Peter Beerli

• PhD
• computational population genetics at Florida State University

Eucalyptus urophylla is one of the most economically important species in the world due to its wood quality and tolerance to water stress. Understanding the genetic composition at the population level of this species is essential for the sustainable and efficient management and utilization of its genetic resources. This study describes the genetic...

The Canary Islands are oceanic islands that encompass a wide diversity of geological ages, sizes, ecological regions, and orographic contexts that determine different isolation frameworks and provide a suitable geographical setting to address questions regarding genetic variation patterns and colonization processes. In the present study, we used nu...

Eucalyptus urophylla is one of the most economically important species in the world due to its wood quality and tolerance to water stress. Understanding the genetic composition at the population level of this species is essential for the sustainable and efficient management and utilization of its genetic resources. This study describes the genetic...

Movement of animals and plants from mainland populations contributes to the genetic diversity and viability of geographically isolated island biota, but also carries risks of pathogen introductions. The bat fauna of the island of Trinidad reflects species diversity on the neighbouring South American mainland and includes the common vampire bat ( De...

A bstract Inferring the evolutionary history of species or populations employing multilocus analysis is gaining ground in phylogenetic analysis. We developed an alignment-free method to infer the multilocus species tree, which is implemented in the Python package T opic C ontml . The method operates in two primary stages. First, it uses probabilist...

Phylogenetic trees are fundamental for understanding evolutionary history. However, finding maximum likelihood trees is challenging due to the complexity of the likelihood landscape and the size of tree space. Based on the Billera-Holmes-Vogtmann (BHV) distance between trees, we describe a method to generate intermediate trees on the shortest path...

Species interactions drive diverse evolutionary outcomes. Speciation by cascade reinforcement represents one example of how species interactions can contribute to the proliferation of species. This process occurs when the divergence of mating traits in response to selection against interspecific hybridization incidentally leads to reproductive isol...

The Carpentarian barrier across north-eastern Australia is a major biogeographic barrier and a generator of biodiversity within the Australian Monsoonal Tropics. Here we present a continent-wide analysis of mitochondrial (control region) and autosomal (14 anonymous loci) sequence and indel variation and niche modelling of brown and black-tailed tre...

Delineating genetically distinct population segments of threatened species and quantifying population connectivity are important steps in developing effective conservation and management strategies aimed at preventing extinction. The gopher frog (Rana capito) is a xeric-adapted, pond-breeding species endemic to the Gulf and Atlantic coastal plains...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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).

MIGRATE-N 3.2.6, runtime conditions and methods. Summary of methods and conditions.

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...

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.

Allelic frequencies of 26 microsatllite loci in the studied populations. Summary of allelic frequencies for all loci and all populations.

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...

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).

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...

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...

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...

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 relate divergence times to past geological events and discuss the relevance of our data for the systematics of eastern Mediterranean water frogs. Location The ea...

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...

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)

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)

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)

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...

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)

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)

Number of sequences used from each geographic region in different stages of the analysis. (0.03 MB PDF)

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)

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)

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)

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...

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...

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...

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...

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)...

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...

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...

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 types of malformations reflecting developmental disturbances, each affecting few individuals overall. Giant tadpoles arre...

IN a recent issue of Genetics, [RoyChoudhury and Stephens (2007)][1] showcased a new method for estimating the population scaled mutation rate θ from microsatellite data; θ is equivalent to four times the effective population size times the mutation rate per generation and can also be viewed as

European water frog hybrids Rana esculenta reproduce hemiclonally, by hybridogenesis: In the germ line they exclude the genome of the parental species Rana lessonae and produce haploid, unrecombined gametes with a genome of the parental species Rana ridibunda. These hybrids coexist with and depend as sexual parasites on the host parental species R....

Unlabelled: Comparison of the performance and accuracy of different inference methods, such as maximum likelihood (ML) and Bayesian inference, is difficult because the inference methods are implemented in different programs, often written by different authors. Both methods were implemented in the program MIGRATE, that estimates population genetic...

The geographical origin of Plasmodium vivax, the most widespread human malaria parasite, is controversial. Although genetic closeness to Asian primate malarias has been confirmed by phylogenetic analyses, genetic similarities between P. vivax and Plasmodium simium, a New World primate malaria, suggest that humans may have acquired P. vivax from New...

The Sobol sequence is the most popular quasirandom se- quence because of its simplicity and efficiency in implementation. We summarize aspects of the scrambling technique applied to Sobols e- quences and propose a new simpler modified scrambling algorithm, called the multi-digit scrambling scheme. Most proposed scrambling methods randomize a single...

Current estimators of gene flow come in two methods; those that estimate parameters assuming that the populations investigated are a small random sample of a large number of populations and those that assume that all populations were sampled. Maximum likelihood or Bayesian approaches that estimate the migration rates and population sizes directly u...

The emergence of virulent Plasmodium falciparumin Africa within the past 6000 years as a result of a cascade of changes in human behavior and mosquito transmission has recently been hypothesized. Here, we provide genetic evidence for a sudden increase in the African malaria parasite population about 10,000 years ago, followed by migration to other...

Single nucleotide polymorphisms (SNPs) represent the most widespread type of sequence variation in genomes, yet they have only emerged recently as valuable genetic markers for revealing the evolutionary history of populations. Their occurrence throughout the genome also makes them ideal for analyses of speciation and historical demography, especial...

Our analysis of the Neanderthal-modern human gene divergence resulted in gene divergence times in a range of 631-789 KY. This gene divergence time is informative, but the biologically more relevant parameter is the time of population divergence, which necessarily occurs after the observed gene divergence when there is any polymorphism in the ancest...

Key Words ancestral polymorphism, coalescence theory, maximum likelihood, molecular clock, sequence saturation s Abstract Molecular clocks have profoundly influenced modern views on the timing of important events in evolutionary history. We review recent advances in es-timating divergence times from molecular data, emphasizing the continuum between...

Directional selection is a major force driving adaptation and evolutionary change. However, the distribution, strength, and tempo of phenotypic selection acting on quantitative traits in natural populations remain unclear across different study systems. We reviewed the literature (1984-1997) that reported the strength of directional selection as in...

A maximum likelihood estimator based on the coalescent for unequal migration rates and different subpopulation sizes is developed. The method uses a Markov chain Monte Carlo approach to investigate possible genealogies with branch lengths and with migration events. Properties of the new method are shown by using simulated data from a four-populatio...

How strong is phenotypic selection on quantitative traits in the wild? We reviewed the literature from 1984 through 1997 for studies that estimated the strength of linear and quadratic selection in terms of standardized selection gradients or differentials on natural variation in quantitative traits for field populations. We tabulated 63 published...

How strong is phenotypic selection on quantitative traits in the wild? We reviewed the literature from 1984 through 1997 for studies that estimated the strength of linear and quadratic selection in terms of standardized selection gradients or differentials on natural variation in quantitative traits for field populations. We tabulated 63 published...

Genotypic variation at six of 67 microsatellite loci we developed from Rana ridibunda, containing di- or trinucleotide simplesequence repeats, confirms the value of microsatellites as an evolutionary genetic tool for studying western Palearctic water frogs, a model system characterized by clonal reproduction in natural hybrid lineages. R. ridibunda...

Molecular methods as applied to the biogeography of single species (phylogeography) or multiple codistributed species (comparative phylogeography) have been productively and extensively used to elucidate common historical features in the diversification of the Earth's biota. However, only recently have methods for estimating population divergence t...

Molecular methods as applied to the biogeography of single species (phylogeography) or multiple codistributed species (comparative phylogeography) have been productively and extensively used to elucidate common historical features in the diversification of the Earth's biota. However, only recently have methods for estimating population divergence t...

Single nucleotide polymorphism (SNP) data can be used for parameter estimation via maximum likelihood methods as long as the way in which the SNPs were determined is known, so that an appropriate likelihood formula can be constructed. We present such likelihoods for several sampling methods. As a test of these approaches, we consider use of SNPs to...

A new method for the estimation of migration rates and effective population sizes is described. It uses a maximum-likelihood framework based on coalescence theory. The parameters are estimated by Metropolis-Hastings importance sampling. In a two-population model this method estimates four parameters: the effective population size and the immigratio...

European water frog hybrids Rana esculenta (Rana ridibunda x Rana lessonae) reproduce hemiclonally, transmitting only their ridibunda genome to gametes. We compared fitness-related larval life-history traits of natural R. esculenta from Poland with those of the two sympatric parental species and of newly generated F1 hybrids. Compared with either p...

2 When population samples of molecular data, such as sequences, are taken, the members of the sample are related by a gene tree whose shape is affected by the population processes, such as genetic drift, change of population size, and migration. Genetic parameters such as recombination also affect that genealogy. Likelihood inference of these param...