A Draft Sequence of the Neandertal Genome

Green, Edward; Krause, Johannes; Briggs, Adrian W.; Maričić, Tomislav; Stenzel, Udo; Kircher, Martin; Patterson, Nick; Li, Heng; Zhai, Weiwei; Fritz, Markus Hsi Yang; Hansen, Nancy F.; Durand, Éric; Malaspinas, Anna-Sapfo; Jensen, Jeffrey D.; Marquès‐Bonet, Tomàs; Alkan, Can; Prüfer, Kay; Meyer, Matthias; Burbano, Hernán A.; Good, Jeffrey M.; Schultz, Rigo; Aximu‐Petri, Ayinuer; Butthof, Anne; Höber, Barbara; Höffner, Barbara; Siegemund, Madien; Weihmann, Antje; Nusbaum, Chad; Lander, Eric S.; Russ, Carsten; Novod, Nathaniel; Affourtit, Jason P.; Egholm, Michael; Verna, Christine; Rudan, Pavao; Brajković, Dejana; Kućan, Željko; Gušić, Ivan; Doronichev, Vladimir B.; Golovanova, Liubov V.; Lalueza-Fox, Carles; Vives, Marco de la Rasilla; Fortea, Javier; Rosas, Antonio; Schmitz, Ralf W.; Johnson, Philip L.; Eichler, Evan E.; Falush, Daniel; Birney, Ewan; Mullikin, James C.; Slatkin, Montgomery; Nielsen, Rasmus; Kelso, Janet; Lachmann, Michael; Reich, David; Pääbo, Svante

doi:10.1126/science.1188021

Cited by 3,560 publications

(3,832 citation statements)

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“…To test for potential recombination events between Australian Taxon A and other Oryza species, we performed a four‐taxon test, also known as the D‐statistic (Durand et al ., 2011; Green et al ., 2010) separately for each chromosome. This test screens the aligned data for two biallelic mutation patterns: ABBA and BABA.…”

Section: Resultsmentioning

confidence: 99%

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

Brożyńska

Copetti

Furtado

et al. 2017

Plant Biotechnology Journal

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SummaryThe related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon‐like population, referred to as Taxon A, and O. meridionalis‐like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short‐ and long‐read next‐generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.

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Section: Resultsmentioning

confidence: 99%

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

Brożyńska

Copetti

Furtado

et al. 2017

Plant Biotechnology Journal

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“…The D -statistic test in genomic analysis was first introduced by Green et al (2010) to evaluate formally whether humans harbour some Neandertal ancestry (Green et al 2010). Recently, it has been used as a convenient statistic for studying locus-specific introgression of genetic material controlling coloration in Heliconius butterflies (Zhang et al 2015).…”

Section: Discussionmentioning

confidence: 99%

Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

Zhang

Wang

et al. 2018

Mycology

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Hypocrealean fungi (Ascomycota) are known for their diversity of lifestyles. Their vital influences on agricultural and natural ecosystems have resulted in a number of sequenced genomes, which provide essential data for genomic analysis. Totally, 45 hypocrealean fungal genomes constructed a phylogeny. The phylogeny showed that plant pathogens in Nectriaceae diverged earliest, followed by animal pathogens in Cordycipitaceae, Ophiocordycipitaceae and Clavicipitaceae with mycoparasites in Hypocreaceae. Insect/nematode pathogens and grass endophytes in Clavicipitaceae diverged at last. Gene families associated with host-derived nutrients are significantly contracted in diverged lineages compared with the ancestral species. Introgression was detected in certain lineages of hypocrealean fungi, and the main functions of the genes located in the introgressed regions are involved in host recognition, transcriptional regulation, stress response and cell growth regulation. These results indicate that contraction of gene families and introgression might be main mechanisms to drive lifestyle differentiation and evolution and host shift of hypocrealean fungi.

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“…2 One of the authors of Mendez et al 2 even proposed that early Homo sapiens mated with 'an unknown archaic species in western Central Africa' . 10 Although either of the two scenarios above may be true, 11,12 there is no scientific support for either one for the Y chromosome. We wondered whether a simpler explanation might exist.…”

Section: Introductionmentioning

confidence: 99%

The ‘extremely ancient’ chromosome that isn’t: a forensic bioinformatic investigation of Albert Perry’s X-degenerate portion of the Y chromosome

Elhaik

Tatarinova

Klyosov³

et al. 2014

Eur J Hum Genet

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Mendez and colleagues reported the identification of a Y chromosome haplotype (the A00 lineage) that lies at the basal position of the Y chromosome phylogenetic tree. Incorporating this haplotype, the authors estimated the time to the most recent common ancestor (TMRCA) for the Y tree to be 338 000 years ago (95% CI ¼ 237 000-581 000). Such an extraordinarily early estimate contradicts all previous estimates in the literature and is over a 100 000 years older than the earliest fossils of anatomically modern humans. This estimate raises two astonishing possibilities, either the novel Y chromosome was inherited after ancestral humans interbred with another species, or anatomically modern Homo sapiens emerged earlier than previously estimated and quickly became subdivided into genetically differentiated subpopulations. We demonstrate that the TMRCA estimate was reached through inadequate statistical and analytical methods, each of which contributed to its inflation. We show that the authors ignored previously inferred Y-specific rates of substitution, incorrectly derived the Y-specific substitution rate from autosomal mutation rates, and compared unequal lengths of the novel Y chromosome with the previously recognized basal lineage. Our analysis indicates that the A00 lineage was derived from all the other lineages 208 300 (95% CI ¼ 163 900-260 200) years ago.

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A Draft Sequence of the Neandertal Genome

Cited by 3,560 publications

References 87 publications

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

The ‘extremely ancient’ chromosome that isn’t: a forensic bioinformatic investigation of Albert Perry’s X-degenerate portion of the Y chromosome

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