Whole‐genome SNP genotyping unveils ancestral and recent introgression in wild and domestic goats

After the domestication of goats around 10,000 years before the present (BP), humans transported goats far beyond the range of their wild ancestor, the bezoar goat. This brought domestic goats into contact with many wild goat species such as ibex and markhor, enabling introgression between domestic and wild goats. To investigate this, while shedding light on the taxonomic status of wild and domestic goats, we analysed genome-wide SNP data of 613 specimens from 14 taxonomic units, including Capra hircus, C. pyrenaica, C. ibex (from Switzerland, Austria, Germany and Slovenia), C. aegagrus aegagrus, C. a. cretica, C. h. dorcas, C. caucasica caucasica, C. c. severtzovi, C. c. cylindricornis, C. falconeri, C. sibirica sibirica, C. s. alaiana and C. nubiana, as well as Oreamnos americanus (mountain goat) as an outgroup. To trace gene flow between domestic and wild goats, we integrated genotype data of local goat breeds from the Alps as well as from countries such as Spain, Greece, Türkiye, Egypt, Sudan, Iran, Russia (Caucasus and Altai) and Pakistan. Our phylogenetic analyses displayed a clear separation between bezoar-type and ibex-type clades with wild goats from the Greek islands of Crete and Youra clustered within domestic goats, confirming their feral origin. Our analyses also revealed gene flow between the lineages of Caucasian tur and domestic goats that most likely occurred before or during early domestication. Within the clade of domestic goats, analyses inferred gene flow between African and Iberian goats. The detected events of introgression were consistent with previous reports and offered interesting insights into the historical relationships among domestic and wild goats.Deutscher Akademischer Austauschdienst http://dx.doi.org/10.13039/501100001655Javna Agencija za Raziskovalno Dejavnost RS http://dx.doi.org/10.13039/501100004329Ministry of Science and Higher Education of the Russian Federation http://dx.doi.org/10.13039/501100012190Peer Reviewe

Whole‐genome SNP genotyping unveils ancestral and recent introgression in wild and domestic goats

After the domestication of goats around 10,000 years before the present (BP), humans transported goats far beyond the range of their wild ancestor, the bezoar goat. This brought domestic goats into contact with many wild goat species such as ibex and markhor, enabling introgression between domestic and wild goats. To investigate this, while shedding light on the taxonomic status of wild and domestic goats, we analysed genome-wide SNP data of 613 specimens from 14 taxonomic units, including Capra hircus, C. pyrenaica, C. ibex (from Switzerland, Austria, Germany and Slovenia), C. aegagrus aegagrus, C. a. cretica, C. h. dorcas, C. caucasica caucasica, C. c. severtzovi, C. c. cylindricornis, C. falconeri, C. sibirica sibirica, C. s. alaiana and C. nubiana, as well as Oreamnos americanus (mountain goat) as an outgroup. To trace gene flow between domestic and wild goats, we integrated genotype data of local goat breeds from the Alps as well as from countries such as Spain, Greece, Türkiye, Egypt, Sudan, Iran, Russia (Caucasus and Altai) and Pakistan. Our phylogenetic analyses displayed a clear separation between bezoar-type and ibex-type clades with wild goats from the Greek islands of Crete and Youra clustered within domestic goats, confirming their feral origin. Our analyses also revealed gene flow between the lineages of Caucasian tur and domestic goats that most likely occurred before or during early domestication. Within the clade of domestic goats, analyses inferred gene flow between African and Iberian goats. The detected events of introgression were consistent with previous reports and offered interesting insights into the historical relationships among domestic and wild goats

Sardines at a junction: seascape genomics reveals ecological and oceanographic drivers of variation in the {NW} Mediterranean Sea

By evaluating genetic variation across the entire genome, one can address existing questions in a novel way while raising new ones. The latter includes how different local environments influence adaptive and neutral genomic variation within and among populations, providing insights into local adaptation of natural populations and their responses to global change. Here, under a seascape genomic approach, ddRAD data of 4609 single nucleotide polymorphisms (SNPs) from 398 sardines (Sardina pilchardus) collected in 11 Mediterranean and one Atlantic site were generated. These were used along with oceanographic and ecological information to detect signals of adaptive divergence with gene flow across environmental gradients. The studied sardines constitute two clusters (FST = 0.07), a pattern attributed to outlier loci, highlighting putative local adaptation. The trend in the number of days with sea surface temperature above 19°C, a critical threshold for successful sardine spawning, was crucial at all levels of population structuring with implications on the species' key biological processes. Outliers link candidate SNPs to the region's environmental heterogeneity. Our findings provide evidence for a dynamic equilibrium in which population structure is maintained by physical and ecological factors under the opposing influences of migration and selection. This dynamic in a natural system warrants continuous monitoring under a seascape genomic approach that might benefit from a temporal and more detailed spatial dimension. Our results may contribute to complementary studies aimed at providing deeper insights into the mechanistic processes underlying population structuring. Those are key to understanding and predicting future changes and responses of this highly exploited species in the face of climate change

Identifying Fishes through DNA Barcodes and Microarrays

Background: International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. Methodology/Principal Findings: This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of ‘‘DNA barcoding’’ and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the ‘‘position of label’’ effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (.90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. Conclusions/Significance: Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products

Unravelling the evolutionary history of European hare (Lepus europaeus Pallas, 1778) in Balkans

Although the European hare (Lepus europaeus) constitutes a main faunal element of open areas with a great socio-economic importance, little is known regarding the species biology, whereas its phylogeographic and population structure remain largely unknown. The study of European hare is interesting since it encompasses some of the most challenging principles in the field of theoretical population genetics. The species is continuously distributed in a variety of habitats occurring at the opposite extreme edges of the habitat variability, while it is characterized by high potential for dispersal and philopatry (females mostly), behavioral mechanisms that can play an important role in shaping the population structure of a species. The present study focuses on the European hare populations distributed in the Balkan peninsula and Cyprus. In an attempt to unravel the evolutionary history of the species and to determine its micro and macro-geographical genetic structure, we combined information acquired from distinct genetic markers, namely 10 nuclear microsatellite loci and partial control region (D-loop) sequences of mitochondrial DNA. Furthermore, we tried to assess the efficacy of current methodology in population genetics. Considering the problems encountered when defining populations and in contrast to what is currently known regarding the species genetic structure, hares of Balkans and Cyprus exhibited high variability and a remarkable genetic structure. The produced phylogenetic relationships coupled with paleogeographic, paleoclimatic and paleontological data allowed us to speculate a phylogeographic hypothesis according to which the species colonized Balkans during Pleistocene. Upon the phylogeographic scenario, an ancestral stock of the European hare inhabited areas of Caucasus where it probably diverged. During the middle and upper Pleistocene, ancestral populations of the species reached Europe following two distinct dispersal routes (north and south coastline of Black Sea) giving rise to the two phylogenetic clades (“eastern” and “western”) that are present today in Balkans. We also reported for the first time the spatial distribution of those highly divergent groups in the area of northeastern Greece where they occur in sympatry. Furthermore, information regarding the reproductive characteristics of Cretan populations revealed their discernible features, indicating a continuous reproduction of hares throughout the year, fact that could also be attributed to their genetic distinctiveness. Conclusively, the multi-dimensional study of European hare populations enabled the definition of the main features responsible for the pattern of diversity observed today in Balkans.Ο Ευρωπαϊκός λαγός (Lepus europaeus), αν και αποτελεί κυρίαρχο στοιχείο της πανίδας των ανοικτών εκτάσεων με ιδιαίτερη οικονομική σημασία, έχει ελάχιστα μελετηθεί ως προς τη βιολογία του, όπου η φυλογεωγραφική και πληθυσμιακή του δομή του παραμένουν, στο μεγαλύτερο τμήμα τους, άγνωστες. Η έλλειψη ολοκληρωμένων μελετών του είδους, ιδιαίτερα στο χώρο της Βαλκανικής χερσονήσου, σε συνδυασμό με το γεγονός ότι μια τέτοια προσπάθεια ενέχει ορισμένες από τις πιο σημαντικές προκλήσεις στο χώρο της θεωρητικής πληθυσμιακής γενετικής, καθιστούν τη μελέτη Ευρωπαϊκού λαγού εξαιρετικής σημασίας με ιδιαίτερο επιστημονικό ενδιαφέρον. Ο Ευρωπαϊκός λαγός, αποτελεί ένα είδος με συνεχή κατανομή που συναντάται σε ποικίλα ενδιαιτήματα, καλύπτοντας τους πόλους της ενδιαιτηματικής ποικιλότητας. Ως είδος χαρακτηρίζεται από μεγάλη ικανότητα διασποράς με έντονη φιλοπατρική συμπεριφορά (κυρίως από τα θηλυκά άτομα), στοιχεία που συνιστούν μηχανισμούς οι οποίοι μπορούν να διαδραματίσουν σημαντικό ρόλο στη διαμόρφωση της πληθυσμιακής δομής ενός είδους. Στα πλαίσια αυτά, σκοπός της παρούσας μελέτης αποτέλεσε η αποκάλυψη της εξελικτικής ιστορίας του Ευρωπαϊκού λαγού στην περιοχή της Βαλκανικής χερσονήσου και της Κύπρου και ο καθορισμός της μικρο- και μακρογεωγραφικής του δομής, ενώ παράλληλα προσεγγίστηκαν ερωτήματα που αφορούν στην αποτελεσματικότητα της υπάρχουσας μεθοδολογίας ανάλυσης πληθυσμών με συνεχή κατανομή. Για το σκοπό αυτό χρησιμοποιήθηκε συνδυασμένη πληροφορία που προήλθε από διάφορους γενετικούς δείκτες, οι οποίοι συνίσταται σε 10 πυρηνικούς μικροδορυφορικούς τόπους και σε τμήμα της περιοχής ελέγχου (D-loop) του μιτοχονδριακού DNA. Η ανάλυση των παραπάνω γενετικών δεδομένων, λαμβάνοντας υπόψη τα γενικότερα προβλήματα καθορισμού πληθυσμιακών μονάδων, υπέδειξε ότι τα υπό μελέτη άτομα χαρακτηρίζονται από σημαντική ποικιλότητα και έντονη δομή με υψηλό βαθμό πολυπλοκότητας, γεγονός που αντιτίθεται στην πλειοψηφία των μελετών που έχουν πραγματοποιηθεί μέχρι σήμερα για το είδος. Οι παραγόμενες φυλογενετικές σχέσεις σε συνδυασμό με τα παλαιογεωγραφικά, παλαιοκλιματικά και παλαιοντολογικά δεδομένα της περιοχής επέτρεψαν τη διατύπωση ενός πιθανού φυλογεωγραφικού σεναρίου που αφορά στον τρόπο με το οποίο το είδος εποίκισε την Ευρώπη κατά τη διάρκεια του Πλειστοκαίνου. Βάσει αυτού, ο Ευρωπαϊκός λαγός εποίκισε τη Βαλκανική από το προγονικό απόθεμα του Καυκάσου, ακολουθώντας δύο διαφορετικές οδούς διασποράς (βόρεια και νότια της Μαύρης Θάλασσας), δίνοντας γένεση στους δύο βασικούς φυλογενετικούς κλάδους («ανατολικό» και «δυτικό») που παρατηρούμε σήμερα στον χώρο της Βαλκανικής. Παράλληλα, κατέστη για πρώτη φορά δυνατός ο καθορισμός του χωροταξικού προτύπου συνύπαρξης των δύο διαφοροποιημένων κλάδων στην περιοχή της βορειοανατολικής Ελλάδας. Τέλος όσον αφορά στην ανάλυση των δεδομένων που σχετίζονται με την αναπαραγωγή του είδους στην Κρήτη, διαπιστώθηκε ότι οι πληθυσμοί του νησιού εμφανίζουν ιδιαιτερότητες, παρουσιάζοντας ισχυρές ενδείξεις συνεχούς αναπαραγωγής, γεγονός που θα μπορούσε να αποδοθεί και στη γενετική τους διακριτότητα. Συμπερασματικά, η πολύπλευρη μελέτη των πληθυσμών λαγού της Βαλκανικής, επέτρεψε τον καθορισμό των κυριότερων παραμέτρων που συνέβαλλαν στο παρόν πρότυπο της διαφοροποίησης του είδους

Revision of the freshwater genus Atyaephyra (Crustacea, Decapoda, Atyidae) based on morphological and molecular data

Atyaephyra de Brito Capello, 1867 was described from the Mediterranean region almost 200 years ago. Since then, the genus has been recorded from various freshwater habitats in Europe, North Africa and the Middle East. Despite its long history, the taxonomic status of Atyaephyra species remains confusing and uncertain. Consequently numerous specimens from the known range of Atyaephyra were analysed using morphological characters and mitochondrial COI sequences in an attempt to clarify the taxonomy of this genus. The present study recognises seven Atyaephyra species, more than twice as many as previously recorded (three), four of which are considered as new. The new species are described, additional information to the original descriptions are provided for the remaining three taxa, while neotypes of A. desmarestii Millet, 1831 and A. stankoi Karaman, 1972 are designated to stabilize their taxonomy. Non-overlapping distinguishing morphological characters are used to discriminate the examined material into five species, e.g., A. desmarestii, A. stankoi, A. orientalis Bouvier, 1913, A. thyamisensis sp. n., A. strymonensis sp. n. In addition, the genetic analysis supports the existence of multiple phylogenetic clades in the broader Mediterranean area and distinguishes two new cryptic species, namely A. tuerkayi sp. n. and A. acheronensis sp. n. The geographic distribution of these species is confirmed and their phylogenetic relationships are described

Evaluation of the evolutionary history of Podarcis cretensis (Sauria; Lacertidae)

info:eu-repo/semantics/publishe

Microsatellite_data_Sagonas_et_al

A file contains the microsatellite data where the Fst-values are based on. The first column entitled Sample-ID includes the abbreviation for specimens as given in File 1

Euclidean_geographical_distances_Sagonas_et_al

Contains the populations Euclidean geographical distance in km. Populations abbreviations as in File 1. Mantel test and Mantel correlogram were estimated based on this matri