Showing papers by "David M. Lambert published in 2015"
••
University of Tartu1, Estonian Biocentre2, University of Cambridge3, University of California, Berkeley4, Arizona State University5, Armenian National Academy of Sciences6, Russian Academy of Sciences7, University of Auckland8, Pennsylvania State University9, University of Winchester10, Wellcome Trust Sanger Institute11, University of Copenhagen12, Kazan Federal University13, Bashkir State University14, Georgia Institute of Technology15, University of Pennsylvania16, Centre national de la recherche scientifique17, Eijkman Institute for Molecular Biology18, Massey University19, University of Dhaka20, Aarhus University21, Griffith University22, Josip Juraj Strossmayer University of Osijek23, Academy of Sciences of Uzbekistan24, Kuban State Medical University25, Nazarbayev University26, L.N.Gumilyov Eurasian National University27, North-Eastern Federal University28, Academy of Medical Sciences, United Kingdom29, Anthony Nolan30, University College London31, University of St Andrews32, University of Kharkiv33, International Burch University34, National Academy of Sciences of Belarus35, Radboud University Nijmegen36, King Abdullah University of Science and Technology37, Stanford University38, University of Arizona39, Stony Brook University40, University Hospital of North Norway41, Estonian Academy of Sciences42
TL;DR: A study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples, infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky, and hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.
Abstract: It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.
325 citations
••
TL;DR: The kiwi genome provides a valuable genomic resource for future genome-wide comparative analyses to other extinct and extant diurnal ratites and there is an enrichment of genes influencing mitochondrial function and energy expenditure among genes that are rapidly evolving specifically on the k Kiwi branch, which may be linked to its nocturnal lifestyle.
Abstract: Kiwi, comprising five species from the genus Apteryx, are endangered, ground-dwelling bird species endemic to New Zealand. They are the smallest and only nocturnal representatives of the ratites. The timing of kiwi adaptation to a nocturnal niche and the genomic innovations, which shaped sensory systems and morphology to allow this adaptation, are not yet fully understood. We sequenced and assembled the brown kiwi genome to 150-fold coverage and annotated the genome using kiwi transcript data and non-redundant protein information from multiple bird species. We identified evolutionary sequence changes that underlie adaptation to nocturnality and estimated the onset time of these adaptations. Several opsin genes involved in color vision are inactivated in the kiwi. We date this inactivation to the Oligocene epoch, likely after the arrival of the ancestor of modern kiwi in New Zealand. Genome comparisons between kiwi and representatives of ratites, Galloanserae, and Neoaves, including nocturnal and song birds, show diversification of kiwi’s odorant receptors repertoire, which may reflect an increased reliance on olfaction rather than sight during foraging. Further, there is an enrichment of genes influencing mitochondrial function and energy expenditure among genes that are rapidly evolving specifically on the kiwi branch, which may also be linked to its nocturnal lifestyle. The genomic changes in kiwi vision and olfaction are consistent with changes that are hypothesized to occur during adaptation to nocturnal lifestyle in mammals. The kiwi genome provides a valuable genomic resource for future genome-wide comparative analyses to other extinct and extant diurnal ratites.
78 citations
••
TL;DR: This in silico study suggests aDNA-associated damage patterns minimally impact variant call accuracy and recovery from short-read alignment, while modest increases in sequencing depth can greatly improve variant recovery.
Abstract: Massively parallel sequencing platforms, featuring high throughput and relatively short read lengths, are well suited to ancient DNA (aDNA) studies. Variant identification from short-read alignment could be hindered, however, by low DNA concentrations common to historic samples, which constrain sequencing depths, and post-mortem DNA damage patterns. We simulated pairs of sequences to act as reference and sample genomes at varied GC contents and divergence levels. Short-read sequence pools were generated from sample sequences, and subjected to varying levels of “post-mortem” damage by adjusting levels of fragmentation and fragmentation biases, transition rates at sequence ends, and sequencing depths. Mapping of sample read pools to reference sequences revealed several trends, including decreased alignment success with increased read length and decreased variant recovery with increased divergence. Variants were generally called with high accuracy, however identification of SNPs (single-nucleotide polymorphisms) was less accurate for high damage/low divergence samples. Modest increases in sequencing depth resulted in rapid gains in total variant recovery, and limited improvements to recovery of heterozygous variants. This in silico study suggests aDNA-associated damage patterns minimally impact variant call accuracy and recovery from short-read alignment, while modest increases in sequencing depth can greatly improve variant recovery.
28 citations
••
TL;DR: Progress is reported on a population genomic study of the Adélie penguin (Pygoscelis adeliae), ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica.
Abstract: Recently, the study of ancient DNA (aDNA) has been greatly enhanced by the development of second-generation DNA sequencing technologies and targeted enrichment strategies. These developments have allowed the recovery of several complete ancient genomes, a result that would have been considered virtually impossible only a decade ago. Prior to these developments, aDNA research was largely focused on the recovery of short DNA sequences and their use in the study of phylogenetic relationships, molecular rates, species identification and population structure. However, it is now possible to sequence a large number of modern and ancient complete genomes from a single species and thereby study the genomic patterns of evolutionary change over time. Such a study would herald the beginnings of ancient population genomics and its use in the study of evolution. Species that are amenable to such large-scale studies warrant increased research effort. We report here progress on a population genomic study of the Adelie penguin (Pygoscelis adeliae). This species is ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica. This species will enable us to directly address many of the fundamental questions in ecology and evolution.
21 citations
••
TL;DR: The first ages of a selection of Sacred Ibis mummies using 14C methods in order to establish how closely they match the archaeological chronology were reported from museum samples provenience from Saqqara, Roda and Thebes as mentioned in this paper.
14 citations
••
TL;DR: Concentrated hydrochloric acid was shown to dissolve most of the undigested bone and allowed the efficient recovery of DNA fragments <100 bases in length, which can lead to a several‐fold increase in DNA yield when compared to other commonly used methods.
Abstract: The successful extraction of DNA from historical or ancient animal bone is important for the analysis of discriminating genetic markers. Methods used currently rely on the digestion of bone with EDTA and proteinase K, followed by purification with phenol/chloroform and silica bed binding. We have developed a simple concentrated hydrochloric acid-based method that precludes the use of phenol/chloroform purification and can lead to a several-fold increase in DNA yield when compared to other commonly used methods. Concentrated hydrochloric acid was shown to dissolve most of the undigested bone and allowed the efficient recovery of DNA fragments <100 bases in length. This method should prove useful for the recovery of DNAs from highly degraded animal bone, such as that found in historical or ancient samples.
7 citations
••
TL;DR: This work sequencing complete mitochondrial genomes of the relic species Tuatara from ten offshore islands of New Zealand observed a positive relationship that showed a proportional increase in the neutral diversity at synonymous sites, with increasing geographical distance, and a significant negative relationship between the ratio of dC/dS and geographic distance.
Abstract: Population genetic models predict that populations that are geographically close to each other are expected to be genetically more similar to each other compared to those that are widely separate. However the patterns of relationships between geographic distance and molecular divergences at neutral and constrained regions of the genome are unclear. We attempted to clarify this relationship by sequencing complete mitochondrial genomes of the relic species Tuatara (Sphenodon punctatus) from ten offshore islands of New Zealand. We observed a positive relationship that showed a proportional increase in the neutral diversity at synonymous sites (dS), with increasing geographical distance. In contrast we showed that diversity at evolutionarily constrained sites (dC) was elevated in the case of comparisons involving closely located populations. Conversely diversity was reduced in the case of comparisons between distantly located populations. These patterns were confirmed by a significant negative relationship between the ratio of dC/dS and geographic distance. The observed high dC/dS could be explained by the abundance of deleterious mutations in comparisons involving closely located populations, due to the recent population divergence times. Since distantly related populations were separated over long periods of time, deleterious mutations might have been removed by purifying selection.
5 citations
••
01 Jan 2015
TL;DR: In terms of understanding evolutionary processes in the human origins story, much can be gained by employing an approach of splitting the known fossil record into numerous taxonomically recognized species as discussed by the authors.
Abstract: In terms of understanding evolutionary processes in the human origins story, much can be gained by employing an approach of splitting the known fossil record into numerous taxonomically recognised species. By focusing on variation in fossil specimens, as defined by differences in characters in both time and space, we can start to explore possible evolutionary relationships among the range of fossil specimens. The opposite approach, of lumping such taxonomically species will potentially obscure interesting differentiation, resulting in the possible loss of understanding for important phylogenetic relationships (Groves, 1989a). Whether such taxonomically recognised species are biologically real or not is exceedingly difficult to establish in the fossil record, however, splitting fossils into divisions based on character traits enables the effective testing of hypotheses regarding the validity of such species.
4 citations
••
TL;DR: This study reports a total of five nearly complete mitochondrial genomes, which were sequenced by Sanger and Next Generation DNA sequencing methods and revealed distinct clustering of tuatara populations from the north and south islands of New Zealand.
Abstract: Tuatara are the sister taxon to the Squamata (including lizards and snakes) and are regarded as the most distinctive surviving reptilian genus. They are currently inhabits on offshore islands around New Zealand and have been recognized as a species in need of active conservation management. In this study, we report a total number of five nearly complete mitochondrial genomes, which were sequenced by Sanger and Next Generation DNA sequencing methods. Our phylogenomic analysis revealed distinct clustering of tuatara populations from the north and south islands of New Zealand.
3 citations