Author
David M. Lambert
Other affiliations: Massey University, University of the Witwatersrand, University of Edinburgh ...read more
Bio: David M. Lambert is an academic researcher from Griffith University. The author has contributed to research in topics: Population & Ancient DNA. The author has an hindex of 46, co-authored 202 publications receiving 9449 citations. Previous affiliations of David M. Lambert include Massey University & University of the Witwatersrand.
Topics: Population, Ancient DNA, Molecular evolution, DNA barcoding, Pygoscelis
Papers published on a yearly basis
Papers
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Duke University1, University of Texas at Austin2, Heidelberg Institute for Theoretical Studies3, American Museum of Natural History4, Beijing Genomics Institute5, Xi'an Jiaotong University6, New Mexico State University7, University of Sydney8, University of California9, Uppsala University10, University of Copenhagen11, Okinawa Institute of Science and Technology12, University of Georgia13, Griffith University14, Catalan Institution for Research and Advanced Studies15, Joint Institute for Nuclear Research16, Oak Ridge National Laboratory17, Aarhus University18, Washington University in St. Louis19, University of California, Santa Cruz20, Cardiff University21, Kunming Institute of Zoology22, China Agricultural University23, Tulane University24, Louisiana State University25, Copenhagen Zoo26, Federal University of Pará27, Oregon Health & Science University28, Technical University of Denmark29, Canterbury Museum30, Curtin University31, Novosibirsk State University32, Smithsonian Institution33, National University of Singapore34, National Museum of Natural History35, Nova Southeastern University36, Occidental College37, University of Edinburgh38, Harvard University39, University of California, San Francisco40, University of Florida41, University of Illinois at Urbana–Champaign42
TL;DR: A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
Abstract: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
1,624 citations
University of Copenhagen1, University of California, Berkeley2, Technical University of Denmark3, Estonian Biocentre4, Imperial College London5, University of Cambridge6, Chinese Academy of Sciences7, Stanford University8, Murdoch University9, National Autonomous University of Mexico10, University of Western Australia11, Kitasato University12, University of Bern13, University of Chicago14, University of Toulouse15, Leiden University16, University College London17, Griffith University18, Max Planck Society19, University of British Columbia20, Estonian Academy of Sciences21
TL;DR: It is shown that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago, which is separate from the one that gave rise to modern Asians 25, thousands of years ago.
Abstract: We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.
656 citations
Swiss Institute of Bioinformatics1, University of Copenhagen2, University of Bern3, Griffith University4, Pompeu Fabra University5, Instituto Gulbenkian de Ciência6, Wellcome Trust Sanger Institute7, Aarhus University8, University of California, Berkeley9, Max Planck Society10, Technical University of Denmark11, King Abdullah University of Science and Technology12, University of Cambridge13, ETH Zurich14, Monash University Malaysia Campus15, Centre national de la recherche scientifique16, University of Porto17, University College London18, Papua New Guinea Institute of Medical Research19, University of Papua New Guinea20, University of Otago21, Wellcome Trust Centre for Human Genetics22, Estonian Biocentre23, University of Oxford24, University of Western Australia25, Yale University26, University of California, San Francisco27
TL;DR: A population expansion in northeast Australia during the Holocene epoch associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama–Nyungan languages is inferred.
Abstract: The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama–Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25–40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10–32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama–Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51–72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.
389 citations
University of Cambridge1, University of Bologna2, Estonian Biocentre3, University of Bristol4, Harvard University5, King Abdullah University of Science and Technology6, University of Tartu7, University of Montpellier8, Massey University9, University of Auckland10, Pennsylvania State University11, University of California, San Francisco12, Biodesign Institute13, Arizona State University14, University of Southampton15, University of Montana16, National Academy of Sciences of Belarus17, Wellcome Trust Sanger Institute18, Kuban State Medical University19, University of Georgia20, University of Copenhagen21, Griffith University22, Academy of Sciences of Uzbekistan23, L.N.Gumilyov Eurasian National University24, University of Dhaka25, University of Pennsylvania26, Georgia Institute of Technology27, Russian Academy of Sciences28, Academy of Medical Sciences, United Kingdom29, Royal Free Hospital30, University of Kharkiv31, Centre national de la recherche scientifique32, Eijkman Institute for Molecular Biology33, North-Eastern Federal University34, Josip Juraj Strossmayer University of Osijek35, Armenian National Academy of Sciences36, University of Winchester37, University Hospital Heidelberg38, Novosibirsk State University39, Bashkir State University40, International Burch University41, Russian Academy42, University College London43, James Cook University44, University of Papua New Guinea45, Max Planck Society46, University of California, Berkeley47, Estonian Academy of Sciences48
TL;DR: A genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa earlier than 75,000 years ago is found.
Abstract: High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.
336 citations
Estonian Biocentre1, University of Tartu2, 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, Bashkir State University13, Kazan Federal 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
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TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
11,521 citations
TL;DR: In this paper, the authors introduce a new approach to perform relaxed phylogenetic analysis, which can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times.
Abstract: In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of “relaxed phylogenetics.” Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.
5,812 citations
01 Aug 2000
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.
4,833 citations
TL;DR: This paper showed that the likelihood equations used by versions 1.0 and 2.0 of CERVUS to accommodate genotyping error miscalculate the probability of observing an erroneous genotype.
Abstract: Genotypes are frequently used to identify parentage. Such analysis is notoriously vulnerable to genotyping error, and there is ongoing debate regarding how to solve this problem. Many scientists have used the computer program CERVUS to estimate parentage, and have taken advantage of its option to allow for genotyping error. In this study, we show that the likelihood equations used by versions 1.0 and 2.0 of CERVUS to accommodate genotyping error miscalculate the probability of observing an erroneous genotype. Computer simulation and reanalysis of paternity in Rum red deer show that correcting this error increases success in paternity assignment, and that there is a clear benefit to accommodating genotyping errors when errors are present. A new version of CERVUS (3.0) implementing the corrected likelihood equations is available at http://www.fieldgenetics.com.
4,562 citations
TL;DR: The approach to utilizing available RNA-Seq and other data types in the authors' manual curation process for vertebrate, plant, and other species is summarized, and a new direction for prokaryotic genomes and protein name management is described.
Abstract: The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.
4,104 citations