1
|
Tavares FDS, Oliveira da Silva W, Ferguson-Smith MA, Klautau AGCDM, Oliveira JM, Rodrigues ALF, Melo-Santos G, Pieczarka JC, Nagamachi CY, Noronha RCR. Ancestral chromosomal signatures of Paenungulata (Afroteria) reveal the karyotype of Amazonian manatee (Trichechus inunguis, Sirenia: Trichechidae) as the oldest among American manatees. BMC Genomics 2023; 24:38. [PMID: 36694120 PMCID: PMC9872332 DOI: 10.1186/s12864-023-09129-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/11/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Chromosomal painting in manatees has clarified questions about the rapid evolution of sirenians within the Paenungulata clade. Further cytogenetic studies in Afrotherian species may provide information about their evolutionary dynamics, revealing important insights into the ancestral karyotype in the clade representatives. The karyotype of Trichechus inunguis (TIN, Amazonian manatee) was investigated by chromosome painting, using probes from Trichechus manatus latirostris (TML, Florida manatee) to analyze the homeologies between these sirenians. RESULTS A high similarity was found between these species, with 31 homologous segments in TIN, nineteen of which are whole autosomes, besides the X and Y sex chromosomes. Four chromosomes from TML (4, 6, 8, and 9) resulted in two hybridization signals, totaling eight acrocentrics in the TIN karyotype. This study confirmed in TIN the chromosomal associations of Homo sapiens (HSA) shared in Afrotheria, such as the 5/21 synteny, and in the Paenungulata clade with the syntenies HSA 2/3, 8/22, and 18/19, in addition to the absence of HSA 4/8 common in eutherian ancestral karyotype (EAK). CONCLUSIONS TIN shares more conserved chromosomal signals with the Paenungulata Ancestral Karyotype (APK, 2n = 58) than Procavia capensis (Hyracoidea), Loxodonta africana (Proboscidea) and TML (Sirenia), where TML presents less conserved signals with APK, demonstrating that its karyotype is the most derived among the representatives of Paenungulata. The chromosomal changes that evolved from APK to the T. manatus and T. inunguis karyotypes (7 and 4 changes, respectively) are more substantial within the Trichechus genus compared to other paenungulates. Among these species, T. inunguis presents conserved traits of APK in the American manatee genus. Consequently, the karyotype of T. manatus is more derived than that of T. inunguis.
Collapse
Affiliation(s)
- Flávia Dos Santos Tavares
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Pará, Belém, Brazil
| | - Willam Oliveira da Silva
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Pará, Belém, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Jairo Moura Oliveira
- Zoological Park of Santarém - Universidade da Amazônia (ZOOUNAMA), Pará, Santarém, Brazil
| | - Angélica Lúcia Figueiredo Rodrigues
- Instituto de Biologia e Conservação de Mamíferos Aquáticos da Amazônia, Universidade Federal Rural da Amazônia (UFRA), Pará, Belém, Brazil
- Secretaria de Educação Do Estado Do Pará (SEDUC-PA), Belém, Brazil
| | - Gabriel Melo-Santos
- Instituto de Biologia e Conservação de Mamíferos Aquáticos da Amazônia, Universidade Federal Rural da Amazônia (UFRA), Pará, Belém, Brazil
- Laboratório de Ecologia Marinha e Conservação, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Ecologia de Aves e Comportamento Animal, Universidade Estadual do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Pará, Belém, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Pará, Belém, Brazil
| | - Renata Coelho Rodrigues Noronha
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará (UFPA), Pará, Belém, Brazil.
| |
Collapse
|
2
|
Noronha RCR, Almeida BRR, Chagas MCS, Tavares FS, Cardoso AL, Bastos CEMC, Silva NKN, Klautau AGCM, Luna FO, Attademo FLN, Lima DS, Sabioni LA, Sampaio MIC, Oliveira JM, do Nascimento LAS, Martins C, Vicari MR, Nagamachi CY, Pieczarka JC. Karyotypes of Manatees: New Insights into Hybrid Formation ( Trichechus inunguis × Trichechus m. manatus) in the Amazon Estuary. Genes (Basel) 2022; 13:1263. [PMID: 35886048 PMCID: PMC9323068 DOI: 10.3390/genes13071263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 02/01/2023] Open
Abstract
Great efforts have been made to preserve manatees. Recently, a hybrid zone was described between Trichechus inunguis (TIN) and the Trichechus manatus manatus (TMM) in the Amazon estuary. Cytogenetic data on these sirenians are limited, despite being fundamental to understanding the hybridization/introgression dynamics and genomic organization in Trichechus. We analyzed the karyotype of TMM, TIN, and two hybrid specimens ("Poque" and "Vitor") by classical and molecular cytogenetics. G-band analysis revealed that TMM (2n = 48) and TIN (2n = 56) diverge by at least six Robertsonian translocations and a pericentric inversion. Hybrids had 2n = 50, however, with Autosomal Fundamental Number (FNA) = 88 in "Poque" and FNA = 74 in "Vitor", and chromosomal distinct pairs in heterozygous; additionally, "Vitor" exhibited heteromorphisms and chromosomes whose pairs could not be determined. The U2 snDNA and Histone H3 multi genes are distributed in small clusters along TIN and TMM chromosomes and have transposable Keno and Helitron elements (TEs) in their sequences. The different karyotypes observed among manatee hybrids may indicate that they represent different generations formed by crossing between fertile hybrids and TIN. On the other hand, it is also possible that all hybrids recorded represent F1 and the observed karyotype differences must result from mechanisms of elimination.
Collapse
Affiliation(s)
- Renata C. R. Noronha
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
| | - Bruno R. R. Almeida
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
- Campus Itaituba, Instituto Federal de Educação, Ciência e Tecnologia do Pará, Itaituba 68183-300, PA, Brazil
| | - Monique C. S. Chagas
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
| | - Flávia S. Tavares
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
| | - Adauto L. Cardoso
- Laboratório Genômica Integrativa, Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu 18618-970, SP, Brazil; (A.L.C.); (C.M.)
| | - Carlos E. M. C. Bastos
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
| | - Natalia K. N. Silva
- Campus Tucuruí, Universidade do Estado do Pará, Tucuruí 68455-210, PA, Brazil;
| | - Alex G. C. M. Klautau
- Centro Nacional de Pesquisa e Conservação da Biodiversidade Marinha do Norte, Instituto Chico Mendes de Conservação da Biodiversidade, Belém 66635-110, PA, Brazil;
| | - Fábia O. Luna
- Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos, Instituto Chico Mendes de Conservação de Biodiversidade, Santos 11050-031, SP, Brazil; (F.O.L.); (F.L.N.A.)
| | - Fernanda L. N. Attademo
- Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos, Instituto Chico Mendes de Conservação de Biodiversidade, Santos 11050-031, SP, Brazil; (F.O.L.); (F.L.N.A.)
- Departamento de Zoologia, Programa de Pós-Graduação em Biologia Animal/PPBA, Laboratório de Ecologia Comportamento e Conservação/LECC, Universidade Federal de Pernambuco/UFPE, Recife 50670-901, PE, Brazil
| | - Danielle S. Lima
- Grupo de Pesquisa em Mamíferos Aquáticos Amazônicos, Instituto de Desenvolvimento Sustentável Mamirauá, Estrada do Bexiga, Tefé 69553-225, AM, Brazil; (D.S.L.); (L.A.S.)
- Rede de Pesquisa e Conservação de Sirênios no Estuário Amazônico, Macapá 68903-197, AP, Brazil
| | - Luiz A. Sabioni
- Grupo de Pesquisa em Mamíferos Aquáticos Amazônicos, Instituto de Desenvolvimento Sustentável Mamirauá, Estrada do Bexiga, Tefé 69553-225, AM, Brazil; (D.S.L.); (L.A.S.)
- Rede de Pesquisa e Conservação de Sirênios no Estuário Amazônico, Macapá 68903-197, AP, Brazil
- Campus Porto Grande, Instituto Federal de Educação Ciência e Tecnologia do Amapá, Rodovia BR 210, Km 103, s/n, Zona Rural, Porto Grande 68997-000, AP, Brazil
| | - Maria I. C. Sampaio
- Instituto de Estudos Costeiros, Campus Bragança, Universidade Federal do Pará, Bragança 68600-000, PA, Brazil;
| | - Jairo Moura Oliveira
- Zoological Park of Santarém, ZOOUNAMA, Universidade da Amazônia, Santarém 68030-150, PA, Brazil;
| | | | - Cesar Martins
- Laboratório Genômica Integrativa, Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu 18618-970, SP, Brazil; (A.L.C.); (C.M.)
| | - Marcelo R. Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil;
| | - Cleusa Y. Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
| | - Julio C. Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil; (B.R.R.A.); (M.C.S.C.); (F.S.T.); (C.E.M.C.B.); (C.Y.N.); (J.C.P.)
| |
Collapse
|
3
|
Karyotypical Confirmation of Natural Hybridization between Two Manatee Species, Trichechus manatus and Trichechus inunguis. Life (Basel) 2022; 12:life12050616. [PMID: 35629284 PMCID: PMC9145575 DOI: 10.3390/life12050616] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/17/2022] [Accepted: 04/18/2022] [Indexed: 01/20/2023] Open
Abstract
Two species of manatees are found in Northern Brazil—the Antillean manatee (Trichechus manatus), which is found along the coast from Florida to Northeastern Brazil, and the Amazonian manatee (Trichechus inunguis), endemic to the Amazon drainage basin. These species show a sympatric distribution in the region of the Marajó Archipelago, an estuarine area surrounding the Amazon River mouth. There is evidence of the occurrence of interspecific hybrids in this area, based on mitochondrial DNA analyses, although the use of nuclear markers has not corroborated this proposal. Considering that these species show very distinct karyotypes, despite being closely related (2n = 48 in T. manatus and 2n = 56 in T. inunguis), hybrids would present distinct chromosome numbers. Based on this, we conducted cytogenetic analyses using classic and molecular techniques in three calves found stranded in the Marajó Island and Amapá coast. The results showed that one of them, morphologically classified as T. inunguis, presented the correspondent karyotype, with 2n = 56. However, the other two, which were phenotypically similar to T. manatus, showed 2n = 49. Despite the same diploid number, their G-banding patterns revealed some differences. The results of the distribution of some microsatellite sequences have also confirmed the heterozygosity of some chromosomal pairs in these two individuals. These results are the first indubitable confirmation of the occurrence of natural hybrids between T. manatus and T. inunguis, and also brings about some issues concerning the viability of hybrids, considering that these two individuals do not correspond to an F1 hybrid, but instead, both presented a possible F2 karyotype.
Collapse
|
4
|
Valeri MP, Dias GB, do Espírito Santo AA, Moreira CN, Yonenaga-Yassuda Y, Sommer IB, Kuhn GCS, Svartman M. First Description of a Satellite DNA in Manatees' Centromeric Regions. Front Genet 2021; 12:694866. [PMID: 34504514 PMCID: PMC8421680 DOI: 10.3389/fgene.2021.694866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/30/2021] [Indexed: 11/18/2022] Open
Abstract
Trichechus manatus and Trichechus inunguis are the two Sirenia species that occur in the Americas. Despite their increasing extinction risk, many aspects of their biology remain understudied, including the repetitive DNA fraction of their genomes. Here we used the sequenced genome of T. manatus and TAREAN to identify satellite DNAs (satDNAs) in this species. We report the first description of TMAsat, a satDNA comprising ~0.87% of the genome, with ~684bp monomers and centromeric localization. In T. inunguis, TMAsat showed similar monomer length, chromosome localization and conserved CENP-B box-like motifs as in T. manatus. We also detected this satDNA in the Dugong dugon and in the now extinct Hydrodamalis gigas genomes. The neighbor-joining tree shows that TMAsat sequences from T. manatus, T. inunguis, D. dugon, and H. gigas lack species-specific clusters, which disagrees with the predictions of concerted evolution. We detected a divergent TMAsat-like homologous sequence in elephants and hyraxes, but not in other mammals, suggesting this sequence was already present in the common ancestor of Paenungulata, and later became a satDNA in the Sirenians. This is the first description of a centromeric satDNA in manatees and will facilitate the inclusion of Sirenia in future studies of centromeres and satDNA biology.
Collapse
Affiliation(s)
- Mirela Pelizaro Valeri
- Laboratório de Citogenômica Evolutiva, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Guilherme Borges Dias
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Alice Alves do Espírito Santo
- Laboratório de Citogenômica Evolutiva, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Camila Nascimento Moreira
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Yatiyo Yonenaga-Yassuda
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Iara Braga Sommer
- Centro Nacional de Pesquisa e Conservação da Biodiversidade Marinha do Nordeste, Instituto Chico Mendes de Conservação da Biodiversidade, Brasília, Brazil
| | - Gustavo C. S. Kuhn
- Laboratório de Citogenômica Evolutiva, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marta Svartman
- Laboratório de Citogenômica Evolutiva, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| |
Collapse
|
5
|
Barros HMDDR, Meirelles ACO, Luna FO, Marmontel M, Cordeiro-Estrela P, Santos N, Astúa D. Cranial and chromosomal geographic variation in manatees (Mammalia: Sirenia: Trichechidae) with the description of the Antillean manatee karyotype in Brazil. J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12153] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Helen M. D. do R. Barros
- Laboratório de Mastozoologia; Departamento de Zoologia/CB; Universidade Federal de Pernambuco; Recife PE Brazil
- Laboratório de Genética e Citogenética Animal; Departamento de Genética/CB; Universidade Federal de Pernambuco; Recife PE Brazil
| | - Ana C. O. Meirelles
- Programa de Mamíferos Marinhos; Associação de Pesquisa e Preservação de Ecossistemas Aquáticos; Caucaia CE Brazil
| | - Fábia O. Luna
- Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos; Instituto Chico Mendes de Conservação da Biodiversidade; Itamaracá PE Brazil
| | - Miriam Marmontel
- Grupo de Pesquisa em Mamíferos Aquáticos Amazônicos; Instituto de Desenvolvimento Sustentável Mamirauá; Tefé AM Brazil
| | - Pedro Cordeiro-Estrela
- Laboratório de Mamíferos/Coleção de Mamíferos; Departamento de Sistemática e Ecologia/CCEN; Universidade Federal da Paraíba; João Pessoa PB Brazil
| | - Neide Santos
- Laboratório de Genética e Citogenética Animal; Departamento de Genética/CB; Universidade Federal de Pernambuco; Recife PE Brazil
| | - Diego Astúa
- Laboratório de Mastozoologia; Departamento de Zoologia/CB; Universidade Federal de Pernambuco; Recife PE Brazil
| |
Collapse
|
6
|
Dynamics of vertebrate sex chromosome evolution: from equal size to giants and dwarfs. Chromosoma 2015; 125:553-71. [DOI: 10.1007/s00412-015-0569-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/09/2015] [Accepted: 12/10/2015] [Indexed: 11/26/2022]
|
7
|
Hunter ME, Mignucci-Giannoni AA, Tucker KP, King TL, Bonde RK, Gray BA, McGuire PM. Puerto Rico and Florida manatees represent genetically distinct groups. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0414-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
8
|
Svartman M, Stanyon R. The chromosomes of Afrotheria and their bearing on mammalian genome evolution. Cytogenet Genome Res 2012; 137:144-53. [PMID: 22868637 DOI: 10.1159/000341387] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Afrotheria is the clade of placental mammals that, together with Xenarthra, Euarchontoglires and Laurasiatheria, represents 1 of the 4 main recognized supraordinal eutherian clades. It reunites 6 orders of African origin: Proboscidea, Sirenia, Hyracoidea, Macroscelidea, Afrosoricida and Tubulidentata. The apparently unlikely relationship among such disparate morphological taxa and their possible basal position at the base of the eutherian phylogenetic tree led to a great deal of attention and research on the group. The use of biomolecular data was pivotal in Afrotheria studies, as they were the basis for the recognition of this clade. Although morphological evidence is still scarce, a plethora of molecular data firmly attests to the phylogenetic relationship among these mammals of African origin. Modern cytogenetic techniques also gave a significant contribution to the study of Afrotheria, revealing chromosome signatures for the group as a whole, as well as for some of its internal relationships. The associations of human chromosomes HSA1/19 and 5/21 were found to be chromosome signatures for the group and provided further support for Afrotheria. Additional chromosome synapomorphies were also identified linking elephants and manatees in Tethytheria (the associations HSA2/3, 3/13, 8/22, 18/19 and the lack of HSA4/8) and elephant shrews with the aardvark (HSA2/8, 3/20 and 10/17). Herein, we review the current knowledge on Afrotheria chromosomes and genome evolution. The already available data on the group suggests that further work on this apparently bizarre assemblage of mammals will provide important data to a better understanding on mammalian genome evolution.
Collapse
Affiliation(s)
- M Svartman
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | | |
Collapse
|
9
|
Pardini A, O'Brien P, Fu B, Bonde R, Elder F, Ferguson-Smith M, Yang F, Robinson T. Chromosome painting among Proboscidea, Hyracoidea and Sirenia: support for Paenungulata (Afrotheria, Mammalia) but not Tethytheria. Proc Biol Sci 2007; 274:1333-40. [PMID: 17374594 PMCID: PMC1914331 DOI: 10.1098/rspb.2007.0088] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Despite marked improvements in the interpretation of systematic relationships within Eutheria, particular nodes, including Paenungulata (Hyracoidea, Sirenia and Proboscidea), remain ambiguous. The combination of a rapid radiation, a deep divergence and an extensive morphological diversification has resulted in a limited phylogenetic signal confounding resolution within this clade both at the morphological and nucleotide levels. Cross-species chromosome painting was used to delineate regions of homology between Loxodonta africana (2n=56), Procavia capensis (2n=54), Trichechus manatus latirostris (2n=48) and an outgroup taxon, the aardvark (Orycteropus afer, 2n=20). Changes specific to each lineage were identified and although the presence of a minimum of 11 synapomorphies confirmed the monophyly of Paenungulata, no change characterizing intrapaenungulate relationships was evident. The reconstruction of an ancestral paenungulate karyotype and the estimation of rates of chromosomal evolution indicate a reduced rate of genomic repatterning following the paenungulate radiation. In comparison to data available for other mammalian taxa, the paenungulate rate of chromosomal evolution is slow to moderate. As a consequence, the absence of a chromosomal character uniting two paenungulates (at the level of resolution characterized in this study) may be due to a reduced rate of chromosomal change relative to the length of time separating successive divergence events.
Collapse
Affiliation(s)
- A.T Pardini
- Evolutionary Genomics Group, Department of Botany and Zoology, University of StellenboschPrivate Bag X1, Matieland, 7602 Stellenbosch, South Africa
| | - P.C.M O'Brien
- Centre for Veterinary Science, University of CambridgeCambridge CB3 0ES, UK
| | - B Fu
- Centre for Veterinary Science, University of CambridgeCambridge CB3 0ES, UK
| | - R.K Bonde
- U.S. Geological Survey, Florida Integrated Science CentreGainesville, FL 32605-3574, USA
| | - F.F.B Elder
- Department of Pathology, Cytogenetics LaboratoryUT Southwestern Medical Centre, Dallas, TX 75235, USA
| | - M.A Ferguson-Smith
- Centre for Veterinary Science, University of CambridgeCambridge CB3 0ES, UK
| | - F Yang
- Centre for Veterinary Science, University of CambridgeCambridge CB3 0ES, UK
| | - T.J Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, University of StellenboschPrivate Bag X1, Matieland, 7602 Stellenbosch, South Africa
- Author for correspondence ()
| |
Collapse
|
10
|
Chromosome painting in the manatee supports Afrotheria and Paenungulata. BMC Evol Biol 2007; 7:6. [PMID: 17244368 PMCID: PMC1784077 DOI: 10.1186/1471-2148-7-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Accepted: 01/23/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sirenia (manatees, dugongs and Stellar's sea cow) have no evolutionary relationship with other marine mammals, despite similarities in adaptations and body shape. Recent phylogenomic results place Sirenia in Afrotheria and with elephants and rock hyraxes in Paenungulata. Sirenia and Hyracoidea are the two afrotherian orders as yet unstudied by comparative molecular cytogenetics. Here we report on the chromosome painting of the Florida manatee. RESULTS The human autosomal and X chromosome paints delimited a total of 44 homologous segments in the manatee genome. The synteny of nine of the 22 human autosomal chromosomes (4, 5, 6, 9, 11, 14, 17, 18 and 20) and the X chromosome were found intact in the manatee. The syntenies of other human chromosomes were disrupted in the manatee genome into two to five segments. The hybridization pattern revealed that 20 (15 unique) associations of human chromosome segments are found in the manatee genome: 1/15, 1/19, 2/3 (twice), 3/7 (twice), 3/13, 3/21, 5/21, 7/16, 8/22, 10/12 (twice), 11/20, 12/22 (three times), 14/15, 16/19 and 18/19. CONCLUSION There are five derived chromosome traits that strongly link elephants with manatees in Tethytheria and give implicit support to Paenungulata: the associations 2/3, 3/13, 8/22, 18/19 and the loss of the ancestral eutherian 4/8 association. It would be useful to test these conclusions with chromosome painting in hyraxes. The manatee chromosome painting data confirm that the associations 1/19 and 5/21 phylogenetically link afrotherian species and show that Afrotheria is a natural clade. The association 10/12/22 is also ubiquitous in Afrotheria (clade I), present in Laurasiatheria (clade IV), only partially present in Xenarthra (10/12, clade II) and absent in Euarchontoglires (clade III). If Afrotheria is basal to eutherians, this association could be part of the ancestral eutherian karyotype. If afrotherians are not at the root of the eutherian tree, then the 10/12/22 association could be one of a suite of derived associations linking afrotherian taxa.
Collapse
|
11
|
Pause KC, Bonde RK, McGuire PM, Zori RT, Gray BA. G-banded karyotype and ideogram for the North Atlantic right whale (Eubalaena glacialis). J Hered 2006; 97:303-6. [PMID: 16598035 DOI: 10.1093/jhered/esj033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Published cytogenetic data for extant cetacean species remain incomplete. In a review of the literature, we found karyotypic information for 6 of the 13 tentatively recognized species of the suborder Mysticeti (baleen whales). Among those yet to be described is the critically endangered North Atlantic right whale (Eubalaena glacialis). Herein, we describe and propose a first-generation G-banded karyotype and ideogram for this species (2n = 42), obtained from peripheral blood chromosome preparations from a stranded male calf. This information may prove useful for future genetic mapping projects and for interspecific and intraspecific genomic comparisons by techniques such as zoo-FISH.
Collapse
Affiliation(s)
- Kimberly C Pause
- Department of Biochemistry and Molecular Biology, Box 100245 University of Florida Health Science Center, University of Florida, Gainesville, FL 32610, USA
| | | | | | | | | |
Collapse
|
12
|
Vianna JA, Bonde RK, Caballero S, Giraldo JP, Lima RP, Clark A, Marmontel M, Morales-Vela B, De Souza MJ, Parr L, Rodríguez-Lopez MA, Mignucci-Giannoni AA, Powell JA, Santos FR. Phylogeography, phylogeny and hybridization in trichechid sirenians: implications for manatee conservation. Mol Ecol 2006; 15:433-47. [PMID: 16448411 DOI: 10.1111/j.1365-294x.2005.02771.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Abstract The three living species of manatees, West Indian (Trichechus manatus), Amazonian (Trichechus inunguis) and West African (Trichechus senegalensis), are distributed across the shallow tropical and subtropical waters of America and the western coast of Africa. We have sequenced the mitochondrial DNA control region in 330 Trichechus to compare their phylogeographic patterns. In T. manatus we observed a marked population structure with the identification of three haplotype clusters showing a distinct spatial distribution. A geographic barrier represented by the continuity of the Lesser Antilles to Trinidad Island, near the mouth of the Orinoco River in Venezuela, appears to have restricted the gene flow historically in T. manatus. However, for T. inunguis we observed a single expanding population cluster, with a high diversity of very closely related haplotypes. A marked geographic population structure is likely present in T. senegalensis with at least two distinct clusters. Phylogenetic analyses with the mtDNA cytochrome b gene suggest a clade of the marine Trichechus species, with T. inunguis as the most basal trichechid. This is in agreement with previous morphological analyses. Mitochondrial DNA, autosomal microsatellites and cytogenetic analyses revealed the presence of hybrids between the T. manatus and T. inunguis species at the mouth of the Amazon River in Brazil, extending to the Guyanas and probably as far as the mouth of the Orinoco River. Future conservation strategies should consider the distinct population structure of manatee species, as well as the historical barriers to gene flow and the likely occurrence of interspecific hybridization.
Collapse
Affiliation(s)
- Juliana A Vianna
- Laboratory of Biodiversity and Molecular Evolution (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|