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  1. Article ; Online: Median-joining network analysis of SARS-CoV-2 genomes is neither phylogenetic nor evolutionary.

    Sánchez-Pacheco, Santiago J / Kong, Sungsik / Pulido-Santacruz, Paola / Murphy, Robert W / Kubatko, Laura

    Proceedings of the National Academy of Sciences of the United States of America

    2020  Volume 117, Issue 23, Page(s) 12518–12519

    MeSH term(s) Betacoronavirus ; COVID-19 ; Coronavirus Infections ; Humans ; Pandemics ; Phylogeny ; Pneumonia, Viral ; Severe acute respiratory syndrome-related coronavirus ; SARS-CoV-2
    Keywords covid19
    Language English
    Publishing date 2020-05-07
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2007062117
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    Zs.A 1148: Show issues Location:
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  2. Article ; Online: On the use of median-joining networks in evolutionary biology.

    Kong, Sungsik / Sánchez-Pacheco, Santiago J / Murphy, Robert W

    Cladistics : the international journal of the Willi Hennig Society

    2015  Volume 32, Issue 6, Page(s) 691–699

    Abstract: Median-joining (MJ) was proposed as a method for phylogeographical analysis and is enjoying increasing popularity. Herein, we evaluate the efficacy of the approach as originally intended. We show that median-joining networks (MJNs) are theoretically ... ...

    Abstract Median-joining (MJ) was proposed as a method for phylogeographical analysis and is enjoying increasing popularity. Herein, we evaluate the efficacy of the approach as originally intended. We show that median-joining networks (MJNs) are theoretically untenable for evolutionary inference, and that confusion has afflicted their use for over 15 years. The approach has two obvious shortcomings: its reliance on distance-based phenetics (overall similarity instead of character transformations) and the lack of rooting (no direction or history). Given that evolution involves both change and time, and the absence of rooting removes time (ancestor-descendant relationships) from the equation, the approach cannot yield defensible evolutionary interpretations. We also examine the impact of MJ analyses on evolutionary biology via an analysis of citations and conclude that the spread of MJNs through the literature is difficult to explain, especially given the availability of character-based analyses.
    Language English
    Publishing date 2015-12-19
    Publishing country United States
    Document type Letter
    ZDB-ID 1462608-1
    ISSN 1096-0031 ; 0748-3007
    ISSN (online) 1096-0031
    ISSN 0748-3007
    DOI 10.1111/cla.12147
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  3. Article: Median-joining network analysis of SARS-CoV-2 genomes is neither phylogenetic nor evolutionary

    Sánchez-Pacheco, Santiago J / Kong, Sungsik / Pulido-Santacruz, Paola / Murphy, Robert W / Kubatko, Laura

    Proc Natl Acad Sci U S A

    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #32381733
    Database COVID19

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  4. Article ; Online: Undermining Colombia's peace and environment.

    Salazar, Alejandro / Salazar, Juan F / Sánchez-Pacheco, Santiago J / Sanchez, Adriana / Lasso, Eloisa / Villegas, Juan C / Arias, Paola A / Poveda, Germán / Rendón, Ángela M / Uribe, Maria R / Pérez, Juan C / Dukes, Jeffrey S

    Science (New York, N.Y.)

    2021  Volume 373, Issue 6552, Page(s) 289–290

    Language English
    Publishing date 2021-07-15
    Publishing country United States
    Document type Letter
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.abj8367
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    Zs.A 27: Show issues Location:
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  5. Article: Formal recognition of the species of

    Sánchez-Pacheco, Santiago J / Nunes, Pedro M Sales / Marques-Souza, Sergio / Rodrigues, Miguel T / Murphy, Robert W

    ZooKeys

    2017  , Issue 691, Page(s) 149–162

    Abstract: ... ...

    Abstract Oreosaurus
    Language English
    Publishing date 2017-08-17
    Publishing country Bulgaria
    Document type Journal Article
    ZDB-ID 2445640-8
    ISSN 1313-2970 ; 1313-2989
    ISSN (online) 1313-2970
    ISSN 1313-2989
    DOI 10.3897/zookeys.691.13595
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Extreme mito-nuclear discordance in a peninsular lizard: the role of drift, selection, and climate.

    Bernardo, Pedro Henrique / Sánchez-Ramírez, Santiago / Sánchez-Pacheco, Santiago J / Álvarez-Castañeda, Sergio Ticul / Aguilera-Miller, Eduardo Felipe / Mendez-de la Cruz, Fausto Roberto / Murphy, Robert W

    Heredity

    2019  Volume 123, Issue 3, Page(s) 359–370

    Abstract: Nuclear and mitochondrial genomes coexist within cells but are subject to different tempos and modes of evolution. Evolutionary forces such as drift, mutation, selection, and migration are expected to play fundamental roles in the origin and maintenance ... ...

    Abstract Nuclear and mitochondrial genomes coexist within cells but are subject to different tempos and modes of evolution. Evolutionary forces such as drift, mutation, selection, and migration are expected to play fundamental roles in the origin and maintenance of diverged populations; however, divergence may lag between genomes subject to different modes of inheritance and functional specialization. Herein, we explore whole mitochondrial genome data and thousands of nuclear single nucleotide polymorphisms to evidence extreme mito-nuclear discordance in the small black-tailed brush lizard, Urosaurus nigricaudus, of the Peninsula of Baja California, Mexico and southern California, USA, and discuss potential drivers. Results show three deeply divergent mitochondrial lineages dating back to the later Miocene (ca. 5.5 Ma) and Pliocene (ca. 2.8 Ma) that likely followed geographic isolation due to trans-peninsular seaways. This contrasts with very low levels of genetic differentiation in nuclear loci (F
    MeSH term(s) Animal Migration ; Animals ; California ; Cell Nucleus/genetics ; Female ; Gene Flow ; Genetic Drift ; Genetic Variation ; Genome, Mitochondrial ; Inheritance Patterns ; Lizards/genetics ; Male ; Mexico ; Mitochondria/genetics ; Polymorphism, Single Nucleotide ; Reproductive Isolation ; Selection, Genetic
    Language English
    Publishing date 2019-03-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2423-5
    ISSN 1365-2540 ; 0018-067X
    ISSN (online) 1365-2540
    ISSN 0018-067X
    DOI 10.1038/s41437-019-0204-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Ub I Zs.154: Show issues Location:
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  7. Article: Formal recognition of the species of Oreosaurus (Reptilia, Squamata, Gymnophthalmidae) from the Sierra Nevada de Santa Marta, Colombia

    Sánchez-Pacheco, Santiago J / Nunes, Pedro M. Sales / Marques-Souza, Sergio / Rodrigues, Miguel T / Murphy, Robert W

    ZooKeys. 2017 Aug. 17, v. 691

    2017  

    Abstract: Oreosaurus is one of the two genera extracted from the former Riama sensu lato, which was recently recognized as polyphyletic. Oreosaurus is a small clade (five named and two undescribed species) of montane gymnophthalmid lizards and exhibits an ... ...

    Abstract Oreosaurus is one of the two genera extracted from the former Riama sensu lato, which was recently recognized as polyphyletic. Oreosaurus is a small clade (five named and two undescribed species) of montane gymnophthalmid lizards and exhibits an exceptional distributional pattern. Its nominal and undescribed species are discontinuously distributed on the Cordillera de la Costa of Venezuela, the tepuis from the Chimantá massif in Venezuela, the highlands of the island of Trinidad, and the Sierra Nevada de Santa Marta in Colombia (SNSM). Herein, we describe the species of Oreosaurus that is endemic to the SNSM. Historically, this species associates with two names that are currently nomina nuda: Proctoporus serranus and P. specularis . Formal nomenclatural recognition of Oreosaurus serranus sp. n. renders specularis a permanently unavailable name for this taxon. Oreosaurus serranus sp. n. is the sister of all remaining congeners, and differs primarily from them in having only one pair of genial scales, as well as a unique pattern of scutellation. We provide an identification key to the species of Oreosaurus.
    Keywords Serranus ; Squamata ; polyphyly ; taxonomic keys ; Colombia ; Trinidad and Tobago ; Venezuela
    Language English
    Dates of publication 2017-0817
    Size p. 149-162.
    Publishing place Pensoft Publishers
    Document type Article
    Note NAL-light
    ZDB-ID 2445640-8
    ISSN 1313-2970 ; 1313-2989
    ISSN (online) 1313-2970
    ISSN 1313-2989
    DOI 10.3897/zookeys.691.13595
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: The advertisement calls of three Eleutherodactylus species from Hispaniola (Anura: Eleutherodactylidae)

    Galvis, Pedro A. / Caorsi, Valentina Zaffaroni / Sánchez-Pacheco, Santiago J. / Rada, Marco

    Bioacoustics. 2018 Jan. 02, v. 27, no. 1 p.1-12

    2018  

    Abstract: We provide detailed descriptions of the poorly known advertisement calls of Eleutherodactylus abbotti, E. flavescens and E. inoptatus, three rain frogs endemic to the Caribbean island of Hispaniola. We compare these three advertisement calls to those of ... ...

    Abstract We provide detailed descriptions of the poorly known advertisement calls of Eleutherodactylus abbotti, E. flavescens and E. inoptatus, three rain frogs endemic to the Caribbean island of Hispaniola. We compare these three advertisement calls to those of closely related and/or geographically proximate Eleutherodactylus species. The call of E. abbotti lasts 0.5–6 s and consists of four notes that differ in amplitude and duration, with a mean dominant frequency of 4527 Hz. In turn, the call of E. flavescens, endemic to the Dominican Republic, lasts 0.02–0.09 s and consists of two different notes with dominant frequencies of 2288 and 3025 Hz. In contrast, the call of E. inoptatus lasts 0.25–0.39 s and is composed of a single multi-pulsed note with two harmonics, the first one with a dominant frequency of 660 Hz and the second one with a dominant frequency of 1220 Hz. These congeneric species occur sympatrically over large areas below 1000 m elevation and are commonly encountered together, which suggests that, in addition to interspecific variation (e.g. body size), the remarkable differences in their calls (e.g. dominant frequency) may be due to partitioning of the acoustic environment.
    Keywords Eleutherodactylus ; bioacoustics ; body size ; interspecific variation ; rain ; Caribbean ; Dominican Republic ; Hispaniola ; Haiti ; Eleutherodactylus abbotti ; E. flavescens ; E. inoptatus ; rain frogs ; vocalizations
    Language English
    Dates of publication 2018-0102
    Size p. 1-12.
    Publishing place Taylor & Francis
    Document type Article ; Online
    Note NAL-light
    ISSN 2165-0586
    DOI 10.1080/09524622.2016.1260053
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Formal recognition of the species of Oreosaurus (Reptilia, Squamata, Gymnophthalmidae) from the Sierra Nevada de Santa Marta, Colombia

    Santiago J. Sánchez-Pacheco / Pedro M. Sales Nunes / Miguel T. Rodrigues / Robert W. Murphy

    ZooKeys, Vol 691, Iss , Pp 149-

    2017  Volume 162

    Abstract: Oreosaurus is one of the two genera extracted from the former Riama sensu lato, which was recently recognized as polyphyletic. Oreosaurus is a small clade (five named and two undescribed species) of montane gymnophthalmid lizards and exhibits an ... ...

    Abstract Oreosaurus is one of the two genera extracted from the former Riama sensu lato, which was recently recognized as polyphyletic. Oreosaurus is a small clade (five named and two undescribed species) of montane gymnophthalmid lizards and exhibits an exceptional distributional pattern. Its nominal and undescribed species are discontinuously distributed on the Cordillera de la Costa of Venezuela, the tepuis from the Chimantá massif in Venezuela, the highlands of the island of Trinidad, and the Sierra Nevada de Santa Marta in Colombia (SNSM). Herein, we describe the species of Oreosaurus that is endemic to the SNSM. Historically, this species associates with two names that are currently nomina nuda: Proctoporus serranus and P. specularis. Formal nomenclatural recognition of Oreosaurus serranus sp. n. renders specularis a permanently unavailable name for this taxon. Oreosaurus serranus sp. n. is the sister of all remaining congeners, and differs primarily from them in having only one pair of genial scales, as well as a unique pattern of scutellation. We provide an identification key to the species of Oreosaurus.
    Keywords Zoology ; QL1-991
    Subject code 590
    Language English
    Publishing date 2017-08-01T00:00:00Z
    Publisher Pensoft Publishers
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: The advertisement calls of three hylid frogs from Hispaniola

    Galvis, Pedro A / Caorsi, Valentina Zaffaroni / Sánchez-Pacheco, Santiago J / Rada, Marco

    Bioacoustics. 2016 Jan. 2, v. 25, no. 1

    2016  

    Abstract: In this study, we provide detailed descriptions of the previously unknown advertisement calls of Osteopilus dominicensis and Hypsiboas heilprini, as well as a complete redescription of that of O. pulchrilineatus, three of the four hylid frogs known from ... ...

    Abstract In this study, we provide detailed descriptions of the previously unknown advertisement calls of Osteopilus dominicensis and Hypsiboas heilprini, as well as a complete redescription of that of O. pulchrilineatus, three of the four hylid frogs known from the Caribbean island of Hispaniola. The call of O. dominicensis is composed of a single multi-pulsed note with a mean dominant frequency of 2058 Hz. In contrast, the call of O. pulchrilineatus consists of two different pulsed notes (the second repeated many times in one call) with a mean dominant frequency of 2950 and 2060 Hz, respectively. The call of H. heilprini, in turn, is a trill consisting of multi-pulsed notes (emitted in a consecutive series) with a mean dominant frequency of 1738 Hz. We compare these three calls to those of closely related species.
    Keywords Hypsiboas ; bioacoustics ; frequency ; frogs ; redescriptions ; Caribbean ; Hispaniola
    Language English
    Dates of publication 2016-0102
    Size p. 89-97.
    Publishing place Taylor & Francis
    Document type Article
    Note NAL-light
    ISSN 2165-0586
    DOI 10.1080/09524622.2015.1116410
    Database NAL-Catalogue (AGRICOLA)

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