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

Molecular phylogeny and phylogeography of the “Podarcis tauricus” (Sauria: Lacertidae) species subgroup

Podarcis wall-lizards are included phylogenetically into the Balkan species group and into the “P. tauricus” species subgroup that consists of P. gaigeae, P. melisellensis, P. milensis and P. tauricus. This subgroup is distributed in the western and south Balkans, an area that is considered as an herpetofauna biodiversity hotspot. A plethora of endemic species can be found closely to the external Hellenides (Pindos mountain range) that comprise one of the most important biogeographic barriers in the Balkan Peninsula. The four focal species are characterized by obscure phylogenetic relationships among them, as well as among their populations. The general scope of the present thesis is to investigate the evolutionary history of the “P. tauricus” species subgroup by using a dataset containing samples from the entire species distribution and by producing different types of genetic and genomic data (Sanger sequencing, Next Generation Sequencing, Microsatellites). In order to achieve the above goal a large variety of analyses were performed that includes phylogenetic analyses (Second Chapter), phylogenomic analyses (Third Chapter), population structure analyses (Forth Chapter), species delimitation (Fifth Chapter), species distribution modelling (Fifth Chapter), divergence time estimations (Sixth Chapter), construction of mitochondrial haplotype networks (Sixth Chapter), and demographic analyses (Sixth Chapter). According to the results of the phylogenetic and phylogenomic analyses the “P. tauricus” species subgroup consists of five major phylogenetic clades that correspond to the taxa (in an order of evolutionary diversification) P. melisellensis, P. milensis, P. gaigeae, P. t. ionicus and P. t. tauricus/P. t. thasopulae. The taxon of P. t. ionicus displays hidden genetic diversity, comprising of five geographically isolated phylogenetic subclades with genetic distances of species level among them. In the context of taxonomical revision within the “P. tauricus” species subgroup and in congruence with the results of the species delimitation we propose the synonymy between some of the subspecies and the existence of a distinct Greek-Albanian species (or species complex) with the provisional name P. ionicus. The relationships among the subclades (a – e) of P. ionicus are resolved with the help of the genomic data in the following order of evolutionary diversification: subclade α (south Ionian islands), subclade e (southwestern Albania, northwestern Greece and western Peloponnisos), subclade c (northeastern Peloponnisos) and subclade d (central and southeastern Peloponnisos). Subclade b (western central Greece) is either a sister subclade to subclade a (Sanger sequencing), or closely related to subclade d (ddRADseq data). The results of population structure analyses shown that there is a general concordance between the revealed clusters and the phylogenetic clades and subclades (or group of them). Most of the resulted clusters consisted of pure individuals (>90% assignment probability), however in some cases it was observed that the daughter clusters of a parental one (e.g. the case of P. t. tauricus) contained also a small percentage of non-pure individuals originated from a different geographic area. Furthermore, there were cases in which individuals originated from the same geographic locality were grouping within different clusters. The species distribution analyses revealed that, in general, there are distinct putative distributions based on the environmental data among the taxa of the focal species subgroup. Finally, taking into account all the above data and analyses and in combination with the existing knowledge on the Paleogeography and the Paleoclimatology of the Balkans a phylogeographic scenario is proposed, which is taking place in several main stages. Before ~14-9 my the ancestral of “P. tauricus” species subgroup started to colonize the Balkan peninsula. The first divergence event happened at ~8-7 with the ancestror of P. melisellensis being isolated south of the Dinarides. Before ~7-6 my ago the distribution of the ancestor of the rest of the species includes the eastern and western to the External Hellenides continental Greece, Peloponnisos, central Greece, Skyros area, and Milos area. At ~5-4 mya the end of the Messinian salinity crisis caused the isolation of the aforementioned areas and the diversification of the isolated populations inhabiting these areas led to the forming of P. milensis, P. gaigeae, P. t. ionicus and P. t. tauricus / P. t. thasopulae. Before ~4-3 my the diversification of P. melisellensis and P. ionicus into their subclades is happening and during the time period of ~2,5-0,018 mya the populations were experienced the affection of the glacial and inter-glacial cycles of Pleistocene that formed in a great manner the current genetic diversity of the species. After the end of the last glacial period (~18.000 years ago) and until today the populations started to expand gradually, especially at their northern distribution limits.Οι «τοιχόσαυρες» του γένους Podarcis φυλογενετικά συμπεριλαμβάνονται στη «Βαλκανική» ομάδα ειδών και στην υποομάδα ειδών «P. tauricus» που περιλαμβάνει τα είδη P. gaigeae, P. melisellensis, P. milensis και P. tauricus. Η υποομάδα αυτή κατανέμεται στα δυτικά και νότια Βαλκάνια, μια περιοχή η οποία θεωρείται κέντρο υψηλής βιοποικιλότητας (biodiversity hotspot) ερπετοπανίδας. Πληθώρα ενδημικών ειδών συναντάται κοντά στις Εξωτερικές Ελληνίδες της ηπειρωτικής Ελλάδας (οροσειρά Πίνδου), οι οποίες αποτελούν έναν από τους σημαντικότερους βιογεωγραφικούς φραγμούς στη βαλκανική χερσόνησο. Οι φυλογενετικές σχέσεις μεταξύ των τεσσάρων υπό εξέταση ειδών, αλλά και μεταξύ των πληθυσμών εντός των ειδών δεν έχουν μέχρι στιγμής επιλυθεί. Στην παρούσα διατριβή γενικός στόχος ήταν η διερεύνηση της εξελικτικής ιστορίας της υποομάδας ειδών «P. tauricus» κάνοντας χρήση ενός συνόλου δειγμάτων που περιλαμβάνει άτομα από το μεγαλύτερο μέρος της κατανομής των ειδών μελέτης και παράγοντας γενετικά και γενωμικά δεδομένα διαφορετικού τύπου (αλληλούχιση Sanger, Νέα Γενιά Αλληλούχισης, Μικροδορυφορικά). Για την επίτευξη του ανωτέρου στόχου πραγματοποιήθηκε μια μεγάλη ποικιλία αναλύσεων η οποία περιλαμβάνει φυλογενετικές αναλύσεις (Δεύτερο Κεφάλαιο), φυλογενωμικές αναλύσεις (Τρίτο Κεφάλαιο), εκτιμήσεις πληθυσμιακής δομής (Τέταρτο Κεφάλαιο), οριοθέτηση ειδών (Πέμπτο Κεφάλαιο), μοντελοποίηση χωρικών κατανομών (Πέμπτο Κεφάλαιο), εκτίμηση χρόνων απόκλισης (Έκτο Κεφάλαιο), κατασκευή δικτύων μιτοχονδριακών απλοτύπων (Έκτο Κεφάλαιο) και δημογραφικές αναλύσεις (Έκτο Κεφάλαιο). Σύμφωνα με τα αποτελέσματα των φυλογενετικών και φυλογενωμικών αναλύσεων, η υποομάδα ειδών «P. tauricus» εμπεριέχει πέντε κύριους φυλογενετικούς κλάδους οι οποίοι ταυτίζονται με τα taxa (κατά σειρά εξελικτικής διαφοροποίησης) P. melisellensis, P. milensis, P. gaigeae, P. t. ionicus και P. t. tauricus/P. t. thasopulae. To taxon P. t. ionicus εμφανίζει κρυμμένη γενετική ποικιλότητα, αποτελούμενο από πέντε, γεωγραφικά διακριτούς, φυλογενετικούς υποκλάδους με τις γενετικές αποστάσεις μεταξύ τους να φτάνουν σε διαειδικά επίπεδα. Στο πλαίσιο της ταξινομικής αναθεώρησης της υποομάδας ειδών «P. tauricus» και σε συμφωνία με τα αποτελέσματα των αναλύσεων της οριοθέτησης ειδών προτείνεται η συνωνυμία κάποιων αναγνωρισμένων υποειδών της υποομάδας και η ύπαρξη ενός διακριτού ελληνοαλβανικού φυλογενετικού είδους ονόματι, προσωρινά, σύμπλεγμα ειδών (species complex) «P. ionicus». Οι σχέσεις μεταξύ των υποκλάδων (a – e) του taxon P. ionicus επιλύονται με τη βοήθεια των γενωμικών δεδομένων με τη σειρά διαφοροποίησης να έχει ως εξής: υποκλάδος α (νότια Επτάνησα), υποκλάδος e (νοτιοδυτική Αλβανία, βορειοδυτική Ελλάδα και δυτική Πελοπόννησος), υποκλάδος c (βορειοανατολική Πελοπόννησος) και υποκλάδος d (κεντρική και νοτιοανατολική Πελοπόννησος). Ο υποκλάδος b (δυτική Στερεά Ελλάδα) εμφανίζεται είτε ως αδελφό taxon με τον υποκλάδο a (δεδομένα Sanger), είτε ως συγγενικό με τον υποκλάδο d (δεδομένα ddRADseq). Τα αποτελέσματα των αναλύσεων ανίχνευσης πληθυσμιακής δομής έδειξαν ότι σε γενικές γραμμές οι ομαδοποιήσεις (clusters) που αναγνωρίστηκαν αντιστοιχούν στους κύριους φυλογενετικούς κλάδους και υποκλάδους (ή ομάδες αυτών). Οι ομαδοποιήσεις αυτές στην πλειονότητά τους αποτελούταν από αμιγή άτομα (>90% πιθανότητα σωστής αντιστοίχισης), ωστόσο παρατηρήθηκαν περιπτώσεις όπου οι θυγατρικές ομαδοποιήσεις μιας πατρικής ομαδοποίησης (π.χ., η περίπτωση του taxon P. t. tauricus) αποτελούνταν από ένα μικρό ποσοστό μη αμιγών ατόμων που προέρχονταν από διαφορετική γεωγραφική περιοχή. Επιπλέον, παρατηρήθηκαν και περιπτώσεις στις οποίες άτομα ίδιας γεωγραφικής προέλευσης να ομαδοποιούνται σε διαφορετικές συναθροίσεις. Οι αναλύσεις χωρικής κατανομής έδειξαν ότι, ως ένα βαθμό, υπάρχουν διακριτές δυνητικές κατανομές βάσει περιβαλλοντικών συνθηκών μεταξύ των taxa της παραπάνω υποομάδας, παρατήρηση που ενισχύει την υπόθεση διάκρισης του taxon P. t. ionicus ως είδος ή ομάδα ειδών. Τέλος, βάσει όλων των παραπάνω δεδομένων και αναλύσεων και βάσει της υπάρχουσας γνώσης για την παλαιογεωγραφία και παλαιοκλιματολογία των Βαλκανίων, το φυλογεωγραφικό σενάριο που προτείνεται μπορεί να περιγραφτεί συνοπτικά σε μια σειρά σταδίων. Πριν από ~14-9 εκατομμύρια χρόνια γίνεται η αποίκιση των Βαλκανίων από την προγονική μορφή της υποομάδας ειδών «P. tauricus». Το πρώτο γεγονός διαφοροποίησης συμβαίνει πριν από ~8-7 εκατομμύρια χρόνια όταν νότια των Διναρίδων απομονώνεται ο πρόγονος του είδους P. melisellensis. Την περίοδο πριν από ~7-6 εκατομμύρια χρόνια η κατανομή του προγόνου των υπολοίπων ειδών της υποομάδας περιλαμβάνει τις περιοχές ανατολικά και δυτικά των Εξωτερικών Ελληνίδων, την Πελοπόννησο, την περιοχή της Σκύρου και την περιοχή της Μήλου. Στα ~5-4 εκατομμύρια χρόνια, λόγω του τέλους της κρίσης της αλατότητας του Μεσσηνίου, συμβαίνει η απομόνωση των ανωτέρω περιοχών και η επακόλουθη διαφοροποίηση των απομονωμένων πληθυσμών στα taxa P. milensis, P. gaigeae, P. t. ionicus και P. t. tauricus / P. t. thasopulae. Ακολουθεί η διαφοροποίηση του είδους P. melisellensis και του taxon P. t. ionicus στους υποκλάδους τους πριν από ~4-3 εκατομμύρια χρόνια. Στο διάστημα ~2,5-0,018 εκατομμύρια χρόνια πριν η επίδραση των πλειστοκαινικών παγετωδών και μεσοπαγετωδών περιόδων είναι έντονη διαμορφώνοντας σε μεγάλο βαθμό τη σημερινή γενετική ποικιλότητα των πληθυσμών. Μετά το τέλος της τελευταίας παγετώδους περιόδου (~18.000 χρόνια πριν) και μέχρι σήμερα οι πληθυσμοί αρχίζουν και εξαπλώνονται σταδιακά, ιδιαίτερα προς τα βόρεια των κατανομών τους.Λέξεις κλειδιά: Βαλκανική χερσόνησος, Οριοθέτηση ειδών, Παγετωνικά καταφύγια, Πληθυσμιακή δομή, Σύμπλεγμα ειδών, Φυλογενωμικ

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

Hidden diversity in the Podarcis tauricus (Sauria, Lacertidae) species subgroup in the light of multilocus phylogeny and species delimitation

The monophyletic species subgroup of Podarcis tauricus is distributed in the western and southern parts of the Balkans, and includes four species with unresolved and unstudied inter- and intra-specific phylogenetic relationships. Using sequence data from two mitochondrial and three nuclear genes and applying several phylogenetic methods and species delimitation approaches to an extensive dataset, we have reconstructed the phylogeny of the Podarcis wall lizards in the Balkans, and re-investigated the taxonomic status of the P. tauricus species subgroup. Multilocus analyses revealed that the aforementioned subgroup consists of five major clades, with P. melisellensis as its most basal taxon. Monophyly of P. tauricus sensu stricto is not supported, with one of the subspecies (P. t. ionicus) displaying great genetic diversity (hidden diversity or cryptic species). It comprises five, geographically distinct, subclades with genetic distances on the species level. Species delimitation approaches revealed nine species within the P. tauricus species subgroup (P. melisellensis, P. gaigeae, P. milensis, and six in the P. tauricus complex), underlining the necessity of taxonomic re-evaluation. We thus synonymize some previously recognized subspecies in this subgroup, elevate P. t. tauricus and P. g. gaigeae to the species level and suggest a distinct Albanian-Greek clade, provisionally named as the P. ionicus species complex. The latter clade comprises five unconfirmed candidate species that call for comprehensive studies in the future.Molecular Phylogenetics and Evolution (2017), 106: 6-1

Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system

The Balkan Peninsula constitutes a biodiversity hotspot with high levels of species richness and endemism. The complex geological history of the Balkans in conjunction with the climate evolution are hypothesized as the main drivers generating this biodiversity. We investigated the phylogeography, historical demography, and population structure of closely related wall-lizard species from the Balkan Peninsula and southeastern Europe to better understand diversification processes of species with limited dispersal ability, from Late Miocene to the Holocene. We used several analytical methods integrating genome-wide SNPs (ddRADseq), microsatellites, mitochondrial and nuclear DNA data, as well as species distribution modelling. Phylogenomic analysis resulted in a completely resolved species level phylogeny, population level analyses confirmed the existence of at least two cryptic evolutionary lineages and extensive within species genetic structuring. Divergence time estimations indicated that the Messinian Salinity Crisis played a key role in shaping patterns of species divergence, whereas intraspecific genetic structuring was mainly driven by Pliocene tectonic events and Quaternary climatic oscillations. The present work highlights the effectiveness of utilizing multiple methods and data types coupled with extensive geographic sampling to uncover the evolutionary processes that shaped the species over space and time