166 Works

Data from: A recent local sweep at the PHYA locus in the Northern European Spiterstulen population of Arabidopsis lyrata

Tuomas Toivainen, Tanja Pyhäjärvi, Anne Niittyvuopio & Outi Savolainen
Northern and central European Arabidopsis lyrata ssp. petraea populations are locally adapted to prevailing climatic conditions through differences in timing of life history events. The timing of flowering, and in perennials, the timing of growth cessation influence fitness. Phytochrome A may have an important role in regulating these life-history traits as it perceives changes in daylength. We asked, whether PHYA has contributed to local adaptation to the northern conditions in A. l. petraea. To search...

Data from: Bayesian adaptive Markov Chain Monte Carlo estimation of genetic parameters

Boby Mathew, Andrea M. Bauer, Petri Koistinen, Tobias C. Reetz, Jens Léon & Mikko J. Sillanpää
Accurate and fast estimation of genetic parameters that underlie quantitative traits using mixed linear models with additive and dominance effects is of great importance in both natural and breeding populations. Here we propose a new fast adaptive Markov Chain Monte Carlo (MCMC) sampling algorithm for the estimation of genetic parameters in the linear mixed model with several random effects. In the learning phase of our algorithm, we use the hybrid Gibbs sampler to learn the...

Data from: Demographic histories and genetic diversities of Fennoscandian marine and landlocked ringed seal subspecies

Tommi Nyman, Mia Valtonen, Jouni Aspi, Minna Ruokonen, Mervi Kunnasranta & Jukka U. Palo
Island populations are on average smaller, genetically less diverse, and at a higher risk to go extinct than mainland populations. Low genetic diversity may elevate extinction probability, but the genetic component of the risk can be affected by the mode of diversity loss, which, in turn, is connected to the demographic history of the population. Here, we examined the history of genetic erosion in three Fennoscandian ringed seal subspecies, of which one inhabits the Baltic...

Data from: Cuckoo parasitism in a cavity nesting host: near absent egg-rejection in a northern redstart population under heavy apparent (but low effective) brood parasitism

Robert L. Thomson, Jere Tolvanen & Jukka T. Forsman
Brood parasite - host systems continue to offer insights into species coevolution. A notable system is the redstart Phoenicurus phoenicurus parasitized by the “redstart-cuckoo” Cuculus canorus gens. Redstarts are the only regular cuckoo hosts that breed in cavities, which challenges adult cuckoos in egg laying and cuckoo chicks in host eviction. We investigated parasitism in this system and found high overall parasitism rates (31.1% of 360 redstart nests), but also that only 33.1% of parasitism...

Data from: Sex allocation conflict between queens and workers in Formica pratensis wood ants predicts seasonal sex ratio variation

Heikki Helanterä, Jonna Kulmuni & Pekka Pamilo
Sex allocation theory predicts parents should adjust their investment in male and female offspring in a way that increases parental fitness. This has been shown in several species and selective contexts. Yet, seasonal sex ratio variation within species and its underlying causes are poorly understood. Here we study sex allocation variation in the wood ant Formica pratensis. This species displays conflict over colony sex ratio as workers and queens prefer different investment in male and...

Data from: Selection for population specific adaptation has shaped patterns of variation in the photoperiod pathway genes in Arabidopsis lyrata during post glacial colonization

Tiina M. Mattila, Esa A. Aalto, Tuomas Toivainen, Anne Niittyvuopio, Susanna Piltonen, Helmi Kuittinen & Outi Savolainen
Spatially varying selection can lead to population-specific adaptation, which is often recognized at the phenotypic level; however, the genetic evidence is weaker in many groups of organisms. In plants, environmental shifts that occur due to colonization of a novel environment may require adaptive changes in the timing of growth and flowering, which are often governed by location-specific environmental cues such as day length. We studied locally varying selection in 19 flowering time loci in nine...

Data from: No biotic homogenisation across decades but consistent effects of landscape position and pH on macrophyte communities in boreal lakes

Marja Lindholm, Janne Alahuhta, Jani Heino & Heikki Toivonen
It has been predicted that spatial beta diversity shows a decreasing trend in the Anthropocene due to increasing human impact, causing biotic homogenisation. We aimed to discover if vascular aquatic macrophyte communities show different spatial patterns in beta diversity in relation to land use and environmental characteristics in different decades from 1940s to 2010s. We aimed to discover if spatial structures differ between species-, phylogeny- and functional-based beta diversity. We used presence-absence data of aquatic...

Data from: Reproduction under light pollution: maladaptive response to spatial variation in artificial light in a glow-worm

Christina Elgert, Juhani Hopkins, Arja Kaitala & Ulrika Candolin
The amount of artificial light at night is growing worldwide, impacting the behaviour of nocturnal organisms. Yet, we know little about the consequences of these behavioural responses for individual fitness and population viability. We investigated if females of the common glow-worm Lampyris noctiluca – which glow in the night to attract males – mitigate negative effects of artificial light on mate attraction by adjusting the timing and location of glowing to spatial variation in light...

Data from: Genome-wide meta-analysis of sciatica in Finnish population

Susanna Lemmelä, Svetlana Solovieva, Rahman Shiri, Christian Benner, Markku Heliövaara, Johannes Kettunen, Verneri Anttila, Samuli Ripatti, Markus Perola, Ilkka Seppälä, Markus Juonala, Mika Kähönen, Veikko Salomaa, Jorma Viikari, Olli Raitakari, Terho Lehtimäki, Aarno Palotie, Eira Viikari-Juntula, Kirsti Husgafvel-Pursiainen, Olli T. Raitakari & Eira Viikari-Juntura
Sciatica or the sciatic syndrome is a common and often disabling low back disorder in the working-age population. It has a relatively high heritability but poorly understood molecular mechanisms. The Finnish population is a genetic isolate where small founder population and bottleneck events have led to enrichment of certain rare and low frequency variants. We performed here the first genome-wide association (GWAS) and meta-analysis of sciatica. The meta-analysis was conducted across two GWAS covering 291...

Data from: Statistical forecasting of current and future circum-Arctic ground temperatures and active layer thickness

Juha Aalto, Olli Karjalainen, Jan Hjort & Miska Luoto
Mean annual ground temperature (MAGT) and active layer thickness (ALT) are key to understanding the evolution of the ground thermal state across the Arctic under climate change. Here a statistical modeling approach is presented to forecast current and future circum-Arctic MAGT and ALT in relation to climatic and local environmental factors, at spatial scales unreachable with contemporary transient modeling. After deploying an ensemble of multiple statistical techniques, distance-blocked cross-validation between observations and predictions suggested excellent...

Data from: Short- and mid-wavelength artificial light influences the flash signals of Aquatica ficta fireflies (Coleoptera: Lampyridae)

Avalon C.S. Owens, Victor B. Meyer-Rochow, En-Cheng Yang & Avalon Celeste Stevahn Owens
Urbanization can radically disrupt natural ecosystems through alteration of the sensory environment. Habitat disturbances are predicted to favor behaviorally flexible species capable of adapting to altered environments. When artificial light at night (ALAN) is introduced into urban areas, it has the potential to impede reproduction of local firefly populations by obscuring their bioluminescent courtship signals. Whether individual fireflies can brighten their signals to maintain visibility against an illuminated background remains unknown. In this study, we...

An ancient and eroded social supergene is widespread across Formica ants

Alan Brelsford, Jessica Purcell, Amaury Avril, Patrick Tran Van, Junxia Zhang, Timothée Brütsch, Liselotte Sundström, Heikki Helanterä & Michel Chapuisat
Supergenes, clusters of tightly linked genes, play a key role in the evolution of complex adaptive variation. While supergenes have been identified in many species, we lack an understanding of their origin, evolution and persistence. Here, we uncover 20-40 MY of evolutionary history of a supergene associated with polymorphic social organization in Formica ants. We show that five Formica species exhibit homologous divergent haplotypes spanning 11 Mbp on chromosome 3. Despite the size of the...

Population genomics reveals repeated signals of adaptive divergence in the Atlantic salmon of northeastern Europe

Ksenia Zueva, Jaakko Lumme, Alexey Veselov, Craig Primmer & Victoria Pritchard
Our ability to examine genetic variation across entire genomes have enabled many studies searching for the genetic basis of local adaptation. These studies have identified numerous loci as candidates for differential local selection, however relatively few have examined the overlap among candidate loci identified from independent studies of the same species in different geographic areas or evolutionary lineages. We used an allelotyping approach with a 220K SNP array to characterize the population genetic structure of...

Data from: Divergence of Arctic shrub growth associated with sea ice decline

Agata Buchwal, Patrick F. Sullivan, Marc Macias-Fauria, Eric Post, Isla H. Myers-Smith, Julienne C. Stroeve, Daan Blok, Ken D. Tape, Bruce C. Forbes, Pascale Ropars, Esther Lévesque, Bo Elberling, Sandra Angers-Blondin, Joseph S. Boyle, Stéphane Boudreau, Noémie Boulanger-Lapointe, Cassandra Gamm, Martin Hallinger, Grzegorz Rachlewicz, Amanda Young, Pentti Zetterberg & Jeffrey M. Welker
Arctic sea ice extent (SIE) is declining at an accelerating rate with a wide range of ecological consequences. However, determining sea ice effects on tundra vegetation remains a challenge. In this study, we examined the universality or lack thereof in tundra shrub growth responses to changes in SIE and summer climate across the Pan-Arctic, taking advantage of 23 tundra shrub-ring chronologies from 19 widely distributed sites (56⁰-83⁰N).

Estimating migration of the cold-tolerant leaf beetle Gonioctena quinquepunctata inside a mountain range in a spatially explicit context

Chedly Kastally, Simon Dellicour, Olivier J. Hardy, Marius Gilbert & Patrick Mardulyn
The cold-tolerant leaf beetle Gonioctena quinquepunctata displays a large but fragmented European distribution and is restricted to mountain regions in the southern part of its range. Using a RAD-seq-generated large SNP data set (> 10,000 loci), we investigated the geographic distribution of genetic variation within the Vosges mountains, where the species is common. To translate this pattern of variation in an estimate of its capacity to disperse, we simulated SNP data under a spatially explicit...

Stochastic processes and ecological connectivity drive stream invertebrate community responses to short-term drought

Romain Sarremejane, Amélie Truchy, Brendan McKie, Heikki Mykrä, Richard Johnson, Ari Huusko, Ryan Sponseller & Timo Muotka
1. Community responses to and recovery from disturbances depend on local (e.g. presence of refuges) and regional (connectivity to recolonization sources) factors. Droughts are becoming more frequent in boreal regions, and are likely to constitute a severe disturbance for boreal stream communities where organisms largely lack adaptations to such hydrological extremes. 2. We conducted an experiment in 24 seminatural stream flumes to assess the effects of local and regional factors on the responses of benthic...

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The abundance of small mammals is positively linked to survival from nest depredation but negatively linked to local recruitment of a ground nesting precocial bird

Veli-Matti Pakanen, Veli-Matti Pakanen, Risto Tornberg, Eveliina Airaksinen, Nelli Rönkä & Kari Koivula
Generalist predators using small mammals as their primary prey are suggested to shift hunting alternative prey such as bird nests, when small mammals are in short supply (the alternative prey hypothesis, APH). Nest survival and survival of young individuals should be positively linked to small mammal abundance and negatively linked to predator abundance, but little information exists from survival of chicks, especially until recruitment. We test these predictions of the APH using 13 years (2002-2014)...

Additional file 7 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 7. Figure S4: ctDNA statuses and disease-related events of patients during follow-up periods. Swimmer plot illustrating the ctDNA statuses, adjuvant therapies, and pathological events of all patients. Abbreviations: LUAD – lung adenocarcinoma, LUSC - lung squamous-cell carcinoma, AT – adjuvant therapy.

Additional file 9 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 9. Figure S6: ctDNA testing, LDCT scans, and disease-related events of patients during follow-up periods. . Swimmer plot illustrating the first positive ctDNA testing, the last negative LDCT scans, and pathological events of patients that experienced recurrence or deceased. B). The original and adjusted time intervals between the first positive ctDNA testing and final LDCT scans that detected disease recurrence. Abbreviations: LDCT – low-dose computed tomography, LUAD – lung adenocarcinoma, LUSC - lung...

Additional file 8 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 8. Figure S5: Prognostic values of ctDNA detection based on clonal and subclonal mutations. A). The recurrence-free survival analysis of patients stratified by ctDNA detection based on only clonal mutation profiles. B). The recurrence-free survival analysis of patients stratified by ctDNA detection based on all clonal and subclonal mutations.

Additional file 3 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 3. Table S3: Performance of three strategies.

Additional file 2 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 2. Table S2: Adjuvant treatment information.

Additional file 9 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 9. Figure S6: ctDNA testing, LDCT scans, and disease-related events of patients during follow-up periods. . Swimmer plot illustrating the first positive ctDNA testing, the last negative LDCT scans, and pathological events of patients that experienced recurrence or deceased. B). The original and adjusted time intervals between the first positive ctDNA testing and final LDCT scans that detected disease recurrence. Abbreviations: LDCT – low-dose computed tomography, LUAD – lung adenocarcinoma, LUSC - lung...

Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Abstract Background Circulating tumor DNA (ctDNA) has been proven as a marker for detecting minimal residual diseases following systemic therapies in mid-to-late-stage non-small-cell lung cancers (NSCLCs) by multiple studies. However, fewer studies cast light on ctDNA-based MRD monitoring in early-to-mid-stage NSCLCs that received surgical resection as the standard of care. Methods We prospectively recruited 128 patients with stage I–III NSCLCs who received curative surgical resections in our Lung Cancer Tempo-spatial Heterogeneity prospective cohort. Plasma samples...

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