Microsatellite_scores-67cheetahs

Scores of 67 cheetahs screened at 18 microsatellite loc

Redefining the timing and circumstances of the chicken's introduction to Europe and north-west Africa

Little is known about the early history of the chicken (Gallus gallus domesticus), including the timing and circumstances of its introduction into new cultural environments. To evaluate its spatio-temporal spread across Eurasia and north-west Africa, the authors radiocarbon dated 23 chicken bones from presumed early contexts. Three-quarters returned dates later than those suggested by stratigraphy, indicating the importance of direct dating. The results indicate that chickens did not arrive in Europe until the first millennium BC. Moreover, a consistent time-lag between the introduction of chickens and their consumption by humans suggests that these animals were initially regarded as exotica and only several centuries later recognised as a source of ‘food’

Relative frequencies of OC (<i>Ovis aries/orientalis</i>+<i>Capra hircus/aegagrus</i>), <i>Bos taurus/primigenius</i>, and <i>Sus scrofa</i> in Neolithic assemblages (see Table S2 for data).

<p>Sites labeled and colored after <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099845#pone-0099845-g001" target="_blank">Fig. 1</a>. X's represent mean values for each region.</p

Changes in mean size through time for <i>Ovis</i>, <i>Capra</i>, <i>Bos</i>, and <i>Sus</i> (based on LSI of breadth and depth measurements)(for data see Tables S3–6).

<p>Vertical lines represent standard deviations. Colors reflect geographic location of site (after <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099845#pone-0099845-g001" target="_blank">Fig. 1</a>). Values to the left of the vertical axis represent means for each region. Key sites are labeled (after <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099845#pone-0099845-g001" target="_blank">Fig. 1</a>).</p

Plots showing relationship between body size (mean LSI) and %juvenile (based on long bone fusion) for <i>Ovis</i>, <i>Capra</i>, <i>Bos</i>, and <i>Sus</i> (for data see Tables S3–6).

<p>Colors reflect geographic location of site (after <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099845#pone-0099845-g001" target="_blank">Fig. 1</a>). “W” indicates assemblages representing wild populations. Key sites are labeled (after <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099845#pone-0099845-g001" target="_blank">Fig. 1</a>). For <i>Capra</i>, dark blue marks represent Zagros sites Asiab, ZC Shanidar, and Shanidar Mousterian.</p

Map of Turkey showing the location of sites mentioned in this analysis.

<p>Arrows indicate potential routes for the spread of domestic animals outside of the Fertile Crescent. Dates indicate an approximation of the first appearance of domesticated sheep/goat (O/C), cattle (<i>Bos</i>), and pigs (<i>Sus</i>) in six regions of Turkey. Dotted lines indicate boundaries where the listed domestic animals were not part of initial Neolithic economies. Southeast Region (purple) = 1. Hasankeyf, 2. Körtik Tepe, 3. Hallan Çemi, 4. Çayönü Tepesi, 5. Cafer Höyük, 6. Nevalı Çori, 7. Göbekli Tepe, 8. Yeni Mahalle, 9. Mureybet; South Region (blue) = 10. Üçağızlı, 11.Domuztepe, 12.Direkli Cave, 13.Yumuktepe; Central Region (red) = 14. Köşk Höyük, 15. Aşıklı Höyük, 16. Musular, 17. Güvercinkayası, 18. Pınarbaşı, 19. Çatalhöyük, 20. Boncuklu; Lakes Region (orange) =  21. Suberde, 22. Erbaba, 23. Höyücek, 24. Bademağacı; West/Coast Region (yellow) =  25. Karain B, 26. Öküzini, 27. Çukuriçi, 28. Ulucak; Northwest Region (green) =  29. Orman Fidanlığı, 30. Barcın, 31. Menteşe, 32. Ilıpınar, 33. Pendik, 34. Fikirtepe, 35. Yenikapı, 36. Hoca Çesme.</p

Phylogenetic tree of the mitochondrial control region of the Eurasiatic wild ass constructed through BEAST analysis.

<p>The corresponding <i>E</i>. <i>asinus</i> DNA region was used as an outgroup. The estimated median height of the nodes is indicated in red, in kiloyears (kyears), and the thickness of the lines is proportional to the posterior clade probability (the scale is represented). The mean substitution rate averaged across the whole tree is 8.5 E-8 substitutions per site per million years (95% HPD interval: 2.1–18.8 E-8). The colors of the box surrounding each individual sequence follow the same convention as in the sPCA analysis displayed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174216#pone.0174216.g001" target="_blank">Fig 1</a>. The names of the deduced clades are indicated in italics. The symbols following each sequence name indicated the origin of the sample (Square: Archeological; Triangle: Historical; Circle: Modern), and the red circles indicate the modern dziggetais (see text). For an enlarged representation of the tree containing the names of the sequences, the 95% HPD of the node height values, the posterior probabilities of the nodes and their bootstrap values by ML analysis, see Fig H in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174216#pone.0174216.s002" target="_blank">S2 File</a>.</p

Geographic distribution of the analyzed kiangs and dziggetais and maximum likelihood phylogeny of the <i>K/KD</i> clades.

<p><b>(A)</b> The map indicates the current areas of distribution of kiangs (pink) and dziggetais (orange) as determined by IUCN [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174216#pone.0174216.ref003" target="_blank">3</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174216#pone.0174216.ref004" target="_blank">4</a>], as well as the location of the collected wild samples. Symbols and colors schemes are used to represent the various samples and populations. The southern Tibetan reserves populated by kiangs (Nyalam, Gyirong, Ngamring and Tingri; [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174216#pone.0174216.ref054" target="_blank">54</a>]), are represented by green circles, whereas the blue circles indicate the kiang samples collected north of Tibet [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174216#pone.0174216.ref049" target="_blank">49</a>]. The dziggetai samples analyzed herein, as well as those from the Kalamaili natural reserve [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174216#pone.0174216.ref054" target="_blank">54</a>], whose mitogenomes belong to the <i>D1</i> and <i>D2</i> clades are indicated by white circles and stars, respectively, whereas those belonging to the <i>KD</i> clade are represented by red circles. Differences in the East-West distribution of the Dziggetai <i>D1</i> and <i>D2</i> clades are observed, although it is unclear how these correlate with the East-West distributions observed for microsatellite markers in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174216#pone.0174216.ref076" target="_blank">76</a>]. <b>(B)</b> The ML phylogeny of the kiang and dziggetai sequences of the <i>KD</i> and <i>K</i> clades was performed with PHYML [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174216#pone.0174216.ref035" target="_blank">35</a>] using the full contiguous 295-bp-long HVR sequence. The bootstrap values of the nodes are indicated (1000 bootstraps). The red, green and blue circles indicate the geolocalized dziggetais, northern Tibetan kiangs, southern Tibetan kiangs, respectively, as in panel A. The modern kiang from zoos are represented with black circles whereas the historical kiang specimens are represented with a grey triangle. See also Table E in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174216#pone.0174216.s001" target="_blank">S1 File</a> for the summary statistics of the kiang and dzigettai populations analyzed here.</p

Median joining network analysis (A) and maximum likelihood analysis based on PHYML (B).

<p>The names of the deduced clades are indicated in italics. The colors of the box with the clade name follow the same convention as in the sPCA analysis displayed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174216#pone.0174216.g001" target="_blank">Fig 1</a>.</p

Measurements of intrapopulation diversity.

<p>Measurements of intrapopulation diversity.</p