1
|
Description of the Type Specimen of the Extinct Tenerife Giant Rat (Canariomys bravoi). J MAMM EVOL 2022. [DOI: 10.1007/s10914-021-09594-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
2
|
Renom P, de-Dios T, Civit S, Llovera L, Sánchez-Gracia A, Lizano E, Rando JC, Marquès-Bonet T, Kergoat GJ, Casanovas-Vilar I, Lalueza-Fox C. Genetic data from the extinct giant rat from Tenerife (Canary Islands) points to a recent divergence from mainland relatives. Biol Lett 2021; 17:20210533. [PMID: 34932923 PMCID: PMC8692034 DOI: 10.1098/rsbl.2021.0533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Evolution of vertebrate endemics in oceanic islands follows a predictable pattern, known as the island rule, according to which gigantism arises in originally small-sized species and dwarfism in large ones. Species of extinct insular giant rodents are known from all over the world. In the Canary Islands, two examples of giant rats, †Canariomys bravoi and †Canariomys tamarani, endemic to Tenerife and Gran Canaria, respectively, disappeared soon after human settlement. The highly derived morphological features of these insular endemic rodents hamper the reconstruction of their evolutionary histories. We have retrieved partial nuclear and mitochondrial data from †C. bravoi and used this information to explore its evolutionary affinities. The resulting dated phylogeny confidently places †C. bravoi within the African grass rat clade (Arvicanthis niloticus). The estimated divergence time, 650 000 years ago (95% higher posterior densities: 373 000–944 000), points toward an island colonization during the Günz–Mindel interglacial stage. †Canariomys bravoi ancestors would have reached the island via passive rafting and then underwent a yearly increase of mean body mass calculated between 0.0015 g and 0.0023 g; this corresponds to fast evolutionary rates (in darwins (d), ranging from 7.09 d to 2.78 d) that are well above those observed for non-insular mammals.
Collapse
Affiliation(s)
- Pere Renom
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona 08003, Spain
| | - Toni de-Dios
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona 08003, Spain.,University of Tartu, Institute of Genomics, Estonian Biocentre, Tartu 51010, Estonia
| | - Sergi Civit
- Departament of Genetics, Microbiology and Statistics-Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona 08028, Spain
| | - Laia Llovera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona 08003, Spain
| | - Alejandro Sánchez-Gracia
- Departament of Genetics, Microbiology and Statistics-Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona 08028, Spain
| | - Esther Lizano
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona 08003, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona 08193, Spain
| | - Juan Carlos Rando
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, La Laguna 38206, Tenerife, Spain
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona 08003, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona 08193, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona 08010, Spain.,CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona 08036, Spain
| | - Gael J Kergoat
- CBGP, INRAE, IRD, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Isaac Casanovas-Vilar
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona 08193, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona 08003, Spain
| |
Collapse
|
3
|
Izquierdo-Rico MJ, Moros-Nicolás C, Pérez-Crespo M, Laguna-Barraza R, Gutiérrez-Adán A, Veyrunes F, Ballesta J, Laudet V, Chevret P, Avilés M. ZP4 Is Present in Murine Zona Pellucida and Is Not Responsible for the Specific Gamete Interaction. Front Cell Dev Biol 2021; 8:626679. [PMID: 33537315 PMCID: PMC7848090 DOI: 10.3389/fcell.2020.626679] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
Mammalian eggs are surrounded by an extracellular matrix called the zona pellucida (ZP). This envelope participates in processes such as acrosome reaction induction, sperm binding, protection of the oviductal embryo, and may be involved in speciation. In eutherian mammals, this coat is formed of three or four glycoproteins (ZP1–ZP4). While Mus musculus has been used as a model to study the ZP for more than 35 years, surprisingly, it is the only eutherian species in which the ZP is formed of three glycoproteins Zp1, Zp2, and Zp3, Zp4 being a pseudogene. Zp4 was lost in the Mus lineage after it diverged from Rattus, although it is not known when precisely this loss occurred. In this work, the status of Zp4 in several murine rodents was tested by phylogenetic, molecular, and proteomic analyses. Additionally, assays of cross in vitro fertilization between three and four ZP rodents were performed to test the effect of the presence of Zp4 in murine ZP and its possible involvement in reproductive isolation. Our results showed that Zp4 pseudogenization is restricted to the subgenus Mus, which diverged around 6 MYA. Heterologous in vitro fertilization assays demonstrate that a ZP formed of four glycoproteins is not a barrier for the spermatozoa of species with a ZP formed of three glycoproteins. This study identifies the existence of several mouse species with four ZPs that can be considered suitable for use as an experimental animal model to understand the structural and functional roles of the four ZP proteins in other species, including human.
Collapse
Affiliation(s)
- Mª José Izquierdo-Rico
- Department of Cell Biology and Histology, Faculty of Medicine, University of Murcia, Murcia, Spain.,Institute for Biomedical Research of Murcia (IMIB-Arrixaca), Murcia, Spain.,International Excellence Campus for Higher Education and Research "Campus Mare Nostrum", Murcia, Spain
| | - Carla Moros-Nicolás
- Department of Cell Biology and Histology, Faculty of Medicine, University of Murcia, Murcia, Spain.,Institute for Biomedical Research of Murcia (IMIB-Arrixaca), Murcia, Spain.,International Excellence Campus for Higher Education and Research "Campus Mare Nostrum", Murcia, Spain
| | - Míriam Pérez-Crespo
- Department of Animal Reproduction, Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Madrid, Spain
| | - Ricardo Laguna-Barraza
- Department of Animal Reproduction, Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Madrid, Spain
| | - Alfonso Gutiérrez-Adán
- Department of Animal Reproduction, Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Madrid, Spain
| | - Frédéric Veyrunes
- Institut des Sciences de l'Evolution, UMR5554 CNRS/Université Montpellier/IRD/EPHE, Montpellier, France
| | - José Ballesta
- Department of Cell Biology and Histology, Faculty of Medicine, University of Murcia, Murcia, Spain.,Institute for Biomedical Research of Murcia (IMIB-Arrixaca), Murcia, Spain.,International Excellence Campus for Higher Education and Research "Campus Mare Nostrum", Murcia, Spain
| | - Vincent Laudet
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Pascale Chevret
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Manuel Avilés
- Department of Cell Biology and Histology, Faculty of Medicine, University of Murcia, Murcia, Spain.,Institute for Biomedical Research of Murcia (IMIB-Arrixaca), Murcia, Spain.,International Excellence Campus for Higher Education and Research "Campus Mare Nostrum", Murcia, Spain
| |
Collapse
|
4
|
Revisiting the Foraging Ecology and Extinction History of Two Endemic Vertebrates from Tenerife, Canary Islands. QUATERNARY 2019. [DOI: 10.3390/quat2010010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We used carbon (δ13C) and nitrogen (δ15N) isotopes to examine the foraging ecology of Tenerife giant rats (Canariomys bravoi) and lizards (Gallotia goliath) in northwestern Tenerife, which until recently, were the island’s largest terrestrial vertebrates. We combined new isotope data for 28 C. bravoi and 14 G. goliath with published regional data for both species and then compared these with data for co-occurring extant taxa and modern C3 plants. Isotope data suggest both extinct species relied primarily on C3 resources and were trophic omnivores. However, the two species appear to have partitioned their resources when living in sympatry. Isotopic overlap between C. bravoi and Rattus spp., and between G. goliath, extant Gallotia galloti, and introduced rabbits (Oryctolagus cuniculus) suggests reliance on similar foods. We radiocarbon dated four C. bravoi and two G. goliath with the most extreme isotope values. These new dates do not settle the question of what triggered the demise of either species. Nevertheless, the data are most consistent with anthropogenically-induced extinction. Temporal isotopic trends contradict expectations if regional climate were responsible, and confidence intervals for radiocarbon dates suggest it is highly likely that both species were present when humans first settled the island.
Collapse
|
5
|
Woods R, Marr MM, Brace S, Barnes I. The Small and the Dead: A Review of Ancient DNA Studies Analysing Micromammal Species. Genes (Basel) 2017; 8:E312. [PMID: 29117125 PMCID: PMC5704225 DOI: 10.3390/genes8110312] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/13/2017] [Accepted: 10/13/2017] [Indexed: 02/06/2023] Open
Abstract
The field of ancient DNA (aDNA) has recently been in a state of exponential growth, largely driven by the uptake of Next Generation Sequencing (NGS) techniques. Much of this work has focused on the mammalian megafauna and ancient humans, with comparatively less studies looking at micromammal fauna, despite the potential of these species in testing evolutionary, environmental and taxonomic theories. Several factors make micromammal fauna ideally suited for aDNA extraction and sequencing. Micromammal subfossil assemblages often include the large number of individuals appropriate for population level analyses, and, furthermore, the assemblages are frequently found in cave sites where the constant temperature and sheltered environment provide favourable conditions for DNA preservation. This review looks at studies that include the use of aDNA in molecular analysis of micromammal fauna, in order to examine the wide array of questions that can be answered in the study of small mammals using new palaeogenetic techniques. This study highlights the bias in current aDNA studies and assesses the future use of aDNA as a tool for the study of micromammal fauna.
Collapse
Affiliation(s)
- Roseina Woods
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Melissa M Marr
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| |
Collapse
|
6
|
Pagès M, Fabre PH, Chaval Y, Mortelliti A, Nicolas V, Wells K, Michaux JR, Lazzari V. Molecular phylogeny of South-East Asian arboreal murine rodents. ZOOL SCR 2015. [DOI: 10.1111/zsc.12161] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marie Pagès
- Unité de génétique de la conservation; Institut de Botanique; Université de Liège; 4000 Liège (Sart Tilman) Belgique
- INRA; UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro); Campus International de Baillarguet, CS 30016 34988 Montferrier-sur-Lez Cedex France
- Institut des Sciences de l’Évolution de Montpellier; Université de Montpellier; CNRS; IRD; EPHE; 34095 Montpellier France
| | - Pierre-Henri Fabre
- Harvard Museum of Comparative Zoology; 26 Oxford Street Cambridge MA 02138 USA
- Smithsonian Institution; PO Box 37012, MRC 108 Washington DC 20013-7012 USA
| | - Yannick Chaval
- INRA; UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro); Campus International de Baillarguet, CS 30016 34988 Montferrier-sur-Lez Cedex France
| | - Alessio Mortelliti
- Department of Wildlife, Fisheries, and Conservation Biology; University of Maine; 5755 Nutting Hall, Room 228 Orono ME 04469 USA
| | - Violaine Nicolas
- Institut de Systématique, Évolution, Biodiversité; ISYEB - UMR 7205, CNRS; MNHN; UPMC; EPHE; Muséum national d'Histoire naturelle; Sorbonne Universités 57 rue Cuvier, CP 51 75005 Paris France
| | - Konstans Wells
- Environmental Futures Research Institute; Griffith University; Brisbane Qld 4111 Australia
| | - Johan R. Michaux
- Unité de génétique de la conservation; Institut de Botanique; Université de Liège; 4000 Liège (Sart Tilman) Belgique
- CIRAD; TA C- 22/E - Campus international de Baillarguet 34398 Montpellier Cedex 5 France
| | - Vincent Lazzari
- Institut de paléoprimatologie; Paléontologie Humaine: Evolution et paléoenvironnements - UMR CNRS 7262 INEE; 86022 6 rue Michel Brunet Poitier France
| |
Collapse
|
7
|
Opatova V, Arnedo MA. Spiders on a Hot Volcanic Roof: Colonisation Pathways and Phylogeography of the Canary Islands Endemic Trap-Door Spider Titanidiops canariensis (Araneae, Idiopidae). PLoS One 2014; 9:e115078. [PMID: 25494329 PMCID: PMC4262472 DOI: 10.1371/journal.pone.0115078] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 11/03/2014] [Indexed: 11/19/2022] Open
Abstract
Studies conducted on volcanic islands have greatly contributed to our current understanding of how organisms diversify. The Canary Islands archipelago, located northwest of the coast of northern Africa, harbours a large number of endemic taxa. Because of their low vagility, mygalomorph spiders are usually absent from oceanic islands. The spider Titanidiops canariensis, which inhabits the easternmost islands of the archipelago, constitutes an exception to this rule. Here, we use a multi-locus approach that combines three mitochondrial and four nuclear genes to investigate the origins and phylogeography of this remarkable trap-door spider. We provide a timeframe for the colonisation of the Canary Islands using two alternative approaches: concatenation and species tree inference in a Bayesian relaxed clock framework. Additionally, we investigate the existence of cryptic species on the islands by means of a Bayesian multi-locus species delimitation method. Our results indicate that T. canariensis colonised the Canary Islands once, most likely during the Miocene, although discrepancies between the timeframes from different approaches make the exact timing uncertain. A complex evolutionary history for the species in the archipelago is revealed, which involves two independent colonisations of Fuerteventura from the ancestral range of T. canariensis in northern Lanzarote and a possible back colonisation of southern Lanzarote. The data further corroborate a previously proposed volcanic refugium, highlighting the impact of the dynamic volcanic history of the island on the phylogeographic patterns of the endemic taxa. T. canariensis includes at least two different species, one inhabiting the Jandia peninsula and central Fuerteventura and one spanning from central Fuerteventura to Lanzarote. Our data suggest that the extant northern African Titanidiops lineages may have expanded to the region after the islands were colonised and, hence, are not the source of colonisation. In addition, T. maroccanus may harbour several cryptic species.
Collapse
Affiliation(s)
- Vera Opatova
- Institut de Recerca de la Biodiversitat & Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
- * E-mail:
| | - Miquel A. Arnedo
- Institut de Recerca de la Biodiversitat & Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
| |
Collapse
|
8
|
Chevret P, Robinson TJ, Perez J, Veyrunes F, Britton-Davidian J. A phylogeographic survey of the pygmy mouse Mus minutoides in South Africa: taxonomic and karyotypic inference from cytochrome b sequences of museum specimens. PLoS One 2014; 9:e98499. [PMID: 24905736 PMCID: PMC4048158 DOI: 10.1371/journal.pone.0098499] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 05/03/2014] [Indexed: 11/25/2022] Open
Abstract
The African pygmy mice (Mus, subgenus Nannomys) are a group of small-sized rodents that occur widely throughout sub-Saharan Africa. Chromosomal diversity within this group is extensive and numerous studies have shown the karyotype to be a useful taxonomic marker. This is pertinent to Mus minutoides populations in South Africa where two different cytotypes (2n = 34, 2n = 18) and a modification of the sex determination system (due to the presence of a Y chromosome in some females) have been recorded. This chromosomal diversity is mirrored by mitochondrial DNA sequences that unambiguously discriminate among the various pygmy mouse species and, importantly, the different M. minutoides cytotypes. However, the geographic delimitation and taxonomy of pygmy mice populations in South Africa is poorly understood. To address this, tissue samples of M. minutoides were taken and analysed from specimens housed in six South African museum collections. Partial cytochrome b sequences (400 pb) were successfully amplified from 44% of the 154 samples processed. Two species were identified: M. indutus and M. minutoides. The sequences of the M. indutus samples provided two unexpected features: i) nuclear copies of the cytochrome b gene were detected in many specimens, and ii) the range of this species was found to extend considerably further south than is presently understood. The phylogenetic analysis of the M. minutoides samples revealed two well-supported clades: a Southern clade which included the two chromosomal groups previously identified in South Africa, and an Eastern clade that extended from Eastern Africa into South Africa. Congruent molecular phylogenetic and chromosomal datasets permitted the tentative chromosomal assignments of museum specimens within the different clades as well as the correction of misidentified museum specimens.
Collapse
Affiliation(s)
- Pascale Chevret
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, Villeurbanne, France
- * E-mail:
| | - Terence J. Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Julie Perez
- Institut des Sciences de l’Evolution de Montpellier, UMR CNRS 5554, Université Montpellier 2, Montpellier, France
| | - Frédéric Veyrunes
- Institut des Sciences de l’Evolution de Montpellier, UMR CNRS 5554, Université Montpellier 2, Montpellier, France
| | - Janice Britton-Davidian
- Institut des Sciences de l’Evolution de Montpellier, UMR CNRS 5554, Université Montpellier 2, Montpellier, France
| |
Collapse
|
9
|
Rando JC, Pieper H, Alcover JA. Radiocarbon evidence for the presence of mice on Madeira Island (North Atlantic) one millennium ago. Proc Biol Sci 2014; 281:20133126. [PMID: 24523273 DOI: 10.1098/rspb.2013.3126] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Owing to the catastrophic extinction events that occurred following the Holocene arrival of alien species, extant oceanic island biotas are a mixture of recently incorporated alien fauna and remnants of the original fauna. Knowledge of the Late Quaternary pristine island faunas and a reliable chronology of the earliest presence of alien species on each archipelago are critical in understanding the magnitude and tempo of Quaternary island extinctions. Until now, two successive waves of human arrivals have been identified in the North Atlantic Macaronesian archipelagos (Azores, Madeira, Selvagens, Canary and Cape Verde Islands): 'aboriginal', which is limited to the Canary Islands around two millennia ago, and 'colonial', from the fourteenth century onwards. New surveys in Ponta de São Lourenço (Madeira Island) have allowed us to obtain and date ancient bones of mice. The date obtained (1033 ± 28 BP) documents the earliest evidence for the presence of mice on the island. This date extends the time frame in which the most significant ecological changes occurred on the island. It also suggests that humans could have reached Madeira before 1036 cal AD, around four centuries before Portugal officially took possession of the island.
Collapse
Affiliation(s)
- Juan Carlos Rando
- Departamento de Biología Animal (Zoología), Universidad de La Laguna Tenerife, , Canary Islands, Spain, Ulmenstrasse 21, Schwentinental 24223, Germany, Departament de Biodiversitat i Conservació, IMEDEA (CSIC-UIB), Cr Miquel Marquès 21, Esporles, Mallorca, Balearic Islands 07190, Spain, Department of Mammalogy, American Museum of Natural History, , New York, NY 10024-5192, USA
| | | | | |
Collapse
|
10
|
Galan M, Pagès M, Cosson JF. Next-generation sequencing for rodent barcoding: species identification from fresh, degraded and environmental samples. PLoS One 2012; 7:e48374. [PMID: 23144869 PMCID: PMC3492341 DOI: 10.1371/journal.pone.0048374] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 09/25/2012] [Indexed: 11/18/2022] Open
Abstract
Rodentia is the most diverse order among mammals, with more than 2,000 species currently described. Most of the time, species assignation is so difficult based on morphological data solely that identifying rodents at the specific level corresponds to a real challenge. In this study, we compared the applicability of 100 bp mini-barcodes from cytochrome b and cytochrome c oxidase 1 genes to enable rodent species identification. Based on GenBank sequence datasets of 115 rodent species, a 136 bp fragment of cytochrome b was selected as the most discriminatory mini-barcode, and rodent universal primers surrounding this fragment were designed. The efficacy of this new molecular tool was assessed on 946 samples including rodent tissues, feces, museum samples and feces/pellets from predators known to ingest rodents. Utilizing next-generation sequencing technologies able to sequence mixes of DNA, 1,140 amplicons were tagged, multiplexed and sequenced together in one single 454 GS-FLX run. Our method was initially validated on a reference sample set including 265 clearly identified rodent tissues, corresponding to 103 different species. Following validation, 85.6% of 555 rodent samples from Europe, Asia and Africa whose species identity was unknown were able to be identified using the BLASTN program and GenBank reference sequences. In addition, our method proved effective even on degraded rodent DNA samples: 91.8% and 75.9% of samples from feces and museum specimens respectively were correctly identified. Finally, we succeeded in determining the diet of 66.7% of the investigated carnivores from their feces and 81.8% of owls from their pellets. Non-rodent species were also identified, suggesting that our method is sensitive enough to investigate complete predator diets. This study demonstrates how this molecular identification method combined with high-throughput sequencing can open new realms of possibilities in achieving fast, accurate and inexpensive species identification.
Collapse
Affiliation(s)
- Maxime Galan
- Institut national de la recherche agronomique, Joint Research Unit Centre de Biologie pour la Gestion des Populations (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, Montferrier-sur-Lez, France.
| | | | | |
Collapse
|
11
|
Latinne A, Waengsothorn S, Rojanadilok P, Eiamampai K, Sribuarod K, Michaux JR. Combined mitochondrial and nuclear markers revealed a deep vicariant history for Leopoldamys neilli, a cave-dwelling rodent of Thailand. PLoS One 2012; 7:e47670. [PMID: 23118888 PMCID: PMC3485250 DOI: 10.1371/journal.pone.0047670] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 09/19/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Historical biogeography and evolutionary processes of cave taxa have been widely studied in temperate regions. However, Southeast Asian cave ecosystems remain largely unexplored despite their high scientific interest. Here we studied the phylogeography of Leopoldamys neilli, a cave-dwelling murine rodent living in limestone karsts of Thailand, and compared the molecular signature of mitochondrial and nuclear markers. METHODOLOGY/PRINCIPAL FINDINGS We used a large sampling (n = 225) from 28 localities in Thailand and a combination of mitochondrial and nuclear markers with various evolutionary rates (two intronic regions and 12 microsatellites). The evolutionary history of L. neilli and the relative role of vicariance and dispersal were investigated using ancestral range reconstruction analysis and Approximate Bayesian computation (ABC). Both mitochondrial and nuclear markers support a large-scale population structure of four main groups (west, centre, north and northeast) and a strong finer structure within each of these groups. A deep genealogical divergence among geographically close lineages is observed and denotes a high population fragmentation. Our findings suggest that the current phylogeographic pattern of this species results from the fragmentation of a widespread ancestral population and that vicariance has played a significant role in the evolutionary history of L. neilli. These deep vicariant events that occurred during Plio-Pleistocene are related to the formation of the Central Plain of Thailand. Consequently, the western, central, northern and northeastern groups of populations were historically isolated and should be considered as four distinct Evolutionarily Significant Units (ESUs). CONCLUSIONS/SIGNIFICANCE Our study confirms the benefit of using several independent genetic markers to obtain a comprehensive and reliable picture of L. neilli evolutionary history at different levels of resolution. The complex genetic structure of Leopoldamys neilli is supported by congruent mitochondrial and nuclear markers and has been influenced by the geological history of Thailand during Plio-Pleistocene.
Collapse
Affiliation(s)
- Alice Latinne
- Laboratoire de génétique des microorganismes, Institut de Botanique, University of Liège, Liège, Belgium.
| | | | | | | | | | | |
Collapse
|