Published in Molecular biology and evolution
Mitochondrial DNA (mtDNA) is a universal hallmark of aerobic eukaryotes. That is why the recent suggestion by John et al. (2019) that the aerobic dinoflagellate Amoebophrya sp. strain AT5 (Syndiniales) lacks mtDNA was so remarkable. Here, by reanalysing recently published genomic and transcriptomic data from three Amoebophrya strains, we provide ev...
Published in Molecular biology and evolution
Horizontal gene transfer (HGT) is central to prokaryotic evolution. However, little is known about the "scale" of individual HGT events. In this work, we introduce the first computational framework to help answer the following fundamental question: How often does more than one gene get horizontally transferred in a single HGT event? Our method, cal...
Published in Molecular biology and evolution
Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with LBA artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despit...
Published in Molecular biology and evolution
Recent pangenome studies have revealed a large fraction of the gene content within a species exhibits presence-absence variation (PAV). However, coding regions alone provide an incomplete assessment of functional genomic sequence variation at the species level. Little to no attention has been paid to noncoding regulatory regions in pangenome studie...
Published in Molecular biology and evolution
Rhodopsin, the light-sensitive visual pigment expressed in rod photoreceptors, is specialized for vision in dim light environments. Aquatic environments are particularly challenging for vision due to the spectrally-dependent attenuation of light, which can differ greatly in marine and freshwater systems. Among fish lineages that have successfully c...
Published in Molecular biology and evolution
Prions, proteins that can convert between structurally and functionally distinct states and serve as non-Mendelian mechanisms of inheritance, were initially discovered and only known in eukaryotes, and consequently considered to likely be a relatively late evolutionary acquisition. However, the recent discovery of prions in bacteria and viruses has...
Published in Molecular biology and evolution
dadi is a popular but computationally intensive program for inferring models of demographic history and natural selection from population genetic data. I show that running dadi on a Graphics Processing Unit can dramatically speed computation compared to the CPU implementation, with minimal user burden. Motivated by this speed increase, I also exten...
Published in Molecular biology and evolution
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, we contrast populations of the European sub-species Arabidopsis lyrata ssp petraea, which expanded its Norther...
Published in Molecular biology and evolution
Evolutionarily young genes are usually preferentially expressed in the testis across species. While it is known that older genes are generally more broadly expressed than younger genes, the properties that shaped this pattern are unknown. Older genes may gain expression across other tissues uniformly, or faster in certain tissues than others. Using...
Published in Molecular biology and evolution
India represents an intricate tapestry of population substructure shaped by geography, language, culture and social stratification. While geography closely correlates with genetic structure in other parts of the world, the strict endogamy imposed by the Indian caste system and the large number of spoken languages add further levels of complexity to...
