Accurate microRNA target prediction correlates with protein repression levels

MicroRNAs are small endogenously expressed non-coding RNA molecules that regulate target gene expression through translation repression or messenger RNA degradation. MicroRNA regulation is performed through pairing of the microRNA to sites in the messenger RNA of protein coding genes. Since experimental identification of miRNA target genes poses difficulties, computational microRNA target prediction is one of the key means in deciphering the role of microRNAs in development and diseas

Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic

BACKGROUND: Debated aspects in speciation research concern the amount of gene flow between incipient species under secondary contact and the modes by which post-zygotic isolation accumulates. Secondary contact zones of allopatric lineages, involving varying levels of divergence, provide natural settings for comparative studies, for which the Aegean (Eastern Mediterranean) geography offers unique scenarios. In Palearctic green toads (Bufo viridis subgroup or Bufotes), Plio-Pleistocene (~ 2.6 Mya) diverged species show a sharp transition without contemporary gene flow, while younger lineages, diverged in the Lower-Pleistocene (~ 1.9 Mya), admix over tens of kilometers. Here, we conducted a fine-scale multilocus phylogeographic analysis of continental and insular green toads from the Aegean, where a third pair of taxa, involving Mid-Pleistocene diverged (~ 1.5 Mya) mitochondrial lineages, earlier tentatively named viridis and variabilis, (co-)occurs. RESULTS: We discovered a new lineage, endemic to Naxos (Central Cyclades), while coastal islands and Crete feature weak genetic differentiation from the continent. In continental Greece, both lineages, viridis and variabilis, form a hybrid swarm, involving massive mitochondrial and nuclear admixture over hundreds of kilometers, without obvious selection against hybrids. CONCLUSIONS: The genetic signatures of insular Aegean toads appear governed by bathymetry and Quaternary sea level changes, resulting in long-term isolation (Central Cyclades: Naxos) and recent land-bridges (coastal islands). Conversely, Crete has been isolated since the end of the Messinian salinity crisis (5.3 My) and Cretan populations thus likely result from human-mediated colonization, at least since Antiquity, from Peloponnese and Anatolia. Comparisons of green toad hybrid zones support the idea that post-zygotic hybrid incompatibilities accumulate gradually over the genome. In this radiation, only one million years of divergence separate a scenario of complete reproductive isolation, from a secondary contact resulting in near panmixia

Next-generation sequencing yields the complete mitochondrial genome of the endangered Milos viper Macrovipera schweizeri (Reptilia, Viperidae)

The Milos viper, Macrovipera schweizeri, is an endangered viperid snake found on four Aegean islands (Greece). Its complete mitochondrial genome, the first reported for the genus Macrovipera, was assembled through next-generation sequencing. Its total length is 17,152 bp and includes 22 tRNAs, two ribosomal RNA genes, 13 protein-coding genes and two control regions, showing the typical gene-arrangement for Viperidae. Eight tRNAs and ND3 are encoded on the light strand, while all other genes are encoded on the heavy strand. A mitogenomic phylogeny that included Macrovipera schweizeri and 13 other viperid genera returned an unresolved relationship among the genera Macrovipera, Daboia and Vipera.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant agreement no. 656006 (Project Acronym: CoPhyMed).Peer reviewe

Contribution to the study of phylogeography in the Eastern Mediterranean: the case of the fossorial snake Typhlops vermicularis Merrem, 1820

The current study focuses on the phylogeography of the snake Typhlops vermicularis that is distributed in the eastern Mediterranean region. This area has a complex geological and climatic history that has affected the phylogeny and biogeography of several organisms. The scope of the current study was to assess the phylogenetic relationships among the populations of the studied species with the use of molecular markers and to answer questions regarding the processes that affected the history of animal taxa in the eastern Mediterranean. Basic methods of phylogenetic analysis and network analysis were followed while divergence times were estimated with a strict molecular-clock approach. According to the results of the present study Τ. vermicularis includes ten mitochondrial clades which represent ten Evolutionary Significant Units (ESUs). Genetic divergence levels imply one or more genetic bottleneck or founder effects. It seems that during the Late Neogene this species distribution followed many circles of expansion and shrinkage with the sudden and intense transitions from wetter to more arid conditions acting as a vicariant agent. During the non-favourable periods (arid and cold) several regions acted as refugia for Τ. Vermicularis. Among the Τ. vermicularis ESUs clade A (Jordan. S. Syria) is genetically differentiated from the others and could represent a separate species.Στην παρούσα διατριβή εξετάζεται η φυλογεωγραφία του φιδιού Typhlops vermicularis το οποίο εξαπλώνεται στην ανατολική Μεσόγειο. Η περιοχή αυτή έχει μια πολύπλοκη γεωλογική και κλιματική ιστορία που έχει επηρεάσει τη φυλογένεση και τη βιογεωγραφία πολλών οργανισμών. Σκοπός της διατριβής ήταν να αποσαφηνιστούν οι φυλογενετικές σχέσεις μεταξύ των πληθυσμών του είδους με τη χρήση μοριακών δεικτών και να προσεγγιστούν βασικά ερωτήματα που αφορούν στις διεργασίες που καθόρισαν ή επηρέασαν την ιστορία των ζωικών οργανισμών της ανατολικής Μεσογείου. Ακολουθήθηκαν βασικές μέθοδοι φυλογενετικής ανάλυσης και κατασκευής δικτύων ενώ οι χρόνοι απόσχισης των φυλογενετικών κλάδων εκτιμήθηκαν με την προσέγγιση του αυστηρού μοριακού ρολογιού. Σύμφωνα με τα αποτελέσματα της διατριβής το Τ. vermicularis περιλαμβάνει δέκα μιτοχονδριακούς κλάδους οι οποίοι αντιστοιχούν σε ισάριθμες Εξελικτικά Σημαντικές Μονάδες (ΕΣΜ). Τα επίπεδα γενετικής διαφοροποίησης υποδηλώνουν πιθανή ύπαρξη ενός ή περισσοτέρων φαινομένων γενετικής στενωπού ή ιδρύσεως. Μπορεί να εξαχθεί το συμπέρασμα ότι κατά το Ύστερο Νεογενές η κατανομή του είδους ακολούθησε πολλούς κύκλους επέκτασης και συρρίκνωσης με τις απότομες και έντονες μεταβάσεις από πιο υγρές σε πιο ξηρές συνθήκες να δρουν ως βικαριανιστικός παράγοντας. Κατά τη διάρκεια των μη ευνοϊκών περιόδων (ξηρών και ψυχρών) πολλές περιοχές λειτούργησαν ως καταφύγια για το Τ. vermicularis. Μεταξύ των ΕΣΜ του Τ. vermicularis ο κλάδος Α (Ιορδανία, Ν. Συρία) είναι γενετικά πολύ διαφοροποιημένος από τους υπολοίπους και μπορεί να θεωρηθεί ξεχωριστό είδος

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Disentangling cryptic diversity is important for evolutionary and biogeographical research and conservation planning. In some cases, close examination of the morphology of taxa enables their accurate distinction, but often this is only possible by genetic analysis. In the present study we used geometric morphometrics and genetic analysis of two mitochondrial markers (CO1 and 12S) to explore cryptic diversity within the land snail species Albinaria lycica distributed in a limited area in SW Turkey. Our analyses revealed large and higher than anticipated genetic and morphometric differences between and within the two A. lycica subspecies, which supports our hypothesis that cryptic diversity in such a small geographical scale can occur. Moreover, the correlation of geographic distances with morphometric and genetic ones suggests an isolation-bydistance pattern of population structure. These results confirm earlier studies showing the power of multidisciplinary approaches to characterizing the enormous, and often cryptic, diversity of clausiliid land snails

Blanus aporus F. Werner 1898

<i>Blanus aporus</i> F. Werner, 1898 <p>TYPE LOCALITY: “bei Mersina” (= near Mersin, now Içel)</p> <p>LECTOTYPE (by present designation): NMW 12310.</p> <p>PARALECTOTYPES: BM 1946.8.2.15-16; MZUT 2119 (formerly 2439, quoted by Alexander as IMZUT).</p> <p> Just three types have been located, out of ten studied by F. Werner. NMW 12310, a single individual, is the only “Mersina” specimen in Vienna collection; other specimens of <i>Blanus</i> from Mersin or its vicinity were collected from 1963-1967 and thus cannot be referred to Werner’s material (H. Grillitsch <i>in litt.</i>). Werner was Professor at the University of Vienna; he distributed many of his types among museums in other countries; only after his death, his legacy in the form of a fragmentary private collection was bought by the Vienna museum (H. Grillitsch <i>in litt.</i>), therefore the fate of the other seven specimens of the type-series is currently not known.</p> <p> According to Alexander (1966) the specimen ZMB 19887 (quoted as ZMU) is perhaps a type as well, but Gans <i>et al.</i> (1997) do not list this specimen between their catalogue of the types in the Zoological Museum, Berlin.</p> <p>The lectotype here designated was overlooked in the type-catalogue of Vienna Museum (Tiedemann & Häupl 1980).</p> <p> <i>B. aporus</i> was regarded by recent authors as a subspecies of <i>B. strauchi</i>. On the basis of morphological evidences shown by Alexander (1966) and Zaloğlu (1968), the high genetic divergence and the lack of shared haplotypes for the nuclear marker from both <i>B. strauchi</i> and the eastern clade, this taxon is better regarded at the species rank. The geographic boundaries need to be investigated; the border between <i>B. s. bedriagae</i> and <i>B. aporus</i> probably lies between Antalya and Kaş, while the border between <i>B. aporus</i> and the easternmost taxon lies between Içel and Kozan.</p>Published as part of <i>Sindaco, Roberto, Kornilios, Panagiotis, Sacchi, Roberto & Lymberakis, Petros, 2014, Taxonomic reassessment of Blanus strauchi (Bedriaga, 1884) (Squamata: Amphisbaenia: Blanidae), with the description of a new species from south-east Anatolia (Turkey), pp. 311-326 in Zootaxa 3795 (3)</i> on page 320, DOI: 10.11646/zootaxa.3795.3.6, <a href="http://zenodo.org/record/230932">http://zenodo.org/record/230932</a&gt

Blanus strauchi subsp. bedriagae Boulenger 1884

<i>Blanus strauchi bedriagae</i> (Boulenger, 1884) <p> <i>Blanus bedriagae</i> Boulenger, 1884.</p> <p>TYPE LOCALITY: “from the river Xanthus, Asia Minor ”.</p> <p>SYNTYPES: BM 1946.8.2.14, 1946.8.2.30, 1946.8.31.84-93 (according to Alexander 1966 the series currently consists of only specimens 85-93, but ZIL 6679 - now ZISP -, coming from the British Museum in 1885, may represent the missing specimen).</p> <p> <i>B. strauchi</i> is the available name for the populations of western Anatolia (presumably west of the Antalya area) and the Greek Islands. Two subspecies can be recognized on the basis of both morphological and genetic data: <i>B. s. strauchi</i> (Bedriaga, 1884) in the West and in most of Greek islands, and <i>B. s. bedriagae</i> Boulenger, 1884, in the East (including Kastellorizo Island). The boundary between these subspecies lies between Ula (Muğla province) and Fethiye.</p>Published as part of <i>Sindaco, Roberto, Kornilios, Panagiotis, Sacchi, Roberto & Lymberakis, Petros, 2014, Taxonomic reassessment of Blanus strauchi (Bedriaga, 1884) (Squamata: Amphisbaenia: Blanidae), with the description of a new species from south-east Anatolia (Turkey), pp. 311-326 in Zootaxa 3795 (3)</i> on page 320, DOI: 10.11646/zootaxa.3795.3.6, <a href="http://zenodo.org/record/230932">http://zenodo.org/record/230932</a&gt

Cryptic diversity and molecular systematics of the Aegean Ophiomorus skinks (Reptilia: Squamata), with the description of a new species

In recent years, great attention has been devoted to the discovery and description of cryptic species, especially using DNA markers and new statistical approaches. Genetic data are useful for discovering new lineages that can then be treated as hypotheses to be tested using morphology. Here, we use multilocus genetic data and a thorough sampling to delimit species within the Greek legless skink. Phylogenetic analyses reveal high levels of genetic diversity, suggesting that Ophiomorus punctatissimus includes at least two species, East and West of the Aegean Sea. Moreover, species delimitation methods support at least two and up to five species within the western O.punctatissimus, and this result is shared among single-locus (ABGD, PTP, and GMYC) and multilocus coalescent (BPP) methods. We examined whether the two allopatric lineages exhibit morphological differentiation, but the different preservation methods used for the examined material led to inconclusive results. However, morphological conservatism in this semi-fossorial limbless skink possibly also played a key role. Finally, we formally recognize the East Aegean taxon as a separate species and we provide a differential diagnosis based on DNA diagnostic characters

Blanus alexandri Sindaco, Kornilios, Sacchi & Lymberakis, 2014, sp. nov.

<i>Blanus alexandri</i> sp. nov. <p> <i>Holotype.</i> MCCI-R1632. An adult collected on 26 April 2011, approximately 3.6 km NE of Derik (Mardin province, Turkey) at 37.3891°N – 40.2980E °, m 1161 a.s.l. (Fig. 6).</p> <p> <i>Paratypes.</i> MCCI-R1633. An adult collected on 28 April 2011, approximately 3 km NE of Karalar village (Şırnak prov., Turkey) at 37.3153°N, 41.7037°E, m 831 a.s.l.</p> <p>MCCI-R1634. An adult collected on 1 May 2011, approximately 1.5 km SE of Yukariokcular (Hatay province, Turkey) at 36.0778°N, 36.1518°E, m 562 a.s.l.</p> <p>MCCI-R1635 (1–3). Three specimens collected on 2 May 2011, approximately 1.3 km E of Sungur (Hatay province, Turkey) at 36.0083°N, 36.1218°E, m 944 a.s.l.</p> <p>MSNG 57582. An adult collected on 24 May 2012 between Yesilçe and Isikli (Gaziantep province, Turkey) at 37.1611°N, 37.2135°E, m 1081 a.s.l.</p> <p>MSNG 57583. A specimen collected on 24 May 2012 2 km W of Akdam (Adana Province, Turkey), at 37.5515°N, 35.5937°E, m 932 a.s.l.</p> <p>MCCI-R1678. A specimen collected on 24 May 2012 0.7 km SSW of Akarca Koyu (Adana Province, Turkey) at 37.5615°N, 35.6367°E, m 736 a.sl.</p> <p> <b>Diagnosis.</b> <i>B. alexandri</i> <b>sp. nov.</b> is easily distinguishable from the allopatric <i>B. strauchi bedriagae</i> by having a low number of precloacal pores (usually 3+3, more rarely 3+2 or 2+2, in a single specimen MCCI-R1678: 4+4; N = 8), widely separated by two preanal scales, while <i>B. s. bedriagae</i> has 10 – rarely 8 - precloacal pores arranged in a continuous row or very rarely separated by a single scale. Moreover <i>B. alexandri</i> has three infralabials, instead of two of <i>B. s. bedriagae</i>.</p> <p> Also <i>B. s. strauchi</i> has the precloacal pores widely separated, but the number is higher than in <i>B. alexandri</i>, since it has 4+4 precloacal pores in 18 out of 19 examined specimens.</p> <p> There are no obvious morphological differences between <i>B. alexandri</i> and <i>B. aporus</i>, which differ by having more body annuli, less dorsal segments and ventral segments at midbody.</p> <p> The larger specimen (MCCI-R1635/1) has a SVL = 200 mm, a size reached also by other taxa of the <i>B. strauchi</i> complex (Alexander 1966).</p> <p>Colour in life goes from grey to black; large specimens show more or less depigmented areas of the body (Fig. 6).</p> <p> Genetically, <i>B. alexandri</i> is clearly differentiated from the other two species, appearing as a distinct, strongly monophyletic unit in the mitochondrial phylogeny. The genetic divergence between this species and <i>B. strauchi</i> and <i>B. aporus</i> is very high (mean <i>p</i> -distance values are 12.7% and 10.3%, respectively), equal to or above the species-level when compared to <i>Blanus</i> species-pairs and other squamate reptiles for the same molecular marker (PRLR). The populations of <i>B. alexandri</i> are also genetically distinct on the basis of an independent nuclear marker, showing no apparent gene-flow, i.e. heterozygotes or shared alleles.</p> <p> <b>Description of the holotype.</b> Snout-vent length 162 mm, tail length 18.0 mm, head length 7.8 mm, head width 5.7 mm, prefrontal length 3.0 mm, prefrontal width 3.0 mm, 110 body annuli, 18 caudal annuli, 3+3 precloacal pores, 17 dorsal body segments and 17 ventral body segments. The prefontral scale is large, hardly wider than longer. The nostrils open in the anterior third of the nasal scale that is the first and bigger of the three supralabials; the second supralabial enters the prefrontal scale; the third supralabial scale is the smaller. The small ocular scales are in contact with five scales, including the prefrontal, the first and second supralabial.</p> <p>Following the prefontral plate there are three pairs of quadrangular plates on the occipital region, their size decreasing from anteriors to posteriors.</p> <p>The mental plate is a little bit bigger than the postmental. Infralabials three, the first smaller and the third bigger. Between the second and third infralabials and the postmental scale there are two post-genial rows of four (the anterior) and five (the posterior) quadrangular scales. The lateral shields of the first post-genial row is in very narrow contact with the postmental shield.</p> <p>Scales on the neck are smaller than the dorsal ones; the first rows are quadrangular or slightly wider than long; the scales on the trunk are elongated, the dorsal narrower than the ventral.</p> <p>The lateral sulci are well marked and the dorsal sulcus is visible from about 1/8 of the SVL until the proximal part of the tail.</p> <p>Colour in alcohol is greyish with pinkish intersegmental sutures, the vent is ligher than the dorsum.</p> <p> <b>Variation.</b> Variation in measurements and scale counts and measurements is shown in Table 4.</p> <p> The arrangement of scales is variable, also for scale arrangement diagnostic for other taxa (i.e. <i>B. s. strauchi</i> and <i>B. s. bedriagae</i>), as already stated by Alexander (1966).</p> <p>Large specimens are usually less coloured and can be partially depigmentated (i.e. MCCI-R1635/1).</p> <p> <b>Distribution.</b> Specimens genetically identified occur between Akdam (Adana province) in the west, and Karalar (Şırnak province) in the east. It is likely that the populations of northern Iraq, Syria and Lebanon belong to this species.</p> <p> <b>Derivatio nominis.</b> The species is named in honour of A. Allan Alexander, who made the most valuable study on the <i>Blanus strauchi</i> complex and realized that the eastern populations could be distinguished from the Cilician taxon <i>aporus</i>.</p>Published as part of <i>Sindaco, Roberto, Kornilios, Panagiotis, Sacchi, Roberto & Lymberakis, Petros, 2014, Taxonomic reassessment of Blanus strauchi (Bedriaga, 1884) (Squamata: Amphisbaenia: Blanidae), with the description of a new species from south-east Anatolia (Turkey), pp. 311-326 in Zootaxa 3795 (3)</i> on pages 321-322, DOI: 10.11646/zootaxa.3795.3.6, <a href="http://zenodo.org/record/230932">http://zenodo.org/record/230932</a&gt