Abstract
The Monteiro is a feral pig found in the Brazilian Pantanal ecosystem. The goal of this research is to generate data and knolewdge related to animal populations wich can be used for management and development of an in vitro conservation program for animal resourses at Pantanal ecosystem. The present study evaluated animals sampled from 10 distinct locations within the region, using 19 microsatellite markers (N = 189) and the control region of mitochondrial DNA (mtDNA) (N = 392). Low genetic differences were found between populations with the microsatellite data. The FST range was between 0.009 and 0.063 (p-value < 0.05). The Mantel test corroborated with previous results, as low correlations between genetic and geographic distances were observed (r2 = 0.2309, p = 0.06). Bayesian analysis for genetic structure identification placed the Monteiro pigs into three main clusters (MOB, Pop 1 and all others Pantanal populations). Most of the Monteiro pigs share a single European haplotype as seen by mtDNA analyses. This haplotype is not exclusive, as it is shared with other swine populations (commercial and other locally adapted breeds). Monteiro populations from different geographic locations within Pantanal are not isolated and can be considered as a large unique population. Since animals roam freely to seek food and water, or even due to seasonal flooding of their habitat, the Monteiro populations presented absence of major genetic structure and evidence of high gene flow. These results can be used to create a management plan and in situ and ex situ conservation program for conservation and use of the Monteiro breed in the Pantanal ecosystem.
Similar content being viewed by others
References
Alderson L (1999) Criteria for the recognition and prioritisation of breeds of special genetic importance. Anim Genet Resour 33:1–9
Alves E, Ovilo C, Rodriguez MC, Silio L (2003) Mitochondrial DNA sequence variation and phylogenetic relationships among Iberian pigs and other domestic and wild pig populations. Anim Genet 34:319–324
Amos W, Hoffman JI, Frodsham A, Zhang L, Best S, Hill AVS (2006) Automated binning of microsatellite alleles: problems and solutions. Mol Ecol Notes 7:10–14. https://doi.org/10.1111/j.1471-8286.2006.01560.x
Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge, MA
Ayizanga RA, Kayang BB, Adomako K, Adenyo C, Inoue-Murayama M, Asamoah L (2016) Genetic diversity of some Ghanaian pigs based on microsatellite markers. Livest Res Rural Dev 28:24
Bandelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48. https://doi.org/10.1093/oxfordjournals.molbev.a026036
Bruford MW (2009) Future-proofing genetic units for conservation: time's up for subspecies as the debate gets out of neutral! In: Rizzoli A, Vernesi C, Bertorelle G, Hauffe HC, Bruford MW (eds) Population genetics for animal conservation. Conservation biology. Cambridge University Press, Cambridge, pp 227–240
Burgos-Paz W et al (2013a) Worldwide genetic relationships of pigs as inferred from X chromosome SNPs. Anim Genet 44:130–138. https://doi.org/10.1111/j.1365-2052.2012.02374.x
Burgos-Paz W et al (2013b) Porcine colonization of the Americas: a 60k SNP story. Heredity (Edinb) 110:321–330
Cavalcante Neto A (2010) Origem do suíno casco-de-burro e sua relação genética com populações ibéricas e americanas, Universidade Estadual Paulista
Cowled BD, Giannini F, Beckett SD, Woolnough A, Barry S, Randall L, Garner G (2009) Feral pigs: predicting future distributions. Wildl Res 36:242–251
Crandall KA, Bininda-Emonds ORP, Mace GM, Wayne RK (2000) Considering evolutionary processes in conservation biology. Trends Ecol Evol 15:290–295. https://doi.org/10.1016/S0169-5347(00)01876-0
Desbiez ALJ, Bodmer RE, Tomas WM (2010) Mammalian densities in a neotropical wetland subject to extreme climatic events. Biotropica 42:372–378. https://doi.org/10.1111/j.1744-7429.2009.00601.x
Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361. https://doi.org/10.1007/s12686-011-9548-7
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
Excoffier L, Lischer HE (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x
Frankham R, Ballou JD, Briscoe DA (2010) Introduction to conservation genetics, 2nd edn. Cambridge University Press, Cambridge
Groenen MAM et al (2012) Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491:393. https://doi.org/10.1038/nature11622
Gutierrez JP, Royo LJ, Alvarez I, Goyache F (2005) MolKin v2.0: a computer program for genetic analysis of populations using molecular coancestry information. J Hered 96:718–721. https://doi.org/10.1093/jhered/esi118
Holsinger KE, Weir BS (2009) Genetics in geographically structured populations: defining, estimating and interpreting F(ST). Nat Rev Genet 10:639–650. https://doi.org/10.1038/nrg2611
Kim TH et al (2005) Genetic structure of pig breeds from Korea and China using microsatellite loci analysis. J Anim Sci 83:2255–2263. https://doi.org/10.2527/2005.83102255x
Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I (2015) Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Mol Ecol Resour 15:1179–1191. https://doi.org/10.1111/1755-0998.12387
Larson G et al (2005) Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 307:1618–1621. https://doi.org/10.1126/science.1106927
Laval G et al (2000) Genetic diversity of eleven European pig breeds. Genet Select Evol 32:187–203. https://doi.org/10.1186/1297-9686-32-2-187
Li M et al (2014) Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication. Sci Rep 4:4678. https://doi.org/10.1038/srep04678
Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452. https://doi.org/10.1093/bioinformatics/btp187
Mariante ADS, Albuquerque M, Egito AA, McManus C, Lopes MA, Paiva SR (2009) Present status of the conservation of livestock genetic resources in Brazil. Livest Sci 120(3):204–212
Mantel N (1967) The detection of disease clustering and a generalized regression approach. Can Res 27:209
Osei-Amponsah R, Skinner BM, Adjei DO, Bauer J, Larson G, Affara NA, Sargent CA (2017) Origin and phylogenetic status of the local Ashanti Dwarf pig (ADP) of Ghana based on genetic analysis. BMC Genom 18:193. https://doi.org/10.1186/s12864-017-3536-6
Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel Population genetic software for teaching and research: an update. Bioinformatics 28:2537–2539. https://doi.org/10.1093/bioinformatics/bts460
Peakall ROD, Smouse PE (2005) genalex 6: genetic analysis in Excel Population genetic software for teaching and research. Mol Ecol Notes 6:288–295. https://doi.org/10.1111/j.1471-8286.2005.01155.x
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Ramírez O et al (2009) Integrating Y-chromosome, mitochondrial, and autosomal data to analyze the origin of pig breeds. Mol Biol Evol 26:2061–2072. https://doi.org/10.1093/molbev/msp118
Reynolds J, Weir BS, Cockerham CC (1983) Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105:767
Ritland K (1996) Estimators for pairwise relatedness and individual inbreeding coefficients. Genet Res 67:175–185
Scandura M, Iacolina L, Apollonio M (2011) Genetic diversity in the European wild boar Sus scrofa: phylogeography, population structure and wild x domestic hybridization. Mammal Rev 41:125–137. https://doi.org/10.1111/j.1365-2907.2010.00182.x
Silva EC et al (2011) Patterns of genetic diversity of local pig populations in the State of Pernambuco. Brazil Rev Bras Zootecn 40:1691–1699
Slarkin M (1985) Gene flow in natural populations. Annu Rev Ecol Syst 16:393–430. https://doi.org/10.1146/annurev.es.16.110185.002141
Sollero BP et al (2009) Genetic diversity of Brazilian pig breeds evidenced by microsatellite markers. Livest Sci 123:8–15. https://doi.org/10.1016/j.livsci.2008.09.025
Souza CA (2011) Padrões de Diversidade mitocondrial e nuclear em raças de suínos naturalizadas do Brazil. Universidade Católica de Brasília
Souza CA, Paiva SR, Pereira RW, Guimarães SEF, Dutra WM Jr, Murata LS, Mariante AS (2009) Iberian origin of Brazilian local pig breeds based on Cytochrome b (MT-CYB) sequence. Anim Genet 40:759–762. https://doi.org/10.1111/j.1365-2052.2009.01899.x
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729. https://doi.org/10.1093/molbev/mst197
Ursing BM, Arnason U (1998) The complete mitochondrial DNA sequence of the pig (Sus scrofa). J Mol Evol 47:302–306. https://doi.org/10.1007/PL00006388
Vilaça ST et al (2014) Mitochondrial phylogeography of the European wild boar: the effect of climate on genetic diversity and spatial lineage sorting across Europe. J Biogeogr 41:987–998. https://doi.org/10.1111/jbi.12268
Acknowledgements
This work was supported by CAPES (Coordination of Superior Level Staff Improvement), CNPq (National Council for Scientific and Technological Development), Embrapa (Brazilian Agricultural Research Corporation) and INCT Pecuaria (MCT/FINEP/CNPq/FAPEMIG). We also thank Embrapa Swine and Poultry, Embrapa Pantanal and EMATER-DF for the biological material. We wish to thank Aderbal Cavalcante Neto for the unpublished mtDNA sequences from locally adapted breeds; and Potira Hermuche from Brasilia University for the map on Fig. 1.
Author information
Authors and Affiliations
Contributions
CM, ARC and SRP designed study; material preparation and data collection were performed by ECS, UP and CAS; data analysis were performed by ECS; original draft preparation by CM and DAF; writing, review and editing by CM, DAF, ARC, UP and SRP.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Ethical approval
All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.
Informed consent
Informed consent was obtained from all individuals participants included in the study.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Silva, E.C., McManus, C., Piovezan, U. et al. Phylogeography of feral Monteiro pig in the Brazilian Pantanal Ecosystem. Genetica 148, 183–193 (2020). https://doi.org/10.1007/s10709-020-00099-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10709-020-00099-y