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Matthew Collins
Works at University of York
Attended University of Wales, Bangor
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Just for fun I created a low res animated GIF of the data in 

Leslie, S., et al.  2015. The fine-scale genetic structure of the British population. Nature 519, 309–314.

http://www.nature.com/nature/journal/v519/n7543/full/nature14230.html
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Did farming cause a bottleneck in #male #genetic diversity?

When people abandoned a hunter-gatherer lifestyle and became agriculturalists, initially some 10,000 years ago, they gave up a lot of things.

This significant shift in the way they obtained their food was probably not something they elected to do. Instead, population pressure and diminishing resources forced people into developing new intensified forms of subsistence. This meant people became more sedentary.
Not only did these new arrangements result in the emergence of new social structures and new technological innovations, but it also had some very negative outcomes.

As people intensified their subsistence strategies and became sedentary there was an increase in population size.

In fact, Y chromosome genetic data suggests this reduction at around 8,000 to 4,000 years ago. Essentially there was a genetic bottleneck in male genetic diversity at that time which cannot be easily explained through natural selection.

A lot happened when humanity turned to agriculture.

Originally published: Genome Research
When people abandoned a hunter-gatherer lifestyle and became agriculturalists, initially some 10,000 years ago, they gave up a lot of things. This significant shift in the way they obtained their food was probably not something they ...
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University of York offers Paperpile to all its staff and students.
Organise your research using Paperpile! Posted on 14 April 2015. Paperpile, our newest reference management tool, lets you manage your research library, create quick citations, and collaborate with others on papers and reference lists. Paperpile is a simple but powerful web-based reference ...
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...not to mention a responsive IT team who listen to staff and their needs :)
 
The UCSC Archaeological Research Center presents:
1st Annual Research Conference 
Archaeological Genetics: Genomic Approaches to Our Past
April 14th, 2015
UC Santa Cruz, Porter College
George P. Hitchcock Lounge

Since the first studies 30 years ago, the analysis of ancient DNA from biological specimens found in archaeological contexts has propelled our understanding of the evolution of our species, how humans diverged and interacted in the past, how biology and culture coevolved, how environmental changes impacted on past ecosystems, and also how diseases evolved and spread throughout the ancient world. Recent developments in molecular genetics now provide insights into biological processes unthinkable just 10 years ago. Ancient DNA researchers using these new methods have been able to reconstruct complete genomes of Neanderthals and other extinct species as old as 700,000 years, reconstruct past oral and gut microbiomes allowing incredible insights into past diets and health, to study complex evolutionary processes of adaptation to physical stressors in real-time, study ancient gene expression patterns, and to reconstruct complex patterns of admixture between human populations worldwide granting us a much better picture of how different cultures and regions interacted with each other. Indeed, ancient DNA research has reached the Age of Genomics. The UCSC Archaeological Research Center is hosting a public research conference on Paleogenomics with talks by major leaders in the field. These scientists will present a range of contributions that modern Paleogenomics has made to archaeological efforts to solve the riddles of our collective past.
Speakers Include:

• Lars Fehren-Schmitz (UC Santa Cruz) 

• Ed Green (UC Santa Cruz) 

• Wolfgang Haak (University of Adelaide) 

• Johannes Krause (University of Tubingen, Max-Plank-Institute for Science of Human History) 

• Beth Shapiro (UC Santa Cruz) 

• Pontus Skoglund (Harvard Medical School) 

• Christina Warinner (University of Oklahoma) 

Conference Program

Opening Remarks (1:00-1:30)

• 1:00-1:05 – Opening Comments – J. Cameron Monroe (ARC Director)

• 1:05-1:30 – “Archaeology and Paleogenomics: A New Vision for the Past – Lars Fehren-Schmitz

Session 1 (1:30- 2:30)

• 1:30-2:00 – “Molecular Paleopathology: New insights into ancient Diseases” – Johannes Krause

• 2:00-2:30 – “Reconstructing Our Ancient Microbial Self” – Christina Warinner

Coffee Break (2:30-2:45)

Session 2 (2:45-3:45)

• 2:45-3:15 – “European prehistory at the interface of archaeology and genetics” - Wolfgang Haak

• 3:15-3:45 – “Reconstructing human population history using ancient genomes: the peopling of the Americas” – Pontus Skoglund

Coffee Break (3:45 – 4:00)

Session 3 (4:00-5:00)

• 4:00-4:30 – “Paleoecology and past Biodiversity” – Beth Shapiro

• 4:30-5:00 – “The genomics of extinct Hominins” – Ed Green Closing Comments

• 5:00-5:15 – Concluding Remarks (Lars Fehren-Schmitz)

Reception (5:15-6:00) 
Conference Registration · Event Calendar · Types of Events · Feedback. UC Santa Cruz, 1156 High Street, Santa Cruz, Ca 95064 ©2014 Regents of the University of California. All Rights Reserved.. 128.114.113.115. Privacy Policy and Terms of Use.
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ZooMS tracks Viking Trade
This paper presents the results of the use of a minimally destructive biomolecular technique to explore the resource networks behind one of the first specialized urban crafts in early mediaeval northern Europe: the manufacture of composite combs of deer antler. The research incorporates the largest application of species identification by peptide mass fingerprinting (ZooMS) to a mediaeval artefact assemblage: specifically to collections of antler combs, comb manufacturing waste, and raw antler from Ribe, Aarhus, and Aggersborg. It documents the early use of reindeer (Rangifer tarandus) antler, from the 780s ad at the latest, presenting the earliest unambiguous evidence for exchange-links between urban markets in the southern North Sea region and the Scandinavian Peninsula. The results demonstrate that the common conceptual distinction between urban hinterlands and long-distance trade conceals a vital continuity. Long-range networks were vital to urban activities from the first appearance of towns in this part of the world, preceding the historically documented maritime expansion of the Viking Age. We consequently suggest that urbanism is more appropriately defined and researched in terms of network dynamics than as a function of circumscribed catchment areas or hinterlands.
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The development of farming traditions has long interested archaeologists worldwide, and the relationship of this process with human movement has become increasingly refined in recent years. Here we examine this issue in a case study that concerns the longstanding question of the spread of maize agriculture and Mississippian cultural traditions throughout much of the Eastern U.S. Although it has long been common to interpret the development of Mississippian maize agriculturalists partially as a result of human migration, there have been very few direct studies of the problem. We do so here by analyzing human tooth enamel from burials for δ13C and 87Sr/86Sr. Our results suggest that Fort Ancient societies adopted maize agriculture quickly with the initial sites consuming high levels of maize. The intensity of maize consumption may have declined over time, however, in contrast to the current model. There is clear evidence for the presence of non-local individuals at early Fort Ancient sites, particularly Turpin, with the majority being attributable to neighboring Mississippian regions. These developments occurred at the largest sites located by the mouths of the Great and Little Miami Rivers where the most abundant Mississippian house styles and objects are concentrated.
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On the subject of dog domestication, here's a video by one of the aDNA researchers taken from Science Special Collection:
https://www.youtube.com/watch?v=IO9kBIZY8tg
Special Science Collection:
http://www.sciencemag.org/site/extra/dogs/?intcmp=magazine
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Matthew Collins

Bib Ref Management  - 
 
+Paperpile the gateway drug to collaborative writing on line?

My University, the +University of York has recently provided a site-wide licence for Paperpile an onlline reference management tool which integrates with Google Scholar and Google Drive.  
http://www.york.ac.uk/it-services/it/software/a-z/paperpile/

for the most recent review of Paperpile see
http://www.drsustainable.com/5-reasons-why-paperpile-is-my-new-reference-manger-of-choice/

It works like other bibliographic software - inserting and formatting references (to GoogleDocs) and creating bibliographies.  Its killer implementation is integration with Google Scholar. 

Most academics use Google Scholar.  Paperpile effectively extends Google Scholar, by adding buttons that can be clicked to add articles, storing the PDFs on Google Drive.  If you already have the article and the PDF these are indicated by the ticked button and the blue text icon respectively.  You can then view the reference in Paperpile or the PDF by clicking on them directly.   All the PDFs are renamed, indexed and stored in a Paperpile folder on your Google Drive. 

Once you are addicted to Paperpile the strengths of collaborative writing soon become evident. Multiple authors add their references to a shared Google document and you can easily incorporate any missing articles into your Paperpile.  Clicking on an article tells you which co-author inserted it, opens up a link of all the articles and offers the option of importing just that one article or all cited articles to your Paperpile account.  

The articles that are inserted by Paperpile are hot-linked to the resource. Indeed as an educator you can use this to check if a student really could have read an article they cited (when you try to add to your Paperpile and realise it lurks behind a paywall).  
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Matthew Collins
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Elegant and interesting work. 
Analysis of baby skeletons could help predict medical problems among contemporary children, says archaeologist
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"The real solution to the postdoc problem... lies in dramatically changing the composition of labs to make them smaller, with a higher ratio of permanent staff scientists to trainees" 
There is a growing number of postdocs and few places in academia for them to go. But change could be on the way.
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Matthew Collins
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The introduction of next-generation sequencing methods has broadened the scope and utility of ancient DNA (aDNA) research, and is opening up exciting new applications in Quaternary science. Palaeogenomes – partial or complete genome sequences for extinct taxa – are now available for Neanderthals and Denisovans, various megafauna, and preserved microorganisms. The analysis of aDNA in sediments, including cores in which there are no visible macro- or microfossils, is helping to reconstruct past ecosystems, especially in Arctic regions where aDNA preservation is relatively good. In this review we follow the development of aDNA research over the last 30 years, showing how the problems caused by contamination of ancient samples with modern DNA have gradually been overcome, and highlighting those technical challenges that still exist. We then survey the current standing of palaeogenomics and sedimentary aDNA studies, and indicate how these fields might be developed further in coming years.
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In his circles
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743 people
Brendon Wilkins's profile photo
Benjamin Elliott's profile photo
Joke Reumers's profile photo
Arthur Clune's profile photo
Henry Rothwell's profile photo
Cellular Computing's profile photo
Muchblue.com's profile photo
Melanie Macrae's profile photo
Anita Radini's profile photo
Education
  • University of Wales, Bangor
    Zoology, 1979 - 1982
  • University of Glasgow
    Geology, 1983 - 1986
  • Leiden University
    Biochemistry, 1986 - 1990
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University of York account
Introduction
Professor of Archaeology
Member of BioArCh
Work
Occupation
BioArCh Department of Archaeology
Employment
  • University of York
    Department of Archaeology, present
  • Vriije Universiteit, Amsterdam
    Bijzonder Hoogleerar, 2015
  • University of Newcastle upon Tyne
    Biogeochemist, 1992 - 2003
  • Bristol University
    PDRA, 1990 - 1992
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Male
Excellent Jamaican food, great fun
Public - 6 months ago
reviewed 6 months ago
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