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Thread: Important papers for newbies to Population Genetics

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    11 out of 11 members found this post helpful.

    Important papers for newbies to Population Genetics

    I hope this thread will prove helpful for newbies to population genetics.

    This is some essential reading for newbies:

    Lazaridis et al 2014:http://www.nature.com/nature/journal...ture13673.html

    Gamba et al: https://www.nature.com/articles/ncomms6257

    Haak et al 2015:https://www.biorxiv.org/content/early/2015/02/10/013433

    Lazaridis et al 2016: https://www.biorxiv.org/content/early/2016/06/16/059311

    Iain Mathiesen et al 2015:https://www.biorxiv.org/content/early/2017/05/30/135616

    Olalde et al: https://www.biorxiv.org/content/early/2017/05/09/135962

    Cassidy et al:http://www.pnas.org/content/113/2/368.full

    Scheuenemann et al (with Johanes Krause): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5459999/

    Lazaridis et al: https://reich.hms.harvard.edu/sites/...ure23310_0.pdf


    If you have questions I'm sure people will help out. Also, if you have specific questions about a particular topic and can't find the relevant papers through the search engine, we'll try to lend a hand.

    Ed. Lipson et al and as disccused here (also from the Reich Lab):
    https://www.biorxiv.org/content/early/2017/03/06/114488

    https://www.eupedia.com/forum/thread...ghlight=Lipson

    Ed. Free version of Lazaridis et al 2014: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4170574/

    For all the other links, if the complete paper doesn't pop up, look to the right and click on download pdf.
    Last edited by Angela; 13-12-17 at 17:59.


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    Quote Originally Posted by Angela View Post
    I hope this thread will prove helpful for newbies to population genetics.

    This is some essential reading for newbies:


    Lazaridis et al 2014:http://www.nature.com/nature/journal...ture13673.html

    Gamba et al: https://www.nature.com/articles/ncomms6257

    Haak et al 2015:https://www.biorxiv.org/content/early/2015/02/10/013433

    Lazaridis et al 2016: https://www.biorxiv.org/content/early/2016/06/16/059311

    Iain Mathiesen et al 2015:https://www.biorxiv.org/content/early/2017/05/30/135616

    Olalde et al: https://www.biorxiv.org/content/early/2017/05/09/135962

    Cassidy et al:http://www.pnas.org/content/113/2/368.full

    Scheuenemann et al (with Johanes Krause): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5459999/


    If you have questions I'm sure people will help out. Also, if you have specific questions about a particular topic and can't find the relevant papers through the search engine, we'll try to lend a hand.
    Nice compilation


    Sent from my iPhone using Eupedia Forum
    Last edited by Angela; 11-11-17 at 17:01.

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    Wow, thanks!

    Sent from my SM-G900F using Eupedia Forum mobile app

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    1 out of 1 members found this post helpful.
    Balkan Genetics:
    http://journals.plos.org/plosone/art...l.pone.0105090

    It was discussed here:
    https://www.eupedia.com/forum/thread...eway-to-Europe

    The Geography of Recent Ancestry across Europe: Ralph and Coop et al-based on IBD analysis
    http://journals.plos.org/plosbiology...l.pbio.1001555
    Last edited by Angela; 27-11-17 at 23:13.

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    I will read this in my free time, thank you!!

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    1 out of 1 members found this post helpful.
    Review of ancient genomics by Pontus Skoglund and Iain Mathiesen:
    https://www.dropbox.com/s/ddzg6q5e14...20Genomics.pdf

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    1 out of 1 members found this post helpful.
    Also essential reading...

    Kilinc et al:
    http://www.cell.com/current-biology/...822(16)30850-8

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    2 out of 2 members found this post helpful.

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    1 out of 1 members found this post helpful.
    Some I forgot to include:
    Hoffmanova et al: https://www.biorxiv.org/content/early/2015/11/25/032763

    An oldy but a goody: the paper on Otzi
    https://www.nature.com/articles/ncomms1701

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    A tutorial on how not to over-interpret Structure and Admixture...

    See: https://www.biorxiv.org/content/bior...66431.full.pdf

    I've posted on this before, but some people just won't listen.

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    Quote Originally Posted by Angela View Post
    I hope this thread will prove helpful for newbies to population genetics.

    This is some essential reading for newbies:

    Lazaridis et al 2014:http://www.nature.com/nature/journal...ture13673.html

    Gamba et al: https://www.nature.com/articles/ncomms6257

    Haak et al 2015:https://www.biorxiv.org/content/early/2015/02/10/013433

    Lazaridis et al 2016: https://www.biorxiv.org/content/early/2016/06/16/059311

    Iain Mathiesen et al 2015:https://www.biorxiv.org/content/early/2017/05/30/135616

    Olalde et al: https://www.biorxiv.org/content/early/2017/05/09/135962

    Cassidy et al:http://www.pnas.org/content/113/2/368.full

    Scheuenemann et al (with Johanes Krause): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5459999/

    Lazaridis et al: https://reich.hms.harvard.edu/sites/...ure23310_0.pdf


    If you have questions I'm sure people will help out. Also, if you have specific questions about a particular topic and can't find the relevant papers through the search engine, we'll try to lend a hand.

    Ed. Lipson et al and as disccused here (also from the Reich Lab):
    https://www.biorxiv.org/content/early/2017/03/06/114488

    https://www.eupedia.com/forum/thread...ghlight=Lipson
    Any reason why its asking me to pay 200 dollars to subscribe to read the actual paper, besides a abstract? With the exception of the Gamba paper, most are asking me to pay for full access to the paper.

    Anywhere I can access this without forking over 200 beans?

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    1 out of 1 members found this post helpful.
    Quote Originally Posted by Dibran View Post
    Any reason why its asking me to pay 200 dollars to subscribe to read the actual paper, besides a abstract? With the exception of the Gamba paper, most are asking me to pay for full access to the paper.

    Anywhere I can access this without forking over 200 beans?
    Dibran, the only link that doesn't either show or allow for the viewing of the entire paper is the first one, Lazaridis et al 2014. I'll try to find free, legal access for it. For the rest, if the whole paper doesn't pop up, then just look to the right and click on download pdf.

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    1 out of 1 members found this post helpful.
    Quote Originally Posted by Angela View Post
    Dibran, the only link that doesn't either show or allow for the viewing of the entire paper is the first one, Lazaridis et al 2014. I'll try to find free, legal access for it. For the rest, if the whole paper doesn't pop up, then just look to the right and click on download pdf.
    Here is the link for the free version of Lazaridis et al 2014. I'll edit my original post.
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4170574/

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    1 out of 1 members found this post helpful.
    @Dibran,

    You're welcome.

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    Quote Originally Posted by Angela View Post
    Dibran, the only link that doesn't either show or allow for the viewing of the entire paper is the first one, Lazaridis et al 2014. I'll try to find free, legal access for it. For the rest, if the whole paper doesn't pop up, then just look to the right and click on download pdf.

    Ahh, thank you. Just noticed now that you mentioned PDF icon.

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    Quote Originally Posted by Angela View Post
    Here is the link for the free version of Lazaridis et al 2014. I'll edit my original post.
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4170574/

    Thank you so much!

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    In Olalde et al, Anatolia Neolithic is modeled as a mixture of the blue component highest in Levantine Neolithic and the red component representing European hunter gatherers, but in Lazaridis et al Anatolia Neolithic is a mixture of the previous two plus Iran Neolithic, yes I can see the small amount of the green component but that's not as high as the 38% mentioned in the last paper, how to explain this ?




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    1 out of 1 members found this post helpful.
    Paper on the Stone Age Plague from the Krause group:

    Valtuena et al: "The Stone Age Plague: 1000 years of Persistence in Eurasia"
    https://www.biorxiv.org/content/bior...94243.full.pdf

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    See also: Rui Mariniano et al about Roman Era Britain
    "Genomic signals of migration and continuity in Britain before the Anglo-Saxons:
    https://www.nature.com/articles/ncomms10326


    It was discussed by us here:
    https://www.eupedia.com/forum/thread...nd-Anglo-Saxon


    See also: Torsten Gunther et al
    "Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation"

    It was discussed here at these links:

    https://www.eupedia.com/forum/thread...ic-Scandinavia

    https://www.eupedia.com/forum/thread...ic+Scandinavia




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    1 out of 1 members found this post helpful.
    Another important paper:
    Alyssa Mittnik et al
    "The Genetic Pre-history of the Baltic Sea Region"
    https://www.nature.com/articles/s41467-018-02825-9


    It's discussed here:
    https://www.eupedia.com/forum/thread...tic-Sea-Region

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    I thought of adding this here, because I believe it is a very powerful finding of modern population genetics: populations at the four corners of the quadrangle (WHG, EHG, Natufians, Iran_N) had differentiation of FST=0.08-0.15, comparable to the value of 0.09-0.13 seen between present-day West Eurasians and East Asians (Han). In contrast, by the Bronze Age, genetic differentiation between pairs of West Eurasian populations had reached its present-day low levels, today, FST is ≤0.025 for 95% of the pairs of West Eurasian populations and ≤0.046 for all pairs. These results point to a demographic process that established high differentiation across West Eurasia and then reduced this differentiation over time.


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    Good Afternoon: thank you for the opportunity to be a part of this forum. I've been both a consultant and a writer as well as a host of others. yet my recent discoveries of sources and programahas made my current journey of retirement one of a passionate curiosity and a committment to discovery. Currently the Celttic world's truthand myths has incresed my hunger. having spent some time with this source I'm excited> Thanks again and I'll look forwar to sharing even if I'm sure that I should start slow.

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    Iron side
    thanks for the information it's really exciting to see how much information that has been procecessedsince my days of writng a newspaper column and being assigne a high scool genetic seminar.

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    Population replacement in Early Neolithic Britain:

    https://www.eupedia.com/forum/thread...nc-Cheddar-Man

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    1 out of 1 members found this post helpful.
    This is the link to the paper on the ancient Lombards:

    Understanding 6th Century Barbarian Social Organization and Migration through Paleogenomics
    https://www.biorxiv.org/content/bior...68250.full.pdf

    This is our discussion on it.
    https://www.eupedia.com/forum/thread...light=Lombards


    This is the shareable link for the official Nature version of Mathiesen et al on the genetics of Southeastern Europe. Thanks to Iosif Lazaridis for requesting it.

    https://www.nature.com/articles/natu...izVSR-LMRmndg0

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