1
|
Beklemisheva VR, Lemskaya NA, Prokopov DY, Perelman PL, Romanenko SA, Proskuryakova AA, Serdyukova NA, Utkin YA, Nie W, Ferguson-Smith MA, Yang F, Graphodatsky AS. Maps of Constitutive-Heterochromatin Distribution for Four Martes Species (Mustelidae, Carnivora, Mammalia) Show the Formative Role of Macrosatellite Repeats in Interspecific Variation of Chromosome Structure. Genes (Basel) 2023; 14:489. [PMID: 36833416 PMCID: PMC9957230 DOI: 10.3390/genes14020489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Constitutive-heterochromatin placement in the genome affects chromosome structure by occupying centromeric areas and forming large blocks. To investigate the basis for heterochromatin variation in the genome, we chose a group of species with a conserved euchromatin part: the genus Martes [stone marten (M. foina, 2n = 38), sable (M. zibellina, 2n = 38), pine marten (M. martes, 2n = 38), and yellow-throated marten (M. flavigula, 2n = 40)]. We mined the stone marten genome for the most abundant tandem repeats and selected the top 11 macrosatellite repetitive sequences. Fluorescent in situ hybridization revealed distributions of the tandemly repeated sequences (macrosatellites, telomeric repeats, and ribosomal DNA). We next characterized the AT/GC content of constitutive heterochromatin by CDAG (Chromomycin A3-DAPI-after G-banding). The euchromatin conservatism was shown by comparative chromosome painting with stone marten probes in newly built maps of the sable and pine marten. Thus, for the four Martes species, we mapped three different types of tandemly repeated sequences critical for chromosome structure. Most macrosatellites are shared by the four species with individual patterns of amplification. Some macrosatellites are specific to a species, autosomes, or the X chromosome. The variation of core macrosatellites and their prevalence in a genome are responsible for the species-specific variation of the heterochromatic blocks.
Collapse
Affiliation(s)
- Violetta R. Beklemisheva
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Natalya A. Lemskaya
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Dmitry Yu. Prokopov
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Polina L. Perelman
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Svetlana A. Romanenko
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anastasia A. Proskuryakova
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Natalya A. Serdyukova
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Yaroslav A. Utkin
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Wenhui Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Fentang Yang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
| | - Alexander S. Graphodatsky
- Department of Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| |
Collapse
|
2
|
Genetic relationships among populations of the small Indian mongoose (Urva auropunctata) introduced in Japan. MAMMAL RES 2023. [DOI: 10.1007/s13364-023-00672-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Abstract
The small Indian mongoose, Urva auropunctata, is one of the most notorious invasive species in the world. In Japan, the mongoose was introduced to Amami, Kyushu (Kiire region), and Okinawa Islands. Currently, an eradication program for the Amami population is proving successful. To prevent reinvasion and conserve biodiversity, it would be advantageous to investigate the origin and dispersal history of introduced mongoose populations in Japan. We determined the mitochondrial genome of a mongoose from the Okinawa population and confirmed that the systematic status of the mongoose is Urva auropunctata. We also found two haplotypes of cytochrome b in the Amami population, one of which is common among the Okinawa, Amami, and Kiire populations. Based on our microsatellite analysis, the three populations were genetically different from each other. Furthermore, with a low pairwise FST value, the Kiire population was closer to the Okinawa than the Amami population. Our results suggest that the Okinawa population could be the source of the Amami and Kiire populations. These results align with historical records of mongoose in Japan and clarify its genetic status. Our results should aid the prediction of the pathway through which a new invasion will likely occur.
Collapse
|
3
|
Kargopoulos N, Valenciano A, Abella J, Kampouridis P, Lechner T, Böhme M. The exceptionally high diversity of small carnivorans from the Late Miocene hominid locality of Hammerschmiede (Bavaria, Germany). PLoS One 2022; 17:e0268968. [PMID: 35830447 PMCID: PMC9278789 DOI: 10.1371/journal.pone.0268968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/05/2022] [Indexed: 11/19/2022] Open
Abstract
The present study deals with new material of carnivorans (Mustelidae, Mephitidae, Ailuridae, Potamotheriinae and Viverridae) from the basal Tortonian (Late Miocene, late Astaracian) hominid-bearing locality of Hammerschmiede (Bavaria, Germany). The small carnivoran fauna includes 20 species belonging to nine different subfamilies (Guloninae, Lutrinae, Mellivorinae, Potamotheriinae, Leptarctinae, Mephitinae, Simocyoninae, Genettinae and Viverrinae). The identified forms include: “Martes” sansaniensis, “Martes” cf. munki, “Martes” sp., Circamustela hartmanni n. sp., Laphyctis mustelinus, Guloninae indet., Eomellivora moralesi, Vishnuonyx neptuni, Paralutra jaegeri, Lartetictis cf. dubia, Trocharion albanense, Palaeomeles pachecoi, Proputorius sansaniensis, Proputorius pusillus, Alopecocyon goeriachensis, Simocyoninae indet., Potamotherium sp., Semigenetta sansaniensis, Semigenetta grandis and Viverrictis modica. The new species Circamustela hartmanni n. sp. is differentiated from the other members of the genus by its small size and the morphology of its dental cusps in the upper and lower carnassials. This is one of the highest reported taxonomic diversities for fossil small carnivorans in the Miocene of Europe, including also first and last occurrences for several genera and species. Additionally, the assemblage comprises some rare taxa such as Palaeomeles pachecoi and Eomellivora moralesi. An ecomorphological comparison of the discovered taxa reveals possible cases of competition and niche partitioning.
Collapse
Affiliation(s)
- Nikolaos Kargopoulos
- Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Baden-Württemberg, Germany
- * E-mail: (NK); (AV)
| | - Alberto Valenciano
- Departamento de Ciencias de la Tierra, Universidad de Zaragoza and Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA), Zaragoza, Zaragoza, Spain
- Research and Exhibitions Department, Iziko Museums of South Africa, Cape Town, Western Cape, South Africa
- * E-mail: (NK); (AV)
| | - Juan Abella
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
- Instituto Nacional de Biodiversidad, Quito, Pichincha, Ecuador
| | - Panagiotis Kampouridis
- Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Baden-Württemberg, Germany
| | - Thomas Lechner
- Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Baden-Württemberg, Germany
- Senckenberg Centre for Human Evolution and Paleoenvironment (HEP), Tübingen, Baden-Württemberg, Germany
| | - Madelaine Böhme
- Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Baden-Württemberg, Germany
- Senckenberg Centre for Human Evolution and Paleoenvironment (HEP), Tübingen, Baden-Württemberg, Germany
| |
Collapse
|
4
|
Wolverines (Gulo gulo) in a changing landscape and warming climate: A decadal synthesis of global conservation ecology research. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
5
|
Derežanin L, Blažytė A, Dobrynin P, Duchêne DA, Grau JH, Jeon S, Kliver S, Koepfli KP, Meneghini D, Preick M, Tomarovsky A, Totikov A, Fickel J, Förster DW. Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae. Mol Ecol 2022; 31:2898-2919. [PMID: 35334142 DOI: 10.1111/mec.16443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 03/06/2022] [Accepted: 03/14/2022] [Indexed: 11/28/2022]
Abstract
Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes, as well as searching for species-specific structural variants (SVs). Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observe species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This strongly argues for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.
Collapse
Affiliation(s)
- Lorena Derežanin
- Leibniz Institute for Zoo and Wildlife Research (IZW, Alfred Kowalke Straße 17, 10315, Berlin, Germany
| | - Asta Blažytė
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST, Ulsan, 44919, Republic of Korea
| | - Pavel Dobrynin
- Computer Technologies Laboratory, ITMO University, 49 Kronverkskiy Pr, 197101, Saint Petersburg, Russia
| | - David A Duchêne
- Center for Evolutionary Hologenomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark
| | - José Horacio Grau
- amedes Genetics, amedes Medizinische Dienstleistungen GmbH, Jägerstr. 61, 10117, Berlin, Germany
| | - Sungwon Jeon
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST, Ulsan, 44919, Republic of Korea.,Clinomics Inc, Ulsan, 44919, Republic of Korea
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology, SB RAS, 8/2 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Klaus-Peter Koepfli
- Computer Technologies Laboratory, ITMO University, 49 Kronverkskiy Pr, 197101, Saint Petersburg, Russia.,Smithsonian-Mason School of Conservation, 1500 Remount Road, Front Royal, VA, 22630, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA
| | - Dorina Meneghini
- Leibniz Institute for Zoo and Wildlife Research (IZW, Alfred Kowalke Straße 17, 10315, Berlin, Germany
| | - Michaela Preick
- Institute for Biochemistry and Biology, Faculty of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, OT, Germany
| | - Andrey Tomarovsky
- Computer Technologies Laboratory, ITMO University, 49 Kronverkskiy Pr, 197101, Saint Petersburg, Russia.,Institute of Molecular and Cellular Biology, SB RAS, 8/2 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia.,Novosibirsk State University, 1 Pirogova str, Novosibirsk, 630090, Russia
| | - Azamat Totikov
- Computer Technologies Laboratory, ITMO University, 49 Kronverkskiy Pr, 197101, Saint Petersburg, Russia.,Institute of Molecular and Cellular Biology, SB RAS, 8/2 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia.,Novosibirsk State University, 1 Pirogova str, Novosibirsk, 630090, Russia
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research (IZW, Alfred Kowalke Straße 17, 10315, Berlin, Germany.,Institute for Biochemistry and Biology, Faculty of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, OT, Germany
| | - Daniel W Förster
- Leibniz Institute for Zoo and Wildlife Research (IZW, Alfred Kowalke Straße 17, 10315, Berlin, Germany
| |
Collapse
|
6
|
Abramson NI, Bodrov SY, Bondareva OV, Genelt-Yanovskiy EA, Petrova TV. A mitochondrial genome phylogeny of voles and lemmings (Rodentia: Arvicolinae): Evolutionary and taxonomic implications. PLoS One 2021; 16:e0248198. [PMID: 34797834 PMCID: PMC8604340 DOI: 10.1371/journal.pone.0248198] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 11/03/2021] [Indexed: 01/04/2023] Open
Abstract
Arvicolinae is one of the most impressive placental radiations with over 150 extant and numerous extinct species that emerged since the Miocene in the Northern Hemisphere. The phylogeny of Arvicolinae has been studied intensively for several decades using morphological and genetic methods. Here, we sequenced 30 new mitochondrial genomes to better understand the evolutionary relationships among the major tribes and genera within the subfamily. The phylogenetic and molecular dating analyses based on 11,391 bp concatenated alignment of protein-coding mitochondrial genes confirmed the monophyly of the subfamily. While Bayesian analysis provided a high resolution across the entire tree, Maximum Likelihood tree reconstruction showed weak support for the ordering of divergence and interrelationships of tribal level taxa within the most ancient radiation. Both the interrelationships among tribes Lagurini, Ellobiusini and Arvicolini, comprising the largest radiation and the position of the genus Dinaromys within it also remained unresolved. For the first time complex relationships between genus level taxa within the species-rich tribe Arvicolini received full resolution. Particularly Lemmiscus was robustly placed as sister to the snow voles Chionomys in the tribe Arvicolini in contrast with a long-held belief of its affinity with Lagurini. Molecular dating of the origin of Arvicolinae and early divergences obtained from the mitogenome data were consistent with fossil records. The mtDNA estimates for putative ancestors of the most genera within Arvicolini appeared to be much older than it was previously proposed in paleontological studies.
Collapse
Affiliation(s)
- Natalia I. Abramson
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Semyon Yu. Bodrov
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Olga V. Bondareva
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Evgeny A. Genelt-Yanovskiy
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| | - Tatyana V. Petrova
- Department of Molecular Systematics, Laboratory of Theriology, Zoological Institute RAS, Saint Petersburg, Russia
| |
Collapse
|
7
|
Schwartz MK, Walters AD, Pilgrim KL, Moriarty KM, Slauson KM, Zielinski WJ, Aubry KB, Sacks BN, Zarn KE, Quinn CB, Young MK. Pliocene-Early Pleistocene Geological Events Structure Pacific Martens (Martes caurina). J Hered 2021; 111:169-181. [PMID: 32161974 DOI: 10.1093/jhered/esaa005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 02/10/2020] [Indexed: 11/15/2022] Open
Abstract
The complex topography, climate, and geological history of Western North America have shaped contemporary patterns of biodiversity and species distributions in the region. Pacific martens (Martes caurina) are distributed along the northern Pacific Coast of North America with disjunct populations found throughout the Northwestern Forested Mountains and Marine West Coast Forest ecoregions of the West Coast. Martes in this region have been classified into subspecies; however, the subspecific designation has been extensively debated. In this study, we use genomic data to delineate conservation units of Pacific marten in the Sierra-Cascade-Coastal montane belt in the western United States. We analyzed the mitochondrial genome for 94 individuals to evaluate the spatial distribution and divergence times of major lineages. We further genotyped 401 individuals at 13 microsatellite loci to investigate major patterns of population structure. Both nuclear and mitochondrial DNA suggest substantial genetic substructure concordant with historical subspecies designations. Our results revealed that the region contains 2 distinct mitochondrial lineages: a Cascades/Sierra lineage that diverged from the Cascades/coastal lineage 2.23 (1.48-3.14 mya), consistent with orogeny of the Cascade Mountain chain. Interestingly, Pacific Martes share phylogeographic patterns similar with other sympatric taxa, suggesting that the complex geological history has shaped the biota of this region. The information is critical for conservation and management efforts, and further investigation of adaptive diversity is warranted following appropriate revision of conservation management designations.
Collapse
Affiliation(s)
- Michael K Schwartz
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| | - Ashley D Walters
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| | - Kristine L Pilgrim
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| | - Katie M Moriarty
- National Council for Air and Stream Improvement, Inc., Corvallis, OR
| | - Keith M Slauson
- USDA Forest Service, Pacific Southwest Research Station, Arcata, CA
| | - William J Zielinski
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT.,USDA Forest Service, Pacific Southwest Research Station, Arcata, CA
| | - Keith B Aubry
- USDA Forest Service, Pacific Northwest Research Station, Olympia, WA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA
| | - Katherine E Zarn
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| | - Cate B Quinn
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA
| | - Michael K Young
- USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT
| |
Collapse
|
8
|
Li B, Lu J, Monakhov V, Kang H, Xu Y, An B, Ghani MU, Li M, Peng W, Ma X. Phylogeography of subspecies of the sable (Martes zibellina L.) based on mitochondrial genomes: implications for evolutionary history. Mamm Biol 2021. [DOI: 10.1007/s42991-020-00092-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
9
|
Abstract
Abstract
The subspecies concept is one of the most controversial in Linnean taxonomy. In the past, subspecies were described without a clear conceptual framework, triggering confusion and motivating criticism of the very concept of a subspecies. At present, subspecies are conceived as aggregates of populations that are geographically isolated, are composed of interfertile individuals, and are morphologically diagnosable. The tayra, Eira barbara, was described in 1758 and has had a stable taxonomic history at the species level. However, below the species level, 16 subspecies have been named, with from two to seven subspecies recognized as valid by different authors. None of the subspecies were, however, described within a clear conceptual framework. Using the modern concept of a subspecies, I analyzed subspecies of E. barbara recognized by recent authors. I gathered morphometric data from 155 specimens in mammal collections, georeferenced each specimen, and recorded membership to subspecies assigned by different references and by its location. I gathered climate and geographic data for each location. I analyzed data using Principal Components Analysis (PCA) and analysis of variance (ANOVA). Specimens exhibited sexual dimorphism in size but not in skull shape. I used regression analysis to test for associations between skull shape and size and climate data. Geographic analyses documented that subspecies are not allopatric, violating one of the main properties of the subspecies concept. ANOVA showed significant differences in skull morphology between some pairs of recognized subspecies but not others. However, none of the subspecies segregated in the PCA. Thus, the recognized subspecies could not be diagnosed from morphological data, violating another property of the subspecies concept. Size varied greatly between the sexes using different schemes for recognized subspecies. Climate variables explained between 4% and 6% of size variation for males and females. Skull shape proved not to be geographically variable.
Collapse
Affiliation(s)
- Mauro Ignacio Schiaffini
- CIEMEP, Centro de Investigación Esquel de Montaña y Estepa Patagónica (Universidad Nacional de la Patagonia San Juan Bosco- Consejo Nacional de Investigaciones Científicas y Técnicas), LIEB, Laboratorio de Investigaciones en Evolución y Biodiversidad. Facultad de Ciencias Naturales y Ciencias de la Salud, Universidad Nacional de la Patagonia San Juan Bosco, Esquel, Chubut, Argentina
| |
Collapse
|
10
|
Valenciano A, Govender R. New insights into the giant mustelids (Mammalia, Carnivora, Mustelidae) from Langebaanweg fossil site (West Coast Fossil Park, South Africa, early Pliocene). PeerJ 2020; 8:e9221. [PMID: 32547866 PMCID: PMC7271888 DOI: 10.7717/peerj.9221] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/29/2020] [Indexed: 11/20/2022] Open
Abstract
Giant mustelids are a paraphyletic group of mustelids found in the Neogene of Eurasia, Africa and North America. Most are known largely from dental remains, with their postcranial skeleton mostly unknown. Here, we describe new craniodental and postcranial remains of the large lutrine Sivaonyx hendeyi and the leopard-size gulonine Plesiogulo aff. monspessulanus from the early Pliocene site Langebaanweg, South Africa. The new material of the endemic S. hendeyi, includes upper incisors and premolars, and fragmentary humerus, ulna and a complete astragalus. Its postcrania shares more traits with the living Aonyx capensis than the late Miocene Sivaonyx beyi from Chad. Sivaonyx hendeyi could therefore be tentatively interpreted as a relatively more aquatic taxon than the Chadian species, comparable to A. capensis. The new specimens of Plesiogulo comprise two edentulous maxillae, including one of a juvenile individual with incomplete decidual dentition, and a fragmentary forelimb of an adult individual. The new dental measurements point to this form being amongst the largest specimens of the genus. Both P3-4 differs from the very large species Plesiogulo botori from late Miocene of Kenya and Ethiopia. This confirms the existence of two distinct large species of Plesiogulo in Africa during the Mio/Pliocene, P. botori in the Late Miocene of Eastern Africa (6.1–5.5 Ma) and Plesiogulo aff. monspessulanus at the beginning of the Pliocene in southern Africa (5.2 Ma). Lastly, we report for the first time the presence of both Sivaonyx and Plesiogulo in MPPM and LQSM at Langebaanweg, suggesting that the differences observed from the locality may be produced by sedimentation or sampling biases instead of temporal replacement within the carnivoran guild.
Collapse
Affiliation(s)
- Alberto Valenciano
- Department of Research and Exhibitions, Iziko Museums of South Africa, Cape Town, South Africa.,Department of Biological Science, University of Cape Town, Cape Town, South Africa
| | - Romala Govender
- Department of Research and Exhibitions, Iziko Museums of South Africa, Cape Town, South Africa.,Department of Biological Science, University of Cape Town, Cape Town, South Africa
| |
Collapse
|
11
|
Liu G, Zhao C, Xu D, Zhang H, Monakhov V, Shang S, Gao X, Sha W, Ma J, Zhang W, Tang X, Li B, Hua Y, Cao X, Liu Z, Zhang H. First Draft Genome of the Sable, Martes zibellina. Genome Biol Evol 2020; 12:59-65. [PMID: 32058545 PMCID: PMC7144822 DOI: 10.1093/gbe/evaa029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2020] [Indexed: 11/28/2022] Open
Abstract
Members of genus Martes provide early warning signals about forest ecosystem health and are designated as a Management Indicator Species. As one of the most widespread members in Martes, the sable (Martes zibellina) is a circumboreal small predator found throughout all taiga zoogeographical zones of Eurasia and shows distinct population differentiation and morphological variations. To support further studies on striking local adaptation and population evolution, we present the first sable genome, assembled de novo from an individual originating in the Great Khingan Mountains (China). The assembled genome is 2.42 Gb, consisting of 15,814 scaffolds with a scaffold N50 of 5.20 Mb. Searches for complete Mammalia BUSCO (Benchmarking Universal Single-Copy Ortholog) gene groups found that 95.15% of the curated single-copy orthologs were assembled as complete, suggesting a high level of completeness of the genome. We totally predicted 19,413 protein-coding genes, and 0.82 Gb of repeat sequences was annotated. We also detected 1,257 olfactory receptor genes and found more functional olfactory receptor genes in sable than in other Mustelidae species, which provide a possible genetic explanation for the acute sense of smell of the sable for searching the preys under deep snow. Phylogenetic analyses revealed that the ferret (Mustela putorius furo) and sea otter (Enhydra lutris) form a clade that is sister to the sable, which was dated ∼16.4 Ma. Overall, our study provided the first reference genome for research in a broad range of areas including local adaptations, population evolution, conservation, and management for sable.
Collapse
Affiliation(s)
- Guangshuai Liu
- College of Life Science, Qufu Normal University, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chao Zhao
- College of Life Science, Qufu Normal University, China
| | - Dongming Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Huanxin Zhang
- College of Marine Life Science, Ocean University of China, Qingdao, Shandong, China
| | - Vladimir Monakhov
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Shuai Shang
- College of Marine Life Science, Ocean University of China, Qingdao, Shandong, China
- College of Biological and Environmental Engineering, Binzhou University, China
| | - Xiaodong Gao
- College of Life Science, Qufu Normal University, China
| | - Weilai Sha
- College of Life Science, Qufu Normal University, China
| | - Jianzhang Ma
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Wei Zhang
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Xuexi Tang
- College of Marine Life Science, Ocean University of China, Qingdao, Shandong, China
| | - Bo Li
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Yan Hua
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Xiaofang Cao
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhen Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, China
| |
Collapse
|
12
|
Arslan Y, Demi̇rtaş S, Herman JS, Pustilnik JD, Searle JB, Gündüz İ. The Anatolian glacial refugium and human-mediated colonization: a phylogeographical study of the stone marten (Martes foina) in Turkey. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe Anatolian Peninsula, comprising most of modern Turkey, is situated at the junction of Europe, the Middle East and Asia. Together with its complex geomorphological and climatic history, this has given rise to a rich fauna and flora, which exhibits a wide range of historical biogeographical patterns. The stone marten (Martes foina) is a small carnivore that is found across the temperate Palaearctic region including Anatolia, where it is often associated with habitats modified by humans, but few genetic data exist for this species. We sequenced a 1840-bp region of the mitochondrial genome from 97 martens sampled across the peninsula and intron 7 of the nuclear β-fibrinogen gene from 53 of these. Two mitochondrial lineages were recovered, with overlapping eastern and western distributions, but there was no geographical structure for the autosomal marker. Coalescent analyses indicated that both of the lineages originated during the Last Glacial Maximum, one of them within an eastern Anatolian refugium and the other in a western Anatolian or Balkan refugium. The western lineage colonized most of Europe in the Holocene, while the eastern lineage may be endemic to Anatolia, from where it colonized the Iberian Peninsula via human translocation. The presence of at least one refugial stone marten population highlights the importance of Anatolia to the preservation of genetic variation and biodiversity.
Collapse
Affiliation(s)
- Yağmur Arslan
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
| | - Sadik Demi̇rtaş
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
| | - Jeremy S Herman
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
| | - Jeremy D Pustilnik
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - İslam Gündüz
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
| |
Collapse
|
13
|
Lynch LM. Fossil Calibration of Mitochondrial Phylogenetic Relationships of North American Pine Martens, Martes, Suggests an Older Divergence of M. americana and M. caurina than Previously Hypothesized. J MAMM EVOL 2019. [DOI: 10.1007/s10914-019-09476-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
14
|
Li B, Wu D, Cai Y, Vladimir G M, Zhang W, Xu Y. Genetic individualization of sable ( Martes zibellina L. 1758) using microsatellites. Anim Cells Syst (Seoul) 2018; 22:253-258. [PMID: 30460105 PMCID: PMC6138352 DOI: 10.1080/19768354.2018.1494039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 05/22/2018] [Accepted: 06/21/2018] [Indexed: 10/28/2022] Open
Abstract
Genetic individualization based on non-invasive sampling is crucial for estimating the numbers of individuals in endangered mammalian populations. In sable (Martes zibellina)-poaching cases, identifying the number of animals involved is critical for determining the penalty. In addition, investigating animal numbers for wild sable populations requires genetic individualization when collecting several samples in neighboring regions. Microsatellites have been demonstrated to be reliable markers for individual identification. Thirty-three microsatellite loci derived from Mustelidae were selected to develop a genetic individualization method for sable. Three reference populations containing 54 unrelated sables were used to calculate allele number, allelic frequencies, and the polymorphic information content of each locus. The data were subsequently used to assess the validity of a combination of twelve loci for sable individualization. We defined twelve polymorphic loci that were easy to be amplified and genotyped. Four significant deviations from Hardy-Weinberg equilibrium were observed among the 12 loci in the three populations. The match probability of an individual from the reference populations with a random individual based on the 12 loci was 1.37 × 10-13. Using the combination of the twelve loci provides sufficient power to individualize sables considering the levels of microsatellite polymorphism observed. These loci were successfully applied to a case of sable poaching and provided valid evidence to determine the penalty. The genetic individualization of sable based on these loci might also be useful to investigate the numbers of animals in wild populations.
Collapse
Affiliation(s)
- Bo Li
- College of Wildlife Resources, Northeast Forestry University, Harbin, People's Republic of China.,State Forestry Administration Detecting Center of Wildlife Resources, Harbin, People's Republic of China
| | - Dan Wu
- College of Wildlife Resources, Northeast Forestry University, Harbin, People's Republic of China.,College of Biotechnology and Engineering, West Yunnan University, Lincang, People's Republic of China
| | - Yingying Cai
- College of Wildlife Resources, Northeast Forestry University, Harbin, People's Republic of China
| | - Monakhov Vladimir G
- Institute of Plant and Animal Ecology, Ural Division of RAS, Yekaterinburg, Russia
| | - Wei Zhang
- College of Wildlife Resources, Northeast Forestry University, Harbin, People's Republic of China.,State Forestry Administration Detecting Center of Wildlife Resources, Harbin, People's Republic of China
| | - Yanchun Xu
- College of Wildlife Resources, Northeast Forestry University, Harbin, People's Republic of China.,State Forestry Administration Detecting Center of Wildlife Resources, Harbin, People's Republic of China
| |
Collapse
|
15
|
New Early Miocene Material of Iberictis, the Oldest Member of the Wolverine Lineage (Carnivora, Mustelidae, Guloninae). J MAMM EVOL 2018. [DOI: 10.1007/s10914-018-9445-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
16
|
Evolutionary progression of mitochondrial gene rearrangements and phylogenetic relationships in Strigidae (Strigiformes). Gene 2018; 674:8-14. [PMID: 29940272 DOI: 10.1016/j.gene.2018.06.066] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/30/2018] [Accepted: 06/20/2018] [Indexed: 01/09/2023]
Abstract
The bird mitogenome is generally considered to have a conservative genome size, consistent gene content, and similar gene order. As more mitogenomes are sequenced, mitochondrial (mt) gene rearrangements have been frequently identified among diverse birds. Within two genera (Bubo and Strix) of typical owls (Strigidae, Strigiformes), the rearrangement of the mt gene has been a subject of debate. In the current study, we first sequenced the whole mitogenomes of S. uralensis and B. scandiaca and resequenced the entire mitogenome of B. bubo. By combining our data with previously sequenced mitogenomes in Strigidae, we examined the mt gene rearrangements in the family and attempted to reconstruct the evolutionary progression of these rearrangements. The mitogenomes were then used to review the phylogenies of Strigidae. Most mitogenomes exhibited the ancestral gene order (A) in Strigidae. The ancestral gene order in the previously published mitogenome of B. bubo was found to be incorrect. We determined the mt gene order (the duplicate tRNAThr-CR, B) and discovered two additional mt gene orders (the duplicate tRNAGlu-L-CR and CR, C and D) in the Bubo and Strix genera. Gene order B was likely derived from A by a tandem duplication of the region spanning from tRNAThr to CR. The other two modified gene orders, C and D, were likely derived from B by further degenerations or deletions of one copy of specific duplicated genes. We also preliminarily reconstructed the evolutionary progression of mt gene rearrangements and discussed maintenance of the duplicated CR in the genera. Additionally, the phylogenetic trees based on the mitogenomes supported the division of Strigidae into three subfamilies: Ninoxinae + (Surniinae + Striginae). Within the Striginae clade, the four genera formed a phylogenetic relationship: Otus + (Asio + (Bubo + Strix)). This suggests that Otus firstly diverges in their evolutionary history, and Bubo and Strix show a close relationship. B. bubo, B. blakistoni and B. scandiaca form a clade should be considered members of the same genus. The well-supported topology obtained in our Bayesian inference (BI) and maximum likelihood (ML) analyses of Strigid mitogenomes suggests that these genomes are informative for constructing phylogenetic relationships.
Collapse
|
17
|
Samuels JX, Bredehoeft KE, Wallace SC. A new species of Gulo from the Early Pliocene Gray Fossil Site (Eastern United States); rethinking the evolution of wolverines. PeerJ 2018; 6:e4648. [PMID: 29682423 PMCID: PMC5910791 DOI: 10.7717/peerj.4648] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/30/2018] [Indexed: 11/26/2022] Open
Abstract
The wolverine (Gulo gulo) is the largest living terrestrial member of the Mustelidae; a versatile predator formerly distributed throughout boreal regions of North America and Eurasia. Though commonly recovered from Pleistocene sites across their range, pre-Pleistocene records of the genus are exceedingly rare. Here, we describe a new species of Gulo from the Gray Fossil Site in Tennessee. Based on biostratigraphy, a revised estimate of the age of the Gray Fossil Site is Early Pliocene, near the Hemphillian—Blancan transition, between 4.9 and 4.5 Ma. This represents the earliest known occurrence of a wolverine, more than one million years earlier than any other record. The new species of wolverine described here shares similarities with previously described species of Gulo, and with early fishers (Pekania). As the earliest records of both Gulo and Pekania are known from North America, this suggests the genus may have evolved in North America and dispersed to Eurasia later in the Pliocene. Both fauna and flora at the Gray Fossil Site are characteristic of warm/humid climates, which suggests wolverines may have become ‘cold-adapted’ relatively recently. Finally, detailed comparison indicates Plesiogulo, which has often been suggested to be ancestral to Gulo, is not likely closely related to gulonines, and instead may represent convergence on a similar niche.
Collapse
Affiliation(s)
- Joshua X Samuels
- Department of Geosciences, East Tennessee State University, Johnson City, TN, United States of America.,Don Sundquist Center of Excellence in Paleontology, East Tennessee State University, Johnson City, TN, United States of America
| | - Keila E Bredehoeft
- Don Sundquist Center of Excellence in Paleontology, East Tennessee State University, Johnson City, TN, United States of America
| | - Steven C Wallace
- Department of Geosciences, East Tennessee State University, Johnson City, TN, United States of America.,Don Sundquist Center of Excellence in Paleontology, East Tennessee State University, Johnson City, TN, United States of America
| |
Collapse
|
18
|
Carvalho EL, Wallau GL, Rangel DL, Machado LC, Pereira AB, Victoria FDC, Boldo JT, Pinto PM. Phylogenetic positioning of the Antarctic alga Prasiola crispa (Trebouxiophyceae) using organellar genomes and their structural analysis. JOURNAL OF PHYCOLOGY 2017; 53:908-915. [PMID: 28394430 DOI: 10.1111/jpy.12541] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 01/09/2017] [Indexed: 06/07/2023]
Abstract
Antarctica is one of the most difficult habitats for sustaining life on earth; organisms that live there have developed different strategies for survival. Among these organisms is the green alga Prasiola crispa, belonging to the class Trebouxiophyceae. The literature on P. crispa taxonomy is scarce, and many gaps in the evolutionary relationship with its closest relatives remain. The goal of this study was to analyze the evolutionary relationships between P. crispa and other green algae using plastid and mitochondrial genomes. In addition, we analyzed the synteny conservation of these genomes of P. crispa with those of closely related species. Based on the plastid genome, P. crispa grouped with Prasiolopsis sp. SAG 84.81, another Trebouxiophyceaen species from the Prasiola clade. Based on the mitochondrial genome analysis, P. crispa grouped with other Trebouxiophyceaen species but had a basal position. The structure of the P. crispa chloroplast genome had low synteny with Prasiolopsis sp. SAG 84.81, despite some conserved gene blocks. The same was observed in the mitochondrial genome compared with Coccomyxa subellipsoidea C-169. We were able to establish the phylogenetic position of P. crispa with other species of Trebouxiophyceae using its genomes. In addition, we described the plasticity of these genomes using a structural analysis. The plastid and mitochondrial genomes of P. crispa will be useful for further genetic studies, phylogenetic analysis and resource protection of P. crispa as well as for further phylogenetic analysis of Trebouxiophyceaen green algae.
Collapse
Affiliation(s)
- Evelise Leis Carvalho
- Applied Proteomics Laboratory, University of Pampa, São Gabriel, RS, 97300-000, Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia Centro de Pesquisas Aggeu Magalhães, Fiocruz, Recife, 50740-465, Brazil
| | - Darlene Lopes Rangel
- Applied Proteomics Laboratory, University of Pampa, São Gabriel, RS, 97300-000, Brazil
| | - Laís Ceschini Machado
- Applied Proteomics Laboratory, University of Pampa, São Gabriel, RS, 97300-000, Brazil
| | | | | | | | - Paulo Marcos Pinto
- Applied Proteomics Laboratory, University of Pampa, São Gabriel, RS, 97300-000, Brazil
| |
Collapse
|
19
|
Sapp SG, Gupta P, Martin MK, Murray MH, Niedringhaus KD, Pfaff MA, Yabsley MJ. Beyond the raccoon roundworm: The natural history of non-raccoon Baylisascaris species in the New World. Int J Parasitol Parasites Wildl 2017; 6:85-99. [PMID: 28529879 PMCID: PMC5429227 DOI: 10.1016/j.ijppaw.2017.04.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/18/2017] [Indexed: 02/07/2023]
Abstract
A total of 10 species of Baylisascaris, a genus of ascaridoid nematodes, occur worldwide and 6 of them occur in the New World. Most of the Baylisascaris species have a similar life cycle with carnivorous mammals or marsupials serving as definitive hosts and a smaller prey host serving as paratenic (or intermediate) hosts. However, one species in rodents is unique in that it only has one host. Considerable research has been conducted on B. procyonis, the raccoon roundworm, as it is a well-known cause of severe to fatal neurologic disease in humans and many wildlife species. However, other Baylisascaris species could cause larva migrans but research on them is limited in comparison. In addition to concerns related to the potential impacts of larva migrans on potential paratenic hosts, there are many questions about the geographic ranges, definitive and paratenic host diversity, and general ecology of these non-raccoon Baylisascaris species. Here, we provide a comprehensive review of the current knowledge of New World Baylisascaris species, including B. columnaris of skunks, B. transfuga and B. venezuelensis of bears, B. laevis of sciurids, B. devosi of gulonids, B. melis of badgers, and B. potosis of kinkajou. Discussed are what is known regarding the morphology, host range, geographic distribution, ecoepidemiology, infection dynamics in definitive and paratenic hosts, treatment, and control of these under-studied species. Also, we discuss the currently used molecular tools used to investigate this group of parasites. Because of morphologic similarities among larval stages of sympatric Baylisascaris species, these molecular tools should provide critical insight into these poorly-understood areas, especially paratenic and definitive host diversity and the possible risk these parasites pose to the health to the former group. This, paired with traditional experimental infections, morphological analysis, and field surveys will lead to a greater understanding of this interesting and important nematode genus.
Collapse
Affiliation(s)
- Sarah G.H. Sapp
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Pooja Gupta
- Savannah River Ecology Lab, University of Georgia, Aiken, SC, USA
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, USA
| | - Melissa K. Martin
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, USA
| | - Maureen H. Murray
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, USA
| | - Kevin D. Niedringhaus
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Madeleine A. Pfaff
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, USA
| | - Michael J. Yabsley
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, USA
| |
Collapse
|
20
|
Valenciano A, Baskin JA, Abella J, Pérez-Ramos A, Álvarez-Sierra MÁ, Morales J, Hartstone-Rose A. Megalictis, the Bone-Crushing Giant Mustelid (Carnivora, Mustelidae, Oligobuninae) from the Early Miocene of North America. PLoS One 2016; 11:e0152430. [PMID: 27054570 PMCID: PMC4824437 DOI: 10.1371/journal.pone.0152430] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 03/14/2016] [Indexed: 11/18/2022] Open
Abstract
We describe cranial and mandibular remains of three undescribed individuals of the giant mustelid Megalictis ferox Matthew, 1907 from the latest Arikareean (Ar4), Early Miocene mammal fauna of Nebraska, and Wyoming (USA) housed at the American Museum of Natural History (New York, USA). Our phylogenetic hypothesis indicates that Ar4 specimens assigned to M. ferox constitute a monophyletic group. We assign three additional species previously referred to Paroligobunis to Megalictis: M. simplicidens, M. frazieri, and "M." petersoni. The node containing these four species of Megalictis and Oligobunis forms the Oligobuninae. We test the hypothesis that Oligobuninae (Megalictis and Oligobunis) is a stem mustelid taxon. Our results indicate that the Oligobuninae form the sister clade to the crown extant mustelids. Based on the cranium, M. ferox is a jaguar-size mustelid and the largest terrestrial mustelid known to have existed. This new material also sheds light on a new ecomorphological interpretation of M. ferox as a bone-crushing durophage (similar to hyenas), rather than a cat-like hypercarnivore, as had been previously described. The relative large size of M. ferox, together with a stout rostrum and mandible made it one of the more powerful predators of the Early Miocene of the Great Plains of North America.
Collapse
Affiliation(s)
- Alberto Valenciano
- Departamento de Geología Sedimentaria y Cambio Medioambiental, Instituto de Geociencias (CSIC, UCM), Madrid, Spain
- Departamento de Paleontología UCM, Facultad de Ciencias Geológicas UCM, Madrid, Spain
| | - Jon A. Baskin
- Department of Biological and Health Sciences, Texas A&M University-Kingsville, Kingsville, United States of America
| | - Juan Abella
- Universidad Estatal Península de Santa Elena, La Libertad, Santa Elena, Ecuador
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICP, Campus de la UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - Alejandro Pérez-Ramos
- Departamento de Ecología y Geología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - M. Ángeles Álvarez-Sierra
- Departamento de Geología Sedimentaria y Cambio Medioambiental, Instituto de Geociencias (CSIC, UCM), Madrid, Spain
- Departamento de Paleontología UCM, Facultad de Ciencias Geológicas UCM, Madrid, Spain
| | - Jorge Morales
- Departamento de Paleobiología. Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain
| | - Adam Hartstone-Rose
- Department of Cell Biology and Anatomy, University of South Carolina School of Medicine, Columbia, South Carolina, United States of America
- Department of Anthropology, University of South Carolina, Columbia, South Carolina, United States of America
| |
Collapse
|
21
|
Zhao C, Zhang H, Liu G, Yang X, Zhang J. The complete mitochondrial genome of the Tibetan fox (Vulpes ferrilata) and implications for the phylogeny of Canidae. C R Biol 2016; 339:68-77. [PMID: 26868757 DOI: 10.1016/j.crvi.2015.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/30/2015] [Accepted: 11/30/2015] [Indexed: 01/30/2023]
Abstract
Canidae is a family of carnivores comprises about 36 extant species that have been defined as three distinct monophyletic groups based on multi-gene data sets. The Tibetan fox (Vulpes ferrilata) is a member of the family Canidae that is endemic to the Tibetan Plateau and has seldom been in the focus of phylogenetic analyses. To clarify the phylogenic relationship of V. ferrilata between other canids, we sequenced the mitochondrial genome and firstly attempted to clarify the relative phylogenetic position of V. ferrilata in canids using the complete mitochondrial genome data. The mitochondrial genome of the Tibetan fox was 16,667 bp, including 37 genes (13 protein-coding genes, 2 rRNA, and 22 tRNA) and a control region. A comparison analysis among the sequenced data of canids indicated that they shared a similar arrangement, codon usage, and other aspects. A phylogenetic analysis on the basis of the nearly complete mtDNA genomes of canids agreed with three monophyletic clades, and the Tibetan fox was highly supported as a sister group of the corsac fox within Vulpes. The estimation of the divergence time suggested a recent split between the Tibetan fox and the corsac fox and rapid evolution in canids. There was no genetic evidence for positive selection related to high-altitude adaption for the Tibetan fox in mtDNA and following studies should pay more attention to the detection of positive signals in nuclear genes involved in energy and oxygen metabolisms.
Collapse
Affiliation(s)
- Chao Zhao
- College of Life Science, Qufu Normal University, Qufu, China.
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu, China.
| | - Guangshuai Liu
- College of Wildlife Resources, Northeast Forestry University, Harbin, China.
| | - Xiufeng Yang
- College of Life Science, Qufu Normal University, Qufu, China.
| | - Jin Zhang
- College of Life Science, Qufu Normal University, Qufu, China.
| |
Collapse
|
22
|
Moncrief ND, Fies ML. Report of First Specimens ofPekania pennanti(Fisher) from Virginia. Northeast Nat (Steuben) 2015. [DOI: 10.1656/045.022.0417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
23
|
Malyarchuk BA, Derenko MV, Denisova GA. Mitochondrial genome variability in the wolverine (Gulo gulo). RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415090069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
24
|
Vergara M, Basto MP, Madeira MJ, Gómez-Moliner BJ, Santos-Reis M, Fernandes C, Ruiz-González A. Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study. PLoS One 2015; 10:e0134257. [PMID: 26222680 PMCID: PMC4519273 DOI: 10.1371/journal.pone.0134257] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 07/07/2015] [Indexed: 11/20/2022] Open
Abstract
The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a) spatial and non-spatial Bayesian individual-based clustering (IBC) approaches (STRUCTURE, TESS, BAPS and GENELAND), and b) multivariate methods [discriminant analysis of principal components (DAPC) and spatial principal component analysis (sPCA)]. Additionally, because isolation by distance (IBD) is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence of the rivers Ebro, Tagus and Guadiana, suggesting that main watercourses in the Iberian Peninsula may act as semi-permeable barriers to gene flow in stone martens. To our knowledge, this is the first phylogeographic and population genetic study of the species at a broad regional scale. We also wanted to make the case for the importance and benefits of using and comparing multiple different clustering and multivariate methods in spatial genetic analyses of mobile and continuously distributed species.
Collapse
Affiliation(s)
- María Vergara
- Department of Zoology and Animal Cell Biology, Zoology Laboratory, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
- Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Mafalda P. Basto
- CE3C—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - María José Madeira
- Department of Zoology and Animal Cell Biology, Zoology Laboratory, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
- Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Benjamín J. Gómez-Moliner
- Department of Zoology and Animal Cell Biology, Zoology Laboratory, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
- Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Margarida Santos-Reis
- CE3C—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Carlos Fernandes
- CE3C—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Aritz Ruiz-González
- Department of Zoology and Animal Cell Biology, Zoology Laboratory, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
- Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| |
Collapse
|