Genetic variability and history of a native Finnish horse breed

Background: The Finnhorse was established as a breed more than 110 years ago by combining local Finnish landraces. Since its foundation, the breed has experienced both strong directional selection, especially for size and colour, and severe population bottlenecks that are connected with its initial foundation and subsequent changes in agricultural and forestry practices. Here, we used sequences of the mitochondrial control region and genomic single nucleotide polymorphisms (SNPs) to estimate the genetic diversity and differentiation of the four Finnhorse breeding sections: trotters, pony-sized horses, draught horses and riding horses. Furthermore, we estimated inbreeding and effective population sizes over time to infer the history of this breed. Results: We found a high level of mitochondrial genetic variation and identified 16 of the 18 haplogroups described in present-day horses. Interestingly, one of these detected haplogroups was previously reported only in the Przewalski’s horse. Female effective population sizes were in the thousands, but declines were evident at the times when the breed and its breeding sections were founded. By contrast, nuclear variation and effective population sizes were small (approximately 50). Nevertheless, inbreeding in Finnhorses was lower than in many other horse breeds. Based on nuclear SNP data, genetic differentiation among the four breeding sections was strongest between the draught horses and the three other sections (FST=0.007–0.018), whereas based on mitochondrial DNA data, it was strongest between the trotters and the pony-sized and riding horses (ΦST= 0.054–0.068). Conclusions: The existence of a Przewalski’s horse haplogroup in the Finnhorse provides new insights into the domestication of the horse, and this finding supports previous suggestions of a close relationship between the Finnhorse and eastern primitive breeds. The high level of mitochondrial DNA variation in the Finnhorse supports its domestication from a large number of mares but also reflects that its founding depended on many local landraces. Although inbreeding in Finnhorses was lower than in many other horse breeds, the small nuclear effective popula- tion sizes of each of its breeding sections can be considered as a warning sign, which warrants changes in breeding practices.Peer reviewe

Ancient DNA identification of domestic animals used for leather objects in Central Asia during the Bronze Age

The arid climate of many regions within Central Asia often leads to excellent archaeological preservation, especially in sealed funerary contexts, allowing for ancient DNA analyses. While geneticists have looked at human remains, clothes, tools, and other burial objects are often neglected. In this paper, we present the results of an ancient DNA study on Bronze Age leather objects excavated from tombs of the Wupu cemetery in the Hami Oasis and Yanghai cemetery in the Turpan Oasis, both in Xinjiang Uyghur Autonomous Region of northwestern China. In addition to species identification of goat (Capra aegagrus/hircus), sheep (Ovis orientalis/aries), and cattle (Bos primigenius/taurus), mitochondrial haplogroups were determined for several samples. Our results show that Bronze Age domesticated goats and sheep from the Hami and Turpan oases possessed identical or closely related haplotypes to modern domestic animals of this area. The absence of leather produced from wild animals emphasizes the importance of animal husbandry in the cultures of Wupu and Yanghai

A curated DNA barcode reference library for parasitoids of northern European cyclically outbreaking geometrid moths

Large areas of forests are annually damaged or destroyed by outbreaking insect pests. Understanding the factors that trigger and terminate such population eruptions has become crucially important, as plants, plant-feeding insects, and their natural enemies may respond differentially to the ongoing changes in the global climate. In northernmost Europe, climate-driven range expansions of the geometrid moths Epirrita autumnata and Operophtera brumata have resulted in overlapping and increasingly severe outbreaks. Delayed density-dependent responses of parasitoids are a plausible explanation for the 10-year population cycles of these moth species, but the impact of parasitoids on geometrid outbreak dynamics is unclear due to a lack of knowledge on the host ranges and prevalences of parasitoids attacking the moths in nature. To overcome these problems, we reviewed the literature on parasitism in the focal geometrid species in their outbreak range and then constructed a DNA barcode reference library for all relevant parasitoid species based on reared specimens and sequences obtained from public databases. The combined recorded parasitoid community of E. autumnata and O. brumata consists of 32 hymenopteran species, all of which can be reliably identified based on their barcode sequences. The curated barcode library presented here opens up new opportunities for estimating the abundance and community composition of parasitoids across populations and ecosystems based on mass barcoding and metabarcoding approaches. Such information can be used for elucidating the role of parasitoids in moth population control, possibly also for devising methods for reducing the extent, intensity, and duration of outbreaks.publishedVersio

Taxonomy and nomenclature of some Fennoscandian Sawflies, with descriptions of two new species (Hymenoptera, Symphyta)

While working on an identification guide to the sawflies of Fennoscandia, we encountered numerous taxonomic problems, for some of which we present solutions. Dicrostema Benson, 1952 is a new synonym of Phymatoceropsis Rohwer, 1916, and not congeneric with Paracharactus MacGillivray, 1908. Two species occurring in Europe are transferred to Phymatoceropsis. Dolerus aericepsellus Heidemaa and Mutanen sp. nov. and Heptamelus viitasaarii Liston, Mutanen and Prous sp. nov. are described from Finland. Abia brevicornis Leach, 1817 nom. rev. is the valid name of Abia nitens auct. nec Linnaeus, and Abia nitens (Linnaeus, 1758) is the valid name for what has recently been called Abia sericea (Linnaeus, 1767). Tenthredo haemorrhoidalis Fabricius, 1781 is treated as an unplaced species of Hymenoptera, possibly Ichneumonoidea. Calameuta variabilis (Mocsáry, 1886) is the valid name of the species recently generally called C. haemorrhoidalis. Claremontia confusa (Konow, 1886) sp. rev. and Claremontia brevicornis (Brischke, 1883) are distinct species. Dolerus coracinus (Klug, 1818) is the valid name for D. anthracinus auct. Dolerus anthracinus (Klug, 1818) is a valid species similar to D. nitens Zaddach, 1859. Dolerus coruscans Konow, 1890 sp. rev. is a valid species. Dolerus junci (Stephens, 1835) is the valid name for Dolerus cothurnatus auct. Dolerus timidus (Klug, 1818) sp. rev. is distinguished from the similar D. pratensis (Linnaeus, 1758). A neotype is designated for Astatus punctatus Klug, 1803. Lectotypes are designated for 39 nominal species. 29 species group names are new junior synonyms. We present data on some species recently collected for the first time in Finland, including first records for the Palaearctic and West Palaearctic

A curated DNA barcode reference library for parasitoids of northern European cyclically outbreaking geometrid moths

Large areas of forests are annually damaged or destroyed by outbreaking insect pests. Understanding the factors that trigger and terminate such population eruptions has become crucially important, as plants, plant-feeding insects, and their natural enemies may respond differentially to the ongoing changes in the global climate. In northernmost Europe, climate-driven range expansions of the geometrid moths Epirrita autumnata and Operophtera brumata have resulted in overlapping and increasingly severe outbreaks. Delayed density-dependent responses of parasitoids are a plausible explanation for the 10-year population cycles of these moth species, but the impact of parasitoids on geometrid outbreak dynamics is unclear due to a lack of knowledge on the host ranges and prevalences of parasitoids attacking the moths in nature. To overcome these problems, we reviewed the literature on parasitism in the focal geometrid species in their outbreak range and then constructed a DNA barcode reference library for all relevant parasitoid species based on reared specimens and sequences obtained from public databases. The combined recorded parasitoid community of E. autumnata and O. brumata consists of 32 hymenopteran species, all of which can be reliably identified based on their barcode sequences. The curated barcode library presented here opens up new opportunities for estimating the abundance and community composition of parasitoids across populations and ecosystems based on mass barcoding and metabarcoding approaches. Such information can be used for elucidating the role of parasitoids in moth population control, possibly also for devising methods for reducing the extent, intensity, and duration of outbreaks

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.Peer Reviewe

Genomes of the willow-galling sawflies Euura lappo and Eupontania aestiva (Hymenoptera: Tenthredinidae): a resource for research on ecological speciation, adaptation, and gall induction

Hymenoptera is a hyperdiverse insect order represented by over 153,000 different species. As many hymenopteran species perform various crucial roles for our environments, such as pollination, herbivory, and parasitism, they are of high economic and ecological importance. There are 99 hymenopteran genomes in the NCBI database, yet only five are representative of the paraphyletic suborder Symphyta (sawflies, woodwasps, and horntails), while the rest represent the suborder Apocrita (bees, wasps, and ants). Here, using a combination of 10X Genomics linked-read sequencing, Oxford Nanopore long-read technology, and Illumina short-read data, we assembled the genomes of two willow-galling sawflies (Hymenoptera: Tenthredinidae: Nematinae: Euurina): the bud-galling species Euura lappo and the leaf-galling species Eupontania aestiva. The final assembly for E. lappo is 259.85 Mbp in size, with a contig N50 of 209.0 kbp and a BUSCO score of 93.5%. The E. aestiva genome is 222.23 Mbp in size, with a contig N50 of 49.7 kbp and a 90.2% complete BUSCO score. De novo annotation of repetitive elements showed that 27.45% of the genome was composed of repetitive elements in E. lappo and 16.89% in E. aestiva, which is a marked increase compared to previously published hymenopteran genomes. The genomes presented here provide a resource for inferring phylogenetic relationships among basal hymenopterans, comparative studies on host-related genomic adaptation in plant-feeding insects, and research on the mechanisms of plant manipulation by gall-inducing insects.publishedVersio

Datasets and scripts used in the analyses of the article

This zipped folder contains the datasets, R scripts and command files of all analyses of the article. Some intermediate results are also included

The early wasp plucks the flower : Disparate extant diversity of sawfly superfamilies (Hymenoptera: 'Symphyta') may reflect asynchronous switching to angiosperm hosts

The insect order Hymenoptera originated during the Permian nearly 300 Mya. Ancestrally herbivorous hymenopteran lineages today make up the paraphyletic suborder 'Symphyta', which encompasses c. 8200 species with very diverse host-plant associations. We use phylogeny-based statistical analyses to explore the drivers of diversity dynamics within the 'Symphyta', with a particular focus on the hypothesis that diversification of herbivorous insects has been driven by the explosive radiation of angiosperms during and after the Cretaceous. Our ancestral-state estimates reveal that the first symphytans fed on gymnosperms, and that shifts onto angiosperms and pteridophytes - and back - have occurred at different time intervals in different groups. Trait-dependent analyses indicate that average net diversification rates do not differ between symphytan lineages feeding on angiosperms, gymnosperms or pteridophytes, but trait-independent models show that the highest diversification rates are found in a few angiosperm-feeding lineages that may have been favoured by the radiations of their host taxa during the Cenozoic. Intriguingly, lineages-through-time plots show signs of an early Cretaceous mass extinction, with a recovery starting first in angiosperm-associated clades. Hence, the oft-invoked assumption of herbivore diversification driven by the rise of flowering plants may overlook a Cretaceous global turnover in insect herbivore communities during the rapid displacement of gymnosperm- and pteridophyte-dominated floras by angiosperms

The early wasp plucks the flower : Disparate extant diversity of sawfly superfamilies (Hymenoptera: 'Symphyta') may reflect asynchronous switching to angiosperm hosts

The insect order Hymenoptera originated during the Permian nearly 300 Mya. Ancestrally herbivorous hymenopteran lineages today make up the paraphyletic suborder 'Symphyta', which encompasses c. 8200 species with very diverse host-plant associations. We use phylogeny-based statistical analyses to explore the drivers of diversity dynamics within the 'Symphyta', with a particular focus on the hypothesis that diversification of herbivorous insects has been driven by the explosive radiation of angiosperms during and after the Cretaceous. Our ancestral-state estimates reveal that the first symphytans fed on gymnosperms, and that shifts onto angiosperms and pteridophytes - and back - have occurred at different time intervals in different groups. Trait-dependent analyses indicate that average net diversification rates do not differ between symphytan lineages feeding on angiosperms, gymnosperms or pteridophytes, but trait-independent models show that the highest diversification rates are found in a few angiosperm-feeding lineages that may have been favoured by the radiations of their host taxa during the Cenozoic. Intriguingly, lineages-through-time plots show signs of an early Cretaceous mass extinction, with a recovery starting first in angiosperm-associated clades. Hence, the oft-invoked assumption of herbivore diversification driven by the rise of flowering plants may overlook a Cretaceous global turnover in insect herbivore communities during the rapid displacement of gymnosperm- and pteridophyte-dominated floras by angiosperms