Population history, phylogeography, and conservation genetics of the last Neotropical mega-herbivore, the lowland tapir (Tapirus terrestris)

Thoisy, Benoı̂t de; Silva, Anders Gonçalves da; Ruiz‐García, Manuel; Tapia, Andrés; Ramírez, Oswaldo; Arana, Margarita; Quse, Viviana; Paz‐y‐Miño, César; Tobler, Mathias W.; Pedraza, Carlos; Lee, Anne

doi:10.1186/1471-2148-10-278

Cited by 41 publications

(36 citation statements)

References 108 publications

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“…Our results concur partially with previous molecular phylogenies (Norman and Ashley 2000;de Thoisy et al 2010;Steiner and Ryder 2011). The mtDNA gene trees (Cytb, or Cytb þ COI þ COII) show strong support for a unique Neotropical clade, encompassing a strict South American tapir subclade (Fig.…”

Section: Discussionsupporting

confidence: 82%

“…We thank J. Patton (Museum of Vertebrate Zoology, Berkeley, California) for providing data and measurements of tapir skulls from his institution, initial comments, and advising on early stage of this manuscript; J. Vianna (Pontificia Universidad Católica de Chile, Santiago, Chile) and A. A. Nascimento (Universidade Federal de Minas Gerais, Belo Horizonte, Brazil) for participation and discussion in the initial stages of this work; C. Pedraza (Universidad de Los Andes, Bogotá, Colombia), A. Tapia (Universidad Central del Ecuador, Quito, Ecuador), M. R. Garcia (Universidad Javeriana, Bogotá, Colombia), O. Ramirez (Universidad Peruana Cayetano Heredia, Lima, Peru), and A. G. Silva (University of British Columbia Okanagan, Kelowna, Canada), who provided some samples of Neotropical Tapirus (de Thoisy et al 2010); the San Diego Zoo, San Diego, California, which provided a sample of T. indicus; L. Avilla (Federal University of the State of Rio de Janeiro, UNIRIO), who lent us 2 camera-traps; M. Marmontel (Instituto Sustentável Mamirauá, Tefé, Brazil), P. Médici (Tapir Specialist Group, www.tapirs.org), and C. Maria Jacobi (Universidade Federal de Minas Gerais, Belo Horizonte, Brazil), who helped to improve the manuscript text; and L. Emmons (National Museum of Natural History, Smithsonian Institution, Washington, D.C.), who provided many comments and English review of the final text. We thank the biology student G. Braga, who kindly made the life drawings of the male and female specimens of T. kabomani in Supporting Information S6 and S7.…”

Section: Acknowledgmentsmentioning

confidence: 99%

“…Despite popular accounts of the occurrence of more than 1 tapir species in lowland Amazonia, it was assumed that observed diversity of both morphological (Hershkovitz 1954) and molecular (de Thoisy et al 2010) characters represented variations of T. terrestris (Linnaeus, 1758). We present here detailed morphological and molecular (mitochondrial DNA [mtDNA]) comparisons of specimens from western Brazilian Amazon with all other Tapirus species, which indicate the Molecular phylogenetic analyses.-The following total sample numbers, or sequences, or both, were included in the analyses: T. terrestris: n ¼ 52, T. bairdii: n ¼ 3, T. pinchaque: n ¼ 5, T. indicus: n ¼ 4, Tapirus sp.…”

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confidence: 99%

“…The DNA sequences from 3 mtDNA genes (cytochrome b [Cytb], cytochrome oxidase I [COI], and cytochrome oxidase II [COII]) from living Tapirus species were generated and compared to previously published data (Ashley et al 1996;Norman and Ashley 2000;de Thoisy et al 2010). We included a thorough analysis of the Cytb in a large geographic sampling in South America, such as has been shown to be useful in recovering mammalian phylogeny and exposing cryptic species (Baker and Bradley 2006;Redondo et al 2008).…”

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A new species of tapir from the Amazon

Cozzuol

Clozato

Holanda

et al. 2013

Journal of Mammalogy

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All known species of extant tapirs are allopatric: 1 in southeastern Asia and 3 in Central and South America. The fossil record for tapirs, however, is much wider in geographical range, including Europe, Asia, and North and South America, going back to the late Oligocene, making the present distribution a relict of the original one. We here describe a new species of living Tapirus from the Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla in more than 100 years, from both morphological and molecular characters. It is shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque (Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia, where the biota faces increasing threats. Local peoples have long recognized our new species, suggesting a key role for traditional knowledge in understanding the biodiversity of the region.

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Section: Discussionsupporting

confidence: 82%

Section: Acknowledgmentsmentioning

confidence: 99%

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confidence: 99%

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A new species of tapir from the Amazon

Cozzuol

Clozato

Holanda

et al. 2013

Journal of Mammalogy

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“…Also, the ancestors of this population were the first to diverge in all of the trees. The Western Amazon area was also the focus for the dispersion of many other mammalian taxa such as the lowland tapir [102][103][104][105], the jaguar [106], and diverse Neotropical primate genera [107][108][109][110].…”

Section: Strong Genetic Heterogeneity Among Capybara Populations Of Dmentioning

confidence: 99%

Continuous Miocene, Pliocene and Pleistocene Influences on Mitochondrial Diversification of the Capybara (Hydrochoerus Hydrochoeris; Hydrochoeridae, Rodentia): Incapacity to Determine Exclusive Hypotheses on the Origins of the Amazon and Orinoco Diversity for This Species

Ruiz‐García¹,

Luengas-Villamil²,

Pinedo-Castro³

et al. 2016

J Phylogenetics Evol Biol

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The capybara (Hydrochoerus hydrochoeris) is the largest rodent on the world and it is strongly linked to the river systems of a large fraction of South America and part of Central America (Panama). Thus, it is an interesting species to test hypotheses about the origin of the high biodiversity within the Amazon Basin and in a sizeable fraction of the Neotropics. To test these hypotheses, we sequenced two mitochondrial genes (control region and Cytochrome b) of 78 wild capybaras sampled in Colombia, Peru, Ecuador and Brazil. At least, five different "populations" or ESUs were detected in well delimited geographical areas. However, our results do not support the more recent view that two different species of capybara are present (H. hydrochoeris and H. isthmus), unless chromosomal speciation (stasipatric or parapatric) can be demonstrated between these two groups. A Bayesian tree with the aforementioned two mitochondrial genes, and another Bayesian tree with a subset of 25 capybaras for 10 mitochondrial genes, showed that the initial diversification of the mitochondrial haplotype in capybaras was initiated in the Late Miocene. The trees also showed that the other haplotype diversification processes extended into the Pliocene and Pleistocene. We also detected population expansion events during different moments of the Pleistocene. Although some authors strongly suggest that the Miocene diversification explains the extreme biodiversity in the Amazon Basin and in surroundings areas (for instance, the Paleogeography hypothesis), others consider it the result of available forest refugia (Refuge hypothesis) during the Pleistocene. However, our results suggest that both hypotheses (and others, such as the Riverrefuge, the Recent Lagoon and the Hydrogeological Recent Change hypotheses) could have affected the evolution of the capybara to generate the current mitochondrial diversity. Thus, it is difficult to generalize a unique Amazon biota diversification hypothesis because each species or taxon could be affected by different processes and because the temporal antiquity of each taxon in South America is also different. Many mammalian taxa, and others, migrated into South America during the Great American Biotic Interchange (GABI) and their diversification processes in South America were mainly driven by Pleistocene events as those proposed by the Refuge hypothesis. Older taxa within this continent could have begun their current genetics diversification processes earlier, such as in the case of the capybara.

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The genetic population structure of wild western lowland gorillas (Gorilla gorilla gorilla) living in continuous rain forest

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Arandjelovic

Morgan

et al. 2014

American J Primatol

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To understand the evolutionary histories and conservation potential of wild animal species it is useful to assess whether taxa are genetically structured into different populations and identify the underlying factors responsible for any clustering. Landscape features such as rivers may influence genetic population structure, and analysis of structure by sex can further reveal effects of sex-specific dispersal. Using microsatellite genotypes obtained from noninvasively collected fecal samples we investigated the population structure of 261 western lowland gorillas (WLGs) (Gorilla gorilla gorilla) from seven locations spanning an approximately 37,000km2 region of mainly continuous rain forest within Central African Republic (CAR), Republic of Congo and Cameroon. We found our sample to consist of two or three significantly differentiated clusters. The boundaries of the clusters coincided with courses of major rivers. Moreover, geographic distance detoured around rivers better-explained variation in genetic distance than straight line distance. Together these results suggest that major rivers in our study area play an important role in directing WLG gene flow. The number of clusters did not change when males and females were analyzed separately, indicating a lack of greater philopatry in WLG females than males at this scale.

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Population history, phylogeography, and conservation genetics of the last Neotropical mega-herbivore, the lowland tapir (Tapirus terrestris)

Cited by 41 publications

References 108 publications

A new species of tapir from the Amazon

A new species of tapir from the Amazon

Continuous Miocene, Pliocene and Pleistocene Influences on Mitochondrial Diversification of the Capybara (Hydrochoerus Hydrochoeris; Hydrochoeridae, Rodentia): Incapacity to Determine Exclusive Hypotheses on the Origins of the Amazon and Orinoco Diversity for This Species

The genetic population structure of wild western lowland gorillas (Gorilla gorilla gorilla) living in continuous rain forest

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