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Molecular species identification plays a crucial role in archaeology and palaeontology, especially when diagnostic morphological characters are unavailable. Molecular markers have been used in forensic science to trace the geographic origin of wildlife products, such as ivory. So far, only a few studies have applied genetic methods to both identify the species and circumscribe the provenance of historic wildlife trade material. Here, by combining ancient DNA methods and genome skimming on a historical elephantid tooth found in southwestern Portugal, we aimed to identify its species, infer its placement in the elephantid phylogenetic tree, and triangulate its geographic origin. According to our results the specimen dates back to the eighteenth century CE and belongs to a female African forest elephant (non-hybrid Loxodonta cyclotis individual) geographically originated from west—west-central Africa, from areas where one of the four major mitochondrial clades of L. cyclotis is distributed. Historical evidence supports our inference, pointing out that the tooth should be considered as post-Medieval raw ivory trade material between West Africa and Portugal. Our study provides a comprehensive approach to study historical products and artefacts using archaeogenetics and contributes towards enlightening cultural and biological historical aspects of ivory trade in western Europe.

The Galapagos Archipelago is recognized as a natural laboratory for studying evolutionary processes. San Cristóbal was one of the first islands colonized by tortoises, which radiated from there across the archipelago to inhabit 10 islands. Here, we sequenced the mitochondrial control region from six historical giant tortoises from San Cristóbal (five long deceased individuals found in a cave and one found alive during an expedition in 1906) and discovered that the five from the cave are from a clade that is distinct among known Galapagos giant tortoises but closely related to the species from Española and Pinta Islands. The haplotype of the individual collected alive in 1906 is in the same clade as the haplotype in the contemporary population. To search for traces of a second lineage in the contemporary population on San Cristóbal, we closely examined the population by sequencing the mitochondrial control region for 129 individuals and genotyping 70 of these for both 21 microsatellite loci and >12,000 genome-wide single nucleotide polymorphisms [SNPs]. Only a single mitochondrial haplotype was found, with no evidence to suggest substructure based on the nuclear markers. Given the geographic and temporal proximity of the two deeply divergent mitochondrial lineages in the historical samples, they were likely sympatric, raising the possibility that the lineages coexisted. Without the museum samples, this important discovery of an additional lineage of Galapagos giant tortoise would not have been possible, underscoring the value of such collections and providing insights into the early evolution of this iconic radiation.

Background Phlebotomine sand flies (Diptera: Psychodidae) are vectors of Leishmania  spp., protozoan parasites responsible for a group of neglected diseases called leishmaniases. Two sand fly genera, Phlebotomus and Sergentomyia , contain species that are present in the Mediterranean islands of Crete and Cyprus where the visceral (VL), cutaneous (CL) and canine (CanLei) leishmaniases are a public health concern. The risk of transmission of different Leishmania species can be studied in an area by monitoring their vectors. Sand fly species are traditionally identified using morphological characteristics but minute differences between individuals or populations could be overlooked leading to wrong epidemiological predictions. Molecular identification of these important vectors has become, therefore, an essential tool for research tasks concerning their geographical distribution which directly relates to leishmaniasis control efforts. DNA barcoding is a widely used molecular identification method for cataloguing animal species by sequencing a fragment of the mitochondrial gene encoding cytochrome oxidase I. Results DNA barcoding was used to identify individuals of five sand fly species ( Phlebotomus papatasi , P. similis , P. killicki , Sergentomyia minuta , S. dentata ) circulating in the islands of Crete and Cyprus during the years 2011–2014. Phlebotomus papatasi is a known vector of zoonotic CL in the Middle East and it is found in both islands. Phlebotomus similis is the suspected vector of Leishmania tropica in Greece causing anthroponotic CL. Phlebotomus killicki was collected in Cyprus for the first time. Sergentomyia minuta , found to present intraspecific diversity, is discussed for its potential as a Leishmania vector. Molecular identification was consistent with the morphological identification. It successfully identified males and females, which is difficult when using only morphological characters. A phylogenetic tree was constructed based on the barcodes acquired, representing their genetic relationships along with other species from the area studied. All individuals identified were clustered according to their species and subgenus. Conclusions Molecular identification of sand flies via DNA barcoding can accurately identify these medically important insects assisting traditional morphological tools, thus helping to assess their implication in Leishmania transmission.

Land snails and the Aegean Archipelago offer an intriguing combination for studying biodiversity, biogeography and ecology. A region with high environmental and temporal heterogeneity and a tri-continental biotic influence and a group of organisms with low active dispersal abilities, high endemism, as well as the particularity to leave shells as traces of past presence, set an ideal stage for testing biodiversity patterns and exploring multisource threats, especially in the era of the ongoing biodiversity crisis. In this study, we examine Helix godetiana , a large-sized, threatened and endemic land snail of the central and south Aegean Islands. The species has been extirpated from 22 of the 32 islands where it was historically present. We identify potential drivers of its extinction, as Helix godetiana faces several threats across its current range, including competitive exclusion by Cornu aspersum , a species with continuing expansion in the Aegean and climate change disrupting its unusual breeding cycle, which occurs in late spring. Our findings shed light on potentially major, yet previously unexplored, threats on endemic molluscs of the Aegean Islands, a European biodiversity hotspot.

The taxonomy of giant Galapagos tortoises (Chelonoidis spp.) is currently based primarily on morphological characters and island of origin. Over the last decade, compelling genetic evidence has accumulated for multiple independent evolutionary lineages, spurring the need for taxonomic revision. On the island of Santa Cruz there is currently a single named species, C. porteri. Recent genetic and morphological studies have shown that, within this taxon, there are two evolutionarily and spatially distinct lineages on the western and eastern sectors of the island, known as the Reserva and Cerro Fatal populations, respectively. Analyses of DNA from natural populations and museum specimens, including the type specimen for C. porteri, confirm the genetic distinctiveness of these two lineages and support elevation of the Cerro Fatal tortoises to the rank of species. In this paper, we identify DNA characters that define this new species, and infer evolutionary relationships relative to other species of Galapagos tortoises.

Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George—the iconic last member of Chelonoidis abingdonii —and the Aldabra giant tortoise ( Aldabrachelys gigantea ). Comparison of these genomes with those of related species, using both unsupervised and supervised analyses, led us to detect lineage-specific variants affecting DNA repair genes, inflammatory mediators and genes related to cancer development. Our study also hints at specific evolutionary strategies linked to increased lifespan, and expands our understanding of the genomic determinants of ageing. These new genome sequences also provide important resources to help the efforts for restoration of giant tortoise populations. The genomes of two long-lived giant tortoises, including Lonesome George, reveal candidate genes and pathways associated with their development, gigantism and longevity.

The genus Phlebotomus (Diptera: Psychodidae: Phlebotominae) comprises a group of small winged insect species of medical importance. To date, ten species of Phlebotomus are known to be present in Greece; yet their evolutionary history is poorly studied due to the lack of comprehensive phylogenetic and phylogeographic studies. Herein, we aim to clarify the phylogenetic relationships amongst the local species collected from 12 Aegean Islands, Cyprus and Turkey; and to identify which of the palaeogeographic events may have influenced their biogeographic history. Our analyses revealed for the first time the presence of P. cf. major and P. sergenti in the Aegean Islands. All studied local species were retrieved as monophyletic and the mtDNA and nDNA phylogenetic trees indicated a plausible mitochondrial introgression between the closely related species of the P. major complex. From a palaeogeographic viewpoint, the major driving force that shaped the biogeographic history of the studied Phlebotomus species seems to be the dispersal that started in the Oligocene epoch, followed by several speciation events that occurred at the end of Miocene and the Plio-Pleistocene, including multiple dispersal events of Asiatic origin. The Messinian Salinity Crisis, the bimodal Mediterranean climate, and the glacial and interglacial periods were identified as key drivers for the diversification of the local species of Phlebotomus .

The ability of an animal to shed its tail is a widespread antipredator strategy among lizards. The degree of expression of this defense is expected to be shaped by prevailing environmental conditions including local predation pressure. We test these hypotheses by comparing several aspects of caudal autotomy in 15 Mediterranean lizard taxa existing across a swath of mainland and island localities that differ in the number and identity of predator species present. Autotomic ease varied substantially among the study populations, in a pattern that is best explained by the presence of vipers. Neither insularity nor the presence of other types of predators explain the observed autotomy rates. Final concentration of accumulated tail muscle lactate and duration of movement of a shed tail, two traits that were previously thought to relate to predation pressure, are in general not shaped by either predator diversity or insularity. Under conditions of relaxed predation selection, an uncoupling of different aspects of caudal autotomy exists, with some elements (ease of autotomy) declining faster than others (duration of movement, lactate concentration). We compared rates of shed tails in the field against rates of laboratory autotomies conducted under standardized conditions and found very high correlation values (r > 0.96). This suggests that field autotomy rates, rather than being a metric of predatory attacks, merely reflect the innate predisposition of a taxon to shed its tail.

Background The Kastellorizo island group (in the Dodecanese, Greece) is situated in the southeast corner of the Aegean Archipelago. It consists of twenty islets, of which the three largest (Kastellorizo, Ro and Strongyli) and seven smaller ones belong to Greece. Knowledge of the malacofauna on the islands is relatively poor. Only eight species were known prior to the present study, all from the islet of Kastellorizo. Results Here, using the scientific collections at the Natural History Museum of Crete collected mainly by the authors and also by several researchers since 1976, we reappraise the malacofauna of the island group. Thirty-one species were found in total (23 from Kastellorizo, 19 from Ro, 15 from Strongyli, 10 from Agios Georgios, 14 from Agrielia, 6 from Psomi and 10 from Psoradia). Conclusions The fact that there are no endemic snail species in the islands can be accounted for by their proximity to the Turkish coast, their common paleogeography with Turkey until the Late Pleistocene and Holocene, and the influence of humans. All but two species, Mastus etuberculatus and Vitrea riedeliana , are known from the adjacent Turkish coasts. Together with the subfossil species found on the smaller islets, the predominance of different species on each islet suggests a continuous substitution from the source areas of Turkey and the Aegean.

Urban habitats receive an increasing number of species due to anthropogenic activities, mainly transportations. Here, we report a new addition to the herpetofauna of Athens (Greece): a small population of the Pelasgian wall lizard ( Anatololacerta pelasgiana ) was found in a suburb of the Athenian metropolitan area. The species normally occurs in southwestern Anatolia and southeastern Aegean islands and this is the first record in the Greek mainland. Allochthonous species that successfully colonize cities raise new challenges to urban ecology.