Suggested readings

1. Sun et al. 2021 Ancient DNA and multimethod dating confirm the late arrival of anatomically modern humans in southern China.

   • "Genetic studies show the founders of all living non-African populations expanded from Africa ca. 65 to 45 ka. This “late dispersal” model has been challenged by the discovery of isolated AMHs at caves in southern China suggested as early as ca. 120 ka. We assessed the age of early AMH fossils from five caves in this region using ancient DNA analysis and a multimethod geological dating strategy. We found they were much younger than previously suggested, with some remains dating to the Holocene owing to the complex depositional history at these subtropical caves. Current evidence shows AMHs settled southern China within the timeframe set by molecular data of less than ca. 50 to 45 ka and no earlier."

2. Betti et al. 2020 Climate shaped how Neolithic farmers and European hunter-gatherers interacted after a major slowdown from 6,100 BCE to 4,500 BCE.

   • "We identify four axes of [European Neolithic] expansion and observe a slowdown along three axes when crossing the same climatic threshold. This threshold reflects the quality of the growing season, suggesting that Near Eastern crops might have struggled under more challenging climatic conditions. This same threshold also predicts the mixing of farmers and hunter-gatherers as estimated from ancient DNA, suggesting that unreliable yields in these regions might have favoured the contact between the two groups."

3. Immel et al. 2021 Genome-wide study of a Neolithic Wartberg grave community reveals distinct HLA variation and hunter-gatherer ancestry.

   • Studied 42 late-Neolithic genomes from the Wartenberg culture of Europe. A high percentage--40%--of their ancestry was from hunter gatherers, and their HLA alleles were unlike those of modern Europeans. The authors argue that their immune systems were specialized for defense against viruses.

4. Saag et al 2021 Genetic ancestry changes in Stone to Bronze Age transition in the East European plain.

   • "The transition from Stone to Bronze Age in Central and Western Europe was a period of major population movements originating from the Ponto-Caspian Steppe. Here, we report new genome-wide sequence data from 30 individuals north of this area, from the understudied western part of present-day Russia, including 3 Stone Age hunter-gatherers (10,800 to 4250 cal BCE) and 26 Bronze Age farmers from the Corded Ware complex Fatyanovo Culture (2900 to 2050 cal BCE). We show that Eastern hunter-gatherer ancestry was present in northwestern Russia already from around 10,000 BCE. Furthermore, we see a change in ancestry with the arrival of farming—Fatyanovo Culture individuals were genetically similar to other Corded Ware cultures, carrying a mixture of Steppe and European early farmer ancestry. Thus, they likely originate from a fast migration toward the northeast from somewhere near modern-day Ukraine—the closest area where these ancestries coexisted from around 3000 BCE."

5. Fernandes et al. 2020 The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean.

   • "We generated genome-wide ancient-DNA data from the Balearic Islands, Sicily and Sardinia, increasing the number of individuals with reported data from 5 to 66. The oldest individual from the Balearic Islands (~2400 bc) carried ancestry from steppe pastoralists that probably derived from west-to-east migration from Iberia, although two later Balearic individuals had less ancestry from steppe pastoralists. In Sicily, steppe pastoralist ancestry arrived by ~2200 bc. ... Major immigration into Sardinia began in the first millennium bc and, at present, no more than 56–62% of Sardinian ancestry is from its first farmers. This value is lower than previous estimates, highlighting that Sardinia, similar to every other region in Europe, has been a stage for major movement and mixtures of people."

6. van der Valk et al 2019 The genome of the endangered Dryas monkey provides new insights into the evolutionary history of the Vervets.

   • "We show that the [endangered] Dryas monkey represents a sister lineage to the vervets (Chlorocebus sp.) and has diverged from them ∼1.4 Ma with additional bidirectional gene flow ∼750,000–500,000 years ago that has likely involved the crossing of the Congo River. ... We find high genetic diversity and low levels of inbreeding and genetic load in the studied Dryas monkey individual. This suggests that the current population carries sufficient genetic variability for long-term survival and might be larger than currently recognized."

7. Sinding et al. 2020. Arctic-adapted dogs emerged at the Pleistocene-Holocene transition.

   • "This analysis indicates that sled dogs represent an ancient lineage going back at least 9500 years and that wolves bred with the ancestors of sled dogs and precontact American dogs. However, gene flow between sled dogs and wolves likely stopped before ∼9500 years ago."

8. Brandt et al 2018 The effect of balancing selection on population differentiation: a study with HLA genes.

   • "Theory predicts that balancing selection reduces population differentiation, as measured by FST...However, in pairs of closely related populations, where genome-wide differentiation is low, differentiation at HLA is higher than in other genomic regions. Such increased population differentiation at HLA genes for recently diverged population pairs was reproduced in simulations of overdominant selection, as long as the fitness of the homozygotes differs between the diverging populations."

9. Zen, Huber, Davies, and Lohmuller, 2020 Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared to mice and Drosophila melanogaster.

   • "We use improved modeling of weakly deleterious mutations and the demographic history of the outgroup species and ancestral population and estimate that at least 20% of nonsynonymous substitutions between humans and an outgroup species were fixed by positive selection. This estimate is much higher than previous estimates, which did not correct for the sizes of the outgroup species and ancestral population."

10. Byrne et al. 2020 Dutch population structure across space, time and GWAS design.

    • The authors use haplotype sharing to estimate the fine-grained population structure and history of the Dutch population. "Despite superexponential population growth, regional demographic estimates reveal population crashes contemporaneous with the Black Death. Within Dutch and international data, GWAS incorporating fine-grained haplotypic covariates are less confounded than standard methods."

11. Parreira et al. 2020 Genetic consequences of social structure in the golden-crowned sifaka.

    • "We observe high excess of heterozygotes within [social groups (SGs)]. ... While offspring are characterised by a high excess of heterozygotes (FIS < 0), the reproductive pair does not show dramatic departures from Hardy–Weinberg expectations. Moreover, the heterozygosity excess disappears at larger geographic scales (sites and forests). ... Our results suggest that social structure leads to high levels of outbreeding without the need for active inbreeding avoidance mechanisms."

12. Zeberg and Paabo. 2020 The major genetic risk factor for severe COVID-19 is inherited from Neandertals.

    • "A recent genetic association study (Ellinghaus et al. 2020) identified a gene cluster on chromosome 3 as a risk locus for respiratory failure in SARS-CoV-2. Recent data comprising 3,199 hospitalized COVID-19 patients and controls reproduce this and find that it is the major genetic risk factor for severe SARS-CoV-2 infection and hospitalization (COVID-19 Host Genetics Initiative). Here, we show that the risk is conferred by a genomic segment of ~50 kb that is inherited from Neandertals and occurs at a frequency of ~30% in south Asia and ~8% in Europe."

13. Zeberg, et al. 2020. The Neandertal Progesterone Receptor.

    • "The gene encoding the progesterone receptor (PGR) carries introgressed Neandertal haplotypes...[, which] have reached nearly 20% frequency in non-Africans and have been associated with preterm birth... Present-day carriers of the Neandertal haplotypes express higher levels of the receptor. In a cohort of present-day Britons, these carriers have more siblings, fewer miscarriages, and less bleeding during early pregnancy suggesting that the Neandertal progesterone receptor alleles promote fertility. This may explain their high frequency in modern human populations."

14. Hernandez, Shenk, and Perry. 2020 Factors influencing taxonomic unevenness in scientific research: A mixed-methods case study of non-human primate genomic sequence data generation.

    • How do scientists decide which species to focus on in DNA-sequencing studies? This study shows that the most-studied species are those for which there is a large prior literature and that there is a bias in favor of species closely-related to our own.

15. Hicks et al. 2018. Gut microbiomes of wild great apes fluctuate seasonally in response to diet.

    • "Here we use 16S rRNA sequencing to characterize the microbiota of wild western lowland gorillas and sympatric central chimpanzees and demonstrate compositional divergence between the microbiotas of gorillas, chimpanzees, Old World monkeys, and modern humans. We show that gorilla and chimpanzee microbiomes fluctuate with seasonal rainfall patterns and frugivory."