Secretary of State Condoleezza Rice concluded a visit to Beijing during which human rights were discussed -- Shao walked out of Qingpu Prison, on the outskirts of Shanghai. But it is possible that the parole could lead to full freedom sooner than the five years of the remaining term. During those talks, U. In addition, some China specialists noted that with the Olympics next month, Beijing was eager to buff up its image, which recently had been tarnished by deadly riots in Tibet and other incidents in which Chinese lawyers, journalists and human rights activists had been silenced.
On Sunday, Chinese authorities prevented some Chinese lawyers from attending a dinner with two U. Bush has rejected calls that he skip the ceremony, and Rice said this week that she planned to attend the Games as well.
Shao, a naturalized U. He formed a company that was exporting U. That never happened. Pairwise F ST estimates also show that G. S11 - S D -statistic analyses further suggest a complex genetic relationship among G. Overall, our analyses indicate that all RJF subspecies are genetically differentiated, which generally correspond to their geographic ranges and taxonomic classifications.
S17a , consistent with its basal phylogenetic position. These analyses indicate that all of the RJF subspecies diverged from one another substantially earlier than the advent of chicken domestication. We then sought to identify the specific RJF lineage s from which domestic chickens were derived. The phylogeny constructed with all RJFs and domestic chickens supports a monophyletic clade composed of some wild G.
Interestingly, the wild G. S18 and S This finding is consistent with observations that domestic village chickens were hybridized with wild G. Domestic chicken and RJF clades are collapsed and colored according to their geographic ranges and subspecies classifications. RJF subspecies are denoted within rings. Of the five RJF subspecies, individuals of G. S21 - S29 also unequivocally indicate that domestic chickens cluster more closely with G.
S30 and S By combining the monophyletic nature of all domestic chickens, the results from these analyses collectively suggest that chickens were likely domesticated in the Holocene from the G.
For clarity, we only present one result of MSMC for each population pair; more pairs were analyzed and shown in Supplementary information, Figs. S30 , S31 and S48a. GGB G. We also identified two well-defined clades: I and II Fig.
Clade II contains mostly northern, central, and southern Chinese village chickens i. Branches basal to the two clades, but within the total diversity of chickens, include chickens sampled almost exclusively from the Yunnan province of China, Thailand, Vietnam and Indonesia.
These individuals may represent the earliest domestic lineages or have admixed with local RJF subspecies. Our results contradict previous claims that chickens were domesticated in Neolithic northern China 37 and the Indus Valley Civilization made on the basis of suspected chicken remains found at the site of Mohenjo-Daro in Pakistan. Moreover, our mtDNA analyses revealed that the most frequent and dominant haplogroups of South Asian chickens are D and E, which are similar to that from Southeast Asia and China, but seldom detected in G.
S2 and Table S1. MSMC estimate indicates that the divergence time between domestic chickens and G. S30 , similar to that between G. This deeper timeframe of divergence relative to the split between G. Because introgression following domestication is common, 13 we therefore assessed the potential contribution of G. S29 , S33 - S These analyses indicate that G. Taken together, these analyses suggest that G. Alternatively, chickens may have been domesticated from G.
To test this possibility, we used PCAdmix 39 to compare the lengths of haplotype blocks in the genomes of Indian chickens that are shared with both G.
We observed that Indian chickens share significantly smaller haplotype blocks with G. In addition, qpGraph, TreeMix and fastsimicoal2 40 analyses also favor a model in which all domestic chickens were initially derived from G. S38 - S Thus, we show that chickens were unlikely initially domesticated from G. Multiple lines of analyses, including outgroup- f 3 and f 4 statistics, TreeMix and qpGraph, indicate that admixture between RJF subspecies and domestic chickens is common.
For example, Indonesian chickens inherit 1. These admixture signals, however, do not always match expectations based solely on the geographic distributions of each of the RJF subspecies. All these analyses demonstrate that the contribution from G. Previous studies suggested that three additional species of jungle fowls likely contributed to the genetic make-up of modern domestic chickens. S50 - S However, these introgressed fragments occur at very low frequency and are primarily limited to local chickens that inhabit the native ranges of the local wild jungle fowl species e.
It is plausible, however, that a portion of these signals is misleading since our gray jungle fowl samples were obtained from a zoo population, which may have been admixed previously with chickens. Overall, consistent with the previous study, 42 our analyses suggest that though other jungle fowl species have contributed to the genetic make-up of some local chicken populations, the admixed genomic proportions are very limited.
We used our extensive dataset to identify genomic regions that were affected by positive selection in domestic chickens. Through these analyses, we found that genes bearing signal of selection are associated with development of nervous system, muscle and bone as well as regulation of growth, metabolism and reproduction see a discussion of these genes in Supplementary information, Notes and Tables S10 , S FGFR1 Fig. Red dashed line indicates Z -transformed score of 3.
Domestic chickens are generally more fertile, produce more eggs and mature earlier than their wild counterparts. S54 - S GNRH-I is a principal regulator in the reproductive axis controlling onset of puberty and sexual maturity. S59 , suggesting that the two mutations are likely genetically linked.
In this study, we present, to the best of our knowledge, the largest genome sequencing initiative for domestic chickens and all wild jungle fowl sub species at a global scale to date.
Our analyses suggest that domestic chickens were derived initially from the wild RJF subspecies G. A molecular clock analysis suggests that domestic chickens diverged from G. Curiously, the split time between chickens and G. Since our sample set does not include representatives from every single extant population, we have yet to establish how many G.
The results of our whole-genome analyses also indicate that the five RJF subspecies form monophyletic clades. Continuous post-divergence gene flow is found for RJF populations, especially for those with overlapping ranges, similar to numerous wild canid populations. For example, modern G. Following their domestication, chickens were then translocated across Southeast and South Asia where they interbred with highly divergent local RJF subspecies and other jungle fowl species.
Domestic chickens in China, Southeast Asia and South Asia now all possess hybrid genomes that derive up to For example, the genetic make-up of White Leghorns shows a substantial contribution from G. S33 - S Given the evolutionary history of chicken accompanied by episodes of recurrent hybridization, it is not surprising that the mitogenomes of wild relatives and domestic chickens were shared between lineages.
Despite this interbreeding, our analyses identified multiple genes involved in behavior, growth and reproduction in domestic chickens that bear signatures of positive selection. Previous studies have observed similar patterns in other livestock species, 65 , 66 , 67 , 68 , 69 suggesting common genomic features resulting from a close relationship with human.
We observed significant selection signatures on loci related to reproduction. At least for this trait, if not for all genes the timing of the origin of the selective sweeps likely significantly postdates the temporal origins of domestic populations. This result firstly suggests that the mutation arose prior to domestication, but only in G.
Alternatively, this allele could have been introgressed into G. This hypothesis, however, seems less likely given that this allele is found at a very low frequency in other RJF subspecies that have also experienced gene flow from domestic chickens. Analyzing ancient genomes from chicken and RJF spanning a wide timeframe and range is expected to more precisely determine when the selection on these traits first began 18 as well as more precisely pinpoint the geographic and temporal origins and dispersal patterns of domestic chickens.
The novel findings from this study provide new insights into the origin and evolutionary history of domestic chickens. The identification of unique genomic landscapes of all RJF subspecies and three additional jungle fowl species suggests that conservation efforts should be made to safeguard them from extinction. These rich genomic resources will pave the way to facilitate ongoing explorations into the biocultural history of the relationship between humans and chickens as well as the development of fast-growing, high-quality and cost-effective lineages.
We collected bird samples for whole-genome sequencing, including domestic chickens, RJFs Supplementary information, Table S1 ; G. Total genome DNA was extracted and purified from blood or muscle of bird using phenol-chloroform method. Next-generation genome sequencing libraries were constructed according to standard protocol of library preparation kit.
Raw sequencing reads were trimmed using Btrim software 70 to filter out low-quality bases and sequences. Maximum-likelihood tree was built using FastTree program version: 2. The program Beagle 43 was used to impute the missing genotype and phase of genotypes into the haplotypes. The 2-D unfolded site frequency spectrum SFS for each population pair was generated using a modified script from dadi.
Outgroup f 3 - and f 4 -statistics were computed using the threepop and fourpop programs from TreeMix package, 32 respectively. Population splitting and admixture analyses were carried out using TreeMix program. Local ancestry inference was carried out using PCAdmix program version: 1. Haplotype trees for these putatively introgressed fragments were constructed using MEGA7 80 to determine the direction of the introgression. An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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