When bacterial symbionts become associated with their hosts, their genomes are thought to decay inexorably towards an organelle-like fate due to decreased recombination and inefficient selection. Despite extensive theoretical treatment, no empirical study thus far has connected these underlying population genetic processes with long-term evolutionary outcomes. By sampling marine endosymbionts that range from primarily vertical to strictly horizontal transmission, we tested this canonical theory....
Sat Aug 31, 2019 03:00
The wild currant tomato Solanum pimpinellifolium inhabits a wide range of abiotic habitats across its native range of Ecuador and Peru. Although it has served as a key genetic resource for the improvement of domestic cultivars, little is known about the genetic basis of traits underlying local adaptation in this species, nor what abiotic variables are most important for driving differentiation. Here we use redundancy analysis (RDA) and other multivariate statistical methods (structural equation modeling...
Sat Aug 31, 2019 03:00
Abalones, turban snails, top snails, keyhole limpets and slit shells are just some of the diverse marine Vetigastropoda. With major lineages having ancient divergences in the Paleozoic Era, basal nodes in the phylogeny have been largely unresolved. Here we present the first genomic-scale dataset focused on vetigastropods, including a comprehensive sampling of taxa with all superfamilies and about half of the extant families (41 new transcriptomes, 49 total ingroup terminals). Our recovered topology...
Sat Aug 31, 2019 03:00
High mutation rates select for the evolution of mutational robustness where populations inhabit flat fitness peaks with little epistasis, protecting them from a mutational meltdown. Recent evidence suggests that a different effect protects small populations from extinction via the accumulation of deleterious mutations. In drift robustness, populations tend to occupy peaks with steep flanks and positive epistasis between mutations. However, it is not known what happens when mutation rates are high...
Sat Aug 31, 2019 03:00
Adaptation is mediated by phenotypic traits that are often near continuous, and undergo selective pressures that may change with the environment. The dynamics of allelic frequencies at underlying quantitative trait loci (QTL) depend on their own phenotypic effects, but also possibly on other polymorphic loci affecting the same trait, and on environmental change driving phenotypic selection. Most environments include a substantial component of random noise, characterized by both its magnitude and...
Sat Aug 31, 2019 03:00
Ribosomal proteins (RPs) genes encode structure components of ribosomes, the cellular machinery for protein synthesis. A single functional copy has been maintained in most of 78-80 RP families in animals due to evolutionary constraints imposed by gene dosage balance. Some fungal species have maintained duplicate copies in most RP families. How the RP genes were duplicated and maintained in these fungal species, and their functional significance remains unresolved. To address these questions, we identified...
Sat Aug 31, 2019 03:00
In recent years, genome-scan methods have been extensively used to detect signatures of selection and introgression. Here, we compare the latest genome-scan methods with non-parametric k-nearest neighbors (kNN) anomaly detection algorithms, while incorporating pairwise Fixation Index (FST) estimates and pairwise nucleotide differences (dxy) as features. Simulations were performed for both positive directional selection and introgression, with varying parameters, such as recombination rates, population...
Sat Aug 31, 2019 03:00
Plant self-incompatibility (SI) is a genetic system that prevents selfing and enforces outcrossing. Because of strong balancing selection, the genes encoding SI are predicted to maintain extraordinary high levels of polymorphism, both in terms of the number of S-alleles that segregate in SI species and in terms of nucleotide sequence divergence among distinct S-allelic lines. However, because of these two combined features, documenting polymorphism of these genes also presents important methodological...
Sat Aug 31, 2019 03:00
One important question in aging research is how differences in genomics and transcriptomics determine maximum lifespan in various species. Despite recent progress, much is still unclear on the topic, partly due to the lack of samples in non-model organisms and due to challenges in direct comparisons of transcriptomes from different species. The novel ranking-based method that we employ here is used to analyze gene expression in the gray whale and compare its de novo assembled transcriptome with that...
Sun Sep 01, 2019 03:00
Staurozoa is an intriguing lineage of cnidarians bearing both polypoid and medusoid characters in the adult body plan. Miranda et al. (2016) recently provided a massive descriptive effort of specimen collection, sequencing, and character evolution. We recently described the neuromusculature of two staurozoan species: Manania handi and Haliclystus "sanjuanensis." We found that our M. handi samples genetically matched Manania gwilliami samples used in Miranda et al. (2016). Taking advantage of newly-deposited...
Sun Sep 01, 2019 03:00
The most recent version of this paper has been removed owing to copyright violation. Earlier versions of the paper remain available.
Sun Sep 01, 2019 03:00
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