Sun et al. 2021 Ancient DNA and multimethod dating
confirm the late arrival of anatomically modern humans in southern
- "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."
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
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.
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."
Fernandes et al. 2020 The spread of steppe and
Iranian-related ancestry in the islands of the western
- "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."
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."
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
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."
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
- "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."
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
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."
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."
Zeberg, et al. 2020. The Neandertal Progesterone
- "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
Hernandez, Shenk, and Perry. 2020 Factors
influencing taxonomic unevenness in scientific research: A
mixed-methods case study of non-human primate genomic sequence data
- 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
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."