The Winter-Type Allele of HvCEN Is Associated With Earliness Without Severe Yield Penalty in Icelandic Spring Barley (Hordeum vulgare L.).

Icelandic barley genotypes have shown extreme earliness both in flowering and maturity compared to other north European genotypes, whereas earliness is a key trait in adapting barley to northern latitudes. Four genes were partially re-sequenced, which are Ppd-H1, HvCEN, HvELF3, and HvFT1, to better understand the mechanisms underlying this observed earliness. These genes are all known to play a part in the photoperiod response. The objective of this study is to correlate allelic diversity with flowering time and yield data from Icelandic field trials. The resequencing identified two to three alleles at each locus which resulted in 12 haplotype combinations. One haplotype combination containing the winter-type allele of Ppd-H1 correlated with extreme earliness, however, with a severe yield penalty. A winter-type allele in HvCEN in four genotypes correlated with earliness combined with high yield. Our results open the possibility of marker-assisted pyramiding as a rapid way to develop varieties with a shortened time from sowing to flowering under the extreme Icelandic growing conditions and possibly in other arctic or sub-arctic regions.

Author Correction: Spotted phenotypes in horses lost attractiveness in the Middle Ages.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Not a limitless resource: ethics and guidelines for destructive sampling of archaeofaunal remains.

With the advent of ancient DNA, as well as other methods such as isotope analysis, destructive sampling of archaeofaunal remains has increased much faster than the effort to collect and curate them. While there has been considerable discussion regarding the ethics of destructive sampling and analysis of human remains, this dialogue has not extended to archaeofaunal material. Here we address this gap and discuss the ethical challenges surrounding destructive sampling of materials from archaeofaunal collections. We suggest ways of mitigating the negative aspects of destructive sampling and present step-by-step guidelines aimed at relevant stakeholders, including scientists, holding institutions and scientific journals. Our suggestions are in most cases easily implemented without significant increases in project costs, but with clear long-term benefits in the preservation and use of zooarchaeological material.

Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic.

Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

Identification of Ideal Allele Combinations for the Adaptation of Spring Barley to Northern Latitudes.

The northwards expansion of barley production requires adaptation to longer days, lower temperatures and stronger winds during the growing season. We have screened 169 lines of the current barley breeding gene pool in the Nordic region with regards to heading, maturity, height, and lodging under different environmental conditions in nineteen field trials over 3 years at eight locations in northern and central Europe. Through a genome-wide association scan we have linked phenotypic differences observed in multi-environment field trials (MET) to single nucleotide polymorphisms (SNP). We have identified an allele combination, only occurring among a few Icelandic lines, that affects heat sum to maturity and requires 214 growing degree days (GDD) less heat sum to maturity than the most common allele combination in the Nordic spring barley gene pool. This allele combination is beneficial in a cold environment, where autumn frost can destroy a late maturing harvest. Despite decades of intense breeding efforts relying heavily on the same germplasm, our results show that there still exists considerable variation within the current breeding gene pool and we identify ideal allele combinations for regional adaptation, which can facilitate the expansion of cereal cultivation even further northwards.

Population genetic analysis of a global collection of Fragaria vesca using microsatellite markers.

The woodland strawberry, Fragaria vesca, holds great promise as a model organism. It not only represents the important Rosaceae family that includes economically important species such as apples, pears, peaches and roses, but it also complements the well-known model organism Arabidopsis thaliana in key areas such as perennial life cycle and the development of fleshy fruit. Analysis of wild populations of A. thaliana has shed light on several important developmental pathways controlling, for example, flowering time and plant growth, suggesting that a similar approach using F. vesca might add to our understanding on the development of rosaceous species and perennials in general. As a first step, 298 F. vesca plants were analyzed using microsatellite markers with the primary aim of analyzing population structure and distribution of genetic diversity. Of the 68 markers tested, 56 were polymorphic, with an average of 4.46 alleles per locus. Our analysis partly confirms previous classification of F. vesca subspecies in North America and suggests two groups within the subsp. bracteata. In addition, F. vesca subsp. vesca forms a single global population with evidence that the Icelandic group is a separate cluster from the main Eurasian population.

Spotted phenotypes in horses lost attractiveness in the Middle Ages.

Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in ~3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population.

The origin of ambling horses.

Horseback riding is the most fundamental use of domestic horses and has had a huge influence on the development of human societies for millennia. Over time, riding techniques and the style of riding improved. Therefore, horses with the ability to perform comfortable gaits (e.g. ambling or pacing), so-called 'gaited' horses, have been highly valued by humans, especially for long distance travel. Recently, the causative mutation for gaitedness in horses has been linked to a substitution causing a premature stop codon in the DMRT3 gene (DMRT3_Ser301STOP) [1]. In mice, Dmrt3 is expressed in spinal cord interneurons and plays an important role in the development of limb movement coordination [1]. Genotyping the position in 4396 modern horses from 141 breeds revealed that nowadays the mutated allele is distributed worldwide with an especially high frequency in gaited horses and breeds used for harness racing [2]. Here, we examine historic horse remains for the DMRT3 SNP, tracking the origin of gaitedness to Medieval England between 850 and 900 AD. The presence of the corresponding allele in Icelandic horses (9(th)-11(th) century) strongly suggests that ambling horses were brought from the British Isles to Iceland by Norse people. Considering the high frequency of the ambling allele in early Icelandic horses, we believe that Norse settlers selected for this comfortable mode of horse riding soon after arrival. The absence of the allele in samples from continental Europe (including Scandinavia) at this time implies that ambling horses may have spread from Iceland and maybe also the British Isles across the continent at a later date.

Evolutionary sequence comparison of the Mitf gene reveals novel conserved domains.

The microphthalmia-associated transcription factor (MITF) is a member of the MYC family of basic helix-loop-helix leucine zipper transcription factors. The corresponding gene was initially discovered in the mouse based on mutations which affect the development of several different cell types, including melanocytes and retinal pigment epithelium cells. Subsequently, it was shown to be associated with deafness and hypo-pigmentation disorders in humans. More recently, the gene has been shown to be critical in melanoma formation and to play a role in melanocyte stem cell maintenance. Thus, the mouse Mitf gene represents an important model system for the study of human disease as well as an interesting model for the study of transcription factor function in the organism. Here we use the evolutionary relationship of Mitf genes from numerous distantly related species, including vertebrates and invertebrates, to identify novel conserved domains in the Mitf protein and regions of possible functional importance in the 3' untranslated region. We also characterize the nine different 5' exons of the Mitf gene and identify a new 5' exon in the Drosophila Mitf gene. Our analysis sheds new light on the conservation of the Mitf gene and protein and opens the door for further functional analysis.

Interallelic complementation at the mouse Mitf locus.

Mutations at the mouse microphthalmia locus (Mitf) affect the development of different cell types, including melanocytes, retinal pigment epithelial cells of the eye, and osteoclasts. The MITF protein is a member of the MYC supergene family of basic-helix-loop-helix-leucine-zipper (bHLHZip) transcription factors and is known to regulate the expression of cell-specific target genes by binding DNA as homodimer or as heterodimer with related proteins. The many mutations isolated at the locus have different effects on the phenotype and can be arranged in an allelic series in which the phenotypes range from near normal to white microphthalmic animals with osteopetrosis. Previous investigations have shown that certain combinations of Mitf alleles complement each other, resulting in a phenotype more normal than that of each homozygote alone. Here we analyze this interallelic complementation in detail and show that it is limited to one particular allele, Mitf(Mi-white) (Mitf(Mi-wh)), a mutation affecting the DNA-binding domain. Both loss- and gain-of-function mutations are complemented, as are other Mitf mutations affecting the DNA-binding domain. Furthermore, this behavior is not restricted to particular cell types: Both eye development and coat color phenotypes are complemented. Our analysis suggests that Mitf(Mi-wh)-associated interallelic complementation is due to the unique biochemical nature of this mutation.