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CURATOR

I am a scientist specialized in genetics and cell metabolism.

PINBOARD SUMMARY

Genetics show that our species bred with other hominins with outcomes that are still visible today.

In 10 seconds? As Homo sapiens left Africa and dispersed throughout the world they encountered and interbred with other human species, today extinct. These hybridization events may have boosted our evolution and the issue of these encounters is still visible in our DNA.

Don’t believe it? Genetic studies have shown that modern humans met, and even mixed, with other human species that inhabited different regions of the globe. Namely, with Neanderthals in Europe and Asia; Denisovans in the Himalayas and Southeast Asia; Heidelbergensis in Africa; and possibly Floresiensis in Indonesia.

How were those other human species? Neanderthals were stronger than Homo sapiens, had bigger cranial capacities, so probably bigger brains, made stone tools, used fire and it seems they even self-medicated. Denisovans were probably as robust as Neanderthals, but not much is known about their morphology. On the other hand, Heidelbergensis were taller than Neanderthals but had smaller brains, and Homo floresiensis, also referred to as hobbits, were much smaller (about 3.5 feet) and had small brains.

And how did these encounters boost our evolution? Recent results suggest that hybridization between Homo sapiens and other human species may have enabled adaptation to out-of-Africa environments, by providing an important reservoir of advantageous alleles and allowing a faster rate of adaptation than with mutation and selection alone. For instance, it has increased the diversity of the immune repertoire of contemporary Europeans, affecting preferentially responses to viral challenges.

9 ITEMS PINNED

The affinities of Homo floresiensis based on phylogenetic analyses of cranial, dental, and postcranial characters.

Abstract: Although the diminutive Homo floresiensis has been known for a decade, its phylogenetic status remains highly contentious. A broad range of potential explanations for the evolution of this species has been explored. One view is that H. floresiensis is derived from Asian Homo erectus that arrived on Flores and subsequently evolved a smaller body size, perhaps to survive the constrained resources they faced in a new island environment. Fossil remains of H. erectus, well known from Java, have not yet been discovered on Flores. The second hypothesis is that H. floresiensis is directly descended from an early Homo lineage with roots in Africa, such as Homo habilis; the third is that it is Homo sapiens with pathology. We use parsimony and Bayesian phylogenetic methods to test these hypotheses. Our phylogenetic data build upon those characters previously presented in support of these hypotheses by broadening the range of traits to include the crania, mandibles, dentition, and postcrania of Homo and Australopithecus. The new data and analyses support the hypothesis that H. floresiensis is an early Homo lineage: H. floresiensis is sister either to H. habilis alone or to a clade consisting of at least H. habilis, H. erectus, Homo ergaster, and H. sapiens. A close phylogenetic relationship between H. floresiensis and H. erectus or H. sapiens can be rejected; furthermore, most of the traits separating H. floresiensis from H. sapiens are not readily attributable to pathology (e.g., Down syndrome). The results suggest H. floresiensis is a long-surviving relict of an early (>1.75 Ma) hominin lineage and a hitherto unknown migration out of Africa, and not a recent derivative of either H. erectus or H. sapiens.

Pub.: 26 Apr '17, Pinned: 09 May '17

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.

Abstract: Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.

Pub.: 09 Mar '17, Pinned: 09 May '17

Signatures of archaic adaptive introgression in present-day human populations.

Abstract: Comparisons of DNA from archaic and modern humans show that these groups interbred, and in some cases received an evolutionary advantage from doing so. This process - adaptive introgression - may lead to a faster rate of adaptation than is predicted from models with mutation and selection alone. Within the last couple of years, a series of studies have identified regions of the genome that are likely examples of adaptive introgression. In many cases, once a region was ascertained as being introgressed, commonly used statistics based on both haplotype as well as allele frequency information were employed to test for positive selection. Introgression by itself, however, changes both the haplotype structure and the distribution of allele frequencies, thus confounding traditional tests for detecting positive selection. Therefore, patterns generated by introgression alone may lead to false inferences of positive selection. Here we explore models involving both introgression and positive selection to investigate the behavior of various statistics under adaptive introgression. In particular, we find that the number and allelic frequencies of sites that are uniquely shared between archaic humans and specific present-day populations are particularly useful for detecting adaptive introgression. We then examine the 1000 Genomes dataset to characterize the landscape of uniquely shared archaic alleles in human populations. Finally, we identify regions that were likely subject to adaptive introgression and discuss some of the most promising candidate genes located in these regions.

Pub.: 21 Oct '16, Pinned: 09 May '17

The Strength of Selection against Neanderthal Introgression.

Abstract: Hybridization between humans and Neanderthals has resulted in a low level of Neanderthal ancestry scattered across the genomes of many modern-day humans. After hybridization, on average, selection appears to have removed Neanderthal alleles from the human population. Quantifying the strength and causes of this selection against Neanderthal ancestry is key to understanding our relationship to Neanderthals and, more broadly, how populations remain distinct after secondary contact. Here, we develop a novel method for estimating the genome-wide average strength of selection and the density of selected sites using estimates of Neanderthal allele frequency along the genomes of modern-day humans. We confirm that East Asians had somewhat higher initial levels of Neanderthal ancestry than Europeans even after accounting for selection. We find that the bulk of purifying selection against Neanderthal ancestry is best understood as acting on many weakly deleterious alleles. We propose that the majority of these alleles were effectively neutral-and segregating at high frequency-in Neanderthals, but became selected against after entering human populations of much larger effective size. While individually of small effect, these alleles potentially imposed a heavy genetic load on the early-generation human-Neanderthal hybrids. This work suggests that differences in effective population size may play a far more important role in shaping levels of introgression than previously thought.

Pub.: 09 Nov '16, Pinned: 09 May '17