Inference of Ancestral Recombination Graphs through Topological Data Analysis

The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Gal\'apagos Islands.Comment: 33 pages, 12 figures. The accompanying software, instructions and example files used in the manuscript can be obtained from https://github.com/RabadanLab/TARGe

Understanding evolutionary processes during past Quaternary climatic cycles: Can it be applied to the future?

Climate change affected ecological community make-up during the Quaternary which was probably both the cause of, and was caused by, evolutionary processes such as species evolution, adaptation and extinction of species and populations

Morphological evaluation of genetic evidence for a Pleistocene extirpation of eastern African impala

Palaeontology typically relies on fossil studies, in particular morphological differences, to reconstruct and interpret patterns of vertebrate evolution. However, genetic studies of population histories of extant species provide data about past population events (e.g. local extinctions, recolonisations) which are equally relevant to palaeontological questions. This study used morphological traits to evaluate a hypothesis based on genetic evidence that southern African impala (Aepyceros melampus) are the founder population for all other living African impala populations, after an eastern African extirpation event dating to around 200 000 years ago. Measurements of three horn metrics and the presence or absence of a particular dental trait were compared across four regional impala samples. Eastern African impala possess a unique combination of larger horns and a signiicantly higher occurrence of entostyles when compared to other impala populations. These traits are likely to have characterised a small group of founding impala which recolonised this region. This pattern appears consistent with the genetic evidence that a subset of the southern African impala gave rise to the eastern African populations. Other species with complex population histories, such as wildebeest, eland, topi and hartebeest may also therefore be expected to express variation in certain morphological traits in the fossil record because of similar patterns of recolonisations. The process of local extinction and subsequent repopulation over shorter timescales may pass unnoticed in the fossil record, and lineages may appear uninterrupted. Instead, greater morphological variation within a species may be observed, which may be misinterpreted as reflecting a speciation event, or ecophenotypic variation. Combining data from genetic studies and palaeontology may provide further clues as to how faunal dispersals within Africa shaped the morphological variation in the fossil record, and how to best interpret such differences

DNA and pacific commensal models : applications, construction, limitations, and future prospects

Components of the Pacific transported landscape have been used as proxies to trace the prehistoric movement of humans across the Pacific for almost two decades. Analyses of archaeological remains and DNA sequences of plants, animals, and microorganisms moved by or with humans have contributed to understanding prehistoric migration, trade, exchange, and sometimes revealed the geographic origins of particular plants and animals. This paper presents the basic elements of a DNA-based commensal model and discusses the phylogenetic and population genetic approaches these models employ. A clear delineation of the underlying assumptions of these models and the background information required to construct them have yet to appear in the literature. This not only provides a framework with which to construct a commensal model but also highlights gaps in current knowledge. The ways in which commensal models have enriched archaeological reconstructions will be highlighted, as will their current limitations. With these limitations in mind, options will be outlined for augmenting commensal models through the application of established techniques and new technologies in order to provide the best tools for reconstructing ancient human mobility and behavior in the Pacific and beyond

Assessing the preservation of cytosine methylation in ancient DNA from five prehistoric Native American populations

textCytosine methylation of CpG dinucleotides is an important epigenetic mark that regulates gene expression in humans. While methylation patterns in extant populations have been widely studied, few studies have attempted to analyze methylation in ancient DNA. Indeed, it was only recently shown that methyl groups can be preserved in ancient DNA. However, it is unknown how often methylation patterns can be recovered from ancient samples with preserved nuclear DNA. If they are frequently preserved, it may ultimately be possible to infer patterns of gene activity at the population level in ancient times. In this study, I assessed the preservation of cytosine methylation in ancient DNA from the remains of 30 prehistoric Native Americans from California, Illinois, Kentucky, and Mexico. These samples were previously shown to contain endogenous mitochondrial and nuclear DNA. I analyzed the cytosine methylation states of CpG-rich retrotransposons, which are epigenetically inactivated by cytosine methylation in humans. Unmethylated cytosines were converted to uracils by treatment with sodium bisulfite. Bisulfite products were pyrosequenced, and C-to-T conversions at potentially methylated CpG dinucleotides were quantified. I found that cytosine methylation is readily recoverable from human remains with preserved nuclear DNA from various localities over the time depth tested (~6000 years). This study presents the first direct evidence of cytosine methylation in ancient human remains, and suggests that it may be possible to analyze patterns of gene activity in ancient populations.Anthropolog

‘The uses of ethnography in the science of cultural evolution’. Commentary on Mesoudi, A., Whiten, A. and K. Laland ‘Toward a unified science of cultural evolution’

There is considerable scope for developing a more explicit role for ethnography within the research program proposed in the article. Ethnographic studies of cultural micro-evolution would complement experimental approaches by providing insights into the “natural” settings in which cultural behaviours occur. Ethnography can also contribute to the study of cultural macro-evolution by shedding light on the conditions that generate and maintain cultural lineages

Genealogical typing of Neisseria meningitidis

Despite the increasing popularity of multilocus sequence typing (MLST), the most appropriate method for characterizing bacterial variation and facilitating epidemiological investigations remains a matter of debate. Here, we propose that different typing schemes should be compared on the basis of their power to infer clonal relationships and investigate the utility of sequence data for genealogical reconstruction by exploiting new statistical tools and data from 20 housekeeping loci for 93 isolates of the bacterial pathogen Neisseria meningitidis. Our analysis demonstrated that all but one of the hyperinvasive isolates established by multilocus enzyme electrophoresis and MLST were grouped into one of six genealogical lineages, each of which contained substantial variation. Due to the confounding effect of recombination, evolutionary relationships among these lineages remained unclear, even using 20 loci. Analyses of the seven loci in the standard MLST scheme using the same methods reproduced this classification, but were unable to support finer inferences concerning the relationships between the members within each complex

The Family Name as Socio-Cultural Feature and Genetic Metaphor: From Concepts to Methods

A recent workshop entitled The Family Name as Socio-Cultural Feature and Genetic Metaphor: From Concepts to Methods was held in Paris in December 2010, sponsored by the French National Centre for Scientific Research (CNRS) and by the journal Human Biology. This workshop was intended to foster a debate on questions related to the family names and to compare different multidisciplinary approaches involving geneticists, historians, geographers, sociologists and social anthropologists. This collective paper presents a collection of selected communications