Figure 1 - uploaded by Manuel Ruiz-García
Content may be subject to copyright.
Map of the geographical localities where 141 lowland tapirs were sampled to sequence the Cyt-b gene.
Source publication
representing the largest geographical distribution sample of this species studied across of
South America to date. We compare our new data regard to two previous works on population
structure and molecular systematics of T. terrestris. Our data agree with the Thoisy et al.’s work
in (1) the Northern Western Amazon basin was the area with the highes...
Context in source publication
Context 1
... used sequences of the Cyt-b gene, which is commonly used among the molecular markers relevant for phylogeography, biosystematics, and genetic structure studies in mammal populations (Patton et al., 2000). We sequenced 141 individuals of T. terrestris , including more geographical areas and individuals than any previous study (Cozzuol et al., 2013; Thoisy et al., 2010) to determine levels of gene diversity, spatial genetic structure, and demographic changes of T. terrestris in South America. Additionally, 42 tapir individuals from T. terrestris , T. pinchaque , T. bairdii , and the alleged new species, T. kabomani were sequenced at the Cyt-b , COI , and COII genes to compare with the tree showed by Cozzuol et al. (2013) and to show evidence in favor or against of the alleged ‘‘new species’’ T. kabomani . We sequenced a total of 141 individuals of T. terrestris at the Cyt-b gene from nine South American countries including Colombia (42 animals), Venezuela (six individuals), French Guiana (11 individuals), Ecuador (seven animals), Peru (30 animals), Bolivia (11 animals), Brazil (24 animals), Paraguay (one animal), and Argentina (two animals) (Figure 1). Additionally, one animal from the Barcelona Zoo (Spain), five animals from the Cincinnati Zoo (Cincinnati, OH) and one animal of unknown origin were also analyzed. These last seven animals were not included in those analyses where the origin of the animals was necessary. Thirty T. pinchaque (12 haplotypes), 30 T. bairdii (six haplotypes), and one T. indicus samples obtained by the first author were also employed. For the question of T. kabomani , 42 individuals were analyzed: 17 T. terrestris (one from Argentina, two from Bolivia, three from Brazil, five from Ecuador, three from Peru and three from the Cincinnati Zoo), five ‘‘ T. kabomani ’’ (the two Brazilian individuals reported by Cozzuol et al., 2013, and three ‘‘classical morphological’’ T. terrestris sampled by us but with haplotypes related to T. kabomani ; one from San Mart ́n de Amacayacu, Amazon River, Colombia, one from the Mazan River, a tributary from the Napo River, in the Peruvian Amazon and one from near to Tena, upper Napo River, at the Ecuadorian Amazon), 12 T. pinchaque (three Colombian and nine Ecuadorian individuals), and nine T. bairdii (all them from the Darien area in Panama). All these 42 individuals were sequenced for Cyt-b (1140 base pairs, bp) , COI (640 bp), and COII (726 bp) genes summing up 2506 bp. DNA from teeth, bones, muscle, and skins were obtained with the phenol–chloroform procedure (Sambrock et al., 1989), whereas DNA samples from hair and blood were obtained with 10% Chelex Õ 100 resin (Walsh et al., 1991). Amplifications for Cyt-b gene were achieved using primers designed for perissodactyls (Tougard et al., 2001). The amplification conditions employed followed Ruiz-Garc ́a et al. (2012). For the COI and COII genes, the amplification conditions followed Ashley et al. (1996) and Hebert et al. (2003, 2004). All amplifications, including ...
Similar publications
Key words Lanzhou Basin, Early Oligocene, Paraceratheriidae, new species
The critically endangered northern white rhinoceros is believed to be extinct in the wild, with the recent death of the last male leaving only two remaining individuals in captivity. Its extinction would appear inevitable, but the development of advanced cell and reproductive technologies such as cloning by nuclear transfer and the artificial produ...
The Mass, Metabolism and Length Explanation (MMLE) was advanced in 1984 to explain the relationship between metabolic rate and body mass for birds and mammals. This paper reports on a modernized version of MMLE. MMLE deterministically predicts the absolute value of Basal Metabolic Rate (BMR) and body mass for individual animals. MMLE is thus distin...
The vertebrate fossil record from the Dúbravka-Pole site in the territory of Devínska Kobyla consists of Brachypotherium cf. brachypus and Lartetotherium sp. dental and osteological remains. The both taxa lived in swampy to forested land at the shore of shallow brackish sea (or lagoon?) during the Early Sarmatian (MN 7/8). Their occurrence is proba...
Citations
... The separation of drainages East and West of the Andes Divergence time estimation data were compiled from the literature that reported separation events between cis-and trans-Andean lineages, be it contemporary species or nodal divergences (Abe et al., 2014;Cheviron et al., 2005;Collins and Dubach, 2000;Cortés-Ortiz et al., 2003;D'Horta et al., 2013;Dick et al., 2003;Elias et al., 2009;Fernandes et al., 2014;Grau et al., 2005;Gutiérrez et al., 2014;Hardman and Lundberg, 2006;Hernández Torres, 2015;Machado et al., 2014;Miller et al., 2008;Patané et al., 2009;Patel et al., 2011;Picq et al., 2014;Ribas et al., 2005Ribas et al., , 2007Říčan et al., 2013;Ruiz-García et al., 2015;Smith et al., 2014;Voss et al., 2013;Weir and Price, 2011). A total of 54 data points were compiled along with their credible intervals, most frequently HPD intervals. ...
Estimating phylogenies in which branch lengths are expressed in units of absolute time is crucial for testing hypotheses in modern evolutionary biology. However, bioinformatic tools to process data from bayesian divergence time estimation analyses are often not easily adaptable, and documenting methodological choices is not a generalized practice.
The R package tbea is a toolset to integrate biological, geological and paleontological information to optimize the specification of models, their parameters and prior distributions in divergence times estimation analyses. tbea implements statistical models to (i) better translate time information in dating sources into the specified calibration densities, (ii) improve comparisons between prior and posterior distributions for parameters of interest, (iii) carry out inference on origination times for a collection of posterior distributions, (iv) summarize different distributions into a single one, useful e.g. when building secondary calibrations, and (v) improve the reproducibility of divergence time estimation analyses allowing users to document methodological choices.
We illustrate the package functionalities by carrying out two worked examples. One on the phylogenetic relationships and divergence time estimation of South American Saber-Tooth Characins of the family Cynodontidae, and another one on the separation time of drainages East and West of the Andes in South America during the Neogene.
It is expected that the tools herein available will be key when estimating events in time from collections of point estimates, as well as the combination of different posterior densities from the same parameter are useful to justifying the selection of secondary calibration points, or discussing the timing of biogeographic events when multiple sources are available.
... The phylogenetic relationships across all of Tapiridae are currently unresolved; however, the species examined in this study have been the subject of phylogenetic revision over the past 10 years, and relationships are for the most part well established (Cozzuol et al., 2013;Hulbert, 2010;Ruiz-García et al., 2016a;Ruiz-García et al., 2016b). A composite phylogenetic tree was compiled in Mesquite 3.6 (Maddison and Maddison, 2019) based on published tapirid topologies (Colbert, 2005;Cozzuol et al., 2013;Holanda and Ferrero, 2013;Hulbert, 2010;Hulbert and Wallace, 2005). ...
Bite force is often associated with specific morphological features, such as sagittal crests. The presence of a pronounced sagittal crest in some tapirs (Perissodactyla: Tapiridae) was recently shown to be negatively correlated with hard-object feeding, in contrast with similar cranial structures in carnivorans. The aim of this study was to investigate bite forces and sagittal crest heights across a wide range of modern and extinct tapirs and apply a comparative investigation to establish whether these features are correlated across a broad phylogenetic scope. We examined a sample of 71 specimens representing 15 tapir species (five extant, ten extinct) using the dry-skull method, linear measurements of cranial features, phylogenetic reconstruction, and comparative analyses. Tapirs were found to exhibit variation in bite force and sagittal crest height across their phylogeny and between different biogeographical realms, with high-crested morphologies occurring mostly in Neotropical species. The highest bite forces within tapirs appear to be driven by estimates for the masseter - pterygoid muscle complex, rather than predicted forces for the temporalis muscle. Our results demonstrate that relative sagittal crest height is poorly correlated with relative cranial bite force, suggesting high force application is not a driver for pronounced sagittal crests in this sample. The divergent biomechanical capabilities of different contemporaneous tapirids may have allowed multiple species to occupy overlapping territories and partition resources to avoid excess competition. Bite forces in tapirs peak in Pleistocene species, independent of body size, suggesting possible dietary shifts as a potential result of climatic changes during this epoch. This article is protected by copyright. All rights reserved.
... This new species would be distributed in Brazil and Southern Colombia (department of Amazon) in sympatry with T. terrestris. However, a debate on the validity of T. kabomani has been in place (Cozzuol et al. 2014;Ruiz-García et al. 2015a;Ruiz-García et al. 2016;Voss et al. 2014). Given this uncertainty and lack of further information, we decided not to include T. kabomani here until more information resolving the topic is available. ...
... According to Ruiz-García et al. (2016), mountain tapir populations of Colombia and Ecuador experienced a high historical gene flow, which is reflected in their low genetic differentiation, found from the information coming from the sequencing of 15 mitochondrial genes. Although the Colombian population presents a slightly higher nucleotide diversity, these authors did not detect any molecular subspecies or significantly different evolutionary units for T. pinchaque. ...
Twelve species of ungulates are present in Colombia, represented by three species of tapirs, two of peccaries and seven species of deer. A synthesis about the evolutionary and recent history for each of the group is presented, highlighting recent paleontological information for northern South America. Genetic and molecular studies indicate that deer present the greatest uncertainty regarding the number of species and their phylogenetic relationships. By species richness, the Caribbean region, with eight species, is the most diverse, followed by the Andean region with seven, the Orinoquia and Amazonia with six species and finally the Pacific region with four ungulate species. All the species present a greater proportion of their distribution outside protected areas, being two species of Andean ungulates, the mountain tapir (Tapirus pinchaque) and the rabbit deer (Pudu mephistophiles) the only ones reaching 20% of their distribution inside protected areas. Seven species are found in one of the threatened categories of IUCN, in which all species of tapirs are included. Finally, information about hippopotamus (Hippopotamus amphibius) and feral pig (Sus scrofa), alien species with wild populations in Colombia, is presented.
... At the more recent end of the temporal scale, much can be gained through interactions between phylogeographers and ecologists that are interested in the assembly and disassembly of extant (or nearly extant) biotas (Palma et al. 2017); evolutionary biologists with a focus on trait evolution (Cahill et al. 2015) and the mechanics of speciation (Morales et al. 2017;Savić et al. 2017); and conservation biologists needing tools to predict biotic changes across the Anthropocene (Ruiz-García et al. 2016). Each of these disciplines to one degree or another requires an accurate depiction of lineage diversity and geographic distribution, often within and among closely related species. ...
Mammals have played a foundational role in the explosive growth of phylogeography over the past 30 years that it has been a recognized discipline. Novel discoveries of geographic patterns and processes using phylogeographic approaches have integrated disciplines including biogeography, evolutionary biology, ecology, and conservation biology. Here, we use several approaches to survey the scope and influence of phylogeography, beginning with use of a well-studied family of North American rodents to contrast information content derived from DNA-based phylogeography versus a popular older method, allozyme electrophoresis, of assaying genetic variation within and among species across geography. We conclude that phylogeography has elevated the quality of insights attainable regarding, for example, the causal role of Earth history events in processes including lineage divergence, speciation, and adaptive evolution. Next, we use searches of the Web of Science with an array of terms that return information on molecular markers employed, numbers of individuals and localities examined, time frames investigated, historical processes and ways that species and biotas have responded to Earth history, design of phylogeographic studies (e.g., single-taxon versus comparative), and current gaps in taxonomic and geographic sampling. Highlighted results from phylogeographic assays include: an average of 3.3 cryptic lineages per taxonomic species in rodents; a bias in number of studies toward less-diverse biogeographic regions; and a relatively low number of mammalian genera studied. We conclude with predicted and recommended directions for future growth in mammalian phylogeography, including prospects for an increasing role of next generation-based genomics. Los mamíferos han jugado un papel fundamental en el crecimiento explosivo de la filogeografía durante los últimos 30 años, el período en el que esta área de investigación ha sido reconocida como una disciplina independiente. Los descubrimientos novedosos de patrones y procesos usando estrategias filogeográficas han integrado varias disciplinas, incluyendo la biogeografía, la biología evolutiva, la ecología y la biología de conservación. En este artículo usamos varios enfoques para examinar el alcance y la influencia de la filogeografía, comenzando con el uso de una familia de roedores de América del Norte que ha sido bien estudiada, para contrastar la información obtenida con estudios filogeográficos con ADN y con un método antiguo popular, la electroforesis de aloenzimas, para determinar los niveles de variación genética en una especie y en varias especies a través de la geografía. Concluimos que la filogeografía ha incrementado la calidad de las percepciones que se puede obtener acerca de, por ejemplo, el papel causal de los eventos históricos de la tierra en procesos que incluyen la divergencia de linajes, la especiación y la evolución adaptativa. Seguidamente, hicimos búsquedas del sitio de la Internet Web of Science usando varios términos que produjeron información acerca de los marcadores genéticos utilizados, el número de individuos y de localidades examinados, los marcos temporales investigados, los procesos históricos y las maneras en que las especies y las biotas han respondido a la historia de la tierra, el diseño de los estudios filogeográficos (por ejemplo, una sola especie versus proyectos comparativos) y la falta de conocimiento actuales con referencia al muestreo taxonómico y geográfico. Los resultados de los análisis filogeográficos que enfatizamos incluyen: un promedio de 3.3 linajes crípticos por especie taxonómica de roedor; una propensión a conducir estudios en áreas biogeográficas de menor diversidad; y un número relativamente pequeño de los géneros de
... The mitochondrial genes are interesting markers for phylogenetic tasks because they lack introns and include a rapid accumulation of mutations, rapid coalescence time, a negligible recombination rate, and haploid inheritance (Avise et al. 1987). The Cyt-b gene is commonly used among the molecular markers relevant for phylogeography, biosystematics, and genetic structure studies in mammal populations (Lavergne et al. 2010;Ruiz-García et al. 2015). The COI gene has emerged as the standard barcode region for animals, including mammals (www.mammaliabol. ...
We sequenced mitochondrial genes of otter (Lontra longicaudis and Pteronura brasiliensis) and dolphin (Inia sp.) species to provide new systematics data and to test hypotheses that offer explanations as to the Amazon’s biodiversity. Four of the 11 hypotheses tested --Paleogeography (PH), Recent Lagoon (RLH), Hydrogeological Recent Change (HRCH), and Refugia (RH)-- support the evolution of these three species. As part of this comparative phylogenetic study, we also considered the degree of water dependence of each species. For the least water dependent of the three species, L. longicaudis, only HRCH and RH had an influence on genetic structure, although it was relatively minor. For the more water dependent otter species, P. brasiliensis, our analyses stressed the significance of a single PH event along with two lesser important PH events. However, its gene diversification basically occurred during the Pleistocene and our analyses did detect a relatively small influence of HRCH and RH. For the completely water dependent species, Inia, we detected two significant PH events. Its genetic structure was considerably more developed than in either otter species, although the Pleistocene was a very important period of genetic diversification for the pink river dolphins (HRCH and RLH). Each species has ancestors with different geographical origins and genomes with different capacities to colonize—making it difficult to rely on a generalized hypothesis to understand the origins of the Amazon’s extremely rich biodiversity.
... 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]. ...
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.
... Supporting this, Cummings et al., (1995) showed that mitochondrial genomes have higher information content per base than nuclear DNA. The Cyt-b gene is commonly used among the molecular markers relevant for phylogeography, biosystematics, and genetic structure studies in mammalian populations (Lavergne et al., 2010;Ruiz-García et al., 2015a). The COI gene has emerged as the standard barcode region for animals, including mammals (www.mammaliabol.org) ...
... Primer name Primer sequence (5 to 3 ) Amplicon sizes (bp) TPF1 5 -CTAACTCCATAAAACA-3 3,768 TPR1 5 -CAAAATCCTCCGT-3 TPF2 5 -AAACATAAGAAAT-3 4,990 TPR2 5 -ATCAGCCCTCCTTA-3 TPF3 5 -TAGCCTTAATTCAA-3 5,049 TPR3 5 -TAATTTCCCCATTA-3 TPF4 5 -TCAAACCAAAAAGG-3 3,345 TPR4 5 -CAGGTTTGATCCT-3 density (HPD). The time during which the demographic changes were recorded was chosen by the software with a mutation rate of 2.5% per million of year (Ruiz-García et al., 2015). We used IBD Software (version 1.2) (Bohonak, 2002) to determine possible correlation between the genetic distances (Kimura 2P distance; Kimura, 1980) and the geographical distances among these populations. ...
We sampled 45 Andean mountain tapirs (Tapirus pinchaque) from Colombia and Ecuador and sequenced 15 mitochondrial genes (two rRNA and 13 protein codifying genes)—making up 13,939 base pairs, approximately 83.1% of the total mitochondrial DNA's length. The overall sample had low to medium levels of nucleotide diversity with diversity slightly higher for the Colombian population. Both populations experienced high historical gene flow and our genetic heterogeneity analyses revealed a low genetic differentiation between them. Therefore, we did not detect any molecular subspecies, or significantly different evolutionary units for T. pinchaque. This species experienced a population expansion in the last 100,000 years but this expansion was more pronounced in the Ecuadorian population especially in the last 10,000 years, whereas the Colombian population underwent a strong bottleneck in the last 5,000 years. There was no significant spatial trend in genetic structure for the mountain tapir in Colombia and Ecuador. Phylogenetic analyses did not detect any important geographic clade within this species. Temporal split between T. pinchaque and T. terrestris might have occurred around 7–1.5 million years ago (MYA). T. pinchaque and T. terrestris + T. kabomani are two monophyletic clades, suggesting that T. kabomani is not a full species.
... When a statistic was used on a MNJ network, the two most frequent T. terrestris's haplotypes diverged from the main T. pinchaque's haplotype around 1.58 + 0.30 MYA and 1.53 + 0.34 MYA, respectively. García et al., (2015a) showed a Bayesian tree that supported a temporal split of 3.33 MYA between both T. pinchaque and T. terrestris. Also, Ruiz-García et al., (2015b) performed a mitogenomic study of T. pinchaque and determined the temporal split between the ancestors of T. terrestris and T. pinchaque to oscillate from 7.42 to 3.27 MYA (95 % HPD) in a Bayesian tree. ...
We sequenced mitochondrial genes (COI, COII, Cyt-b) of accepted Latin America tapir species (Tapirus pinchaque, T. terrestris and T. bairdii) as well as an alleged new species, T. kabomani.
The mountain tapir (T. pinchaque) is a relatively rare large mammal species. Some population censuses indicate that no more than 2,000 mountain tapirs are left in the wilderness areas of Colombia, Ecuador and Peru. Our results showed that the gene diversity levels are medium to low with respect to other mammals sequenced for the same or similar genes. However, these gene diversity levels are not impoverished, which means that the genetic situation of this species is not as critical as its population censuses suggest. It will be crucial to determine the gene diversity levels in certain populations not included in the current work (the eastern and, possibly, western Andean Cordilleras in Colombia as well as the Tabaconas Namballe National Sanctuary in Peru), because they are probably the smallest populations of this species. On the other hand, the lowland tapir (T. terrestris), the species with the largest geographical distribution in Latin America, showed the highest gene diversity levels of all the other tapir species studied. Additionally, the genetic structure of T. terrestris is clearly more robust than that of T. pinchaque. Different geographic populations of both species showed different demographic trends throughout time. Our results including five samples of T. kabomani showed this taxon to be a haplogroup within T. terrestris, reducing the likelihood of T. kabomani being a new full species. Finally, we also analyzed the influence of diverse Pleistocene climatic changes on the mitochondrial haplotype diversification of T. terrestris and T. pinchaque. The Pleistocene Refugia and the Recent Lake hypotheses probably played integral roles in the evolutionary history of T. terrestris. In contrast, the Pleistocene Refugia hypothesis involving the Andes, which probably played an important part in the genetic diversification of other mammals, did not have a significant impact on T. pinchaque.
... This new species would be distributed in Brazil and Southern Colombia (department of Amazon) in sympatry with T. terrestris. However, a debate on the validity of T. kabomani has been in place (Cozzuol et al. 2014;Ruiz-García et al. 2015a;Ruiz-García et al. 2016;Voss et al. 2014). Given this uncertainty and lack of further information, we decided not to include T. kabomani here until more information resolving the topic is available. ...
... According to Ruiz-García et al. (2016), mountain tapir populations of Colombia and Ecuador experienced a high historical gene flow, which is reflected in their low genetic differentiation, found from the information coming from the sequencing of 15 mitochondrial genes. Although the Colombian population presents a slightly higher nucleotide diversity, these authors did not detect any molecular subspecies or significantly different evolutionary units for T. pinchaque. ...
