Inferring the Demographic History of African Farmers and Pygmy Hunter–Gatherers Using a Multilocus Resequencing Data Set

Investigations into the upper palaeolithic settlement history of Europe have made significant advances over the past decades in several fields. As a result of the reappraisal of old collections and the excavation of ‘new’ sites, an extensive data set has become available which can be used to study aspects of the organization of palaeolithic hunter-gatherers. The improvement of absolute and relative dating methods has provided the archaeologist with a more solid chronological framework. Additionally, innovations in archaeological theory and methodology have led to the exploration of new directions of inquiry. This paper focuses on a well-known example of these new directions: the study ofregionalsettlement-subsistence systems of palaeolithic groups, incorporating the systematic evaluation of archaeological data recovered from substantial areas. A growing number of archaeologists dealing with the upper palaeolithic record and active in various regions throughout Europe is currently engaged in this particular form of analysis (Audouze 1992; Hahn 1987; Julien 1987; Straus 1986; Weniger 1987, 1989).

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Malthusian cycles among semi-sedentary Fisher-Hunter-Gatherers: The socio-economic and demographic history of Housepit 54, Bridge River site, British Columbia

Journal of Anthropological Archaeology ◽

10.1016/j.jaa.2020.101181 ◽

2020 ◽

Vol 59 ◽

pp. 101181 ◽

Cited By ~ 4

Author(s):

Anna Marie Prentiss ◽

Matthew J. Walsh ◽

Thomas A. Foor ◽

Kathryn Bobolinski ◽

Ashley Hampton ◽

...

Keyword(s):

British Columbia ◽

Demographic History ◽

Hunter Gatherers ◽

History Of ◽

River Site

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A Microsatellite-Based Multilocus Screen for the Identification of Local Selective Sweeps

Genetics ◽

10.1093/genetics/160.2.753 ◽

2002 ◽

Vol 160 (2) ◽

pp. 753-763 ◽

Cited By ~ 12

Author(s):

Christian Schlötterer

Keyword(s):

Microsatellite Loci ◽

Selective Sweep ◽

Demographic History ◽

Human Populations ◽

Selective Sweeps ◽

Test Statistic ◽

Data Set ◽

History Of ◽

Microsatellite Mutation ◽

Genomic Regions

AbstractWith the availability of completely sequenced genomes, multilocus scans of natural variability have become a feasible approach for the identification of genomic regions subjected to natural and artificial selection. Here, I introduce a new multilocus test statistic, ln RV, which is based on the ratio of observed variances in repeat number at a set of microsatellite loci in two groups of populations. The distribution of ln RV values captures demographic history of the populations as well as variation in microsatellite mutation among loci. Given that microsatellite loci associated with a recent selective sweep differ from the remainder of the genome, they are expected to fall outside of the distribution of neutral ln RV values. The ln RV test statistic is applied to a data set of 94 loci typed in eight non-African and two African human populations.

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Population dynamics in the Japanese Archipelago since the Pleistocene

10.21203/rs.3.rs-145519/v1 ◽

2021 ◽

Author(s):

Fuzuki Mizuno ◽

Jun Gojobori ◽

Masahiko Kumagai ◽

Hisao Baba ◽

Yasuhiro Taniguchi ◽

...

Keyword(s):

Demographic History ◽

Cultural Transition ◽

Rice Agriculture ◽

Hunter Gatherers ◽

Japanese Archipelago ◽

Mitogenome Sequence ◽

History Of ◽

Complete Mitogenome ◽

Genetic Continuity ◽

The Japanese Archipelago

Abstract The Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome sequence from Palaeolithic human remains. We also obtained those of Neolithic (hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome is potentially an ancestral type of haplogroup M, suggesting it is not only connected to present-day Japanese but also present-day East Asians. There were no changes in the gene pool from the hunting-gathering (Jomon) to the farming cultures (Yayoi), and this is different from in Europe, where there was no genetic continuity between hunter-gatherers and farmers. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.

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Parallel paleogenomic transects reveal complex genetic history of early European farmers

10.1101/114488 ◽

2017 ◽

Cited By ~ 3

Author(s):

Mark Lipson ◽

Anna Szécsényi-Nagy ◽

Swapan Mallick ◽

Annamária Pósa ◽

Balázs Stégmár ◽

...

Keyword(s):

Ancient Dna ◽

Temporal Dynamics ◽

Neolithic Period ◽

Hunter Gatherers ◽

Data Set ◽

Open Questions ◽

Dynamics Of Population ◽

History Of ◽

Population Interactions ◽

Almost All

Ancient DNA studies have established that European Neolithic populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Using the highest-resolution genome-wide ancient DNA data set assembled to date—a total of 177 samples, 127 newly reported here, from the Neolithic and Chalcolithic of Hungary (6000–2900 BCE,n= 98), Germany (5500–3000 BCE,n= 42), and Spain (5500–2200 BCE,n= 37)—we investigate the population dynamics of Neolithization across Europe. We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ances try among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways that gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modeling approaches to elucidate multiple dimensions of historical population interactions.

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Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences

Genome Biology and Evolution ◽

10.1093/gbe/evaa098 ◽

2020 ◽

Vol 12 (7) ◽

pp. 1031-1039 ◽

Cited By ~ 1

Author(s):

Thijessen Naidoo ◽

Jingzi Xu ◽

Mário Vicente ◽

Helena Malmström ◽

Himla Soodyall ◽

...

Keyword(s):

Y Chromosome ◽

Sequence Data ◽

Demographic History ◽

Data Sets ◽

High Coverage ◽

Hunter Gatherers ◽

Data Set ◽

Chromosome Sequence ◽

Shared Ancestry ◽

Chromosome Variant

Abstract Although the human Y chromosome has effectively shown utility in uncovering facets of human evolution and population histories, the ascertainment bias present in early Y-chromosome variant data sets limited the accuracy of diversity and TMRCA estimates obtained from them. The advent of next-generation sequencing, however, has removed this bias and allowed for the discovery of thousands of new variants for use in improving the Y-chromosome phylogeny and computing estimates that are more accurate. Here, we describe the high-coverage sequencing of the whole Y chromosome in a data set of 19 male Khoe-San individuals in comparison with existing whole Y-chromosome sequence data. Due to the increased resolution, we potentially resolve the source of haplogroup B-P70 in the Khoe-San, and reconcile recently published haplogroup A-M51 data with the most recent version of the ISOGG Y-chromosome phylogeny. Our results also improve the positioning of tentatively placed new branches of the ISOGG Y-chromosome phylogeny. The distribution of major Y-chromosome haplogroups in the Khoe-San and other African groups coincide with the emerging picture of African demographic history; with E-M2 linked to the agriculturalist Bantu expansion, E-M35 linked to pastoralist eastern African migrations, B-M112 linked to earlier east-south gene flow, A-M14 linked to shared ancestry with central African rainforest hunter-gatherers, and A-M51 potentially unique to the Khoe-San.

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Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽

10.1093/genetics/164.4.1511 ◽

2003 ◽

Vol 164 (4) ◽

pp. 1511-1518 ◽

Cited By ~ 1

Author(s):

Ning Yu ◽

Michael I Jensen-Seaman ◽

Leona Chemnick ◽

Judith R Kidd ◽

Amos S Deinard ◽

...

Keyword(s):

Nucleotide Diversity ◽

Nuclear Dna ◽

Demographic History ◽

Nuclear Genome ◽

Limited Data ◽

Effective Population ◽

East Central ◽

Dna Diversity ◽

History Of ◽

Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

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Economics of respiratory disease in dairy replacement heifers

Animal Health Research Reviews ◽

10.1017/s1466252320000250 ◽

2020 ◽

Vol 21 (2) ◽

pp. 143-148

Author(s):

Michael W. Overton

Keyword(s):

Respiratory Disease ◽

Milk Production ◽

Incident Case ◽

Data Set ◽

Dairy Heifers ◽

The Usa ◽

History Of ◽

On Farm ◽

The Impact ◽

Selective Culling

AbstractBovine respiratory disease (BRD) is a frequent disease concern in dairy cattle and is most commonly diagnosed in young dairy heifers. The impact of BRD is highly variable, depending on the accuracy and completeness of detection, effectiveness of treatment, and on-farm culling practices. Consequences include decreased rate of weight gain, a higher culling risk either as heifers or as cows, delayed age at first service, delayed age at first calving, and in some cases, lower future milk production. In this data set of 104,100 dairy replacement heifers from across the USA, 36.6% had one or more cases diagnosed within the first 120 days of age with the highest risk of new cases occurring prior to weaning. Comparison of the raising cost for heifers with BRD and those without a recorded history of BRD resulted in an estimated cost per incident case occurring in the first 120 days of age of $252 or $282, depending upon whether anticipated future milk production differences were considered or not. Current market conditions contributed to a cost estimate that is significantly higher than previously published estimates, driven in part by the losses associated with selective culling of a subset of heifers that experienced BRD.

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