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Abstract
Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.
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Craniodental Morphology and Phylogeny of Marsupials. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2022. [DOI: 10.1206/0003-0090.457.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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An Annotated Checklist of Recent Opossums (Mammalia: Didelphidae). BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2022. [DOI: 10.1206/0003-0090.455.1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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A Revision of the Didelphid Marsupial Genus Marmosa Part 4. Species of the Alstoni Group (Subgenus Micoureus). AMERICAN MUSEUM NOVITATES 2021. [DOI: 10.1206/3983.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Mammalian Diversity and Matses Ethnomammalogy in Amazonian Peru Part 4: Bats. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2021. [DOI: 10.1206/0003-0090.451.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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A Revision of the Didelphid Marsupial Genus Marmosa Part 3. A New Species from Western Amazonia, with Redescriptions of M. perplexa Anthony, 1922, and M. germana Thomas, 1904. AMERICAN MUSEUM NOVITATES 2021. [DOI: 10.1206/3969.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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On the Identity of Victoria's Mouse Opossum, Marmosa regina Thomas, 1898. AMERICAN MUSEUM NOVITATES 2020. [DOI: 10.1206/3960.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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A Revision of Philander (Marsupialia: Didelphidae), Part 2: Phylogenetic Relationships and Morphological Diagnosis of P. nigratus Thomas, 1923. AMERICAN MUSEUM NOVITATES 2020. [DOI: 10.1206/3955.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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A Revision of the Didelphid Marsupial Genus MarmosaPart 2. Species of the Rapposa Group (Subgenus Micoureus). BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2020. [DOI: 10.1206/0003-0090.439.1.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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DNA Sequence Data from the Holotype of Marmosa elegans coquimbensis Tate, 1931 (Mammalia: Didelphidae) Resolve its Disputed Relationships. AMERICAN MUSEUM NOVITATES 2020. [DOI: 10.1206/3946.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Minimal genetic divergence among South American samples of the water opossum Chironectes minimus: evidence for transcontinental gene flow? MAMMALIA 2019. [DOI: 10.1515/mammalia-2018-0073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Cytochrome b sequences from South American specimens of the water opossum Chironectes minimus exhibit uncorrected pairwise differences of 0.6% or less among samples collected thousands of kilometers apart (in Guyana, Bolivia and southeastern Brazil). Despite published evidence of population divergence from recent analyses of craniodental morphology, our results suggest extensive gene flow or recent range expansion across the South American landscapes currently occupied by this seldom-collected species.
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A Revision ofPhilander(Marsupialia: Didelphidae), Part 1:P. quica,P. canus, and a New Species from Amazonia. AMERICAN MUSEUM NOVITATES 2018. [DOI: 10.1206/3891.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Mammalian Diversity and Matses Ethnomammalogy in Amazonian Peru Part 2: Xenarthra, Carnivora, Perissodactyla, Artiodactyla, and Sirenia. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2017. [DOI: 10.1206/00030090-417.1.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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A New Species of Nectar-Feeding Bat of the GenusHsunycteris(Phyllostomidae: Lonchophyllinae) from Northeastern Peru. AMERICAN MUSEUM NOVITATES 2017. [DOI: 10.1206/3881.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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MORPHOLOGICAL EVOLUTION IN MUROID RODENTS I. CONSERVATIVE PATTERNS OF CRANIOMETRIC COVARIANCE AND THEIR ONTOGENETIC BASIS IN THE NEOTROPICAL GENUS ZYGODONTOMYS. Evolution 2017; 44:1568-1587. [PMID: 28564313 DOI: 10.1111/j.1558-5646.1990.tb03847.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/1989] [Accepted: 12/22/1989] [Indexed: 11/30/2022]
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MORPHOLOGICAL EVOLUTION IN MUROID RODENTS II. CRANIOMETRIC FACTOR DIVERGENCE IN SEVEN NEOTROPICAL GENERA, WITH EXPERIMENTAL RESULTS FROM ZYGODONTOMYS. Evolution 2017; 46:1918-1934. [DOI: 10.1111/j.1558-5646.1992.tb01178.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/1991] [Accepted: 04/02/1992] [Indexed: 11/27/2022]
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A New Species ofMonodelphis(Didelphimorphia: Didelphidae) from the Brazilian Amazon. AMERICAN MUSEUM NOVITATES 2017. [DOI: 10.1206/3872.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Roosting Ecology of Amazonian Bats: Evidence for Guild Structure in Hyperdiverse Mammalian Communities. AMERICAN MUSEUM NOVITATES 2016. [DOI: 10.1206/3870.1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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A Revised Subgeneric Classification of Short-Tailed Opossums (Didelphidae:Monodelphis). AMERICAN MUSEUM NOVITATES 2016. [DOI: 10.1206/3868.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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A Revision of the Didelphid Marsupial Genus Marmosops, Part 1. Species of the Subgenus Sciophanes. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2016. [DOI: 10.1206/0003-0090-402.1.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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DNA sequencing reveals unexpected Recent diversity and an ancient dichotomy in the American marsupial genusMarmosops(Didelphidae: Thylamyini). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12343] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Phylogenetic relationships of
Chacodelphys
(Marsupialia: Didelphidae: Didelphinae) based on “ancient” DNA sequences. J Mammal 2015. [DOI: 10.1093/jmammal/gyv197] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Morphological character data are inadequate to resolve the evolutionary relationships of the didelphid genus Chacodelphys , which previous phylogenetic analyses have alternatively suggested might be the sister taxon of Lestodelphys and Thylamys (tribe Thylamyini) or of Monodelphis (tribe Marmosini) in the subfamily Didelphinae. Because fresh material of Chacodelphys is unavailable, we extracted DNA from microscopic fragments of soft tissue adhering to the 95-year-old holotype skull of C. formosa. Phylogenetic analyses of the resulting sequence data convincingly resolve Chacodelphys as the sister taxon of Cryptonanus , a genus with which it had not previously been thought to be closely related. This novel clade ( Chacodelphys + Cryptonanus ) belongs to an unnamed thylamyine lineage with Gracilinanus and Lestodelphys + Thylamys , but relationships among these taxa remain to be convincingly resolved.
Los análisis basados en caracteres morfológicos han sido inadecuados para resolver las relaciones evolutivas del género marsupial didélfido Chacodelphys . Previos análisis filogenéticos han sugerido como hipótesis alternativas que Chacodelphys sea el grupo hermano de Lestodelphys y Thylamys (tribu Thylamyini) o de Monodelphis (tribu Marmosini), todos estos géneros pertenecientes a la subfamilia Didelphinae. Debido a la ausencia de material fresco de Chacodelphys , extrajimos ADN de fragmentos microscópicos de tejido adherido al cráneo de 95 años del holotipo de C. formosa . Análisis filogenéticos de las secuencias obtenidas resuelven convincentemente la posición filogenética de Chacodelphys como el taxón hermano de Cryptonanus , un género con el cual nunca antes se había pensado que estuviera cercanamente relacionado. Aunque reconocemos a este nuevo clado ( Chacodelphys + Cryptonanus ) junto con Gracilinanus y Lestodelphys + Thylamys pertenecientes a un linaje sin nombre, las relaciones entre estas taxa siguen sin estar convincentemente resueltas.
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Phylogeography ofMarmosa robinsoni: insights into the biogeography of dry forests in northern South America. J Mammal 2014. [DOI: 10.1644/14-mamm-a-069] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Phylogenetic Relationships of Mouse Opossums (Didelphidae,Marmosa) with a Revised Subgeneric Classification and Notes on Sympatric Diversity. AMERICAN MUSEUM NOVITATES 2014. [DOI: 10.1206/3817.1] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Molecular phylogeny of short-tailed opossums (Didelphidae: Monodelphis ): Taxonomic implications and tests of evolutionary hypotheses. Mol Phylogenet Evol 2014; 79:199-214. [DOI: 10.1016/j.ympev.2014.05.029] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 05/23/2014] [Accepted: 05/26/2014] [Indexed: 02/01/2023]
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Extraordinary claims require extraordinary evidence: a comment on Cozzuol et al. (2013): Fig. 1. J Mammal 2014. [DOI: 10.1644/14-mamm-a-054] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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First South American record of Isthmomys pirrensis (Goldman, 1912) (Rodentia: Cricetidae: Neotominae). CHECK LIST 2014. [DOI: 10.15560/10.3.648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Extraordinary Local Diversity of Disk-Winged Bats (Thyropteridae:Thyroptera) in Northeastern Peru, with the Description of a New Species and Comments on Roosting Behavior. AMERICAN MUSEUM NOVITATES 2014. [DOI: 10.1206/3795.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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THE EARLY DIVERSIFICATION HISTORY OF DIDELPHID MARSUPIALS: A WINDOW INTO SOUTH AMERICA'S “SPLENDID ISOLATION”. Evolution 2013; 68:684-95. [DOI: 10.1111/evo.12290] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 10/01/2013] [Indexed: 11/30/2022]
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A New Species ofMarmosops(Marsupialia: Didelphidae) from the Pakaraima Highlands of Guyana, with Remarks on the Origin of the Endemic Pantepui Mammal Fauna. AMERICAN MUSEUM NOVITATES 2013. [DOI: 10.1206/3778.2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Phylogenetic Relationships of New World Porcupines (Rodentia, Erethizontidae): Implications for Taxonomy, Morphological Evolution, and Biogeography. AMERICAN MUSEUM NOVITATES 2013. [DOI: 10.1206/3769.2] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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A New Species of the Didelphid Marsupial GenusMonodelphisfrom Eastern Bolivia. AMERICAN MUSEUM NOVITATES 2012. [DOI: 10.1206/3740.2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Snake-venom resistance as a mammalian trophic adaptation: lessons from didelphid marsupials. Biol Rev Camb Philos Soc 2012; 87:822-37. [PMID: 22404916 DOI: 10.1111/j.1469-185x.2012.00222.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mammals that prey on venomous snakes include several opossums (Didelphidae), at least two hedgehogs (Erinaceidae), several mongooses (Herpestidae), several mustelids, and some skunks (Mephitidae). As a group, these taxa do not share any distinctive morphological traits. Instead, mammalian adaptations for ophiophagy seem to consist only in the ability to resist the toxic effects of snake venom. Molecular mechanisms of venom resistance (as indicated by biochemical research on opossums, mongooses, and hedgehogs) include toxin-neutralizing serum factors and adaptive changes in venom-targeted molecules. Of these, toxin-neutralizing serum factors have received the most research attention to date. All of the toxin-neutralizing serum proteins discovered so far in both opossums and mongooses are human α1B-glycoprotein homologs that inhibit either snake-venom metalloproteinases or phospholipase A(2) myotoxins. By contrast, adaptive changes in venom-targeted molecules have received far less attention. The best-documented examples include amino-acid substitutions in mongoose nicotinic acetylcholine receptor that inhibit binding by α-neurotoxins, and amino-acid substitutions in opossum von Willebrand factor (vWF) that are hypothesized to weaken the bond between vWF and coagulopathic C-type lectins. Although multiple mechanisms of venom resistance are known from some species, the proteomic complexity of most snake venoms suggests that the evolved biochemical defences of ophiophagous mammals are likely to be far more numerous than currently recognized. Whereas most previous research in this field has been motivated by the potential for medical applications, venom resistance in ophiophagous mammals is a complex adaptation that merits attention from comparative biologists. Unfortunately, evolutionary inference is currently limited by ignorance about many relevant facts that can only be provided by future research.
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Adaptive evolution of the venom-targeted vWF protein in opossums that eat pitvipers. PLoS One 2011; 6:e20997. [PMID: 21731638 PMCID: PMC3120824 DOI: 10.1371/journal.pone.0020997] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 05/16/2011] [Indexed: 11/21/2022] Open
Abstract
The rapid evolution of venom toxin genes is often explained as the result of a biochemical arms race between venomous animals and their prey. However, it is not clear that an arms race analogy is appropriate in this context because there is no published evidence for rapid evolution in genes that might confer toxin resistance among routinely envenomed species. Here we report such evidence from an unusual predator-prey relationship between opossums (Marsupialia: Didelphidae) and pitvipers (Serpentes: Crotalinae). In particular, we found high ratios of replacement to silent substitutions in the gene encoding von Willebrand Factor (vWF), a venom-targeted hemostatic blood protein, in a clade of opossums known to eat pitvipers and to be resistant to their hemorrhagic venom. Observed amino-acid substitutions in venom-resistant opossums include changes in net charge and hydrophobicity that are hypothesized to weaken the bond between vWF and one of its toxic snake-venom ligands, the C-type lectin-like protein botrocetin. Our results provide the first example of rapid adaptive evolution in any venom-targeted molecule, and they support the notion that an evolutionary arms race might be driving the rapid evolution of snake venoms. However, in the arms race implied by our results, venomous snakes are prey, and their venom has a correspondingly defensive function in addition to its usual trophic role.
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Revisionary Notes on Neotropical Porcupines (Rodentia: Erethizontidae) 3. An Annotated Checklist of the Species ofCoendouLacépède, 1799. AMERICAN MUSEUM NOVITATES 2011. [DOI: 10.1206/3720.2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Mammalian Diversity and Matses Ethnomammalogy in Amazonian Peru Part 1: Primates. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2011. [DOI: 10.1206/351.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Species Limits and Phylogenetic Relationships in the Didelphid Marsupial Genus Thylamys Based on Mitochondrial DNA Sequences and Morphology. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2010. [DOI: 10.1206/716.1] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Molecular Systematics of Mouse Opossums (Didelphidae: Marmosa): Assessing Species Limits using Mitochondrial DNA Sequences, with Comments on Phylogenetic Relationships and Biogeography. AMERICAN MUSEUM NOVITATES 2010. [DOI: 10.1206/708.1] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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A New Species of Peropteryx (Chiroptera: Emballonuridae) from Western Amazonia with Comments on Phylogenetic Relationships within the Genus. AMERICAN MUSEUM NOVITATES 2010. [DOI: 10.1206/691.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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A Revision of the Didelphid Marsupial Genus Marmosa Part 1. The Species in Tate's ‘Mexicana’ and ‘Mitis’ Sections and Other Closely Related Forms. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2010. [DOI: 10.1206/334.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Preface: Systematic Mammalogy: Contributions in Honor of Guy G. Musser. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2009. [DOI: 10.1206/0003-0090-331.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Chapter 11. The Six Opossums of Félix de Azara: Identification, Taxonomic History, Neotype Designations, and Nomenclatural Recommendations. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2009. [DOI: 10.1206/582-11.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Phylogenetic Relationships and Classification of Didelphid Marsupials, an Extant Radiation of New World Metatherian Mammals. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2009. [DOI: 10.1206/322.1] [Citation(s) in RCA: 184] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Gardner, A. L. (ed.). 2007 [2008]. Mammals of South America. Volume 1: Marsupials, Xenarthrans, Shrews, and Bats. University of Chicago Press, Chicago, Illinois, and London, United Kingdom, 669 pp. ISBN-13: 978-0-226-28240-4, price (hardbound), $75. J Mammal 2009. [DOI: 10.1644/08-mamm-r-296.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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On the Taxonomic Status ofOryzomys curasoaeMcFarlane and Debrot, 2001, (Rodentia: Cricetidae: Sigmodontinae) with Remarks on the Phylogenetic Relationships ofO. gorgasiHershkovitz, 1971. CARIBB J SCI 2009. [DOI: 10.18475/cjos.v45i1.a11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Base-compositional heterogeneity in the RAG1 locus among didelphid marsupials: implications for phylogenetic inference and the evolution of GC content. Syst Biol 2007; 56:83-96. [PMID: 17366139 DOI: 10.1080/10635150601182939] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Although theoretical studies have suggested that base-compositional heterogeneity can adversely affect phylogenetic reconstruction, only a few empirical examples of this phenomenon, mostly among ancient lineages (with divergence dates > 100 Mya), have been reported. In the course of our phylogenetic research on the New World marsupial family Didelphidae, we sequenced 2790 bp of the RAG1 exon from exemplar species of most extant genera. Phylogenetic analysis of these sequences recovered an anomalous node consisting of two clades previously shown to be distantly related based on analyses of other molecular data. These two clades show significantly increased GC content at RAG1 third codon positions, and the resulting convergence in base composition is strong enough to overwhelm phylogenetic signal from other genes (and morphology) in most analyses of concatenated datasets. This base-compositional convergence occurred relatively recently (over tens rather than hundreds of millions of years), and the affected gene region is still in a state of evolutionary disequilibrium. Both mutation rate and substitution rate are higher in GC-rich didelphid taxa, observations consistent with RAG1 sequences having experienced a higher rate of recombination in the convergent lineages.
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Different patterns of selection on the nuclear genes IRBP and DMP-1 affect the efficiency but not the outcome of phylogeny estimation for didelphid marsupials. Mol Phylogenet Evol 2006; 38:363-80. [PMID: 16054401 DOI: 10.1016/j.ympev.2005.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2005] [Revised: 06/03/2005] [Accepted: 06/07/2005] [Indexed: 11/29/2022]
Abstract
Selection at the protein-level can influence nucleotide substitution patterns for protein-coding genes, which in turn can affect their performance as phylogenetic characters. In this study, we compare two protein-coding nuclear genes that appear to have evolved under markedly different selective constraints and evaluate how selection has shaped their phylogenetic signal. We sequenced 1,100+ bp of exon 6 of the gene encoding dentin matrix protein 1 (DMP1) from most of the currently recognized genera of New World opossums (family: Didelphidae) and compared these data to an existing matrix of sequences from the interphotoreceptor retinoid-binding protein gene (IRBP) and morphological characters. In comparison to IRBP, DMP1 has far fewer sites under strong purifying selection and exhibits a number of sites under positive directional selection. Furthermore, selection on the DMP1 protein appears to conserve short, acidic, serine-rich domains rather than primary amino acid sequence; as a result, DMP1 has significantly different nucleotide substitution patterns from IRBP. Using Bayesian methods, we determined that DMP1 evolves almost 30% faster than IRBP, has 2.5 times more variable sites, has less among-site rate heterogeneity, is skewed toward A and away from CT (IRBP has relatively even base frequencies), and has a significantly lower rate of change between adenine and any other nucleotide. Despite these different nucleotide substitution patterns, estimates of didelphid relationships based on separate phylogenetic analyses of these genes are remarkably congruent whether patterns of nucleotide substitution are explicitly modeled or not. Nonetheless, DMP1 contains more phylogenetically informative characters per unit sequence and resolves more nodes with higher support than does IRBP. Thus, for these two genes, relaxed functional constraints and positive selection appear to improve the efficiency of phylogenetic estimation without compromising its accuracy.
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Holochilus Brandt, 1835, Proechimys J.a. Allen, 1899 And Trinomys Thomas, 1921 (Mammalia, Rodentia): Proposed Conservation By The Designation Of H. Sciureus Wagner, 1842 As The Type Species Of Holochilus. ACTA ACUST UNITED AC 1999. [DOI: 10.5962/bhl.part.23088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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