Sunday, February 17, 2019

Unexplained Allele-Calling Errors May Account for Apparent Denisovan-Neanderthal F1 Genome

David Curtis
https://www.preprints.org
28 August, 2018
(Link)

Abstract

The recent report that DNA extracted from ancient bone must have from the offspring of a female Neanderthal and a male Denisovan depends on the inference that the subject has a high level of heterozygosity for Neanderthal and Denisovan alleles across the genome. Here I point out that the relative frequencies of derived transversion polymorphisms varies markedly between the new specimen, Denisova 11, and two high-coverage Neanderthal genomes. In Denisova 11 the AC and CG polymorphisms are much commoner than the others and are almost twice as common as the AT polymorphism. In the high-coverage Neanderthal genomes the four types of transversion are about equally common, with the AT being slightly commoner than the others. These results suggest that allele-calling errors are frequent and that this may provide an alternative explanation for the observed heterozygosity.

Supplementary and Associated Material

https://www.nature.com/articles/s41586-018-0455-x: Original paper

Tuesday, February 12, 2019

A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots

Daniel J. Lawson, Lucy van Dorp and Daniel Falush
Nature Communications
Volume 9, Article number: 3258 (2018)
(Link)

Abstract

Genetic clustering algorithms, implemented in programs such as STRUCTURE and ADMIXTURE, have been used extensively in the characterisation of individuals and populations based on genetic data. A successful example is the reconstruction of the genetic history of African Americans as a product of recent admixture between highly differentiated populations. Histories can also be reconstructed using the same procedure for groups that do not have admixture in their recent history, where recent genetic drift is strong or that deviate in other ways from the underlying inference model. Unfortunately, such histories can be misleading. We have implemented an approach, badMIXTURE, to assess the goodness of fit of the model using the ancestry “palettes” estimated by CHROMOPAINTER and apply it to both simulated data and real case studies. Combining these complementary analyses with additional methods that are designed to test specific hypotheses allows a richer and more robust analysis of recent demographic history.

Saturday, February 9, 2019

Hole in the Ground

Northland, New Zealand (wikicommons (Link))



















Kendrick Smithyman (wikipedia)
1971
(Link)

Hole in the Ground

Walk out to the ocean mark,
away from language. Hightide noon crouches
browbeaten, sliteyed. We do not recognise
the terms of our occupation,
what they imply. A background noise
wholly fails to overcome another
order, a dimension, of silence.

Breakers are not stopped from falling,
blustering or brawling rank on rank.
Slog inland, through the valley’s big mouth,
recording
pulse of insects and the rocky creek.
You leave behind language, like dead shells
an incompetent syntax, a register
unresponsive. How shall I know
where I stand, until I say what I see?

Made deaf by excess of light,
a colonist’s house, last farm, road’s end,
tires any phrase, itself historical fact
leaning tonguetied towards an inarticulate
feeble macrocarpa. The tree tilts
towards the house. Nobody was at home.
Cattle dogs slept, a muddle of black,
white and tan, on the washhouse verandah.
The tractor did not speak.

Unsophisticated downfall,
soil faces along the beach, cut back
by aggressive weathering, show rubbish
layers of occupation. Up the coast
archaeologists are digging. Fragments
will not yet shape themselves
as discourse. A grassy headland
slides the remains of palisades down
the gradient which becomes a meadow,
all lupin, crossed by the creek’s meanders.
Storms have crabbed bushes, littered
with driftwood to the foot of a rise
on which fall bits of shacks,
a flaking stove, frame of an outhouse
passionately used to near extinction.

Yellow admirals, little blues and day
flying moths speculatively cloud
the stream’s precincts. Above an imitation
weir, where you abandon the bay flats,
the valley begins as glen or dale,
further darkly tightens and is a gorge
overhung by feral peaks and birds’
questioning crying,
which we no doubt misconstrue.

Cattle wander there. The creek lopes round
a flat stage with a fell steep behind;
opposite, cliff sheer to a stream bed of slabs.
Gross bulk of silence, bloodily oozing,
taxes unspoken queries. They bear upon
you, heavy as dialect, an alien grammar.

On that flat is a scar, six or eight feet deep,
not naturally straight. The spoil was
thrown mainly on the north side.
No conceivable function as defence,
incredibly long for a saw-pit,
not feasible as a cattle dip, wrong
location for building a canoe,
too wet for storage, without sign
that it was an oven . . . you tire
conjecture and query. Finally,
guess that it is anomaly,
a taro trench (some plants are in situ,
which may be misleading) of a kind
that Buck, for one, never saw in this country
but describes for islands beyond the Line.
That hardly helps. We do not follow

the terms of our occupation.

Monday, February 4, 2019

Posts on this Blog: Southeast Asia, Australia and the South Western Pacific


Culture: Aboriginal Australia


It is our motherland and it is our backbone: The Yolngu people of northeast Arnhem land, Australia, talk about their culture

The Film "Walkabout"


Culture and Ethnobotany: West Papua

Ethnobotany of the Yali of West Papua

Plumes, Pipes and Valuables: The Papuan Artefact-Trade in Southwest New Guinea, 1845–1888

Collecting and Documenting the Kiwai: Stone Tools
Bamboo Pipes/Flutes/Stamping Tubes: Solomon Islands

The Solomon Islands' Arasuka'aniwara Panpipe Band

'Are'are Music

Pala'wan bamboo flute played by Undu Apäl, Mäkägwaq, Pala'wan, Philippines



Bamboo Uses and Manufacture: Australia

Taxonomic interpretations of Australian native bamboos (Poaceae: Bambuseae) and their biogeographic implications

Australian Aboriginal Bamboo Uses and Manufacture 


Music: Aboriginal Australia

Australian Aboriginal Musical Instruments: The Didjeridu, The Bullroarer and the Gumleaf


Bamboo Uses: Yunnan, Southeast China



Bamboo Uses: Philippines

Schizostachyum Lumampao (Byuyu): Its Diverse Ethno-Botanical Uses By Lubuagan Sub Tribe of Kalinga In North Luzon Philippines



Bamboo Rafts

Ecological Contingency Accounts for Earliest Seagoing in the Western Pacific Ocean

Bamboo Rafts

The Manufacture and Terminology of Temiar Bamboo Rafts

South East Asia Archaeology

Were bamboo tools made in prehistoric Southeast Asia? An experimental view from South China

Characterisation of the use-wear resulting from bamboo working and its importance to address the hypothesis of the existence of a bamboo industry in prehistoric Southeast Asia

The oldest Hoabinhian technocomplex in Asia (43.5 ka) at Xiaodong rockshelter, Yunnan Province, southwest China 

The deep human prehistory of global tropical forests and its relevance for modern conservation

The Hoabinhian of Southeast Asia and its Relationship to Regional Pleistocene Lithic Technologies

Stone Axes and Flake Tools: Evaluations from Two New Guinea Highlands Societies 

World’s earliest ground-edge axe production coincides with human colonisation of Australia

Human Occupation of Northern Australia by 65,000 Years Ago



Physical Anthropology of SE Asia

Additional evidence for early modern human morphological diversity in Southeast Asia at Tam Pa Ling, Laos

Cranio-morphometric and aDNA corroboration of the Austronesian dispersal model in ancient Island Southeast Asia: Support from Gua Harimau, Indonesia

A Re-Examination of Sundadonty Origin Models



Bamboo Phylogeny

Taxonomic interpretations of Australian native bamboos (Poaceae: Bambuseae) and their biogeographic implications 

Towards a complete generic-level plastid phylogeny of the paleotropical woody bamboos (Poaceae: Bambusoideae)

How many genera of vascular plants are endemic to New Caledonia? A critical review based on phylogenetic evidence 



Deconstructing Jared Diamond


The People of Papua New Guinea Speak for Themselves

The Round World Made Flat

Questions for Jared Diamond

Friday, February 1, 2019

Compound-specific radiocarbon dating and mitochondrial DNA analysis of the Pleistocene hominin from Salkhit Mongolia

Thibaut Devièse,
Diyendo Massilani,
Seonbok Yi,
Daniel Comeskey,
Sarah Nagel,
Birgit Nickel,
Erika Ribechini,
Jungeun Lee,
Damdinsuren Tseveendorj,
Byambaa Gunchinsuren,
Matthias Meyer,
Svante Pääbo,
Tom Higham

Nature Communications
Volume 10, Article number: 274 (2019)
(Link) open access

Abstract

A skullcap found in the Salkhit Valley in northeast Mongolia is, to our knowledge, the only Pleistocene hominin fossil found in the country. It was initially described as an individual with possible archaic affinities, but its ancestry has been debated since the discovery. Here, we determine the age of the Salkhit skull by compound-specific radiocarbon dating of hydroxyproline to 34,950–33,900 Cal. BP (at 95% probability), placing the Salkhit individual in the Early Upper Paleolithic period. We reconstruct the complete mitochondrial genome (mtDNA) of the specimen. It falls within a group of modern human mtDNAs (haplogroup N) that is widespread in Eurasia today. The results now place the specimen into its proper chronometric and biological context and allow us to begin integrating it with other evidence for the human occupation of this region during the Paleolithic, as well as wider Pleistocene sequences across Eurasia.