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Molecular phylogenetics and evolution 36건

  1. [해외논문]   CO2: Editorial Board  


    Molecular phylogenetics and evolution v.118 ,pp. IFC , 2018 , 1055-7903 ,

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

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  2. [해외논문]   CO2: Editorial Board   SCI SCIE


    Molecular phylogenetics and evolution v.118 ,pp. IFC - IFC , 2018 , 1055-7903 ,

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  3. [해외논문]   Revisiting the phylogeny of Zoanthidea (Cnidaria: Anthozoa): Staggered alignment of hypervariable sequences improves species tree inference   SCI SCIE

    Swain, Timothy D. (Address: Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL 60208, USA.)
    Molecular phylogenetics and evolution v.118 ,pp. 1 - 12 , 2018 , 1055-7903 ,

    초록

    Abstract The recent rapid proliferation of novel taxon identification in the Zoanthidea has been accompanied by a parallel propagation of gene trees as a tool of species discovery, but not a corresponding increase in our understanding of phylogeny. This disparity is caused by the trade-off between the capabilities of automated DNA sequence alignment and data content of genes applied to phylogenetic inference in this group. Conserved genes or segments are easily aligned across the order, but produce poorly resolved trees; hypervariable genes or segments contain the evolutionary signal necessary for resolution and robust support, but sequence alignment is daunting. Staggered alignments are a form of phylogeny-informed sequence alignment composed of a mosaic of local and universal regions that allow phylogenetic inference to be applied to all nucleotides from both hypervariable and conserved gene segments. Comparisons between species tree phylogenies inferred from all data (staggered alignment) and hypervariable-excluded data (standard alignment) demonstrate improved confidence and greater topological agreement with other sources of data for the complete-data tree. This novel phylogeny is the most comprehensive to date (in terms of taxa and data) and can serve as an expandable tool for evolutionary hypothesis testing in the Zoanthidea. Spanish language abstract available in . Translation by L. O. Swain, DePaul University, Chicago, Illinois, 60604, USA. Highlights A current and comprehensive maximum-likelihood phylogeny of Zoanthidea is proposed. Inference based upon concatenated multi-gene, multi-genomic staggered alignment. Staggered alignment is phylogeny-informed and retains all nucleotides in the analysis. Complete-data tree is more robust and defensible than the hypervariable-excluded tree. Graphical abstract [DISPLAY OMISSION]

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

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  4. [해외논문]   A multilocus view on Mediterranean aeolid nudibranchs (Mollusca): Systematics and cryptic diversity of Flabellinidae and Piseinotecidae   SCI SCIE

    Furfaro, Giulia (Department of Sciences, University “Roma Tre”, Viale G. Marconi 446, I-00146 Rome, Italy ) , Salvi, Daniele (Department of Health, Life and Environmental Sciences, University of L'Aquila, 67100 Coppito, L'Aquila, Italy ) , Mancini, Emiliano (Department of Sciences, University “Roma Tre”, Viale G. Marconi 446, I-00146 Rome, Italy ) , Mariottini, Paolo (Department of Sciences, University “Roma Tre”, Viale G. Marconi 446, I-00146 Rome, Italy)
    Molecular phylogenetics and evolution v.118 ,pp. 13 - 22 , 2018 , 1055-7903 ,

    초록

    Abstract Recent molecular studies revealed high level of endemism and numerous cryptic species within opisthobranchs, with Mediterranean taxa clearly understudied. Here we used genetic data from both mitochondrial and nuclear gene fragments as well as morphological data from taxonomically relevant characters to investigate the phylogenetic relationships and systematics of Mediterranean taxa of the Flabellinidae and Piseinotecidae families. Phylogenetic analyses based on Bayesian and Maximum-Likelihood methods indicate that Flabellinidae and Pisenotecidae taxa and species within the genera Flabellina , Calmella and Piseinotecus do not form monophyletic clades. These results are supported by our morphological analyses which allowed the re-evaluation of the triseriate radula condition in Pisenotecidae and Calmella taxa and their inclusion in the genus Flabellina as Flabellina gaditana comb. nov. (synonym of F. confusa ), Flabellina gabinierei comb. nov. and Flabellina cavolini comb. nov. Species delimitation and barcoding gap analyses allowed uncovering cryptic species within Flabellina gracilis (Alder and Hancock, 1844), F. trophina (Bergh, 1890), F. verrucosa (M. Sars, 1829) and F. ischitana Hirano and Thompson, 1990, the latter with an Atlantic form which is under description. This study corroborates the relevance of combining molecular and morphological data from multiple populations and species in the assessment of nudibranch diversity and classification. Highlights Flabellina confusa is a synonym of Piseinotecus gaditanus . Piseinotecus gaditanus ranked in Flabellinidae as Flabellina gaditana comb. nov . Piseinotecus gabinierei and Calmella cavolini are included in the genus Flabellina . Piseinotecus gabinierei renamed as Flabellina gabinierei comb. nov . Calmella cavolini renamed as Flabellina cavolini comb. nov . The genus Calmella is a synonym of the genus Flabellina . A cryptic species new to science is discovered within Flabellina ischitana . Graphical abstract [DISPLAY OMISSION]

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

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  5. [해외논문]   Multiple transmission chains of coxsackievirus A4 co-circulating in China and neighboring countries in recent years: Phylogenetic and spatiotemporal analyses based on virological surveillance   SCI SCIE

    Chen, Peng (Department of Epidemiology, School of Public Health, Shandong University, No. 44 Wenhuaxi Road, Jinan 250012, People's Republic of China ) , Wang, Haiyan (Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan 250014, People's Republic of China ) , Tao, Zexin (Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan 250014, People's Republic of China ) , Xu, Aiqiang (Department of Epidemiology, School of Public Health, Shandong University, No. 44 Wenhuaxi Road, Jinan 250012, People's Republic of China ) , Lin, Xiaojuan (Shandong Provincial Key Laboratory of Infectious Disease Control and Prevention, Shandong Center for Disease Control and Prevention, No. 16992 Jingshi Road, Jinan 250014, People's Republic of China ) , Zhou, Nan (Department of Epidemiology, School of Public Health, Shandong University, No. 44 Wenhuaxi Road, Jinan 250012, Pe) , Wang, Pei , Wang, Qian
    Molecular phylogenetics and evolution v.118 ,pp. 23 - 31 , 2018 , 1055-7903 ,

    초록

    Abstract Coxsackievirus A4 (CV-A4) has been reported frequently in association with many infectious diseases and cases of hand, foot, and mouth disease potentially associated with CV-A4 infection are also identified. This study summarized the Shandong CV-A4 strains isolated from 25years acute flaccid paralysis surveillance, with an emphasis on exploring the phylogenetic analyses and spatiotemporal dynamics of CV-A4 at the global scale. We sampled 43 CV-A4 isolates and utilized VP1 gene to construct phylogenetic trees. Further extensive Bayesian phylogeographic analysis was carried out to investigate the evolution of CV-A4 and understand the spatiotemporal diffusion around the world using BEAST and SPREAD software. Phylogenetic trees showed that CV-A4 emerged to be more active in recent decades and multiple transmission chains were co-circulating. The molecular clock analysis estimated a mean evolutionary rate of 6.4×10 −3 substitutions/site/year, and the estimated origin of CV-A4 around 1944. The phylogeographic analyses suggested the origin of CV-A4 could be in the USA, however regional dissemination was mainly located around the Asia-Europe region. The spatiotemporal dynamics of CV-A4 exhibited frequent viral traffic among localities, and virus from Shandong province seemed to have played a central role in spreading around China and neighboring countries. Our phylogenetic description and phylogeographic analyses indicate the importance of large spatial- and temporal-scale studies in understanding epidemiological dynamics of CV-A4, particularly the diffusion routes will be of great importance to global control efforts. Highlights CV-A4 is more active in recent decades and multiple transmission chains are co-circulating. Origin of CV-A4 could be in the USA, regional dissemination located around the Asia-Europe region. CV-A4 exhibited frequent viral traffic among localities, spatiotemporal analysis was necessary. Understanding the diffusion routes of CV-A4 will be of great importance to global control efforts. Shandong seemed to play a central role in spreading around China and neighboring countries. Graphical abstract [DISPLAY OMISSION]

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  6. [해외논문]   Evolution in Australia's mesic biome under past and future climates: Insights from a phylogenetic study of the Australian Rock Orchids (Dendrobium speciosum complex, Orchidaceae)   SCI SCIE

    Simpson, Lalita (Australian Tropical Herbarium, Sir Robert Norman Building (E2), James Cook University, Cairns, PO Box 6811, QLD 4878, Australia ) , Clements, Mark A. (Centre for Australian National Biodiversity Research, GPO Box 1700, Canberra, ACT 2601, Australia ) , Crayn, Darren M. (Australian Tropical Herbarium, Sir Robert Norman Building (E2), James Cook University, Cairns, PO Box 6811, QLD 4878, Australia ) , Nargar, Katharina (Australian Tropical Herbarium, Sir Robert Norman Building (E2), James Cook University, Cairns, PO Box 6811, QLD 4878, Australia)
    Molecular phylogenetics and evolution v.118 ,pp. 32 - 46 , 2018 , 1055-7903 ,

    초록

    Abstract The Australian mesic biome spans c. 33° of latitude along Australia’s east coast and ranges and is dissected by historical and contemporary biogeographical barriers. To investigate the impact of these barriers on evolutionary diversification and to predict the impact of future climate change on the distribution of species and genetic diversity within this biome, we inferred phylogenetic relationships within the Dendrobium speciosum complex (Orchidaceae) across its distribution and undertook environmental niche modelling (ENM) under past, contemporary and projected future climates. Neighbor Joining tree inference, NeighborNet and STRUCTURE analyses of Amplified Fragment Length Polymorphism (AFLP) profiles for D. speciosum sampled from across its distribution showed that the complex consists of two highly supported main groups that are geographically separated by the St. Lawrence gap, an area of dry sclerophyll forest and woodland. The presence of several highly admixed individuals identified by the STRUCTURE analysis provided evidence of genetic exchange between the two groups across this gap. Whereas previous treatments have recognised between one to eleven species, the molecular results support the taxonomic treatment of the complex as a single species with two subspecies. The ENM analysis supported the hypothesis that lineage divergence within the complex was driven by past climatic changes. The St. Lawrence gap represented a stronger biogeographic barrier for the D. speciosum complex during the cool and dry glacial climatic conditions of the Pleistocene than under today’s interglacial conditions. Shallow genetic divergence was found within the two lineages, which mainly corresponded to three other biogeographic barriers: the Black Mountain Corridor, Glass House Mountains and the Hunter Valley. Our ENM analyses provide further support for the hypothesis that biogeographic barriers along Australia’s east coast were somewhat permeable to genetic exchange due to past episodic range expansions and contractions caused by climatic change resulting in recurrent contact between previously isolated populations. An overall southward shift in the distribution of the complex under future climate scenarios was predicted, with the strongest effects on the northern lineage. This study contributes to our understanding of the factors shaping biodiversity patterns in Australia’s mesic biome. Highlights The complex consists of two main genetic lineages separated by the St. Lawrence gap. Genetically admixed individuals indicate gene flow across the St. Lawrence gap. A taxonomy consisting of one species and two subspecies is supported. Divergence within the complex was driven by past climatic conditions. Under future climates the most extensive declines are expected for the northern lineage. Graphical abstract [DISPLAY OMISSION]

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  7. [해외논문]   Independent pseudogenization of CYP2J19 in penguins, owls and kiwis implicates gene in red carotenoid synthesis   SCI SCIE

    Emerling, Christopher A.
    Molecular phylogenetics and evolution v.118 ,pp. 47 - 53 , 2018 , 1055-7903 ,

    초록

    Abstract Carotenoids have important roles in bird behavior, including pigmentation for sexual signaling and improving color vision via retinal oil droplets. Yellow carotenoids are diet-derived, but red carotenoids (ketocarotenoids) are typically synthesized from yellow precursors via a carotenoid ketolase. Recent research on passerines has provided evidence that a cytochrome p450 enzyme, CYP2J19, is responsible for this reaction, though it is unclear if this function is phylogenetically restricted. Here I provide evidence that CYP2J19 is the carotenoid ketolase common to Aves using the genomes of 65 birds and the retinal transcriptomes of 15 avian taxa. CYP2J19 is functionally intact and robustly transcribed in all taxa except for several species adapted to foraging in dim light conditions. Two penguins, an owl and a kiwi show evidence of genetic lesions and relaxed selection in their genomic copy of CYP2J19 , and six owls show evidence of marked reduction in CYP2J19 retinal transcription compared to nine diurnal avian taxa. Furthermore, one of the owls appears to transcribe a CYP2J19 pseudogene. Notably, none of these taxa are known to use red carotenoids for sexual signaling and several species of owls and penguins represent the only birds known to completely lack red retinal oil droplets. The remaining avian taxa belong to groups known to possess red oil droplets, are known or expected to deposit red carotenoids in skin and/or plumage, and/or frequently forage in bright light. The loss and reduced expression of CYP2J19 is likely an adaptation to maximize retinal sensitivity, given that oil droplets reduce the amount of light available to the retina. Highlights Recent research implicated CYP2J19 as red carotenoid locus in passerines. Penguins, owls and kiwis have inactivated CYP2J19. Owl retinas transcribe CYP2J19 at lower levels than diurnal birds. Penguins and owls are only birds known to lack red carotenoids. CYP2J19 loss/reduction likely tied to dim light adaptation. Graphical abstract [DISPLAY OMISSION]

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  8. [해외논문]   Evolution of the alternative AQP2 gene: Acquisition of a novel protein-coding sequence in dolphins   SCI SCIE

    Kishida, Takushi (Wildlife Research Center, Kyoto University, 2-24 Tanaka Sekiden-cho, Sakyo, Kyoto 606-8203, Japan ) , Suzuki, Miwa (Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan ) , Takayama, Asuka (Department of Marine Science and Resources, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan)
    Molecular phylogenetics and evolution v.118 ,pp. 54 - 57 , 2018 , 1055-7903 ,

    초록

    Abstract Taxon-specific de novo protein-coding sequences are thought to be important for taxon-specific environmental adaptation. A recent study revealed that bottlenose dolphins acquired a novel isoform of aquaporin 2 generated by alternative splicing (alternative AQP2), which helps dolphins to live in hyperosmotic seawater. The AQP2 gene consists of four exons, but the alternative AQP2 gene lacks the fourth exon and instead has a longer third exon that includes the original third exon and a part of the original third intron. Here, we show that the latter half of the third exon of the alternative AQP2 arose from a non-protein-coding sequence. Intact ORF of this de novo sequence is shared not by all cetaceans, but only by delphinoids. However, this sequence is conservative in all modern cetaceans, implying that this de novo sequence potentially plays important roles for marine adaptation in cetaceans. Highlights Dolphins acquired a de novo protein-coding sequence. Intact ORF of the newly acquired alternative AQP2 is shared only by delphinoids. But the alternative AQP2 sequence is conserved even in non-delphinoid cetaceans. The ‘RNA-first’ model is preferred compared to the ‘ORF-first’ model. This study sheds first light on the evolution of the seawater adaptation in whales. Graphical abstract [DISPLAY OMISSION]

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  9. [해외논문]   Protein backbone flexibility pattern is evolutionarily conserved in the Flaviviridae family: A case of NS3 protease in Flavivirus and Hepacivirus   SCI SCIE

    Palanisamy, Navaneethan (Molecular and Cellular Engineering Group, BioQuant, University of Heidelberg, Heidelberg, Germany ) , Akaberi, Dario (Section of Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden ) , Lennerstrand, Johan (Section of Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden)
    Molecular phylogenetics and evolution v.118 ,pp. 58 - 63 , 2018 , 1055-7903 ,

    초록

    Abstract Viruses belonging to the Flaviviridae family have been an important health concern for humans, animals and birds alike. No specific treatment is available yet for many of the viral infections caused by the members of this family. Lack of specific drugs against these viruses is mainly due to lack of protein structure information. It has been known that protein backbone fluctuation pattern is highly conserved in protein pairs with similar folds, in spite of the lack of sequence similarity. We hypothesized that this concept should also hold true for proteins (especially enzymes) of viruses included in different genera of the Flaviviridae family, as we know that the sequence similarity between them is low. Using available NS3 protease crystal structures of the Flaviviridae family, our preliminary results have shown that the Cα (i.e. backbone) fluctuation patterns are highly similar between Flaviviruses and a Hepacivirus (i.e. hepatitis C virus, HCV). This has to be validated further experimentally. Highlights Cα fluctuation pattern conservation in enzymes of the Flaviviridae family is proposed. Cα fluctuation pattern of NS3 protease is similar within Flaviviruses. Cα fluctuation pattern of NS5 methyltransferase is similar within Flaviviruses. Cα fluctuation pattern of NS3 protease is conserved between Flaviviruses and HCV. Graphical abstract [DISPLAY OMISSION]

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

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  10. [해외논문]   The role of climatic cycles and trans-Saharan migration corridors in species diversification: Biogeography of Psammophis schokari group in North Africa   SCI SCIE

    Gonç (CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal ) , alves, Duarte Vasconcelos (CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal ) , Martí (CNRS-UMR 5175, Centre d'Ecologie Fonctionnelle et Evolutive, 1919 route de Mende, F-34293 Montpellier-Cedex 5, France ) , nez-Freirí (EPHE, PSL Research University, CNRS, UM, SupAgro, IND, INRA, UMR 5175 CEFE, 34293 Montpellier, France ) , a, Fernando (Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, E-08003 Barcelona, Spain ) , Crochet, Pierre-André (CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal) , , Geniez, Philippe , Carranza, Salvador , Brito, José , Carlos
    Molecular phylogenetics and evolution v.118 ,pp. 64 - 74 , 2018 , 1055-7903 ,

    초록

    Abstract Highlands, hydrographic systems and coastal areas have been hypothesised to form corridors across the hyperarid Sahara desert in North Africa, allowing dispersal and gene flow for non-xeric species. Here we aim to provide a genetic test for the trans-Saharan corridor model, and predict the location and stability of ecological-corridors, by combining phylogeography and palaeoclimatic modelling. The model was the Psammophis schokari (Schokari sand racer) group, fast-moving and widely distributed generalist colubrids occurring mostly in arid and semiarid scrublands. We combined dated phylogenies of mitochondrial and nuclear markers with palaeoclimatic modelling. For the phylogeographic analysis, we used 75 samples of P. schokari and P. aegyptius , and Bayesian and Maximum-Likelihood methods. For the ecological models, we used Maxent over the distribution of P. schokari and West African lineages. Models were projected to past conditions (mid Holocene, Last Glacial Maximum and Last Inter-Glacial) to infer climatic stable areas. Climatic stability was predicted to be mostly restricted to coastal areas and not spatially continuous. A putative temporary trans-Saharan corridor was identified in Eastern Sahara, with a more stable one along the Atlantic coast. Six parapatric lineages were identified within P. schokari , four occurring in North Africa. These likely diverged during the Pliocene. The Tamanraset River might have been a vicariant agent. African lineages may have experienced further subsequent diversification during the late Pleistocene. The main P. schokari refugia were probably located along the northern margins of the Sahara, allowing its North-to-South colonization. Trans-Saharan corridors seem to have played a role in P. schokari biogeography, allowing colonization of central Saharan mountains and Sahel. Some might have worked as refugia , and even the most stable corridors may have sections working as filters, depending on each climatic phase. We expect the use of trans-Saharan corridors to decrease for more mesic species or with less dispersal capabilities. Highlights Testing trans-Saharan mesic corridors model and predict their location and stability. We combined phylogeography and palaeoclimate modelling of P. schokari in North Africa. Atlantic corridor predicted to be permanent, others sporadically active. Six parapatric lineages identified, four in North Africa. Divergence in Pliocene. Lineages divergence attributed to climate cycles and possibly Tamanrasset palaeo-river basin. Graphical abstract [DISPLAY OMISSION]

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