cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4616155.v2
title: DNA barcodes for dragonflies and damselflies (Odonata) of Mindanao, Philippines

description: Reliable species identification provides a sounder basis for use of species in the order Odonata as biological indicators and for their conservation, an urgent concern as many species are threatened with imminent extinction. We generated 134 COI barcodes from 36 morphologically identified species of Odonata collected from Mindanao Island, representing 10 families and 19 genera. Intraspecific sequence divergences ranged from 0 to 6.7% with four species showing more than 2%, while interspecific sequence divergences ranged from 0.5 to 23.3% with seven species showing less than 2%. Consequently, no distinct gap was observed between intraspecific and interspecific DNA barcode divergences. The numerous islands of the Philippine archipelago may have facilitated rapid speciation in the Odonata and resulted in low interspecific sequence divergences among closely related groups of species. This study contributes DNA barcodes for 36 morphologically identified species of Odonata reported from Mindanao including 31 species with no previous DNA barcode records.
DOI: 10.6084/m9.figshare.6026732.v2
title: Mitochondrial DNA genetic diversity in six Italian donkey breeds (<i>Equus asinus</i>)

description: Donkeys have played an important role in agricultural land practices and in human historical periods of recent past and, still today, are used as a working power in several world areas. The objective of this study was to identify genetic variability in six Italian donkey breeds using mtDNA D-loop. Fifteen haplotypes, grouped in three haplogroups, were identified. The genetic indices were informative and showed a high population genetic variability. The results of AMOVA analyses based on geographic structuring of Italian populations highlighted that the majority of the observed variance is due to differences among samples within breeds. Comparison among Italian haplotypes and mtDNA D-loop sequences belonging to European domestic and Ethiopian donkeys and wild asses, clearly define two clades referred to Nubian lineage. The results can be useful to complement safeguard planes for donkey breeds that are considered to extinction endangered.
DOI: 10.6084/m9.figshare.3408244
title: Mitochondrial diversity in mountain horse population from the South-Eastern Europe

description: It is believed that population structure of mountain horse breeds is preserved from any genetic introgression, because of their geographical isolation and specific semi-wild life style of husbandry. Till date there are no molecular data for the Balkan horses. In this study we try to give information about some autochthonous mountain horse breeds from Bulgaria. A total of 121 horses from three different mountain massifs are presented: Stara Planina (the Balkan mountain), the Rhodopes and Rila-Pirin massif were genotyped according to mitochondrial D-loop region. The results showed huge diversity of all known haplogroups with exception of C, F and R. West Eurasian haplogroups B, D, M and L were with the highest frequencies. Haplogroups A, J, I, O’P and Q were also observed with the highest frequencies, but not equally distributed among the three populations. Analyses of the horse breeds reveal preserved genetic profile of the Balkan and the Rhodopes mountains populations. In contrast, a Rila-Pirin breed unexpectedly showed mixed profile – a massive genetic introgression with an Asiatic-type haplogroups. A similar mixed Euro-Asiatic haplotype profile possessed the Carpathian mountain pony, although both populations are separated geographically and historically. The genetic pool of three Bulgarian mountain horse populations is highly heterogenic and because of that these breeds should be preserved.
DOI: 10.6084/m9.figshare.3408244.v1
title: Mitochondrial diversity in mountain horse population from the South-Eastern Europe

description: It is believed that population structure of mountain horse breeds is preserved from any genetic introgression, because of their geographical isolation and specific semi-wild life style of husbandry. Till date there are no molecular data for the Balkan horses. In this study we try to give information about some autochthonous mountain horse breeds from Bulgaria. A total of 121 horses from three different mountain massifs are presented: Stara Planina (the Balkan mountain), the Rhodopes and Rila-Pirin massif were genotyped according to mitochondrial D-loop region. The results showed huge diversity of all known haplogroups with exception of C, F and R. West Eurasian haplogroups B, D, M and L were with the highest frequencies. Haplogroups A, J, I, O’P and Q were also observed with the highest frequencies, but not equally distributed among the three populations. Analyses of the horse breeds reveal preserved genetic profile of the Balkan and the Rhodopes mountains populations. In contrast, a Rila-Pirin breed unexpectedly showed mixed profile – a massive genetic introgression with an Asiatic-type haplogroups. A similar mixed Euro-Asiatic haplotype profile possessed the Carpathian mountain pony, although both populations are separated geographically and historically. The genetic pool of three Bulgarian mountain horse populations is highly heterogenic and because of that these breeds should be preserved.
DOI: 10.6084/m9.figshare.6026732.v1
title: Mitochondrial DNA genetic diversity in six Italian donkey breeds (<i>Equus asinus</i>)

description: Donkeys have played an important role in agricultural land practices and in human historical periods of recent past and, still today, are used as a working power in several world areas. The objective of this study was to identify genetic variability in six Italian donkey breeds using mtDNA D-loop. Fifteen haplotypes, grouped in three haplogroups, were identified. The genetic indices were informative and showed a high population genetic variability. The results of AMOVA analyses based on geographic structuring of Italian populations highlighted that the majority of the observed variance is due to differences among samples within breeds. Comparison among Italian haplotypes and mtDNA D-loop sequences belonging to European domestic and Ethiopian donkeys and wild asses, clearly define two clades referred to Nubian lineage. The results can be useful to complement safeguard planes for donkey breeds that are considered to extinction endangered.
DOI: 10.6084/m9.figshare.3750294.v2
title: Structure and variation of the Fringillidae (Aves: Passeriformes) mitochondrial DNA control region and their phylogenetic relationship

description: The control region is the major noncoding segment of animal mitochondrial DNA. To infer the structure and variation of Fringillidae mitochondrial DNA control region, the entire control region sequences of 25 species were analyzed. The length of the control region sequences was very conserved (1230 ± 18) and can be separated into three domains. The frequency of both substitutions and gaps was highest in the third domain and lowest in the central region. The control region has the same flanking gene order from tRNA<sup>Glu</sup> to tRNA<sup>Phe</sup>. Genetic distances between species ranged from 1.80% (between <i>Carduelis pinus</i> and <i>Carduelis spinus</i>) to 25.34% (between <i>Carduelis sinica</i> and <i>Coccothraustes vespertinus</i>). The average genetic distances among the species within the genera varied from 5.11% (<i>Leucosticte</i>) to 14.31% (<i>Carpodacus</i>). The average genetic distances showed insignificantly negative correlation with ts/tv. Domain III is the most variable of the three domains among all the genera. The control region of Fringillidae contains a putative TAS element and the highly conserved CSB-1, and F, E, D, C boxes. However, neither CSB-2 nor CSB-3 could be unambiguously identified in the Fringillidae. The maximum likelihood method was used to construct a phylogenetic tree. Control region analysis demonstrated that some currently recognized genera may be polyphyletic, including <i>Carpodacus, Carduelis</i> and <i>Serinus</i>.
DOI: 10.6084/m9.figshare.5752776
title: DNA barcoding revises a misidentification on mossy frog: new record and distribution extension of <i>Theloderma corticale</i> Boulenger, 1903 (Amphibia: Anura: Rhacophoridae)

description: As an endangered animal group, mossy frog (genus <i>Theloderma</i>) has attracted the attention of biologists and wildlife conservationists. Clarifying the taxonomic status and distribution of each species in <i>Theloderma</i> is important to determine the conservation status for each species, establish appropriate conservation strategies and probe the speciation process. Recently, we discovered a medium-sized species of mossy frog of the genus <i>Theloderma</i> in April 2015 during municipal surveys of amphibians in Dayao Mountain of Jinxiu. It was collected from the water-filled tree cavities. However, there remains some uncertainty about the species determination of the mossy frog in the Yinshan station of Dayao Mountain in Guangxi Province, China. Previously, the mossy frog in Guangxi Province was recognized as <i>Th. kwangsiense</i>. In order to clarify the species status of the mossy frog obtained from Guangxi, we sequenced 2414 bp of the 12S and 16S genes in the sample collected from the Dayao Mountain. Combining all the sequence in NCBI, genetic analyses from the data suggest that the sample from the Dayao Mountain is <i>Th. corticale</i> rather than <i>Th. kwangsiense</i>. It is most likely that the most previous studies had wrong species identification. And, it is the first time we use DNA barcoding to prove that the species obtained from Guangxi is a new distribution of <i>Th. corticale</i>.
DOI: 10.6084/m9.figshare.5752776.v1
title: DNA barcoding revises a misidentification on mossy frog: new record and distribution extension of <i>Theloderma corticale</i> Boulenger, 1903 (Amphibia: Anura: Rhacophoridae)

description: As an endangered animal group, mossy frog (genus <i>Theloderma</i>) has attracted the attention of biologists and wildlife conservationists. Clarifying the taxonomic status and distribution of each species in <i>Theloderma</i> is important to determine the conservation status for each species, establish appropriate conservation strategies and probe the speciation process. Recently, we discovered a medium-sized species of mossy frog of the genus <i>Theloderma</i> in April 2015 during municipal surveys of amphibians in Dayao Mountain of Jinxiu. It was collected from the water-filled tree cavities. However, there remains some uncertainty about the species determination of the mossy frog in the Yinshan station of Dayao Mountain in Guangxi Province, China. Previously, the mossy frog in Guangxi Province was recognized as <i>Th. kwangsiense</i>. In order to clarify the species status of the mossy frog obtained from Guangxi, we sequenced 2414 bp of the 12S and 16S genes in the sample collected from the Dayao Mountain. Combining all the sequence in NCBI, genetic analyses from the data suggest that the sample from the Dayao Mountain is <i>Th. corticale</i> rather than <i>Th. kwangsiense</i>. It is most likely that the most previous studies had wrong species identification. And, it is the first time we use DNA barcoding to prove that the species obtained from Guangxi is a new distribution of <i>Th. corticale</i>.
DOI: 10.6084/m9.figshare.3750294.v1
title: Structure and variation of the Fringillidae (Aves: Passeriformes) mitochondrial DNA control region and their phylogenetic relationship

description: The control region is the major noncoding segment of animal mitochondrial DNA. To infer the structure and variation of Fringillidae mitochondrial DNA control region, the entire control region sequences of 25 species were analyzed. The length of the control region sequences was very conserved (1230 ± 18) and can be separated into three domains. The frequency of both substitutions and gaps was highest in the third domain and lowest in the central region. The control region has the same flanking gene order from tRNA<sup>Glu</sup> to tRNA<sup>Phe</sup>. Genetic distances between species ranged from 1.80% (between <i>Carduelis pinus</i> and <i>Carduelis spinus</i>) to 25.34% (between <i>Carduelis sinica</i> and <i>Coccothraustes vespertinus</i>). The average genetic distances among the species within the genera varied from 5.11% (<i>Leucosticte</i>) to 14.31% (<i>Carpodacus</i>). The average genetic distances showed insignificantly negative correlation with ts/tv. Domain III is the most variable of the three domains among all the genera. The control region of Fringillidae contains a putative TAS element and the highly conserved CSB-1, and F, E, D, C boxes. However, neither CSB-2 nor CSB-3 could be unambiguously identified in the Fringillidae. The maximum likelihood method was used to construct a phylogenetic tree. Control region analysis demonstrated that some currently recognized genera may be polyphyletic, including <i>Carpodacus, Carduelis</i> and <i>Serinus</i>.
DOI: 10.6084/m9.figshare.4592638.v3
title: Geographic variation in the spotted-wing drosophila, <i>Drosophila suzukii</i> (Diptera: Drosophilidae), based on mitochondrial DNA sequences

description: The spotted-wing drosophila (SWD), <i>Drosophila suzukii</i> (Diptera: Drosophilidae), is an economically damaging pest that feeds on most thin-skinned fruits. It was originally native to a few Asian countries, including Korea, but is now found in North America and Europe. In this study, we sequenced portions of the mitochondrial (mt) <i>COI</i> and <i>ND4</i> genes from a total of 195 individuals collected mainly from Korea. We then combined GenBank-registered <i>COI</i> sequences from all ancestral-range and introduced-range populations with our own <i>COI</i> data to assess the worldwide diversity, divergence, and relatedness of SWD haplotypes. A total of 139 haplotypes were obtained from the concatenated <i>COI</i> and <i>ND4</i> sequences. Most haplotypes were confined to single localities, but 12 of them were found in more than two localities, and one haplotype (SWDCN61) was found from Korea to Canada. A dataset combining GenBank sequences with our own data identified a total of 94 worldwide <i>COI</i> haplotypes with a maximum sequence divergence (MSD) of 5.433% (32 bp). Although most haplotypes were found in only a single country, a few haplotypes were found commonly in China, Korea, and Japan; these occurred at a higher frequency and were often involved in introductions. A rough estimate of genetic diversity in each country showed higher diversity in ancestral distributional ranges, but the invasion over Asian countries seems to have been substantial because haplotype diversity was only 2.35 to 3.97-fold lower in the U.S.A, Canada, and Italy than that in the populations’ ancestral ranges.
DOI: 10.6084/m9.figshare.3968913
title: Phylogenetic relationships of <i>D. rudis</i> (Bedriaga, 1886) and <i>D. bithynica</i>(Mehely, 1909) based on microsatellite and mitochondrial DNA in Turkey

description: The spiny-tailed lizard of the genus <i>Darevskia</i> have a series of taxonomic revisions, but still their phylogenetic relationships remain uncertain. In the present study, we have assessed taxonomic relationships among <i>Darevskia bithynica</i> and <i>Darevskia rudis</i> populations through estimation of phylogenetic relationships among 96 specimens using microsatellite DNA (<i>Du215</i>, <i>Du281</i>, <i>Du323</i> and <i>Du418</i> loci) and 53 specimens using mtDNA (16S rRNA and cytb) from main populations in Turkey. Although <i>D. b. bithynica</i> and <i>D. r. mirabilis</i> were separated based on the PCoA analysis at low level from other <i>D. rudis</i> and <i>D. bithynica</i> populations, the distance values of Nei's genetic distance, Nei's unbiased genetic distance, Fst and Linear Fst were not high among taxa in microsatellite DNA. On the other hand, our phylogenetic analyses (NJ, ML, MP and BI) did not separate <i>D. rudis</i> and <i>D. bithynica</i> populations. Finally, most of the topologically identical trees of phylogenetic analyses and microsatellite results showed that the extant populations of <i>D. rudis</i> and <i>D. bithynica</i> were found to be polytomy. Based on our molecular phylogenetic study, <i>D. rudis</i> complex is still ongoing revisions.
DOI: 10.6084/m9.figshare.4592638
title: Geographic variation in the spotted-wing drosophila, <i>Drosophila suzukii</i> (Diptera: Drosophilidae), based on mitochondrial DNA sequences

description: The spotted-wing drosophila (SWD), <i>Drosophila suzukii</i> (Diptera: Drosophilidae), is an economically damaging pest that feeds on most thin-skinned fruits. It was originally native to a few Asian countries, including Korea, but is now found in North America and Europe. In this study, we sequenced portions of the mitochondrial (mt) <i>COI</i> and <i>ND4</i> genes from a total of 195 individuals collected mainly from Korea. We then combined GenBank-registered <i>COI</i> sequences from all ancestral-range and introduced-range populations with our own <i>COI</i> data to assess the worldwide diversity, divergence, and relatedness of SWD haplotypes. A total of 139 haplotypes were obtained from the concatenated <i>COI</i> and <i>ND4</i> sequences. Most haplotypes were confined to single localities, but 12 of them were found in more than two localities, and one haplotype (SWDCN61) was found from Korea to Canada. A dataset combining GenBank sequences with our own data identified a total of 94 worldwide <i>COI</i> haplotypes with a maximum sequence divergence (MSD) of 5.433% (32 bp). Although most haplotypes were found in only a single country, a few haplotypes were found commonly in China, Korea, and Japan; these occurred at a higher frequency and were often involved in introductions. A rough estimate of genetic diversity in each country showed higher diversity in ancestral distributional ranges, but the invasion over Asian countries seems to have been substantial because haplotype diversity was only 2.35 to 3.97-fold lower in the U.S.A, Canada, and Italy than that in the populations’ ancestral ranges.
DOI: 10.6084/m9.figshare.4592629
title: Back from the dead! Resurrection and revalidation of the Indian endemic snake genus <i>Wallophis</i> Werner, 1929 (Squamata: Colubridae) insights from molecular data

description: The monotypic colubrid snake genus <i>Wallophis</i> is revalidated and rediagnosed. Partial sequence for nuclear gene Oocyte maturation factor Mos (c-<i>mos</i>), mitochondrial Nicotinamide adenine dinucleotide dehydrogenase subunit 4 (<i>ND4</i>) and cytochrome b (cyt <i>b</i>) were used to assess phylogenetic relationship. <i>Wallophis brachyura</i> type species for the genus was found to be a member of the Western Palearctic clade of Colubrinae and is recovered as a sister taxa to <i>Wallaceophis gujaratensis</i>. <i>Wallophis</i> differs from <i>Wallaceophis</i> in an uncorrected pairwise p-distance of 17% for mitochondrial <i>ND4</i> gene. <i>Wallaceophis gujaratensis</i> was described in three different spellings in the literature hence we here propose <i>Wallaceophis gujaratensis</i> as the correct spelling for the species based on provisions in the article 24.2.3. of the International Code for Zoological Nomenclature.
DOI: 10.6084/m9.figshare.4592647
title: The heavy strand dilemma of vertebrate mitochondria on genome sequencing age: number of encoded genes or G + T content?

description: The heavy strand dilemma of vertebrate mitochondria on genome sequencing age: number of encoded genes or G + T content?
DOI: 10.6084/m9.figshare.4592647.v1
title: The heavy strand dilemma of vertebrate mitochondria on genome sequencing age: number of encoded genes or G + T content?

description: The heavy strand dilemma of vertebrate mitochondria on genome sequencing age: number of encoded genes or G + T content?
DOI: 10.6084/m9.figshare.3968913.v2
title: Phylogenetic relationships of <i>D. rudis</i> (Bedriaga, 1886) and <i>D. bithynica</i>(Mehely, 1909) based on microsatellite and mitochondrial DNA in Turkey

description: The spiny-tailed lizard of the genus <i>Darevskia</i> have a series of taxonomic revisions, but still their phylogenetic relationships remain uncertain. In the present study, we have assessed taxonomic relationships among <i>Darevskia bithynica</i> and <i>Darevskia rudis</i> populations through estimation of phylogenetic relationships among 96 specimens using microsatellite DNA (<i>Du215</i>, <i>Du281</i>, <i>Du323</i> and <i>Du418</i> loci) and 53 specimens using mtDNA (16S rRNA and cytb) from main populations in Turkey. Although <i>D. b. bithynica</i> and <i>D. r. mirabilis</i> were separated based on the PCoA analysis at low level from other <i>D. rudis</i> and <i>D. bithynica</i> populations, the distance values of Nei's genetic distance, Nei's unbiased genetic distance, Fst and Linear Fst were not high among taxa in microsatellite DNA. On the other hand, our phylogenetic analyses (NJ, ML, MP and BI) did not separate <i>D. rudis</i> and <i>D. bithynica</i> populations. Finally, most of the topologically identical trees of phylogenetic analyses and microsatellite results showed that the extant populations of <i>D. rudis</i> and <i>D. bithynica</i> were found to be polytomy. Based on our molecular phylogenetic study, <i>D. rudis</i> complex is still ongoing revisions.
DOI: 10.6084/m9.figshare.4592629.v3
title: Back from the dead! Resurrection and revalidation of the Indian endemic snake genus <i>Wallophis</i> Werner, 1929 (Squamata: Colubridae) insights from molecular data

description: The monotypic colubrid snake genus <i>Wallophis</i> is revalidated and rediagnosed. Partial sequence for nuclear gene Oocyte maturation factor Mos (c-<i>mos</i>), mitochondrial Nicotinamide adenine dinucleotide dehydrogenase subunit 4 (<i>ND4</i>) and cytochrome b (cyt <i>b</i>) were used to assess phylogenetic relationship. <i>Wallophis brachyura</i> type species for the genus was found to be a member of the Western Palearctic clade of Colubrinae and is recovered as a sister taxa to <i>Wallaceophis gujaratensis</i>. <i>Wallophis</i> differs from <i>Wallaceophis</i> in an uncorrected pairwise p-distance of 17% for mitochondrial <i>ND4</i> gene. <i>Wallaceophis gujaratensis</i> was described in three different spellings in the literature hence we here propose <i>Wallaceophis gujaratensis</i> as the correct spelling for the species based on provisions in the article 24.2.3. of the International Code for Zoological Nomenclature.
DOI: 10.6084/m9.figshare.4506155.v1
title: On the origin of Iberomaurusians: new data based on ancient mitochondrial DNA and phylogenetic analysis of Afalou and Taforalt populations

description: The Western North African population was characterized by the presence of Iberomaurusian civilization at the Epiplaeolithic period (around 20,000 years before present (YBP) to 10,000 YBP). The origin of this population is still not clear: they may come from Europe, Near East, sub-Saharan Africa or they could have evolved <i>in situ</i> in North Africa. With the aim to contribute to a better knowledge of the settlement of North Africa we analysed the mitochondrial DNA extracted from Iberomaurusian skeletons exhumed from the archaeological site of Afalou (AFA) (15,000–11,000 YBP) in Algeria and from the archaeological site of Taforalt (TAF) (23,000–10,800 YBP) in Morocco. Then, we carried out a phylogenetic analysis relating these Iberomaurusians to 61 current Mediterranean populations. The genetic structure of TAF and AFA specimens contains only North African and Eurasian maternal lineages. These finding demonstrate the presence of these haplotypes in North Africa from at least 20,000 YBP. The very low contribution of a Sub-Saharan African haplotype in the Iberomaurusian samples is confirmed. We also highlighted the existence of genetic flows between Southern and Northern coast of the Mediterranean.