Ivan Dario Soto-Calderón

• BSc. Biol, MSc, PhD
• Associate Professor at University of Antioquia

Progress in the acquisition of massive sets of molecular data and in the bioinformatic capabilities for their processing have revolutionised species identification, filling gaps in crucial areas such as taxonomy, phylogenetic inference, biogeography, and even biodiversity conservation. Advanced DNA sequencing and metabarcoding have uncovered previo...

High levels of species diversity and endemism in developing countries contrast with a dramatic expansion of human populations and urban development. This poses a challenge for wildlife and their ability to adapt to transformed and fragmented habitats. In the Neotropics, tamarins and marmosets (Primates: Callitrichidae) have established populations...

Trypanosomes are blood parasites capable of infecting nearly any vertebrate. Many Neotropical primates frequently host trypanosomes and are considered potential reservoirs for Trypanosoma cruzi and other human-pathogenic trypanosomatids. However, diagnostic methods originally developed for detecting these trypanosomatids in humans and domestic spec...

Conservation genetics is the use of genetics to understand and mitigate the threats caused by anthropogenic activities, including habitat loss and fragmentation, wildlife trafficking, and emerging diseases. In this review, we discuss the role of primate conservation genetics in the development of effective conservation strategies, emphasizing the i...

Until now, phylogenetic relationships for the genus Calliandra section Androcallis (Fabaceae) were unresolved. We reconstructed the phylogeny of the section, including previously sequenced species from Central and South America and unexamined species from Colombia. Here, we generated 80 novel DNA sequences of Calliandra species from Colombia for th...

The common opossum ( Didelphis marsupialis ) is a marsupial widely distributed in the Neotropics, where it lives in urbanized environments. The apparent scarcity and fragmentation of available habitat, and high rates of vehicle collisions, may represent barriers to dispersal. To assess the functional connectivity of this species and its potential u...

The common opossum is a marsupial widely distributed in the Neotropics, where it lives in urbanized environments. The apparent scarcity and fragmentation of available habitat, and high rates of vehicle collisions, may represent barriers to dispersal. To assess the functional connectivity of this species and its potential use as a model in urban eco...

Phylogenetic relationships for the genus Calliandra section Androcallis (Fabaceae) were reconstructed, including previously sequenced species from Central and South America and unexamined species from Colombia, one of Calliandra main diversity centers. Here, we generated novel DNA sequences of Calliandra species from Colombia for the nuclear Intern...

This chapter presents an overview of the general characteristics of the Nancy Ma’s owl monkey (Aotus nancymaae) and a case study where we explore the genetic composition of wild populations in northern Peru and its genetic representation in an ex situ population. The species has historically been heavily exploited for biomedical research. On the Co...

During the last century, the critically endangered cotton‐top tamarin ( Saguinus oedipus ) has been threatened by multiple anthropogenic factors that drastically affected their habitat and population size. As the genetic impact of these pressures is largely unknown, this study aimed to establish a genetic baseline with the use of temporal sampling...

High levels of species diversity and endemism in developing countries contrast with high rates of human population expansion and urban development. This poses a challenge for wildlife and their ability to adapt to transformed and fragmented habitats. In the Neotropics, tamarins and marmosets (Primates: Callitrichidae) have established populations i...

The tropical dry forest is one of the world's most threatened ecosystems and is the habitat of the Robinson's Mouse Opossum (Marmosa robinsoni), a small marsupial within the Didelphidae family. This study aimed to describe cases of cuterebriases in free-ranging M. robinsoni by examining individuals caught in live animal traps. Sherman traps were de...

The sabaleta, Brycon henni, is a medium-size fish species found in the Andean range of the Magdalena-Cauca river basin in Colombia, where it is a fishery resource. Recruitment of sabaleta has affected construction of dams with unknown consequences on its genetic diversity and structure. Understanding the current genetic architecture in the dam-infl...

The Barcode of Life initiative was originally motivated by the large number of species, taxonomic difficulties and the limited number of expert taxonomists. Colombia has 1,610 freshwater fish species and comprises the second largest diversity of this group in the world. As genetic information continues to be limited, we constructed a reference coll...

Despite the wide distribution of the red howler monkey in Colombia, wild populations are affected by hunting, trafficking, and habitat fragmentation. The diversity and current genetic structure of the species were studied in Otún Quimbaya Fauna and Flora Sanctuary and other regions across northern-central Colombia using noninvasive methods. Genetic...

Aunque la amplificación del gen Helicasa con Cromodominio de Unión a ADN (CHD) ha sido usado para inferir el sexo en guacamayas a partir de sangre y plumas, el uso de muestras no invasivas ha sido poco explorado. Aquí optimizamos un protocolo completo de identificación molecular del sexo en guacamayas (Ara spp.) a partir de muestras de sangre, plum...

The Barcoding was proposed motivated by the mismatch between the low number of taxonomists that contrasts with the large number of species, the method requires the construction of reference collections of DNA sequences that represent existing biodiversity. Freshwater fishes are key indicators for understanding biogeography around the world. Colombi...

Habitat loss and fragmentation, illegal trade, and other anthropogenic activities cause the population decline of wild species including primates. The white-footed tamarin (Saguinus leucopus) is highly affected by habitat loss and illegal traffic in northwest Colombia. Few studies have been carried out on the species levels of genetic diversity and...

Studbooks are databases of individual genealogical records of ex situ populations. Since they are an essential tool in management and planning, we conducted a search of studbook reports to explore historical trends in breeding programs of Neotropical primates and implications for ex situ conservation. We accessed two databases: one made by the Worl...

The great diversity of species in urban centers in Colombia contrasts with the rapid and intense degradation of the habitats where this diversity occurs. Given the importance of these environments for urban biological conservation and the increasing pressure on them, we studied the composition of the mammal community in the basin of La Gómez creek,...

Background: Two biotypes of Aberdeen Angus cattle breed, known as Old Type and New Type, that differ in their origin and beef production are formally recognized. In Colombia, this breed has been commercialized for approximately 80 years. Studies on the origin, kinship and levels of genetic diversity of this breed in Colombian herds are scarce, yet...

http://repository.humboldt.org.co/handle/20.500.11761/35544 En la versión del “Atlas de la biodiversidad de Colombia. Primates” publicado el pasado 24 de julio de 2020 se omitieron los nombres de dos autores: Nelson Fabián Galvis Ramírez y Lina María Valencia. Pedimos disculpas por este error, tanto a los autores como a los lectores. Las especies d...

This article is intended for inclusion in the Special Issue on Primate Hybridization and Hybrid Zones. It was however published in a separate issue, Volume 39 Issue 6 and is available at 10.1007/s10764-018-0044-8.

Incomplete reproductive isolation and hybridization is relatively frequent in primates. However, no cases of hybridization between formally recognized species have been reported in tamarins (genus Saguinus), a highly specious group of Neotropical primates. Here, we provide evidence from different sources to demonstrate three cases of hybridization...

An automated multiplex PCR assay of 10 polymorphic microsatellite loci was optimized here in Senepol bovine cattle. Allele frequencies were estimated for Colombian herds. The power of this set of markers for parentage and kinship analyses was also tested. Population genetic parameters, combined probability of identity (CPI) and combined probabiliti...

Among primates, the Neotropical Callitrichid monkeys (tamarins and marmosets) exhibit a particular ability to adapt to disturbed and urbanized environments. However, little is known about physiological and health status in contrasting ecological contexts. An example of adaptation to urban environments is the white-footed tamarin (Saguinus leucopus)...

Along with howler and capuchin monkeys, white-footed tamarins are the most smuggled primates in North-West Colombia. This is reflected by the large number of confiscated animals and releases into the wild, whose effect on the historical population genetic structure of the species is unknown. We thus aimed to assess natural levels of genetic variati...

Although captive populations of western gorilla have been maintained in the United States for over a century, little is known about the geographic origins and genetic composition of the current zoo population. Furthermore, although previous mitochondrial analyses have shown that free-range gorilla populations exhibit substantial regional differenti...

El tití gris (Saguinus leucopus) es un primate catalogado En Peligro de extinción por la Unión Internacional para la Conservación de la Naturaleza (UICN). Sin embargo, el género Saguinus exhibe cierta plasticidad adaptativa a parches de bosques perturbados y zonas urbanas. El tití gris fue descrito por primera vez en jurisdicción de Medellín donde...

El tití gris, Saguinus leucopus, es un primate endémico y amenazado de Colombia. Aunque el holotipo de la especie fue descrito por Günther en 1876 en jurisdicción de Medellín, el rápido e intenso desarrollo urbano ha diezmado considerablemente las poblaciones en la región y constreñido la distribución geográfica de la especie. A pesar de esto aún a...

El tití gris (Saguinus leucopus – Callitrichidae) es un primate endémico colombiano que se encuentra en Peligro (EN) (UICN) debido a la pérdida del hábitat y la extracción ilegal. Pocos estudios se han realizado sobre los niveles de diversidad y distribución de la composición genética, fundamentales para entender la historia natural y definir linea...

El estudio de individuos en cautiverio de primates Neotropicales ha permitido conocer aspectos básicos de su biología. Sin embargo las condiciones medioambientales pueden determinar diferencias ecológicas y fisiológicas en poblaciones silvestres. En el caso del tití gris (Saguinus leucopus), primate endémico colombiano, diferentes parámetros fisiol...

The Western and Eastern species of gorillas (Gorilla gorilla and Gorilla beringei) began diverging in the mid-Pleistocene, but in a complex pattern with ongoing gene flow following their initial split. We sequenced the complete mitochondrial genomes of 1 Eastern and 1 Western gorilla to provide the most accurate date for their mitochondrial diverge...

While much of the natural history of Neotropical primates has been revealed through studies conducted in captive individuals, environmental factors may impose ecological and physiological differences in free-range populations. For the white-footed tamarin (Saguinus leucopus), a primate endemic to Northwest Colombia, physiological parameters that ha...

El tití gris (Saguinus leucopus; Cebidae, Callitrichinae) es uno de los primates americanos con más estrecha distribución, siendo endémico del noroeste Colombiano. Aunque se encuentra en Peligro (UICN) debido a la pérdida del hábitat y la extracción ilegal, poco se sabe sobre los niveles de diversidad y distribución de la composición genética, fund...

El gorila occidental de tierras bajas (Gorilla gorilla gorilla) presenta marcada estructura genética donde los diferentes haplogrupos mitocondriales exhiben distribución geográfica restringida. Los gorilas presentes actualmente en zoológicos estadounidenses descienden de gorilas occidentales salvajes capturados entre 1820s y 1970s y aunque presenta...

Wild western lowland gorillas (Gorilla gorilla gorilla) exhibit strong population genetic structure across much of their natural range and mitochondrial haplogroups are geographically well defined. Western gorillas currently present in North American zoos all show high levels of genetic diversity. Captive gorillas in the USA are descended from free...

The White-footed tamarin (Saguinus leucopus) is an endangered species endemic to North-west Colombia. Although there is an ongoing conservation plan, there has not been any systematic study of the population structure, ecological interactions or natural history of this species. This study aims to identify the most prevalent blood and fecal parasite...

Although nuclear copies of mitochondrial DNA (numts) can originate from any portion of the mitochondrial genome, evidence from humans suggests that more variable parts of the mitochondrial genome, such as the mitochondrial control region (MCR), are under-represented in the nucleus. This apparent deficit might arise from the erosion of sequence iden...

https://scholarworks.uno.edu/td/1510/ The mitochondrial control region (MCR) has played an important role as a population genetic marker in many taxa but sequencing of complete eukaryotic genomes has revealed that nuclear integrations of mitochondrial DNA (numts) are abundant and widespread across many taxa. If left undetected, numts can inflate mi...

Por medio del análisis de marcadores genéticos del cromosoma Y, se estudió la composición de los linajes y su distribución en los apellidos más comunes en una muestra de 471 hombres provenientes del municipio de Marinilla (Antioquia) y su zona de influencia y del municipio de Aranzazu (Caldas), y en un grupo de muestras de la población general de M...

Using Y chromosome genetic markers we studied the lineage composition and distribution in the most common surnames in 471 males from the municipality of Marinilla and its zone of influence, the municipality of Aranzazu (department of Caldas) and a group of samples from the general population of Medellin (Antioquia). Despite a variable rate of coanc...

Estimates of genetic divergence are essential for understanding species’ biogeography and taxonomy. The use of such data from mitochondrial DNA (mtDNA) in addressing questions of the evolutionary history of gorillas has lagged behind other great apes, in part because of the prevalence of mitochondrial pseudogenes (“numts”). We determined the comple...

Although nuclear copies of mitochondrial DNA (numts) can originate from any portion of the mitochondrial genome, evidence from humans suggests that more variable parts of the mitochondrial genome, such as the mitochondrial control region (MCR), are under-represented in the nucleus. This apparent deficit might arise from the erosion of sequence iden...

Nuclear copies of mitochondrial DNA (mtDNA), also known as numts, are widely distributed in the genomes of primates at levels that seem to surpass those in other mammalian orders. Sequencing of the human genome has shown that numts can originate from any portion of the mitochondrial genome but it also uncovered an apparent under-representation of n...

The present study set out to evaluate cross-species amplification of 34 bovid microsatellites in six central African duikers: Cephalophus callipygus, C. monticola, C. silvicultor, C. nigrifrons, C. dorsalis and C. leucogaster. Of these loci, 16 amplified across all species and appeared polymorphic when initially tested in polyacrylamide gel electro...

Nuclear integrations of mitochondrial DNA (numts) are widespread among eukaryotes, although their prevalence differs greatly among taxa. Most knowledge of numt evolution comes from analyses of whole-genome sequences of single species or, more recently, from genomic comparisons across vast phylogenetic distances. Here we employ a comparative approac...

The mitochondrial control region (MCR) has played an important role as a population genetic marker in many taxa. However, inadvertent amplification of nuclear integrations of mitochondrial DNA (NUMTs) can inflate estimates of mitochondrial diversity and mislead phylogenetic and population genetic analyses. NUMTs are thought to integrate by non-homo...

The present study compares the effect of three storage media (silica, RNAlater®, ethanol) and time to extraction (1 week, 1 month and 3 months) on mitochondrial and nuclear marker amplification success in faecal DNA extracts from a sympatric community of small to medium-sized Central African forest ungulates (genera Cephalophus, Tragelaphus, Hyemos...

The standardized use of mitochondrial cytochrome c oxidase subunit I (COI) gene sequences as DNA barcodes has been widely promoted as a high-throughput method for species identification and discovery. Species delimitation has been based on the following criteria: (1) monophyletic association and less frequently (2) a minimum 10x greater divergence...

Mitochondrial DNA (mtDNA) has traditionally been the main source of data for population genetics and molecular systematics studies of mammalian populations. However, sequencing of complete eukaryotic genomes has called to attention the abundance and widespread distribution of nuclear copies of mitochondrial DNA (numts) that can potentially confound...

Surname frequency (isonymy) is used as a marker of paternal lineage and is used to characterize human population structure. Principles of isonymy were used to determine the genetic structure, migration rates, ancestry relations and origins of populations. This analysis was applied to two historically related local populations which currently are co...

Introducción. La utilización de la frecuencia de apellidos como marcadores de linajes paternos ha permitido caracterizar poblaciones. Los principios de isonimia se han empleado para determinar el grado de estructuración genética, las tasas de migraciones y las relaciones de ancestría y origen entre poblaciones. Este análisis se aplicó a dos poblaci...

Although it is well established that Hispanics generally have a mixed Native American, African, and European ancestry, the dynamics of admixture at the foundation of Hispanic populations is heterogeneous and poorly documented. Genetic analyses are potentially very informative for probing the early demographic history of these populations. Here we e...

En la región noroccidental de Colombia se encuentra localizada la población Paisa, la cual fue fundada mediante un fuerte proceso de mestizaje a mediados del siglo XVII y creció en relativo estado de aislamiento que ha determinado la formación de una cultura claramente diferenciable. Como consecuencia de dicho proceso demográfico, fueron introducid...

Diferentes estudios sugieren que ciertas regiones de Antioquia han estado aisladas geográficamente, desde su fundación en la colonia, hasta principios del siglo XX. La información existente sobre MZI, uno de los núcleos principales de poblamiento en Antioquia, es incipiente e incluso anecdótica. A pesar de que se cuenta con variosestudios histórico...

We recently used Y-chromosome and mtDNA markers to assess the ethnic background of the population of Antioquia in North West Colombia. This population has a history of isolation and since its founding in the 16th-17th centuries has expanded over a thousand times (to a current size of about 3-4 million). A Native American ancestry was detected in ab...

We are conducting genetic mapping studies in the populations of the Central Valley of Costa Rica (CVCR) and of Antioquia (Colombia). These two populations were established in the 16-17th centuries mostly by the admixture of a small number of Spanish and Native Americans founders. Since their establishment these two populations have remained relativ...

Objectives: To characterize a sample of families and trios from an isolated colombian population, in order to map loci involved in vulnerability to Bipolar Mood Disorder type-I (BD-I). Methods: Trios and pedigrees using FIGS-DIGS interviews to family members and possibly affected were collected. Power to detect linkage (PDL) was estimated by simula...

To evaluate sex-specific differences in gene flow between Native American populations from South America and between those populations and recent immigrants to the New World, we examined the genetic diversity at uni- and biparental genetic markers of five Native American populations from Colombia and in published surveys from native South Americans...

Historical and genetic evidences suggest that the recently founded population of Antioquia (Colombia) is potentially useful for the genetic mapping of complex traits. This population was established in the 16th-17th centuries through the admixture of Amerinds, Europeans, and Africans and grew in relative isolation until the late 19th century. To ex...

The short variant of a functional length polymorphism in the promoter region of the serotonin transporter has been associated with several behavioural and psychiatric traits, including bipolar mood disorder. The same short allele has also been implicated as a modifier of the bipolar phenotype. Here we evaluate the etiologic/modifier role of this po...

In order to examine mtDNA diversity in Colombian Amerinds we performed a combined RFLP and D-loop sequence analysis of 73 individuals from 17 Native populations. In each sample we collected sequence data for D-loop hypervariable segments 1 and 2 and typed 5 RFLPs (the 4 sites diagnostic of lineages A to D and the HaeIII site at position 16,517). Th...

We have examined the frequency of a functional length polymorphism in the promoter region of the serotonin transporter (5-HTTLPR) in a case/control sample for bipolar mood disorder type 1. Patients (N=98) and controls (N=104) were collected from the isolated population of Antioquia, Colombia. Cases were evaluated using the Diagnostic Interview for...

To evaluate the proposed higher migration rate of females throughout human evolution (Nat. Genet. 20: 270, 1998)we examined the level of within and between population diversity in 5 Colombian Native American populations. Markers examined included: mtDNA (5 RFLPs), autosomal (11 microsatellites, 5 beta globin gene cluster RFLPs and the MHC DQA1 locu...

We have examined the frequency of a functional length polymorphism in the promoter region of the serotonin transporter (5-HTTLPR) in a case/control sample for bipolar mood disorder type 1. Patients (N=98) and controls (N= 104) were collected from the isolated population of Antioquia, Colombia. Cases were evaluated using the Diagnostic Interview for...