Dependence of paracentric inversion rate on tract length

BACKGROUND: We develop a Bayesian method based on MCMC for estimating the relative rates of pericentric and paracentric inversions from marker data from two species. The method also allows estimation of the distribution of inversion tract lengths. RESULTS: We apply the method to data from Drosophila melanogaster and D. yakuba. We find that pericentric inversions occur at a much lower rate compared to paracentric inversions. The average paracentric inversion tract length is approx. 4.8 Mb with small inversions being more frequent than large inversions. If the two breakpoints defining a paracentric inversion tract are uniformly and independently distributed over chromosome arms there will be more short tract-length inversions than long; we find an even greater preponderance of short tract lengths than this would predict. Thus there appears to be a correlation between the positions of breakpoints which favors shorter tract lengths. CONCLUSION: The method developed in this paper provides the first statistical estimator for estimating the distribution of inversion tract lengths from marker data. Application of this method for a number of data sets may help elucidate the relationship between the length of an inversion and the chance that it will get accepted

Genomic signatures of population decline in the malaria mosquito Anopheles gambiae

Population genomic features such as nucleotide diversity and linkage disequilibrium are expected to be strongly shaped by changes in population size, and might therefore be useful for monitoring the success of a control campaign. In the Kilifi district of Kenya, there has been a marked decline in the abundance of the malaria vector Anopheles gambiae subsequent to the rollout of insecticide-treated bed nets. To investigate whether this decline left a detectable population genomic signature, simulations were performed to compare the effect of population crashes on nucleotide diversity, Tajima's D, and linkage disequilibrium (as measured by the population recombination parameter ρ). Linkage disequilibrium and ρ were estimated for An. gambiae from Kilifi, and compared them to values for Anopheles arabiensis and Anopheles merus at the same location, and for An. gambiae in a location 200 km from Kilifi. In the first simulations ρ changed more rapidly after a population crash than the other statistics, and therefore is a more sensitive indicator of recent population decline. In the empirical data, linkage disequilibrium extends 100-1000 times further, and ρ is 100-1000 times smaller, for the Kilifi population of An. gambiae than for any of the other populations. There were also significant runs of homozygosity in many of the individual An. gambiae mosquitoes from Kilifi. These results support the hypothesis that the recent decline in An. gambiae was driven by the rollout of bed nets. Measuring population genomic parameters in a small sample of individuals before, during and after vector or pest control may be a valuable method of tracking the effectiveness of interventions

Maximum likelihood estimates of pairwise rearrangement distances

Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. In the case of bacteria, distances can be estimated using a range of different evolutionary models, from single nucleotide polymorphisms to large-scale genome rearrangements. In the case of sequence evolution models (such as the Jukes-Cantor model and associated metric) have been used to correct pairwise distances. Similar correction methods for genome rearrangement processes are required to improve inference. Current attempts at correction fall into 3 categories: Empirical computational studies, Bayesian/MCMC approaches, and combinatorial approaches. Here we introduce a maximum likelihood estimator for the inversion distance between a pair of genomes, using the group-theoretic approach to modelling inversions introduced recently. This MLE functions as a corrected distance: in particular, we show that because of the way sequences of inversions interact with each other, it is quite possible for minimal distance and MLE distance to differently order the distances of two genomes from a third. This has obvious implications for the use of minimal distance in phylogeny reconstruction. The work also tackles the above problem allowing free rotation of the genome. Generally a frame of reference is locked, and all computation made accordingly. This work incorporates the action of the dihedral group so that distance estimates are free from any a priori frame of reference.Comment: 21 pages, 7 figures. To appear in the Journal of Theoretical Biolog

Dynamics of Genome Rearrangement in Bacterial Populations

Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic bacteria such as Yersinia pestis, which causes bubonic and pneumonic plague, often exhibit a high degree of genomic rearrangement. The recent availability of several Yersinia genomes offers an unprecedented opportunity to study the evolution of genome structure and arrangement. We introduce a set of statistical methods to study patterns of rearrangement in circular chromosomes and apply them to the Yersinia. We constructed a multiple alignment of eight Yersinia genomes using Mauve software to identify 78 conserved segments that are internally free from genome rearrangement. Based on the alignment, we applied Bayesian statistical methods to infer the phylogenetic inversion history of Yersinia. The sampling of genome arrangement reconstructions contains seven parsimonious tree topologies, each having different histories of 79 inversions. Topologies with a greater number of inversions also exist, but were sampled less frequently. The inversion phylogenies agree with results suggested by SNP patterns. We then analyzed reconstructed inversion histories to identify patterns of rearrangement. We confirm an over-representation of “symmetric inversions”—inversions with endpoints that are equally distant from the origin of chromosomal replication. Ancestral genome arrangements demonstrate moderate preference for replichore balance in Yersinia. We found that all inversions are shorter than expected under a neutral model, whereas inversions acting within a single replichore are much shorter than expected. We also found evidence for a canonical configuration of the origin and terminus of replication. Finally, breakpoint reuse analysis reveals that inversions with endpoints proximal to the origin of DNA replication are nearly three times more frequent. Our findings represent the first characterization of genome arrangement evolution in a bacterial population evolving outside laboratory conditions. Insight into the process of genomic rearrangement may further the understanding of pathogen population dynamics and selection on the architecture of circular bacterial chromosomes

Inferring Histories of Adaptive Divergence with Gene Flow: Genetic, Demographic and Geographic Effects.

As genomic data is increasingly available even for non-model organisms, the traditional boundaries among fields such as phylogenetics, phylogeography and genetics of adaptation are disappearing. This thesis provides a synthetic framework for studying ecological genomics, which considers selective processes (such as adaptation to new niches) and neutral processes (such as population size changes due to environmental shifts) simultaneously. Conventionally, studies that look for targets of selection on a genome assume a simple demographic model without validations from the species' ecological or phylogeographic histories. The work demonstrates that one cannot reliably identify selection unless realistic demographic histories are inferred for the species or even a specific genomic region. In particular, I investigate the evolutionary history of large polymorphic inversions in Anopheles gambiae, which maintains adaptive divergence among ecologically divergent populations. By modeling the unique origin and introgression histories of each inversion, I am able to identify target regions of selection within inversions through training discriminant functions with pure drift versus selection simulations. The thesis also extends the existing theory of local adaptation model via chromosomal inversions to consider the source of inversion variation, as well as evaluates the likelihood of such adaptations under different parameter spaces. The findings are particularly important for understanding mosaic genomic evolution in the early stages of speciation, where accumulation of divergence is dampened by gene flow. Finally, I examine how historical events, such as habitat contractions or recolonization, influence current genetic pattern and the application of spatially-explicit demographic modeling under Approximate Bayesian Computation statistics to distinguish different phylogeographic scenarios. The work represents a flexible framework for researchers to translate dynamic phylogeographic hypotheses into testable coalescent models by integrating all the available information of the species, such as distribution records, habitat preference, paleo-climate models, and competition between species. In general, with the amount of information as well as inherent heterogeneity of genomic data, this thesis contributes to the ongoing paradigm shift from studying separate evolutionary processes towards a holistic analysis of the interactions of selective and neutral processes under a rigorous statistical framework.PHDEcology and Evolutionary BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/111443/1/heqixin_1.pd

A new genus of neobatrachian frog from southern Patagonian forests, Argentina and Chile

In 1975 Lynch named a new species of frog based on two specimens from Puerto Eden, Wellington Island, southern Chile, tentatively allocated to the genus Telmatobius. Telmatobius grandisonae Lynch was later included by the same author in his genus Atelognathus. Based on a reappraisal of the type material and the description of the internal and external morphology, karyotype, tadpole morphology and molecular evidence from recently discovered specimens collected at Lago del Desierto, southern Argentina, we describe the monotypic genus Chaltenobatrachus, with Telmatobius grandisonae (Lynch) serving as the type species. Chaltenobatrachus differs from Atelognathus mainly in having a uniform bright green dorsal coloration, with brown to reddish warts; orange iris with gold spots; fingers with interdigital membrane; frontoparietals well developed, small nasals; well ossified sphenethmoid; anteriorly expanded homosternum; skin of tadpole transparent; oral disc with protruding anterior and lateral papillae; diploid number 2n = 32 chromosomes. The genetic distances between Chaltenobatrachus and Atelognathus meet or exceed most other intergeneric comparisons.Fil: Basso, Nestor Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; ArgentinaFil: Úbeda, Carmen A.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Bunge, Maria M.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigaciones en Biodiversidad y Medioambiente. Universidad Nacional del Comahue. Centro Regional Universidad Bariloche. Instituto de Investigaciones en Biodiversidad y Medioambiente; ArgentinaFil: Martinazzo Giménez, Liza Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentin

Models and analyses of chromosome evolution

textAt the core of evolutionary biology stands the study of divergence between populations and the formation of new species. This dissertation applies a diverse array of theoretical and statistical approaches to study how chromosomes evolve. In the first chapter, I build models that predict the amount of neutral genetic variation in chromosomal inversions involved in local adaptation, providing a foundation for future studies on the role of these rearrangements in population divergence. In the second chapter, I use a large dataset of the geographic variation in frequency of a chromosomal inversion to infer natural selection and non-random mating, revealing that this inversion could be implicated in strong reproductive isolation between subpopulations of a single species. In the third chapter, I use coalescent models for recombining sex chromosomes coupled with approximate Bayesian computation to estimate the recombination rate between X and Y chromosomes in European tree frogs. This novel approach allows me to infer a rate so low that would have been hard to detect with empirical methods. In the fourth chapter, I study the theoretical conditions that favor the evolution of a chromosome fusion that reduces recombination between locally adapted alleles.Ecology, Evolution and Behavio