From wild horses to domestic horses: a European perspective

There is a period of some 5000 years or so in the prehistory of Europe when horse populations were greatly depleted and perhaps even disappeared in many places. Before this time, during the Upper Palaeolithic, wild horses were common; after, during the Bronze Age, domestic horses were being raised and used across Europe. What happened in between is uncertain, in part because of the sketchy archaeological record. Debates continue as to the origins (the when, where and how) of Europe's domestic horses, including whether horse husbandry dispersed only from habitats favourable to horses on the Eurasian steppes or whether there was local domestication in temperate Europe. This paper reviews the evidence for the transition from wild horses to domestic horses in Europe.

Analysis of DNA polymorphism in ancient barley herbarium material: validation of the KASP SNP genotyping platform

The availability of crop specimens archived in herbaria and old seed collections represent valuable resources for the analysis of plant genetic diversity and crop domestication. The ability to extract ancient DNA (aDNA) from such samples has recently allowed molecular genetic investigations to be undertaken in ancient materials. While analyses of aDNA initially focused on the use of markers which occur in multiple copies such as the internal transcribed spacer region (ITS) within ribosomal DNA and those requiring amplification of short DNA regions of variable length such as simple sequence repeats (SSRs), emphasis is now moving towards the genotyping of single nucleotide polymorphisms (SNPs), traditionally undertaken in aDNA by Sanger sequencing. Here, using a panel of barley aDNA samples previously surveyed by Sanger sequencing for putative causative SNPs within the flowering-time gene PPD-H1, we assess the utility of the Kompetitive Allele Specific PCR (KASP) genotyping platform for aDNA analysis. We find KASP to out-perform Sanger sequencing in the genotyping of aDNA samples (78% versus 61% success, respectively), as well as being robust to contamination. The small template size (≥46 bp) and one-step, closed-tube amplification/genotyping process make this platform ideally suited to the genotypic analysis of aDNA, a process which is often hampered by template DNA degradation and sample cross-contamination. Such attributes, as well as its flexibility of use and relatively low cost, make KASP particularly relevant to the genetic analysis of aDNA samples. Furthermore, KASP provides a common platform for the genotyping and analysis of corresponding SNPs in ancient, landrace and modern plant materials. The extended haplotype analysis of PPD-H1 undertaken here (allelic variation at which is thought to be important for the spread of domestication and local adaptation) provides further resolution to the previously identified geographic cline of flowering-time allele distribution, illustrating how KASP can be used to aid genetic analyses of aDNA from plant species. We further demonstrate the utility of KASP by genotyping ten additional genetic markers diagnostic for morphological traits in barley, shedding light on the phenotypic traits, alleles and allele combinations present in these unviable ancient specimens, as well as their geographic distributions.

The population dynamics of disease on short and long time-scales

Observational evidence is scarce concerning the distribution of plant pathogen population sizes or densities as a function of time-scale or spatial scale. For wild pathosystems we can only get indirect evidence from evolutionary patterns and the consequences of biological invasions.We have little or no evidence bearing on extermination of hosts by pathogens, or successful escape of a host from a pathogen. Evidence over the last couple of centuries from crops suggest that the abundance of particular pathogens in the spectrum affecting a given host can vary hugely on decadal timescales. However, this may be an artefact of domestication and intensive cultivation. Host-pathogen dynamics can be formulated mathematically fairly easily–for example as SIR-type differential equation or difference equation models, and this has been the (successful) focus of recent work in crops. “Long-term” is then discussed in terms of the time taken to relax from a perturbation to the asymptotic state. However, both host and pathogen dynamics are driven by environmental factors as well as their mutual interactions, and both host and pathogen co-evolve, and evolve in response to external factors. We have virtually no information about the importance and natural role of higher trophic levels (hyperpathogens) and competitors, but they could also induce long-scale fluctuations in the abundance of pathogens on particular hosts. In wild pathosystems the host distribution cannot be modelled as either a uniform density or even a uniform distribution of fields (which could then be treated as individuals). Patterns of short term density-dependence and the detail of host distribution are therefore critical to long-term dynamics. Host density distributions are not usually scale-free, but are rarely uniform or clearly structured on a single scale. In a (multiply structured) metapopulation with coevolution and external disturbances it could well be the case that the time required to attain equilibrium (if it exists) based on conditions stable over a specified time-scale is longer than that time-scale. Alternatively, local equilibria may be reached fairly rapidly following perturbations but the meta-population equilibrium be attained very slowly. In either case, meta-stability on various time-scales is a more relevant than equilibrium concepts in explaining observed patterns.

Care in the community? Interpretations of a fractured goat bone from Neolithic Jarmo, Iraq

A case study of a goat metatarsal exhibiting a complex diaphyseal fracture from Pottery Neolithic Jarmo in the Central Zagros region of the eastern Fertile Crescent is here described and analysed. The Central Zagros is one of the areas with the earliest evidence for goat domestication. The significance of the pathology may be viewed within the context of domestic goat ecology in the landscape of Jarmo, potentially impacting browsing behaviour (goats raise themselves on their hind limbs to browse) and movement with the herd in the landscape (the terrain around Jarmo is very steep in places, which would be difficult for an animal to navigate on three legs). In the light of this, possible levels of care that the Neolithic human community may have afforded this animal are discussed – from a situation where therapeutic intervention may have occurred, to one of stall confinement of the animal to allow the pathology to heal, to a position of simple awareness of the condition – and how this impacts on our understanding of changes in attitudes towards animals through the process of domestication.

Putting the P in Ptilotus: a phosphorus accumulating herb native to Australia

Background and Aims Ptilotus polystachyus (green mulla mulla; ptilotus) is a short-lived perennial herb that occurs widely in Australia in arid and semi-arid regions with nutrient poor soils. As this species shows potential for domestication, its response to addition of phosphorus (P) and nitrogen (N) was compared to a variety of the domesticated exotic perennial pasture herb Cichorium intybus (chicory), ‘Puna’. Methods Pots were filled with 3 kg of an extremely nutrient-deficient sterilized field soil that contained 3 mg kg−1 mineral N and 2 mg kg−1 bicarbonate-extractable P. The growth and P and N accumulation of ptilotus and chicory in response to seven rates of readily available phosphorus (0–300 mg P pot−1) and nitrogen (N) (0–270 mg N pot−1) was examined. Key Results Ptilotus grew extremely well under low P conditions: shoot dry weights were 23, 6 and 1·7 times greater than for chicory at the three lowest levels of P addition, 0, 15 and 30 mg P pot−1, respectively. Ptilotus could not downregulate P uptake. Concentrations of P in shoots approached 4 % of dry weight and cryo-scanning electron microscopy and X-ray microanalysis showed 35–196 mm of P in cell vacuoles in a range of tissues from young leaves. Ptilotus had a remarkable tolerance of high P concentrations in shoots. While chicory exhibited symptoms of P toxicity at the highest rate of P addition (300 mg P pot−1), no symptoms were present for ptilotus. The two species responded in a similar manner to addition of N. Conclusions In comparison to chicory, ptilotus demonstrated an impressive ability to grow well under conditions of low and high P availability. Further study of the mechanisms of P uptake and tolerance in ptilotus is warranted.

Identification and validation of candidate genes associated with domesticated and improved traits in soybean

Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses. Of the 1489 candidate domestication genes (CDGs) within these CDRs, a total of 330 CDGs were related to the above four traits in the domestication, gene ontology (GO) enrichment, gene expression, and pathway analyses. Eighteen, 60, 66, and 10 of the 330 CDGs were significantly associated with the above four traits, respectively. Of 134 traitassociated CDGs, 29 overlapped with previous CDGs, 11 were consistent with candidate genes in previous trait association studies, and 66 were covered by the domesticated and improved quantitative trait loci or their adjacent regions, having six common CDGs, such as one functionally characterized gene Glyma15 g17480 (GmZTL3). Of the 68 seed size (SS) and SOC CDGs, 37 were further confirmed by gene expression analysis. In addition, eight genes were found to be related to artificial selection during modern breeding. Therefore, this study provides an integrated method for efficiently identifying CDGs and valuable information for domestication and genetic research.