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Thread: New DNA Papers

  1. #1471
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    The Lithuanian reference genome LT1

    The Lithuanian reference genome LT1 - a human de novo genome assembly with short and long read sequence and Hi-C data
    Hui-Su Kim, Asta Blazyte, Sungwon Jeon, Changhan Yoon, Yeonkyung Kim, Changjae Kim, Dan Bolser, Ji-Hye Ahn, Jeremy S Edwards, Jong Bhak

    Abstract
    We present LT1, the first high-quality human reference genome from the Baltic States. LT1 is a female de novo human reference genome assembly constructed using 57× of ultra-long nanopore reads and 47× of short paired-end reads. We also utilized 72 Gb of Hi-C chromosomal mapping data to maximize the assembly′s contiguity and accuracy. LT1′s contig assembly was 2.73 Gbp in length comprising of 4,490 contigs with an N50 value of 13.4 Mbp. After scaffolding with Hi-C data and extensive manual curation, we produced a chromosome-scale assembly with an N50 value of 138 Mbp and 4,699 scaffolds. Our gene prediction quality assessment using BUSCO identify 89.3% of the single-copy orthologous genes included in the benchmarking set. Detailed characterization of LT1 suggested it has 73,744 predicted transcripts, 4.2 million autosomal SNPs, 974,000 short indels, and 12,330 large structural variants. These data are shared as a public resource without any restrictions and can be used as a benchmark for further in-depth genomic analyses of the Baltic populations.
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  3. #1472
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    The structure, function and evolution of a complete human chromosome 8

    The structure, function and evolution of a complete human chromosome 8
    Glennis A. Logsdon, Mitchell R. Vollger, PingHsun Hsieh, Yafei Mao, Mikhail A. Liskovykh, Sergey Koren, Sergey Nurk, Ludovica Mercuri, Philip C. Dishuck, Arang Rhie, Leonardo G. de Lima, Tatiana Dvorkina, David Porubsky, William T. Harvey, Alla Mikheenko, Andrey V. Bzikadze, Milinn Kremitzki, Tina A. Graves-Lindsay, Chirag Jain, Kendra Hoekzema, Shwetha C. Murali, Katherine M. Munson, Carl Baker, Melanie Sorensen, Alexandra M. Lewis, Urvashi Surti, Jennifer L. Gerton, Vladimir Larionov, Mario Ventura, Karen H. Miga, Adam M. Phillippy & Evan E. Eichler

    Abstract
    The complete assembly of each human chromosome is essential for understanding human biology and evolution. Here we use complementary long-read sequencing technologies to complete the linear assembly of human chromosome 8. Our assembly resolves the sequence of five previously long-standing gaps, including a 2.08-Mb centromeric α-satellite array, a 644-kb copy number polymorphism in the β-defensin gene cluster that is important for disease risk, and an 863-kb variable number tandem repeat at chromosome 8q21.2 that can function as a neocentromere. We show that the centromeric α-satellite array is generally methylated except for a 73-kb hypomethylated region of diverse higher-order α-satellites enriched with CENP-A nucleosomes, consistent with the location of the kinetochore. In addition, we confirm the overall organization and methylation pattern of the centromere in a diploid human genome. Using a dual long-read sequencing approach, we complete high-quality draft assemblies of the orthologous centromere from chromosome 8 in chimpanzee, orangutan and macaque to reconstruct its evolutionary history. Comparative and phylogenetic analyses show that the higher-order α-satellite structure evolved in the great ape ancestor with a layered symmetry, in which more ancient higher-order repeats locate peripherally to monomeric α-satellites. We estimate that the mutation rate of centromeric satellite DNA is accelerated by more than 2.2-fold compared to the unique portions of the genome, and this acceleration extends into the flanking sequence.
    Last edited by pmokeefe; 04-07-2021 at 07:36 PM.
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  5. #1473
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    An efficient method for inferring large human pedigrees from genotype data

    Bonsai: An efficient method for inferring large human pedigrees from genotype data
    Ethan MacNeil Jewett, Kimberly F McManus, William A Freyman, Adam Auton

    Abstract
    Pedigree inference from genotype data is a challenging problem, particularly when pedigrees are sparsely sampled and individuals may be distantly related to their closest genotyped relatives. We present a new method that infers small pedigrees of close relatives and then assembles them into larger pedigrees. To assemble large pedigrees, we introduce several new formulas and tools including a new likelihood for the degree separating two small pedigrees, a method for detecting individuals who share background identity-by-descent (IBD) that does not reflect recent common ancestry, and a method for identifying the ancestral branches through which distant relatives are connected. Our method also takes several new approaches that help to improve the accuracy and efficiency of pedigree inference. In particular, we incorporate age information directly into the likelihood rather than using ages only for consistency checks and we employ a heuristic branch-and-bound-like approach to more efficiently explore the space of possible pedigrees. Together, these approaches make it possible to construct large pedigrees that are challenging or intractable for current inference methods. The new method, Bonsai, is available at https://github.com/23andMe/bonsaitree.

    Competing Interest Statement
    The authors are employees of 23andMe, Inc., and hold stock or stock options in 23andMe.
    YFull: YF14620 (Dante Labs 2018)

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  7. #1474
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    https://science.sciencemag.org/content/372/6538/165

    The primitive brain of early Homo

    Abstract
    The brains of modern humans differ from those of great apes in size, shape, and cortical organization, notably in frontal lobe areas involved in complex cognitive tasks, such as social cognition, tool use, and language. When these differences arose during human evolution is a question of ongoing debate. Here, we show that the brains of early Homo from Africa and Western Asia (Dmanisi) retained a primitive, great ape–like organization of the frontal lobe. By contrast, African Homo younger than 1.5 million years ago, as well as all Southeast Asian Homo erectus, exhibited a more derived, humanlike brain organization. Frontal lobe reorganization, once considered a hallmark of earliest Homo in Africa, thus evolved comparatively late, and long after Homo first dispersed from Africa.

    Neurofunctional implications
    In modern human brains, the inferior frontal lobe is an important neurofunctional substrate for advanced social cognition, toolmaking and tool use, and articulated language (2, 47, 48). We may thus ask whether its evolutionary reorganization around 1.7 to 1.5 Ma was accompanied by major changes in technocultural performance. The earliest evidence for Mode II (Acheulean) technocultures in Africa [1.76 Ma (49, 50)] largely coincides with incipient frontal lobe reorganization, and Mode I and Mode II lithic technologies were used concurrently during the critical time period (51). We hypothesize that this pattern reflects interdependent processes of brain-culture coevolution (52), where cultural innovation triggered changes in cortical interconnectivity (4, 53) and ultimately in external frontal lobe topography. On the other hand, the cerebral innovations that characterize Homo at ~1.5 Ma might have constituted the foundations of the “language-ready” brain of later Homo species (54).

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  9. #1475
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    Qiyan Wang, Jing Zhao, Zheng Ren, Jin Sun, Guanglin He, Jianxin Guo, Hongling Zhang, Jingyan Ji, Yubo Liu, Meiqing Yang, Xiaomin Yang, Jinwen Chen, Kongyang Zhu, Rui Wang, Yingxiang Li, Gang Chen, Jiang Huang, and Chuan-Chao Wang, "Male-Dominated Migration and Massive Assimilation of Indigenous East Asians in the Formation of Muslim Hui People in Southwest China." Frontiers in Genetics, 11 January 2021. https://doi.org/10.3389/fgene.2020.618614

    The origin and diversification of Muslim Hui people in China via demic or simple cultural diffusion is a long-going debate. We here generated genome-wide data at nearly 700,000 single nucleotide polymorphisms (SNPs) from 45 Hui and 14 Han Chinese individuals collected from Guizhou province in southwest China. We applied principal component analysis (PCA), ADMIXTURE, f-statistics, qpWave, and qpAdm analysis to infer the population genetic structure and admixture history. Our results revealed the Guizhou Hui people have a limited amount of West Eurasian related ancestry at a proportion of 6%, but show massive genetic assimilation with indigenous southern Han Chinese and Tibetan or Tungusic/Mongolic related northern East Asians. We also detected a high frequency of North Asia or Central Asia related paternal Y-chromosome but not maternal mtDNA lineages in Guizhou Hui. Our observation supports the cultural diffusion has played a vital role in the formation of Hui people and the migration of Hui people to southwest China was probably a sex-biased male-driven process.

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  11. #1476
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    https://www.nature.com/articles/s41431-021-00875-0

    Fine-scale population structure in five rural populations from the Spanish Eastern Pyrenees using high-coverage whole-genome sequence data
    Iago Maceda, Miguel Martín Álvarez, Georgios Athanasiadis, Raúl Tonda, Jordi Camps, Sergi Beltran, Agustí Camps, Jordi Fàbrega, Josefina Felisart, Joan Grané, José Luis Remón, Jordi Serra, Pedro Moral & Oscar Lao

    Abstract
    The area of the Spanish Pyrenees is particularly interesting for studying the demographic dynamics of European rural areas given its orography, the main traditional rural condition of its population and the reported higher patterns of consanguinity of the region. Previous genetic studies suggest a gradient of genetic continuity of the area in the West to East axis. However, it has been shown that micro-population substructure can be detected when considering high-quality NGS data and using spatial explicit methods. In this work, we have analyzed the genome of 30 individuals sequenced at 40× from five different valleys in the Spanish Eastern Pyrenees (SEP) separated by less than 140 km along a west to east axis. Using haplotype-based methods and spatial analyses, we have been able to detect micro-population substructure within SEP not seen in previous studies. Linkage disequilibrium and autozygosity analyses suggest that the SEP populations show diverse demographic histories. In agreement with these results, demographic modeling by means of ABC-DL identify heterogeneity in their effective population sizes despite of their close geographic proximity, and suggests that the population substructure within SEP could have appeared around 2500 years ago. Overall, these results suggest that each rural population of the Pyrenees could represent a unique entity.

    Data are available upon request to the corresponding author.
    Ελευθερία ή θάνατος.

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  13. #1477
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    Upcoming dissertation.

    Bayesian adventures among human mitochondrial lineages

    A mitochondrion is a cytoplasmic organelle responsible for the energy production of the eukaryotic cells. Mitochondria contain their own genome, mitochondrial DNA (mtDNA), which is a double-stranded circular molecule. Due to mitochondria’s essential role in metabolism, a cell can contain hundreds of thousands of copies of mitochondrial DNA, depending upon the cell’s energy requirements. In mammals, mtDNA is generally maternally inherited, meaning that it is transmitted from a mother to all of her descendants. Although mtDNA constitutes only a small fraction of the cell genome, it has several qualities which make it widely used in population genetic studies such as uniparental inheritance, and the fact that the mitochondrial genome does not recombine. Moreover, mtDNA has a mutation rate ten times higher than that of the nuclear genome and therefore allows us to trace back matrilineal lineages through generations and subsequently make inferences about maternal ancestors.

    The human mtDNA sequence consists of approximately 16,570 base pairs and also contains both a coding region and a non-coding control region, the latter constituting around 7% of the whole mtDNA genome. Since mtDNA does not undergo recombination, an individual’s mitochondrial haplotype can be determined simply by the direct sequencing of target amplicons. Haplotypes containing certain defining variants are considered to be descendants of a common ancestor and are classified into haplogroups. The geographical distribution of haplogroups among contemporary populations is well-known – for instance, the majority of Europeans exhibit mitochondrial lineages H, U, J, K, T and V. Ancient DNA research has uncovered that lineage U was already highly prevalent among the earliest hunter-gatherer settlers of Europe, whereas the gradual spread of agriculture from the Near East that started approximately 10,000 years ago brought along new people and hence also novel mitochondrial lineages (H, J, K and T). Previous studies have stated that compared with other European populations, contemporary Finns do not seem to be an exception in terms of mitochondrial genome pool. This is rather surprising, since other genetic markers have revealed that contemporary Finns are characterized by a strong Eastern genetic influence and are distinguishable from other Europeans. Moreover, the evident East-West distinction within Finland, apparent in Y-chromosomes and autosomes, has not been previously identified in the mtDNA.

    This thesis outlines the mitochondrial DNA variation among present-day Finns in a Bayesian framework. The aims were to evaluate if Finns display a homogeneous geographical distribution of haplogroups and if the mtDNA composition of Finns resembles that of other European populations, as previously suggested. While no spatial differences have previously been detected in the mitochondrial haplogroup frequencies within Finland, a clear geographical distinction arose when clustering haplogroups into ‘hunter-gatherer’ (U and V) and ‘farmer’ associated lineages (H, J, K and T). Whereas the farmer related haplogroups were notably more common in Southwestern Finland, the hunter-gatherer lineages had higher densities in the Northeastern parts compared to the Southwest. Furthermore, utilization of the complete mitochondrial genomes allowed for reassessing the Finnish mtDNA pool on a larger scale. One third of the subhaplogroups in Finland today were characteristic only of Finns, i.e. these lineages were virtually absent from other populations. When further partitioning the Finnish samples based on their inclusion in ‘local’ and ‘non-local’ lineages, two notably different demographic trajectories were obtained. The population history for Finn-characteristic lineages was more in accordance with what is known through other data types, such as Y-chromosomal and archaeological data. In general, the observed geographical within-country deviation in the Finnish mtDNA pool and the high proportion of Finn-characteristic lineages reflected the signals reported from other genetic markers.

    Alongside Finnish mtDNA, this thesis explores the molecular rate variation among the different subhaplogroups of lineage U. Unexpectedly, a noteworthy discrepancy emerged from the tip calibrated phylogenies: haplogroup U5b had a notably lower substitution rate when compared to U2, U4 and U5a. This lineage-specificity in the rates most likely arose, at least to some extent, from differences in past population dynamics. In particular, U4 and U5a have been associated with the rapid population expansion which occurred during the Bronze Age, whereas the frequency of U5b has remained rather stable. Subsequently, the observed rate of deviation influences the divergence estimates for subhaplogroups, suggesting that U5b emerged considerably earlier than U5a. Since molecular rates are fundamental to several population genetic analyses and the timing of divergence and demographic events relies heavily on the rate used, more attention should be paid to the interlineage molecular rate variation.

    The results of this thesis demonstrate not only the importance of using complete mtDNA genomes and the appropriate molecular rate, but also the relevance of approaching the data from new angles when assessing the demographic past of mitochondrial lineages.

    https://helda.helsinki.fi/handle/10138/328569

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