Intra- and inter-annual uranium concentration variability in a Belizean stalagmite controlled by prior aragonite precipitation: A new tool for reconstructing hydro-climate using aragonitic speleothems

Aragonitic speleothems are increasingly utilised as palaeoclimate archives due to their amenability to high precision U–Th dating. Proxy records from fast-growing aragonitic stalagmites, precisely dated to annual timescales, can allow investigation of climatic events occurring on annual or even sub-annual timescales with minimal chronological uncertainty. However, the behaviour of many trace elements, such as uranium, in aragonitic speleothems has not thus far been as well constrained as in calcitic speleothems. Here, we use uranium concentration shifts measured across primary calcite-to-aragonite mineralogical transitions in speleothems to calculate the distribution coefficient of uranium in aragonitic speleothems (derived DU = 3.74 ± 1.13). Because our calculated DU is considerably above 1 increased prior aragonite precipitation due to increased karst water residence time should strongly control stalagmite aragonite U/Ca values. Consequently, uranium concentrations in aragonitic speleothems should act as excellent proxies for effective rainfall. We test this using a high-resolution ICP-MS derived trace element dataset from a Belizean stalagmite. YOK-G is an aragonitic stalagmite from Yok Balum cave in Belize with an extremely robust monthly-resolved chronology built using annual δ13C cycles. We interpret seasonal U/Ca variations in YOK-G as reflecting changes in the amount and seasonality of prior aragonite precipitation driven by variable rainfall amounts. The U/Ca record strongly suggests that modern drying has occurred in Belize, and that this drying was primarily caused by a reduction in wet season rainfall. This is consistent with published stable isotope data from YOK-G also very strongly suggesting modern rainfall reductions, previously interpreted as the result of southward ITCZ displacement. Our results strongly suggest that U/Ca values in aragonitic speleothems are excellent proxies for rainfall variability. This new tool, combined with the exceptional chronological control characteristic of aragonitic stalagmites and the high spatial resolution afforded by modern microanalytical techniques, should facilitate the construction of new exquisitely resolved rainfall records, providing rare insights into seasonality changes as well as long-term changes in local recharge conditions

COnstructing Proxy Records from Age models (COPRA)

Reliable age models are fundamental for any palaeoclimate reconstruction. Available interpolation procedures between age control points are often inadequately reported, and very few translate age uncertainties to proxy uncertainties. Most available modeling algorithms do not allow incorporation of layer counted intervals to improve the confidence limits of the age model in question. We present a framework that allows detection and interactive handling of age reversals and hiatuses, depth-age modeling, and proxy-record reconstruction. Monte Carlo simulation and a translation procedure are used to assign a precise time scale to climate proxies and to translate dating uncertainties to uncertainties in the proxy values. The presented framework allows integration of incremental relative dating information to improve the final age model. The free software package COPRA1.0 facilitates easy interactive usage

Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14th century

We report genome-wide data for 33 Ashkenazi Jews (AJ), dated to the 14th century, following a salvageexcavation at the medieval Jewish cemetery of Erfurt, Germany. The Erfurt individuals are geneticallysimilar to modern AJ and have substantial Southern European ancestry, but they show more variabilityin Eastern European-related ancestry than modern AJ. A third of the Erfurt individuals carried the samenearly-AJ-specific mitochondrial haplogroup and eight carried pathogenic variants known to affect AJtoday. These observations, together with high levels of runs of homozygosity, suggest that the Erfurtcommunity had already experienced the major reduction in size that affected modern AJ. However, theErfurt bottleneck was more severe, implying substructure in medieval AJ. Together, our results suggestthat the AJ founder event and the acquisition of the main sources of ancestry pre-dated the 14th centuryand highlight late medieval genetic heterogeneity no longer present in modern AJ

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

Background Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals. Results Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle. Conclusions This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought

Understanding language evolution : beyond Pan-centrism

Language does not fossilize but this does not mean that the language's evolutionary timeline is lost forever. Great apes provide a window back in time on our last prelinguistic ancestor's communication and cognition. Phylogeny and cladistics implicitly conjure Pan (chimpanzees, bonobos) as a superior (often the only) model for language evolution compared with earlier diverging lineages, Gorilla and Pongo (orangutans). Here, in reviewing the literature, it is shown that Pan do not surpass other great apes along genetic, cognitive, ecologic, or vocal traits that are putatively paramount for language onset and evolution. Instead, revived herein is the idea that only by abandoning single-species models and learning about the variation among great apes, there might be a chance to retrieve lost fragments of the evolutionary timeline of language.PostprintPeer reviewe

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis

<p>Abstract</p> <p>Background</p> <p>The Gene Ontology (GO) Consortium organizes genes into hierarchical categories based on biological process, molecular function and subcellular localization. Tools such as GoMiner can leverage GO to perform ontological analysis of microarray and proteomics studies, typically generating a list of significant functional categories. Two or more of the categories are often redundant, in the sense that identical or nearly-identical sets of genes map to the categories. The redundancy might typically inflate the report of significant categories by a factor of three-fold, create an illusion of an overly long list of significant categories, and obscure the relevant biological interpretation.</p> <p>Results</p> <p>We now introduce a new resource, RedundancyMiner, that de-replicates the redundant and nearly-redundant GO categories that had been determined by first running GoMiner. The main algorithm of RedundancyMiner, MultiClust, performs a novel form of cluster analysis in which a GO category might belong to several category clusters. Each category cluster follows a "complete linkage" paradigm. The metric is a similarity measure that captures the overlap in gene mapping between pairs of categories.</p> <p>Conclusions</p> <p>RedundancyMiner effectively eliminated redundancies from a set of GO categories. For illustration, we have applied it to the clarification of the results arising from two current studies: (1) assessment of the gene expression profiles obtained by laser capture microdissection (LCM) of serial cryosections of the retina at the site of final optic fissure closure in the mouse embryos at specific embryonic stages, and (2) analysis of a conceptual data set obtained by examining a list of genes deemed to be "kinetochore" genes.</p

Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis

BACKGROUND: Massive Parallel Sequencing methods (MPS) can extend and improve the knowledge obtained by conventional microarray technology, both for mRNAs and short non-coding RNAs, e.g. miRNAs. The processing methods used to extract and interpret the information are an important aspect of dealing with the vast amounts of data generated from short read sequencing. Although the number of computational tools for MPS data analysis is constantly growing, their strengths and weaknesses as part of a complex analytical pipe-line have not yet been well investigated. PRIMARY FINDINGS: A benchmark MPS miRNA dataset, resembling a situation in which miRNAs are spiked in biological replication experiments was assembled by merging a publicly available MPS spike-in miRNAs data set with MPS data derived from healthy donor peripheral blood mononuclear cells. Using this data set we observed that short reads counts estimation is strongly under estimated in case of duplicates miRNAs, if whole genome is used as reference. Furthermore, the sensitivity of miRNAs detection is strongly dependent by the primary tool used in the analysis. Within the six aligners tested, specifically devoted to miRNA detection, SHRiMP and MicroRazerS show the highest sensitivity. Differential expression estimation is quite efficient. Within the five tools investigated, two of them (DESseq, baySeq) show a very good specificity and sensitivity in the detection of differential expression. CONCLUSIONS: The results provided by our analysis allow the definition of a clear and simple analytical optimized workflow for miRNAs digital quantitative analysis

Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq

Transcription is the first step connecting genetic information with an organism's phenotype. While expression of annotated genes in the human brain has been characterized extensively, our knowledge about the scope and the conservation of transcripts located outside of the known genes' boundaries is limited. Here, we use high-throughput transcriptome sequencing (RNA-Seq) to characterize the total non-ribosomal transcriptome of human, chimpanzee, and rhesus macaque brain. In all species, only 20–28% of non-ribosomal transcripts correspond to annotated exons and 20–23% to introns. By contrast, transcripts originating within intronic and intergenic repetitive sequences constitute 40–48% of the total brain transcriptome. Notably, some repeat families show elevated transcription. In non-repetitive intergenic regions, we identify and characterize 1,093 distinct regions highly expressed in the human brain. These regions are conserved at the RNA expression level across primates studied and at the DNA sequence level across mammals. A large proportion of these transcripts (20%) represents 3′UTR extensions of known genes and may play roles in alternative microRNA-directed regulation. Finally, we show that while transcriptome divergence between species increases with evolutionary time, intergenic transcripts show more expression differences among species and exons show less. Our results show that many yet uncharacterized evolutionary conserved transcripts exist in the human brain. Some of these transcripts may play roles in transcriptional regulation and contribute to evolution of human-specific phenotypic traits

South-to-north migration preceded the advent of intensive farming in the Maya region

This is the final version. Available on open access from Nature Research via the DOI in this recordData availability: The aligned sequences have been deposited in the European Nucleotide Archive database under accession code PRJEB49391. The processed genotype data used in analysis are available online on the Nature Communications website as Supplementary Data 9.The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations. After ~5,600 cal. BP a previously unknown human dispersal from the south made a major demographic impact on the region, contributing more than 50% of the ancestry of all later individuals. This new ancestry derived from a source related to present-day Chibchan speakers living from Costa Rica to Colombia. Its arrival corresponds to the first clear evidence for forest clearing and maize horticulture in what later became the Maya region.Alphawood FoundationNational Science Foundation (NSF)National Institutes of Health (NIH)John Templeton FoundationPaul G. Allen Family Foundatio