scholarly journals Phylogeography of Rhinella spinulosa (Anura: Bufonidae) in northern Chile

2010 ◽  
Vol 31 (1) ◽  
pp. 85-96 ◽  
Author(s):  
Luis Pastenes ◽  
Michel Sallaberry ◽  
Claudio Correa ◽  
Alberto Veloso ◽  
Marco Méndez
Keyword(s):  
Mitochondrial Control Region ◽  
Phylogeographic Structure ◽  
Demographic Expansion ◽  
The Andes ◽  
Haplotype Networks ◽  
Extreme North ◽  
High Degree ◽  
Geologic Activity ◽  
Mismatch Distributions ◽  
Entire Distribution

AbstractThe southern part of the Altiplano of the Andes Range is characterized by a complex hydrography, due to an intense geologic activity and the effects of the Pleistocene glaciations. This has produced a high degree of diversity at the species level in some aquatic taxa (e.g., fish and amphibians), which suggests that these same processes have produced divergence at the intraspecific level in co-distributed taxa. We investigated the genetic variation in populations of the anuran Rhinella spinulosa which represent its entire distribution in the extreme north of Chile (17°44′S-23°47′S). Haplotype networks of the mitochondrial control region recognized two main lineages, one of which is distributed from the northern boundary of Chile to the Salar de Alconcha and the other from the Salar de Carcote to the locality of Tilomonte. The northern lineage showed little phylogeographic structure; a few very frequent haplotypes are widely distributed. The southern lineage had greater structure, due principally to the high divergence of the populations from the eastern springs of the Salar de Atacama. Fu's Fs test and the mismatch distributions suggested that most of the populations of both lineages are in the process of demographic expansion. The spatial distribution of the genetic variability was correlated with the hydrography and the paleoclimatological data available for the region, which suggested that geographic expansions followed by periods of contraction of population ranges, together with sporadic floods may explain the observed phylogeographic patterns.

scholarly journals Multiple drainage reversal episodes and glacial refugia in a Patagonian fish revealed by sequenced microsatellites

2020 ◽  
Vol 287 (1928) ◽  
pp. 20200468 ◽  
Author(s):  
Daniel E. Ruzzante ◽  
Annie P. Simons ◽  
Gregory R. McCracken ◽  
Evelyn Habit ◽  
Sandra J. Walde
Keyword(s):  
Glacial Refugia ◽  
Phylogeographic Structure ◽  
Glacial Cycles ◽  
Multiple Systems ◽  
Biogeographic Patterns ◽  
The Andes ◽  
The Pacific ◽  
Historical Processes ◽  
Microsatellite Dna Markers ◽  
Analytical Approaches

The rise of the southern Andes and the Quaternary glacial cycles influenced the landscape of Patagonia, affecting the phylogeographic and biogeographic patterns of its flora and fauna. Here, we examine the phylogeography of the freshwater fish, Percichthys trucha, using 53 sequenced microsatellite DNA markers . Fish ( n = 835) were collected from 16 river systems (46 locations) spanning the species range on both sides of the Andes. Eleven watersheds drain to the Pacific, five of which are trans-Andean (headwaters east of Andes). The remaining five drainages empty into the Atlantic. Three analytical approaches (neighbour-joining tree, hierarchical AMOVAs, S tructure ) revealed evidence of historic drainage reversals: fish from four of the five trans-Andean systems (Puelo, Futalaufquen/Yelcho, Baker, Pascua) exhibited greater genetic similarity with Atlantic draining systems than with Pacific systems with headwaters west of Andes. Present-day drainage (Pacific versus Atlantic) explained only 5% of total genetic variance, while ancestral drainage explained nearly 27% of total variance. Thus, the phylogeographic structure of P. trucha is consistent with episodes of drainage reversal in multiple systems and suggests a major role for deglaciation in the genetic and indeed the geographical distribution of P. trucha in Patagonia. The study emphasizes the significant role of historical processes in the current pattern of genetic diversity and differentiation in a fish from a southern temperate region.

scholarly journals Genetic History of Hepatitis C Virus in East Asia

2008 ◽  
Vol 83 (2) ◽  
pp. 1071-1082 ◽  
Author(s):  
Oliver G. Pybus ◽  
Eleanor Barnes ◽  
Rachel Taggart ◽  
Philippe Lemey ◽  
Peter V. Markov ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
20Th Century ◽  
Statistical Tests ◽  
Phylogeographic Structure ◽  
Rate Variation ◽  
Human Populations ◽  
Serum Samples ◽  
History Of ◽  
High Degree

ABSTRACT The hepatitis C virus (HCV), which currently infects an estimated 3% of people worldwide, has been present in some human populations for several centuries, notably HCV genotypes 1 and 2 in West Africa and genotype 6 in Southeast Asia. Here we use newly developed methods of sequence analysis to conduct the first comprehensive investigation of the epidemic and evolutionary history of HCV in Asia. Our analysis includes new HCV core (n = 16) and NS5B (n = 14) gene sequences, obtained from serum samples of jaundiced patients from Laos. These exceptionally diverse isolates were analyzed in conjunction with all available reference strains using phylogenetic and Bayesian coalescent methods. We performed statistical tests of phylogeographic structure and applied a recently developed “relaxed molecular clock” approach to HCV for the first time, which indicated an unexpectedly high degree of rate variation. Our results reveal a >1,000-year-long development of genotype 6 in Asia, characterized by substantial phylogeographic structure and two distinct phases of epidemic history, before and during the 20th century. We conclude that HCV lineages representing preexisting and spatially restricted strains were involved in multiple, independent local epidemics during the 20th century. Our analysis explains the generation and maintenance of HCV diversity in Asia and could provide a template for further investigations of HCV spread in other regions.

Distributional patterns of raptors along altitudinal gradients in the northern Andes and effects of forest fragmentation

1996 ◽  
Vol 12 (4) ◽  
pp. 535-560 ◽  
Author(s):  
Jean-Marc Thiollay
Keyword(s):  
Forest Fragmentation ◽  
Habitat Preferences ◽  
Tropical Species ◽  
Habitat Types ◽  
Grassland Species ◽  
The Andes ◽  
Small Set ◽  
Peninsular Effect ◽  
High Degree ◽  
Made In

ABSTRACTA survey of the diurnal raptor community (46 resident species) at five altitudinal levels from 100 to 4600 m was made in Venezuela using 106 1-km2sample quadrats and then compared with similar censuses (211 plots) in southwestern Colombia and eastern Ecuador. Six habitat types were defined and habitat preferences were measured from every encountered birds and from the association between individual abundances and the coverage of habitat types on plots. The overall species richness steeply declined with elevation in all three countries. The raptor community consisted mostly of tropical species that rapidly decreased in both abundance and frequency of occurrence with elevation. A small set of subtropical-temperate forest specialists partly replaced them at mid-elevation and only two species occurred in the paramo of Venezuela, against 5–7 in the other countries. Although originally the gradients were probably almost completely covered with forest, a large part of the raptor community is now composed of grassland species, three of them extending from the lowlands to the tree line. The relative impoverishment of the Venezuelan community, especially at upper levels, is attributed to a peninsular effect at the narrow extreme northern tip of the Andes and perhaps also to former forest fragmentation. Within some species, different subspecies had discrete altitudinal distributions and interspecific competition may explain differences in the range extension of some species between countries. Today, however, accelerating deforestation may result in a severe decline of forest-interior species and a probable reduction in the altitudinal range of at least some of them. Species naturally associated with forest gaps or edges usually tolerate a high degree of forest fragmentation and degradation but only one of them may become abundant in heavily human-altered woodlands. Few grassland specialists have become more widely distributed in the increasingly deforested landscapes.

Comparative phylogeography, morphological boundaries and climate envelopes of two sympatric widespread Bromeliaceae from the southern Andes

2020 ◽  
Vol 192 (4) ◽  
pp. 726-743
Author(s):  
Lucia V Castello ◽  
Jorge O Chiapella ◽  
Michael H J Barfuss ◽  
Walter Till ◽  
M Paula Quiroga ◽  
...  
Keyword(s):  
Arid Regions ◽  
High Genetic Diversity ◽  
North Central ◽  
Mountain Environments ◽  
The Andes ◽  
Genetic Groups ◽  
Morphological Studies ◽  
Haplotype Networks ◽  
Discriminant Analyses

Abstract We studied the epiphytic species Tillandsia capillaris and T. virescens that grow as neotenic forms with autogamous and cleistogamous flowers. They have expanded in Andean mountain environments, where they grow sympatrically across most of their ranges in arid regions of Peru, central-western Bolivia and north-central Argentina and Chile. We studied the relationships between the two species and populations within each of them, the morphological boundaries and the climatic characterization of distinct genetic entities. We analysed 125 and 102 individuals from 25 and 27 populations of T. virescens and T. capillaris, respectively, by means of haplotype networks, phylogenetic and genetic structure analyses, using the plastid gene ycf1 (c. 4500 bp) to define genetic groups. Morphological studies by discriminant analyses and correlation with climatic variables extracted from WorldClim were used to test differentiations among the genetic groups within each species. We confirm that T. capillaris is a distinct entity and that T. virescens consists of three groups that diverged by vicariance from widespread ancestors. The high genetic diversity found in both species is consistent with the complex geography of the Andes and the Pleistocene glaciation cycles that have driven ecological speciation in both species reflected in the timing of divergence of the clusters.

Population genetic structure of long-tailed pygmy rice rats (Oligoryzomys longicaudatus) from Argentina and Chile based on the mitochondrial control region

2010 ◽  
Vol 88 (1) ◽  
pp. 23-35 ◽  
Author(s):  
Raúl E. González-Ittig ◽  
Hernán J. Rossi-Fraire ◽  
Gustavo E. Cantoni ◽  
Eduardo R. Herrero ◽  
Rosendo Benedetti ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Control Region ◽  
Phylogenetic Trees ◽  
Mitochondrial Control Region ◽  
The Andes ◽  
Single Clade ◽  
The Last Glacial Maximum ◽  
Oligoryzomys Longicaudatus ◽  
The Last Glacial

The rodent Oligoryzomys longicaudatus (Bennett, 1832) (Rodentia, Cricetidae) inhabits southern forests of Argentina and Chile, a region severely affected by glaciations during the Pleistocene–Holocene periods. We evaluate here the diversity of the mitochondrial control region to characterize the genetic structure of this species from forests and bushy areas of seven populations from Argentina and four populations from Chile. Statistical analyses showed shallow haplotype trees and mismatch distributions compatible with recent range expansions. The presence of “private” haplotypes indicates that current levels of gene flow among populations of each country would be low to moderate. Significant differences in haplotype frequencies were detected between eastern and western populations, indicating that the Andes mountains would be an effective geographic barrier for gene flow despite the existing valleys that could act as corridors for dispersion. A single clade containing all the haplotypes was recovered in the phylogenetic trees, suggesting postglacial dispersion from a single refugium during the Last Glacial Maximum. The higher effective size and levels of polymorphism in populations from Chile suggest that the refugium was located in this country. The asymmetric gene flow from Chile to Argentina may reflect a recent colonization of the eastern populations.

scholarly journals Analysis of mitochondrial control region nucleotide sequences from Baffin Bay beluga, (Delphinapterus leucas): detecting pods or sub-populations?

2002 ◽  
Vol 4 ◽  
pp. 39 ◽  
Author(s):  
Per Jakob Palsbøll ◽  
Mads Peter Heide-Jørgensen ◽  
Martine Bérubé
Keyword(s):  
Population Structure ◽  
Control Region ◽  
Genetic Heterogeneity ◽  
Mitochondrial Control Region ◽  
Delphinapterus Leucas ◽  
Significant Heterogeneity ◽  
Management Units ◽  
Baffin Bay ◽  
The One ◽  
High Degree

We report the results of an analysis of the variation in the nucleotide sequence of the mitochondrial control region obtained in 218 samples collected from belugas, Delphinapterus leucas, around the Baffin Bay. We detected multiple instances of significant heterogeneity in the distribution of genetic variation among the analyzed mitochondrial control region sequences on a spatial as well as temporal scale indicating a high degree of maternal population structure. The detection of significant levels of heterogeneity between samples collected in different years but within the same area and season was unexpected. Re-examination of earlier results presented by Brown Gladden and coworkers also revealed temporal genetic heterogeneity within the one area where sufficient (n>15) samples were collected in multiple years. These findings suggest that non-random breeding and maternally directed site-fidelity are not the sole causes of genetic heterogeneity among belugas but that a matrilineal pod structure might cause significant levels of genetic heterogeneity as well, even within the same area. We propose that a maternal pod structure, which has been shown to be the cause of significant genetic heterogeneity in other odontocetes, may add to the overall level of heterogeneity in the maternally inherited DNA and hence that much of the spatial heterogeneity observed in this and previous studies might be attributed to pod rather than population structure. Our findings suggest that it is important to estimate the contribution of pod structure to overall heterogeneity before defining populations or management units in order to avoid interpreting heterogeneity due to sampling of different pods as different populations/management units.

Subsistence Continuity Linked to Consumption of Marine Protein in the Formative Period in the Interfluvic Coast of Northern Chile: Re-Assessing Contacts with Agropastoral Groups from Highlands

Radiocarbon ◽  
2015 ◽  
Vol 57 (4) ◽  
pp. 679-688 ◽  
Author(s):  
Pedro Andrade ◽  
Ricardo Fernandes ◽  
Katia Codjambassis ◽  
Josefina Urrea ◽  
Laura Olguín ◽  
...  
Keyword(s):  
Material Culture ◽  
Formative Period ◽  
Marine Resources ◽  
Northern Chile ◽  
Social Changes ◽  
The Andes ◽  
Radiocarbon Data ◽  
High Degree ◽  
Bone Remains ◽  
Marine Protein

From material culture evidence dating as early as 7500 cal BC, it has been established that populations from the interfluvic coast in northern Chile adapted to a maritime economic livelihood. During the 2nd millennium BC, local populations began to experience major social changes arising mainly from an increase in contacts with agropastoral populations from the highlands of the Andes. New radiocarbon data and stable isotope (δ15Ncol, δ13Ccol, and δ13Cap) analyses of human bone remains from interfluvic coastal individuals were obtained. The data showed that these individuals, at the time of contact with highland populations, maintained a mode of subsistence relying principally on marine protein. This suggests that, although instances of social change may have arisen, the livelihoods linked to the consumption of marine resources would have remained constant, demonstrating a high degree of resistance in changing local lifestyles.

Multiple Pleistocene refugia in the widespread Patagonian tree Embothrium coccineum (Proteaceae)

2011 ◽  
Vol 59 (4) ◽  
pp. 299 ◽  
Author(s):  
Romina Vidal-Russell ◽  
Cintia P. Souto ◽  
Andrea C. Premoli
Keyword(s):  
Population Size ◽  
Dna Sequences ◽  
Phylogeographic Structure ◽  
Mountain Range ◽  
Pollen Record ◽  
The South ◽  
Effective Population ◽  
The Andes ◽  
Chloroplast Dna Sequences ◽  
The Impact

Embothrium coccineum J.R.Forst. & G.Forst is an endemic tree of the Patagonian temperate forest. The objective of this study is to evaluate the impact of last glaciation events on the genetic structure of this widespread and ecologically tolerant species, to postulate possible refugial areas. Phylogeographic analyses were performed using chloroplast DNA sequences (trnL-trnF spacer and ndhC-trnV spacer) from individuals collected in 34 populations along the total range of the species, and these results were compared with a similar study in Nothofagus. A total of 22 haplotypes were found, three of which were widely distributed while 13 were found at only one location. Historical demography suggests a long period of stable effective population size, decreasing gradually towards the Last Glacial Maximum (LGM), followed by an increase in population size that stabilised 2500 years ago. The phylogeographic analyses reflect recent events of colonisation after the LGM from multiple refugia. In the northern area of its distribution probably the species survived in several pockets within the Andes mountain range and in Cordillera de la Costa in Chile. In the south, it is suggested that Embothrium survived the glacial period at the edge of the glaciers. These findings are in agreement with the fossil pollen record that shows 10 000-year-old grains in the south, suggesting colonisation from nearby areas when ice retreated. Embothrium is a coloniser that naturally occurs as scattered individuals within mixed forests. Hence, the shallow phylogeographic structure reported here reflects a Pleistocene signature highly impacted by drift resulting in the randomly fixation of new variants reducing the cpDNA structure.

Small marsupial, big dispersal? Broad- and fine-scale genetic structure of an endangered marsupial from the Australian arid zone

2018 ◽  
Vol 66 (3) ◽  
pp. 214 ◽  
Author(s):  
Amanda L. McLean ◽  
Steven J. B. Cooper ◽  
Melanie L. Lancaster ◽  
Glen Gaikhorst ◽  
Cathy Lambert ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Arid Zone ◽  
Mitochondrial Control Region ◽  
Climatic Conditions ◽  
Phylogeographic Structure ◽  
Mammal Species ◽  
Heterogeneous Distribution ◽  
Resource Pulses ◽  
Significant Genetic Structure

The irregular nature of rainfall in the Australian arid and semiarid zones results in a heterogeneous distribution of resources in both time and space. The mammal species that reside in these regions are uniquely adapted to these climatic conditions, often occurring in naturally low densities and increasing significantly in numbers following major rainfall events. We investigated how these adaptations may influence genetic diversity and gene flow across the landscape in an endangered semiarid/arid-zone marsupial, the sandhill dunnart (Sminthopsis psammophila), from three known populations in southern Australia. Analyses of mitochondrial control region (CR) sequences and microsatellite loci revealed that S. psammophila had maintained similar levels of genetic diversity to other sympatric Sminthopsis species despite its endangered status. There was no evidence for significant phylogeographic structure within the species, but each population was genetically differentiated, based on the frequency of microsatellite alleles and CR haplotypes, suggesting that they should be considered as distinct Management Units for conservation. At a fine spatial scale, no significant genetic structure or sex-biased dispersal was detected within a study site of 240km2. These findings suggest that both sexes are highly mobile, which allows individuals to locate localised resource patches when they become available. We detected evidence of a genetic bottleneck within the population, possibly caused by a recent drought. Our study highlights the importance of maintaining connectivity across the landscape for semiarid- and arid-zone species to enable them to track resource pulses and maintain genetic diversity.

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