112 Works

Effects of primary seed dormancy on life-time fitness of Arabidopsis thaliana in the field

Jon Ågren
Background and Aims Seed dormancy determines the environmental niche of plants in seasonal environments, and has consequences for plant performance that potentially go far beyond the seed and seedling stages. In this study, we examined the cascading effects of seed dormancy on the expression of subsequent life-history traits and fitness in the annual herb Arabidopsis thaliana. Methods We planted seeds of >200 recombinant inbred lines (RIL) derived from a cross between two locally adapted populations...

Context dependent variation in corticosterone and phenotypic divergence of Rana arvalis populations along an acidification gradient

Katja Räsänen, Jelena Mausbach & Anssi Laurila
Background Physiological processes, as immediate responses to the environment, are important mechanisms of phenotypic plasticity and can influence evolution at ecological time scales. In stressful environments, physiological stress responses of individuals are initiated and integrated via the release of hormones, such as corticosterone (CORT). In vertebrates, CORT influences energy metabolism and resource allocation to multiple fitness traits (e.g. growth and morphology) and can be an important mediator of rapid adaptation to environmental stress, such as...

The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

Bilena L.B. Almeida, Mohamed N.M. Bahrudeen, Vatsala Chauhan, Suchintak Dash, Vinodh Kandavalli, Antti Häkkinen, Jason Lloyd-Price, Cristina S.D. Palma, Ines S.C. Baptista, Abhishekh Gupta, Juha Kesseli, Eric Dufour, Olli-Pekka Smolander, Matti Nykter, Petri Auvinen, Howard T. Jacobs, Samuel M.D. Oliveira & Andre S. Ribeiro
The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the...

A polygenic architecture with habitat-dependent effects underlies ecological differentiation in Silene

Susanne Gramlich, Xiaodong Liu, C. Alex Buerkle, Adrien Favre & Sophie Karrenberg
Ecological differentiation can drive speciation but it is unclear how the genetic architecture of habitat-dependent fitness contributes to lineage divergence. We investigated the genetic architecture of cumulative flowering, a fitness component, in second-generation hybrids between Silene dioica and S. latifolia transplanted into the natural habitat of each species. We used reduced-representation sequencing and Bayesian Sparse Linear Mixed Models (BSLMMs) to analyze the genetic control of cumulative flowering in each habitat. Our results point to a...

Data from: Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Hollis Dahn, Jacquelyn Mountcastle, Jennifer Balacco, Sylke Winkler, Iliana Bista, Anthony Schmitt, Olga Vinnere Pettersson, Giulio Formenti, Karen Oliver, Michelle Smith, Wenhua Tan, Anne Kraus, Stephen Mac, Lisa Komoroske, Tanya Lama, Andrew Crawford, Robert Murphy, Samara Brown, Alan Scott, Phillip Morin, Erich Jarvis & Olivier Fedrigo
Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different...

Habitat shapes diversity of gut microbiomes in a wild population of blue tits Cyanistes caeruleus

Szymon Drobniak, Mariusz Cichoń, Katarzyna Janas, Julia Barczyk, Lars Gustafsson, Magdalena Zagalska-Neubauer, Szymon M. Drobniak & Magdalena Zagalska‐Neubauer
Microbiome constitutes and important axis of individual variation that, together with genes and the environment, influences an individual’s physiology and fitness. Microbiomes are dependent not only on an individual’s body condition but also on external factors, such as diet or stress levels, and as such can be involved into feedbacks between the external ecological factors and internal physiology. In our study we used a wild population of blue tits (Cyanistes caeruleus) to investigate the impact...

Experimental sexual selection affects the evolution of physiological and life history traits

Martin D. Garlovsky, Luke Holman, Andrew L. Brooks, Rhonda R. Snook & Zorana K. Novicic
Sexual selection and sexual conflict are expected to affect all aspects of the phenotype, not only traits that are directly involved in reproduction. Here, we show coordinated evolution of multiple physiological and life history traits in response to long-term experimental manipulation of the mating system in populations of Drosophila pseudoobscura. Development time was extended under polyandry relative to monogamy in both sexes, potentially due to higher investment in traits linked to sexual selection and sexual...

Changes in testing and incidence of Chlamydia trachomatis and Neisseria gonorrhoeae – the possible impact of the COVID-19 pandemic in the three Scandinavian countries

Lovisa Ivarsson, Magdalena de Arriba Sánchez de la Campa, Karin Elfving, Hong Yin, Karolina Gullsby, Lisa Stark, Berit Andersen, Steen Hoffmann, Åsa Gylfe, Magnus Unemo & Björn Herrmann
This study aimed to investigate what impact the COVID-19 pandemic and its associated restrictions had on Chlamydia trachomatis and Neisseria gonorrhoeae infections in Sweden, Denmark and Norway, countries with very different governmental strategies for handling this pandemic. Retrospective analysis of data collected via requests to Swedish regions and to health authorities in Denmark and Norway. The data were collected for the years 2018–2020 and the data from Sweden were more detailed. When the pandemic restrictions...

ISIMIP2b Simulation Data from the Local Lakes Sector

Rafael Marcé, Donald Pierson, Daniel Mercado-Bettin, Wim Thiery, Sebastiano Piccolroaz, Bronwyn Woodward, Richard Iestyn Woolway, Zeli Tan, Georgiy Kirillin, Tom Shatwell, Raoul-Marie Couture, Marianne Côté, Damien Bouffard, Carl Love Mikael Råman Vinnå, Martin Schmid & Jacob Schewe
The Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) provides a framework for the collation of a set of consistent, multi-sector, multi-scale climate-impact simulations, based on scientifically and politically relevant historical and future scenarios. This framework serves as a basis for robust projections of climate impacts, as well as facilitating model evaluation and improvement, allowing for advanced estimates of the biophysical and socio-economic impacts of climate change at different levels of global warming. It also provides a...

Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus)

Stefan Prost, Ana Paula Machado, Julia Zumbroich, Lisa Preier, Sarita Mahtani-Williams, René Meißner, Katerina Guschanski, Jaelle C. Braeley, Carlos Rodriguez Fernandes, Paul Vercammen, Luke T. B. Hunter, Alexei V. Abramov, Martin Plasil, Petr Horin, Lena Godsall-Botriell, Paul Bottriell, Desire Lee Dalton, Antoinette Kotze & Pamela Burger
We live in a world characterised by biodiversity loss and global environmental change. The extinction of large carnivores can have ramifying effects on ecosystems like an uncontrolled increase in wild herbivores, which in turn can have knock-on impacts on vegetation regeneration and communities. Cheetahs (Acinonyx jubatus) serve important ecosystem functions as apex predators; yet, they are quickly heading towards an uncertain future. Threatened by habitat loss, human-wildlife conflict, and illegal trafficking, there are only approximately...

A baseline for the genetic stock identification of Atlantic herring, Clupea harengus, in ICES Divisions 6.a, 7.b-c

Edward Farrell, Leif Andersson, Dorte Bekkevold, Neil Campbell, Jens Carlsson, Maurice Clarke, Afra Egan, Arild Folkvord, Michael Gras, Susan Mærsk Lusseau, Steven Mackinson, Cormac Nolan, Steven O'Connell, Michael O'Malley, Martin Pastoors, Mats Pettersson & Emma White
Atlantic herring in ICES Divisions 6.a, 7.b-c comprises at least three populations, distinguished by temporal and spatial differences in spawning, which have until recently been managed as two stocks defined by geographic delineators. Outside of spawning the populations form mixed aggregations, which are the subject of acoustic surveys. The inability to distinguish the populations has prevented the development of separate survey indices and separate stock assessments. A panel of 45 SNPs, derived from whole genome...

Additional file 1 of Identification of HMGB2 associated with proliferation, invasion and prognosis in lung adenocarcinoma via weighted gene co-expression network analysis

Xie Qiu, Wei Liu, Yifan Zheng, Kai Zeng, Hao Wang, Haijun Sun & Jianhua Dai
Additional file 1: Table S1. Clinical informations and IHC score of patients with LUAD.

Pollinator and host sharing lead to hybridization and introgression in Panamanian free-standing figs, but not in their pollinator wasps

Jordan Satler, Allen Herre, Tracy Heath, Carlos Machado, Adalberto Gomez, Charlotte Jander, Deren Eaton & John Nason
Obligate pollination mutualisms, in which plant and pollinator lineages depend on each other for reproduction, often exhibit high levels of species-specificity. However, cases in which two or more pollinator species share a single host species (host sharing), or two or more host species share a single pollinator species (pollinator sharing), are known to occur in the current ecological time. Further, evidence for host switching in evolutionary time is increasingly being recognized in these systems. The...

Additional file 2 of Genome-associations of extended-spectrum ß-lactamase producing (ESBL) or AmpC producing E. coli in small and medium pig farms from Khon Kaen province, Thailand

João Pires, Laura Huber, Rachel A. Hickman, Simon Dellicour, Kamonwan Lunha, Thongpan Leangapichart, Jatesada Jiwakanon, Ulf Magnusson, Marianne Sunde, Josef D. Järhult & Thomas P. Van Boeckel
Additional file 2: Table S2. ESBL AMPC farm metadata.

Additional file 4 of Oxidative stress genes in patients with esophageal squamous cell carcinoma: construction of a novel prognostic signature and characterization of tumor microenvironment infiltration

Wei Liu, Hao-Shuai Yang, Shao-Yi Zheng, Hong-He Luo, Yan-Fen Feng & Yi-Yan Lei
Additional file 4: Table S3. The results of univariate Cox proportional hazards regression analyses between clinical features and risk score in the training, testing, and entire sets.

Additional file 5 of Oxidative stress genes in patients with esophageal squamous cell carcinoma: construction of a novel prognostic signature and characterization of tumor microenvironment infiltration

Wei Liu, Hao-Shuai Yang, Shao-Yi Zheng, Hong-He Luo, Yan-Fen Feng & Yi-Yan Lei
Additional file 5: Table S4. The results of univariate Cox proportional hazards regression analyses between clinical features and risk score in the training, testing, and entire sets.

Prevalence and risk factors for sexual dysfunction in young women following a cancer diagnosis – a population-based study

Lena Wettergren, Lars E. Eriksson, Charlotta Bergström, Christel Hedman, Johan Ahlgren, Karin E. Smedby, Kristina Hellman, Roger Henriksson & Claudia Lampic
Self-reported sex problems among women diagnosed with reproductive and nonreproductive cancers before the age of 40 are not fully understood. This study aimed to determine sexual dysfunction in young women following a cancer diagnosis in relation to women of the general population. Furthermore, to identify factors associated with sexual dysfunction in women diagnosed with cancer. A population-based cross-sectional study with 694 young women was conducted 1.5 years after being diagnosed with cancer (response rate 72%)....

Impact of spontaneous liposome modification with phospholipid polymer-lipid conjugates on protein interactions

Haruna Suzuki, Anna Adler, Tianwei Huang, Akiko Kuramochi, Yoshiro Ohba, Yuya Sato, Naoko Nakamura, Vivek Anand Manivel, Kristina N Ekdahl, Bo Nilsson, Kazuhiko Ishihara & Yuji Teramura
Liposome surface coating has been studied to avoid the immunological responses caused by the complement system, and alternative materials to poly(ethylene glycol) (PEG) have been explored recently since the production of anti-PEG IgM antibodies has been found in humans. We previously reported a liposome coating with poly(2-methacryloyloxyethyl phosphorylcholine) (poly(MPC))-conjugated lipids (PMPC-lipids) and demonstrated its protective effect on blood protein interactions. Here, we attempted to modify the liposome surface by exogenously adding PMPC-lipids, which were spontaneously...

Additional file 10 of Evolution patterns of NBS genes in the genus Dendrobium and NBS-LRR gene expression in D. officinale by salicylic acid treatment

Jiapeng Yang, Caijun Xiong, Siyuan Li, Cheng Zhou, Lingli Li, Qingyun Xue, Wei Liu, Zhitao Niu & Xiaoyu Ding
Additional file 10.

Additional file 9 of MP4: a machine learning based classification tool for prediction and functional annotation of pathogenic proteins from metagenomic and genomic datasets

Ankit Gupta, Aditya S. Malwe, Gopal N. Srivastava, Parikshit Thoudam, Keshav Hibare & Vineet K. Sharma
Additional file 9. Table S5: Performance of MP4, MP3 and VirulentPred on real dataset-1.

Additional file 7 of Evolution patterns of NBS genes in the genus Dendrobium and NBS-LRR gene expression in D. officinale by salicylic acid treatment

Jiapeng Yang, Caijun Xiong, Siyuan Li, Cheng Zhou, Lingli Li, Qingyun Xue, Wei Liu, Zhitao Niu & Xiaoyu Ding
Additional file 7.

Integrating top-down and bottom-up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone

Matthew Streisfeld, Sean Stankowski, Madeline Chase & Hanna McIntosh
Understanding the phenotypic and genetic architecture of reproductive isolation is a longstanding goal of speciation research. In several systems, large-effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine ‘top-down’ and ‘bottom-up’ approaches with demographic modeling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to...

Conflict over the eukaryote root resides in strong outliers, mosaics and missing data sensitivity of site-specific (CAT) mixture models

Caesar Al Jewari & Sandra Baldauf
Abstract Phylogenetic reconstruction using concatenated loci (“phylogenomics” or “supermatrix phylogeny”) is a powerful tool for solving evolutionary splits that are poorly resolved in single gene/protein trees (SGTs). However, recent phylogenomic attempts to resolve the eukaryote root have yielded conflicting results, along with claims of various artefacts hidden in the data. We have investigated these conflicts using two new methods for assessing phylogenetic conflict. ConJak uses whole marker (gene or protein) jackknifing to assess deviation from...

WGS for patient specific MRD in pediatric ALL

Cecilia Arthur, Fatemah Rezayee, Nina Mogensen, Leonie Saft, Richard Rosenquist Brandell, Magnus Nordenskjöld, Arja Harila-Saari, Emma Tham & Gisela Barbany
Data from a study of six children with acute lymphoblastic leukemia (four patients with precursor B-cell ALL (Acute lymphoblastic leukemia) and two patients with T-cell ALL). None had stratifying genetics or central nervous system involvement. The study was approved by the Ethical Review Board at Stockholm County and written informed consent was obtained from the patients’ guardians.
The data consits of BAM-files from whole-genome sequencing (WGS) of diagnostic bone marrow samples (30X coverage on...

Cryptic species in a colorful genus: integrative taxonomy of the bush robins (Aves, Muscicapidae, Tarsiger) suggests two overlooked species

Yang Liu, Chentao Wei, George Sangster, Urban Olsson, Pamela Rasmussen, Lars Svensson, Cheng-Te Yao, Geoff Carey, Paul Leader, Ruiying Zhang, Guoling Chen, Gang Song, Fumin Lei, David Wilcove & Per Alström
Several cryptic avian species have been validated by recent integrative taxonomic efforts in the Sino-Himalayan mountains, indicating that avian diversity in this global biodiversity hotspot may be underestimated. In the present study,we investigated species limits in the genus Tarsiger, the bush robins, a group of montane forest specialists with high species richness in the Sino-Himalayan region. Based on comprehensive sampling of all 11 subspecies of the six currently recognized species, we applied an integrative taxonomic...

Registration Year

  • 2022

Resource Types

  • Dataset


  • Uppsala University
  • Fudan University
  • Capital Medical University
  • Central South University
  • Jilin University
  • Hainan Medical University
  • Shanghai University of Traditional Chinese Medicine
  • Zhengzhou University
  • Chinese Academy of Medical Sciences & Peking Union Medical College
  • Army Medical University