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Post by djoser-xyyman on Apr 20, 2019 20:11:02 GMT -5
Ancient genomes indicate population replacement in Early Neolithic BritainSelina Brace1,15, Chris Stringer 1, David Reich The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain circa 4000 bc, a millennium after they appeared in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition
remain unclear. We assembled genome-wide data from 6 Mesolithic and 67 Neolithic individuals found in Britain, dating 8500–2500 bc. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European huntergatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect
no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithicindividuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by circa 6000 bc. StoneHenge woman  mesolithic Briton Cheddar Man 
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Post by djoser-xyyman on Apr 20, 2019 20:41:56 GMT -5
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Post by djoser-xyyman on Apr 20, 2019 20:50:36 GMT -5
quote:
"To explore variation in pigmentation of European populations,
we predicted pigmentation in higher-coverage Mesolithic and
Neolithic Europeans using HIrisplex-S29. We infer that Cheddar
Man mostly probably had blue/green eyes, dark brown (possibly
black) hair and dark or dark to black skin, whereas our highestcoverage
Early Neolithic individual had brown eyes, black (possibly
dark brown) hair and dark to intermediate skin (see Supplementary
Data 3). Together with the pigmentation prediction outcomes we
obtained for Loschbour and La Braña, these results imply that different
pigmentation levels co-existed in Europe by around 6000 bc."
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Post by djoser-xyyman on Apr 20, 2019 20:53:18 GMT -5
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Post by djoser-xyyman on Apr 20, 2019 21:59:57 GMT -5
Megalithic tombs in western and northern Neolithic Europe were linked to a kindred society Federico Sánchez-Quintoa, www.pnas.org/content/pnas/early/2019/04/09/1818037116.full.pdfData Availability. Raw sequencing reads produced for this study have been deposited in the European Nucleotide Archive (accession no. PRJEB31045). |
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Post by djoser-xyyman on Apr 20, 2019 22:10:10 GMT -5
www.cureffi.org/2013/02/01/the-decoy-genome/The decoy genome Feb 1, 2013 • ericminikel At the CHGR retreat earlier this week I bumped into Ben Neale and mentioned I’d been aligning unmapped reads to virus genomes. He told me I could do much better: Heng Li, inventor of BWA, has created an entire ‘decoy genome’ to capture reads from human exome or whole genome sequencing that fail to align to the human reference genome. The Broad Institute hosts a copy of this decoy genome. With that in mind, let’s return to Broad’s repository of files. If you’re just starting alignment now, you can use hs37d5.fa.gz, which is all of human genome b37 plus the decoy, and if you’ve already done alignment and you just want to realign the unmapped reads you can use hs37d5ss.fa.gz, which is just the decoy. Here I’ll consider the case of realigning unmapped reads to the decoy. step 1. prep files hs37d5ss.fa.gz is the decoy reference genome; you still need to gunzip it and bwa index it which takes < 1 minute because it’s pretty small. wget ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5ss.fa.gzgunzip hs37d5ss.fa.gz bwa index hs37d5ss.fa You’ll also want to pull the unmapped reads out of your original BAM files: samtools view -f 0x04 -h -b original.bam -o unmapped.bam For me, starting with BAMs of 30-50M reads, about 10% of which are unmapped, this takes ~10 minutes per BAM.
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Post by djoser-xyyman on Apr 20, 2019 22:19:19 GMT -5
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Post by anansi on Apr 21, 2019 9:35:19 GMT -5
(But but but!! the agriculturalist are supposed to be depigmented cuz they carried the gene for "lite skin") I've actually heard that argument, that yes, Hg Europeans were black, but the more advanced Neolithic farmer types were the civilizers and therefore "white"
Now What!!¿
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Post by djoser-xyyman on Apr 21, 2019 12:57:19 GMT -5
Keep in mind Kenyans carry derived SLC24A5(heterogenous) like Europeans(homogenous) but are one of the darkest people on the planet. Paupans carry derived SLC45A2 like Europeans but are also one of the darkest people on the planet, Point?! Apparently you need to carry ALL the derived depigmented homogeneous genes to be lilly white.
I haven't parsed through the Supplementals only the main study. But they are admitting that yes, HG were definitely black in complexion(really dark), but the new incoming farmers were a tard lighter than HG. And yes, they carried genes for lighter skin. Maybe heterogenous for SLC24A5. So they are not lilly white. SLC45A2 seemed to arrived earlier. So Europe was still multicolored around 4000bc but by the Bronze age depigmentation was in overdrive.
Nevertheless - They are playing the same sampling game. They refuse to include Africa(North) in their sampling plan when Mota(Ethiopian Hunter gatherer) genes are rich in Iberia and North of Italy. Modern African genes are rich in Iberia. They just can't help themselves....these Europeans.
Now, why Am I talking hs37dB? Well apparently they are playing games with the human reference used in this sample sets. I never heard of hs37db until this study. I can't find a LiftOver file to convert to hg19. These damn Europeans and their games.
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Post by djoser-xyyman on Apr 21, 2019 19:28:22 GMT -5
quote:
"We infer no Central European admixture in Neolithic farmers from
Wales. However, we caution that the model fits are poor and so
these inferences should be considered preliminary.
We inferred some notable geographic structure in WHG
admixture proportions among the British Early Neolithic individuals
(see Supplementary Table 4 for statistical comparison of
inferred WHG admixture proportions); those from Wales retain
the lowest levels of WHG admixture, followed by those from
South-West and Central England."
To those who don't get it, plot this on a map. This implies there was no island hopping. It is BS. Africans Neolithic migrated from the West of the UK not across the Mediterranean Sea
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Post by djoser-xyyman on Apr 21, 2019 19:35:00 GMT -5
quote:
"One explanation for the British Neolithic cline in WHG ancestry
is that a single population moved across Britain from a western
entry point and progressively admixed with local hunter-gatherers.
This scenario is consistent with the western distribution of megalithic
cultures along the Atlantic seaboard31, and is supported by
radiocarbon evidence suggesting a marginally earlier date for
the arrival of ANF ancestry in the west of Britain1.
Evidence for only low levels of WHG introgression among
British Early Neolithic people is striking"
To those who are geographically challenge. They are confirming that the new incoming farmers did NOT arrive from the Mediterranean Sea. They came from the West. ie This genetic pattern is also confirmed by Megalithic structures. The structures in the west were built first ie prior to those in the EAst. The Neolithics arrived in Britain first landing in Wales.
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Post by djoser-xyyman on Apr 21, 2019 19:55:33 GMT -5
looking at the Supplementals Data2 table. The pigmentation profile is shockingly primarily black skin genotype!!!! Wow We know from previous studies eg Rym Kefi. That mtDNA H in Iberia is a subset what is found in North Africa. MtDNA R/N/H in North Africa is derived from East Africa. Now they are adding the nails to the coffin. UK Neolithics came from Iberia. The migration entry was the West in the UK NOT the East  |
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Post by zarahan on Apr 21, 2019 20:22:26 GMT -5
Good roundup.
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