Enamel thickness trends in Plio-Pleistocene hominin mandibular molars

Enamel thickness continues to be an important morphological character in hominin systematics and is frequently invoked in dietary reconstructions of Plio-Pleistocene hominin taxa. However, to date, the majority of published data on molar enamel thickness of Pliocene and early Pleistocene hominins derive from naturally fractured random surfaces of a small number of specimens. In this study we systematically analyze enamel thickness in a large sample of Plio-Pleistocene fossil hominins (n ¼ 99), extant hominoids (n ¼ 57), and modern humans (n ¼ 30). Based on analysis of 2D mesial planes of section derived from microtomography, we examine both average and relative enamel thickness, and the distribution of enamel across buccal, occlusal, and lingual components of mandibular molars. Our results confirm the trend of increasing enamel thickness during the Pliocene that culminates in the thick enamel of the robust Australopithecus species, and then decreases from early Homo to recent modern humans. All hominin taxa share a regional average enamel thickness pattern of thick occlusal enamel and greater buccal than lingual enamel thickness. Pan is unique in exhibiting the thinnest average enamel thickness in the occlusal basin. Statistical analysis indicates that among Pliocene hominins enamel thickness is a weak taxonomic discriminator. The data underlying these results are included in a table in the Supplementary Online Material

The origins and spread of domestic horses from the Western Eurasian steppes

This is the final version. Available on open access from Nature Research via the DOI in this recordData availability: All collapsed and paired-end sequence data for samples sequenced in this study are available in compressed fastq format through the European Nucleotide Archive under accession number PRJEB44430, together with rescaled and trimmed bam sequence alignments against both the nuclear and mitochondrial horse reference genomes. Previously published ancient data used in this study are available under accession numbers PRJEB7537, PRJEB10098, PRJEB10854, PRJEB22390 and PRJEB31613, and detailed in Supplementary Table 1. The genomes of ten modern horses, publicly available, were also accessed as indicated in their corresponding original publications57,61,85-87.NOTE: see the published version available via the DOI in this record for the full list of authorsDomestication of horses fundamentally transformed long-range mobility and warfare. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling at Botai, Central Asia around 3500 BC. Other longstanding candidate regions for horse domestication, such as Iberia and Anatolia, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC driving the spread of Indo-European languages. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture

The mules that are not mules - metrics, morphology, archaeogenomics and mtDNA d-loop diversity in equids from Roman Switzerland

Mules (Equus asinus x Equus caballus) represent first-generation hybrids between a female horse (mare) and a male donkey (jack). They are generally considered to have first appeared north of the Alps with Roman influence, a time period in which written and iconographic sources support their key role for transport and traction, both in farming and the military. The archaeozoological evidence for mules is, however, contentious as faunal assemblages are difficult to assign to either parental species or hybrids based on morphometric data alone. Here we leverage low-coverage DNA sequence data and Zonkey computational analyses to assess the occurrence of mules within Roman equid faunal assemblages in the alpine foreland. While morphological data previously assigned 17 remains to mules, successful DNA analysis of 12 remains revealed that 11 were in fact horses, one female and ten males. Eight mtDNA d-loop haplogroups were identified and genetic diversity within Roman equids corresponds to non-threatened modern local breeds. Two remains genetically identified as mules belonged to haplogroups F and I. Our results suggest that the importance of mules in the Roman archaeological record of the alpine foreland, and probably elsewhere, may have been previously over-estimated. Whether this is true for other regions of the Roman Empire needs to be evaluated. Further genomic testing for equid species and their hybrids and molecular sexing will improve our knowledge on this important issue

Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine Fl-hybrids in archaeological assemblages

Horses, asses and zebras, can produce first-generation Fl-hybrids, despite their striking karyotypic and phenotypic differences. Such Fl-hybrids are mostly infertile, but often present characters of considerable interest to breeders. They were extremely valued in antiquity, and commonly represented in art and on coinage. However, hybrids appear relatively rarely in archaeological faunal assemblages, mostly because identification based on morphometric data alone is extremely difficult. Here, we developed a methodological framework that exploits high-throughput sequencing data retrieved from archaeological material to identify Fl-equine hybrids. Our computational methodology is distributed in the open-source Zonkey pipeline, now part of PALEOMIX (https://github.com/MikkelSchubert/paleomix), together with full documentation and examples. Using both synthetic and real sequence datasets, from living and ancient Fl-hybrids, we find that Zonkey shows high sensitivity and specificity, even with limited sequencing efforts. Zonkey is thus well suited to the identification of equine Fl-hybrids in the archaeological record, even in cases where DNA preservation is limited. Zonlcey can also help determine the sex of ancient animals, and allows species identification, which advantageously complements morphological data in cases where material is fragmentary and/or multiple candidate equine species coexisted in sympatry. (C) 2016 Elsevier Ltd. All rights reserved

Zonkey:a simple, accurate and sensitive pipeline to genetically identify equine Fl-hybrids in archaeological assemblages

Horses, asses and zebras, can produce first-generation F1-hybrids, despite their striking karyotypic and phenotypic differences. Such F1-hybrids are mostly infertile, but often present characters of considerable interest to breeders. They were extremely valued in antiquity, and commonly represented in art and on coinage. However, hybrids appear relatively rarely in archaeological faunal assemblages, mostly because identification based on morphometric data alone is extremely difficult. Here, we developed a methodological framework that exploits high-throughput sequencing data retrieved from archaeological material to identify F1-equine hybrids. Our computational methodology is distributed in the open-source Zonkey pipeline, now part of PALEOMIX (https://github.com/MikkelSchubert/paleomix), together with full documentation and examples. Using both synthetic and real sequence datasets, from living and ancient F1-hybrids, we find that Zonkey shows high sensitivity and specificity, even with limited sequencing efforts. Zonkey is thus well suited to the identification of equine F1-hybrids in the archaeological record, even in cases where DNA preservation is limited. Zonkey can also help determine the sex of ancient animals, and allows species identification, which advantageously complements morphological data in cases where material is fragmentary and/or multiple candidate equine species coexisted in sympatry

Experimental conditions improving in-solution target enrichment for ancient DNA

High-throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best-suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture-enrichment methods represent cost-effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MYbaits in-solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA, probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self-annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains.No Full Tex