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Diversification of Amazonian spiny tree rats in genus Makalata (Rodentia, Echimyidae): Cryptic diversity, geographic structure and drivers of speciation. PLoS One 2022; 17:e0276475. [PMID: 36520936 PMCID: PMC9754209 DOI: 10.1371/journal.pone.0276475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 10/10/2022] [Indexed: 12/23/2022] Open
Abstract
Amazonian mammal diversity is exceptionally high, yet new taxonomic discoveries continue to be made and many questions remain for understanding its diversification through time and space. Here we investigate the diversification of spiny rats in the genus Makalata, whose species are strongly associated with seasonally flooded forests, watercourses and flooded islands. We use a biogeographical approach based on a mitochondrial cytochrome b gene through divergence time estimation and reconstruction of ancestral areas and events. Our findings indicate an ancient origin of Makalata for the Guiana Shield and Eastern Amazonia as ancestral area. A first cladogenetic event led to a phylogeographic break into two broader clades of Makalata through dispersal, implying a pattern of western/Eastern Amazonian clades coinciding with the Purus Arch (middle Miocene). Most of subclades we infer originated between the late Pliocene to the early Pleistocene, with few recent exceptions in the early Pliocene through dispersal and vicariant events. The hypothesis of rivers as dispersal barriers is not corroborated for Makalata, as expected for mammalian species associated with seasonally flooded environments. We identify two key events for the expansion and diversification of Makalata species: the presence of geologically stable areas in the Guiana and Brazilian shields and the transition from lacustrine conditions in western Amazonia (Acre system) to a river system, with the establishment of the Amazon River transcontinental system and its tributaries. Our results are congruent with older geological scenarios for the Amazon basin formation (Miocene), but we do not discard the influence of recent dynamics on some speciation events and, mainly, on phylogeographic structuring processes.
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Chacón-Pacheco JJ, Lozano-Flórez J, Avendaño-Maldonado LJ, Racero-Casarrubia J, Montoya-Patiño L, Ramírez-Chaves HE. Rarity and conservation status of the Colombian Speckled Tree Rat, Pattonomys semivillosus (I. Geoffroy, 1838). MAMMALIA 2022. [DOI: 10.1515/mammalia-2022-0070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
The Colombian Speckled Tree Rat, Pattonomys semivillosus, is a little-known rodent endemic to the Lower Magdalena River basin at the Caribbean Coast of Colombia. To date it is the only species of Pattonomys documented in the country. We provide information on the rarity, and conservation status of P. semivillosus based on the current and potential distribution, population density and size using information from the literature, new records, and museum vouchers. We confirmed 66 occurrences that belong to 25 localities in six departments (Atlántico, Bolívar, Cesar, La Guajira, Magdalena, Santander, and Sucre) in northern Colombia, including 18 new localities not previously reported in the literature, mostly in the highly threatened Tropical Dry Forest ecosystem. The population density in three sites of Department of Cesar was 5.4 ind/km2, 5.9 ind/km2, and 32.4 ind/km2. The species matches with the Category D of rarity, and we suggest an update to the threatened assessment (from Least Concern to Near Threatened). This information will contribute to update the current IUCN assessment of the species.
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Affiliation(s)
- Julio J. Chacón-Pacheco
- Grupo de Investigación Biodiversidad Unicórdoba , Universidad de Córdoba , Carrera 6 No. 76-103, Cod. Postal 230002 , Montería , Córdoba , Colombia
- Laboratorio de Ecología Funcional Unidad de Ecología y Sistemática (UNESIS), Laboratorio de Ecología Funcional, Facultad de Ciencias , Pontificia Universidad Javeriana , Cod. Postal 110231 , Bogotá , Colombia
| | - Julián Lozano-Flórez
- Colecciones biológicas , Instituto de Investigación de Recursos Biológicos Alexander von Humboldt , Carrera 8 # 15-08, Villa de Leyva , Boyacá , Colombia
| | - Luis Jose Avendaño-Maldonado
- Grupo de Investigación Biodiversidad del Caribe Colombiano , Semillero de Mastozoología, Universidad del Atlántico , Carrera 30 No. 8-49 , Puerto Colombia , Atlántico , Colombia
| | - Javier Racero-Casarrubia
- Grupo de Investigación Biodiversidad Unicórdoba , Universidad de Córdoba , Carrera 6 No. 76-103, Cod. Postal 230002 , Montería , Córdoba , Colombia
| | | | - Héctor Emilio Ramírez-Chaves
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales , Universidad de Caldas, y Centro de Museos, Museo de Historia Natural, Universidad de Caldas , Calle 65 # 26-10 , Manizales , Caldas , Colombia
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3
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Phylogenetic, Allometric, and Ecological Factors Affecting Morphological Variation in the Scapula and Humerus of Spiny Rats (Rodentia: Echimyidae). J MAMM EVOL 2022. [DOI: 10.1007/s10914-022-09617-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
AbstractLocomotion, as a fundamental function in mammals directly associated with the use of ecological resources, is expected to have anatomical structures functionally committed that evolved under intense selective pressure, possibly carrying specializations for different locomotor habits. Among caviomorph rodents, the family Echimyidae stands out for having the greatest species richness, with relatively well-resolved phylogenetic relationships, wide variation in body mass, and remarkable diversity of locomotor habits, including arboreal, scansorial, semi-aquatic, semifossorial, and terrestrial forms. Thus, Echimyidae constitutes a promising model for understanding how phylogenetic, allometric, and ecological factors affect the evolution of postcranial structures directly linked to locomotor function. We investigated the influence of these three factors on scapular and humeral morphological variation in 38 echimyid species using two-dimensional geometric morphometry and phylogenetically informed comparative methods. Scapular and humeral shape variation had a low correlation with body mass and structure size, conveying a small or negligible allometric effect. Conversely, a significant moderate to strong phylogenetic signal was detected in both structures, suggesting that an important part of their morphometric variation results from shared evolutionary history. Notably, morphological variation of the scapula was extensively structured by phylogeny, without the marked influence of locomotor habits, suggesting that its shape may be a suitable taxonomic marker. Finally, locomotor habits were important in structuring the morphological variation of the humerus. Our results suggest that the morphologies of the scapula and humerus, despite being anatomically and functionally interconnected, were differentially shaped by ecological factors associated with locomotor habits.
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Miranda CL, Nunes MDS, Farias IP, Silva MNFD, Rossi RV, Eler E, Feldberg E, da Silva RDF, de Oliveira TG, Nagamachi CY, Pieczarka JC. A molecular and chromosomic meta‐analysis approach and its implications for the taxonomy of the genus
Makalata
Husson, 1978 (Rodentia, Echimyidae) including an amended diagnosis for
M. macrura
(Wagner, 1842). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cleuton Lima Miranda
- Museu Paraense Emílio GoeldiUniversidade Federal do Pará Belém Brazil
- Laboratório de Evolução e Genética Animal Departamento de Genética Instituto de Ciências Biológicas Universidade Federal do Amazonas Manaus Brazil
| | - Mario da Silva Nunes
- Laboratório de Evolução e Genética Animal Departamento de Genética Instituto de Ciências Biológicas Universidade Federal do Amazonas Manaus Brazil
| | - Izeni Pires Farias
- Laboratório de Evolução e Genética Animal Departamento de Genética Instituto de Ciências Biológicas Universidade Federal do Amazonas Manaus Brazil
| | | | - Rogério Vieira Rossi
- Departamento de Biologia e Zoologia Instituto de Biociências Universidade Federal de Mato Grosso Cuiabá Brazil
| | - Eduardo Eler
- Laboratório de Genética Animal Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
| | - Eliana Feldberg
- Laboratório de Genética Animal Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
| | | | | | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética Instituto de Ciências Biológicas Universidade Federal do Pará Belém, Pará Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética Instituto de Ciências Biológicas Universidade Federal do Pará Belém, Pará Brazil
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Malcher SM, Pieczarka JC, Pereira AL, do Amaral PJS, Rossi RV, Saldanha J, Nagamachi CY. New karyotype for Mesomys stimulax (Rodentia, Echimyidae) from the Brazilian Amazon: A case for species complex? Ecol Evol 2021; 11:7125-7131. [PMID: 34188799 PMCID: PMC8216883 DOI: 10.1002/ece3.7583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 11/17/2022] Open
Abstract
Mesomys Wagner, 1845 (Rodentia, Echimyidae, Eumysopinae) currently has four recognized species, three of which occur in Brazil: Mesomys hispidus (probably a species complex), M. occultus, and M. stimulax. Mesomys leniceps is found in montane forests of northern Peru. Mesomys stimulax, the focus of the present study, has a distribution that is restricted to the central and eastern Amazonia south of the Amazon River, extending from the left bank of the Tapajós River to the right bank of the Tocantins River, and south to the southeast portion of Pará State. The genus presents karyotypes with diploid number 2n = 60 and Fundamental Number (FN) = 116 for M. hispidus and M. stimulax, and 2n = 42, FN = 54 for M. occultus. We studied the karyotype of a female specimen of M. stimulax collected from the Tapirapé-Aquiri National Forest, Marabá, Pará, Brazil, in the Xingu/Tocantins interfluvium. The obtained karyotype (2n = 60 and FN = 110) differs from that described in the literature for both M. stimulax and M. hispidus by exhibiting more biarmed chromosomes, probably due to pericentric inversions and/or centromeric repositioning, and exhibiting differences in the amount and distribution of constitutive heterochromatin (CH). These results suggest that, similar to what has already been proposed for M. hispidus, M. stimulax may represent a species complex and/or cryptic species. The mechanisms of chromosomal diversification in Mesomys and the biogeographic implications are discussed reinforcing the need for broad systematic review for Mesomys.
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Affiliation(s)
- Stella Miranda Malcher
- Laboratório de CitogenéticaCentro de Estudos Avançados da BiodiversidadeInstituto de Ciências BiológicasUniversidade Federal do ParáBelémBrasil
| | - Julio Cesar Pieczarka
- Laboratório de CitogenéticaCentro de Estudos Avançados da BiodiversidadeInstituto de Ciências BiológicasUniversidade Federal do ParáBelémBrasil
| | | | | | - Rogério Vieira Rossi
- Laboratório de MastozoologiaInstituto de BiociênciasUniversidade Federal do Mato GrossoCuiabáBrasil
| | - Juliane Saldanha
- Laboratório de MastozoologiaInstituto de BiociênciasUniversidade Federal do Mato GrossoCuiabáBrasil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de CitogenéticaCentro de Estudos Avançados da BiodiversidadeInstituto de Ciências BiológicasUniversidade Federal do ParáBelémBrasil
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Abreu EF, Jung DMH, Christoff AU, Valiati VH, Jansa SA, Percequillo AR. Systematics of Brucepattersonius Hershkovitz, 1998 (Rodentia, Sigmodontinae): molecular species delimitation and morphological analyses suggest an overestimation in species diversity. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1890270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Edson Fiedler Abreu
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, 13418900, SP, Brazil
| | - Diego Marques Henriques Jung
- Laboratório de Genética e Biologia Molecular, Universidade do Vale do Rio dos Sinos, São Leopoldo, 93022750, RS, Brazil
| | - Alexandre Uarth Christoff
- Laboratório de Genética e Biologia Molecular, Universidade do Vale do Rio dos Sinos, São Leopoldo, 93022750, RS, Brazil
| | - Victor Hugo Valiati
- Laboratório de Genética e Biologia Molecular, Universidade do Vale do Rio dos Sinos, São Leopoldo, 93022750, RS, Brazil
| | - Sharon A. Jansa
- Department of Ecology, Evolution, and Behavior and Bell Museum of Natural History, University of Minnesota, St Paul, 55108, MN, USA
| | - Alexandre Reis Percequillo
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, 13418900, SP, Brazil
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Netto TFDS, Tavares WC. Historical, allometric and ecological effects on the shape of the lumbar vertebrae of spiny rats (Rodentia: Echimyidae). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
In mammals, the lumbar vertebrae are important for sustaining the trunk, for allowing the trunk to flex and extend, and, during locomotion, for transferring forces from the sacroiliac region to the anterior region of the body. The Echimyidae is a group that comprises spiny rats, the coypu and hutias. It is the caviomorph rodent family with the greatest ecological diversity and species richness, as well as having a wide variation in body mass. Thus, echimyid rodents provide a promising model for understanding how phylogenetic, allometric and ecological factors associated with locomotion affect the evolution of the post-cranial skeleton. To assess the effect of these three factors on the morphology of the lumbar vertebrae, the penultimate lumbar vertebra of 26 echimyid species was photographed under five views and submitted to phylogenetically informed comparative analysis using 2D geometric morphometrics. Vertebral shape variation showed a low correlation with body mass and vertebral size, and a low to moderate phylogenetic signal. Remarkably, locomotory habit had a strong influence on lumbar morphology, particularly when analysed in lateral view. Our results indicate that the echimyid penultimate lumbar vertebra is potentially useful for future ecomorphological studies on living and fossil small mammals.
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Affiliation(s)
- Thomas Furtado Da Silva Netto
- Programa de Pós-Graduação em Biodiversidade e Biologia Evolutiva, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, S/N, Cidade Universitária, Rio de Janeiro, RJ, Brazil
- Laboratório de Mastozoologia, Departamento de Zoologia, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, S/N, Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - William Corrêa Tavares
- Programa de Pós-Graduação em Biodiversidade e Biologia Evolutiva, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, S/N, Cidade Universitária, Rio de Janeiro, RJ, Brazil
- Laboratório de Mastozoologia, Departamento de Zoologia, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, S/N, Cidade Universitária, Rio de Janeiro, RJ, Brazil
- Campus Duque de Caxias Professor Geraldo Cidade, Universidade Federal do Rio de Janeiro, Rodovia Washington Luiz, Km 104,5, Santa Cruz da Serra, Duque de Caxias, RJ, Brazil
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Lebedev VS, Kovalskaya Y, Solovyeva EN, Zemlemerova ED, Bannikova AA, Rusin MY, Matrosova VA. Molecular systematics of the Sicista tianschanica species complex: a contribution from historical DNA analysis. PeerJ 2021; 9:e10759. [PMID: 33520475 PMCID: PMC7810041 DOI: 10.7717/peerj.10759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/22/2020] [Indexed: 11/20/2022] Open
Abstract
The Tianshan birch mouse Sicista tianschanica is an endemic of the Central Asian mountains and has previously been shown to include several karyomorphs (“Terskey”, “Talgar”, “Dzungar”); however, the taxonomic status of these forms has remained uncertain. We examined the genetic variation in S. tianschanica based on historical DNA samples from museum collections, including the type series. Mitochondrial and nuclear data indicated that the species complex includes two major clades: Northern (N) and Southern (S) (cytb distance 13%). The N clade corresponds to the “Dzungar” karyomorph (Dzungar Alatau, Tarbagatay). The S clade is comprised of four lineages (S1–S4) divergent at 6–8%; the relationships among which are resolved incompletely. The S1 lineage is found in eastern Tianshan and corresponds to the nominal taxon. The S2 is distributed in central and northern Tianshan and corresponds to the “Terskey” karyomorph. The S3 is restricted to Trans-Ili Alatau and belongs to the “Talgar” karyomorph. The S4 is represented by a single specimen from southeastern Dzungar Alatau with "Talgar" karyotype. No interlineage gene flow was revealed. The validity of S. zhetysuica (equivalent to the N clade) is supported. Based on genetic and karyotypic evidence, lineages S2 and S3 are described as distinct species. The status of the S4 requires further investigation.
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Affiliation(s)
| | - Yulia Kovalskaya
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | | | - Elena D Zemlemerova
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Anna A Bannikova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail Yu Rusin
- Research and International Cooperation Department, Kiev Zoo, Kiev, Ukraine.,Schmalhausen Institute of Zoology, Kiev, Ukraine
| | - Vera A Matrosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Tavares WC, Pessôa LM. Effects of size, phylogeny and locomotor habits on the pelvic and femoral morphology of South American spiny rats (Rodentia: Echimyidae). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The rodent family Echimyidae (spiny rats, hutias and coypu) is notable for its high phylogenetic and ecological diversity, encompassing ~100 living species with body mass ranging from 70 to 4500 g, including arboreal, epigean (non-arboreal or scansorial), fossorial and semi-aquatic taxa. In view of this diversity, it was hypothesized that echimyid morphological variation in the pelvis and femur should reflect: (1) allometric association with body mass; (2) morphofunctional specializations for the different locomotor habits; and (3) phylogenetic history. To test these propositions, we examined 30 echimyid species, in addition to eight species of two other octodontoid families, Abrocomidae and Octodontidae. Pelvic and femoral variation was assessed with linear morphometry, using bivariate and multivariate statistical methods, part of which was phylogenetically informed. Approximately 80% of the total variation among echimyids was explained by body mass, and some univariate measurements were found potentially to be effective as body mass estimators after simple allometric procedures, notably in the pelvis. Even considering the significant phylogenetic signal, variation in shape was largely structured by locomotor habits, mainly in the pelvis, suggesting that the echimyid hindlimb diversification was driven, in part, by selective pressures related to locomotor habits. Finally, echimyid femoral disparity was considerably greater than in other octodontoids, contrasting with their relatively modest cranial variation. Thus, this study suggests that hindlimb diversity constitutes a key factor for the exceptional echimyid ecological and phyletic diversification.
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Affiliation(s)
- William Corrêa Tavares
- Campus Duque de Caxias Professor Geraldo Cidade, Universidade Federal do Rio de Janeiro, Duque de Caxias, Rio de Janeiro, Brazil
- Laboratório de Mastozoologia, Departamento de Zoologia, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Pós-Graduação em Biodiversidade e Biologia Evolutiva, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leila Maria Pessôa
- Laboratório de Mastozoologia, Departamento de Zoologia, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Pós-Graduação em Biodiversidade e Biologia Evolutiva, Instituto de Biologia, CCS, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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de Abreu-Jr EF, Pavan SE, Tsuchiya MTN, Wilson DE, Percequillo AR, Maldonado JE. Museomics of tree squirrels: a dense taxon sampling of mitogenomes reveals hidden diversity, phenotypic convergence, and the need of a taxonomic overhaul. BMC Evol Biol 2020; 20:77. [PMID: 32590930 PMCID: PMC7320592 DOI: 10.1186/s12862-020-01639-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/17/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Tree squirrels (Sciuridae, Sciurini), in particular the highly diverse Neotropical lineages, are amongst the most rapidly diversifying branches of the mammal tree of life but also some of the least known. Negligence of this group by systematists is likely a product of the difficulties in assessing morphological informative traits and of the scarcity or unavailability of fresh tissue samples for DNA sequencing. The highly discrepant taxonomic arrangements are a consequence of the lack of phylogenies and the exclusive phenotypic-based classifications, which can be misleading in a group with conservative morphology. Here we used high-throughput sequencing and an unprecedented sampling of museum specimens to provide the first comprehensive phylogeny of tree squirrels, with a special emphasis on Neotropical taxa. RESULTS We obtained complete or partial mitochondrial genomes from 232 historical and modern samples, representing 40 of the 43 currently recognized species of Sciurini. Our phylogenetic analyses-performed with datasets differing on levels of missing data and taxa under distinct analytical methods-strongly support the monophyly of Sciurini and consistently recovered 12 major clades within the tribe. We found evidence that the diversity of Neotropical tree squirrels is underestimated, with at least six lineages that represent taxa to be named or revalidated. Ancestral state reconstructions of number of upper premolars and number of mammae indicated that alternative conditions of both characters must have evolved multiple times throughout the evolutionary history of tree squirrels. CONCLUSIONS Complete mitogenomes were obtained from museum specimens as old as 120 years, reinforcing the potential of historical samples for phylogenetic inferences of elusive lineages of the tree of life. None of the taxonomic arrangements ever proposed for tree squirrels fully corresponded to our phylogenetic reconstruction, with only a few of the currently recognized genera recovered as monophyletic. By investigating the evolution of two morphological traits widely employed in the taxonomy of the group, we revealed that their homoplastic nature can help explain the incongruence between phylogenetic results and the classification schemes presented so far. Based on our phylogenetic results we suggest a tentative supraspecific taxonomic arrangement for Sciurini, employing 13 generic names used in previous taxonomic classifications.
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Affiliation(s)
- Edson Fiedler de Abreu-Jr
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, 13418900, Brazil.
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20013, USA.
| | - Silvia E Pavan
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20013, USA.
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, PA, 66077530, Brazil.
| | - Mirian T N Tsuchiya
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20013, USA
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, 20560, USA
| | - Don E Wilson
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
| | - Alexandre R Percequillo
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, 13418900, Brazil
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, 20013, USA
- Department of Biology and Department of Environmental Science and Policy, George Mason University, Fairfax, VA, 22030, USA
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Álvarez A, Ercoli MD, Olivares AI, De Santi NA, Verzi DH. Evolutionary Patterns of Mandible Shape Diversification of Caviomorph Rodents. J MAMM EVOL 2020. [DOI: 10.1007/s10914-020-09511-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Digging for the spiny rat and hutia phylogeny using a gene capture approach, with the description of a new mammal subfamily. Mol Phylogenet Evol 2019; 136:241-253. [PMID: 30885830 DOI: 10.1016/j.ympev.2019.03.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 02/07/2023]
Abstract
Next generation sequencing (NGS) and genomic database mining allow biologists to gather and select large molecular datasets well suited to address phylogenomics and molecular evolution questions. Here we applied this approach to a mammal family, the Echimyidae, for which generic relationships have been difficult to recover and often referred to as a star phylogeny. These South-American spiny rats represent a family of caviomorph rodents exhibiting a striking diversity of species and life history traits. Using a NGS exon capture protocol, we isolated and sequenced ca. 500 nuclear DNA exons for 35 species belonging to all major echimyid and capromyid clades. Exons were carefully selected to encompass as much diversity as possible in terms of rate of evolution, heterogeneity in the distribution of site-variation and nucleotide composition. Supermatrix inferences and coalescence-based approaches were subsequently applied to infer this family's phylogeny. The inferred topologies were the same for both approaches, and support was maximal for each node, entirely resolving the ambiguous relationships of previous analyses. Fast-evolving nuclear exons tended to yield more reliable phylogenies, as slower-evolving sequences were not informative enough to disentangle the short branches of the Echimyidae radiation. Based on this resolved phylogeny and on molecular and morphological evidence, we confirm the rank of the Caribbean hutias - formerly placed in the Capromyidae family - as Capromyinae, a clade nested within Echimyidae. We also name and define Carterodontinae, a new subfamily of Echimyidae, comprising the extant monotypic genus Carterodon from Brazil, which is the closest living relative of West Indies Capromyinae.
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de Abreu-Júnior EF, Percequillo AR, Geise L, Leite YL, Loss AC. Unveiling the identity of Kerr's Atlantic tree rat, Phyllomys kerri (Rodentia, Echimyidae). Mamm Biol 2018. [DOI: 10.1016/j.mambio.2018.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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