Draft genome of the lowland anoa (Bubalus depressicornis) and comparison with buffalo genome assemblies (Bovidae, Bubalina)

Genomic data for wild species of the genus Bubalus (Asian buffaloes) are still lacking while several whole genomes are currently available for domestic water buffaloes. To address this, we sequenced the genome of a wild endangered dwarf buffalo, the lowland anoa (Bubalus depressicornis), produced a draft genome assembly, and made comparison to published buffalo genomes. The lowland anoa genome assembly was 2.56 Gbp long and contained 103,135 contigs, the longest contig being 337.39 kbp long. N50 and L50 values were 38.73 kbp and 19.83 kbp, respectively, mean coverage was 44x and GC content was 41.74%. Two strategies were adopted to evaluate genome completeness: (i) determination of genomic features with de novo and homology-based predictions using annotations of chromosome-level genome assembly of the river buffalo, and (ii) employment of benchmarking against universal single-copy orthologs (BUSCO). Homology-based predictions identified 94.51% complete and 3.65% partial genomic features. De novo gene predictions identified 32,393 genes, representing 97.14% of the reference's annotated genes, whilst BUSCO search against the mammalian orthologues database identified 71.1% complete, 11.7% fragmented and 17.2% missing orthologues, indicating a good level of completeness for downstream analyses. Repeat analyses indicated that the lowland anoa genome contains 42.12% of repetitive regions. The genome assembly of the lowland anoa is expected to contribute to comparative genome analyses among bovid species. [Abstract copyright: © The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.

Accurate age estimation in small-scale societies

Precise estimation of age is essential in evolutionary anthropology, especially to infer population age structures and understand the evolution of human life history diversity. However, in small-scale societies, such as hunter-gatherer populations, time is often not referred to in calendar years, and accurate age estimation remains a challenge. We address this issue by proposing a Bayesian approach that accounts for age uncertainty inherent to fieldwork data. We developed a Gibbs sampling Markov chain Monte Carlo algorithm that produces posterior distributions of ages for each individual, based on a ranking order of individuals from youngest to oldest and age ranges for each individual. We first validate our method on 65 Agta foragers from the Philippines with known ages, and show that our method generates age estimations that are superior to previously published regression-based approaches. We then use data on 587 Agta collected during recent fieldwork to demonstrate how multiple partial age ranks coming from multiple camps of hunter-gatherers can be integrated. Finally, we exemplify how the distributions generated by our method can be used to estimate important demographic parameters in small-scale societies: here, age-specific fertility patterns. Our flexible Bayesian approach will be especially useful to improve cross-cultural life history datasets for small-scale societies for which reliable age records are difficult to acquire

World-wide distributions of lactase persistence alleles and the complex effects of recombination and selection

The genetic trait of lactase persistence (LP) is associated with at least five independent functional single nucleotide variants in a regulatory region about 14 kb upstream of the lactase gene [-13910*T (rs4988235), -13907*G (rs41525747), -13915*G (rs41380347), -14009*G (rs869051967) and -14010*C (rs145946881)]. These alleles have been inferred to have spread recently and present-day frequencies have been attributed to positive selection for the ability of adult humans to digest lactose without risk of symptoms of lactose intolerance. One of the inferential approaches used to estimate the level of past selection has been to determine the extent of haplotype homozygosity (EHH) of the sequence surrounding the SNP of interest. We report here new data on the frequencies of the known LP alleles in the 'Old World' and their haplotype lineages. We examine and confirm EHH of each of the LP alleles in relation to their distinct lineages, but also show marked EHH for one of the older haplotypes that does not carry any of the five LP alleles. The region of EHH of this (B) haplotype exactly coincides with a region of suppressed recombination that is detectable in families as well as in population data, and the results show how such suppression may have exaggerated haplotype-based measures of past selection

Insights for the melt migration, the volcanic activity and the ultrafast lithosphere delamination related to the Yellowstone plume (Western USA)

The Yellowstone–East Snake River Plain hotspot track has been intensely studied since several decades and is widely considered to result from the interaction of a mantle plume with the North American plate. An integrated conclusive geodynamic interpretation of this extensive data set is however presently still lacking, and our knowledge of the dynamical processes beneath Yellowstone is patchy. It has been argued that the Yellowstone plume has delaminated the lower part of the thick Wyoming cratonic lithosphere. We derive an original dynamic model to quantify delamination processes related to mantle plume–lithosphere interactions. We show that fast (∼300 ka) lithospheric delamination is consistent with the observed timing of formation of successive volcanic centres along the Yellowstone hotspot track and requires (i) a tensile stress regime within the whole lithosphere exceeding its failure threshold, (ii) a purely plastic rheology in the lithosphere when stresses reach this yield limit, (iii) a dense lower part of the 200 km thick Wyoming lithosphere and (iv) a decoupling melt horizon inside the median part of the lithosphere. We demonstrate that all these conditions are verified and that ∼150 km large and ∼100 km thick lithospheric blocks delaminate within 300 ka when the Yellowstone plume ponded below the 200 km thick Wyoming cratonic lithosphere. Furthermore, we take advantage of the available extensive regional geophysical and geological observation data sets to design a numerical 3-D upper-mantle convective model. We propose a map of the ascending convective sheets contouring the Yellowstone plume. The model further evidences the development of a counter-flow within the lower part of the lithosphere centred just above the Yellowstone mantle plume axis. This counter-flow controls the local lithospheric stress field, and as a result the trajectories of feeder dykes linking the partial melting source within the core of the mantle plume with the crust by crosscutting the lithospheric mantle. This counter-flow further explains the 50 km NE shift observed between the mantle plume axis and the present-day Yellowstone Caldera as well as the peculiar shaped crustal magma chambers

Viscoelastic relaxation: A mechanism to explain the decennial large surface displacements at the Laguna del Maule silicic volcanic complex

ilicic systems generate the most explosive eruptions on Earth. In contrast to basaltic systems, they can accumulate large volumes of magma without systematically erupting, confronting the classical interpretation that a volcano inflates when a magmatic intrusion occurs. Understanding the mechanisms of volcanic inflation and unrest is thus one of the most important challenges in volcanic risk assessment. Laguna del Maule (LdM) in the Southern Volcanic Zone (SVZ) of Chile, is one of the most active Holocene silicic complexes in the world and it has been inflating since 2007, accumulating 2 m of uplift without erupting. Several geophysical and geochemical studies conclude that a large crystal rich reservoir would be residing beneath LdM, in consistency with other multi-disciplinary studies showing that such crystal-rich reservoirs (“mush zones”) can be maintained beneath silicic volcanoes, fed by mafic magma recharge from below. Nevertheless, the mechanical state of such reservoirs remains unclear. Here, we characterize for the first time the mechanical properties of such a mush reservoir, able to promote large surface displacements such as those measured at LdM. Using a 3D finite element method we simulate a recharge of magma at the base of a crystal rich reservoir, by assuming an overpressurized source surrounded by a large viscoelastic shell. Inversion results show that this model fits the observed temporal and spatial evolution of ground displacements measured with InSAR data and GNSS data between 2007 and 2017. We interpret the temporal behavior of ground displacement at LdM as resulting from two contributions. A magma recharge occurred within the first 4 yr of the active inflation, followed by the viscous response of the large viscoelastic shell, set to a viscosity of 1017 Pas. Compared to a purely elastic solution, our model suggests that up to 50% of the accumulated surface displacement during the ten-year period can be explained by this viscous response, and predicts ongoing displacements 50 yr after the onset of inflation. This model agrees with geophysical and geochemical observations and offers a simple explanation of the temporal evolution of surface displacements. It further allows to reconsider the mechanical behavior of large partially crystallized domains in the upper crust; such significant transient stress transfer over large viscoelastic areas should thus be accounted for in other studies of silicic volcanic complexes

Investigating mitochondrial DNA relationships in Neolithic Western Europe through serial coalescent simulations

Recent ancient DNA studies on European Neolithic human populations have provided persuasive evidence of a major migration of farmers originating from the Aegean, accompanied by sporadic hunter-gatherer admixture into early Neolithic populations, but increasing toward the Late Neolithic. In this context, ancient mitochondrial DNA data collected from the Neolithic necropolis of Gurgy (Paris Basin, France), the largest mitochondrial DNA sample obtained from a single archeological site for the Early/Middle Neolithic period, indicate little differentiation from farmers associated to both the Danubian and Mediterranean Neolithic migration routes, as well as from Western European hunter-gatherers. To test whether this pattern of differentiation could arise in a single unstructured population by genetic drift alone, we used serial coalescent simulations. We explore female effective population size parameter combinations at the time of the colonization of Europe 45000 years ago and the most recent of the Neolithic samples analyzed in this study 5900 years ago, and identify conditions under which population panmixia between hunter-gatherers/Early-Middle Neolithic farmers and Gurgy cannot be rejected. In relation to other studies on the current debate of the origins of Europeans, these results suggest increasing hunter-gatherer admixture into farmers' group migrating farther west in Europe.European Journal of Human Genetics advance online publication, 28 December 2016; doi:10.1038/ejhg.2016.180

Latitudinal gradient in dairy production with the introduction of farming in Atlantic Europe

International audienceThe introduction of farming had far-reaching impacts on health, social structure and demography. Although the spread of domesticated plants and animals has been extensively tracked, it is unclear how these nascent economies developed within different environmental and cultural settings. Using molecular and isotopic analysis of lipids from pottery, here we investigate the foods prepared by the earliest farming communities of the European Atlantic seaboard. Surprisingly, we find an absence of aquatic foods, including in ceramics from coastal sites, except in the Western Baltic where this tradition continued from indigenous ceramic using hunter-gatherer-fishers. The frequency of dairy products in pottery increased as farming was progressively introduced along a northerly latitudinal gradient. This finding implies that early farming communities needed time to adapt their economic practices before expanding into more northerly areas. Latitudinal differences in the scale of dairy production might also have influenced the evolution of adult lactase persistence across Europe

Impact of Selection and Demography on the Diffusion of Lactase Persistence

BACKGROUND: The lactase enzyme allows lactose digestion in fresh milk. Its activity strongly decreases after the weaning phase in most humans, but persists at a high frequency in Europe and some nomadic populations. Two hypotheses are usually proposed to explain the particular distribution of the lactase persistence phenotype. The gene-culture coevolution hypothesis supposes a nutritional advantage of lactose digestion in pastoral populations. The calcium assimilation hypothesis suggests that carriers of the lactase persistence allele(s) (LCT*P) are favoured in high-latitude regions, where sunshine is insufficient to allow accurate vitamin-D synthesis. In this work, we test the validity of these two hypotheses on a large worldwide dataset of lactase persistence frequencies by using several complementary approaches. METHODOLOGY: We first analyse the distribution of lactase persistence in various continents in relation to geographic variation, pastoralism levels, and the genetic patterns observed for other independent polymorphisms. Then we use computer simulations and a large database of archaeological dates for the introduction of domestication to explore the evolution of these frequencies in Europe according to different demographic scenarios and selection intensities. CONCLUSIONS: Our results show that gene-culture coevolution is a likely hypothesis in Africa as high LCT*P frequencies are preferentially found in pastoral populations. In Europe, we show that population history played an important role in the diffusion of lactase persistence over the continent. Moreover, selection pressure on lactase persistence has been very high in the North-western part of the continent, by contrast to the South-eastern part where genetic drift alone can explain the observed frequencies. This selection pressure increasing with latitude is highly compatible with the calcium assimilation hypothesis while the gene-culture coevolution hypothesis cannot be ruled out if a positively selected lactase gene was carried at the front of the expansion wave during the Neolithic transition in Europe