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Jiménez R, Burgos M, Barrionuevo FJ. The Biology and Evolution of Fierce Females (Moles and Hyenas). Annu Rev Anim Biosci 2023; 11:141-162. [PMID: 36130099 DOI: 10.1146/annurev-animal-050622-043424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Talpid moles and spotted hyenas have become the paradigms of anatomical and behavioral female masculinization. Females of many mole species develop ovotestes that produce testosterone, show external genitalia that resemble that of males, and close their vaginal orifice after every estrus, and female spotted hyenas lack an external vaginal orifice and develop a pseudoscrotum and a large pseudopenis through which they urinate, mate, and give birth. We review current knowledge about several significant aspects of the biology and evolution of these females, including (a) their specific study methods; (b) their unique anatomical features, and how these peculiarities influence certain physiological functions; and (c) the role that steroid hormones as well as genetic and environmental factors may have in urogenital system development, aggressive behavior, and social dominance. Nevertheless, both mole and hyena females are exceptionally efficient mothers, so their peculiar genitalia should not call into question their femininity.
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Affiliation(s)
- Rafael Jiménez
- Department of Genetics, Institute of Biotechnology, and Center of Biomedical Research (CIBM), University of Granada, Armilla, Granada, Spain; , ,
| | - Miguel Burgos
- Department of Genetics, Institute of Biotechnology, and Center of Biomedical Research (CIBM), University of Granada, Armilla, Granada, Spain; , ,
| | - Francisco J Barrionuevo
- Department of Genetics, Institute of Biotechnology, and Center of Biomedical Research (CIBM), University of Granada, Armilla, Granada, Spain; , ,
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2
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Demirtaş S, Budak M, Korkmaz EM, Searle JB, Bilton DT, Gündüz İ. The complete mitochondrial genome of Talpa martinorum (Mammalia: Talpidae), a mole species endemic to Thrace: genome content and phylogenetic considerations. Genetica 2022; 150:317-325. [PMID: 36029420 DOI: 10.1007/s10709-022-00162-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 08/04/2022] [Indexed: 11/04/2022]
Abstract
The complete mitogenome sequence of Talpa martinorum, a recently described Balkan endemic mole, was assembled from next generation sequence data. The mitogenome is similar to that of the three other Talpa species sequenced to date, being 16,835 bp in length, and containing 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, an origin of L-strand replication, and a control region or D-loop. Compared to other Talpa mitogenomes sequenced to date, that of T. martinorum differs in the length of D-loop and stop codon usage. TAG and T-- are the stop codons for the ND1 and ATP8 genes, respectively, in T. martinorum, whilst TAA acts as a stop codon for both ND1 and ATP8 in the other three Talpa species sequenced. Phylogeny reconstructions based on Maximum Likelihood and Bayesian inference analyses yielded phylogenies with similar topologies, demonstrating that T. martinorum nests within the western lineage of the genus, being closely related to T. aquitania and T. occidentalis.
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Affiliation(s)
- Sadık Demirtaş
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
| | - Mahir Budak
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Ertan M Korkmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853-2701, USA
| | - David T Bilton
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, Devon, PL4 8AA, UK.,Department of Zoology, University of Johannesburg, Auckland Park, PO Box 524, Johannesburg, 2006, South Africa
| | - İslam Gündüz
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey.
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3
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Escoda L, Castresana J. The genome of the Pyrenean desman and the effects of bottlenecks and inbreeding on the genomic landscape of an endangered species. Evol Appl 2021; 14:1898-1913. [PMID: 34295371 PMCID: PMC8288019 DOI: 10.1111/eva.13249] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/19/2021] [Accepted: 04/27/2021] [Indexed: 01/23/2023] Open
Abstract
The Pyrenean desman (Galemys pyrenaicus) is a small semiaquatic mammal endemic to the Iberian Peninsula. Despite its limited range, this species presents a strong genetic structure due to past isolation in glacial refugia and subsequent bottlenecks. Additionally, some populations are highly fragmented today as a consequence of river barriers, causing substantial levels of inbreeding. These features make the Pyrenean desman a unique model in which to study the genomic footprints of differentiation, bottlenecks and extreme isolation in an endangered species. To understand these processes, the complete genome of the Pyrenean desman was sequenced and assembled using a Bloom filter-based approach. An analysis of the 1.83 Gb reference genome and the sequencing of five additional individuals from different evolutionary units allowed us to detect its main genomic characteristics. The population differentiation of the species was reflected in highly distinctive demographic trajectories. In addition, a severe population bottleneck during the postglacial recolonization of the eastern Pyrenees created one of the lowest genomic heterozygosity values recorded in a mammal. Moreover, isolation and inbreeding gave rise to a high proportion of runs of homozygosity (ROH). Despite these extremely low levels of genetic diversity, two key multigene families from an eco-evolutionary perspective, the major histocompatibility complex and olfactory receptor genes, showed heterozygosity excess in the majority of individuals, revealing that functional diversity can be maintained up to a certain extent. Furthermore, these two classes of genes were significantly less abundant than expected within ROH. In conclusion, the genomic landscape of each analysed Pyrenean desman turned out to be strikingly distinctive and was a clear reflection of its recent ancestry and current conservation conditions. These results may help characterize the genomic health of each individual, and can be crucial for the conservation and management of the species.
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Affiliation(s)
- Lídia Escoda
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
| | - Jose Castresana
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
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Zhu L, Qing-Qing W, Xue-Ting J, Wen-Jing J, Xin-Xu Z, Qian-Qian Y, Jun-Sheng Z, Zhong-Wan P. Sequencing and analysis of the complete mitochondrial genome of the lesser bandicoot rat ( Bandicota bengalensis) from China and its phylogenetic analysis. Mitochondrial DNA B Resour 2021; 6:2063-2065. [PMID: 34212099 PMCID: PMC8218843 DOI: 10.1080/23802359.2021.1942273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
The complete mitogenome sequence of the lesser bandicoot rat (Bandicota bengalensis Gray and Hardwicke, 1833) was determined using long PCR. The genome was 16,327 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand is A (34.2%), C (24.9%), T (28.5%) and G (12.4%). The base compositions present clearly the A-T skew, which is most obviously in the control region and protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees. This study verifies the evolutionary status of Bandicota bengalensis in Muridae at the molecular level. The mitochondrial genome would be a significant supplement for the Bandicota bengalensis genetic background. The two Bandicota species formed a monophyletic group with the high bootstrap value (100%) in all examinations.
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Affiliation(s)
- Liu Zhu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Wang Qing-Qing
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Jiang Xue-Ting
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Jiang Wen-Jing
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Zhao Xin-Xu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Yao Qian-Qian
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Zhang Jun-Sheng
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Piao Zhong-Wan
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
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Zhao XX, Piao ZW, Yang QJ, Zhang Q, Yao QQ, Zhang JS, Liu Z. Sequencing and analysis of the complete mitochondrial genome of Ochotona hyperborea from China and its phylogenetic analysis. Mitochondrial DNA B Resour 2021; 6:1805-1807. [PMID: 34124354 PMCID: PMC8174475 DOI: 10.1080/23802359.2021.1934137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/15/2021] [Indexed: 12/05/2022] Open
Abstract
The complete mitogenome sequence of Ochotona hyperborea was determined using long PCR. The genome was 17,063 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one origin of L strand replication, and one control region. The overall base composition of the heavy strand is A (31.1%), C (28.7%), T (26.3%), and G (13.9%). The base compositions present clearly the A-T skew, which is most obvious in the control region and protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ, and Bayesian analyses yielded identical phylogenetic trees. This study verifies the evolutionary status of Ochotona hyperborea in Ochotonidae at the molecular level. The mitochondrial genome would be a significant supplement for the Ochotona hyperborea genetic background. The eight Ochotona species formed a monophyletic group with the high bootstrap value (100%) in all examinations.
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Affiliation(s)
- Xin-Xu Zhao
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, PR China
| | - Zhong-Wan Piao
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, PR China
| | - Qiao-Jiang Yang
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, PR China
| | - Qi Zhang
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, PR China
| | - Qian-Qian Yao
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, PR China
| | - Jun-Sheng Zhang
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, PR China
| | - Zhu Liu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, PR China
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Cai H, Wang QQ, Zhao XX, Yao QQ, Wu N, Zhang JS, Liu Z. Sequencing and analysis of the complete mitochondrial genome of Micromys erythrotis from China and its phylogenetic analysis. Mitochondrial DNA B Resour 2021; 6:1617-1620. [PMID: 34027072 PMCID: PMC8118456 DOI: 10.1080/23802359.2021.1926353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/02/2021] [Indexed: 11/04/2022] Open
Abstract
The complete mitogenome sequence of Micromys erythrotis was determined using long PCR. The genome was 16,238 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand is A (33.7%), C (24.8%), T (29.1%) and G (12.4%). The base compositions present clearly the A-T skew, which is most obviously in the control region and protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees. This study verifies the evolutionary status of Micromys erythrotis in Muridae at the molecular level. The mitochondrial genome would be a significant supplement for the Micromys erythrotis genetic background.
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Affiliation(s)
- He Cai
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Qing-Qing Wang
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Xin-Xu Zhao
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Qian-Qian Yao
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Ning Wu
- Ningan Jiangnan School, Ningan, P.R. China
| | - Jun-Sheng Zhang
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Zhu Liu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
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Lamelas L, Aleix-Mata G, Rovatsos M, Marchal JA, Palomeque T, Lorite P, Sánchez A. Complete Mitochondrial Genome of Three Species of the Genus Microtus (Arvicolinae, Rodentia). Animals (Basel) 2020; 10:E2130. [PMID: 33207831 PMCID: PMC7696944 DOI: 10.3390/ani10112130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/09/2020] [Accepted: 11/14/2020] [Indexed: 11/17/2022] Open
Abstract
The 65 species of the genus Microtus have unusual sex-related genetic features and a high rate of karyotype variation. However, only nine complete mitogenomes for these species are currently available. We describe the complete mitogenome sequences of three Microtus, which vary in length from 16,295 bp to 16,331 bp, contain 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes and a control region. The length of the 13 PCGs and the coded proteins is the same in all three species, and the start and stop codons are conserved. The non-coding regions include the L-strand origin of replication, with the same sequence of 35 bp, and the control region, which varies between 896 bp and 930 bp in length. The control region includes three domains (Domains I, II and III) with extended termination-associated sequences (ETAS-1 and ETAS-2) in Domain I. Domain II and Domain III include five (CSB-B, C, D, E and F) and three (CSB-1, CSB-2, and CSB-3) conserved sequence blocks, respectively. Phylogenetic reconstructions using the mitochondrial genomes of all the available Microtus species and one representative species from another genus of the Arvicolinae subfamily reproduced the established phylogenetic relationships for all the Arvicolinae genera that were analyzed.
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Affiliation(s)
- Luz Lamelas
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
| | - Gaël Aleix-Mata
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic;
| | - Juan Alberto Marchal
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
| | - Antonio Sánchez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
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Jun-Sheng Z, Bo-Qi L, Qiao-Jiang Y, Qi Z, Chen W, Zhu L. Sequencing and analysis of the complete mitochondrial genome of Ochotona coreana from China and its phylogenetic analysis. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1731353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Zhang Jun-Sheng
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Li Bo-Qi
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Yang Qiao-Jiang
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Zhang Qi
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Wang Chen
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Liu Zhu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
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The complete mitochondrial genome of Talpa aquitania (Talpidae; Insectivora), a mole species endemic to northern Spain and southern France. Mol Biol Rep 2020; 47:2397-2403. [PMID: 32034626 DOI: 10.1007/s11033-020-05296-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/08/2020] [Accepted: 01/30/2020] [Indexed: 10/25/2022]
Abstract
The complete mitogenome sequence of Talpa aquitania, a recently described Talpa species, was assembled using whole-genome sequencing data. It varies in length from 16,776 to 16,846 bp, contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one origin of L-strand replication, and a control region. In the control region, which varied from 1320 to 1390 bp, we identified the extended termination-associated sequence (ETAS-1 and ETAS-2) and the conserved sequence blocks (CSB-1, 2, 3, B, C, D, E, F). In addition, this region includes a 10 bp tandem repeat DNA sequence, with a variable number of repeats that suggest the existence of heteroplasmy. Phylogeny reconstructions based on Maximum Likelihood, Neighbor-joining and Bayesian inference analyses yielded phylogenies with similar topologies demonstrating that T. aquitania and T. occidentalis are sister species.
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Zhu L, Qiao-Jiang Y, Chun-Yu X, Chen W, Qing-Qing W, Wen-Jing J. Sequencing and analysis of the complete mitochondrial genome of Blarinella griselda from China and its phylogenetic analysis. Mitochondrial DNA B Resour 2020; 5:965-967. [PMID: 33366829 PMCID: PMC7748876 DOI: 10.1080/23802359.2020.1715305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 01/07/2020] [Indexed: 11/05/2022] Open
Abstract
The complete mitogenome sequence of Blarinella griselda was determined using long PCR. The genome was 16,947 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand is A (33.1%), C (22.6%), T (31.6%) and G (12.7%). The base compositions present clearly the A-T skew, which is most obviously in the control region and protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees. This study verifies the evolutionary status of Blarinella griselda in Soricidae at the molecular level. The mitochondrial genome would be a significant supplement for the Blarinella griselda genetic background. The three Blarinella species formed a monophyletic group with the high bootstrap value (100%) in all examinations.
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Affiliation(s)
- Liu Zhu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Yang Qiao-Jiang
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Xu Chun-Yu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Wang Chen
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Wang Qing-Qing
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Jiang Wen-Jing
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
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Sansalone G, Colangelo P, Loy A, Raia P, Wroe S, Piras P. Impact of transition to a subterranean lifestyle on morphological disparity and integration in talpid moles (Mammalia, Talpidae). BMC Evol Biol 2019; 19:179. [PMID: 31510915 PMCID: PMC6739959 DOI: 10.1186/s12862-019-1506-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 08/30/2019] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Understanding the mechanisms promoting or constraining morphological diversification within clades is a central topic in evolutionary biology. Ecological transitions are of particular interest because of their influence upon the selective forces and factors involved in phenotypic evolution. Here we focused on the humerus and mandibles of talpid moles to test whether the transition to the subterranean lifestyle impacted morphological disparity and phenotypic traits covariation between these two structures. RESULTS Our results indicate non-subterranean species occupy a significantly larger portion of the talpid moles morphospace. However, there is no difference between subterranean and non-subterranean moles in terms of the strength and direction of phenotypic integration. CONCLUSIONS Our study shows that the transition to a subterranean lifestyle significantly reduced morphological variability in talpid moles. However, this reduced disparity was not accompanied by changes in the pattern of traits covariation between the humerus and the mandible, suggesting the presence of strong phylogenetic conservatism within this pattern.
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Affiliation(s)
- Gabriele Sansalone
- Form, Evolution and Anatomy Research Laboratory, Zoology, School of Environmental and Rural Sciences, University of New England, Armidale, NSW 2351 Australia
- Department of Sciences, Roma Tre University, Largo San Leonardo Murialdo 1, I-00146 Rome, Italy
| | - Paolo Colangelo
- National Research Council, Institute of Research on Terrestrial Ecosystems, Via Salaria km 29.300, 00015 Monterotondo (Rome), Italy
| | - Anna Loy
- Environmetrics Lab, Dipartimento STAT, Università del Molise, I-86090 Pesche, Italy
| | - Pasquale Raia
- Università degli Studi di Napoli Federico II, Department of Earth Sciences, Environment and Resources, L.go San Marcellino 10, 80138 Naples, Italy
| | - Stephen Wroe
- Form, Evolution and Anatomy Research Laboratory, Zoology, School of Environmental and Rural Sciences, University of New England, Armidale, NSW 2351 Australia
| | - Paolo Piras
- Dipartimento di Scienze Cardiovascolari,Respiratorie, Nefrologiche, Anestesiologiche e Geriatriche, “Sapienza”, Università di Roma, Via del Policlinico 155, 00161 Rome, Italy
- Dipartimento di Ingegneria Strutturale e Geotecnica, Sapienza, Università di Roma, Via Eudossiana 18, 00100 Rome, Italy
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12
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Zhi-Min J, Ke-Song Q, Bo-Qi L, Jun-Sheng Z, He C, Jin-Xun L, Zhu W, Zhu L. Sequencing and analysis of the complete mitochondrial genome of Crocidura tanakae from China and its phylogenetic analysis. Mitochondrial DNA B Resour 2019; 4:2791-2793. [PMID: 33365730 PMCID: PMC7706458 DOI: 10.1080/23802359.2019.1659118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 07/31/2019] [Indexed: 11/05/2022] Open
Abstract
The complete mitogenome sequence of Crocidura tanakae was determined using long PCR. The genome was 16,969 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand is A (32.5%), C (22.3%), T (31.9%), and G (13.3%). The base compositions present clearly the A-T skew, which is most obviously in the control region and protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ, and Bayesian analyses yielded identical phylogenetic trees. The five Crocidura species formed a monophyletic group with the high bootstrap value (100%) in all examinations. This study verifies the evolutionary status of C. tanakae in Soricidae at the molecular level. The mitochondrial genome would be a significant supplement for the C. tanakae genetic background.
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Affiliation(s)
- Jin Zhi-Min
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, People’s Republic of China
| | - Qin Ke-Song
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, People’s Republic of China
| | - Li Bo-Qi
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, People’s Republic of China
| | - Zhang Jun-Sheng
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, People’s Republic of China
| | - Cai He
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, People’s Republic of China
| | - Li Jin-Xun
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, People’s Republic of China
| | - Wang Zhu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, People’s Republic of China
| | - Liu Zhu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, People’s Republic of China
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Zhu L, Yang B, Yi S, Qi Z, He C, Sheng Z, Jin-Xun L, Zhu W. Sequencing and analysis of the complete mitochondrial genome of Chodsigoa hoffmanni from China and its phylogenetic analysis. Mitochondrial DNA B Resour 2019; 4:2438-2440. [PMID: 33365576 PMCID: PMC7687604 DOI: 10.1080/23802359.2019.1637294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 06/22/2019] [Indexed: 11/22/2022] Open
Abstract
The complete mitogenome sequence of Chodsigoa hoffmanni was determined using long PCR. The genome was 17,138 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one origin of L strand replication, and one control region. The overall base composition of the heavy strand is A (32.8%), C (24.4%), T (29.8%), and G (13.0%). The base compositions present clearly the A-T skew, which is most obviously in the control region and protein-coding genes. Mitochondrial genome analyses based on MP, ML, NJ, and Bayesian analyses yielded identical phylogenetic trees. Chodsigoa hoffmanni is the first species to have been reported on the mitochondrial genome in Chodsigoa genus. This study verifies the evolutionary status of C. hoffmanni in Soricidae at the molecular level. The mitochondrial genome would be a significant supplement for the C. hoffmanni genetic background.
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Affiliation(s)
- Liu Zhu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Bai Yang
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Sheng Yi
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Zhang Qi
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Cai He
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Zhang Sheng
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Li Jin-Xun
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Wang Zhu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
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Zhu L, Ao-nan W, Jiao-Jiao L. Sequencing and analysis of the complete mitochondrial genome of the large mole (Mogera robusta) from China. MITOCHONDRIAL DNA PART B 2019. [DOI: 10.1080/23802359.2019.1601520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Liu Zhu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Wang Ao-nan
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
| | - Li Jiao-Jiao
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, P.R. China
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15
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Quaglietta L, Beja P. Direct observations of vertebrate killing and consumption by the endangered Pyrenean desman (Galemys pyrenaicus). MAMMALIA 2018. [DOI: 10.1515/mammalia-2018-0111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The Pyrenean desman (Galemys pyrenaicus) is a globally endangered semiaquatic mammal species restricted to Southwest Europe. It is thought to mostly predate on aquatic prey, particularly macroinvertebrates; yet anecdotal information and recent genetic-based findings suggest higher flexibility in its trophic niche. Here, we report on direct observations of wild-caught Pyrenean desmans attacking, killing and consuming live fish (trout – Salmo trutta fario) and amphibians (Iberian frog – Rana iberica) in semi-captivity conditions providing unquestionable evidence (photos and videos) of vertebrate attack, killing, handling and consumption by the species. This illustrates the species’ ability to kill and eat vertebrates, corroborating recent evidence on its trophic flexibility.
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Affiliation(s)
- Lorenzo Quaglietta
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos , Universidade do Porto , Vairão, 4485-661 Vairão , Portugal
- CEABN/InBIO, Centro de Ecologia Aplicada “Prof Baeta Neves”, Instituto Superior de Agronomia , Universidade de Lisboa , Lisbon , Portugal
| | - Pedro Beja
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos , Universidade do Porto , Vairão, 4485-661 Vairão , Portugal
- CEABN/InBIO, Centro de Ecologia Aplicada “Prof Baeta Neves”, Instituto Superior de Agronomia , Universidade de Lisboa , Lisbon , Portugal
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16
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Gutiérrez J, Lamelas L, Aleix-Mata G, Arroyo M, Marchal JA, Palomeque T, Lorite P, Sánchez A. Complete mitochondrial genome of the Iberian Mole Talpa occidentalis (Talpidae, Insectivora) and comparison with Talpa europaea. Genetica 2018; 146:415-423. [PMID: 30145730 DOI: 10.1007/s10709-018-0033-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 08/01/2018] [Indexed: 12/23/2022]
Abstract
The complete mitogenome of Talpa occidentalis, the Iberian mole, was sequenced using a combination of the Illumina and Sanger methods. The 16,962 bp genome obtained contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region. Thirty-seven identical repetitions of a 10-nucleotide (CACACGTACG) repeat element were identified in the non-coding control region (D-loop). The number, order, and orientation of the mitochondrial genes are the same as in T. europaea, the only mitogenome published so far for this genus. These two mitogenomes differ only at the repeat element included in the control region. The phylogeny obtained for the Talpidae species using the protein-coding genes of these mitogenomes agrees with the current classification of this family.
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Affiliation(s)
- Juana Gutiérrez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Luz Lamelas
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Gaël Aleix-Mata
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - María Arroyo
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Juan Alberto Marchal
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Antonio Sánchez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain.
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Influence of Evolutionary Allometry on Rates of Morphological Evolution and Disparity in strictly Subterranean Moles (Talpinae, Talpidae, Lipotyphla, Mammalia). J MAMM EVOL 2017. [DOI: 10.1007/s10914-016-9370-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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18
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He K, Shinohara A, Helgen KM, Springer MS, Jiang XL, Campbell KL. Talpid Mole Phylogeny Unites Shrew Moles and Illuminates Overlooked Cryptic Species Diversity. Mol Biol Evol 2016; 34:78-87. [PMID: 27795230 DOI: 10.1093/molbev/msw221] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The mammalian family Talpidae (moles, shrew moles, desmans) is characterized by diverse ecomorphologies associated with terrestrial, semi-aquatic, semi-fossorial, fossorial, and aquatic-fossorial lifestyles. Prominent specializations involved with these different lifestyles, and the transitions between them, pose outstanding questions regarding the evolutionary history within the family, not only for living but also for fossil taxa. Here, we investigate the phylogenetic relationships, divergence times, and biogeographic history of the family using 19 nuclear and 2 mitochondrial genes (∼16 kb) from ∼60% of described species representing all 17 genera. Our phylogenetic analyses help settle classical questions in the evolution of moles, identify an ancient (mid-Miocene) split within the monotypic genus Scaptonyx, and indicate that talpid species richness may be nearly 30% higher than previously recognized. Our results also uniformly support the monophyly of long-tailed moles with the two shrew mole tribes and confirm that the Gansu mole is the sole living Asian member of an otherwise North American radiation. Finally, we provide evidence that aquatic specializations within the tribes Condylurini and Desmanini evolved along different morphological trajectories, though we were unable to statistically reject monophyly of the strictly fossorial tribes Talpini and Scalopini.
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Affiliation(s)
- Kai He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Department of Biological Sciences, University of Manitoba, Winnipeg, MN , Canada
| | - Akio Shinohara
- Department of Bio-resources, Division of Biotechnology, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Kristofer M Helgen
- National Museum of Natural History Smithsonian Institution, Washington, DC
| | - Mark S Springer
- Department of Biology, University of California, Riverside, CA
| | - Xue-Long Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Kevin L Campbell
- Department of Biological Sciences, University of Manitoba, Winnipeg, MN , Canada
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Brace S, Thomas JA, Dalén L, Burger J, MacPhee RDE, Barnes I, Turvey ST. Evolutionary History of the Nesophontidae, the Last Unplaced Recent Mammal Family. Mol Biol Evol 2016; 33:3095-3103. [PMID: 27624716 DOI: 10.1093/molbev/msw186] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The mammalian evolutionary tree has lost several major clades through recent human-caused extinctions. This process of historical biodiversity loss has particularly affected tropical island regions such as the Caribbean, an area of great evolutionary diversification but poor molecular preservation. The most enigmatic of the recently extinct endemic Caribbean mammals are the Nesophontidae, a family of morphologically plesiomorphic lipotyphlan insectivores with no consensus on their evolutionary affinities, and which constitute the only major recent mammal clade to lack any molecular information on their phylogenetic placement. Here, we use a palaeogenomic approach to place Nesophontidae within the phylogeny of recent Lipotyphla. We recovered the near-complete mitochondrial genome and sequences for 17 nuclear genes from a ∼750-year-old Hispaniolan Nesophontes specimen, and identify a divergence from their closest living relatives, the Solenodontidae, more than 40 million years ago. Nesophontidae is thus an older distinct lineage than many extant mammalian orders, highlighting not only the role of island systems as "museums" of diversity that preserve ancient lineages, but also the major human-caused loss of evolutionary history.
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Affiliation(s)
- Selina Brace
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | | | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Joachim Burger
- Institute of Anthropology Johannes Gutenberg-University, Anselm-Franz-von-Bentzel-Weg 7, Mainz, Germany
| | - Ross D E MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Samuel T Turvey
- Zoological Society of London, Institute of Zoology, London, United Kingdom
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20
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Montelli S, Peruffo A, Patarnello T, Cozzi B, Negrisolo E. Back to Water: Signature of Adaptive Evolution in Cetacean Mitochondrial tRNAs. PLoS One 2016; 11:e0158129. [PMID: 27336480 PMCID: PMC4919058 DOI: 10.1371/journal.pone.0158129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 06/11/2016] [Indexed: 11/29/2022] Open
Abstract
The mitochondrion is the power plant of the eukaryotic cell, and tRNAs are the fundamental components of its translational machinery. In the present paper, the evolution of mitochondrial tRNAs was investigated in the Cetacea, a clade of Cetartiodactyla that retuned to water and thus had to adapt its metabolism to a different medium than that of its mainland ancestors. Our analysis focussed on identifying the factors that influenced the evolution of Cetacea tRNA double-helix elements, which play a pivotal role in the formation of the secondary and tertiary structures of each tRNA and consequently manipulate the whole translation machinery of the mitochondrion. Our analyses showed that the substitution pathways in the stems of different tRNAs were influenced by various factors, determining a molecular evolution that was unique to each of the 22 tRNAs. Our data suggested that the composition, AT-skew, and GC-skew of the tRNA stems were the main factors influencing the substitution process. In particular, the range of variation and the fluctuation of these parameters affected the fate of single tRNAs. Strong heterogeneity was observed among the different species of Cetacea. Finally, it appears that the evolution of mitochondrial tRNAs was also shaped by the environments in which the Cetacean taxa differentiated. This latter effect was particularly evident in toothed whales that either live in freshwater or are deep divers.
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Affiliation(s)
- Stefano Montelli
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro (PD), Italy
| | - Antonella Peruffo
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro (PD), Italy
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro (PD), Italy
| | - Bruno Cozzi
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro (PD), Italy
| | - Enrico Negrisolo
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro (PD), Italy
- * E-mail:
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21
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Khwanmunee J, Leelawatwattana L, Prapunpoj P. Gene structure and evolution of transthyretin in the order Chiroptera. Genetica 2015; 144:71-83. [PMID: 26681450 DOI: 10.1007/s10709-015-9879-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 12/13/2015] [Indexed: 11/26/2022]
Abstract
Bats are mammals in the order Chiroptera. Although many extensive morphologic and molecular genetics analyses have been attempted, phylogenetic relationships of bats has not been completely resolved. The paraphyly of microbats is of particular controversy that needs to be confirmed. In this study, we attempted to use the nucleotide sequence of transthyretin (TTR) intron 1 to resolve the relationship among bats. To explore its utility, the complete sequences of TTR gene and intron 1 region of bats in Vespertilionidae: genus Eptesicus (Eptesicus fuscus) and genus Myotis (Myotis brandtii, Myotis davidii, and Myotis lucifugus), and Pteropodidae (Pteropus alecto and Pteropus vampyrus) were extracted from the retrieved sequences, whereas those of Rhinoluphus affinis and Scotophilus kuhlii were amplified and sequenced. The derived overall amino sequences of bat TTRs were found to be very similar to those in other eutherians but differed from those in other classes of vertebrates. However, missing of amino acids from N-terminal or C-terminal region was observed. The phylogenetic analysis of amino acid sequences suggested bat and other eutherian TTRs lineal descent from a single most recent common ancestor which differed from those of non-placental mammals and the other classes of vertebrates. The splicing of bat TTR precursor mRNAs was similar to those of other eutherian but different from those of marsupial, bird, reptile and amphibian. Based on TTR intron 1 sequence, the inferred evolutionary relationship within Chiroptera revealed more closely relatedness of R. affinis to megabats than to microbats. Accordingly, the paraphyly of microbats was suggested.
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Affiliation(s)
- Jiraporn Khwanmunee
- Department of Biochemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Ladda Leelawatwattana
- Department of Biochemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Porntip Prapunpoj
- Department of Biochemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand.
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22
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Doronina L, Churakov G, Shi J, Brosius J, Baertsch R, Clawson H, Schmitz J. Exploring Massive Incomplete Lineage Sorting in Arctoids (Laurasiatheria, Carnivora). Mol Biol Evol 2015; 32:3194-204. [PMID: 26337548 DOI: 10.1093/molbev/msv188] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Freed from the competition of large raptors, Paleocene carnivores could expand their newly acquired habitats in search of prey. Such changing conditions might have led to their successful distribution and rapid radiation. Today, molecular evolutionary biologists are faced, however, with the consequences of such accelerated adaptive radiations, because they led to sequential speciation more rapidly than phylogenetic markers could be fixed. The repercussions being that current genealogies based on such markers are incongruent with species trees.Our aim was to explore such conflicting phylogenetic zones of evolution during the early arctoid radiation, especially to distinguish diagnostic from misleading phylogenetic signals, and to examine other carnivore-related speciation events. We applied a combination of high-throughput computational strategies to screen carnivore and related genomes in silico for randomly inserted retroposed elements that we then used to identify inconsistent phylogenetic patterns in the Arctoidea group, which is well known for phylogenetic discordances.Our combined retrophylogenomic and in vitro wet lab approach detected hundreds of carnivore-specific insertions, many of them confirming well-established splits or identifying and solving conflicting species distributions. Our systematic genome-wide screens for Long INterspersed Elements detected homoplasy-free markers with insertion-specific truncation points that we used to distinguish phylogenetically informative markers from conflicting signals. The results were independently confirmed by phylogenetic diagnostic Short INterspersed Elements. As statistical analysis ruled out ancestral hybridization, these doubly verified but still conflicting patterns were statistically determined to be genomic remnants from a time of ancestral incomplete lineage sorting that especially accompanied large parts of Arctoidea evolution.
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Affiliation(s)
- Liliya Doronina
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany
| | - Gennady Churakov
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Jingjing Shi
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany
| | - Jürgen Brosius
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany Institute of Evolutionary and Medical Genomics, Brandenburg Medical School (MHB), Neuruppin, Germany
| | - Robert Baertsch
- Department of Biomolecular Engineering, University of California, Santa Cruz
| | - Hiram Clawson
- Department of Biomolecular Engineering, University of California, Santa Cruz
| | - Jürgen Schmitz
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany
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23
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Tu F, Fan Z, Murphy RW, Chen S, Zhang X, Yan C, Liu Y, Sun Z, Fu J, Liu S, Yue B. Molecular phylogenetic relationships among Asiatic shrewlike moles inferred from the complete mitogenomes. J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12081] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Feiyun Tu
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife; College of Life Sciences; Sichuan University; Chengdu China
- Jiangxi Academy of Forestry; Nanchang China
| | - Zhenxin Fan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife; College of Life Sciences; Sichuan University; Chengdu China
| | - Robert W. Murphy
- Centre for Biodiversity and Conservation Biology; Royal Ontario Museum; Toronto M5S, 2C6 Canada
| | - Shunde Chen
- College of Life Sciences; Sichuan Normal University; Chengdu China
| | - Xiuyue Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife; College of Life Sciences; Sichuan University; Chengdu China
| | - Chaochao Yan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife; College of Life Sciences; Sichuan University; Chengdu China
| | - Yang Liu
- Sichuan Academy of Forestry; Chengdu China
| | - Zhiyu Sun
- Sichuan Academy of Forestry; Chengdu China
| | | | | | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife; College of Life Sciences; Sichuan University; Chengdu China
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24
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Shinohara A, Kawada SI, Son NT, Koshimoto C, Endo H, Can DN, Suzuki H. Molecular phylogeny of East and Southeast Asian fossorial moles (Lipotyphla, Talpidae). J Mammal 2014. [DOI: 10.1644/13-mamm-a-135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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25
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Tu F, Liu S, Liu Y, Sun Z, Yin Y, Yan C, Lu L, Yue B, Zhang X. Complete mitogenome of Chinese shrew moleUropsilus soricipes(Milne-Edwards, 1871) (Mammalia: Talpidae) and genetic structure of the species in the Jiajin Mountains (China). J NAT HIST 2014. [DOI: 10.1080/00222933.2013.842012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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26
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Mirceta S, Signore AV, Burns JM, Cossins AR, Campbell KL, Berenbrink M. Evolution of mammalian diving capacity traced by myoglobin net surface charge. Science 2013; 340:1234192. [PMID: 23766330 DOI: 10.1126/science.1234192] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Extended breath-hold endurance enables the exploitation of the aquatic niche by numerous mammalian lineages and is accomplished by elevated body oxygen stores and adaptations that promote their economical use. However, little is known regarding the molecular and evolutionary underpinnings of the high muscle myoglobin concentration phenotype of divers. We used ancestral sequence reconstruction to trace the evolution of this oxygen-storing protein across a 130-species mammalian phylogeny and reveal an adaptive molecular signature of elevated myoglobin net surface charge in diving species that is mechanistically linked with maximal myoglobin concentration. This observation provides insights into the tempo and routes to enhanced dive capacity evolution within the ancestors of each major mammalian aquatic lineage and infers amphibious ancestries of echidnas, moles, hyraxes, and elephants, offering a fresh perspective on the evolution of this iconic respiratory pigment.
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Affiliation(s)
- Scott Mirceta
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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27
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Igea J, Aymerich P, Fernández-González A, González-Esteban J, Gómez A, Alonso R, Gosálbez J, Castresana J. Phylogeography and postglacial expansion of the endangered semi-aquatic mammal Galemys pyrenaicus. BMC Evol Biol 2013; 13:115. [PMID: 23738626 PMCID: PMC3682870 DOI: 10.1186/1471-2148-13-115] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 05/28/2013] [Indexed: 01/20/2023] Open
Abstract
Background Species with strict ecological requirements may provide new insights into the forces that shaped the geographic variation of genetic diversity. The Pyrenean desman, Galemys pyrenaicus, is a small semi-aquatic mammal that inhabits clean streams of the northern half of the Iberian Peninsula and is endangered in most of its geographic range, but its genetic structure is currently unknown. While the stringent ecological demands derived from its aquatic habitat might have caused a partition of the genetic diversity among river basins, Pleistocene glaciations would have generated a genetic pattern related to glacial refugia. Results To study the relative importance of historical and ecological factors in the genetic structure of G. pyrenaicus, we used mitochondrial and intronic sequences of specimens covering most of the species range. We show, first, that the Pyrenean desman has very low levels of genetic diversity compared to other mammals. In addition, phylogenetic and dating analyses of the mitochondrial sequences reveal a strong phylogeographic structure of a Middle Pleistocene origin, suggesting that the main lineages arose during periods of glacial isolation. Furthermore, both the spatial distribution of nuclear and mitochondrial diversity and the results of species distribution modeling suggest the existence of a major glacial refugium in the northwestern part of the Iberian Peninsula. Finally, the main mitochondrial lineages show a striking parapatric distribution without any apparent exchange of mitochondrial haplotypes between the lineages that came into secondary contact (although with certain permeability to nuclear genes), indicating incomplete mixing after the post-glacial recolonization. On the other hand, when we analyzed the partition of the genetic diversity among river basins, the Pyrenean desman showed a lower than expected genetic differentiation among main rivers. Conclusions The analysis of mitochondrial and intronic markers in G. pyrenaicus showed the predominant effects of Pleistocene glaciations on the genetic structure of this species, while the distribution of the genetic diversity was not greatly influenced by the main river systems. These results and, particularly, the discovery of a marked phylogeographic structure, may have important implications for the conservation of the Pyrenean desman.
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Affiliation(s)
- Javier Igea
- Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta 37, Barcelona 08003, Spain
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28
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Lu L, Tu F, Yan C, Zhang X, Yue B, Zeng T. The complete mitochondrial genome sequence of Shrew Gymnure,Neotetracus sinensis. ACTA ACUST UNITED AC 2012. [DOI: 10.3109/19401736.2012.744976] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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29
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Tu F, Fan Z, Chen S, Yin Y, Li P, Zhang X, Liu S, Yue B. The complete mitochondrial genome sequence of the Gracile shrew mole,Uropsilus gracilis(Soricomorpha: Talpidae). ACTA ACUST UNITED AC 2012; 23:382-4. [DOI: 10.3109/19401736.2012.696634] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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30
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Crumpton N, Thompson RS. The Holes of Moles: Osteological Correlates of the Trigeminal Nerve in Talpidae. J MAMM EVOL 2012. [DOI: 10.1007/s10914-012-9213-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Piras P, Sansalone G, Teresi L, Kotsakis T, Colangelo P, Loy A. Testing convergent and parallel adaptations in talpids humeral mechanical performance by means of geometric morphometrics and finite element analysis. J Morphol 2012; 273:696-711. [DOI: 10.1002/jmor.20015] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 01/06/2012] [Accepted: 01/29/2012] [Indexed: 11/07/2022]
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Del Cerro I, Marmi J, Ferrando A, Chashchin P, Taberlet P, Bosch M. Nuclear and mitochondrial phylogenies provide evidence for four species of Eurasian badgers (Carnivora). ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2010.00436.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Morueta-Holme N, Fløjgaard C, Svenning JC. Climate change risks and conservation implications for a threatened small-range mammal species. PLoS One 2010; 5:e10360. [PMID: 20454451 PMCID: PMC2861593 DOI: 10.1371/journal.pone.0010360] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 03/16/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Climate change is already affecting the distributions of many species and may lead to numerous extinctions over the next century. Small-range species are likely to be a special concern, but the extent to which they are sensitive to climate is currently unclear. Species distribution modeling, if carefully implemented, can be used to assess climate sensitivity and potential climate change impacts, even for rare and cryptic species. METHODOLOGY/PRINCIPAL FINDINGS We used species distribution modeling to assess the climate sensitivity, climate change risks and conservation implications for a threatened small-range mammal species, the Iberian desman (Galemys pyrenaicus), which is a phylogenetically isolated insectivore endemic to south-western Europe. Atlas data on the distribution of G. pyrenaicus was linked to data on climate, topography and human impact using two species distribution modeling algorithms to test hypotheses on the factors that determine the range for this species. Predictive models were developed and projected onto climate scenarios for 2070-2099 to assess climate change risks and conservation possibilities. Mean summer temperature and water balance appeared to be the main factors influencing the distribution of G. pyrenaicus. Climate change was predicted to result in significant reductions of the species' range. However, the severity of these reductions was highly dependent on which predictor was the most important limiting factor. Notably, if mean summer temperature is the main range determinant, G. pyrenaicus is at risk of near total extinction in Spain under the most severe climate change scenario. The range projections for Europe indicate that assisted migration may be a possible long-term conservation strategy for G. pyrenaicus in the face of global warming. CONCLUSIONS/SIGNIFICANCE Climate change clearly poses a severe threat to this illustrative endemic species. Our findings confirm that endemic species can be highly vulnerable to a warming climate and highlight the fact that assisted migration has potential as a conservation strategy for species threatened by climate change.
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Affiliation(s)
- Naia Morueta-Holme
- Ecoinformatics and Biodiversity Group, Department of Biological Sciences, Aarhus University, Aarhus, Denmark.
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A sex determination protocol for the Iberian desman (Galemys pyrenaicus) based on a three primer amplification of DBX and DBY fragments with non-invasive samples. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9913-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Kawada SI, Li S, Wang YX, Mock OB, Oda SI, Campbell KL. Karyotype Evolution of Shrew Moles (Soricomorpha: Talpidae). J Mammal 2008. [DOI: 10.1644/07-mamm-a-105.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Carmona FD, Motokawa M, Tokita M, Tsuchiya K, Jiménez R, Sánchez-Villagra MR. The evolution of female mole ovotestes evidences high plasticity of mammalian gonad development. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2008; 310:259-66. [DOI: 10.1002/jez.b.21209] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Zardoya R, Suárez M. Sequencing and phylogenomic analysis of whole mitochondrial genomes of animals. Methods Mol Biol 2008; 422:185-200. [PMID: 18629668 DOI: 10.1007/978-1-59745-581-7_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mitochondrial genomes (mtDNA) of animals are circular molecules of relatively small size, compactly organized, and generally encoding genes for 2 rRNAs, 22 tRNAs, and 13 proteins that are required for mitochondrial function. Methods of mtDNA isolation take advantage of its physical localization apart from the nuclear genome (centrifugation at low speed efficiently separates mitochondria from nuclei) and of its structure (alkaline lysis differentially precipitates linear nuclear DNA, but not circular mtDNA). Furthermore, the recent development of robust long-PCR techniques has boosted high-throughput determination of complete sequences of animal mtDNAs. The exponentially growing number of complete animal mitochondrial genomes deposited in GenBank allows a phylogenomic approach to disentangle phylogenetic relationships among main animal phyla, and provides extensive new data to gain insights on the molecular mechanisms underlying genome evolution.
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Affiliation(s)
- Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain
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Goswami A, Prochel J. Ontogenetic Morphology and Allometry of the Cranium in the Common European Mole (Talpa europaea). J Mammal 2007. [DOI: 10.1644/06-mamm-a-315r.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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