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Ruiz-García M, Pinedo-Castro M, Albino A, Arias-Vásquez JY, Castellanos A, Shostell JM. Invalidation of taxa within the silvery wooly monkey ( Lagothrix lagothricha poeppigii, Atelidae, Primates). Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:147-162. [PMID: 32329402 DOI: 10.1080/24701394.2020.1757084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The systematics of the Humboldt's wooly monkeys (L. lagothricha; Atelidae) is essential to preserve this Neotropical primate species. Traditionally, four morphological subspecies have been described, which recently have been molecularly confirmed. However, no population genetics studies have been carried out throughout the geographical distribution of one of these subspecies, Lagothrix lagothricha poeppigii. For this reason, we analyzed nine mitochondrial genes of L. l. poeppigii mainly collected from the Ecuadorian and Peruvian Amazon in order to better understand the evolutionary history of this taxon. The mitochondrial genetic diversity levels (haplotype and nucleotide diversity) we estimated are likely the highest yet reported for L. lagothricha. Our results did not detect important genetic structure within L. l. poeppigii. Furthermore, our phylogenetic analyses did not detect any relevant molecular cluster in the area where Groves hypothesized the existence of L. poeppigii castelnaui. Therefore, based on these data, castelnaui is not a valid taxon from a molecular perspective. The most differentiated subpopulation within L. l. poeppigii was from Morona-Santiago province (Ecuador) and had a genetic distance of 0.8-1.2% relative to the other subpopulations studied. However, this genetic distance range is within the variability found within a population. We estimated the mitochondrial temporal diversification within L. l. poeppigii to have occurred during the Pleistocene, 1.8-1.2 million years ago. Similarly, all our analyses detected a strong Pleistocene female population expansion for this taxon. Diverse spatial genetic analyses, perhaps with the exception of Monmonier's Algorithm, did not detect differentiated taxa within the area analyzed for L. l. poeppigii. These genetics results could be of importance to conservation efforts to preserve this taxon as one unit.
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Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones-Biología Evolutiva. Unidad de Genética. Departamento de Biología. Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.,Instituto Nacional de Biodiversidad (INABIO), Quito, Ecuador
| | - Myreya Pinedo-Castro
- Laboratorio de Genética de Poblaciones-Biología Evolutiva. Unidad de Genética. Departamento de Biología. Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Aymara Albino
- Laboratorio de Genética de Poblaciones-Biología Evolutiva. Unidad de Genética. Departamento de Biología. Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Jessica Yanina Arias-Vásquez
- Laboratorio de Genética de Poblaciones-Biología Evolutiva. Unidad de Genética. Departamento de Biología. Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Armando Castellanos
- Instituto Nacional de Biodiversidad (INABIO), Quito, Ecuador.,Andean Bear Fundation, Quito, Ecuador
| | - Joseph Mark Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, Crookston, MN, USA
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Molecular Phylogenetics of Bradypus (Three-Toed Sloth, Pilosa: Bradypodidae, Mammalia) and Phylogeography of Bradypus variegatus (Brown-Throated Three-Toed Sloth) with Mitochondrial Gene Sequences. J MAMM EVOL 2019. [DOI: 10.1007/s10914-019-09465-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Ruiz-García M, Pinedo-Castro M, Shostell JM. Mitogenomics of the jaguarundi (Puma yagouaroundi, Felidae, Carnivora): Disagreement between morphological subspecies and molecular data. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2018.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Ruiz-García M, Pinedo-Castro M, Shostell JM. Small spotted bodies with multiple specific mitochondrial DNAs: existence of diverse and differentiated tigrina lineages or species (Leopardus spp: Felidae, Mammalia) throughout Latin America. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:993-1014. [PMID: 29157065 DOI: 10.1080/24701394.2017.1404041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We analysed two sets of mitochondrial (mt) DNA data from tigrinas (traditionally, Leopardus tigrinus) we sampled in Costa Rica, Venezuela, Colombia, Ecuador, Peru, Bolivia, northwestern and northeastern Argentina and southern Brazil. Additionally, the analysis included some GenBank sequences from southern, central and northeastern Brazil. The first mt set (mt ATP8+mt 16S rRNA with 41 tigrina) revealed the existence of seven different tigrina-like haplogroups. They could represent, at least, 4-6 different tigrina species following the Phylogenetic Species Concept (PSC). In the second mt set (mitogenomics with 18 tigrinas), we detected six different tigrina-like haplogroups. They could represent 4-5 different tigrina species - including a possible full new species, which has gone previously unnoticed to the world of science both morphologic and molecularly. Coat patterns of several of these different tigrinas support the molecular differences. We also detected intense hybridization in many Andean tigrina with margays (Leopardus wiedii) and ocelots (Leopardus pardalis) as well as hybridization of one Bolivian tigrina with Leopardus geoffroyi. Similar hybridization was found for many of the southern Brazilian tigrina (Leopardus guttulus). All of the temporal split estimates for these tigrina haplogroups, together with those of the Leopardus species recognized to date, began in the late Pliocene but mostly occurred during the Pleistocene. In agreement with the existence of multiple species within the traditional L. tigrinus species, we detected strong and significant spatial structure in the two mt data sets. There were clear circular clines. A major part of the analyses detected more genetic resemblance between the Central American + trans Andean Colombian and Ecuadorian tigrina (L. oncilla) with the most geographically distant tigrina from central and southern Brazil (L. guttulus; pure individuals not hybridized with L. geoffroyi). In comparison, the Andean tigrina taxa had intermediate geographical origins but were highly genetically differentiated both from the Central American + trans Andean Colombian-Ecuadorian tigrina and from the central and southern Brazilian tigrina.
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Affiliation(s)
- Manuel Ruiz-García
- a Departamento de Biología, Facultad de Ciencias , Laboratorio de Genética de Poblaciones-Biología Evolutiva, Unidad de Genética, Pontificia Universidad Javeriana , Bogotá , Colombia
| | - Myreya Pinedo-Castro
- a Departamento de Biología, Facultad de Ciencias , Laboratorio de Genética de Poblaciones-Biología Evolutiva, Unidad de Genética, Pontificia Universidad Javeriana , Bogotá , Colombia
| | - Joseph Mark Shostell
- b Math, Science and Technology Department , University of Minnesota Crookston , Crookston , MN , USA
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Luna-Marín KP, Angulo-Silva VM, Hernández-Torres J, Ruiz-García M. Genetic Relationships and Spatial Genetic Structure Among Populations of Rhodnius prolixus (Hemiptera: Reduviidae) in Colombia and Venezuela Based on Mitochondrial Cytochrome-b Sequences. NEOTROPICAL ENTOMOLOGY 2017; 46:341-355. [PMID: 27889871 DOI: 10.1007/s13744-016-0470-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 11/15/2016] [Indexed: 06/06/2023]
Abstract
One hundred twenty Rhodnius prolixus (Stal) (Hemiptera: Reduviidae) specimens from 6 Colombian Departments and 1 Venezuelan State had 594-bp of the mitochondrial cytochrome-b gene sequenced to improve the understanding of evolutionary processes that shape the main vector of Chagas disease. The levels of genetic diversity for this species were low-medium with reference to other bugs. The genetic heterogeneity among the populations was very limited which means there has been extensive gene flow and/or very recent split processes. The overall sample as well as some individual populations showed evidence of recent population expansions (with the exception of Arauca, which yielded evidence of a bottleneck for a mismatch distribution). This expansion (11,000 or 2000-25,000 year ago depending of two procedures employed) coincides with the ending of the last intense glacial conditions during the Pleistocene and the beginning of the Holocene that had a warmer and wetter climate. Some of our autocorrelation analyses (AIDA and Genetic Landscape Interpolation Analysis) indicated local patches of high genetic similarity but no globally significant spatial structure. We did show an original haplotype distributed throughout the entirety of the geographical area studied.
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Affiliation(s)
- K P Luna-Marín
- Centro de Investigaciones en Enfermedades Tropicales (CINTROP), Univ Industrial de Santander (UIS), Bucaramanga, Colombia
- Lab de Genética de Poblaciones Molecular y Biología Evolutiva, Unidad de Genética, Depto de Biología, Facultad de Ciencias, Pontificia Univ Javeriana, Cra 7ª No 43-82, Bogotá, DC, Colombia
| | - V M Angulo-Silva
- Centro de Investigaciones en Enfermedades Tropicales (CINTROP), Univ Industrial de Santander (UIS), Bucaramanga, Colombia
| | - J Hernández-Torres
- Lab de Biología Molecular (CINBIN), Escuela de Biología, Univ Industrial de Santander (UIS), Bucaramanga, Colombia
| | - M Ruiz-García
- Lab de Genética de Poblaciones Molecular y Biología Evolutiva, Unidad de Genética, Depto de Biología, Facultad de Ciencias, Pontificia Univ Javeriana, Cra 7ª No 43-82, Bogotá, DC, Colombia.
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PEÑA-CRUZ AF, SANDOVAL ARANGO S, PATIÑO MONTOYA A, BEDOYA M, RODRÍGUEZ ORTIZ A, ORJUELA VASQUEZ J, ORTEGA A, F. LÓPEZ J, MOLINA HENAO E, GUZMÁN A, GIL J, CÁRDENAS HENAO H. Genetic Analysis of the Cat Population of North and South of Cali, Colombia. ACTA BIOLÓGICA COLOMBIANA 2014. [DOI: 10.15446/abc.v20n1.41610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Brochero H, Li C, Wilkerson R, Conn JE, Ruiz-García M. Genetic structure of Anopheles (Nyssorhynchus) marajoara (Diptera: Culicidae) in Colombia. Am J Trop Med Hyg 2010; 83:585-95. [PMID: 20810825 DOI: 10.4269/ajtmh.2010.09-0482] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Five Anopheles marajoara Galvão and Damasceno populations, representing diverse ecological conditions, were sampled throughout Colombia and analyzed using nine hypervariable DNA microsatellite loci. The overall genetic diversity (H = 0.58) was lower than that determined for some Brazilian populations using the same markers. The Caquetá population (Colombia) had the lowest gene diversity (H = 0.48), and it was the only population at Hardy-Weinberg equilibrium. Hardy-Weinberg disequilibrium in the remaining four populations was probably caused by the Wahlund effect. The assignment analyses showed two incompletely isolated gene pools separated by the Eastern Andean cordillera. However, other possible geographical barriers (rivers and other mountains) did not play any role in the moderate genetic heterogeneity found among these populations (F(ST) = 0.069). These results are noteworthy, because this species is a putative malaria vector in Colombia.
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Affiliation(s)
- Helena Brochero
- Laboratorio de Entomología, Instituto Nacional de Salud, Bogotá DC, Colombia
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Ruiz-Garcia M, Payán E, Murillo A, Alvarez D. DNA microsatellite characterization of the jaguar (Panthera onca) in Colombia. Genes Genet Syst 2006; 81:115-27. [PMID: 16755135 DOI: 10.1266/ggs.81.115] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Colombian jaguar population is thought to contain two different subspecies, Panthera onca centralis and Panthera onca onca. The genetic structure of this population was evaluated using 12 microsatellite loci (n = 62 samples). In addition, 22 jaguar DNA samples from Guatemala, Paraguay, Perú, Bolivia, Venezuela and Brazil were analyzed for these microsatellite loci (n = 84 samples). The results of this study indicate six primary themes. First, the levels of gene diversity were very high. Second, the majority of the loci analyzed showed an absence of Hardy-Weinberg equilibrium, probably due to the Wahlund effect (= population subdivision). Third, several microsatellite loci showed significant heterogeneity between the two supposed subspecies in the country. Nevertheless, gene flow was present between them, and heterogeneity was relatively low, although the assignment analyses showed good classification of the jaguars studied into their respective subspecies. Fourth, the long-term historical effective population sizes were calculated through a maximum likelihood procedure for single and multi-step mutation models. Fifth, seven out of twelve DNA microsatellites studied significantly deviated from a single-step mutation model. However, the overall mean multi-step mutation percentage for these 12 DNA microsatellites was only 6%. Therefore, 94% of mutations were uni-step. Sixth, no bottleneck events were detected in the Colombian jaguar population overall.
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Affiliation(s)
- Manuel Ruiz-Garcia
- Laboratory of Molecular Population Genetics (Grupo de Genética de Poblaciones-Biología Evolutiva), Unidad de Genética, Departamento de Biología. Facultad de Ciencias, Pontificia Universidad Javeriana, Colombia.
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Ruiz-García M, Orozco-terWengel P, Castellanos A, Arias L. Microsatellite Analysis of the Spectacled Bear (Tremarctos ornatus) Across its Range Distribution. Genes Genet Syst 2005; 80:57-69. [PMID: 15824457 DOI: 10.1266/ggs.80.57] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA samples of the spectacled bear (Tremarctos ornatus) from five Andean countries, Venezuela, Colombia, Ecuador, Peru and Bolivia, were analyzed for nine microsatellite loci. Seven of them were polymorphic, which led us to investigate several population-genetic parameters. Private alleles and significant differences in gene frequencies were found among the populations studied, which demonstrated the extent of genetic differentiation among the spectacled bear populations. The levels of gene diversity measured with these microsatellites were rather modest in this species. Hardy-Weinberg disequilibrium was especially found for the overall and the Ecuadorian samples, and might be due to the Wahl-und effect or consanguinity. Significant genetic heterogeneity was mainly observed among the Colombian and the Ecuadorian populations. Markov chain Monte Carlo simulations clearly showed that two different gene pools were present, one present in the Venezuelan-Colombian bears and other in the Ecuadorian ones.
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Affiliation(s)
- Manuel Ruiz-García
- Laboratory of Molecular Population Genetics (Grupo de Genética de Poblaciones-Biología Evolutiva), Unidad de Genética, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogota DC, Colombia
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Ruiz-Garcia M. Molecular population genetic analysis of the spectacled bear (Tremarctos ornatus) in the northern Andean area. Hereditas 2004; 138:81-93. [PMID: 12921159 DOI: 10.1034/j.1601-5223.2003.01578.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Eighty-two Andean bear samples obtained in three South American Andean countries were analyzed using five hypervariable microsatellite markers. Neither the overall sample nor the samples coming from each of the countries analyzed were in Hardy-Weinberg equilibrium. This is attributable to the Wahlund effect caused by a fragmentation of the bear populations. The genetic variability levels found were in general low for this kind of molecular markers (H = 0.38 for the global population). The situation of the Ecuadorian bear population seems to be endangered (H = 0.24). This is the lowest level recorded for any bear population. The genetic heterogeneity among the three populations was large and highly significant (F(ST) = 0.39; R(ST) = 0.32-0.49). Likewise, the gene flow estimates were remarkably low among these populations (Nm = 0.2-0.3). This means that the populations are strongly isolated. Different methods were applied to determine the effective numbers in these populations. A significant spatial structure of the genotypes was analyzed with different procedures. In all cases, an isolation-by-distance structure was detected. This could be a consequence of the original South America colonization. There was no evidence for a recent genetic bottleneck. This could mean that the low heterozygosity and the population fragmentation could be explained by ancient events related to the bear colonization, with the arrival of humans beings in the Americas, and/or with the glacial maximum, 16.000-30.000 years ago.
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Affiliation(s)
- Manuel Ruiz-Garcia
- Unidad de Genètica, Departamento de Biología, Facultad de Ciencias, Pontifica Universidad Javeriana, Bogotá DC, Colombia.
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Say L, Bonhomme F, Desmarais E, Pontier D. Microspatial genetic heterogeneity and gene flow in stray cats (Felis catus L.): a comparison of coat colour and microsatellite loci. Mol Ecol 2003; 12:1669-74. [PMID: 12755894 DOI: 10.1046/j.1365-294x.2003.01824.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We analysed levels of genetic differentiation between nine local urban colonies of stray cats using eight coat colour and nine microsatellite loci. Both types of markers revealed a strong differentiation between colonies (FST = 0.15 and 0.09 for coat colour and microsatellite loci, respectively). Three coat colour loci showed extreme levels of genetic differentiation comparatively to other loci and are strongly suspected to be under divergent selective pressures. Microsatellite loci showed significant heterozygote deficiency within colonies (FIS = 0.14), suggesting that coat colour loci are not appropriate to investigate genetic structure at a fine scale because coat colour allele frequencies are based on Hardy-Weinberg equilibrium. The reported pattern conformed to that predicted from the social structuring of cat colonies: aggressive exclusion of immigrants, inbreeding and very low dispersal rate.
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Affiliation(s)
- Ludovic Say
- UMR-CNRS 5558 'Biométrie et Biologie évolutive', Université Claude Bernard Lyon I, 43, boulevard du 11 novembre 1918, 69622 Villeurbanne, France
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Ruiz-Garcia M, Montilla M, Nicholls S, Alvarez D. Population genetic analysis of Colombian Trypanosoma cruzi isolates revealed by enzyme electrophoretic profiles. Mem Inst Oswaldo Cruz 2001; 96:31-51. [PMID: 11285474 DOI: 10.1590/s0074-02762001000100005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
Although Colombia presents an enormous biological diversity, few studies have been conducted on the population genetics of Trypanosoma cruzi. This study was carried out with 23 Colombian stocks of this protozoa analyzed for 13 isoenzymatic loci. The Hardy-Weinberg equilibrium, the genetic diversity and heterogeneity, the genetic relationships and the possible spatial structure of these 23 Colombian stocks of T. cruzi were estimated. The majority of results obtained are in agreement with a clonal population structure. Nevertheless, two aspects expected in a clonal structure were not discovered in the Colombian T. cruzi stocks. There was an absence of given zymodemes over-represented from a geographical point of view and the presumed temporal stabilizing selective phenomena was not observed either in the Colombian stocks sampled several times through the years of the study. Some hypotheses are discussed in order to explain the results found.
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Affiliation(s)
- M Ruiz-Garcia
- Unidad de Genética (Genética de Poblaciones-Biología Evolutiva), Departamento de Biologia, Facultad de Ciencias, Pontifica Universidad Javerina, Bogotá DC, Colombia.
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Ruiz-Garcia M. Genetic microstructure in two Spanish cat populations. II: gametic disequilibrium and spatial autocorrelation. Genes Genet Syst 2000; 75:281-92. [PMID: 11245221 DOI: 10.1266/ggs.75.281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In a previous publication, we described some aspects of the microgenetic structure of two Spanish cat populations (in Barcelona and Alicante). In the present study, the possible existence ofgametic disequilibrium and spatial genetic structure for these populations, at the coat colour pattern and length genes O, A, T D, L, S and W, was analyzed. There was little gametic disequilibrium between pairs of these loci, despite certain pairs that showed significant systematic gametic disequilibrium (a-d and O-S), which appears to show the action of natural selection on domestic cat populations. Nevertheless, we believe that the major cause of the small amount of gametic disequilibrium found was probably a combination of gene drift and gene flow. The results obtained here were clearly in disagreement with those of Hedrick (1985), who concluded that epistatic selection was the cause of the gametic disequilibrium that he found in cat populations. We also found that although Hardy-Weinberg equilibrium could not be demonstrated, the gametic disequilibrium statistics were not affected by this fact, adding credence to the estimates obtained. We found no genetic spatial structure inside the city of Barcelona, as shown by analysis of the spatial autocorrelation of the individual loci, and analysis of the coordinates of the two first axes of a multidimensional scale. However, some gametic disequilibrium statistics showed certain spatial patterns, which leads us to consider the possibility of several evolutionary processes acting upon some of Barcelona's cat colonies.
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Affiliation(s)
- M Ruiz-Garcia
- Unidad De Genetica (Biologia Evolutiva), Departamento De Biologia, Facultad De Ciencias, Pontificia Universidad Javeriana, Bogota DC Colombia.
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