Mario Vargas-Ramírez

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• Ph. D.
• Professor (Associate) at National University of Colombia

The mitochondrial genome of three Trachemys medemi was sequenced and annotated for the first time. The mitochondrial genome is a circular DNA molecule of 16,711–16,810 bp in size, with 60.9% AT content. It includes 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and the non-coding control region. The genome composition is characterized by a...

Introduction: Turtles are extensively harvested to supply the demand for food, pets, and products. Conservation strategies often involve the release of seized individuals and ex-situ breeding programs. However, several traded species have particular genetic characteristics, and the origins of captive individuals are often unknown. Despite their pot...

The South American rattlesnake corresponds to a species complex, and debates persist regarding its systematics and taxonomy. Similarly, the understanding of its phylogeography has been incomplete, due to a lack of information concerning northwestern populations. This knowledge gap hinders the development of conservation strategies to address threat...

Amazon parrots stand out as one of the most illegally traded Psittacids in the neotropics. However, the lack of effective tools for determining the geographical origin of confiscated individuals has impeded the development of well-informed release programmes. In this study, we evaluated the efficacy of the cytochrome oxidase subunit I (COI) gene to...

Supplementary figures

Supplementary tables

The genus Helicops Wagler, 1828 comprises 20 species of semiaquatic snakes. It is mostly distributed in the cis-Andean region of South America, with only two trans-Andean species (H. danieli, H. scalaris). Helicops danieli is endemic to Colombia and occurs through most of the trans-Andean region. Herein two mitochondrial and two nuclear genomic mar...

During the second third of last century, the Orinoco Crocodile (Crocodylus intermedius) underwent a hunting process driven by the demand from the North American, European, and Japanese leather industry, resulting in a sharp decline of its populations. Currently, only two known remaining populations of this Critically Endangered species persist in t...

Trachemys is a speciose genus of freshwater turtles distributed from the Great Lakes in North America across the southeastern USA, Mexico and Central America to the Rio de la Plata in South America, with up to 13 continental American species and 11 additional subspecies. Another four species with three additional subspecies occur on the West Indies...

The savannah side-necked turtle Podocnemis vogli is a species restricted to the savannas of the Orinoco basin in Colombia and Venezuela. Because of its apparent abundance, it is currently categorized as Least Concern (LC) by the IUCN Red List. However, throughout its distribution range, several populations have been extirpated or individuals in rem...

Kinosternon is the most speciose genus of extant turtles, with 22 currently recognized species, distributed across large parts of the Americas. Most species have small distributions, but K. leucostomum and K. scorpioides range from Mexico to South America. Previous studies have found discordance between mitochondrial and nuclear phylogenies in some...

Conservation actions for threatened species and populations aim to preserve their genetic diversity and prevent issues such as inbreeding or outbreeding depressions. This perspective has been incorporated into the management plans proposed for the critically endangered Orinoco crocodile (Crocodylus intermedius) in Colombia. A previous study, which...

Dwarf caiman species of the genus Paleosuchus (Paleosuchus palpebrosus and Paleosuchus trigonatus) are old, widespread crocodilian lineages with populations affected by habitat modification. For both species, phylogeographical studies revealing crucial information have already been performed, but for important ecoregions, such as the Orinoco, knowl...

Recovering of Crocodylus intermedius populations in Colombia

A purpose of ex-situ populations is the preservation of genetic variation, but this is a challenging task since genetic diversity is commonly lost through each generation, and so the establishment of management guidelines should be a high priority. Fifty years ago, the National University of Colombia began a breeding program in the Roberto Franco T...

Wide-ranging species are seldom considered conservation priorities, yet they have the potential to harbour genetically deeply differentiated units across environments or ecological barriers, including some that warrant taxonomic recognition. Documenting such cryptic genetic diversity is especially important for wide-ranging species that are in decl...

The Anolis heterodermus group is a complex of lizard species from the highlands of the northernmost South American Andes. We assessed the species diversity of the group using a molecular dataset and a deep morphological study to infer evolutionary relationships within this species group. The analyses identified several unknown evolutionary lineages...

Morphological traits from blood stages have been the gold standard for determining haemos- poridian parasite species. However, the status of some taxa and the value of such traits in para- sites from reptiles remain contentious. The scarce sampling of these species worsens the situation, and several taxa lack molecular data. A survey was performed...

El caimán llanero (Crocodylus intermedius) constituye un auténtico cocodrilo de agua dulce que se distribuye las tierras bajas de la Orinoquia, compartida por Colombia y Venezuela. Durante el primer tercio del siglo pasado (1929-década de los 60) la especie estuvo sometida a una fuerte presión por cacería comercial que la llevó al borde la extinció...

Adeleorinid parasites commonly infect turtles and tortoises in nature. Currently, our knowledge about such parasites is extremely poor. Their characterization is based on morphological and molecular approaches using the 18S rDNA molecular marker. However, there is a limitation with the 18S rDNA due to its slow rate of evolution. For that reason, th...

The New World genus Micrurus contains more than 80 currently recognized species of venomous coral snakes. The taxonomy of the South American M. lemniscatus complex is controversial. Within this group, M. lemniscatus, M. carvalhoi, M. diutius, M. frontifasciatus, and M. helleri have been treated either as distinct species or subspecies of M. lemnisc...

Further to the debate associated with the viability of land-bound mammals being able to colonize remote frontiers by way of long-distance over-water dispersal, observations are documented of monkeys (red howlers, Alouatta seniculus) occupying free-standing trees within a large floating island on the Magdalena River in north-west Colombia. Also, we...

Coral snakes of the genus Micrurus have been recorded as prey of rapacious birds, some mammals and other snakes, but so far not as prey of fishes. The black spotted piranha, Pygocentrus cariba, is an opportunistic predator that feeds mainly on fishes, occasionally on other vertebrates, but has so far not been reported to prey on snakes. Herein, bas...

Thirteen species of Neotropical bats of the genus Micronycteris are currently recognized and are allocated to four subgenera Leuconycteris , Micronycteris , Schizonycteris , and Xenonectes . Despite that, the presence of polyphyletic clades in molecular phylogenies suggests that its diversity is underestimated. Additionally, the incorrect identific...

In northern South America, amphisbaenians are rarely seen among the herpetofauna.Thus, general knowledge about them is very poor. During a herpetological survey in 2012 at Casanare, Colombia, we found two specimens of an unusual Amphisbaena. A third specimen sharing the same morphotype labeled Amphisbaena sp. from Vichada department was found depos...

In northern South America, amphisbaenians are rarely seen among the herpetofauna.Thus, general knowledge about them is very poor. During a herpetological survey in 2012 at Casanare, Colombia, we found two specimens of an unusual Amphisbaena . A third specimen sharing the same morphotype labeled Amphisbaena sp. from Vichada department was found depo...

Haemogregarines (Adeleorina) have a high prevalence in turtles. Nevertheless, there is only one Hepatozoon species described that infects Testudines so far; it is Hepatozoon fitzsimonsi which infects the African tortoise Kinixys belliana. Colombia harbours a great diversity of chelonians; however, most of them are threatened. It is important to ide...

Haemosporida are diverse vector-borne parasites associated with terrestrial vertebrates. Driven by the interest in species causing malaria (genus Plasmodium), the diversity of avian and mammalian haemosporidian species has been extensively studied, relying mostly on mitochondrial genes, particularly cytochrome b. However, parasites from reptiles ha...

A new species of Pristimantis (Craugastoridae, subgenus Pristimantis) is described from a relict and unexplored cloud forest in the western slope from Cordillera Oriental of the Colombian Andes. The specific name was chosen by consensus expert scientists and local people. Pristimantis chamezensis sp. nov. is easily distinguished from congeneric spe...

The Apaporis caiman (Caiman crocodilus apaporiensis) has been of particular interest due to its highly differentiated morphology. However, no molecular research has been done to clarify its taxonomy. We characterized the genetic variation within C. crocodilus by assessing the evolutionary trajectory of Apaporis caiman populations using mitochondria...

Introducción: Recientemente ha tomado relevancia el uso de especímenes de museo como fuente de información genética para desarrollar estudios que resuelven preguntas taxonómicas, ecológicas, demográficas y evolutivas a diversas escalas temporales y geográficas. Sin embargo, material genético obtenido a partir de ejemplares depositados en coleccione...

The matamata is one of the most charismatic turtles on earth, widely distributed in northern South America. Debates have occurred over whether or not there should be two subspecies or species recognized due to its geographic variation in morphology. Even though the matamata is universally known, its natural history, conservation status and biogeogr...

Using different sources of evidence (i.e., integrative taxonomy), we describe a new species of Hyloxalus, Hyloxalus arliensis sp. nov. The new species occurs in the middle Magdalena River valley on slopes between the Cordillera Central and Cordillera Oriental of the Andes of Colombia. Previously, the new species was referred to as Hyloxalus “Ibagué...

Guías etnobiológicas de Colombia es una publicación periódica, que nace como resultado de las investigaciones multidiciplinares del grupo estudiantil "MUI" de la Facultad de Ciencias de la Universidad Nacional de Colombia. El objetivo de estas guías de campo es mostrar la cosmovisión de grupos étnicos y resaltar la importancia de su conservación cu...

The genus Haemocystidium was described in 1904 by Castellani and Willey. However, several studies considered it a synonym of the genera Plasmodium or Haemoproteus. Recently, molecular evidence has shown the existence of a monophyletic group that corresponds to the genus Haemocystidium. Here, we further explore the clade Haemocystidium spp. by study...

Landscape genomic signatures indicate reduced gene flow and forest-associated adaptive divergence in an endangered neotropical turtle Running title: Landscape genomics of a neotropical turtle ABSTRACT Human-induced transformations of ecosystems usually result in fragmented populations subject to increased extinction risk. Fragmentation is also ofte...

Human‐induced transformations of ecosystems usually result in fragmented populations subject to increased extinction risk. Fragmentation is also often associated with novel environmental heterogeneity, which in combination with restricted gene flow may increase the opportunity for local adaptation. To manage at‐risk populations in these landscapes,...

RESUMEN Hasta el momento se ha llevado a cabo un estu-dio en filogenética molecular de la familia Po-docnemididae y varios estudios filogeográficos y de genética de poblaciones para cinco espe-cies. Se presenta una revisión de los principales aportes de estas investigaciones. Los estudios realizados han proporcionado información re-levante enmarcad...

A new species of frog of the genus Hyloxalus from a high Andean forest of the central parts of the Cordillera Oriental, Colombia is recognized and described using integrative taxonomy. Using phylogenetic analyses of 2590 base pairs (bp) of mitochondrial DNA, Hyloxalus felixcoperari sp. nov. was shown to belong to a lineage of the subpunctatus clade...

Population fragmentation is one of the most concerning consequences of habitat fragmentation, as small and isolated populations suffer increased genetic drift and inbreeding. However, the extent to which habitat fragmentation leads to population fragmentation depends not only on the landscape structure, but also on the response of organisms to it....

Studying phylogeographic histories in wide-ranging species provides key insights into those processes shaping current species’ distributions and genetic structuring. In this work, we extend previous sampling and analyse data from three mitochondrial genes to explore in-depth the phylogeography of the spur-thighed tortoise (Testudo graeca), the most...

Supporting Information

Recent studies indicate that hybridization in animals occurs more frequently than previously thought and that it may play an important evolutionary role. Chelonians are capable of extensive hybridization, raising the question how chelonian species evolve and maintain genetic integrity despite hybridization. Here, we use two sister species with para...

For decades, the genus Pelomedusa has been thought of as containing only a single species that is widely distributed in sub-Saharan Africa, the Arabian Peninsula, and Madagascar. However, ten species and up to five candidate species have been recognized recently. For these taxa, ecological information is scarce and distribution ranges are often onl...

The objective of our study was to review and quantify the level of knowledge of the biology of tortoise and freshwater turtle species of Colombia based on studies conducted in the country. We used the resulting rankings in knowledge, in combination with IUCN threat category, presence in protected areas, and endemism, to propose conservation priorit...

Anolis heterodermus is a poorly known, high elevation anole lizard from northern Andes, currently under threat due to habitat destruction. Although it has been suggested that this taxon corresponds to a species complex, different evolutionary lineages have not been identified. We examined phylogenetic relationships between individuals of A. heterod...

Along the Prado River, at southeast of Colombia, there is a population of Podocnemis lewyana, an endemic and endangered river turtle. Relative abundance, population structure and conservation threats were determined using field data obtained in 2007 and 2009. Relative abundance was estimated by turtle catch per unit of time, which was used to compa...

Using nearly range-wide sampling, we analyze up to 1848 bp of mitochondrial DNA of 183 helmeted terrapins and identify a minimum of 12 deeply divergent species-level clades. Uncorrected p distances of these clades equal or clearly exceed those between the currently recognized species of Pelusios, the genus most closely related to Pelomedusa. We cor...

Taxonomía y sistemática Podocenmis lewyana fue descrita por Duméril (1852) con base en tres especímenes sintipo, con la localidad tipo en Santa Fe de Bogotá. Después, Williams (1954) identificó uno de estos sintipos como un ejemplar de la especie Podocnemis vogli, y designó otro de los sintipos remanentes como lectotipo. En una filogenia molecular...

We examined differentiation within the Colombian wood turtle Rhinoclemmys melanosterna, and among R. melanosterna and the closely allied species R. diademata, R. funerea and R. punctularia, based on 1060 base pairs of the mitochondrial cyt b gene. We also assessed the phylogenetic relationships among these species using 2050 bp of mtDNA (partial cy...

Weak genetic divergence between the two South American toad-headed turtles Mesoclemmys dahli and M. zuliae Abstract. Mesoclemmys dahli and M. zuliae are two endangered, little-known toad-headed turtles with small distribution ranges in Colombia and Venezuela, respectively. Using the mitochondrial cytochrome b gene as a marker, we investigate their...

We analyse phylogeny, systematics and biogeography of slider turtles (Trachemys spp.) using sequence data of four mitochondrial genes (3242 bp) and five nuclear loci (3396 bp) of most South American and southern Central American taxa and representatives of northern Central American, West Indian and North American slider species (16 species and subs...

Fritz, U., Alcalde, L., Vargas-Ramírez, M., Goode, E.V., Fabius-Turoblin, D.U. & Praschag, P. (2012). Northern genetic richness and southern purity, but just one species in the Chelonoidis chilensis complex. —Zoologica Scripta, 41, 220–232. The Chelonoidis chilensis complex, the sister group of the famous Galápagos tortoises, is a widely distribute...

Podocnemis lewyana is an endangered endemic river turtle of Colombia. Using ten unlinked polymorphic microsatellite loci and a 691-bp-long DNA fragment corresponding to the more variable portion of the mitochondrial control region, we investigated genetic diversity and population structure throughout its range. Both neutral markers showed extremely...

We re-examine the phylogenetic position of Pelusios williamsi by merging new sequences with an earlier published data set of all Pelusios species, except the possibly extinct P. seychellensis, and the nine previously identified lineages of the closely allied genus Pelomedusa (2054 bp mtDNA, 2025 bp nDNA). Furthermore, we include new sequences of Pe...

We re-examine the phylogenetic position of Pelusios williamsi by merging new sequences with an earlier published data set of all Pelusios species, except the possibly extinct P. seychellensis, and the nine previously identified lineages of the closely allied genus Pelomedusa (2054 bp mtDNA, 2025 bp nDNA). Furthermore, we include new sequences of Pe...

Fritz, U., Branch, W. R., Hofmeyr, M. D., Maran, J., Prokop, H., Schleicher, A., Široký, P., Stuckas, H., Vargas-Ramírez, M., Vences, M. & Hundsdörfer, A. K. (2010). Molecular phylogeny of African hinged and helmeted terrapins (Testudines: Pelomedusidae: Pelusios and Pelomedusa). —Zoologica Scripta, 40, 115–125. With 18 currently recognised species...

By using three different molecular systematic approaches (phylogeny, phylogeography and population genetics) of different turtles groups of the families Podocnemididae, Pelomedusidae and Testudinidae from South America and Africa this study aimed at: (1) reconstructing and revealing among and within species relationships, (2) increasing the knowled...

Using sequence data of the mitochondrial cytochrome b gene, we investigated phylogeographic differentiation of the Amazonian tortoise species Chelonoidis carbonaria and C. denticulata. While C. carbonaria is generally restricted to savannah habitats and adjacent forests, C. denticulata is associated with wet tropical and subtropical forests. Our st...

We investigated the phylogeographic differentiation of the widely distributed African helmeted terrapin Pelomedusa subrufa based on 1503 base pairs of mitochondrial DNA (partial cyt b and ND4 genes with adjacent tRNAs) and 1937 bp of nuclear DNA (partial Rag1, Rag2, R35 genes). Congruent among different analyses, nine strongly divergent mitochondri...

Podocnemis lewyana, the Magdalena River turtle (Family Podocnemididae), is a medium to large-sized river turtle confined to the Sinú, San Jorge, Cauca, and Magdalena river drain-ages in Colombia, making it a biogeographic anomaly, being the only South American podocnemid turtle to occur northwest of the Andes Mountains instead of inhabiting the Ori...

suMMary. – Podocnemis lewyana, the Magdalena River turtle (Family Podocnemididae), is a medium to large-sized river turtle confined to the Sinú, San Jorge, Cauca, and Magdalena river drain-ages in Colombia, making it a biogeographic anomaly, being the only South American podocnemid turtle to occur northwest of the Andes Mountains instead of inhabit...

Known-locality samples of Geoemyda spengleri from three Chinese provinces (Guangdong, Guangxi, Hainan) and northern Vietnam provide clear evidence for phylogeographic structure in a southern Chinese chelonian species. Within southern China two clades of mitochondrial haplotypes from east and west of the Xi Jiang together form the sister group to ha...

This phase aimed at the continuity of the educational program and support of the next step of biological research; collection and assessment of biological information. Its objectives were: 1) - Educational program (EP). To continue with the educational program strategies, engaging a larger percentage of the community of the Prado municipality, Uppe...

The eight extant podocnemidid species are the last survivors of a speciose ancient group of turtles known to have existed since the Cretaceous. One species, representing the monotypic genus Erymnochelys, occurs on Madagascar; the remaining seven species are confined to South America (Peltocephalus: one species; Podocnemis: six species). Phylogeneti...

Podocnemis Lewyana; The Magdalena’s river turtle, is a fresh water threatened-endemic turtle species from the so-called Uraba-Magdalena eco-region in Colombia. It is considered endangered species (EN) in the IUCN red list. It has also been put in Appendix II of the CITES convention. Local fishing communities have been consuming its meat and eggs fo...

The Magdalena River Turtle (Podocnemis lewyana) is a Colom-bian endemic species, endangered due to human exploitation and habitat destruction. To date, this species is poorly known ecologi-cally and data on its genetic diversity are lacking. Here we report on the fi rst genetic survey of the species across its distribution range. We obtained mitoch...

This pilot project aimed at collecting and analyzing preliminary biological and social base information of the Magdalena’s river turtle Podocnemis Lewyana, for the creation and implementation of adequate and coherent actions towards its protection and conservation. The three main goals were: 1) to investigate the genetic variability and examine the...

Herpetológicamente, el Guanía es el departamento menos conocido de Colombia; además, es de interés por su posición geográfica, entre los Llanos y los bosques del Amazonas. Adicionalmente, esta situado en el límite occidental de la región Guyana. Registramos 27 especies de ranas para el departamento (22 de ellas de los alrededores de la comunidad La...

The Eastern limit of the Vichada and Guainía departments of Colombia falls within the Guyana shield and it’s perhaps the least known biotic region of the country. In order to increase the knowledge on the herpetofauna of the region, this study was performed with the following goals: (i) to register the present species of amphibians and reptiles, (i...