Sunday 28 June 2020

Chicken origins: closing in with new genomic evidence

wild Gallus gallus spadiceus
The past week saw the publication of a landmark genomic study on chickens (Wang et al 2020, Cell Research), which clarifies much about origins, and focuses some questions for further research. For a news summary see Lawler's Science piece.

It is transformative because it includes a substantial sample of genomes from across all of the wild subspecies of Red Jungle Fowl (142 wild red jungle fowls) and other wild Gallus species. The first thing to note is that is does support the reality of these different wild taxa. They aren’t merely geographical feral populations derived from escaped chickens, but they are differentiated from each other, making it reasonable to ask which population(s) are ancestral to domesticated chickens. In addition there has, of course, been gene flow via introgressions with domesticated chickens, but this has been on a more limited scale. So the answer to big question (of origins) appears to be Gallus gallus spadiceus. G. g. spadiceus is geographically focused on Burma, Yunnan, Guangxi, northern Thailand and bits of Laos. This struck me as the most surprising—this geographical derivation. If one favours a Chinese origins then you would look to G. g. jaboulliei (of the Guangdong and Fujian and perhaps further north in the past); if one favours an Indus domestication then one looks to G. g. murghii. Previously I have accepted the likelihood of an Indus Chicken domestication and a spread through India in post-Harappan times (e.g. Fuller 2006). This now appears unlikely. Instead it probably means that wild jungle fowls attracted attention in the Harappan period as pretty birds that were captured sometimes, traded, etc.,but not really domesticated subsistence species. Presumably the first Bronze Age Mesopotamian and Ramesside Egyptian “chickens” were actually pet wild jungle fowl-- fancy exotic birds-- and not connected to chickens as we understand them now. The "multi-colored birds of Meluhha" that were imported to Mesopotamia at the end of the Third Millennium BC from the Indus region, are plausible painted ivory statuettes of murghii jungle fowl (see, e.g. During-Caspers 1990).

These new genetic data also make it clear that as chickens spread out of their northern SE Asian homeland they did pickup some genetic material through introgression with local wild jungle fowl (such as G. g. murghii in northern India) and even grey jungle fowl in South India (the source of yellow legs: G. sonneratii). This process can be called “introgressive capture” and it is widespread in most livestock and many crops. This process has sometimes confused genetic studies into inferring multiple domestications, but with more genomic data it can now be disentangled (see Larson and Fuller 2014). 

It is also quite exciting that they have some genetic loci that might be under positive selection as part of the domestication process. One of the real mysteries with animal domestication is what constitutes domestication in a genetic sense in terms of adaptations. In plant it is well known that certain genes for seed dispersal, growth habit, dormancy, grain size, etc. were selected. We can find this evidence genetically and tie it to morphological changes in the archaeobotanical record. There is so far nothing equivalent in animals that links genetic loci to the morphological adaptations we see with animal domestication. So on a more theoretical level this may be the first step to actually starting to unravel the genetics of animal domestication.

These raises fascinating questions then about the contexts in which G. g spadiceus was domesticated—what kinds of human societies and agricultural economies did it interact with in its wild form and how did it get incorporated into ecology of human settlements. Equally at what period and in what contexts did these early chickens then spread. Their phylogenetic results suggest the first wave of chickens spread through SE Asia and SW China only.  Sadly we know little about the Neolithic in Myanmar, or Guangxi or Southern Yunnan; we do have some data from northern Yunnan where Chinese millet and rice agriculture (with pigs) arrives from the North around 2600 BC. One presumes there was some further Southern diffusion towards the China/Burma borderlands. And perhaps it was in these borderland zones where early sedentary rice/millet farmers began to isolate some G. g. spadiceus populations that came feed within the human settlement niche. As hypothesized in Larson and Fuller (2014), chickens likely followed a commensal pathway to domestication. But we now need to refine the map (right). And work out when this happened.


There estimate of the age of the last common ancestor of domesticated chickens and G. g. spadiceus 9500 BP (+/- 3000). But I would regard domestication any time between 10000 BC and 4500 BC as highly unlikely. As the authors themselves not in the first paragraph of their discussion such genetic estimates of domestication age tend to be over estimates (by upto 15,000 years!), so these are not exactly reliable.  In fact I would regard the tendency genetic coallesence ages as to tell us anyting about the timing of domestication to be a highly  misleading tradition that is entrenched in genetics but has little to back it up. Take the example of rice (Oryza sativa), where the genetic estimate of last common ancestor of cultivated rice and modern wild population is ca. 18,000 (Choi et al 2017). But archaeologically even the more generous estimates are ~10,000 (and more like 7,000-6500 by more cautious approaches). I suspect a more general problem is that what is being picked up the last major cladogenetic event that structured wild populations and not domestication itself. Often this can be expected to be something climatic, so 9500 BP is telling us something about how Early Holocene climatic changes—which restructured vegetation in big ways—restructured wild jungle fowl. Then it was one of these localized population that millennia later got domesticated. In all likelihood that localized population that was actually domesticated won’t exist anymore. It is also worth noting that the reality of domestication bottlenecks is itself somewhat dubious and is in the past year or two come to be questioned. Where ancient DNA is available (e.g. maize, sorghum, barley) it is demonstrable that no such bottleneck occurred and age estimates (see Allaby, Ware and Kistler 2019) that conceive some sort of a bottleneck may not be really telling up about domestication. 

Given what we know of the archaeology of SE Asia, one would tend think the initial  domestication and spread of chicken is unlikely earlier than the grain-based Neolithic that starts around 2500 BC (in southern bits of China) and reaches southern Thailand at 2000 BC. However, as far as I know there are no archaeological chicken finds at early sites. So I wonder whether the first spread of domesticated chicken might represent a secondary later spread perhaps closer to 1000 BC (the period when Bronze working spread southwards from China); this might also be the period when new crops spread like sticky rice. It may be that at that time chickens also spread rapidly via trade routes to India. I have long argued (e.g. Fuller 2007) that in South India the Dravidian linguistics suggest arrival of chickens after the South, South-Central and Central languages had fully diverged (which is something like 3000 years ago). Not long after this there are good chicken terminologies in Sanskrits and Prakrits from the 1st Millennium BC, so it makes sense that chickens really only became established as livestock in India at around that time, and of course it is the later Iron Age when they first turn up in the west , such as the Hellenistic era evidence from the Levant (Perry-Gal et al 2015), or as an exotic animal in western Europe (Sykes 2012).

18 comments:

Unknown said...

My name is Mrs Aisha Mohamed, am a Citizen Of Qatar.Have you been looking for a loan?Do you need an urgent personal loan or business loan?contact Dr James Eric Finance Home he help me with a loan of $42,000 some days ago after been scammed of $2,800 from a woman claiming to been a loan lender but i thank God today that i got my loan worth $42,000.Feel free to contact the company for a genuine financial service. Email:(financialserviceoffer876@gmail.com) call/whats-App Contact Number +918929509036 Dr James Eric Finance Pvt Ltd

Zara Blogs said...

There is a comment of a very different way, when I like your comment, thanks for this post.
Call Girls In Gurugram
Call Girls Sector 1
Call Girls In Noida
Call Girls Sushant Lok
Call Girls Palam Vihar
CAll Girls Huda Metro
Call Girls Phase 1
Call Girls phase 2
Call Girls phase 3

Martyn Cornell said...

Man, you really need to install some anti-spam software

Anonymous said...

I'm Serenity Autumn, currently living in Texas city, USA. I am a widow at the moment with Four kids and i was stuck in a financial situation in May 2019 and i needed to refinance and pay my bills. I tried seeking loans from various loan firms both private and corporate but never with success, and most banks declined my credit. But as God would have it, I was introduced to a woman of God a private loan lender who gave me a loan of 850,000.00 USD and today am a business owner and my kids are doing well at the moment, if you must contact any firm with reference to securing a loan without collateral , no credit check, no co signer with just 2% interest rate and better repayment plans and schedule, please contact Mrs Mr Bejamin Lee On Email 247officedept@gmail.com   And Whats-App +1-989-394-3740. He doesn't know that am doing this but am so happy now and i decided to let people know more about him and also i want God to bless him more.

AlexKath said...

Get Hemp teabags boxes from The Customize Boxes. The Custom Hemp Tea Bags Boxes are designed in a way by our specialist that they are fulfilling dual purposes: attracting the customers and saving the item packed inside.

Anonymous said...

Mr Pedro is absolutely incredible. He’s been so responsive, so patient & honest, and just wonderful at his job as a loan officer. I will buy every future house with him if I ever move to DC. He’s just the absolute best.”
I will recommend anyone here looking for a loan to contact a loan officer Pedro on Email... pedroloanss@gmail.com

Debi Mitchell said...

My name is Debi Mitchell! I'm here to testify about Mr Larry Blank ATM Cards which can withdraw money from any ATM machines all over the world. I applied for the Blank Card to my greatest surprise I have used it to get 24,000 dollars. You can withdrawal up to $1,200 per day. You can also use it to shop online and attach it to your PayPal account. The card is already been hack, loaded and programmed with fund. If you want to get one for yourself, contact him via his email: (Larrypatrick_k@aol.com) Do not miss this great opportunity.

urgent loan said...

Do you need Finance? Are you looking for Finance? Are you looking for finance to enlarge your business? We help individuals and companies to obtain finance for business expanding and to setup a new business ranging any amount. Get finance at affordable interest rate of 3%, Do you need this finance for business and to clear your bills? Then send us an email now for more information contact us now via (financialserviceoffer876@gmail.com) whats-App +918929509036 Dr James Eric Finance Pvt Ltd Thanks

Cyberz_Phoenix said...

Cyberz Phoenix is a Group of Multinational Hackers & Spammers. We make sure by all means necessary that our clients get the best of services on A PAYMENT.
Rather than send money and trust a criminal to fulfill your deal. You'll get excellent customer service.
That's a 100% guarantee.

BEWARE OF FRAUDSTARS
if you have been a VICTIM,
Contact:
Telegram : @Cyberz_Phoenix
ICQ : @1001829652
WICKR : @cyberzphoenix for directives.
Here, it's always a win for you.
Without any Reasonable doubts, it is no news that Cyberz Phoennix offer one of the best services.

Amongst others, services we offer are listed as follows :

Fresh and valid USA SSN leads :
>> SSN+DOB
>> SSN+DOB+DL
>> Premium high score fullz (also included relative info)

TUTORIALS AVAILABLE FOR
SPAMMING
CARDING
CASHOUTS
MOBILE DEPOSITS
>APPLE PAY & ANDROID TAP CASH
>BANK TRANSFER
>HOW TO CASHOUT DUMPS+PINS
>MOBILE DEPOSIT

>SAFE SOCKS5 (USA)
>SMTP Linux Root
-->DUMPS+PINS
(How to use & create dumps with pins track 1 & 2)

>SERVER I.P's & proxies in bulk
>USA EMAILS Combo
>Fresh Leads for tax returns & w-2 form filling
>CC's with CVV's (vbv & non-vbv)
>USA Photo ID'S (Front & back)
>Payment mode BTC, ETH, LTC, & USDT

Contact:
Telegram : @Cyberz_Phoenix
ICQ : @1001829652
WICKR : @cyberzphoenix

Roses Ronan said...

I have already been studying the good key points located on your website and immediately got a terrible feeling I never thanked the blog owner for those tips.
Heathrow airport cheap parking

The Eagle Security said...

Thanks for sharing this interesting post with us. We as The Eagle Security provide Mobile Petrol Services striving to become the best security service provider in Toronto. We are here for all your security needs

Custom Popcorn Boxes said...

Interest Post .Custom Popcorn Boxes provides custom and cost-efficient Food boxes for all kinds of personal and professional requirements.

Mozell R Robinson said...

I've lost thousands to these fake hackers, please don't fall for any of them, it's taken me months to find a genuine hacker who's services are cheap and affordables.  Thank you cyprushacker! you and your crew are the bomb ,the work you did on my spouse's accounts was simply phenomenal! Hey if you ever need to get into your spouse's account, improve credit points, clear criminal records,tax, protection from spyware or simply have a score to settle or any other issues that need addressing, completely secure and fast!!contact by email..... (wizardcyprushacker@gmail.com) whatsapp +1 (424) 209-7204 don't forget to tell him Elizebeth Willams refer you to him.
Thank you.

Anonymous said...

Thank you for writing this quality informational content. Your writing technique is impressive and enjoyable to read. If you want about custom packaging box with logo.

hyper leauge said...

Thanks for giving us such productive Informatoin

Anonymous said...

NAME|SSN|DOB|DL|ADDRESS|EMAIL|PHONENUMBER|WORKHISTORY|ACCOUNTDETAILS
Fresh Fullz & Fresh Spammed

CCNUMBER|MM|YYYY|CVV|NAME|SSN|DOB|ADDRESS|EMAIL|PHONENUMBER
CC fullz with CVV

High Credit Scores Pros 700+
EIN Business Fullz

ICQ 752822040
WA/TG +92 317 272 1122
TG @leadsupplier
Skype/Wickr @peeterhacks

Spamming All fresh Tools & Tutorials
Hacking Stuff
Carding Methods & Cashout Methods
Loan Methods
SMTP's/RDP's/SHELLS/Brutes/C-panels
Key-Loggers/Kali-Linux Full Package
Courses for D**K/D**P Web
SQLi Injector
Combos/I.P's/Proxies
Logs/HQ Emails

ICQ/TG @killhacks
WA +92 317 272 1122
exploit.tools4u at gmail dot com

Pedro Santa Cruz said...

<Investment is one of the best ways to achieve financial freedom. For a beginner there are so many challenges you face. It’s hard to know how to get started. Trading the Crypto market has really been a life changer for me. I almost gave up on crypto currency at some point not until I got a proficient trader Bernie Doran, he gave me all the information required to succeed in trading. I made more profit than I could ever imagine. I’m not here to converse much but to share my testimony, I invested $2000.00 and got back $21,500.00 within 5 days of investment. His strategies and signals are the best and I have gained more knowledge.
If you are new to cryptocurrency. You can reach to him on Telegram: @BERNIE_FX
Or through Email : Bernie.doranfx01@gmail.com

Linda Anthony said...

I'd like to express my sincere gratitude to the woman who commented on how she used DWOH to recover her bitcoin and return it to her wallet. Coincidentally, I experienced a similar issue and, after losing a total of $88,000 on a phony cryptocurrency investment platform, I felt compelled to contact them for assistance. Today, I can attest to their authenticity because, as I type this, I have my lost bitcoin back in my CoinBase wallet and am in tears of joy. Please get in touch with DWOH using the following information via Email Address: dwchzone@gmail.com OR Whats-App: +1 (803) 392-1735 if you're having withdrawal issues, wish to recover, or want to confirm a website is legitimate before investing.