@article{15099, abstract = {Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems.}, author = {Johannesson, Kerstin and Faria, Rui and Le Moan, Alan and Rafajlović, Marina and Westram, Anja M and Butlin, Roger K. and Stankowski, Sean}, issn = {1362-4555}, journal = {Trends in Genetics}, number = {4}, pages = {337--351}, publisher = {Elsevier}, title = {{Diverse pathways to speciation revealed by marine snails}}, doi = {10.1016/j.tig.2024.01.002}, volume = {40}, year = {2024}, } @article{886, abstract = {The factors that determine the tempo and mode of protein evolution continue to be a central question in molecular evolution. Traditionally, studies of protein evolution focused on the rates of amino acid substitutions. More recently, with the availability of sequence data and advanced experimental techniques, the focus of attention has shifted toward the study of evolutionary trajectories and the overall layout of protein fitness landscapes. In this review we describe the effect of epistasis on the topology of evolutionary pathways that are likely to be found in fitness landscapes and develop a simple theory to connect the number of maladapted genotypes to the topology of fitness landscapes with epistatic interactions. Finally, we review recent studies that have probed the extent of epistatic interactions and have begun to chart the fitness landscapes in protein sequence space.}, author = {Kondrashov, Dmitry and Kondrashov, Fyodor}, issn = {1362-4555}, journal = {Trends in Genetics}, keywords = {Mimsatch repair, Chromatin structure, Replication fork, Cancer therapy}, number = {1}, pages = {24 -- 33}, publisher = {Elsevier}, title = {{Topological features of rugged fitness landscapes in sequence space}}, doi = {10.1016/j.tig.2014.09.009}, volume = {31}, year = {2015}, } @article{7744, author = {Robinson, Matthew Richard and Wray, Naomi R. and Visscher, Peter M.}, issn = {0168-9525}, journal = {Trends in Genetics}, number = {4}, pages = {124--132}, publisher = {Elsevier}, title = {{Explaining additional genetic variation in complex traits}}, doi = {10.1016/j.tig.2014.02.003}, volume = {30}, year = {2014}, } @article{6135, abstract = {Many organisms have stress response pathways, components of which share homology with players in complex human disease pathways. Research on stress response in the nematode worm Caenorhabditis elegans has provided detailed insights into the genetic and molecular mechanisms underlying complex human diseases. In this review we focus on four different types of environmental stress responses – heat shock, oxidative stress, hypoxia, and osmotic stress – and on how these can be used to study the genetics of complex human diseases. All four types of responses involve the genetic machineries that underlie a number of complex human diseases such as cancer and neurodegenerative diseases, including Alzheimer's and Parkinson's. We highlight the types of stress response experiments required to detect the genes and pathways underlying human disease and suggest that studying stress biology in worms can be translated to understanding human disease and provide potential targets for drug discovery.}, author = {Rodriguez, Miriam and Snoek, L. Basten and de Bono, Mario and Kammenga, Jan E.}, issn = {0168-9525}, journal = {Trends in Genetics}, number = {6}, pages = {367--374}, publisher = {Elsevier}, title = {{Worms under stress: C. elegans stress response and its relevance to complex human disease and aging}}, doi = {10.1016/j.tig.2013.01.010}, volume = {29}, year = {2013}, } @article{6148, author = {Kammenga, Jan E. and Phillips, Patrick C. and de Bono, Mario and Doroszuk, Agnieszka}, issn = {0168-9525}, journal = {Trends in Genetics}, number = {4}, pages = {178--185}, publisher = {Elsevier}, title = {{Beyond induced mutants: using worms to study natural variation in genetic pathways}}, doi = {10.1016/j.tig.2008.01.001}, volume = {24}, year = {2008}, } @article{12201, abstract = {The development of plant lateral organs is interesting because, although many of the same genes seem to be involved in the early growth of primordia, completely different gene combinations are required for the complete development of organs such as leaves and stamens. Thus, the genes common to the development of most organs, which generally form and polarize the primordial ‘envelope’, must at some stage interact with those that ‘install’ the functional content of the organ – in the case of the stamen, the four microsporangia. Although distinct genetic pathways of organ initiation, polarity establishment and setting up the reproductive cell line can readily be recognized, they do not occur sequentially. Rather, they are activated early and run in parallel. There is evidence for continuing crosstalk between these pathways.}, author = {Feng, Xiaoqi and Dickinson, Hugh G.}, issn = {0168-9525}, journal = {Trends in Genetics}, keywords = {Genetics}, number = {10}, pages = {503--510}, publisher = {Elsevier BV}, title = {{Packaging the male germline in plants}}, doi = {10.1016/j.tig.2007.08.005}, volume = {23}, year = {2007}, } @article{876, abstract = {Alternative splicing is thought to be a major source of functional diversity in animal proteins. We analyzed the evolutionary conservation of proteins encoded by alternatively spliced genes and predicted the ancestral state for 73 cases of alternative splicing (25 insertions and 48 deletions). The amino acid sequences of most of the inserts in proteins produced by alternative splicing are as conserved as the surrounding sequences. Thus, alternative splicing often creates novel isoforms by the insertion of new, functional protein sequences that probably originated from noncoding sequences of introns.}, author = {Kondrashov, Fyodor and Koonin, Eugene}, issn = {1362-4555}, journal = {Trends in Genetics}, number = {3}, pages = {115 -- 119}, publisher = {Elsevier}, title = {{Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences}}, doi = {10.1016/S0168-9525(02)00029-X}, volume = {19}, year = {2003}, }