Tuomas Hämälä
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View article: Kinetochore and ionomic adaptation to whole-genome duplication in Cochlearia shows evolutionary convergence in three autopolyploids
Kinetochore and ionomic adaptation to whole-genome duplication in Cochlearia shows evolutionary convergence in three autopolyploids Open
Whole-genome duplication (WGD) occurs in all kingdoms and impacts speciation, domestication, and cancer outcome. However, doubled DNA management can be challenging for nascent polyploids. The study of within-species polyploidy (autopolyplo…
View article: Impact of whole-genome duplications on structural variant evolution in Cochlearia
Impact of whole-genome duplications on structural variant evolution in Cochlearia Open
Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGD…
View article: A combination of conserved and diverged responses underlies Theobroma cacao’s defense response to Phytophthora palmivora
A combination of conserved and diverged responses underlies Theobroma cacao’s defense response to Phytophthora palmivora Open
Background Plants have complex and dynamic immune systems that have evolved to resist pathogens. Humans have worked to enhance these defenses in crops through breeding. However, many crops harbor only a fraction of the genetic diversity pr…
View article: Impact of whole-genome duplications on structural variant evolution in the plant genus<i>Cochlearia</i>
Impact of whole-genome duplications on structural variant evolution in the plant genus<i>Cochlearia</i> Open
Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. All angiosperms have undergone ancient WGDs, and today stable polyploids account for a substantial portion of both wild and domesticated pl…
View article: Kinetochore and ionomic adaptation to whole genome duplication
Kinetochore and ionomic adaptation to whole genome duplication Open
Transforming genomic and cellular landscapes in a single generation, whole genome duplication (WGD) brings fundamental challenges, but is also associated with diversification. How is WGD tolerated, and what processes commonly evolve to sta…
View article: Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of Arabidopsis lyrata
Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of Arabidopsis lyrata Open
Understanding what factors influence plastic and genetic variation is valuable for predicting how organisms respond to changes in the selective environment. Here, using gene expression and DNA methylation as molecular phenotypes, we study …
View article: Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis
Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis Open
The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhiz…
View article: Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of<i>Arabidopsis lyrata</i>
Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of<i>Arabidopsis lyrata</i> Open
Understanding what factors influence plastic and genetic variation is valuable for predicting how organisms respond to changes in the selective environment. Here, using gene expression and DNA methylation as molecular phenotypes, we study …
View article: Genomic structural variants constrain and facilitate adaptation in natural populations of <i>Theobroma cacao</i> , the chocolate tree
Genomic structural variants constrain and facilitate adaptation in natural populations of <i>Theobroma cacao</i> , the chocolate tree Open
Significance Genomic structural variants (SVs) are frequent contributors to adaptation and speciation, but our understanding of their overall fitness consequences is limited, with data and analyses primarily available for humans and short-…
View article: Maintenance of Adaptive Dynamics and No Detectable Load in a Range-Edge Outcrossing Plant Population
Maintenance of Adaptive Dynamics and No Detectable Load in a Range-Edge Outcrossing Plant Population Open
During range expansion, edge populations are expected to face increased genetic drift, which in turn can alter and potentially compromise adaptive dynamics, preventing the removal of deleterious mutations and slowing down adaptation. Here,…
View article: Maintenance of adaptive dynamics and no detectable load in a range-edge outcrossing plant population
Maintenance of adaptive dynamics and no detectable load in a range-edge outcrossing plant population Open
During range expansion, edge populations are expected to face increased genetic drift, which in turn can alter and potentially compromise adaptive dynamics, preventing the removal of deleterious mutations and slowing down adaptation. Here,…
View article: Biased Gene Conversion Constrains Adaptation in <i>Arabidopsis thaliana</i>
Biased Gene Conversion Constrains Adaptation in <i>Arabidopsis thaliana</i> Open
Reduction of fitness due to deleterious mutations imposes a limit to adaptive evolution. By characterizing features that influence this genetic load we may better understand constraints on responses to both natural and human-mediated selec…
View article: Pleiotropy facilitates local adaptation to distant optima in common ragweed (Ambrosia artemisiifolia)
Pleiotropy facilitates local adaptation to distant optima in common ragweed (Ambrosia artemisiifolia) Open
Pleiotropy, the control of multiple phenotypes by a single locus, is expected to slow the rate of adaptation by increasing the chance that beneficial alleles also have deleterious effects. However, a prediction arising from classical theor…
View article: Ragweed transcriptome
Ragweed transcriptome Open
Isoform- and gene-level transcriptomes for common ragweed.After filtering out low quality reads and sequencing adapters with Trimmomatic, a total of 11.8 million read pairs from a single genotype (from Oklahoma) were used in the transcript…
View article: Impact of demography on linked selection in two outcrossing Brassicaceae species
Impact of demography on linked selection in two outcrossing Brassicaceae species Open
Genetic diversity is shaped by mutation, genetic drift, gene flow, recombination, and selection. The dynamics and interactions of these forces shape genetic diversity across different parts of the genome, between populations and species. H…
View article: Local adaptation under gene flow: Recombination, conditional neutrality and genetic trade-offs shape genomic patterns in<i>Arabidopsis lyrata</i>
Local adaptation under gene flow: Recombination, conditional neutrality and genetic trade-offs shape genomic patterns in<i>Arabidopsis lyrata</i> Open
Short-scale local adaptation is a complex process involving selection, migration and drift. The expected effects on the genome are well grounded in theory, but examining these on an empirical level has proven difficult, as it requires info…