<?xml version="1.0" encoding="ISO-8859-1"?><article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<front>
<journal-meta>
<journal-id>2007-3364</journal-id>
<journal-title><![CDATA[Therya]]></journal-title>
<abbrev-journal-title><![CDATA[Therya]]></abbrev-journal-title>
<issn>2007-3364</issn>
<publisher>
<publisher-name><![CDATA[Asociación Mexicana de Mastozoología A.C.]]></publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id>S2007-33642023000100181</article-id>
<article-id pub-id-type="doi">10.12933/therya-23-2243</article-id>
<title-group>
<article-title xml:lang="en"><![CDATA[An 1896 specimen helps clarify the phylogenetic placement of the Mexican endemic Hooper&#8217;s deer mouse]]></article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname><![CDATA[Castañeda-Rico]]></surname>
<given-names><![CDATA[Susette]]></given-names>
</name>
<xref ref-type="aff" rid="Aff"/>
<xref ref-type="aff" rid="Aaf"/>
<xref ref-type="aff" rid="A a"/>
<xref ref-type="aff" rid="A3"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname><![CDATA[Edwards]]></surname>
<given-names><![CDATA[Cody W.]]></given-names>
</name>
<xref ref-type="aff" rid="Aff"/>
<xref ref-type="aff" rid="Aaf"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname><![CDATA[Hawkins]]></surname>
<given-names><![CDATA[Melissa T. R.]]></given-names>
</name>
<xref ref-type="aff" rid="Aff"/>
</contrib>
<contrib contrib-type="author">
<name>
<surname><![CDATA[Maldonado]]></surname>
<given-names><![CDATA[Jesús E.]]></given-names>
</name>
<xref ref-type="aff" rid="Aff"/>
<xref ref-type="aff" rid="Aaf"/>
<xref ref-type="aff" rid="A a"/>
<xref ref-type="aff" rid="A3"/>
</contrib>
</contrib-group>
<aff id="Af1">
<institution><![CDATA[,Smithsonian-Mason School of Conservation  ]]></institution>
<addr-line><![CDATA[ ]]></addr-line>
<country>U.S.A.</country>
</aff>
<aff id="Af2">
<institution><![CDATA[,Smithsonian National Zoo and Conservation Biology Institute Center for Conservation Genomics ]]></institution>
<addr-line><![CDATA[Washington DC ]]></addr-line>
<country>U.S.A.</country>
</aff>
<aff id="Af3">
<institution><![CDATA[,George Mason University Department of Biology ]]></institution>
<addr-line><![CDATA[Fairfax ]]></addr-line>
<country>USA</country>
</aff>
<aff id="Af4">
<institution><![CDATA[,National Museum of Natural History Department of Vertebrate Zoology Division of Mammals]]></institution>
<addr-line><![CDATA[Washington DC ]]></addr-line>
<country>U.S.A.</country>
</aff>
<pub-date pub-type="pub">
<day>00</day>
<month>00</month>
<year>2023</year>
</pub-date>
<pub-date pub-type="epub">
<day>00</day>
<month>00</month>
<year>2023</year>
</pub-date>
<volume>14</volume>
<numero>1</numero>
<fpage>181</fpage>
<lpage>195</lpage>
<copyright-statement/>
<copyright-year/>
<self-uri xlink:href="http://www.scielo.org.mx/scielo.php?script=sci_arttext&amp;pid=S2007-33642023000100181&amp;lng=en&amp;nrm=iso"></self-uri><self-uri xlink:href="http://www.scielo.org.mx/scielo.php?script=sci_abstract&amp;pid=S2007-33642023000100181&amp;lng=en&amp;nrm=iso"></self-uri><self-uri xlink:href="http://www.scielo.org.mx/scielo.php?script=sci_pdf&amp;pid=S2007-33642023000100181&amp;lng=en&amp;nrm=iso"></self-uri><abstract abstract-type="short" xml:lang="en"><p><![CDATA[Abstract Hooper&#8217;s deer mouse, Peromyscus hooperi, is the sole member of the Peromyscus hooperi species group. This species is endemic to México where it is restricted to the grassland transition zone in the states of Coahuila, Zacatecas, and San Luis Potosí. Previous studies using mitochondrial and nuclear genes (Cytb, Adh1-I2, Fgb-I7 and Rbp3) did not resolve the phylogenetic relationships of this relatively poorly known species. It was hypothesized that P. hooperi is sister to P. crinitus, and these two taxa are related to P. melanotis, P. polionotus, P. maniculatus, P. keeni, P. leucopus, P. gossypinus, P. eremicus, P. californicus, and Osgoodomys banderanus. Based on morphological characters, karyotypes, and allozymes, P. hooperi does not align with either subgenera Haplomylomys or Peromyscus. However, its unique characteristics (e. g., phallus, karyotype) have been recognized, and therefore it has been retained as its own species group. To better resolve the phylogenetic placement of P. hooperi, we performed target-enrichment and high-throughput sequencing and obtained several thousand nuclear ultraconserved elements and a complete mitogenome from a specimen collected in 1896 by Nelson and Goldman in Coahuila, México. We compared these data with 21 other species of neotomines using genome-wide data. Contrary to previous studies, we found high nodal support for the placement of P. hooperi as sister to a clade that includes Podomys floridanus, Neotomodon alstoni, Habromys simulatus, H. ixtlani, Peromyscus mexicanus, P. megalops, P. melanophrys, P. perfulvus, P. aztecus, P. attwateri, P. pectoralis, and P. boylii. We dated a Pliocene divergence of P. hooperi from its sister group at approximately 3.98 mya, and after the split of P. crinitus at ca. 4.31 mya from other peromyscines. We demonstrated that genome-wide data improve the phylogenetic signal, independently of taxon sampling, for a phylogenetically problematic species such as P. hooperi. We recommend that future genomic studies expand taxon sampling, including members of the subgenus Haplomylomys, to confirm the phylogenetic relationships of P. hooperi and the genetic status of its populations.]]></p></abstract>
<abstract abstract-type="short" xml:lang="es"><p><![CDATA[Resumen El ratón de Hooper Peromyscus hooperi, es el único miembro del grupo de especies que lleva su mismo nombre. Es una especie endémica de México que se encuentra restringida a las zonas de transición de pastizales en los estados de Coahuila, Zacatecas y San Luis Potosí. Estudios previos en los que se han analizado genes mitocondriales y nucleares (Cytb, Adh1-I2, Fgb-I7 y Rbp3) no han podido resolver las relaciones filogenéticas de esta especie poco conocida. Sin embargo, se ha sugerido que P. hooperi podría ser la especie hermana de P. crinitus, y estar cercanamente relacionada con P. melanotis, P. polionotus, P. maniculatus, P. keeni, P. leucopus, P. gossypinus, P. eremicus, P. californicus y Osgoodomys banderanus. Con base en datos morfológicos, cariotipos y aloenzimas, no se ha podido determinar si esta especie se encuentra más estrechamente relacionada con el subgénero Haplomylomys o Peromyscus. Sin embargo, las características únicas de P. hooperi (e. g., falo, cariotipo) han sido reconocidas, por lo que se ha mantenido en su propio grupo de especies. Con el objetivo de proveer nueva evidencia sobre la posición filogenética de P. hooperi, utilizamos el método de captura por hibridación y secuenciación masiva para obtener miles de elementos ultraconservados y el genoma mitocondrial de un ejemplar colectado en 1896 por Nelson y Goldman en Coahuila, México. Además, analizamos datos genómicos de 21 especies de neotominos. Contrario a estudios previos, encontramos altos valores de soporte en el nodo que posiciona a P. hooperi como la especie hermana del clado que incluye a Podomys floridanus, Neotomodon alstoni, Habromys simulatus, H. ixtlani, Peromyscus mexicanus, P. megalops, P. melanophrys, P. perfulvus, P. aztecus, P. attwateri, P. pectoralis y P. boylii. Datamos la divergencia de P. hooperi de su grupo hermano hace aproximadamente 3.98 millones de años, después de la divergencia de P. crinitus y de otros peromiscinos hace aproximadamente 4.31 millones de años, ambos eventos durante el Plioceno. Nuestro estudio es un claro ejemplo de que analizar datos a nivel del genoma mejoran la señal filogenética, independientemente del número de taxones, para especies cuyas relaciones filogenéticas son conflictivas o se encuentran poco resueltas como en el caso de P. hooperi. Sin embargo, recomendamos que futuros estudios genómicos incluyan un muestreo taxonómico más amplio, sobre todo de miembros del subgénero Haplomylomys, para confirmar las relaciones filogenéticas de P. hooperi y el estatus genético de sus poblaciones.]]></p></abstract>
<kwd-group>
<kwd lng="en"><![CDATA[Historical DNA]]></kwd>
<kwd lng="en"><![CDATA[genomics]]></kwd>
<kwd lng="en"><![CDATA[mitogenomes]]></kwd>
<kwd lng="en"><![CDATA[museum specimens]]></kwd>
<kwd lng="en"><![CDATA[Peromyscus, Pliocene-Pleistocene]]></kwd>
<kwd lng="en"><![CDATA[ultraconserved elements]]></kwd>
</kwd-group>
</article-meta>
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