Origin and Evolution of Deleterious Mutations in Horses

International audienc

Horse males became over-represented in archaeological assemblages during the Bronze Age

International audienceHighlights 1. We generated low-coverage DNA sequence data for 19 new Upper Paleolithic horses from Goyet and Trou Magritte, Belgium. 2. We determined their molecular sex together with that of 249 previously-published horse archaeological remains spanning the last 40,000 years across Eurasia. 3. Osseous archaeological and paleontological assemblages showed balanced male:female sex ratios up until ~3,900 years cal. BP. 4. Archeological assemblages post-3,900 years cal. BP became strongly biased towards males (approximately ~79%), underlining a strong shift in animal gender representation that occurred during the Bronze Age

Equine herpesvirus 4 infected domestic horses associated with Sintashta spoke-wheeled chariots around 4,000 years ago

Equine viral outbreaks have disrupted the socio-economic life of past human societies up until the late 19th century and continue to be of major concern to the horse industry today. With a seroprevalence of 60–80 per cent, equine herpesvirus 4 (EHV-4) is the most common horse pathogen on the planet. Yet, its evolutionary history remains understudied. Here, we screen the sequenced data of 264 archaeological horse remains to detect the presence of EHV-4. We recover the first ancient EHV-4 genome with 4.2× average depth-of-coverage from a specimen excavated in the Southeastern Urals and dated to the Early Bronze Age period, approximately 3,900 years ago. The recovery of an EHV-4 virus outside the upper respiratory tract not only points to an animal particularly infected but also highlights the importance of post-cranial bones in pathogen characterisation. Bayesian phylogenetic reconstruction provides a minimal time estimate for EHV-4 diversification to around 4,000 years ago, a time when modern domestic horses spread across the Central Asian steppes together with spoke-wheeled Sintashta chariots, or earlier. The analyses also considerably revise the diversification time of the two EHV-4 subclades from the 16th century based solely on modern data to nearly a thousand years ago. Our study paves the way for a robust reconstruction of the history of non-human pathogens and their impact on animal health

Mammoth and Elephant Phylogenetic Relationships: Mammut Americanum, the Missing Outgroup

At the morphological level, the woolly mammoth has most often been considered as the sister-species of Asian elephants, but at the DNA level, different studies have found support for proximity with African elephants. Recent reports have increased the available sequence data and apparently solved the discrepancy, finding mammoths to be most closely related to Asian elephants. However, we demonstrate here that the three competing topologies have similar likelihood, bayesian and parsimony supports. The analysis further suggests the inadequacy of using Sirenia or Hyracoidea as outgroups. We therefore argue that orthologous sequences from the extinct American mastodon will be required to definitively solve this long-standing question

AdapterRemoval v2:rapid adapter trimming, identification, and read merging

BACKGROUND: As high-throughput sequencing platforms produce longer and longer reads, sequences generated from short inserts, such as those obtained from fossil and degraded material, are increasingly expected to contain adapter sequences. Efficient adapter trimming algorithms are also needed to process the growing amount of data generated per sequencing run. FINDINGS: We introduce AdapterRemoval v2, a major revision of AdapterRemoval v1, which introduces (i) striking improvements in throughput, through the use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support, (ii) the ability to handle datasets containing reads or read-pairs with different adapters or adapter pairs, (iii) simultaneous demultiplexing and adapter trimming, (iv) the ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets, and (v) native gzip and bzip2 support. CONCLUSIONS: We show that AdapterRemoval v2 compares favorably with existing tools, while offering superior throughput to most alternatives examined here, both for single and multi-threaded operations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13104-016-1900-2) contains supplementary material, which is available to authorized users