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Oliveira da Silva W, Malcher SM, Ferguson-Smith MA, O'Brien PCM, Rossi RV, Geise L, Pieczarka JC, Nagamachi CY. Chromosomal rearrangements played an important role in the speciation of rice rats of genus Cerradomys (Rodentia, Sigmodontinae, Oryzomyini). Sci Rep 2024; 14:545. [PMID: 38177653 PMCID: PMC10766967 DOI: 10.1038/s41598-023-50861-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/27/2023] [Indexed: 01/06/2024] Open
Abstract
Rodents of the genus Cerradomys belong to tribe Oryzomyini, one of the most diverse and speciose groups in Sigmodontinae (Rodentia, Cricetidae). The speciation process in Cerradomys is associated with chromosomal rearrangements and biogeographic dynamics in South America during the Pleistocene era. As the morphological, molecular and karyotypic aspects of Myomorpha rodents do not evolve at the same rate, we strategically employed karyotypic characters for the construction of chromosomal phylogeny to investigate whether phylogenetic relationships using chromosomal data corroborate the radiation of Cerradomys taxa recovered by molecular phylogeny. Comparative chromosome painting using Hylaeamys megacephalus (HME) whole chromosome probes in C. langguthi (CLA), Cerradomys scotii (CSC), C. subflavus (CSU) and C. vivoi (CVI) shows that karyotypic variability is due to 16 fusion events, 2 fission events, 10 pericentric inversions and 1 centromeric repositioning, plus amplification of constitutive heterochromatin in the short arms of the X chromosomes of CSC and CLA. The chromosomal phylogeny obtained by Maximum Parsimony analysis retrieved Cerradomys as a monophyletic group with 97% support (bootstrap), with CSC as the sister to the other species, followed by a ramification into two clades (69% of branch support), the first comprising CLA and the other branch including CVI and CSU. We integrated the chromosome painting analysis of Eumuroida rodents investigated by HME and Mus musculus (MMU) probes and identified several syntenic blocks shared among representatives of Cricetidae and Muridae. The Cerradomys genus underwent an extensive karyotypic evolutionary process, with multiple rearrangements that shaped extant karyotypes. The chromosomal phylogeny corroborates the phylogenetic relationships proposed by molecular analysis and indicates that karyotypic diversity is associated with species radiation. Three syntenic blocks were identified as part of the ancestral Eumuroida karyotype (AEK): MMU 7/19 (AEK 1), MMU 14 (AEK 10) and MMU 12 (AEK 11). Besides, MMU 5/10 (HME 18/2/24) and MMU 8/13 (HME 22/5/11) should be considered as signatures for Cricetidae, while MMU 5/9/14, 5/7/19, 5 and 8/17 for Sigmodontinae.
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Affiliation(s)
- Willam Oliveira da Silva
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Stella Miranda Malcher
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Patricia Caroline Mary O'Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Rogério Vieira Rossi
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal do Mato Grosso (UFMT), Mato Grosso, Brazil
| | - Lena Geise
- Departamento de Zoologia, Laboratório de Mastozoologia, Universidade do Estado do 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), Belém, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil.
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da Silva NKN, Nagamachi CY, Rodrigues LRR, O’Brien PCM, Yang F, Ferguson-Smith MA, Pieczarka JC. Chromosome painting and phylogenetic analysis suggest that the genus Lophostoma (Chiroptera, Phyllostomidae) is paraphyletic. Sci Rep 2022; 12:19514. [PMID: 36376355 PMCID: PMC9663435 DOI: 10.1038/s41598-022-21391-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/27/2022] [Indexed: 11/15/2022] Open
Abstract
The subfamily Phyllostominae (Chiroptera, Phyllostomidae) comprises 10 genera of Microchiroptera bats from the Neotropics. The taxonomy of this group is controversial due to incongruities in the phylogenetic relationships evident from different datasets. The genus Lophostoma currently includes eight species whose phylogenetic relationships have not been resolved. Integrative analyzes including morphological, molecular and chromosomal data are powerful tools to investigate the phylogenetics of organisms, particularly if obtained by chromosomal painting. In the present work we performed comparative genomic mapping of three species of Lophostoma (L. brasiliense 2n = 30, L. carrikeri 2n = 26 and L. schulzi 2n = 26), by chromosome painting using whole chromosome probes from Phyllostomus hastatus and Carollia brevicauda; this included mapping interstitial telomeric sites. The karyotype of L. schulzi (LSC) is a new cytotype. The species L. brasiliense and L. carrikeri showed interstitial telomeric sequences that probably resulted from expansions of repetitive sequences near pericentromeric regions. The addition of chromosomal painting data from other species of Phyllostominae allowed phylogeny construction by maximum parsimony, and the determination that the genera of this subfamily are monophyletic, and that the genus Lophostoma is paraphyletic. Additionally, a review of the taxonomic status of LSC is suggested to determine if this species should be reclassified as part of the genus Tonatia.
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Affiliation(s)
- Natalia Karina Nascimento da Silva
- grid.271300.70000 0001 2171 5249Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará Brazil ,grid.442052.5Departamento de Morfofuncional, Universidade do Estado do Pará, Tucuruí, Pará Brazil
| | - Cleusa Yoshiko Nagamachi
- grid.271300.70000 0001 2171 5249Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará Brazil
| | - Luis Reginaldo Ribeiro Rodrigues
- grid.448725.80000 0004 0509 0076Laboratório de Genética & Biodiversidade, Instituto de Ciências da Educação, Universidade Federal do Oeste do Pará, Santarém, Pará Brazil
| | - Patricia Caroline Mary O’Brien
- grid.5335.00000000121885934Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, UK
| | - Fengtang Yang
- grid.10306.340000 0004 0606 5382Cytogenetics Facility, Wellcome Trust Sanger Institute, Hinxton, UK ,grid.27255.370000 0004 1761 1174School of Life Sciences and Medicine, Shandong University, Jinan, China
| | - Malcolm Andrew Ferguson-Smith
- grid.5335.00000000121885934Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, UK
| | - Julio Cesar Pieczarka
- grid.271300.70000 0001 2171 5249Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará Brazil
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Oliveira da Silva W, Rosa CC, Ferguson-Smith MA, O'Brien PCM, Saldanha J, Rossi RV, Pieczarka JC, Nagamachi CY. The emergence of a new sex-system (XX/XY 1Y 2) suggests a species complex in the "monotypic" rodent Oecomys auyantepui (Rodentia, Sigmodontinae). Sci Rep 2022; 12:8690. [PMID: 35610291 PMCID: PMC9130129 DOI: 10.1038/s41598-022-12706-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 05/11/2022] [Indexed: 11/15/2022] Open
Abstract
X-autosome translocation (XY1Y2) has been reported in distinct groups of vertebrates suggesting that the rise of a multiple sex system within a species may act as a reproductive barrier and lead to speciation. The viability of this system has been linked with repetitive sequences located between sex and autosomal portions of the translocation. Herein, we investigate Oecomys auyantepui, using chromosome banding and Fluorescence In Situ Hybridization with telomeric and Hylaeamys megacephalus whole-chromosome probes, and phylogenetic reconstruction using mtDNA and nuDNA sequences. We describe an amended karyotype for O. auyantepui (2n = 64♀65♂/FNa = 84) and report for the first time a multiple sex system (XX/XY1Y2) in Oryzomyini rodents. Molecular data recovered O. auyantepui as a monophyletic taxon with high support and cytogenetic data indicate that O. auyantepui may exist in two lineages recognized by distinct sex systems. The Neo-X exhibits repetitive sequences located between sex and autosomal portions, which would act as a boundary between these two segments. The G-banding comparisons of the Neo-X chromosomes of other Sigmodontinae taxa revealed a similar banding pattern, suggesting that the autosomal segment in the Neo-X can be shared among the Sigmodontinae lineages with a XY1Y2 sex system.
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Affiliation(s)
- Willam Oliveira da Silva
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Celina Coelho Rosa
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, UK
| | - Patricia Caroline Mary O'Brien
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, UK
| | - Juliane Saldanha
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal do Mato Grosso (UFMT), Cuiabá, Mato Grosso, Brazil
| | - Rogério Vieira Rossi
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal do Mato Grosso (UFMT), Cuiabá, Mato Grosso, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil.
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de Sousa RF, Venere PC, Faria KDC. Comparative cytogenetics of two species of Dermanura (Chiroptera, Phyllostomidae) in Midwestern Brazil. COMPARATIVE CYTOGENETICS 2021; 15:89-99. [PMID: 33868592 PMCID: PMC8035126 DOI: 10.3897/compcytogen.v15i2.60577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
Dermanura Gervais, 1856 is represented by small frugivorous bats of the Stenodermatinae subfamily. The taxonomy of this group presents controversies and has been subject to changes, especially since the morphological characters evaluated have left gaps that are difficult to fill regarding good species characterization. Previous studies performed in Dermanura cinerea Gervais, 1856 found that the karyotype of this species has a diploid number of chromosomes equal to 30 and 56 autosomal arms. The objective of the present study was to describe, for the first time, the karyotypes of the species Dermanura anderseni (Osgood, 1916) and Dermanura gnoma (Handley, 1987) based on classical cytogenetic markers. For both species, the diploid number found was 2n = 30 and NFa = 56. Two pairs of chromosomes showed markings of the nucleolus organizing regions (AgNORs) in the species D. anderseni and only one pair in D. gnoma, differing from what has already been described for D. cinerea. The two species analyzed here also showed differences in the sex chromosome system, with D. gnoma showing a neo-XY type system while in D. anderseni the classic XY sexual system was observed. In both species, visualization of the constitutive heterochromatin occurred in the pericentromeric region of all chromosomes, as well as in the short arms of the subtelocentric chromosomes. The present work represents an important expansion of karyotypic information for the subfamily Stenodermatinae, bringing chromosomal features that are possible to use in the taxonomic implications of the group.
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Affiliation(s)
- Ricardo Firmino de Sousa
- Instituto de Ciências Biológicas, Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Federal do Mato Grosso – UFMT. Av. Fernando Corrêa da Costa, n° 2367, Bairro Boa Esperança. Cuiabá – MT, BrazilUniversidade Federal do Mato GrossoCuiabáBrazil
- Faculdade de Ciências Agrárias, Biológicas e Sociais Aplicadas, Universidade do Estado de Mato Grosso, Av. Prof. Dr. Renato Figueiro Varella, s/n, Nova Xavantina, MT, BrazilUniversidade Federal do Mato GrossoCuiabáBrazil
| | - Paulo Cesar Venere
- Instituto de Ciências Biológicas, Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Federal do Mato Grosso – UFMT. Av. Fernando Corrêa da Costa, n° 2367, Bairro Boa Esperança. Cuiabá – MT, BrazilUniversidade Federal do Mato GrossoCuiabáBrazil
| | - Karina de Cassia Faria
- Faculdade de Ciências Agrárias, Biológicas e Sociais Aplicadas, Universidade do Estado de Mato Grosso, Av. Prof. Dr. Renato Figueiro Varella, s/n, Nova Xavantina, MT, BrazilUniversidade Federal do Mato GrossoCuiabáBrazil
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Oliveira da Silva W, Pieczarka JC, Rodrigues da Costa MJ, Ferguson-Smith MA, O'Brien PCM, Mendes-Oliveira AC, Rossi RV, Nagamachi CY. Chromosomal phylogeny and comparative chromosome painting among Neacomys species (Rodentia, Sigmodontinae) from eastern Amazonia. BMC Evol Biol 2019; 19:184. [PMID: 31601183 PMCID: PMC6785907 DOI: 10.1186/s12862-019-1515-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 09/16/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Neacomys genus is predominantly found in the Amazon region, and belongs to the most diverse tribe of the Sigmodontinae subfamily (Rodentia, Cricetidae, Oryzomyini). The systematics of this genus and questions about its diversity and range have been investigated by morphological, molecular (Cytb and COI sequences) and karyotype analysis (classic cytogenetics and chromosome painting), which have revealed candidate species and new distribution areas. Here we analyzed four species of Neacomys by chromosome painting with Hylaeamys megacephalus (HME) whole-chromosome probes, and compared the results with two previously studied Neacomys species and with other taxa from Oryzomyini and Akodontini tribes that have been hybridized with HME probes. Maximum Parsimony (MP) analyses were performed with the PAUP and T.N.T. software packages, using a non-additive (unordered) multi-state character matrix, based on chromosomal morphology, number and syntenic blocks. We also compared the chromosomal phylogeny obtained in this study with molecular topologies (Cytb and COI) that included eastern Amazonian species of Neacomys, to define the phylogenetic relationships of these taxa. RESULTS The comparative chromosome painting analysis of the seven karyotypes of the six species of Neacomys shows that their diversity is due to 17 fusion/fission events and one translocation, pericentric inversions in four syntenic blocks, and constitutive heterochromatin (CH) amplification/deletion of six syntenic autosomal blocks plus the X chromosome. The chromosomal phylogeny is consistent with the molecular relationships of species of Neacomys. We describe new karyotypes and expand the distribution area for species from eastern Amazonia and detect complex rearrangements by chromosome painting among the karyotypes. CONCLUSIONS Our phylogeny reflects the molecular relationships of the Akodontini and Oryzomyini taxa and supports the monophyly of Neacomys. This work presents new insights about the chromosomal evolution of this group, and we conclude that the karyotypic divergence is in accord with phylogenetic relationships.
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Affiliation(s)
- Willam Oliveira da Silva
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Julio Cesar Pieczarka
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Marlyson Jeremias Rodrigues da Costa
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Patricia Caroline Mary O'Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Rogério Vieira Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso (UFMT), Cuiabá, Mato Grosso, Brazil
| | - Cleusa Yoshiko Nagamachi
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil.
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Solari S, Sotero-Caio CG, Baker RJ. Advances in systematics of bats: towards a consensus on species delimitation and classifications through integrative taxonomy. J Mammal 2019. [DOI: 10.1093/jmammal/gyy168] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Sergio Solari
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Cibele G Sotero-Caio
- Departamento de Genética, Universidade Federal de Pernambuco, Cidade Universitária, Recife, PE, Brazil
| | - Robert J Baker
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
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Benathar TCM, Nagamachi CY, Rodrigues LRR, O’Brien PCM, Ferguson-Smith MA, Yang F, Pieczarka JC. Karyotype, evolution and phylogenetic reconstruction in Micronycterinae bats with implications for the ancestral karyotype of Phyllostomidae. BMC Evol Biol 2019; 19:98. [PMID: 31064342 PMCID: PMC6505122 DOI: 10.1186/s12862-019-1421-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 04/11/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The Micronycterinae form a subfamily of leaf-nosed bats (Phyllostomidae) that contains the genera Lampronycteris Sanborn, 1949, and Micronycteris Gray, 1866 (stricto sensu), and is characterized by marked karyotypic variability and discrepancies in the phylogenetic relationships suggested by the molecular versus morphological data. In the present study, we investigated the chromosomal evolution of the Micronycterinae using classical cytogenetics and multidirectional chromosome painting with whole-chromosomes probes of Phyllostomus hastatus and Carollia brevicauda. Our goal was to perform comparative chromosome mapping between the genera of this subfamily and explore the potential for using chromosomal rearrangements as phylogenetic markers. RESULTS The Micronycterinae exhibit great inter- and intraspecific karyotype diversity, with large blocks of telomere-like sequences inserted within or adjacent to constitutive heterochromatin regions. The phylogenetic results generated from our chromosomal data revealed that the Micronycterinae hold a basal position in the phylogenetic tree of the Phyllostomidae. Molecular cytogenetic data confirmed that there is a low degree of karyotype similarity between Lampronycteris and Micronycteris specimens analyzed, indicating an absence of synapomorphic associations in Micronycterinae. CONCLUSIONS We herein confirm that karyotypic variability is present in subfamily Micronycterinae. We further report intraspecific variation and describe a new cytotype in M. megalotis. The cytogenetic data show that this group typically has large blocks of interstitial telomeric sequences that do not appear to be correlated with chromosomal rearrangement events. Phylogenetic analysis using chromosome data recovered the basal position for Micronycterinae, but did not demonstrate that it is a monophyletic lineage, due to the absence of common chromosomal synapomorphy between the genera. These findings may be related to an increase in the rate of chromosomal evolution during the time period that separates Lampronycteris from Micronycteris.
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Affiliation(s)
| | - C. Y. Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Av. Perimetral, sn. Guamá, Belém, Pará 66077 Brasil
- CNPq, Brasilia, Brazil
| | - L. R. R. Rodrigues
- Laboratório de Genética e Biodiversidade, ICED, Universidade Federal do Oeste do Pará, Belém, Brasil
| | - P. C. M. O’Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - M. A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - F. Yang
- Cytogenetics Facility, Welcome Trust Sanger Institute, Hinxton, UK
| | - J. C. Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Av. Perimetral, sn. Guamá, Belém, Pará 66077 Brasil
- CNPq, Brasilia, Brazil
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Oliveira da Silva W, Rodrigues da Costa MJ, Pieczarka JC, Rissino J, Pereira JC, Ferguson-Smith MA, Nagamachi CY. Identification of two independent X-autosome translocations in closely related mammalian (Proechimys) species. Sci Rep 2019; 9:4047. [PMID: 30858413 PMCID: PMC6411977 DOI: 10.1038/s41598-019-40593-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 02/19/2019] [Indexed: 11/13/2022] Open
Abstract
Multiple sex chromosome systems have been described for several mammalian orders, with different species from the same genus sharing the same system (e.g., X1X2Y or XY1Y2). This is important because the translocated autosome may be influenced by the evolution of the recipient sex chromosome, and this may be related to speciation. It is often thought that the translocation of an autosome to a sex chromosome may share a common origin among phylogenetically related species. However, the neo-X chromosomes of Proechimys goeldii (2n = 24♀, 25♂/NFa = 42) and Proechimys gr. goeldii (2n = 16♀, 17♂/NFa = 14) have distinct sizes and morphologies that have made it difficult to determine whether they have the same or different origins. This study investigates the origins of the XY1Y2 sex chromosome determination system in P. goeldii (PGO) and P. gr. goeldii (PGG) and elucidates the chromosomal rearrangements in this low-diploid-number group of Proechimys species. Toward this end, we produced whole-chromosome probes for P. roberti (PRO; 2n = 30♂/NFa = 54) and P. goeldii (2n = 25♂/NFa = 42) and used them in comparative chromosomal mapping. Our analysis reveals that multiple translocations and inversions are responsible for the karyotype diversity of these species, with only three whole-chromosomes conserved between PRO and PGO and eight between PGO and PGG. Our data indicate that multiple sex chromosome systems have originated twice in Proechimys. As small populations are prone to the fixation of chromosomal rearrangements, we speculate that biological features of Rodentia contribute to this fixation. We also highlight the potential of these rodents as a model for studying sex chromosome evolution.
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Affiliation(s)
- Willam Oliveira da Silva
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, ICB, Universidade Federal do Pará, Belém, Pará, Brazil.,Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Julio Cesar Pieczarka
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Jorge Rissino
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Jorge C Pereira
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Cleusa Yoshiko Nagamachi
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, ICB, Universidade Federal do Pará, Belém, Pará, Brazil.
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Gomes AJB, Nagamachi CY, Rodrigues LRR, Ferguson-Smith MA, Yang F, O'Brien PCM, Pieczarka JC. Chromosomal evolution and phylogeny in the Nullicauda group (Chiroptera, Phyllostomidae): evidence from multidirectional chromosome painting. BMC Evol Biol 2018; 18:62. [PMID: 29699485 PMCID: PMC5921544 DOI: 10.1186/s12862-018-1176-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 04/11/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The family Phyllostomidae (Chiroptera) shows wide morphological, molecular and cytogenetic variation; many disagreements regarding its phylogeny and taxonomy remains to be resolved. In this study, we use chromosome painting with whole chromosome probes from the Phyllostomidae Phyllostomus hastatus and Carollia brevicauda to determine the rearrangements among several genera of the Nullicauda group (subfamilies Gliphonycterinae, Carolliinae, Rhinophyllinae and Stenodermatinae). RESULTS These data, when compared with previously published chromosome homology maps, allow the construction of a phylogeny comparable to those previously obtained by morphological and molecular analysis. Our phylogeny is largely in agreement with that proposed with molecular data, both on relationships between the subfamilies and among genera; it confirms, for instance, that Carollia and Rhinophylla, previously considered as part of the same subfamily are, in fact, distant genera. CONCLUSIONS The occurrence of the karyotype considered ancestral for this family in several different branches suggests that the diversification of Phyllostomidae into many subfamilies has occurred in a short period of time. Finally, the comparison with published maps using human whole chromosome probes allows us to track some syntenic associations prior to the emergence of this family.
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Affiliation(s)
- Anderson José Baia Gomes
- Laboratório de Citogenética, CEABIO, ICB, Universidade Federal do Pará, Av. Bernardo Sayão, sn. Guamá, Belém, Pará, 66075-900, Brazil.,Instituto Federal do Pará, Abaetetuba, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, CEABIO, ICB, Universidade Federal do Pará, Av. Bernardo Sayão, sn. Guamá, Belém, Pará, 66075-900, Brazil.,CNPQ Researcher, Brasilia, Brazil
| | | | - Malcolm Andrew Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, UK
| | - Fengtang Yang
- Cytogenetics Facility, Welcome Trust Sanger Institute, Hinxton, UK
| | - Patricia Caroline Mary O'Brien
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, UK
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, CEABIO, ICB, Universidade Federal do Pará, Av. Bernardo Sayão, sn. Guamá, Belém, Pará, 66075-900, Brazil. .,CNPQ Researcher, Brasilia, Brazil.
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10
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Chromosomal Evolution in Chiroptera. Genes (Basel) 2017; 8:genes8100272. [PMID: 29027987 PMCID: PMC5664122 DOI: 10.3390/genes8100272] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 01/05/2023] Open
Abstract
Chiroptera is the second largest order among mammals, with over 1300 species in 21 extant families. The group is extremely diverse in several aspects of its natural history, including dietary strategies, ecology, behavior and morphology. Bat genomes show ample chromosome diversity (from 2n = 14 to 62). As with other mammalian orders, Chiroptera is characterized by clades with low, moderate and extreme chromosomal change. In this article, we will discuss trends of karyotypic evolution within distinct bat lineages (especially Phyllostomidae, Hipposideridae and Rhinolophidae), focusing on two perspectives: evolution of genome architecture, modes of chromosomal evolution, and the use of chromosome data to resolve taxonomic problems.
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11
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de Sotero-Caio CG, Cabral-de-Mello DC, Calixto MDS, Valente GT, Martins C, Loreto V, de Souza MJ, Santos N. Centromeric enrichment of LINE-1 retrotransposons and its significance for the chromosome evolution of Phyllostomid bats. Chromosome Res 2017; 25:313-325. [PMID: 28916913 DOI: 10.1007/s10577-017-9565-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 08/24/2017] [Accepted: 08/28/2017] [Indexed: 10/18/2022]
Abstract
Despite their ubiquitous incidence, little is known about the chromosomal distribution of long interspersed elements (LINEs) in mammalian genomes. Phyllostomid bats, characterized by lineages with distinct trends of chromosomal evolution coupled with remarkable ecological and taxonomic diversity, represent good models to understand how these repetitive sequences contribute to the evolution of genome architecture and its link to lineage diversification. To test the hypothesis that LINE-1 sequences were important modifiers of bat genome architecture, we characterized the distribution of LINE-1-derived sequences on genomes of 13 phyllostomid species within a phylogenetic framework. We found massive accumulation of LINE-1 elements in the centromeres of most species: a rare phenomenon on mammalian genomes. We hypothesize that expansion of these elements has occurred early in the radiation of phyllostomids and recurred episodically. LINE-1 expansions on centromeric heterochromatin probably spurred chromosomal change before the radiation of phyllostomids into the extant 11 subfamilies and contributed to the high degree of karyotypic variation observed among different lineages. Understanding centromere architecture in a variety of taxa promises to explain how lineage-specific changes on centromere structure can contribute to karyotypic diversity while not disrupting functional constraints for proper cell division.
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Affiliation(s)
- Cibele Gomes de Sotero-Caio
- Departamento de Genética, Laboratório de Genética e Citogenética Animal e Humana, UFPE-Universidade Federal de Pernambuco, Av. da Engenharia s/n; Cidade Universitária, Recife, PE, CEP:50740-600, Brazil. .,Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
| | - Diogo Cavalcanti Cabral-de-Mello
- Departamento de Biologia, Grupo de Estudos em Citogenômica e Evolução Animal, UNESP-Universidade Estadual Paulista, Instituto de Biociências, Rio Claro, SP, Brazil
| | - Merilane da Silva Calixto
- Departamento de Genética, Laboratório de Genética e Citogenética Animal e Humana, UFPE-Universidade Federal de Pernambuco, Av. da Engenharia s/n; Cidade Universitária, Recife, PE, CEP:50740-600, Brazil.,Centro de Saúde e Tecnologia, Unidade Acadêmica de Ciências Biológicas, UFCG-Universidade Federal de Campina Grande, Patos, PB, Brazil
| | - Guilherme Targino Valente
- Departamento de Bioprocessos e Biotecnologia da Faculdade de Ciências Agronômicas, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Cesar Martins
- Departamento de Morfologia, Laboratório Genômica Integrativa, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Vilma Loreto
- Departamento de Genética, Laboratório de Genética e Citogenética Animal e Humana, UFPE-Universidade Federal de Pernambuco, Av. da Engenharia s/n; Cidade Universitária, Recife, PE, CEP:50740-600, Brazil
| | - Maria José de Souza
- Departamento de Genética, Laboratório de Genética e Citogenética Animal e Humana, UFPE-Universidade Federal de Pernambuco, Av. da Engenharia s/n; Cidade Universitária, Recife, PE, CEP:50740-600, Brazil
| | - Neide Santos
- Departamento de Genética, Laboratório de Genética e Citogenética Animal e Humana, UFPE-Universidade Federal de Pernambuco, Av. da Engenharia s/n; Cidade Universitária, Recife, PE, CEP:50740-600, Brazil
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12
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de Souza ÉMS, Gross MC, Silva CEFE, Sotero-Caio CG, Feldberg E. Heterochromatin variation and LINE-1 distribution in Artibeus (Chiroptera, Phyllostomidae) from Central Amazon, Brazil. COMPARATIVE CYTOGENETICS 2017; 11:613-626. [PMID: 29114357 PMCID: PMC5672158 DOI: 10.3897/compcytogen.v11i4.14562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/09/2017] [Indexed: 06/07/2023]
Abstract
Species in the subgenus Artibeus Leach, 1821 are widely distributed in Brazil. Conserved karyotypes characterize the group with identical diploid number and chromosome morphology. Recent studies suggested that the heterochromatin distribution and accumulation patterns can vary among species. In order to assess whether variation can also occur within species, we have analyzed the chromosomal distribution of constitutive heterochromatin in A. planirostris (Spix, 1823) and A. lituratus (Olfers, 1818) from Central Amazon (North Brazil) and contrasted our findings with those reported for other localities in Brazil. In addition, Ag-NOR staining and FISH with 18S rDNA, telomeric, and LINE-1 probes were performed to assess the potential role that these different repetitive markers had in shaping the current architecture of heterochromatic regions. Both species presented interindividual variation of constitutive heterochromatin. In addition, in A. planirostris the centromeres of most chromosomes are enriched with LINE-1, colocated with pericentromeric heterochromatin blocks. Overall, our data indicate that amplification and differential distribution of the investigated repetitive DNAs might have played a significant role in shaping the chromosome architecture of the subgenus Artibeus.
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Affiliation(s)
- Érica Martinha Silva de Souza
- Programa de Pós-graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, Aleixo, 69.060-001 Manaus, AM, Brazil
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, Aleixo, 69.060-001 Manaus, AM, Brazil
| | - Maria Claudia Gross
- Universidade Federal da Integração Latino Americana, Laboratório de Genética, Av. Tarquínio Joslin dos Santos, 1000, Jardim Universitário, 85857-190, Foz do Iguaçu, PR, Brazil
| | - Carlos Eduardo Faresin e Silva
- Programa de Pós-graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, Aleixo, 69.060-001 Manaus, AM, Brazil
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, Aleixo, 69.060-001 Manaus, AM, Brazil
| | - Cibele Gomes Sotero-Caio
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA 79409
- Laboratório de Genética e Citogenética Animal e Humana, Departamento de Genética, Universidade Federal de Pernambuco, Av. da Engenharia s/n; Cidade Universitária; CEP:50740-600; Recife-PE, Brazil
| | - Eliana Feldberg
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, Aleixo, 69.060-001 Manaus, AM, Brazil
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de Araújo REF, Nagamachi CY, da Costa MJR, Noronha RCR, Rodrigues LRR, Pieczarka JC. First description of multivalent ring structures in eutherian mammalian meiosis: new chromosomal characterization of Cormura brevirostris (Emballonuridae, Chiroptera). Genetica 2016; 144:407-15. [PMID: 27300547 DOI: 10.1007/s10709-016-9909-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 06/01/2016] [Indexed: 11/26/2022]
Abstract
Twelve specimens of the bat Cormura brevirostris (Emballonuridae: Chiroptera) were collected from four localities in the Brazilian Amazon region and analyzed by classical and molecular cytogenetics. The diploid number and autosomal fundamental number were as previously reported (2n = 22 and FNa = 40, respectively). Fluorescence in situ hybridization using rDNA probes and silver nitrate technique demonstrated the presence of two NOR sites and the presence of internal telomeric sequences at pericentromeric regions of all chromosomes with exception of Y. Based on meiotic studies and chromosome banding we suggest that the sex chromosome pair of C. brevirostris was equivocally identified as it appears in the literature. Meiotic analysis demonstrated that at diplotene-diakinesis the cells had a ring conformation involving four chromosome pairs. This suggests the occurrence of multiple reciprocal translocations among these chromosomes, which is a very rare phenomenon in vertebrates, and has never been described in Eutheria.
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Affiliation(s)
- Ramon Everton Ferreira de Araújo
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, UFPA-Belém, ICB, 3º Andar. Av. Augusto Corrêa SN, Bairro Guamá, Belém, Pará, 66.075-900, Brazil
- CAPES Doctorship Scholarship -Neuroscience and Cellular Biology - UFPA, Belém, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, UFPA-Belém, ICB, 3º Andar. Av. Augusto Corrêa SN, Bairro Guamá, Belém, Pará, 66.075-900, Brazil
- CNPq Researcher, Brasília, Brazil
| | - Marlyson Jeremias Rodrigues da Costa
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, UFPA-Belém, ICB, 3º Andar. Av. Augusto Corrêa SN, Bairro Guamá, Belém, Pará, 66.075-900, Brazil
| | - Renata Coelho Rodrigues Noronha
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, UFPA-Belém, ICB, 3º Andar. Av. Augusto Corrêa SN, Bairro Guamá, Belém, Pará, 66.075-900, Brazil
- CNPq Researcher, Brasília, Brazil
| | - Luís Reginaldo Ribeiro Rodrigues
- Laboratório de Genética and Biodiversidade, Instituto de Ciências da Educação, Universidade Federal do Oeste do Pará, Santarém, Brazil
- PPG Recursos Naturais da Amazônia - UFOPA, Santarém, Brazil
| | - Julio César Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, UFPA-Belém, ICB, 3º Andar. Av. Augusto Corrêa SN, Bairro Guamá, Belém, Pará, 66.075-900, Brazil.
- CNPq Researcher, Brasília, Brazil.
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14
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Chromosomal phylogeny of Vampyressine bats (Chiroptera, Phyllostomidae) with description of two new sex chromosome systems. BMC Evol Biol 2016; 16:119. [PMID: 27260645 PMCID: PMC4893233 DOI: 10.1186/s12862-016-0689-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 05/23/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The subtribe Vampyressina (sensu Baker et al. 2003) encompasses approximately 43 species and seven genera and is a recent and diversified group of New World leaf-nosed bats specialized in fruit eating. The systematics of this group continues to be debated mainly because of the lack of congruence between topologies generated by molecular and morphological data. We analyzed seven species of all genera of vampyressine bats by multidirectional chromosome painting, using whole-chromosome-painting probes from Carollia brevicauda and Phyllostomus hastatus. Phylogenetic analyses were performed using shared discrete chromosomal segments as characters and the Phylogenetic Analysis Using Parsimony (PAUP) software package, using Desmodontinae as outgroup. We also used the Tree Analysis Using New Technology (TNT) software. RESULTS The result showed a well-supported phylogeny congruent with molecular topologies regarding the sister taxa relationship of Vampyressa and Mesophylla genera, as well as the close relationship between the genus Chiroderma and Vampyriscus. CONCLUSIONS Our results supported the hypothesis that all genera of this subtribe have compound sex chromosome systems that originated from an X-autosome translocation, an ancestral condition observed in the Stenodermatinae. Additional rearrangements occurred independently in the genus Vampyressa and Mesophylla yielding the X1X1X2X2/X1X2Y sex chromosome system. This work presents additional data supporting the hypothesis based on molecular studies regarding the polyphyly of the genus Vampyressa and its sister relationship to Mesophylla.
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15
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Baker RJ, Solari S, Cirranello A, Simmons NB. Higher Level Classification of Phyllostomid Bats with a Summary of DNA Synapomorphies. ACTA CHIROPTEROLOGICA 2016. [DOI: 10.3161/15081109acc2016.18.1.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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16
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Sotero-Caio CG, Volleth M, Hoffmann FG, Scott L, Wichman HA, Yang F, Baker RJ. Integration of molecular cytogenetics, dated molecular phylogeny, and model-based predictions to understand the extreme chromosome reorganization in the Neotropical genus Tonatia (Chiroptera: Phyllostomidae). BMC Evol Biol 2015; 15:220. [PMID: 26444412 PMCID: PMC4594642 DOI: 10.1186/s12862-015-0494-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/22/2015] [Indexed: 11/18/2022] Open
Abstract
Background Defining factors that contributed to the fixation of a high number of underdominant chromosomal rearrangements is a complex task because not only molecular mechanisms must be considered, but also the uniqueness of natural history attributes of each taxon. Ideally, detailed investigation of the chromosome architecture of an organism and related groups, placed within a phylogenetic context, is required. We used multiple approaches to investigate the dynamics of chromosomal evolution in lineages of bats with considerable karyotypic variation, focusing on the different facets contributing to fixation of the exceptional chromosomal changes in Tonatia saurophila. Integration of empirical data with proposed models of chromosome evolution was performed to understand the probable conditions for Tonatia’s karyotypic evolution. Results The trajectory of reorganization of chromosome blocks since the common ancestor of Glossophaginae and Phyllostominae subfamilies suggests that multiple tandem fusions, as well as disruption and fusions of conserved phyllostomid chromosomes were major drivers of karyotypic reshuffling in Tonatia. Considerable variation in the rates of chromosomal evolution between phyllostomid lineages was observed. Thirty–nine unique fusions and fission events reached fixation in Tonatia over a short period of time, followed by ~12 million years of chromosomal stasis. Physical mapping of repetitive DNA revealed an unusual accumulation of LINE-1 sequences on centromeric regions, probably associated with the chromosomal dynamics of this genus. Conclusions Multiple rearrangements have reached fixation in a wave-like fashion in phyllostomid bats. Different biological features of Tonatia support distinct models of rearrangement fixation, and it is unlikely that the fixations were a result of solely stochastic processes in small ancient populations. Increased recombination rates were probably facilitated by expansion of repetitive DNA, reinforced by aspects of taxon reproduction and ecology. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0494-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Marianne Volleth
- Department of Human Genetics, Otto-von-Guericke University, Magdeburg, Germany.
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi, MS, USA. .,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, USA.
| | - LuAnn Scott
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA.
| | - Holly A Wichman
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA.
| | - Fengtang Yang
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
| | - Robert J Baker
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
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17
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Volleth M, Loidl J, Mayer F, Yong HS, Müller S, Heller KG. Surprising Genetic Diversity inRhinolophus luctus(Chiroptera: Rhinolophidae) from Peninsular Malaysia: Description of a New Species Based on Genetic and Morphological Characters. ACTA CHIROPTEROLOGICA 2015. [DOI: 10.3161/15081109acc2015.17.1.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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18
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Ribas TFA, Rodrigues LRR, Nagamachi CY, Gomes AJB, Rissino JDD, O'Brien PCM, Yang F, Ferguson-Smith MA, Pieczarka JC. Phylogenetic reconstruction by cross-species chromosome painting and G-banding in four species of Phyllostomini tribe (Chiroptera, Phyllostomidae) in the Brazilian Amazon: an independent evidence for monophyly. PLoS One 2015; 10:e0122845. [PMID: 25806812 PMCID: PMC4373847 DOI: 10.1371/journal.pone.0122845] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 02/17/2015] [Indexed: 11/18/2022] Open
Abstract
The subfamily Phyllostominae comprises taxa with a variety of feeding strategies. From the cytogenetic point of view, Phyllostominae shows different rates of chromosomal evolution between genera, with Phyllostomus hastatus probably retaining the ancestral karyotype for the subfamily. Since chromosomal rearrangements occur rarely in the genome and have great value as phylogenetic markers and in taxonomic characterization, we analyzed three species: Lophostoma silvicola (LSI), Phyllostomus discolor (PDI) and Tonatia saurophila (TSA), representing the tribe Phyllostomini, collected in the Amazon region, by classic and molecular cytogenetic techniques in order to reconstruct the phylogenetic relationships within this tribe. LSA has a karyotype of 2n=34 and FN=60, PDI has 2n=32 and FN=60 and TSA has 2n=16 and FN=20. Comparative analysis using G-banding and chromosome painting show that the karyotypic complement of TSA is highly rearranged relative to LSI and PHA, while LSI, PHA and PDI have similar karyotypes, differing by only three chromosome pairs. Nearly all chromosomes of PDI and PHA were conserved in toto, except for chromosome 15 that was changed by a pericentric inversion. A strongly supported phylogeny (bootstrap=100 and Bremer=10 steps), confirms the monophyly of Phyllostomini. In agreement with molecular topologies, TSA was in the basal position, while PHA and LSI formed sister taxa. A few ancestral syntenies are conserved without rearrangements and most associations are autapomorphic traits for Tonatia or plesiomorphic for the three genera analyzed here. The karyotype of TSA is highly derived in relation to that of other phyllostomid bats, differing from the supposed ancestral karyotype of Phyllostomidae by multiple rearrangements. Phylogenies based on chromosomal data are independent evidence for the monophyly of tribe Phyllostomini as determined by molecular topologies and provide additional support for the paraphyly of the genus Tonatia by the exclusion of the genus Lophostoma.
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Affiliation(s)
| | | | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
- CNPQ Researcher, Belém, Pará, Brazil
| | | | | | | | - Fengtang Yang
- Cytogenetics Facility, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | | | - Julio Cesar Pieczarka
- Laboratório de Citogenética, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
- CNPQ Researcher, Belém, Pará, Brazil
- * E-mail:
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19
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Sotero-Caio CG, Volleth M, Gollahon LS, Fu B, Cheng W, Ng BL, Yang F, Baker RJ. Chromosomal evolution among leaf-nosed nectarivorous bats--evidence from cross-species chromosome painting (Phyllostomidae, Chiroptera). BMC Evol Biol 2013; 13:276. [PMID: 24369737 PMCID: PMC3880000 DOI: 10.1186/1471-2148-13-276] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/19/2013] [Indexed: 11/10/2022] Open
Abstract
Background New World leaf-nosed bats, Phyllostomidae, represent a lineage of Chiroptera marked by unprecedented morphological/ecological diversity and extensive intergeneric chromosomal reorganization. There are still disagreements regarding their systematic relationships due to morphological convergence among some groups. Their history of karyotypic evolution also remains to be documented. Results To better understand the evolutionary relationships within Phyllostomidae, we developed chromosome paints from the bat species Macrotus californicus. We tested the potential of these paints as phylogenetic tools by looking for chromosomal signatures in two lineages of nectarivorous phyllostomids whose independent origins have been statistically supported by molecular phylogenies. By examining the chromosomal homologies defined by chromosome painting among two representatives of the subfamily Glossophaginae (Glossophaga soricina and Anoura cultrata) and one species from the subfamily Lonchophyllinae (Lonchophylla concava), we found chromosomal correspondence in regions not previously detected by other comparative cytogenetic techniques. We proposed the corresponding human chromosomal segments for chromosomes of the investigated species and found two syntenic associations shared by G. soricina and A. cultrata. Conclusion Comparative painting with whole chromosome-specific paints of M. californicus demonstrates an extensive chromosomal reorganization within the two lineages of nectarivorous phyllostomids, with a large number of chromosomes shared between M. californicus and G. soricina. We show that the evolution of nectar-feeding bats occurs mainly by reshuffling of chiropteran Evolutionarily Conserved Units (ECUs). Robertsonian fusions/fissions and inversions seem to be important modifiers of phyllostomid karyotypes, and autapomorphic character states are common within species. Macrotus californicus chromosome paints will be a valuable tool for documenting the pattern of karyotypic evolution within Phyllostomidae radiation.
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Affiliation(s)
- Cibele G Sotero-Caio
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA.
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Patterns of rDNA and telomeric sequences diversification: contribution to repetitive DNA organization in Phyllostomidae bats. Genetica 2013; 142:49-58. [PMID: 24368540 DOI: 10.1007/s10709-013-9753-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 12/17/2013] [Indexed: 10/25/2022]
Abstract
Chromosomal organization and the evolution of genome architecture can be investigated by physical mapping of the genes for 45S and 5S ribosomal DNAs (rDNAs) and by the analysis of telomeric sequences. We studied 12 species of bats belonging to four subfamilies of the family Phyllostomidae in order to correlate patterns of distribution of heterochromatin and the multigene families for rDNA. The number of clusters for 45S gene ranged from one to three pairs, with exclusively location in autosomes, except for Carollia perspicillata that had in X chromosome. The 5S gene all the species studied had only one site located on an autosomal pair. In no species the 45S and 5S genes collocated. The fluorescence in situ hybridization (FISH) probe for telomeric sequences revealed fluorescence on all telomeres in all species, except in Carollia perspicillata. Non-telomeric sites in the pericentromeric region of the chromosomes were observed in most species, ranged from one to 12 pairs. Most interstitial telomeric sequences were coincident with heterochromatic regions. The results obtained in the present work indicate that different evolutionary mechanisms are acting in Phyllostomidae genome architecture, as well as the occurrence of Robertsonian fusion during the chromosomal evolution of bats without a loss of telomeric sequences. These data contribute to understanding the organization of multigene families and telomeric sequences on bat genome as well as the chromosomal evolutionary history of Phyllostomidae bats.
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Ribas TFA, Rodrigues LRR, Nagamachi CY, Gomes AJB, Benathar TCM, O'Brien PCM, Yang F, Ferguson-Smith MA, Pieczarka JC. Two new cytotypes reinforce that Micronycteris hirsuta Peters, 1869 does not represent a monotypic taxon. BMC Genet 2013; 14:119. [PMID: 24359225 PMCID: PMC3878135 DOI: 10.1186/1471-2156-14-119] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 12/10/2013] [Indexed: 11/10/2022] Open
Abstract
Background The genus Micronycteris is a diverse group of phyllostomid bats currently comprising 11 species, with diploid number (2n) ranging from 26 to 40 chromosomes. The karyotypic relationships within Micronycteris and between Micronycteris and other phyllostomids remain poorly understood. The karyotype of Micronycteris hirsuta is of particular interest: three different diploid numbers were reported for this species in South and Central Americas with 2n = 26, 28 and 30 chromosomes. Although current evidence suggests some geographic differentiation among populations of M. hirsuta based on chromosomal, morphological, and nuclear and mitochondrial DNA markers, the recognition of new species or subspecies has been avoided due to the need for additional data, mainly chromosomal data. Results We describe two new cytotypes for Micronycteris hirsuta (MHI) (2n = 26 and 25, NF = 32), whose differences in diploid number are interpreted as the products of Robertsonian rearrangements. C-banding revealed a small amount of constitutive heterochromatin at the centromere and the NOR was located in the interstitial portion of the short arm of a second pair, confirmed by FISH. Telomeric probes hybridized to the centromeric regions and weakly to telomeric regions of most chromosomes. The G-banding analysis and chromosome painting with whole chromosome probes from Carollia brevicauda (CBR) and Phyllostomus hastatus (PHA) enabled the establishment of genome-wide homologies between MHI, CBR and PHA. Conclusions The karyotypes of Brazilian specimens of Micronycteris hirsuta described here are new to Micronycteris and reinforce that M. hirsuta does not represent a monotypic taxon. Our results corroborate the hypothesis of karyotypic megaevolution within Micronycteris, and strong evidence for this is that the entire chromosome complement of M. hirsuta was shown to be derivative with respect to species compared in this study.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Julio C Pieczarka
- Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará, Campus do Guamá, Av, Perimetral, sn, Guamá, Belém, Pará, 66075-900, Brazil.
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