Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

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Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.Peer reviewe

Author Correction: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch.

In the version of this article initially published, there was a mistake in the calculation of the nucleotide mutation rate per site per generation: 1 × 10−9 mutations per site per generation was used, whereas 9.5 × 10−9 was correct. This error affects the interpretation of population-size changes over time and their possible correspondence with known geological events, as shown in the original Fig. 4 and supporting discussion in the text, as well as details in the Supplementary Note. Neither the data themselves nor any other results are affected. Figure 4 has been revised accordingly. Images of the original and corrected figure panels are shown in the correction notice

Tangled worlds:the Swedish, the Sámi, and the reindeer

Abstract Reindeer pastoralism developed among the indigenous Sámi of northern Fennoscandia, but the established colonial relationship with Sweden brought on an expanded use of reindeer. Tradesmen, priests, and officials of Swedish origin benefited from domesticated reindeer in many ways — trading reindeer products and using reindeer as transport during winter trips to marketplaces. Reindeer were, therefore, in many ways focal in the encounters between the Sámi and the Swedish. In this paper, we use zooarchaeology, stable isotope analysis, and ancient DNA analysis to interpret reindeer remains from towns, marketplaces, and agrarian settlements in medieval and early modern northern Fennoscandia. We argue that reindeer played important roles in contacts and encounters. The Sámi, the Swedish, and the reindeer formed a multispecies community. The exploration of the relationships in this multispecies community captures the complexity of human and human-animal relationships in colonial encounters. Moreover, it emphasizes the importance and agency of animals in colonial histories

Understanding environmental change through the lens of trait-based, functional, and phylogenetic biodiversity in freshwater ecosystems

Abstract In the era of the Anthropocene, environmental change is accelerating biodiversity loss across ecosystems on Earth, among which freshwaters are likely the most threatened. Different biodiversity facets in the freshwater realm suffer from various environmental changes that jeopardize the ecosystem functions and services important for humankind. In this work we examine how environmental changes (e.g., climate change, eutrophication, or invasive species) affect trait-based, functional, and phylogenetic diversity of biological communities. We first developed a simple conceptual model of the possible relationships between environmental change and these three diversity facets in freshwaters and, secondly, systematically reviewed articles where these relationships had been investigated in different freshwater ecosystems. Finally, we highlighted research gaps from the perspectives of organisms, ecosystems, stressors, and geographical locations. Our conceptual model suggested that both natural factors and global change operating at various spatial scales influence freshwater community structure and ecosystem functioning. The relationships between biodiversity and environmental change depend on geographical region, organism group, spatial scale, and environmental change gradient length. The systematic review revealed that environmental change impacts biodiversity patterns in freshwaters, but there is no single type of biodiversity response to the observed global changes. Natural stressors had different, even contradictory, effects (i.e., multiple, negative, and positive) on biodiversity compared with anthropogenic stressors. Anthropogenic stressors more often decreased biodiversity, although eutrophication and climate change affected freshwater ecosystems in a complex, more multi-dimensional way. The research gaps we identified were related, for example, to the low number of community-based biodiversity studies, the lack of information on true phylogenies for all freshwater organism groups, the missing evaluations whether species traits are phylogenetically conserved, and the geographical biases in research (i.e., absence of studies from Africa, Southern Asia, and Russia). We hope that our review will stimulate more research on the less well-known facets and topics of biodiversity loss in highly vulnerable freshwater ecosystems

Self-rated psychopathic traits in a sample of treatment-seeking adolescent girls with internalizing and externalizing disorders:comparisons to girls in the community

Abstract Background: Psychopathy research has thus far focused mostly on child, male, and delinquent samples, but the results are most likely non-generalizable to adolescent girls with mental health disorders. Aim: The present study aimed to compare self-rated psychopathic traits between female psychiatric outpatients and girls in the community, and to investigate how psychopathic traits relate to psychiatric disorders. Method: The outpatient sample comprised 163 girls aged 15–17-years recruited from municipal mental health services. Psychiatric diagnoses were assessed based on the ICD-10 classification. The community sample comprised 355 girls from secondary, vocational, and high schools. The Youth Psychopathic trait Inventory (YPI) served as a self-assessment tool. Results: Treatment-seeking girls exhibit a more impulsive and irresponsible lifestyle than do girls in the community. Girls with externalizing psychopathology, unlike those with an internalizing disorder, exhibit more deficient affective experience than do girls in the community. Psychopathic traits associate with having a psychiatric disorder, a depressive disorder, ADHD, and a conduct disorder. Conclusions: The psychiatric examination of treatment-seeking adolescent girls would likely benefit from screening for psychopathy and its underlying components

Reindeer from Sámi offering sites document the replacement of wild reindeer genetic lineages by domestic ones in Northern Finland starting from 1400 to 1600 AD

Abstract Reindeer herding emerged among the indigenous Sámi of Northern Fennoscandia between ca. 800 and 1500 CE. While the details of the reindeer domestication process are still actively debated, it has been hypothesized that the transition to reindeer herding affected Sámi ritual practice, especially animal offerings given at various sacred sites. To explore this hypothesis, we analyzed DNA from reindeer bone samples dating to ca. 1200–1700 CE from Sámi offering sites located in present-day Northern Finland as well as from samples originating from ancient dwelling site in Southern Finland and Kola Peninsula, Russia. The results show that haplotypes related to wild Finnish forest reindeer (Rangifer tarandus fennicus) began to be replaced by haplotypes common in modern domesticated reindeer in the faunal assemblages from offering sites starting between 1400 and 1600 CE. The results suggest that, although the role of reindeer herding in the economy of the Sámi communities varied greatly, the transition to reindeer herding may have affected ritual practices, testifying to a shared way of reciprocating with the land and animals

Museum specimens of a landlocked pinniped reveal recent loss of genetic diversity and unexpected population connections

Abstract The Saimaa ringed seal (Pusa hispida saimensis) is endemic to Lake Saimaa in Finland. The subspecies is thought to have originated when parts of the ringed seal population of the Baltic region were trapped in lakes emerging due to postglacial bedrock rebound around 9000 years ago. During the 20th century, the population experienced a drastic human-induced bottleneck. Today encompassing a little over 400 seals with extremely low genetic diversity, it is classified as endangered. We sequenced sections of the mitochondrial control region from 60 up to 125-years-old museum specimens of the Saimaa ringed seal. The generated dataset was combined with publicly available sequences. We studied how genetic variation has changed through time in this subspecies and how it is phylogenetically related to other ringed seal populations from the Baltic Sea, Lake Ladoga, North America, Svalbard, and the White Sea. We observed temporal fluctuations in haplotype frequencies and loss of haplotypes accompanied by a recent reduction in female effective population size. In apparent contrast with the traditionally held view of the Baltic origin of the population, the Saimaa ringed seal mtDNA variation also shows affinities to North American ringed seals. Our results suggest that the Saimaa ringed seal has experienced recent genetic drift associated with small population size. The results further suggest that extant Baltic ringed seal is not representative of the ancestral population of the Saimaa ringed seal, which calls for re-evaluation of the deep history of this subspecies

Animal remains from Saami offering places:glimpses of human-animal relations from Finnish Lapland AD 1000–1900

Abstract We present the results of 41 AMS and 49 stable isotope determinations of animal bones retrieved at seven Saami offering places or sieiddit from Finnish Lapland. The offered remains are dominated by reindeer, but other wild and domesticated species were also present. AMS dates and artefacts suggest that six of the studied sieiddit were being utilized as offering places by the 13th century, and that votive activity continued with varying intensity until around 1900. The AMS dates and stable isotope analyses of the sieidi bones produced interesting, somewhat unexpected, results that reflect various aspects of human-animal interaction in Finnish Lapland. In addition to information about Finland’s sieidi sites in terms of utilization chronology and the species offered at them, the study provides a major body of new data from animal species that lived in Finnish Lapland during AD 1000–1900