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Hawkins MTR, Hofman CA, Callicrate T, McDonough MM, Tsuchiya MTN, Gutiérrez EE, Helgen KM, Maldonado JE. In-solution hybridization for mammalian mitogenome enrichment: pros, cons and challenges associated with multiplexing degraded DNA. Mol Ecol Resour 2015. [PMID: 26220248 DOI: 10.1111/1755-0998.12448] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we present a set of RNA-based probes for whole mitochondrial genome in-solution enrichment, targeting a diversity of mammalian mitogenomes. This probes set was designed from seven mammalian orders and tested to determine the utility for enriching degraded DNA. We generated 63 mitogenomes representing five orders and 22 genera of mammals that yielded varying coverage ranging from 0 to >5400X. Based on a threshold of 70% mitogenome recovery and at least 10× average coverage, 32 individuals or 51% of samples were considered successful. The estimated sequence divergence of samples from the probe sequences used to construct the array ranged up to nearly 20%. Sample type was more predictive of mitogenome recovery than sample age. The proportion of reads from each individual in multiplexed enrichments was highly skewed, with each pool having one sample that yielded a majority of the reads. Recovery across each mitochondrial gene varied with most samples exhibiting regions with gaps or ambiguous sites. We estimated the ability of the probes to capture mitogenomes from a diversity of mammalian taxa not included here by performing a clustering analysis of published sequences for 100 taxa representing most mammalian orders. Our study demonstrates that a general array can be cost and time effective when there is a need to screen a modest number of individuals from a variety of taxa. We also address the practical concerns for using such a tool, with regard to pooling samples, generating high quality mitogenomes and detail a pipeline to remove chimeric molecules.
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Affiliation(s)
- Melissa T R Hawkins
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA.,Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA.,Department of Environmental Science & Policy, George Mason University, Fairfax, VA, 22030, USA
| | - Courtney A Hofman
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA.,Program in Human Ecology and Archaeobiology, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA.,Department of Anthropology, University of Maryland, College Park, MD, 20742, USA
| | - Taylor Callicrate
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA.,Department of Animal & Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Molly M McDonough
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA.,Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Mirian T N Tsuchiya
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA.,Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA.,Department of Environmental Science & Policy, George Mason University, Fairfax, VA, 22030, USA
| | - Eliécer E Gutiérrez
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA.,Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Kristofer M Helgen
- Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
| | - Jesus E Maldonado
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20008, USA.,Division of Mammals, National Museum of Natural History, MRC 108, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-7012, USA
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Bryja J, Mikula O, Šumbera R, Meheretu Y, Aghová T, Lavrenchenko LA, Mazoch V, Oguge N, Mbau JS, Welegerima K, Amundala N, Colyn M, Leirs H, Verheyen E. Pan-African phylogeny of Mus (subgenus Nannomys) reveals one of the most successful mammal radiations in Africa. BMC Evol Biol 2014; 14:256. [PMID: 25496476 PMCID: PMC4280006 DOI: 10.1186/s12862-014-0256-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 11/27/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rodents of the genus Mus represent one of the most valuable biological models for biomedical and evolutionary research. Out of the four currently recognized subgenera, Nannomys (African pygmy mice, including the smallest rodents in the world) comprises the only original African lineage. Species of this subgenus became important models for the study of sex determination in mammals and they are also hosts of potentially dangerous pathogens. Nannomys ancestors colonized Africa from Asia at the end of Miocene and Eastern Africa should be considered as the place of their first radiation. In sharp contrast with this fact and despite the biological importance of Nannomys, the specimens from Eastern Africa were obviously under-represented in previous studies and the phylogenetic and distributional patterns were thus incomplete. RESULTS We performed comprehensive genetic analysis of 657 individuals of Nannomys collected at approximately 300 localities across the whole sub-Saharan Africa. Phylogenetic reconstructions based on mitochondrial (CYTB) and nuclear (IRBP) genes identified five species groups and three monotypic ancestral lineages. We provide evidence for important cryptic diversity and we defined and mapped the distribution of 27 molecular operational taxonomic units (MOTUs) that may correspond to presumable species. Biogeographical reconstructions based on data spanning all of Africa modified the previous evolutionary scenarios. First divergences occurred in Eastern African mountains soon after the colonization of the continent and the remnants of these old divergences still occur there, represented by long basal branches of M. (previously Muriculus) imberbis and two undescribed species from Ethiopia and Malawi. The radiation in drier lowland habitats associated with the decrease of body size is much younger, occurred mainly in a single lineage (called the minutoides group, and especially within the species M. minutoides), and was probably linked to aridification and climatic fluctuations in middle Pliocene/Pleistocene. CONCLUSIONS We discovered very high cryptic diversity in African pygmy mice making the genus Mus one of the richest genera of African mammals. Our taxon sampling allowed reliable phylogenetic and biogeographic reconstructions that (together with detailed distributional data of individual MOTUs) provide a solid basis for further evolutionary, ecological and epidemiological studies of this important group of rodents.
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Affiliation(s)
- Josef Bryja
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Research Facility Studenec, Studenec 122, 675 02, Koněšín, Czech Republic.
| | - Ondřej Mikula
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
| | - Yonas Meheretu
- Department of Biology, College of Natural and Computational Sciences, Mekelle University, Tigray, Ethiopia.
| | - Tatiana Aghová
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | | | - Vladimír Mazoch
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
| | | | - Judith S Mbau
- College of Agriculture and Veterinary Sciences, University of Nairobi, Nairobi, Kenya.
| | - Kiros Welegerima
- Department of Biology, College of Natural and Computational Sciences, Mekelle University, Tigray, Ethiopia.
| | - Nicaise Amundala
- University of Kisangani, Eastern Province, Kisangani, DR, Congo.
| | - Marc Colyn
- CNRS UMR 6552/53, Université de Rennes 1, Station Biologique, Paimpont, France.
| | - Herwig Leirs
- Evolutionary Ecology Group, Biology Department, University of Antwerp, Antwerpen, Belgium.
| | - Erik Verheyen
- Evolutionary Ecology Group, Biology Department, University of Antwerp, Antwerpen, Belgium.
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, Brussels, Belgium.
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Veyrunes F, Perez J, Borremans B, Gryseels S, Richards LR, Duran A, Chevret P, Robinson TJ, Britton-Davidian J. A new cytotype of the African pygmy mouse Mus minutoides in Eastern Africa. Implications for the evolution of sex-autosome translocations. Chromosome Res 2014; 22:533-43. [PMID: 25159220 DOI: 10.1007/s10577-014-9440-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 07/31/2014] [Accepted: 08/17/2014] [Indexed: 11/27/2022]
Abstract
The African pygmy mice (genus Mus, subgenus Nannomys) are recognized for their highly conserved morphology but extensive chromosomal diversity, particularly involving sex-autosome translocations, one of the rarest chromosomal rearrangements among mammals. It has been shown that in the absence of unambiguous diagnostic morphological traits, sex-autosome translocations offer accurate taxonomic markers. For example, in Mus minutoides, irrespective of the diploid number (which ranges from 2n = 18 to 34), all specimens possess the sex-autosome translocations (X.1) and (Y.1) that are unique to this species. In this study, we describe a new cytotype that challenges this view. Males are characterized by the translocation (Y.1) only, while females carry no sex-autosome translocation, the X chromosome being acrocentric. Hence, although sex-autosome translocations (X.1) and (Y.1) are still diagnostic when one or both are present, their absence does not rule out M. minutoides. This cytotype has a large distribution, with specimens found in Tanzania and in the eastern part of South Africa. The nonpervasive distribution of Rb(X.1) provides an opportunity to investigate different evolutionary scenarios of sex-autosome translocations using a phylogenetic framework and the distribution of telomeric repeats. The results tend to support a scenario involving a reversal event, i.e., fusion then fission of Rb(X.1), and highlighted the existence of a new X1X1X2X2/X1X2Y sex chromosome system, confirming the remarkable diversity of neo-sex chromosomes and sex determination systems in the African pygmy mice.
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Affiliation(s)
- F Veyrunes
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier 2, UMR CNRS 5554, Montpellier, France,
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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.
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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
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