Mallorca. Both these range extensions may result from very recent natural colonisations or even from accidental human introduction. Recency of origin of Iberian and Balearic populations is indicated by uniformity of their mtDNA even across large distances, and its great similarity to that of populations in source regions. Isolated populations assigned to M. cucullatus in the Hoggar mountains (southern Algeria) and Western Sahara are probably relicts from quite recent periods of climatic amelioration in the North African desert.

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.

Phylogeography of the Madeiran endemic lizard Lacerta dugesii inferred from mtDNA sequences

Partial sequences from two mitochondrial DNA genes, cytochrome b and 12S rRNA, were used to assess the phylogenetic relationships of populations of Lacerta dugesii from the volcanic Atlantic islands of Madeira, the Desertas, Porto Santo, and the Selvagens. All four-island groups are genetically distinguishable and populations within each contain similar degrees of genetic diversity. Molecular clock estimates suggest that the islands were colonized much later after their emergence compared to other Atlantic islands, possibly due to their greater geographical isolation. Mismatch analysis of all populations is consistent with exponential growth, as expected after colonization of empty niches. The Selvagens contain genetic substructuring between the islets.

Evolution on oceanic islands: molecular phylogenetic approaches to understanding pattern and process

By their very nature oceanic island ecosystems offer great opportunities for the study of evolution and have for a long time been recognized as natural laboratories for studying evolution owing to their discrete geographical nature and diversity of species and habitats. The development of molecular genetic methods for phylogenetic reconstruction has been a significant advance for evolutionary biologists, providing a tool for answering questions about the diversity among the flora and fauna on such islands. These questions relate to both the origin and causes of species diversity both within an archipelago and on individual islands. Within a phylogenetic framework one can answer fundamental questions such as whether ecologically and/or morphologically similar species on different islands are the result of island colonization or convergent evolution. Testing hypotheses about ages of the individual species groups or entire community assemblages is also possible within a phylogenetic framework. Evolutionary biologists and ecologists are increasingly turning to molecular phylogenetics for studying oceanic island plant and animal communities and it is important to review what has been attempted and achieved so far, with some cautionary notes about interpreting phylogeographical pattern on oceanic islands.

Relationships and evolution of the North African geckos, Geckonia and Tarentola (Reptilia: Gekkonidae), based on mitochondrial and nuclear DNA sequences

Mitochondrial (cytochrome b and 12S rRNA) and nuclear (c-mos) genes, analyzed by a variety of methods, indicate that the distinctive northwest African gecko Geckonia chazaliae is a member of the Tarentola clade, being most closely related to the species of the western Canary and Cape Verde islands. Relationships in Tarentola as a whole are as follows: (T. americana ((T. mauritanica, T. angustimentalis) ((T. deserti, T. boehmei) ((T. b. boettgeri-South (T. b. boettgeri-North (T. b. bischoffi, T. b. hierrensis))) ((T. annularis, T. ephippiata) (Geckonia, T. delalandii, T. gomerensis, Cape Verde species)))))); nearly all nodes have high bootstrap support. Results confirm that T. americana of Cuba and the Bahamas separated at the most basal dichotomy of the phylogeny and give no positive support for the monophyly of the subgenera Tarentola s. str. and Makariogecko. The latter includes Geckonia and the subgenus Sahelogecko. Continental Tarentola appear to have invaded the Sahara desert from its northern edge. They have also colonized groups of Atlantic islands five times: a single invasion of the West Indies and three of the Canary islands, one of which then went on to invade the Cape Verde archipelago. The phylogeny corroborates anatomical evidence that the ground-dwelling Geckonia had a climbing ancestry, something that is paralleled in some southern African terrestrial gekkonids related to Pachydactylus. Distinctive derived features of Geckonia occur in other gekkonids that are ground dwelling in arid habitats and may be functionally related to this environment. The evolution of such features indicates that, although Tarentola is generally very uniform and may have been so for over 10 million years, this is not due to any overwhelming phylogenetic constraint. G. chazaliae should be included in Tarentola, as Tarentola chazaliae.