Neolithic East Asians tamed leopard cats

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Leopard cat
(CC: F. Spangenberg - Der Irbis)

It's hard to say that cats are domestic at all, tamed is probably a better concept. Some would of course argue that it is cats who have tamed us humans, debatable I guess.

In any case this relationship has not been restricted to the common cat (Felis silvestris catus) but it has been known now that ancient East Asians managed to establish the same kind of relationship with a local feline of similar characteristics: the leopard cat (Prionailurus bengalensis). However at some point the Western cat took over and nothing remains of that ancient domestication event.

Jean-Denis Vigne et al., Earliest “Domestic” Cats in China Identified as Leopard Cat (Prionailurus bengalensis). PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0147295]

Abstract

The ancestor of all modern domestic cats is the wildcat, Felis silvestris lybica, with archaeological evidence indicating it was domesticated as early as 10,000 years ago in South-West Asia. A recent study, however, claims that cat domestication also occurred in China some 5,000 years ago and involved the same wildcat ancestor (F. silvestris). The application of geometric morphometric analyses to ancient small felid bones from China dating between 5,500 to 4,900 BP, instead reveal these and other remains to be that of the leopard cat (Prionailurus bengalensis). These data clearly indicate that the origins of a human-cat ‘domestic’ relationship in Neolithic China began independently from South-West Asia and involved a different wild felid species altogether. The leopard cat’s ‘domestic’ status, however, appears to have been short-lived—its apparent subsequent replacement shown by the fact that today all domestic cats in China are genetically related to F. silvestris.

Goat genetics suggest that two populations were domesticated

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Licia Colli, Hovirang Lancioni et al., Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability. BMC Genomics 2015. Open access → LINK [doi:10.1186/s12864-015-2342-2]

Abstract

Background

The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA).

Results

We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ~460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ~12–10 ka ago.

Conclusions

Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (~130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds.

Note: "Southeastern Anatolia" should read Northern Kurdistan, as the Turkish official concept of Anatolia wildly goes beyond the actual Anatolia or Asia Minor peninsula into Upper Mesopotamia. Also Anatolia Peninsula was not involved, as far as we know, in the Early Neolithic and only cow domestication, which is of a later date, can be tracked to that region. The oldest known goats are from the M'lafatian culture of the Zagros (Jarmo and such). The same happens with sheep and pigs.

An archaic human population surviving in SW China until at least 14,000 years ago

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Just a femur but looks like it. Homo heidelbergensis (Denisovan)?

Darren Curnoe, Xueping Li et al. A Hominin Femur with Archaic Affinities from the Late Pleistocene of Southwest China. PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0143332]

Abstract

The number of Late Pleistocene hominin species and the timing of their extinction are issues receiving renewed attention following genomic evidence for interbreeding between the ancestors of some living humans and archaic taxa. Yet, major gaps in the fossil record and uncertainties surrounding the age of key fossils have meant that these questions remain poorly understood. Here we describe and compare a highly unusual femur from Late Pleistocene sediments at Maludong (Yunnan), Southwest China, recovered along with cranial remains that exhibit a mixture of anatomically modern human and archaic traits. Our studies show that the Maludong femur has affinities to archaic hominins, especially Lower Pleistocene femora. However, the scarcity of later Middle and Late Pleistocene archaic remains in East Asia makes an assessment of systematically relevant character states difficult, warranting caution in assigning the specimen to a species at this time. The Maludong fossil probably samples an archaic population that survived until around 14,000 years ago in the biogeographically complex region of Southwest China.

Ancient DNA confirms that dogs were first domesticated in Southeast Asia

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I have already argued for this scenario several times (as opposed to the Neolithic West Asian one, which just makes no sense and rather seems to represent a secondary layer of dog genetics), so I'm very glad that ancient DNA research can confirm it even further.

Guo-Dong Wang, Out of southern East Asia: the natural history of domestic dogs across the world. Cell Research 2015. Open access → LINK [doi:10.1038/cr.2015.147]

Abstract

The origin and evolution of the domestic dog remains a controversial question for the scientific community, with basic aspects such as the place and date of origin, and the number of times dogs were domesticated, open to dispute. Using whole genome sequences from a total of 58 canids (12 gray wolves, 27 primitive dogs from Asia and Africa, and a collection of 19 diverse breeds from across the world), we find that dogs from southern East Asia have significantly higher genetic diversity compared to other populations, and are the most basal group relating to gray wolves, indicating an ancient origin of domestic dogs in southern East Asia 33 000 years ago. Around 15 000 years ago, a subset of ancestral dogs started migrating to the Middle East, Africa and Europe, arriving in Europe at about 10 000 years ago. One of the out of Asia lineages also migrated back to the east, creating a series of admixed populations with the endemic Asian lineages in northern China before migrating to the New World. For the first time, our study unravels an extraordinary journey that the domestic dog has traveled on earth.

I will dare, once again, to challenge the age guesstimates and suggest that they are in fact notably older, maybe even double the proposed age. Notice that I tentatively associate the domestication of dogs with the massive secondary "out of SE Asia" expansion led by Y-DNA haplogroup K2 and mtDNA haplogroup R, which probably took place, at least in my understanding, at some point between the Toba catastrophe (c. 74 Ka BP) and the beginnings of the Upper Paleolithic in Western Eurasia (c. 50 Ka BP), so, yeah, c. 65 or 60 Ka BP is a good age estimate for me, more so considering that we already know of domesticated dogs far from SE Asia, in 33,000 BP.

See also:

• 33,000 years old dog from Altai is directly related to modern dogs
• Did dogs contribute decisively to our success vs. Neanderthals?
• Dog domesticated in SE Asia (claims new study)
• Y-DNA macro-haplogroup K-M526 originated in Indonesia
• Synthesis of the early colonization of Asia and Australasia by Homo sapiens (haploid genetics)

Genetic structure of pearl millet, an African cereal

Quickies

Zhenbin Hu et al., Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): Comparative analysis of global accessions and Senegalese landraces. BMC genomics 2015. Open access → LINK [doi:10.1186/s12864-015-2255-0]

Abstract

Background

Pearl millet is a staple food for people in arid and semi-arid regions of Africa and South Asia due to its high drought tolerance and nutritional qualities. A better understanding of the genomic diversity and population structure of pearl millet germplasm is needed to support germplasm conservation and genetic improvement of this crop. Here we characterized two pearl millet diversity panels, (i) a set of global accessions from Africa, Asia, and the America, and (ii) a collection of landraces from multiple agro-ecological zones in Senegal.

Results

We identified 83,875 single nucleotide polymorphisms (SNPs) in 500 pearl millet accessions, comprised of 252 global accessions and 248 Senegalese landraces, using genotyping by sequencing (GBS) of PstI-MspI reduced representation libraries. We used these SNPs to characterize genomic diversity and population structure among the accessions. The Senegalese landraces had the highest levels of genetic diversity (π), while accessions from southern Africa and Asia showed lower diversity levels. Principal component analyses and ancestry estimation indicated clear population structure between the Senegalese landraces and the global accessions, and among countries in the global accessions. In contrast, little population structure was observed across in the Senegalese landraces collections. We ordered SNPs on the pearl millet genetic map and observed much faster linkage disequilibrium (LD) decay in Senegalese landraces compared to global accessions. A comparison of pearl millet GBS linkage map with the foxtail millet (Setaria italica) and sorghum (Sorghum bicolor) genomes indicated extensive regions of synteny, as well as some large-scale rearrangements in the pearl millet lineage.

Conclusions

We identified 83,875 SNPs as a genomic resource for pearl millet improvement. The high genetic diversity in Senegal relative to other regions of Africa and Asia supports a West African origin of this crop, followed by wide diffusion. The rapid LD decay and lack of confounding population structure along agro-ecological zones in Senegalese pearl millet will facilitate future association mapping studies. Comparative population genomics will provide insights into panicoid crop evolution and support improvement of these climate-resilient crops.

Fig. 4

The genetic relatedness of pearl millet accessions. a F-statistic (F _ST ) between populations with different origins. The circles indicate the countries of origin, and the values represent the F _ST between accessions from the two countries. The thickness of the lines is proportional to the value of F _ST . b Genetic relatedness among 500 accessions assessed with the neighbor joining method. Global accessions are colored by countries of origin, and Senegalese landraces are colored by regions of origin

See also: Review of Tropical Neolithic flows (a most important agricultural development in the African and Asian Tropics).

Patrilineages of Panama

Quickies

Viola Grugni et al., Exploring the Y Chromosomal Ancestry of Modern Panamanians. PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0144223]

Abstract

Geologically, Panama belongs to the Central American land-bridge between North and South America crossed by Homo sapiens >14 ka ago. Archaeologically, it belongs to a wider Isthmo-Colombian Area. Today, seven indigenous ethnic groups account for 12.3% of Panama’s population. Five speak Chibchan languages and are characterized by low genetic diversity and a high level of differentiation. In addition, no evidence of differential structuring between maternally and paternally inherited genes has been reported in isthmian Chibchan cultural groups. Recent data have shown that 83% of the Panamanian general population harbour mitochondrial DNAs (mtDNAs) of Native American ancestry. Considering differential male/female mortality at European contact and multiple degrees of geographical and genetic isolation over the subsequent five centuries, the Y-chromosome Native American component is expected to vary across different geographic regions and communities in Panama. To address this issue, we investigated Y-chromosome variation in 408 modern males from the nine provinces of Panama and one indigenous territory (the comarca of Kuna Yala). In contrast to mtDNA data, the Y-chromosome Native American component (haplogroup Q) exceeds 50% only in three populations facing the Caribbean Sea: the comarca of Kuna Yala and Bocas del Toro province where Chibchan languages are spoken by the majority, and the province of Colón where many Kuna and people of mixed indigenous-African-and-European descent live. Elsewhere the Old World component is dominant and mostly represented by western Eurasian haplogroups, which signal the strong male genetic impact of invaders. Sub-Saharan African input accounts for 5.9% of male haplotypes. This reflects the consequences of the colonial Atlantic slave trade and more recent influxes of West Indians of African heritage. Overall, our findings reveal a local evolution of the male Native American ancestral gene pool, and a strong but geographically differentiated unidirectional sex bias in the formation of local modern Panamanian populations.

Fig 1. Spatial distributions of Y-chromosome components in Panama.

Bars show Native American (violet), West Eurasian/North African (green), sub-Saharan African (yellow) and South Asian (light blue) components in each province or comarca. In grey the Y-chromosome portion with discordant haplogroup predictions.

How different is Howieson Port Middle Paleolithic tech from its neighbors and successors?

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That's what a recently published paper discusses. Oh, by the way, context for the casual reader: Howieson Port and related industries are among the oldest ones in South Africa, yet they are very advanced for their time, suggesting that our species was innovating in ways that our (now essentially extinct) cousins were not doing. See also: this entry on African Middle Paleolithic.

Paloma de la Peña, Refining Our Understanding of Howiesons Poort Lithic Technology: The Evidence from Grey Rocky Layer in Sibudu Cave (KwaZulu-Natal, South Africa). Open access → LINK [doi:10.1371/journal.pone.0143451]

Abstract

The detailed technological analysis of the youngest Howiesons Poort occupation in Sibudu Cave, layer Grey Rocky, has shown the importance of blade production (with different knapping methods involved), but also of flaking methods in coarse grained rock types. Moreover, new strategies of bifacial production and microlithism were important. Grey Rocky lithic technology shows a really versatile example of reduction strategies that were highly influenced by the characteristics of the rock types. This lithic assemblage is another example of the technological variability linked to the Howiesons Poort technocomplex. The reasons for this variability are still difficult to elucidate. Discrepancies between sites might be for different reasons: diachronic variations, functional variations, organizational variations or maybe different regional variations within what has been recognized traditionally and typologically as Howiesons Poort. The technological comparison of the Grey Rocky assemblage with assemblages from other Howiesons Poort sites demonstrates that there are common technological trends during the late Pleistocene, but they still need to be properly circumscribed chronologically. On the one hand, Howiesons Poort characteristics such as the bifacial production in quartz are reminiscent of production in some Still Bay or pre-Still Bay industries and the flake production or the prismatic blade production described here could be a point in common with pre-Still Bay and post-Howiesons Poort industries. On the other hand, the detailed analysis of the Grey Rocky lithics reinforces the particular character of this Howiesons Poort technocomplex, yet it also shows clear technological links with other Middle Stone Age assemblages.

A Magdalenian campsite map from Catalonia

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A neat curiosity from the Ice Age:

Marcos García Díez & Manuel Vaquero, Looking at the Camp: Paleolithic Depiction of a Hunter-Gatherer Campsite. PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0143002]

Abstract

Landscapes and features of the everyday world were scarcely represented in Paleolithic art, especially those features associated with the human landscape (huts and campsites). On the contrary, other figurative motifs (especially animals) and signs, traditionally linked to the magic or religious conceptions of these hunter-gatherer societies, are the predominant themes of Upper Paleolithic art. This paper seeks to present an engraved schist slab recently found in the Molí del Salt site (North-eastern Iberia) and dated at the end of the Upper Paleolithic, ca. 13,800 years ago. This slab displays seven semicircular motifs that may be interpreted as the representation of dome-shaped huts. The analysis of individual motifs and the composition, as well as the ethnographic and archeological contextualization, suggests that this engraving is a naturalistic depiction of a hunter-gatherer campsite. Campsites can be considered the first human landscape, the first area of land whose visible features were entirely constructed by humans. Given the social meaning of campsites in hunter-gatherer life-styles, this engraving may be considered one of the first representations of the domestic and social space of a human group.

Archaeologists studying Monte Verde claim an age of 18 Ka BP and add some detail

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I'm going in this and upcoming short entries through my backlog. You are warned.

New archaeology from Monte Verde (Chile) suggests a date of 18 Ka BP (slightly older than the oldest known North American site) and also that it was a transiting site for highly mobile peoples and not a main base, as they were not using superior local lithics but bringing their own.

Tom D. Dillehay et al. New Archaeological Evidence for an Early Human Presence at Monte Verde, Chile. PLoS ONE 2015. Open access → LINK [doi:10.1371/journal.pone.0141923]

Abstract

Questions surrounding the chronology, place, and character of the initial human colonization of the Americas are a long-standing focus of debate. Interdisciplinary debate continues over the timing of entry, the rapidity and direction of dispersion, the variety of human responses to diverse habitats, the criteria for evaluating the validity of early sites, and the differences and similarities between colonization in North and South America. Despite recent advances in our understanding of these issues, archaeology still faces challenges in defining interdisciplinary research problems, assessing the reliability of the data, and applying new interpretative models. As the debates and challenges continue, new studies take place and previous research reexamined. Here we discuss recent exploratory excavation at and interdisciplinary data from the Monte Verde area in Chile to further our understanding of the first peopling of the Americas. New evidence of stone artifacts, faunal remains, and burned areas suggests discrete horizons of ephemeral human activity in a sandur plain setting radiocarbon and luminescence dated between at least ~18,500 and 14,500 cal BP. Based on multiple lines of evidence, including sedimentary proxies and artifact analysis, we present the probable anthropogenic origins and wider implications of this evidence. In a non-glacial cold climate environment of the south-central Andes, which is challenging for human occupation and for the preservation of hunter-gatherer sites, these horizons provide insight into an earlier context of late Pleistocene human behavior in northern Patagonia.

Notice that Monte Verde is quite towards the south and, in Ice Age contexts, it was a rather extreme environment, barely outside of the glaciers. I wonder what they looked for in such a remote place, even if they probably only went there in summer.

Most Africans do not have significant Eurasian admixture

This is major news: the authors of the study on the ancient East African genome of Mota have recanted their conclusions. In a correction note echoed by Nature they say:

Erratum'to'Gallego'Llorente'et'al.'2015'

The results presented in the Report “Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent“ were affected by a bioinformatics error. A script necessary to convert the input produced by samtools v0.1.19 to be compatible with PLINK was not run when merging the ancient genome, Mota, with the contemporary populations SNP panel, leading to homozygote positions to the human reference genome being dropped as missing data (the analysis of admixture with Neanderthals and Denisovans was not affected). When those positions were included, 255,922 SNP out of 256,540 from the contemporary reference panel could be called in Mota. The conclusion of a large migration into East Africa from Western Eurasia, and more precisely from a source genetically close to the early Neolithic farmers, is not affected. However, the geographic extent of the genetic impact of this migration was overestimated: the Western Eurasian backflow mostly affected East Africa and only a few SubUSaharan populations; the Yoruba and Mbuti do not show higher levels of Western Eurasian ancestry compared to Mota.

We thank Pontus Skoglund and David Reich for letting us know about this problem.

This makes much better sense admittedly. I strongly appreciate the willingness of Gallego, Jones et al. for publicly amending their wrong as quickly as possible. It's said that erring is human but correcting is only for the wise.