Peter Beerli

Peter Beerli
Florida State University | FSU · Department of Scientific Computing

PhD

About

107
Publications
21,340
Reads
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13,264
Citations
Citations since 2016
12 Research Items
4569 Citations
20162017201820192020202120220200400600
20162017201820192020202120220200400600
20162017201820192020202120220200400600
20162017201820192020202120220200400600
Introduction
I distribute a computer program to infer parameters of population genetic models ( MIGRATE at http://popgen.sc.fsu.edu) using Bayesian inference and the coalescent. I DISAGREE WITH Researchgate-SELF ARCHIVING POLICY BECAUSE I DO NOT CONSIDER THE Researchgate SITE AS MY PERSONAL WEBSPACE BUT A MERE POINTER TO MY WEBSITE. You can download my self-archived papers from MY OWN website: http://people.sc.fsu.edu/~pbeerli/Beerli_Lab/Papers.html
Additional affiliations
April 2003 - present
Florida State University
Position
  • computational population genetics
Description
  • We develop methods and software to estimate parameters of population genetic models based on the coalescence, and also work on model selection procedures for such models.
April 1994 - March 2003
University of Washington Seattle
Position
  • structured coalescence
Education
August 1987 - January 1994
University of Zurich
Field of study
  • Zoology

Publications

Publications (107)
Article
Full-text available
Background Human cutaneous leishmaniasis caused by Leishmania (Viannia) braziliensis is highly prevalent in the Peruvian jungle, where it affects military forces deployed to fight against drug trafficking and civilian people that migrate from the highland to the lowland jungle for economic activities such as mining, agriculture, construction, and c...
Preprint
Full-text available
A bstract Phylogenetic trees are fundamental for understanding the evolutionary history of a set of species. The local neighborhoods of a phylogenetic tree provide important information, but since trees are high-dimensional objects, characterizing these neighborhoods is difficult. Based on the Billera-Holmes-Vogtmann (BHV) distance between pairs of...
Article
Full-text available
Divergence time estimation from multilocus genetic data has become common in population genetics and phylogenetics. We present a new Bayesian inference method that treats the divergence time as a random variable. The divergence time is calculated from an assembly of splitting events on individual lineages in a genealogy. The time for such a splitti...
Preprint
Full-text available
The terms population size and population density are often used interchangeably, when in fact they are quite different. When viewed in a spatial landscape, density is defined as the number of individuals within a square unit of distance, while population size is simply the total count of a population. In discrete population genetics models, the eff...
Article
Full-text available
Many evolutionary biologists collect genetic data from natural populations and then need to investigate the relationship among these populations to compare different biogeographic hypotheses. MIGRATE, a useful tool for exploring relationships between populations and comparing hypotheses, has existed since 1998. Throughout the years, it has steadily...
Preprint
Divergence time estimation from multilocus genetic data has become common in population genetics and phylogenetics. We present a new Bayes inference method that treats the divergence time as a random variable. The divergence time is calculated from an assembly of splitting events on individual lineages in a genealogy. The waiting time for such a sp...
Article
Full-text available
An approach to the coalescent, the fractional coalescent (f-coalescent), is introduced. The derivation is based on the discrete-time Cannings population model in which the variance of the number of offspring depends on the parameter α. This additional parameter α affects the variability of the patterns of the waiting times; values of α<1 lead to an...
Preprint
A new approach to the coalescent, the fractional coalescent ( f -coalescent), is introduced. Two derivations are presented: first, the f -coalescent is based on an extension of the discrete-time Wright-Fisher model. In this extension, for the population of size N , the probability that two randomly selected individuals have the same parent in the p...
Article
With anthropogenic impacts rapidly advancing into deeper waters, there is growing interest in establishing deep-sea marine protected areas (MPAs) or reserves. Reserve design depends on estimates of connectivity and scales of dispersal for the taxa of interest. Deep-sea taxa are hypothesized to disperse greater distances than shallow-water taxa, whi...
Article
Full-text available
Evaluating marginal likelihood is the most critical and computationally expensive task, when conducting Bayesian model averaging to quantify parametric and model uncertainties. The evaluation is commonly done by using Laplace approximations to evaluate semianalytical expressions of the marginal likelihood or by using Monte Carlo (MC) methods to eva...
Article
Full-text available
The swamp type of the Asian water buffalo is assumed to have been domesticated by about 4000 years BP, following the introduction of rice cultivation. Previous localizations of the domestication site were based on mitochondrial DNA (mtDNA) variation within China, accounting only for the maternal lineage. We carried out a comprehensive sampling of C...
Article
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The genetic diversity and phylogeography of maternal lineages in Ursus arctos Linnaeus, 1758 (the brown bear) have been studied extensively over the last two decades; however, sampling has largely been limited to the northern Holarctic, and was possibly biased towards lineages that recolonized the vast expanses of the north as the Last Glacial Maxi...
Article
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Sperm and eggs have interacting proteins on their surfaces that influence their compatibility during fertilization. These proteins are often polymorphic within species, producing variation in gamete affinities. We first demonstrate the fitness consequences of various sperm binding protein (Bindin) variants in the sea urchin Strongylocentrotus purpu...
Article
Full-text available
Population genetic analyses often require the estimation of parameters such as population size and migration rates. In the 1960s, enzyme electrophoresis was developed; it was the first method to gather co-dominant data from many individuals in many populations relatively easily. Summary statistics methods, such as allele-frequency based F-statistic...
Article
Full-text available
Humpback whales (Megaptera novaeangliae) annually undertake the longest migrations between seasonal feeding and breeding grounds of any mammal. Despite this dispersal potential, discontinuous seasonal distributions and migratory patterns suggest that humpbacks form discrete regional populations within each ocean. To better understand the worldwide...
Article
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Introduced species have the potential to outperform natives via the introduction of new para-sites to which the native ecosystem is vulnerable. Cryptic diversity within an invasive species can obscure invasion patterns and confound proper man-agement measures. The aim of this study is to use coalescent theory based methodology to trace recent route...
Article
Most modern population genetics inference methods are based on the coalescence framework. Methods that allow estimating parameters of structured populations commonly insert migration events into the genealogies. For these methods the calculation of the coalescence probability density of a genealogy requires a product over all time periods between e...
Article
Full-text available
Introduced species have the potential to outperform natives via the introduction of new parasites to which the native ecosystem is vulnerable. Cryptic diversity within an invasive species can obscure invasion patterns and confound proper management measures. The aim of this study is to use coalescent theory based methodology to trace recent routes...
Article
Full-text available
Variation patterns of allozymes and of ND3 haplotypes of mitochondrial DNA reveal a zone of genetic transition among western Palearctic water frogs extending across northeastern Greece and European Turkey. At the western end of the zone, allozymes characteristic of Central European frogs known as Pelophylax ridibundus predominate, whereas at the ea...
Article
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There are many large, easy-to-observe anseriform birds (ducks, geese, and swans) in northern Australia and New Guinea and they often gather in large numbers. Yet, the structure of their populations and their regional movements are poorly understood. Lack of understanding of population structure limits our capacity to understand source-sink dynamics...
Article
Full-text available
Water frogs inhabiting Cyprus represent a distinct evolutionary species of Messinian origin that is formally described in this paper. The systematic status of Cypriot frogs is evidenced by specific characters in their mitochondrial (mt) and nuclear (nu) DNA sequences, and the fact that they form a well supported monophyletic clade in both mtDNA and...
Article
Full-text available
Water frogs inhabiting Cyprus represent a distinct evolutionary species of Messinian origin that is formally described in this paper. The systematic status of Cypriot frogs is evidenced by specific characters in their mitochondrial (mt) and nuclear (nu) DNA sequences, and the fact that they form a well supported monophyletic clade in both mtDNA and...
Article
Full-text available
Cave animals converge evolutionarily on a suite of troglomorphic traits, the best known of which are eyelessness and depigmentation. We studied 11 cave and 10 surface populations of Astyanax mexicanus in order to better understand the evolutionary origins of the cave forms, the basic genetic structuring of both cave and surface populations, and the...
Data
A detailed hydrological map of the El Abra region. El Abra region map with the indication of surface and subsurface water divide. Points at, or near, base level (orange line) are indicated by solid circles; fish-inhabited pools by solid circles closer to the high water profile (blue dotted line) (adapted from Mitchell et al. 1977).
Data
MIGRATE-N 3.2.6, runtime conditions and methods. Summary of methods and conditions.
Data
Estimates of gene flow based on Bayesian inferences of migration rates and population sizes. Results of MIGRATE-N 3.2.6 on Astyanax mexicanus population clusters within each geographical region. Mutation scaled immigration rate, M, between different population groups. M is the ratio of the immigration rate over the mutation rate. The central box of...
Data
Summary statistics for 26 microsatellite loci of Astyanax mexicanus populations. Table summarizing the microsatellite data. Mean sample size over all loci (n); Ap is the mean number of alleles per locus, expected (He) and observed (Ho) heterozygosity, FIS. Bold FISvalues are estimates significantly different from zero after Bonferroni correction.
Data
Allelic frequencies of 26 microsatllite loci in the studied populations. Summary of allelic frequencies for all loci and all populations.
Data
Summary of the proposed models and conclusions of the paper. Proposed model with five independent origins of cave adapted Astyanax in NE Mexico as estimated by the data. The first wave of surface fish led to three independent subterranean invasion events establishing the "old" cave populations. The second wave gave rise to two independent invasions...
Data
Genetic isolation by distance. Results of the Mantel test for correlation between genetic distance (Fst/(1-Fst)) and geographic distance for populations of the El Abra region (O1 - O8) (R2 = 0.625, P = 0.01).
Article
Full-text available
Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these appro...
Conference Paper
The computations of likelihood or posterior distribution of parameters of complex population genetics models are common tasks in computational biology. The numerical results of these approaches are often found by Monte Carlo simulations. Much of the recent work of Monte Carlo approaches to population genetics problems has used pseudorandom sequence...
Article
Full-text available
Anastrepha suspensa (Loew) (Diptera: Tephritidae), the Caribbean fruit fly, is indigenous to Florida and the Greater Antilles where it causes economic losses in fruit crops, including citrus. Because of the geographic separation of many of its native locations and anecdotal descriptions of regional differences in host preferences, there have been q...
Article
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AIM: Our aims were to assess the phylogeographic patterns of genetic diversity in eastern Mediterranean water frogs and to estimate divergence times using different geological scenarios. We related divergence times to past geological events and discuss the relevance of our data for the systematics of eastern Mediterranean water frogs. LOCATION: The...
Chapter
Full-text available
Water frogs [genus Pelophylax (Rana)] that occur around the eastern Mediterranean Sea provide an opportunity to study early stages of speciation. The geography of the eastern Mediterranean region has changed dramatically since the Middle Miocene as a result of motions of adjoining lithospheric plates and regional-scale vertical crustal motions (upl...
Data
Full-text available
Estimates for immigration (columns) and emigration (rows) rates between each pair of regions measured in terms of migration events per lineage per year. (0.03 MB PDF)
Data
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Estimates using proportional sampling for immigration (columns) and emigration (rows) rates between each pair of regions measured in terms of migration events per lineage per year. (0.03 MB PDF)
Data
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Estimates using an alternative geographical grouping for immigration (columns) and emigration (rows) rates between each pair of regions measured in terms of migration events per lineage per year. (0.03 MB PDF)
Data
Changes in antigenic diversity and the McDonald-Kreitman related index (MKR) for varying strengths of strain competition and antigenic mutation rates. (A) Mean Shannon diversity was measured for 40 years of simulation. Shannon diversity ranges from zero when a single circulating antigenic variant is present at each time point, to approximately 3.5n...
Data
Regional genetic diversity π arrayed below the diagonal, measured in terms of 10−3 substitutions per site, and regional FST arrayed above diagonal, with 95% confidence intervals determined by 1000 bootstrap replicates. (0.09 MB PDF)
Data
Full-text available
Distribution of 4355 influenza A (H3N2) samples across countries of origin. Circles are colored according to our regional partitioning. Circle areas are proportional to sample count of the full dataset before any resampling took place. (0.26 MB PDF)
Data
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Number of sequences used from each geographic region in different stages of the analysis. (0.03 MB PDF)
Data
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Estimates using a 1000-fold larger prior for immigration (columns) and emigration (rows) rates between each pair of regions measured in terms of migration events per lineage per year. (0.03 MB PDF)
Data
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Estimates for the timescale of coalescence (in years) and the effective population size (in number of individuals) of each region, assuming overlapping generations and an infectious period (generation time) of 5 days. (0.04 MB PDF)
Data
Full-text available
Mean estimates and 95% credible intervals for effective population size Ne, rate of migration m and trunk proportion for each region in simulated data sets based on 500 samples from the North, 500 samples from the South and 100 samples from the Tropics over a 10 year period. (0.06 MB PDF)
Article
Full-text available
Author Summary Infections by the influenza A virus show highly seasonal patterns in temperate regions. Winter is flu season. Over the course of the autumn and winter, a small number of initial infections grow to encompass a significant proportion of the population. At the end of the winter, infection disappears. It has been suggested that the strai...
Article
Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best appr...
Article
For many biological investigations, groups of individuals are genetically sampled from several geographic locations. These sampling locations often do not reflect the genetic population structure. We describe a framework using marginal likelihoods to compare and order structured population models, such as testing whether the sampling locations belo...
Article
Full-text available
A 5' truncated non-LTR CR1-like retrotransposon, named RanaCR1, was identified in the serum albumin intron-1 (SAI-1) of at least seven species of western Palearctic water frogs (WPWF). Based on sequence similarity of the carboxy-terminal region (CTR) of ORF2 and/or the highly conserved 3' untranslated region (3' UTR), RanaCR1-like elements occur al...
Article
Full-text available
Large pelagic fishes are generally thought to have little population genetic structuring based on their cosmopolitan distribution, large population sizes and high dispersal capacities. However, gene flow can be influenced by ecological (e.g. homing behaviour) and physical (e.g. present-day ocean currents, past changes in sea temperature and levels)...
Article
Claviceps purpurea is an important pathogen of grasses and source of novel chemical compounds. Three groups within this species (G1, G2 and G3) have been recognized based on habitat association, sclerotia and conidia morphology, as well as alkaloid production. These groups have further been supported by Random Amplification of Polymorphic DNA (RAPD...
Article
Interspecies transfer of mitochondrial (mt) DNA is a common phenomenon in plants, invertebrates and vertebrates, normally linked with hybridization of closely related species in zones of sympatry or parapatry. In central Europe, in an area north of 48 degrees N latitude and between 8 degrees and 22 degrees E longitude, western Palaearctic water fro...
Article
Full-text available
Rana esculenta progeny from experimental crosses (using R. esculenta from natural lineages and F1Rana ridibunda × Rana lessonae), reared in artificial ponds and in cages immersed in natural breeding ponds, showed three different t