The Wall Lizards of the Balkan Peninsula: Tackling Questions at the Interphase of Phylogenomics and Population Genomics

[Abstract] Wall lizards of the genus Podarcis (Sauria, Lacertidae) are the predominant reptile group in southern Europe, including 24 recognized species. Mitochondrial DNA data have shown that, with the exception of P. muralis, the Podarcis species distributed in the Balkan peninsula form a species group that is further sub-divided into two subgroups: the one of “P. tauricus” consisting of P. tauricus, P. milensis, P. gaigeae, and P. melisellensis, and the other of “P. erhardii” comprising P. erhardii, P. levendis, P. cretensis, and P. peloponnesiacus. In an attempt to explore the Balkan Podarcis phylogenomic relationships, assess the levels of genetic structure and to re-evaluate the number of extant species, we employed phylogenomic and admixture approaches on ddRADseq (double digested Restriction site Associated DNA sequencing) genomic data. With this efficient Next Generation Sequencing approach, we were able to obtain a large number of genomic loci randomly distributed throughout the genome and use them to resolve the previously obscure phylogenetic relationships among the different Podarcis species distributed in the Balkans. The obtained phylogenomic relationships support the monophyly of both aforementioned subgroups and revealed several divergent lineages within each subgroup, stressing the need for taxonomic re-evaluation of Podarcis’ species in Balkans. The phylogenomic trees and the species delimitation analyses confirmed all recently recognized species (P. levendis, P. cretensis, and P. ionicus) and showed the presence of at least two more species, one in P. erhardii and the other in P. peloponnesiacus.This study was funded by NSFR 2007-2013 programme for development, European Social Fund, Operational Programme, Education and Lifelong Learning investing in knowledge society, Ministry of Education and Religious Affairs, Managing Authority, Co-financed by Greece and the European Union. Part of this work was funded by the Klaus Tschira Foundation, by the Ministry of Science and Innovation of Spain (PID2019-104184RB-I00 / AEI / 10.13039/501100011033), and by the Xunta de Galicia and FEDER funds of the EU under the Centro de Investigación de Galicia accreditation 2019-2022 (ED431G 2019/01)Xunta de Galicia; ED431G 2019/0

Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean

We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term “the expanding mobility model.” Interestingly, this increase in inter-regional divergence can be captured by outgroup-f$_3$-based genetic distances, but not by the commonly used F$_{ST}$ statistic, due to the sensitivity of F$_{ST}$, but not outgroup-f$_3$, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene

Identification of wild-caught phlebotomine sand flies from Crete and Cyprus using DNA barcoding

Abstract 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

Barn Owl (Tyto alba) prey in Evros (Greece) and the discovery of a new mammal for the Greek fauna

Rallis, Nikolaos Kiamos ı Petros Lymberakis ı Georgios, Poulakakis, Nikos (2019): Barn Owl (Tyto alba) prey in Evros (Greece) and the discovery of a new mammal for the Greek fauna. Journal of Natural History 53 (27): 1691-1705, DOI: 10.1080/00222933.2019.165882

A molecular phylogeny and phylogeography of Greek Aegean Island sand flies of the genus Phlebotomus (Diptera: Psychodidae)

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

Molecular identification and geographic origin of a post-Medieval elephant finding from southwestern Portugal using high-throughput sequencing

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

Mitochondrial sequences of the extinct Cypriot pygmy hippopotamus confirm its phylogenetic placement

The Cypriot pygmy hippopotamus is an extinct Mediterranean species that inhabited the island of Cyprus during the Late Pleistocene. This iconic species last appears at the archaeological site of Akrotiri Aetokremnos, dated to similar to 12 500 cal. BP. Taxonomically, the Cypriot pygmy hippopotamus has been assigned to Hippopotamus minor, which, based on morphology, is more closely related to the common hippopotamus (Hippopotamus amphibius; today present only in Sub-Saharan Africa) than to the West African pygmy hippopotamus (Choeropsis liberiensis). Despite adverse conditions for preservation that greatly reduce the likelihood of DNA preservation in subfossil samples from hot environments, we recovered and analysed ancient DNA from petrous bones excavated from Akrotiri Aetokremnos. By whole mitogenome hybridization capture and exhaustive high-throughput sequencing, we were able to investigate the molecular phylogeny and taxonomic status of the Cypriot pygmy hippopotamus. The results of our low-coverage ancient mitogenomic analyses support the close phylogenetic affinity of H. minor to H. amphibius, with their divergence estimated at similar to 1.36 or 1.58 Mya, depending on the molecular dating method. To our knowledge, this study constitutes the first step towards reconstruction of the molecular phylogeny of Mediterranean Hippopotaminae