Sunday, May 13, 2018

Ancient humans settled the Philippines 700,000 years ago

Lizzie Wade
ScienceMag



"In what some scientists are calling a “one-in-a-million find,” archaeologists have discovered a cache of butchered rhino bones and dozens of stone tools on the Philippines’s largest island, Luzon. The find pushes back the earliest evidence for human occupation of the Philippines by more than 600,000 years, and it has archaeologists wondering who exactly these ancient humans were—and how they crossed the deep seas that surrounded that island and others in Southeast Asia."

read more

Monday, April 23, 2018

Human activity patterns at the Horokazawa Toma Upper Paleolithic stone tool manufacturing site in the Shirataki obsidian source area: Combining excavation with experimentation

Hideaki Kimura, Evgeny Girya
Quaternary International
Volume 397, 18 March 2016, Pages 448-473
(Link)

Abstract

The Horokazawa site locality Toma (HT) is an Upper Paleolithic archeological site situated on a hillside near the Shirataki Akaishiyama obsidian source area, the largest in Japan. Excavations at HT over a period of more than 20 years have produced more than 570,000 artifacts from an area of less than 100 m2. The Horokazawa Toma lithic assemblage was characterized by the Yubetsu technique, which was used to manufacture microblades in Siberia, the Far East, and North America. The assemblage at HT has been dated to the period just after the last glacial maximum, around 15,000 years ago, and when the microblade industry was flourishing in Eastern Asia. As flakes and chips account for 98% of the lithic artifacts, the site was evidently a lithic workshop. In this study, along with examination of excavated materials we identified the source of excavated materials by macroscopic observation and nondestructive analyses, and we experimentally replicated the manufacturing technique to analyze the activities carried at this workshop and infer the distribution network of raw materials and worked stone, beginning with the acquisition of the obsidian.

The obsidian came from the East Atelier and Ajisainotaki (especially) sources near the summit of Mt. Akaishiyama. Large angular and slab-like nodules from these sources were likely collected at Hidarinosawa being closer to HT, brought to HT, and processed into large bifaces and boat-shaped blanks for microblade manufacture. Many of these products were exported to other sites. We showed by experiment that the first and second spalls efficiently removed from a large biface by the block-on-block technique. A similar microblade industry based on Shirataki obsidian is found at sites in the Yubetsu River drainage, below HT, and other sites in Hokkaido. In fact, Shirataki obsidian is found at remote sites such as Akatsuki site (eastern part of Hokkaido) and Sokol site (on Sakhalin island), suggesting that raw materials were exchanged between groups of people over long distances. This large distribution network was supported by mass production of blanks for microblade manufacturing at the Toma locality of the Horokazawa site.

Two Islands in the Ocean: Prehistoric Obsidian Exchange between Sakhalin and Hokkaido, Northeast Asia

Yaroslav V. Kuzmin, Michael D. Glascock
Journal of Island and Coastal Archaeology
Volume 2, 2007, Issue 1
(Link)
 
Obsidian exchange patterns were studied on Sakhalin Island which connects Japan with mainland Asia. One hundred-eighty-two specimens of obsidian, including 157 artifacts from 75 sites on Sakhalin, ranging in age from the early Upper Paleolithic (ca. 19,400-17,800 RYBP) to the Okhotsk cultural complex (ca. 1400-800 RYBP), and 25 geological samples from Hokkaido Island (Japan), were examined by neutron activation analysis. Geochemical data suggest that all the obsidian artifacts from known sources found in Sakhalin archaeological sites were brought from Hokkaido sources. Widespread use of Hokkaido obsidian by Sakhalin inhabitants shows that long-distance contacts and exchange have taken place in Northeast Asia since at least the Upper Paleolithic. Although this obsidian transport could have been land-based during the Pleistocene, people had to use watercraft to cross La Pérouse Strait during the past 10,000 years. The distance of raw material transport was about 250-300 km in the early Upper Paleolithic, but increased up to 1000 km by the end of the Upper Paleolithic, the Neolithic, and later periods.

Sunday, April 22, 2018

Discovery of circa 115,000-year-old bone retouchers at Lingjing, Henan, China

Luc Doyon, Zhanyang Li, Hao Li, Francesco d’Errico
PLOS One
Published: March 12, 2018
(Link) open access

Abstract

Most Chinese lithic industries dated between 300,000 and 40,000 are characterized by the absence of Levallois debitage, the persistence of core-and-flake knapping, the rarity of prepared cores, their reduction with direct hard hammer percussion, and the rarity of retouched flakes. Here we report the discovery of seven bone soft hammers at the early hominin Lingjing site (Xuchang County, Henan) dated to 125,000–105,000. These artefacts represent the first instance of the use of bone as raw material to modify stone tools found at an East Asian early Late Pleistocene site. Three types of soft hammers are identified. The first consists of large bone flakes resulting from butchery of large herbivores that were utilized as such for expedient stone tools retouching or resharpening. The second involved the fracture of weathered bone from medium size herbivores to obtain elongated splinters shaped by percussion into sub-rectangular artefacts. Traces observed on these objects indicate intensive and possibly recurrent utilization, which implies their curation over time. The last consists of antler, occasionally used. Lingjing bone tools complement what we know about archaic hominin cultural adaptations in East Asia and highlight behavioural consistencies that could not be inferred from other cultural proxies. This discovery provides a new dimension to the debate surrounding the existence of the Middle Palaeolithic in the region. The attribution of East Asian sites to the Middle Palaeolithic assumes that cultural traits such as the Levallois method represent evolutionary hallmarks applicable to regions of the world different from those in which they were originally found. Here, we promote an approach that consists in identifying, possibly from different categories of material culture, the original features of each regional cultural trajectory and understanding the behavioural and cognitive implications they may have had for past hominin populations.

Geology and quaternary environments of the Tategahana Paleolithic site in Nojiri-ko (Lake Nojiri), Nagano, central Japan

Y. Kondo, Y. Takeshita, T. Watanabe, M. Seki, Nojiri-ko Excavation Reserch Group
Quaternary International
Available online 2 January 2018
(Link) available for purchase from ScienceDirect for $36 (US)

Abstract

Excavation of the Tategahana Paleolithic site at Nojiri-ko (Lake Nojiri), central Japan, began in 1962, and the 21st excavation was performed in 2014. The Upper Pleistocene to Holocene fluvio-lacustrin Nojiri-ko Formation is distributed in and around Nojiri-ko. Fossils such as those of Naumann's elephant (Palaeoloxodon naumanni) and Yabe's giant deer (Sinomegaceros yabei), representing the ice age in Japan, have been excavated there in large quantities; at least 46 Naumann's elephants have been found. The fossils have been excavated in strata dating to 37.9–60.4 ka, comparable to MIS 3. Analysis of fossil pollen assemblages indicates that the vegetation at the time was a mixture of coniferous and broad-leaved trees. Bone instruments and spiral flakes made from elephant and deer bones, and stone tools created from stone, not found in the peripheral region, have been excavated from the Nojiri-ko Formation, and concentrated clusters of different types of fossilized elephant bones have been found.

The top horizon containing elephant remains is 37.9 ka old, and thus older than MIS 2 (the Last Glacial Maximum), making it unlikely that Naumann's elephant disappeared from Nojiri-ko only because of climatic cooling. Findings strongly suggest that the occurrence of these large mammal fossils is the result of human activity. The Tategahana Paleolithic site provides important insights into the transitional phase from Asian Paleanthropine to Homo sapiens in Japan.
 
Excepts from the paper:

Archaeological materials

Three horizons have yielded bone flake tools: the U3 unit of the Umibata Sand and Silt Member and the T1 to T3 and T4 units of the Tategahana Sand Member. Typical spiral flakes from the T7 unit of the Tategahana Sand Member were detached from the long bones of S. yabei. These spiral flakes show a higher probability of being the by-product of bone marrow procurement by humans, because a percussion point is evident on the surface of each flake (Ono and Nojiri-ko Excavation Research Group, 1986) (Fig. 8). 

The stone artifacts obtained from the Tategahana excavation site include edge-damaged flakes, a retouched flake, intact flakes, and cores and scrapers.

Three concentrations of large bones, such as the skulls and shoulder blades of P. naumanni, associated with spear-shaped wooden tools and large pebbles have been recognized. This circumstantial evidence emphasizes the likelihood that the site was not a settlement but a butchering or “kill” site. (Ono, 2001, 2004; Ono et al., 2002).

The artifact assemblages obtained from the U3 unit of the Umibata Sand and Silt Member to the T7 unit of the Tategahana Sand Member are distinguished by bone tools and coarse, small, lithic flake tools (Anthropology and Archaeology Research Group for Nojiri-ko Excavation, 2006).


Figure 8, Artefacts from the Tategahana site [with dates]



 Discussion

The question of whether humans lived in the Japanese Islands 40,000 years ago has so far been answered in the negative, based on the results of DNA analyses and anthropological studies using archaeological materials. Izuho and Kaifu (2015) suggest that the UP suddenly emerged in different regions of Japan around 38 ka ago, signaling the arrival of Homo sapiens in this part of eastern Asia.

This time corresponds to the upper age limit of archaeological materials and fossils from the Nojiri-ko Formation. Mitochondrial DNA analyses of the Japanese people have established the existence of various local population groups in the Japanese Islands no more than 40 ka ago (Shinoda, 2015). However, a mammoth kill site discovered in West Siberia was estimated to have an age of 45 ka(Pitulko et al., 2016). This important discovery shows that humans had reached Siberia by that time, and necessitates a DNA-analysis based review of the age of human diffusion. The discovery of moose fossils in the Nojiri-ko Formation indicates that moose moved from Siberia to Honshu Island. The possibility that humans crossed from Siberia to Honshu Island earlier than 45 ka ago is undeniable.

Tsutsumi (2011) notes that it is difficult to judge whether the archaeological materials from the Nojiri-ko Formation are indicative of human activity.

Bone material with a spiral fracture was recently found in the Nojiri-ko excavation and examined by Ono (2001), and the number of spiral flakes found has increased over time (Anthropology and Archaeological Research Group for Nojiri-ko Excavation, 2003). Norton et al. (2009) examined the cut marks on fossils from the Nojiri-ko Formation and determined that hunting had occurred around Nojiri-ko about 40 ka ago. However, Iwase et al. (2015) stated that these conclusions were not based on an accurate examination of other factors that were probably associated with the megafaunal demise. Nevertheless, the Nojiri-ko excavation did reveal that large mammals such as Naumann's elephant moved to Nojiri-ko between the two periods of coldest climate [Marine Isotope Stage (MIS) 4 and MIS 2], and human remains dated to the same time have been excavated from the formation. It is therefore reasonable to hypothesize that large mammals and humans moved to Nojiri-ko when the climate was relatively warm (i.e., in MIS 3). Considering the climate and environment 40 ka ago, it is certainly possible that humans coexisted with large mammals around Nojiri-ko.

Tuesday, April 17, 2018

On the presence of Late Pleistocene wapiti, Cervus canadensis Erxleben, 1777 (Cervidae, Mammalia) in the Palaeolithic site Climăuți II (Moldova)

Roman Croitor, Theodor Obada

Contributions to Zoology, 87 (1) 1-10 (2018)
(Link) pdf

Abstract

This article reports antler remains from the Late Paleolithic site of Climăuți II (Republic of Moldova) confirming the presence of wapiti Cervus canadensis in the Late Pleistocene of Western Eurasia. The occurrence of wapiti in the East Carpathian area by 20 ky BP coincides with the local extinction of Megaloceros giganteus, Crocuta spelaea, and Ursus spelaeus, and substitution of local forest reindeer with grazing tundra-steppe Rangifer tarandus constantini. We here provide an overview of paleontological data and opinions on the presence of Cervus canadensis in Europe, a discussion on the taxonomic status and systematic position of the extinct deer Cervus elaphus palmidactyloceros, and propose a dispersal model for wapiti in Europe during the Late Pleistocene.

Saturday, March 31, 2018

The Special Challenges of Being Both a Scientist and a Mom

Rebecca Calisi
Scientific American
March 30, 2018
(Link)

From the article:

"Being a woman, a scientist and now a mother in a system created for and by white men with stay-at-home partners obviously has its problems. Many of us are either pushed out or decide to set sail for smoother waters. Sometimes when I hear exclamations of “we need to inspire more women to pursue the sciences!” I think: We’re here! We want to do science! But how can we when, to advance, we’re forced to run at double the speed of our male colleagues on a career track clouded by bias and covered in LEGOs?

"Sometimes people ask me why I bother to stay in a career so hostile to women. I remind them the culture is changing, more quickly in some places than others. I also remind them it is not just science or academia in general that harbors this sex-biased hostility. My friends in law, business and entertainment have horrified me with unjust tales from their workplaces. And yet many of us stay the course, determined to both overcome and overturn obstacles in our paths to pursue our goals and passions. We do so by standing on the shoulders of fierce women who came before us, our forward momentum toward a destination made visible by their efforts, a hand hopefully extended behind us to pull up those even less privileged.

"A few months ago I traveled across the country to attend a scientific conference. For me, if science were a town, conferences would be the town square. Thousands of people from all over the world convened at this particular conference to present their work, learn of the latest research findings and technologies, develop new ideas and collaborations, find inspiration, meet with granting agencies, recruit trainees, find jobs and in general be part of a greater community. I had always loved attending conferences for these reasons.

"Unfortunately, in the past few years that had become more difficult for me due to pregnancy, breast-feeding, and child care issues and responsibilities. But now, at this particular meeting, pregnancies and breast-feeding were behind me. I was a faculty member at an institution I loved, making a decent salary. My husband, also a new professor, was caring for our children back at home in collaboration with responsible day care providers we could finally afford. I leaned against a wall inside the conference center, warmed by sunlight streaming in from a nearby window. I took a deep breath, slowly sipped my hot tea and scrolled hungrily through the scientific program. I had survived. I was back.

"In between lectures and poster presentations, I wondered around the conference hall in search of their lactation room. Though I no longer needed it, I was still curious to see if it had improved from the previous year. Last time, to reach the lactation room required an epic journey away from the main conference hall. Most nursing moms forewent the pilgrimage, instead ducking into nearby corners to feed their babies or pump milk in bathrooms so as to make it to their presentations in time. Pumping milk in a bathroom is a nasty affair, one that I’ve written about. Would you want your meal made in a bathroom?

"As I continued my search, I was happy to see child care was available on location, which is undeniably an incredibly helpful resource for attendees with children in tow. Be that as it may, those arguably in the most sensitive period of their career stage—namely graduate students, postdocs and new faculty—are usually the ones in need of these services the most and yet cannot afford them. When I was a postdoc, I couldn’t even afford to buy an extra plane ticket for my child to fly to a conference with me, let alone pay for child care once I got there.

(read more)

Blog note:

Among a number of topics confronting women scientists, the article mentions the lack of support for breast feeding mothers at conferences.  In addition to many conferences and work places having no, or inadequate, lactation rooms, most science, technology, engineering and medicine (STEM) work places have no on-site day care.  Adding to this complexity is the fact that not only childcare, but spring break, fall break and summer programs for older children are beyond the means of most middle class family incomes.

Most STEM work places expect their employees to work at least until 6pm, but schools close before 4pm.  The burden of having to leave work early to pick children up from school usually falls on the parent with the lower salary (usually the mother.)  Employees who leave work earlier than 6pm are often viewed negatively.  In fact, this is one of the gendered inequalities mentioned in a class action lawsuit against Qualcomm in 2016:  women engineers were viewed negatively for leaving work before 6pm and were penalized in their pay and advancement opportunities for it.

In a society that purports to care about families, I marvel at the paucity of childcare and maternal care.  For most families today, it is not possible to get by on one income.  On the surface, we constantly promote STEM careers to both girls and boys.  Yet, beyond monitoring hiring statistics in STEM careers, our policies to address the causes of the attrition rate for women in STEM from high school onward are almost non-existent. 

The Scientific American article also mentions the lack of healthcare for mothers once they have given birth.  It is a little known fact that birth injuries are widely under diagnosed, and under treated, and have serious life long negative health impacts for mothers [1].

In addition to gender discrimination, gender based harassment, unconscious bias, lack of maternal support before and after giving birth in a myriad of ways, mothers are further penalized for taking time out to take care of their young children.  Once mothers do attempt to re-enter the workforce, there are almost no programs in universities or industry to facilitate this.  There is no evidence at all that corporations are interested in hiring this cohort of often highly trained and experienced women scientists and engineers.  Speaking from my own experience, in spite of my having had a Master's Degree in electrical engineering, and about ten years of work experience, my experience of trying to re-enter my engineering career after being a full time mom could be the basis for a lengthy tragicomedy.  This very negative experience of re-entering the workforce is more than five years behind me, but I still have people down grading my worth as an engineer because I took time out to be a mom. 

I often hear my colleagues (almost all male) bring up differences in career outcomes for women because of some underlying biological difference.  These arguments circle around biologically, genetically or hormonally based differences that lead to women's lack of confidence, lack of aggression, excessive sociability and agreeability, propensity to be more altruistic than men, greater "hysteria", and greater verbal ability versus mathematical or spatial ability.

You could break each of these characteristics down, spend the next century creating studies and collecting statistics, and find that some of these differences have a subtle basis in reality.  But these would be subtle effects, whereas being blocked from being hired, paid, developed, mentored, funded and promoted are not subtle in their impact on women in STEM, and on society.  Being asked to choose between a STEM career and a family has a not subtle large negative effect on the advancement of women engineers and scientists, on family incomes and on overall economic productivity. Poor maternal care has a not subtle large negative affect on all mothers, including women in STEM, and on their families.

Until these large effects are addressed, I am not interested in discussing the subtle differences between men and women.  Researchers who say they are interested in discussing gender disparities, yet focus on the possibility of biology and genetics as the primary cause of the disparity, as opposed to the large, not subtle, negative experiences of women and mothers in the STEM workplace, are highly insincere, not objective, and do cause great harm to women, families and society.

Marnie Dunsmore
3/31/2018

[1] Maternal birth trauma: why should it matter to urogynaecologists?; Dietz, Hans P.; Wilson, Peter D.; Milsom, Ian; Current Opinion in Obstetrics and Gynecology: October 2016 - Volume 28 - Issue 5 - p 441–448

Friday, March 30, 2018

Efficiently inferring the demographic history of many populations with allele count data

John A. Kamm, Jonathan Terhorst, Richard Durbin, and Yun S. Song
biorxiv
March 22, 2018
(Link) pdf

Abstract

The sample frequency spectrum (SFS), or histogram of allele counts, is an important summary statistic in evolutionary biology, and is often used to infer the history of population size changes, migrations, and other demographic events affecting a set of populations. The expected multipopulation SFS under a given demographic model can be efficiently computed when the populations in the model are related by a tree, scaling to hundreds of populations. Admixture, back-migration, and introgression are common natural processes that violate the assumption of a tree-like population history, however, and until now the expected SFS could be computed for only a handful of populations when the demographic history is not a tree. In this article, we present a new method for efficiently computing the expected SFS and linear functionals of it, for demographies described by general directed acyclic graphs. This method can scale to more populations than previously possible for complex demographic histories including admixture. We apply our method to an 8-population SFS to estimate the timing and strength of a proposed “basal Eurasian” admixture event in human history. We implement and release our method in a new open-source software package momi2.

[Introduction, Method and Background sections omitted.  Please see the paper for these sections.]

Application

We tested our method on a demographic inference problem in human genetics that is currently of interest.  Lazaridis et al. (2014) showed that genetic variation in present-day Europeans suggests an admixture model involving three ancestral meta-populations: Ancient North Eurasian (ANE), Western Hunter Gatherers (WHG), and Early European Farmers (EEF). They also showed that EEF contains ancestry from a source that is an outgroup to all non-African populations, and yet shares much of the genetic drift common to non-African populations; they dubbed this ancestry component as “Basal Eurasian” ancestry. Later work (Lazaridis et al., 2016) showed that Basal Eurasian ancestry is shared by ancient and contemporary Middle Eastern populations, and is correlated with a decrease in Neanderthal ancestry, implying that Basal Eurasian ancestry contains lower levels of Neanderthal admixture when compared with non-Basal ancestry. The results from Lazaridis et al. (2014, 2016) were based on several related methods for modeling covariances in population allele frequencies, most notably qpGraph and qpAdm (Patterson et al., 2012; Haak et al., 2015). These methods are computationally efficient and robust, but are unable to infer the timing of demographic events.

We applied momi2 to estimate the strength and timing of basal Eurasian admixture into early European farmers, and the split time of the basal Eurasian lineage. To do this, we built a demographic model relating 12 samples from 8 populations, shown in Figure 2. These samples consisted of the Altai Neanderthal (Prüfer et al., 2014); the 45,000 year old Ust’Ishim man from Siberia (Fu et al., 2014); 3 present-day populations (Mbuti, Sardinian, Han) with 3, 2, and 2 samples respectively; and 3 ancient samples representing the European ancestry components identified by Lazaridis et al. (2014): a 7,500 year old sample from the Linearbandkeramik (LBK) culture (representing EEF), an 8,000 year old sample from the Loschbour rock shelter in Luxembourg (representing WHG), and the 24,000 year old Mal’ta boy (“MA1”) from Siberia (representing ANE). After data cleaning, our dataset consisted of 2:4  106 autosomal transversion SNPs. See Appendix A.3 for more details about the data.

To construct the topology of the model in Figure 2, we first obtained a tree by neighbor joining (Saitou and Nei, 1987), then added 3 extra admixture events reflecting prior knowledge, as well as a recent Neanderthal population decline starting at the Mbuti-Eurasian split. We inferred split times, population sizes (including the Neanderthal decline), and admixture times and proportions by maximizing a composite likelihood, given by the product of the likelihoods at every SNP:
 

and was computed by momi2. The low-coverage of the MA1 sample and the deep divergence of the Neanderthal sample may cause bias in SFS entries where only these samples contain derived alleles; we thus excluded these entries and corrected the normalizing constant appropriately (see Appendix A.3).
We used automatic differentiation to compute the gradient (, which we used to search for the optimum of log likelihood. We constructed nonparametric bootstrap confidence intervals by splitting the genome into 100 equally sized blocks, resampling these blocks to create 300 bootstrap datasets, and re-inferring the demography for each bootstrap dataset. We also used 300 parametric bootstraps to assess how well we could infer the demography under simulated data; for each parametric bootstrap dataset, we used msprime (Kelleher et al., 2016) to simulate ten 300 Mb chromosomes from our initial point estimate, and re-inferred the demography. Note the nonparametric bootstrap is better able to account for model misspecification, and we use it for all confidence intervals reported below.


Our inferred demography, along with nonparametric bootstrap re-estimates, are shown in Figure 2 and Table 2. Our parametric bootstrap estimates are shown in Figure 3. We inferred a pulse of 0.094 (95% CI of 0.049-0.174) from the ghost Basal Eurasian population to EEF ancestry (LBK), substantially less than the 0.44 inferred by (Lazaridis et al., 2014). This admixture was inferred to occur 33.7 kya (95% CI of 10.8-41.1 kya), shortly after the Loschbour-LBK split at 37.7 kya (95% CI of 32.2-42.3 kya). The split time of the ghost Basal Eurasian lineage from other Eurasians was inferred at 79.8 kya (95% CI of 67.4-101 kya). Other parameters were broadly in line with previous estimates, such as a Mbuti-Eurasian split of 96 kya, a Han-European split of 50 kya, a Neanderthal split of 696 kya, and Eurasians deriving 0.03 of their ancestry from Neanderthal (Terhorst et al., 2017; Green et al., 2010; Meyer et al., 2016).

[Please see the paper for the remainder of the Application discussion.]

Wednesday, March 28, 2018

The Chiquihuite Cave in Zacatecas, Mexico: Cultural Components, Lithic Industry and the Role of This Pleistocene Site in the Peopling of America

Ciprian Ardelean
ANNUAL MEETING of the Society for American Archaeology
Washington, DC,
April 11-15, 2018
(Link)

Abstract

The high altitude Pleistocene site of Chiquihuite Cave, in the Central-Northern Mexican Highlands, is slowly turning into one of the most important players on the sensitive stage of the debates about the earliest human presence in North America. After the first three exploration seasons and before the imminent continuation of the excavations at this multi-component archaeological site, we can surely talk about several important Late Pleistocene, older-than-Clovis occupational phases. Dozens of radiocarbon and luminescence dates confirm the chronological sequence of this prehistoric locality spanning over millennia. The sediments produced chemical signatures of human presence, as well as interesting palaeonvironmental indicators. The complicated lithic industry at the Cave, based on silicified limestone, shows a large array of taxonomic units, revealing strange but consistent technological approaches: flakes and blades, scrapers, burinated points, points on transversal flakes, bifacial and unifacial tools, intentionally fractured calcite and quartz laminae and so on. The explorations at Chiquihuite are the result of an international and interdisciplinary effort. Novel techniques have been implemented and the results produced a complex view of the ancient archaeological record. Dennis Stanford himself and the Smithsonian Institution played an important role at the very beginning of this scientific endeavor.

Tuesday, March 27, 2018

Detecting archaic introgression without archaic reference genomes

Laurits Skov, Ruoyun Hui, Asger Hobolth, Aylwyn Scally, Mikkel Heide Schierup, Richard Durbin
bioRxiv
March 16, 2018
(Link)

Abstract

Human populations out of Africa have experienced at least two bouts of introgression from archaic humans, Neandertal and Denisovans. In Papuans there is prior evidence of both these introgressions. Here we present a new approach to detect segments of individual genomes of archaic origin without using an archaic reference genome. The approach is based on the detection of genomic regions with a high SNV density of SNVs not seen in unadmixed populations. We show using simulations that this provides a powerful approach to identifying segments of archaic introgression with a small rate of false detection. Furthermore our approach is able to accurately infer admixture proportions and divergence time of human and archaic populations. We apply the model to detect archaic introgression in 89 Papuans and show how the identified segments can be assigned to likely Neandertal or Denisovan origin. We report more Denisovan admixture than previous studies and directly find a shift in size distribution of fragments of Neandertal and Denisovan origin that is compatible with a difference in admixture time. Furthermore we identify small amounts of Denisova ancestry in West Eurasians, South East Asians and South Asians.

Sunday, March 25, 2018

Investigating Ancient Hominin ABO Haplotype Structure From Modern Populations

Keolu Fox, Ian B. Stanaway, Jill Johnsen and Deborah A. Nickerson
AAPA 2018, Meeting Program Abstracts
April 11-14, 2018
http://physanth.org/annual-meetings/annual-meeting-2018/

Abstract

Characterizing variation in the ABO gene is important in transfusion and transplantation medicine because variants in ABO have significant consequences with regard to recipient compatibility. While many believe that the genetics of the ABO locus is well understood, little is known about the impact of novel, rare variation in the ABO gene. Here, we analyze next-generation sequence derived coding variation in ~2,500 individuals from 28 populations, including two ancient hominins (Neanderthal and Denisovan). We hypothesize that imputed ABO types from the 1,000 Genomes Project will recapitulate previous estimates based on serologically derived ABO blood types (Cavalli-Sforza et al., 1994) and allow us to impute ABO haplotype structure in ancient hominins. Through our analysis, we validated previous estimates of ABO blood type based on serology. We identified common variants known to influence ABO function, including those known to the common A and B haplotype as well as a common deletion that leads to the O genotype. We also identified rare population specific coding variants within ABO including single nucleotide/missense variants and insertion/deletions. We then used those haplotypes to impute ABO blood type for both ancient hominins.

These analyses are important for future studies of human blood group genes to (1) improve the specificity of blood typing at both the clinical and research level by identifying rare functional alleles that might result in atypical serological patterns, (2) illuminate ABO gene architecture on a global scale, and (3) assess the potential for introgression of ancient ABO haplotypes found in contemporary human populations.

Saturday, March 24, 2018

Ecological niche models of human land use in Pleistocene Southeast Asia must account for both overall climate and environmentally specific variables

Alexandra J Zachwieja and Laura L. Shackleford
AAPA 2018, Meeting Program Abstracts
April 11-14, 2018
http://physanth.org/annual-meetings/annual-meeting-2018/

Abtract

Ecological niche models (ENM) have long been used to predict species distributions in the biological
sciences. However, their use in paleoanthropological reconstructions of hominin niches is relatively recent and has focused largely on out of Africa dispersals and human occupation in Europe and Central Asia. These studies have shown that the most important variables to predict human land use are moderate temperature, rainfall, and access to fresh water. We apply these predictors to both mainland and island Southeast Asian landscapes during the harsh climate fluctuations of the Last Glacial Maximum (LGM). We validate our ENM using known fossil human occupation sites (n=20) to construct potential human land use maps in an area where glacial climate likely influenced human diet, mobility within habitats, and dispersal to new environments. We compare human land-use outputs from two popular ENM programs, Genetic Algorithm for Rule-Set Production (GARP) and Maximum Entropy Modeling (MaxEnt), to determine which program is more beneficial for studying human land use and dispersal across time and geography. Using only these parameters, both models suggest much of Southeast Asia was amenable to human use during the LGM.

However, other environmental variables, particularly vegetation type, are likely necessary to fully understand past human land use. Rainforest environments have been considered patchier food sources than savannah environments in modern populations, and both environments were widespread in this time and place. We suggest further analysis accounting for additional environmental variables is necessary to gain a full understanding of human land use in Pleistocene Southeast Asia.

Friday, March 23, 2018

Morphological characteristics of the “phylogenetically primitive” Liang Bua, Flores, mandibles match past and present regional Homo sapiens populations

Robett B. Eckhardt, Sakdapong Chavanaves, Kenneth J. Hsu, and Macie J. Henneberg
AAPA 2018, Meeting Program Abstracts
April 11-14, 2018
http://physanth.org/annual-meetings/annual-meeting-2018/

Abstract

Since the first announcement of their discovery in 2004, the bones from Liang Bua (LB), Indonesia, often have been characterized as phylogenetically primitive. However, LB bones fall into the time range for Homo sapiens, whether the original 95,000-120 ka or the revised 100,000-60,000 ka dates, and also are well within more recently-suggested ranges for our species based on 315±34 ka date for Jebel Irhoud. Within those time spans, salient morphological characteristics of the LB1 and LB6 mandibles, for example, can be matched in H. sapiens populations of the region. In extant Flores Rampasa, 93.4% have neutral or negative chins (Hastuti & Jacob, 2007). In Eastern Australian aboriginal mandibles (Larnach & Macintosh, 1971), 37.9% show negative chins; internally, a superior transverse torus ranges from slight in 47.7% to marked in 9.8%; digastric fossa ranges from slight in 37.7% to marked in 28.5%. Pertinent comparative data also are provided by the regional fossil record. At Zhirendong, South China (>100 ka), the Zhiren 3 mandible combines corpus robusticity with an inferior transverse torus lingually. From Minatogawa Fissure, Okinawa (19.9-21.8 ka), Mtg 1 exhibits a rounded external chin labially with a lingually large, deep genioglossal fossa demarcating a weak superior transverse torus from a strong inferior torus. Retromolar sulci are found in Mtg A and Mtg C, as well as in Song Keplek 5, a Holocene human skeleton from Java. Hypothetical African Plio-Pleistocene Homo ancestry for the LB hominins is unnecessary given the existence of morphologically comparable real human populations spatially and temporally closer.