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Genetic variability of populations of the white-eared opossum, Didelphis albiventris Lund 1840 (Didelphimorphia; Didelphidae) in Brazil

Variabilidade genética de populações de gambá de orelha branca, Didelphis albiventris Lund 1840 (Didelphimorphia; Didelphidae) no Brasil

Abstract

Didelphis albiventris are found throughout Northeast and Central Brazil to central-southern Uruguay and it was subject of few studies in a population level. Given this, the present study investigated the genetic variability of the species using the mitochondrial molecular marker cytochrome oxidase c subunit I. We analyzed samples from the different biomes within three Brazilian regions: Northeast (Caatinga , Cerrado, and Atlantic Forest), Southeast (Cerrado , Atlantic Forest, Cerrado/Atlantic Forest, and Cerrado/Caatinga ecotones) and South (Pampa and Atlantic Forest). Software BAPs retrieved five distinct demes: dm 1, dm 2, and dm 5 that occurs in South, Northeast and Southeast regions respectively and the dm 3 and dm 4 are wide distributed in Northeast and Southeast. Population analysis performed with AMOVA, haplotype network and Mantel test estimated the veracity of the demes. The FST shows structuring for the five demes, with dm 1 (South region) isolated from the others, however the other analysis showed the Northeast/Southeast demes (dm 2-5) united, diagnosing gene flow between them, mainly at the transitional zones, in areas as far away as areas with similar latitude interval (Southeast vs South) that was not detected gene flow. In the haplotype network, the mutational steps was conclusive in split dm1 from dm 2-5 with 15 mutational steps and the Mantel test was moderated, which is explained by genetic similarity despite the great geographic distances (Northeast/Southeast). Thus, our analysis recognized two different lineages (South and Northeast/Southeast) and indicate that the biomes were not decisive in their isolation. The sharing of demes at the transitional zones and in areas with high latitudinal intervals reflects a recent ancestral polymorphism for D. albiventris. The plasticity in the occupation of the space by this species contributes in its wide dispersion capability, that is, geographical distribution. Our results revealed important implications for the management of D. albiventris in these transitional zones areas where demes were shared.

Keywords:
marsupials; COI; population diversity; geographic lineages

Resumo

Didelphis albiventris é encontrada em todo o Nordeste e região central do Brasil até o centro-sul do Uruguai e foi alvo de poucos estudos em nível populacional. Dessa forma, o presente estudo, investiga a variabilidade genética da espécie usando o marcador molecular citocromo c oxidase subunidade I. Analisou-se amostras de diferentes biomas de três regiões brasileiras: Nordeste (Caatinga, Cerrado e Floresta Atlântica), Sudeste (Cerrado, Floresta Atlântica, ecótonos Cerrado/Floresta Atlântica e Cerrado/Caatinga) e Sul (Pampa e Floresta Atlântica). O software BAPs recuperou cinco demes distintos: dm 1, dm 2 e dm 5, que ocorrem nas regiões Sul, Nordeste e Sudeste, respectivamente, e os dm 3 e dm 4, que são amplamente distribuído no Nordeste e Sudeste. Análises populacionais realizadas com AMOVA, rede de haplótipo e teste de Mantel estimaram a veracidade das demes. O FST mostrou estruturação para as cinco demes, com dm 1 (região Sul) isolada das demais, entretanto as outras análises mostraram as demes Nordeste/Sudeste (dm 2-5) unidos, diagnosticando fluxo gênico entre elas, principalmente em zonas de transição, em áreas tão distante quanto áreas com similar intervalo de latitude (Sudeste e Sul), onde não foram detectado fluxo gênico. Na rede de haplótipo, os passos mutacionais foram conclusivos em separar dm 1 do dm 2-5 com 15 passos mutacionais, e o teste de Mantel foi moderado, o que é explicado pela similaridade genética apesar da grande distância geográfica (Nordeste/Sudeste). Assim, duas linhagens diferentes (Sul e Sudeste/Nordeste) foram encontradas, indicando que os biomas não foram decisivos em seus isolamentos. Os compartilhamentos das demes, em zonas de transição e em áreas com elevados intervalos de latitude, refletem um polimorfismo ancestral recente para D. albiventris. A plasticidade na ocupação do espaço por esta espécie contribui em sua ampla capacidade de dispersão, ou seja, distribuição geográfica. Nossos resultados revelam importantes implicações para o manejo de D. albiventris nessas áreas de zonas de transição, onde as demes são compartilhadas.

Palavras-chave:
marsupiais; COI; diversidade populacional; linhagens geográficas

1. Introduction

The marsupials of the genus Didelphis Linnaeus, 1758 are a small non-volant mammals that are an essential component of natural communities and good indicators of environmental changes and its degree of conservation (Conde y Vera and Rocha, 2006 CONDE Y VERA, C.F. and ROCHA, C.F., 2006. Habitat disturbance and small mammal richness and diversity in an Atlantic Rainforest Area in Southeastern Brazil. Brazilian Journal of Biology = Revista Brasileira de Biologia, vol. 66, no. 4, pp. 983-990. http://dx.doi.org/10.1590/S1519-69842006000600005. PMid:17299934.
http://dx.doi.org/10.1590/S1519-6984200...
; Castro, 2012 CASTRO, K.C., 2012. Assembleia de pequenos mamíferos não voadores da floresta nacional do Amapá, Amazônia oriental. Macapá: Universidade Federal do Amapá, 85 p. Dissertação de Mestrado em Biodiversidade Tropical. ; Quintela et al., 2013 QUINTELA, F.M., GONÇALVES, B.I., TRINDADE, G.E., SANTOS, M.B. and TOZETTI, A.M., 2013. Non-volant small mammals (Didelphimorphia, Rodentia) in coastal grasslands of southernmost Brazil. Biota Neotropica, vol. 13, no. 4, pp. 284-289. http://dx.doi.org/10.1590/S1676-06032013000400025.
http://dx.doi.org/10.1590/S1676-0603201...
). In particular, populations of the white-eared opossum (Didelphis albiventris Lund, 1840) tends to increase in density in response to environmental disturbance ( Cáceres et al., 2008 CÁCERES, N.C., CASELLA, J., VARGAS, C.F., PRATES, L.Z., TOMBINI, A.A.M., GOULART, C.S. and LOPES, W.H., 2008. Distribuição geográfica de pequenos mamíferos não voadores nas bacias dos rios Araguaia e Paraná, região centro-sul do Brasil. Iheringia. Série Zoologia, Porto Alegre, vol. 98, no. 2, pp. 173-180. http://dx.doi.org/10.1590/S0073-47212008000200001.
http://dx.doi.org/10.1590/S0073-4721200...
), with associated implications for public health given that this species is a natural reservoir for a number of human diseases such as Chagas disease and leishmaniasis ( Sherlock et al., 1984 SHERLOCK, I.A., MIRANDA, J.C., SADIGURSKY, M. and GRIMALDI JÚNIOR, G., 1984. Natural infection of the opossum Didelphis albiventris (Marsupialia, Didelphidae) with Leishmania donovani, in Brasil. Memorias do Instituto Oswaldo. ; Pinho et al., 2000 PINHO, A.P., CUPOLILLO, E., MANGIA, R.H., FERNANDES, O. and JANSEN, A.M., 2000. Trypanosoma cruzi in the sylvatic environment: distinct transmission cycles involving two sympatric marsupials. Transactions of the Royal Society of Tropical Medicine and Hygiene, vol. 94, no. 5, pp. 509-514. http://dx.doi.org/10.1016/S0035-9203(00)90069-5. PMid:11132378.
http://dx.doi.org/10.1016/S0035-9203(00...
; De Luca et al., 2003 DE LUCA, A.S., VASCONCELOS, H.L. and BARRETT, T.V., 2003. Distribution of sandflies (diptera: phlebotominae) in forest remnants and adjacent matrix habitats in Brazilian Amazonia. Brazilian Journal of Biology = Revista Brasileira de Biologia, vol. 63, no. 3, pp. 401-410. http://dx.doi.org/10.1590/S1519-69842003000300006. PMid:14758699.
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; Bern et al., 2011 BERN, C., KJOS, S., YABSLEY, M.J. and MONTGOMERY, S.P., 2011. Trypanosoma cruzi and Chagas’ Disease in the United States. Clinical Microbiology Reviews, vol. 24, no. 4, pp. 655-681. http://dx.doi.org/10.1128/CMR.00005-11. PMid:21976603.
http://dx.doi.org/10.1128/CMR.00005-11 ...
; Zetun et al., 2014 ZETUN, C.B., LUCHEIS, S.B., TRONCARELLI, M.Z. and LANGONI, H., 2014. Infecção por Trypanosoma cruzi em animais silvestres procedentes de zoológicos do Estado de São Paulo. Veterinária e Zootecnia, vol. 21, no. 1, pp. 139-147. ).

Due to its generalist habit, D. albiventris is highly flexible in the use of space, exploiting a variety of vertical strata and occupying large home ranges ( Almeida et al., 2008 ALMEIDA, A.J., TORQUETTI, C.G. and TALAMONI, A.S., 2008. Use of space by neotropical marsupial Didelphis albiventris (Didelphimorphia: Didelphidae) in an urban forest fragment. Revista Brasileira de Zoologia, vol. 25, no. 2, pp. 214-219. http://dx.doi.org/10.1590/S0101-81752008000200008.
http://dx.doi.org/10.1590/S0101-8175200...
; Sanches et al., 2012 SANCHES, V.Q.A., GOMES, M.M.A., PASSOS, F.C., GRACIOLLI, G. and RIBAS, A.C.A., 2012. Home-range and space use by Didelphis albiventris (Lund 1840) (Marsupialia, Didelphidae) in Mutum Island, Paraná river, Brazil. Biota Neotropica, vol. 12, no. 4, pp. 50-55. http://dx.doi.org/10.1590/S1676-06032012000400004.
http://dx.doi.org/10.1590/S1676-0603201...
). The species is widely distributed in deciduous forests, occurring from northeastern and central Brazil to central and southern Uruguay, as well as in Paraguay, Argentina and Bolivia ( Cerqueira and Tribe, 2008 CERQUEIRA, R. and TRIBE, C.J. 2008 Genus Didelphis. In: A. L. GARDNER, ed. Mammals of South America. 1. Marsupials, xenarthrans, shrews, and bats. Chicago, Illinois: University of Chicago Press, pp. 17-25. ). In Brazil there are records in Caatinga, Cerrado, Pantanal, Pampas habitats and transitional zones between these biomes ( Cerqueira and Tribe, 2008 CERQUEIRA, R. and TRIBE, C.J. 2008 Genus Didelphis. In: A. L. GARDNER, ed. Mammals of South America. 1. Marsupials, xenarthrans, shrews, and bats. Chicago, Illinois: University of Chicago Press, pp. 17-25. ; Paglia et al., 2012 PAGLIA, A.P., FONSECA, G.A.B., RYLANDS, A.B., HERRMANN, G., AGUIAR, L.M.S., CHIARELLO, A.G.C., LEITE, Y.L.R., COSTA, L.P., SICILIANO, S., KIERULFF, M.C.M., MENDES, S.L., TAVARES, V.C., MITTERMEIER, R.A. and PATTON, J.L. 2012. Lista Anotada dos Mamíferos do Brasil/Annotated Checklist of Brazilian Mammals. 2. ed. Arlington: Conservation International, 76 p. Occasional Papers in Conservation Biology, no. 6. ).

Despite the genus Didelphis is common and ecologically successful ( Durant, 2001 DURANT, P., 2001. Black-eared Opossum Didelphis marsupialis (Linnaeus, 1758) from Mérida, Venezuela. Zoocriaderos, vol. 3, no. 3, pp. 07-18. ), little is known about the relationships among of D. albiventris populations, with only two studies available: Sousa et al. (2012) SOUSA, L.C.C., GONTIJO, C.M.F., BOTELHO, H.A. and FONSECA, C.G., 2012. Mitochondrial genetic variability of Didelphis albiventris (Didelphimorphia, Didelphidae) in Brazilian localities. Genetics and Molecular Biology, vol. 35, no. 2, pp. 522-529. http://dx.doi.org/10.1590/S1415-47572012005000035. PMid:22888303.
http://dx.doi.org/10.1590/S1415-4757201...
and Rocha et al. (2015) ROCHA, R.G., FERREIRA, E., LOSS, A.C., HELLER, R., FONSECA, C. and COSTA, L.P., 2015. The Araguaia River as an Important Biogeographical Divide for Didelphid Marsupials in Central Brazil. The Journal of Heredity, vol. 106, no. 5, pp. 593-607. http://dx.doi.org/10.1093/jhered/esv058. PMid:26249652.
http://dx.doi.org/10.1093/jhered/esv058...
. Both works revealed some degree of genetic structuring, the former studied the mitochondrial gene cytochrome c oxidase subunit I (COI) of populations from southern and southeastern Brazil, and the other the mitochondrial gene cytochrome b from few localities in central Brazil.

Mitochondrial DNA have revealed degree of population structure for many species, being the most used molecular marker for tracing the geographic distribution of genealogical lineages ( Avise et al., 1987 AVISE, J.C., ARNOLD, J., BALL, R.M., BERMINGHAM, E., LAMB, T., NEIGEL, J.E., REEB, C.A. and SAUNDERS, N.C., 1987. Intraspecific Phylogeography: The mitochondrial DNA bridge between population genetics and systematics. Annual Reviews, vol. 18, pp. 489-522. ). Males and females of the D. albiventris present similar patterns of dispersal ( Sanches et al., 2012 SANCHES, V.Q.A., GOMES, M.M.A., PASSOS, F.C., GRACIOLLI, G. and RIBAS, A.C.A., 2012. Home-range and space use by Didelphis albiventris (Lund 1840) (Marsupialia, Didelphidae) in Mutum Island, Paraná river, Brazil. Biota Neotropica, vol. 12, no. 4, pp. 50-55. http://dx.doi.org/10.1590/S1676-06032012000400004.
http://dx.doi.org/10.1590/S1676-0603201...
), and the sex of the specimen should be irrelevant to the selection of the molecular marker, consequently the matrilineal inheritance of the mitochondria should not interfere in the analyses. Notably, mitochondrial genes have been used successfully in population-level and phylogenetic studies of small mammals ( Carvalho et al., 2011 CARVALHO, B.A., OLIVEIRA, L.F.B., LANGGUTH, A., FREYGANG, C.C., FERRAZ, R.S. and MATTEVI, M.S., 2011. Phylogenetic relationships and phylogeographic patterns in Monodelphis (Didelphimorphia: Didelphidae). Journal of Mammalogy, vol. 92, no. 1, pp. 121-133. http://dx.doi.org/10.1644/10-MAMM-A-075.1.
http://dx.doi.org/10.1644/10-MAMM-A-075...
; Agrizzi et al., 2012 AGRIZZI, J.A., LOSS, C., FARRO, A.P.C., DUDA, R., COSTA, L.P. and LEITE, Y.L.R., 2012. Molecular diagnosis of atlantic forest mammals using mitochondrial DNA sequences: Didelphid Marsupials. The Open Zoology Journal, vol. 5, no. 1, pp. 2-9. http://dx.doi.org/10.2174/1874336601205010002.
http://dx.doi.org/10.2174/1874336601205...
; Sousa et al., 2012 SOUSA, L.C.C., GONTIJO, C.M.F., BOTELHO, H.A. and FONSECA, C.G., 2012. Mitochondrial genetic variability of Didelphis albiventris (Didelphimorphia, Didelphidae) in Brazilian localities. Genetics and Molecular Biology, vol. 35, no. 2, pp. 522-529. http://dx.doi.org/10.1590/S1415-47572012005000035. PMid:22888303.
http://dx.doi.org/10.1590/S1415-4757201...
; Muller et al., 2013 MÜLLER, L., GONÇALVES, G.L., CORDEIRO-ESTRELA, P., MARINHO, J.R., ALTHOFF, S.L., TESTONI, A.F., GONZÁLEZ, E.M. and FREITAS, T.R., 2013. DNA Barcoding of Sigmodontine Rodents: Identifying Wildlife Reservoirs of Zoonoses. PLoS One, vol. 8, no. 11, pp. 1-12. http://dx.doi.org/10.1371/journal.pone.0080282. PMid:24244670.
http://dx.doi.org/10.1371/journal.pone....
; Rocha et al., 2015 ROCHA, R.G., FERREIRA, E., LOSS, A.C., HELLER, R., FONSECA, C. and COSTA, L.P., 2015. The Araguaia River as an Important Biogeographical Divide for Didelphid Marsupials in Central Brazil. The Journal of Heredity, vol. 106, no. 5, pp. 593-607. http://dx.doi.org/10.1093/jhered/esv058. PMid:26249652.
http://dx.doi.org/10.1093/jhered/esv058...
). In particular, the COI gene has been used as a DNA barcode for the identification of a number of different vertebrate groups ( Hebert et al., 2003 HEBERT, P.D., RATNASINGHAM, N.S. and DEWAARD, J.R., 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings. Biological Sciences, vol. 270, suppl. 1, pp. S96-S99. http://dx.doi.org/10.1098/rsbl.2003.0025. PMid:12952648.
http://dx.doi.org/10.1098/rsbl.2003.002...
), and has contributed important findings on D. albiventris populations ( Sousa et al., 2012 SOUSA, L.C.C., GONTIJO, C.M.F., BOTELHO, H.A. and FONSECA, C.G., 2012. Mitochondrial genetic variability of Didelphis albiventris (Didelphimorphia, Didelphidae) in Brazilian localities. Genetics and Molecular Biology, vol. 35, no. 2, pp. 522-529. http://dx.doi.org/10.1590/S1415-47572012005000035. PMid:22888303.
http://dx.doi.org/10.1590/S1415-4757201...
).

Ecological studies use population and genetic data in attempt to understand the biology of a species. With the scarcity of population genetic information throughout its distribution, especially for the inhabitants of Cerrado and Caatinga , the present work investigated how D. albiventris populations are distributed in Brazil using the COI as a molecular marker: 1. The species possesses populations structured in the Northeast/South axis? 2. There is more than one population per Biome? 3. If yes, they are shared between Biomes or are exclusive for one Biome? Ecotone areas has a different role in the population structure of the species? 4. Is there natural selection or are the populations selectively neutral? 5. In attempt to answer these questions we conducted genetic variability study of populations of the white-eared opossum, D. albiventris.

2. Material and Methods

2.1. Description of the samples

Samples of D. albiventris were obtained from the Northeast, Southeast and South regions of Brazil, between latitudes 04°05’ S and 30º01’ S ( Figure 1 ). A total of 52 samples were obtained in the Northeast region (Paraíba/PB, Sergipe/SE, Pernambuco/PE, Ceará/CE, Piauí/PI and Maranhão/MA), from the Atlantic Forest, Caatinga and Cerrado biomes. Eighty four samples from Southeast (Minas Gerais/MG) from the Atlantic Forest and Cerrado biomes, and the Cerrado/Atlantic Forest and Cerrado/Caatinga ecotones. Six samples from South (Rio Grande do Sul/RS) corresponding to the Pampas and Atlantic Forest ( Figure 1 ; Supplementary Material Supplementary Material Supplementary material accompanies this paper. Table S1. List of the D. albiventris specimens included in this study, their field numbers (BC, PR, FNI, ALN, TNM, T, PNSC, URC, LLLS, and DCN), GenBank accession number (JN), demes, haplotype number (H), locality, geographical coordinates and origin of the samples. This material is available as part of the online article from https://drive.google.com/open?id=17CmDgYMAmHLH0VTD_0c2AM476u2fJRrx ).

Figure 1
Localities from which the samples were obtained for the present study. The demes were defined according to the BAPs software and are represented by geometric figures with numbers (designated in Supplementary Material Supplementary Material Supplementary material accompanies this paper. Table S1. List of the D. albiventris specimens included in this study, their field numbers (BC, PR, FNI, ALN, TNM, T, PNSC, URC, LLLS, and DCN), GenBank accession number (JN), demes, haplotype number (H), locality, geographical coordinates and origin of the samples. This material is available as part of the online article from https://drive.google.com/open?id=17CmDgYMAmHLH0VTD_0c2AM476u2fJRrx ); Biomes are indicated in gray scale.

The samples from the Northeast were obtained in the Universidade Estadual do Maranhão , for which the collecting data are available in Costa et al. (2012) COSTA, J.F., NASCIMENTO, D.C., SANTOS, L.L.L., OLÍMPIO, A.P.M., FRAGA, E.C. and BARROS, M.C. 2012. Pequenos mamíferos não voadores de ocorrência na Área de proteção Ambiental Municipal do Inhamum, Caxias/MA. In: M. C. BARROS, ed. Biodiversidade na área de proteção ambiental municipal do Inhamum. São Luís: UEMA, pp. 117-130. , and from collaborations with the scientific collections of other Brazilian research institutions, such as Universidade Federal da Paraíba (UFPB), Universidade Federal de Sergipe (UFS), Universidade Federal do Piauí (UFPI), and Museu Paraense Emílio Goeldi (MPEG). All samples from Southeast and South were obtained at GenBank from Sousa et al. (2012) SOUSA, L.C.C., GONTIJO, C.M.F., BOTELHO, H.A. and FONSECA, C.G., 2012. Mitochondrial genetic variability of Didelphis albiventris (Didelphimorphia, Didelphidae) in Brazilian localities. Genetics and Molecular Biology, vol. 35, no. 2, pp. 522-529. http://dx.doi.org/10.1590/S1415-47572012005000035. PMid:22888303.
http://dx.doi.org/10.1590/S1415-4757201...
.

2.2. DNA extraction, amplification and sequencing

DNA was extracted from muscle, liver, and ear tissue using the Phenol-Chloroform protocol of Sambrook and Russel (2001) SAMBROOK, K.J. and RUSSEL, D.W., 2001. Molecular Cloning: A laboratory manual . Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. . We amplified and sequenced a fragment of the mtDNA COI gene using the primers LCO1490 and HCO2198 ( Folmer et al., 1994 FOLMER, O., BLACK, M., HOEH, W., LUTZ, R. and VRIJENHOEK, R., 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, vol. 3, no. 5, pp. 294-299. PMid:7881515. ). The COI gene was amplified in 25 μl reactions of PCR, consisting of 4.0 μl of dNTP (1.25 nM), 2.5 μl of buffer (10X), 0.5 μl of MgCl2 (25 nM), 0.25 μl of each primer (200 ng/μl), 0.2 μl of Taq DNA Polymerase 10 x 250 μl (GE Healthcare), and 1 μl of template DNA (100 ng/μl), with the final volume being completed by purified water. The samples were amplified in a Veriti 96 well thermal cycler (Applied Biosystems) with an initial denaturation (94ºC for 3 min), 40 cycles of denaturation (94ºC for 45 s), annealing (48ºC for 45 s), and extension (72ºC for 1 min and 30 s), and a final extension at 72ºC for 3 min. We used the BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems) for sequencing reactions. The sequences were obtained using an ABI 3500 automatic DNA sequencer with associated Sequencing Analysis software (Applied Biosystems).

2.3. Data analysis

The sequences were aligned using Clustal W ( Thompson et al., 1994 THOMPSON, J.D., HIGGINS, D.G. and GIBSON, T.J., 1994. ClustaW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Research, vol. 22, no. 4, pp. 4673-4680. PMid:7984417. ) in BioEdit v7.0.5.2 ( Hall, 1999 HALL, T.A., 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, vol. 41, pp. 95-98. ). The analysis of the variable sites was performed in Mega v6.06 ( Tamura et al., 2013 TAMURA, K., STECHER, G., PETERSON, D., FILIPSKI, A. and KUMAR, S., 2013. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology and Evolution , vol. 30, no. 12, pp. 2725-2729. http://dx.doi.org/10.1093/molbev/mst197. PMid:24132122.
http://dx.doi.org/10.1093/molbev/mst197...
). Haplotype and nucleotide diversity were estimated in DnaSP v4.9 ( Rozas et al., 2003 ROZAS, J., SANCHEZ-DELBARRIO, J.C., MESSENGUER, X., and ROZAS, R., 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, vol. 19, pp. 2496-2427. ), and the groups used for the population analyses were defined using the BAPs software ( Corander et al., 2008 CORANDER, J., MARTTINEN, P., SIRÉN, J. and TANG, J., 2008. Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics , vol. 9, no. 539, pp. 1-14. http://dx.doi.org/10.1186/1471-2105-9-539. PMid:19087322.
http://dx.doi.org/10.1186/1471-2105-9-5...
). In this method, the number of populations is treated as unknown parameter and is directly inferred from the data set without defining a prior estimate, a dendogram were generated using Unweighted Pair Group Method using Arithmetic averages - UPGMA. The populations identified by this software were used to structure the subsequent population analyses. The haplotype networks were produced in NetWork v4.6.1.2 ( Bandelt et al., 1999 BANDELT, H.J., FORSTER, P. and RÖHL, A. 1999. Median-joinng networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, vol. 16, no. 1, pp. 37-48. ). An Analysis of Molecular Variance (AMOVA) was performed in Arlequin v3.5.2.1 ( Excoffier and Lischer, 2010 EXCOFFIER, L. and LISCHER, H.E.L., 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, vol. 10, no. 3, pp. 564-567. http://dx.doi.org/10.1111/j.1755-0998.2010.02847.x. PMid:21565059.
http://dx.doi.org/10.1111/j.1755-0998.2...
) to obtain the index of allelic fixation (FST). The neutrality tests D ( Tajima, 1989 TAJIMA, F. 1989. Statistical methods for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, vol. 123, no. 3, pp. 585-595. ) and Fu’s FS ( Fu, 1997 FU, Y.X., 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, vol. 147, no. 2, pp. 915-925. PMid:9335623. ) were run in Arlequin v3.5.2.1 ( Excoffier and Lischer, 2010 EXCOFFIER, L. and LISCHER, H.E.L., 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, vol. 10, no. 3, pp. 564-567. http://dx.doi.org/10.1111/j.1755-0998.2010.02847.x. PMid:21565059.
http://dx.doi.org/10.1111/j.1755-0998.2...
). The Mantel test, which relates genetic distance to geographic distance, was run in the Alleles in Space software with 10,000 replications ( Miller, 2005 MILLER, M.P., 2005. Alleles In Space: Computer software for the joint analysis of interindividual spatial and genetic information. The Journal of Heredity, vol. 96, no. 6, pp. 722-724. http://dx.doi.org/10.1093/jhered/esi119. PMid:16251514.
http://dx.doi.org/10.1093/jhered/esi119...
).

3. Results

3.1. Molecular characterization and neutrality tests

The study included a total of 142 sequences for the mitochondrial COI gene of D. albiventris , made up of a fragment of 655 bps, of which 624 bps were conserved, 31 were variable, and 21 were informative for parsimony analyses, corresponding to 19 haplotypes.

The sequences plotted in the BAPs software ( Figure 2 ) indicated the existence of five Brazilian demes (dm), as can be seen in the haplotype network and in the map ( Figure 1 e 3 ). The dm 1 occurs in the Pampas and Atlantic Forest biomes (South region; H1 and H2), dm 2 in the Caatinga and Atlantic Forest biomes (Northeast region; H3-H8) and dm 5 Cerrado, Caatinga, Atlantic Forest and ecotones (Southeast regions; H16-H19). The dm 3 (H 9-H13) and dm 4 (H14 and H15) are more widely distributed, being found simultaneously in the Cerrado and Caatinga (Northeast region) and Cerrado, Caatinga, Atlantic Forest (Southeast region). We can observe that some localities present multiple demes: Xacriabá Amerindian Reservations/MG that contains dm 3, dm 4 and dm 5; Caxias/MA dm 3 and dm 4, Belo Horizonte/MG and Nova Lima/MG dm 4 and dm 5 ( Table 1 ).

Figure 2
Didelphis albiventris demes defined through the BAPs software for the COI gene. (a) UPGMA tree using the Nei model. (b) Mixture among the demes obtained, the size of the color bars is proportional to the number of specimens in the populations.
Figure 3
Haplotype network for the COI gene in the D. albiventris demes. The numbers represents the mutational sites between demes, while the size of the circles is proportional to the frequency of occurrence of the haplotype. Biomes: PA - Pampa; AF - Atlantic Forest; CA - Caatinga; CE - Cerrado; CE/CA - Ecotone Cerrado/Caatinga; CE/AF - Ecotone Cerrado/Atlantic Forest. The polygons delimit the haplotypes that comprises each deme.
Table 1
Genetic diversity and the results of the neutrality tests for the COI gene in the D. albiventris demes analyzed.

The total haplotypic diversity (h) was h = 0.846, and varied from h = 0.387 for dm 5 to h = 0.614 for dm 3, while total nucleotide diversity (π) was π = 0.00615, and varied from π = 0.00078 for dm 4 to π = 0.00152 for dm 3 ( Table 1 ). No significant p values were found in any deme for the D test ( Tajima, 1989 TAJIMA, F. 1989. Statistical methods for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, vol. 123, no. 3, pp. 585-595. ), and a significant value for Fu’s FS ( Fu, 1997 FU, Y.X., 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, vol. 147, no. 2, pp. 915-925. PMid:9335623. ) was only recorded for dm 2, indicating that only this deme is influenced by demographic parameters ( Table 1 ).

3.2. Genetic differentiation among demes

AMOVA analyses based on the five demes retrieved by the BAPs analysis ( Table 1 ) indicated that 87.47% of the variation was due to differences among the demes, and 12.53% within the demes, with a highly significant (p = 0.00000) F ST value of 0.87 ( Table 2 ). The pairwise FST values were higher, ranging from 0.7, for dm 2 vs. dm 3, to 0.97 for dm 4 vs. dm 1 ( Table 3 ).

Table 2
Results of the AMOVA for the COI gene for the five Didelphis albiventris demes retrieved from BAPs.
Table 3
Pairwise FST values for the COI gene for five demes of D. albiventris.

The results of the Mantel test for the five demes indicated a moderate degree of correlation between genetic and geographic distances (r = 0.54; p = 0.00001; Figure 4 ). When dm 1 (r = -0.31; p = 0.19), dm 2 (r= -0.13; p = 0.79), and dm 5 (r= -0.04; p = 0.61) were analyzed separately the correlation were low, although dm 3 (r = 0.90; p = 0.001) and dm 4 (r = 0.89; p = 0.001) returned high correlations.

Figure 4
Results of the Mantel test for the correlation between genetic (y) and geographic (x) distances in the COI gene among the D. albiventris demes analyzed.

4. Discussion

Due to the ecological importance of D. albiventris, the investigation of the dynamics of dispersion of its populations through a genetic approach will improve the knowledge and contribute to the establishment of management and conservation measures along its geographical distribution.

Were analyzed the largest sample for this specie to date, and high levels of haplotype diversity (h) and nucleotide diversity (π) were found. Similar results were retrieved in Sousa et al. (2012) SOUSA, L.C.C., GONTIJO, C.M.F., BOTELHO, H.A. and FONSECA, C.G., 2012. Mitochondrial genetic variability of Didelphis albiventris (Didelphimorphia, Didelphidae) in Brazilian localities. Genetics and Molecular Biology, vol. 35, no. 2, pp. 522-529. http://dx.doi.org/10.1590/S1415-47572012005000035. PMid:22888303.
http://dx.doi.org/10.1590/S1415-4757201...
; h = 0.7235; π = 0.0065) for COI and Rocha et al. (2015) ROCHA, R.G., FERREIRA, E., LOSS, A.C., HELLER, R., FONSECA, C. and COSTA, L.P., 2015. The Araguaia River as an Important Biogeographical Divide for Didelphid Marsupials in Central Brazil. The Journal of Heredity, vol. 106, no. 5, pp. 593-607. http://dx.doi.org/10.1093/jhered/esv058. PMid:26249652.
http://dx.doi.org/10.1093/jhered/esv058...
for Cytochrome b (h = 0.876; π = 0.0062), reflecting the high genetic diversity of this species. According to Grant and Bower (1998) GRANT, W.S. and BOWER, B.W., 1998. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. The American Genetic Association, vol. 89, pp. 415-426. high values of h and π combined (above 0.5 and 0.005 respectively) reflects long evolutionary history. In the present study our results shows the haplotypes H11, H14 and H16 widely geographic distributed, suggesting long dispersion time and consequently long evolutionary history, corroborating Grant and Bower (1998) GRANT, W.S. and BOWER, B.W., 1998. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. The American Genetic Association, vol. 89, pp. 415-426. .

By randomly treating allelic frequencies of genetic marker and genetic divergence between groups, the BAPS software retrieved five demes, which are divided between the three regions analyzed, with overlap for demes 3 and 4 in the Northeast and Southeast Brazil. The BAPS was not unanimous in considering the geographic proximity or the biomes to delimit the demes, consequently other population analyzes were carried out to verify if they correspond to different lineages.

In order to identify if there is selective neutrality, tests were performed for the five demes. The results of Tajima’s D were not significant and Fu’s Fs was only significant for dm 2, which contains haplotypes from the Northeast. Significant results for these tests indicate the presence of natural selection or demographic processes among the variants of a nucleotide sequence in a population. Dm 2 is distributed over a wide area, with different kind of biomes which could be interfering in the selective neutrality ( Fu and Li, 1993 FU, Y.X. and LI, W.H., 1993. Statistical tests of neutrality of mutations. Genetics , vol. 133, no. 3, pp. 693-709. PMid:8454210. ; Nielsen 2001 NIELSEN, R., 2001. Statistical tests of selective neutrality in the age of genomics. Heredity, vol. 86, no. Pt 6, pp. 641-647. http://dx.doi.org/10.1046/j.1365-2540.2001.00895.x. PMid:11595044.
http://dx.doi.org/10.1046/j.1365-2540.2...
). No significant results were obtained for these same tests by Sousa et al. (2012) SOUSA, L.C.C., GONTIJO, C.M.F., BOTELHO, H.A. and FONSECA, C.G., 2012. Mitochondrial genetic variability of Didelphis albiventris (Didelphimorphia, Didelphidae) in Brazilian localities. Genetics and Molecular Biology, vol. 35, no. 2, pp. 522-529. http://dx.doi.org/10.1590/S1415-47572012005000035. PMid:22888303.
http://dx.doi.org/10.1590/S1415-4757201...
and Rocha et al. (2015) ROCHA, R.G., FERREIRA, E., LOSS, A.C., HELLER, R., FONSECA, C. and COSTA, L.P., 2015. The Araguaia River as an Important Biogeographical Divide for Didelphid Marsupials in Central Brazil. The Journal of Heredity, vol. 106, no. 5, pp. 593-607. http://dx.doi.org/10.1093/jhered/esv058. PMid:26249652.
http://dx.doi.org/10.1093/jhered/esv058...
, which indicates that this species is relatively constant. It is important to mention that these authors did not study northeastern populations.

The results of the AMOVA for the five demes indicate structuring (FST = 0.87). This structuring is evident in the case of dm 1, which has pairwise FST values of 0.95 to 0.97, indicating possible processes of allele fixation and genetic isolation. Sousa et al. (2012) SOUSA, L.C.C., GONTIJO, C.M.F., BOTELHO, H.A. and FONSECA, C.G., 2012. Mitochondrial genetic variability of Didelphis albiventris (Didelphimorphia, Didelphidae) in Brazilian localities. Genetics and Molecular Biology, vol. 35, no. 2, pp. 522-529. http://dx.doi.org/10.1590/S1415-47572012005000035. PMid:22888303.
http://dx.doi.org/10.1590/S1415-4757201...
also found evidence of population structuring (FST> 91%) in the Southeast and South populations.

The remaining demes analyzed in the AMOVA (dms 2, 3, 4 and 5) had also high pairwise F ST values (0.71 to 0.88). Despite the high FST , the same demes are distributed in different localities, for example: dm 3 are in Caxias/MA and Xacriabá Amerindian Reservations/MG; dm 4 in Caxias/MA, Xacriabá Amerindian Reservations/MG, Belo Horizonte/MG and Nova Lima/MG; dm 5 in Xacriabá Amerindian Reservations/MG, Belo Horizonte/MG and Nova Lima/MG. We can also notice that different demes are in sympatry, for example: dm 3 and dm 4 in Caxias/MA; dm 3, dm 4 and dm 5 in Xacriabá Amerindian Reservations/MG; dm 4 and dm 5 in Belo Horizonte/MG and Nova Lima/MG.

These sympatric demes show that FST are considering different structured population in the same localities. This condition could be explained by the wide distribution of D. albiventris ( Figure 1 ) and by the highly adaptable and generalist habit of the specie, since it is known that altitude and environment do not interferes in the specie distribution ( Aragona and Marinho-Filho, 2009 ARAGONA, M. and MARINHO-FILHO, J., 2009. História natural e biologia reprodutiva de marsupiais no Pantanal, Mato Grosso, Brasil. Zoologia, vol. 26, no. 2, pp. 220-230. http://dx.doi.org/10.1590/S1984-46702009000200004.
http://dx.doi.org/10.1590/S1984-4670200...
). Thus, although FST shows structuring, the connection between demes allows that Northeastern and Southeastern regions belong to the same widespread lineages.

Studies of didelphids have shown population structuring among different Brazilian biomes, for example Carvalho et al. (2011) CARVALHO, B.A., OLIVEIRA, L.F.B., LANGGUTH, A., FREYGANG, C.C., FERRAZ, R.S. and MATTEVI, M.S., 2011. Phylogenetic relationships and phylogeographic patterns in Monodelphis (Didelphimorphia: Didelphidae). Journal of Mammalogy, vol. 92, no. 1, pp. 121-133. http://dx.doi.org/10.1644/10-MAMM-A-075.1.
http://dx.doi.org/10.1644/10-MAMM-A-075...
and Caramaschi et al. (2011) CARAMASCHI, F.P., NASCIMENTO, F.F., CERQUEIRA, R., and BONVICINO, C.R., 2011. Genetic diversity of wild populations of the grey short-tailed opossum, Monodelphis domestica (Didelphimorphia: Didelphidae), in Brazilian landscapes. Biological Journal of the Linnean Society, vol. 104, no. 2, pp. 251-263. , found population structuring of Monodelphis domestica between the Cerrado and Caatinga. In the present study this relationship was not verified, as the demes are not restricted to one specific biome and are dispersed among a number of different biomes. This fact may be associated in differences in home ranges and in ecological characteristics between M. domestica and D. albiventris that could be possible directly related with body size. Didelphis albiventris is the largest Didelphidae weighting 500-2,750g while M. domestica weight 80-120g only. This size difference reflects in greater dispersion capacity ( Reis et al., 2006 REIS, N.R., PERACCHI, A.L., PEDRO, W.A. and LIMA, I.P. 2006. Mamíferos do Brasil. Londrina: Universidade Estadual de Londrina, pp. 437. ; Wang et al., 2009 WANG, Z., HUBBARD, F.J., CLUBB, F.J. and VANDEBERG, J.L., 2009. The Laboratory Opossum ( Monodelphis domestica) as a Natural Mammalian Model for Human Cancer Research. International Journal of Clinical and Experimental Pathology, vol. 2, no. 3, pp. 286-299. PMid:19079623. ) of D. albiventris that increases the gene flow, making population structuring more difficult. In this study, only dm 1 was isolated from the others, but this fact is not associated with biomes, since that deme occurs in Atlantic Forest and Pampa’s biomes.

When comparing the mutational sites among the demes, the haplotype network also shows two lineages with different geographic distributions for D. albiventris in this study: one Southern lineages (dm 1) and the other comprising Northeast/Southeast (demes 2-5) showed shared haplotypes. These two principal lineages are separated by 15 mutational steps. Northeast and Southeast dm’s are separated by few mutational steps (maximum of five, see Figure 3 ), have distribution overlapping between biomes and therefore should be considered as a single lineage.

The gene flow shown in the haplotype network represents an ancestral polymorphism, since the shared haplotypes are distributed over long geographic distances, as can be seen in dm 3 (H11) that occurs in Rio Grande do Piauí/PI (Cerrado) and Xacriabá Amerindian reservations/MG (Cerrado/Caatinga ecotone) (latitudes 07º 45’ S - 14° 53’ S). But the results of the haplotype network did not reveal connection between dm 5 (H16 and18) in Piracema/MG (Atlantic Forest) and dm 1 (H1) Machadinho/RS (Atlantic Forest) which has similar latitude interval (latitudes 20º 30’ S - 27º 34’ S) ( Figure 1 and 3 ; Table S1), another indication of the isolation of these two strains.

The Mantel test indicated a moderate degree of correlation between genetic and geographic distances in the five demes. In this study, with the addition of D. albiventris samples from the Northeast, we obtained a reduction in the correlation obtained by Sousa et al. (2012) SOUSA, L.C.C., GONTIJO, C.M.F., BOTELHO, H.A. and FONSECA, C.G., 2012. Mitochondrial genetic variability of Didelphis albiventris (Didelphimorphia, Didelphidae) in Brazilian localities. Genetics and Molecular Biology, vol. 35, no. 2, pp. 522-529. http://dx.doi.org/10.1590/S1415-47572012005000035. PMid:22888303.
http://dx.doi.org/10.1590/S1415-4757201...
. This reduction in the correlation reinforces the similarity found between demes 2-5, not diagnosed by these authors, and indicates that the Northeast/Southeast lineage is genetically similar although geographically distant.

With the addition of northeastern D. albiventris samples, were possible to conduct broader analyses encompassing a more complete distribution range of the specie. Sousa et al. (2012) SOUSA, L.C.C., GONTIJO, C.M.F., BOTELHO, H.A. and FONSECA, C.G., 2012. Mitochondrial genetic variability of Didelphis albiventris (Didelphimorphia, Didelphidae) in Brazilian localities. Genetics and Molecular Biology, vol. 35, no. 2, pp. 522-529. http://dx.doi.org/10.1590/S1415-47572012005000035. PMid:22888303.
http://dx.doi.org/10.1590/S1415-4757201...
, found patterns of isolation between Southeast and South regions as well as ours analyses, but it represents just a small fraction of the distribution. The addition of Northeast does not interfere in the isolation of the South region from the others, but the Northeast and Southeast are connected. It is important to mention that connection of demes occurs in the transitional areas between biomes, which strengthens the conclusions of Sousa et al. (2012) SOUSA, L.C.C., GONTIJO, C.M.F., BOTELHO, H.A. and FONSECA, C.G., 2012. Mitochondrial genetic variability of Didelphis albiventris (Didelphimorphia, Didelphidae) in Brazilian localities. Genetics and Molecular Biology, vol. 35, no. 2, pp. 522-529. http://dx.doi.org/10.1590/S1415-47572012005000035. PMid:22888303.
http://dx.doi.org/10.1590/S1415-4757201...
and Rocha et al. (2015) ROCHA, R.G., FERREIRA, E., LOSS, A.C., HELLER, R., FONSECA, C. and COSTA, L.P., 2015. The Araguaia River as an Important Biogeographical Divide for Didelphid Marsupials in Central Brazil. The Journal of Heredity, vol. 106, no. 5, pp. 593-607. http://dx.doi.org/10.1093/jhered/esv058. PMid:26249652.
http://dx.doi.org/10.1093/jhered/esv058...
about the importance of the transition zones for research and planning. These areas are considered as hotspots of intraspecific diversity and play an important role in the genetic diversity of species and should be closely investigated ( Smith, 1997 SMITH, T.B., 1997. A role for ecotones in generating rainforest biodiversity. Science , vol. 276, no. 5320, pp. 1855-1857. http://dx.doi.org/10.1126/science.276.5320.1855.
http://dx.doi.org/10.1126/science.276.5...
; Kark et al., 2002 KARK S., MUKERJI, T., SAFRIEL, U.N., NOY-MEIR, I., NISSANI, R. and DARVASI, A., 2002. Peak morphological diversity in an ecotone unveiled in the chukar partridge by a novel Estimator in a Dependent Sample (EDS). Journal of Animal Ecology, vol. 71, pp. 1015-1029. ).

Our results provide important new insights into the population dynamics of small mammals in Brazil. It has long been assumed that these kind of mammals have low vagility, with geographically structured populations and highly divergent genetic traits ( Crisci et al., 2003 CRISCI, J.V., KATIANAS, L. and POSADAS, P. 2003. Historical Biogeography: An introduction . Massachusetts: Havard University Press, 170 p. ). The extensive connection between demes of the Northeast and Southeast for D. albiventris may reflect the ecological plasticity of this species, resembling a medium-large mammal, with large home-range.

In the present work we diagnosed two lineages (Northeast/South axis) for the species D. albiventris and that the biomes do not interfere in the isolation of their demes. However, as an essential finding, the present study evidences extensive contact between demes at the transition zones, serving as reference to the conduction of important insights for the development of management actions.

Supplementary Material

Supplementary material accompanies this paper.

Table S1. List of the D. albiventris specimens included in this study, their field numbers (BC, PR, FNI, ALN, TNM, T, PNSC, URC, LLLS, and DCN), GenBank accession number (JN), demes, haplotype number (H), locality, geographical coordinates and origin of the samples.

This material is available as part of the online article from https://drive.google.com/open?id=17CmDgYMAmHLH0VTD_0c2AM476u2fJRrx

Acknowledgements

We are grateful to Fundação de Amparo à Pesquisa e Desenvolvimento Científico do Maranhão (FAPEMA) for financing this study, and the students of the GENBIMOL (Genetics and Molecular Biology Laboratory, Caxias, Maranhão, Brazil) for their invaluable support in the field. This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior -Brasil (CAPES) - Finance code 001.

  • (With 4 figures)

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Publication Dates

  • Publication in this collection
    25 Oct 2018
  • Date of issue
    Oct-Dec 2019

History

  • Received
    01 Sept 2017
  • Accepted
    10 Feb 2018
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