Kuhner MK. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics 22: 768-770
ABSTRACT We present a Markov chain Monte Carlo coalescent genealogy sampler, LAMARC 2.0, which estimates population genetic parameters
from genetic data. LAMARC can co-estimate subpopulation Θ = 4Neμ, immigration rates, subpopulation exponential growth rates and overall recombination rate, or a user-specified subset of
these parameters. It can perform either maximum-likelihood or Bayesian analysis, and accomodates nucleotide sequence, SNP,
microsatellite or elecrophoretic data, with resolved or unresolved haplotypes. It is available as portable source code and
executables for all three major platforms.
Availability: LAMARC 2.0 is freely available at http://evolution.gs.washington.edu/lamarc
Full-textDOI: · Available from: Mary K Kuhner, Mar 11, 2015
- SourceAvailable from: Matheus Souza Lima-Ribeiro
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- "Estimations were based on Bayesian model using the Markov Chain Monte Carlo ( MCMC ) approach implemented in Lamarc 2 . 1 . 9 software ( Kuhner , 2006 ) . Because of the high number of populations , to estimate growth rate , we constrained migration ( maintained migration constant ) , and migration was estimated in independent runs . "
ABSTRACT: Understanding the dispersal routes of Neotropical savanna tree species is an essential step to unravel the effects of past climate change on genetic patterns, species distribution and population demography. Here we reconstruct the demographic history and dispersal dynamics of the Neotropical savanna tree species Tabebuia aurea to understand the effects of Quaternary climate change on its current spatial patterns of genetic diversity. We sampled 285 individuals from 21 populations throughout Brazilian savannas and sequenced all individuals for three chloroplast intergenic spacers and ITS nrDNA. We analyzed data using a multi-model inference framework by coupling the relaxed random walk model (RRW), ecological niche modeling (ENM) and statistical phylogeography. The most recent common ancestor of T. aurea lineages dated from ∼4.0 ± 2.5 Ma. T. aurea lineages cyclically dispersed from the West toward the Central-West Brazil, and from the Southeast toward the East and Northeast Brazil, following the paleodistribution dynamics shown by the ENMs through the last glacial cycle. A historical refugium through time may have allowed dispersal of lineages among populations of Central Brazil, overlapping with population expansion during interglacial periods and the diversification of new lineages. Range and population expansion through the Quaternary were, respectively, the most frequent prediction from ENMs and the most likely demographic scenario from coalescent simulations. Consistent phylogeographic patterns among multiple modeling inferences indicate a promising approach, allowing us to understand how cyclical climate changes through the Quaternary drove complex population dynamics and the current patterns of species distribution and genetic diversity.Frontiers in Plant Science 09/2015; 6. DOI:10.3389/fpls.2015.00653 · 3.95 Impact Factor
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- "Growth rate and timing of population dynamic changes were estimated from coalescent simulations implemented in LAMARC 2.1.9 (Kuhner 2006). The observed distribution of the number of pair base differences between sequences is indicated by the gray bars, while the expected distribution under a model of sudden demographic expansion is represented by a black line. "
ABSTRACT: The almost complete isolation of Antarctica after the intensification the Antarctic circumpolar current (ACC) during the middle-Miocene has been challenged by recent molecular data showing the existence of allelic exchange across the ACC. For organisms present on both sides of the ACC, two hypotheses have then been discussed to explain the origin of the Antarctic populations: (1) They correspond to recent immigrants from adjacent continents, or (2) they have evolved in situ and have survived the dramatic effects of the last Quaternary glaciations in this region. The red algae Gigartina skottsbergii presents a disjoint distribution and is reported in both Antarctica and southern South America, a distribution pattern that largely exceeds its dispersal capacity. Mitochondrial sequences of the intergenic region Cox2-3 (n = 233) and partial chloroplastic RuBisCo large subunit gene (n = 26) sequences were obtained for individuals from the Chilean sub-Antarctic ecoregion and Antarctic Peninsula localities. The results strongly support the persistence of populations on each side of the Drake Passage during glacial periods and the existence of dispersal barrier due to the ACC. On both sides of the ACC, the last Quaternary glaciations have induced strong bottlenecks that were followed by rapid colonization events.Polar Biology 08/2015; DOI:10.1007/s00300-015-1762-4 · 2.07 Impact Factor
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- "We ran LAMARC 2.1.6 (Kuhner 2006) to calculate most probable estimates (MPE) of h. This is a population parameter that reflects effective population size and mutation rate and equals 4Nel and 2Nel (where Ne is the effective population size and l the mutation rate) for microsatellites and mtDNA, respectively. "
ABSTRACT: Demographic models accounting for operational sex ratio (OSR) show that male numbers can have a substantial influence on the dynamics of wild populations. We used the Cantabrian capercaillie, a forest bird, as a model to assess the effects of the reduction in the number of breeding males (increased OSR) associated to male-biased hunting, on the genetics of the population. We based our assessment in the comparison of the dynamics of neutral markers transmitted by both parents (microsatellites) versus markers transmitted only by females (mitochondrial DNA—mtDNA). Parallel to the analysis of field data, we ran computer simulations to explore how different levels of OSR and two other important demographic factors, population size and connectivity, might influence the dynamics of genetic variation of microsatellites and mtDNA. We found evidence of a genetic bottleneck and low genetic variability affecting microsatellites but not mtDNA early in our study period, when male-biased hunting was more intense. This was followed by a decline in mtDNA variation around 10–20 years later. Simulations suggested that changes in genetic variation associated with high OSR had the closest similarity to those observed at the beginning of our study, whereas a combination of reduced size and migration rate better resembled the patterns found later on. Our findings indicate that male-biased hunting might have triggered the ongoing decline of the Cantabrian capercaillie, on its own or in combination with habitat configuration, and support the need to incorporate OSR into decision making for the management and conservation of exploited populations.Conservation Genetics 06/2015; DOI:10.1007/s10592-015-0747-8 · 1.85 Impact Factor