scholarly journals Molecular evolution of non-fertilizing sperm in Lepidoptera suggests minimal direct involvement in sperm competition

2018 ◽  
Author(s):  
Andrew J. Mongue ◽  
Megan E. Hansen ◽  
Liuqi Gu ◽  
Clyde E. Sorenson ◽  
James R. Walters
Keyword(s):  
Molecular Evolution ◽  
Sperm Competition ◽  
Population Genetic ◽  
Purifying Selection ◽  
Monarch Butterfly ◽  
Adaptive Significance ◽  
Sperm Proteins ◽  
Synonymous Polymorphism ◽  
Molecular Framework ◽  
Population Genetic Analyses

AbstractSperm are among the most variable cells in nature. Some of this variation results from non-adaptive errors in spermatogenesis, but many species consistently produce multiple sperm morphs, the adaptive significance of which remains unknown. Here, we investigate the evolution of dimorphic sperm in Lepidoptera, the butterflies and moths. Males of this order produce both fertilizing sperm and a secondary, non-fertilizing type that lacks DNA. Previous organismal studies suggested a role for non-fertilizing sperm in sperm competition, but this hypothesis has never been evaluated from a molecular framework. We combined published datasets with new sequencing in two species, the monandrous Carolina sphinx moth and the highly polyandrous monarch butterfly. Based on population genetic analyses, we see evidence for increased adaptive evolution in fertilizing sperm, but only in the polyandrous species. This signal comes primarily from a decrease in non-synonymous polymorphism in sperm proteins compared to the rest of the genome, suggesting stronger purifying selection, consistent with selection via sperm competition. Non-fertilizing sperm proteins, in contrast, do not show an effect of mating system and do not appear to evolve differently from the background genome in either species, arguing against the involvement of non-fertilizing sperm in direct sperm competition. Based on our results and previous work, we suggest that non-fertilizing sperm may be used to delay female remating in these insects and decrease the risk of sperm competition rather than directly affect its outcome.

scholarly journals No evidence for intermolecular recombination in human fibroblast and blood mtDNA from individuals with biparental mtDNA transmission

2020 ◽  
Author(s):  
Baoheng Gui ◽  
Zeyu Yang ◽  
Shiyu Luo ◽  
Jesse Slone ◽  
Sushma Nagaraj ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Single Molecule ◽  
Population Genetic ◽  
Genetic Recombination ◽  
Phylogenetic Reconstruction ◽  
Sequencing Technology ◽  
Single Nucleotide ◽  
Genetic Analyses ◽  
Human Mitochondrial Genome ◽  
Population Genetic Analyses

AbstractStrictly maternal inheritance and lack of intermolecular recombination of the human mitochondrial genome (mtDNA) are the assumed preconditions for molecular evolution studies, phylogenetic reconstruction and population genetic analyses. This hypothesis, however, has been challenged by investigations providing evidence for genetic recombination of mtDNA, thus sparking controversy. Using single-molecule real-time (SMRT) sequencing technology, we sequenced the entire mtDNA from blood and fibroblast cells from five individuals with biparental mtDNA transmission in three separate, multiple-generation families. After phasing the single nucleotide polymorphism (SNP) genotypes of mtDNA, no intermolecular recombination between paternal and maternal mtDNA was found when the mtDNA was transmitted in either biparental or maternal mode. Our study provides support for the argument that intermolecular mtDNA recombination is absent or extremely rare in humans. As a consequence, these results support the feasibility of mtDNA-based molecular evolution studies and phylogenetic and population genetic analyses for humans, while also avoiding inaccurate phylogenetic inferences and incorrect rejection of the molecular clock.

scholarly journals Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences

2008 ◽  
Vol 363 (1512) ◽  
pp. 3931-3939 ◽  
Author(s):  
Sang Chul Choi ◽  
Benjamin D Redelings ◽  
Jeffrey L Thorne
Keyword(s):  
Molecular Evolution ◽  
Markov Model ◽  
Stationary Distribution ◽  
Population Genetic ◽  
Amino Acid Level ◽  
Protein Sequences ◽  
Relative Fitness ◽  
Evolutionary Models ◽  
Effective Population ◽  
Stationary Distributions

Models of molecular evolution tend to be overly simplistic caricatures of biology that are prone to assigning high probabilities to biologically implausible DNA or protein sequences. Here, we explore how to construct time-reversible evolutionary models that yield stationary distributions of sequences that match given target distributions. By adopting comparatively realistic target distributions, evolutionary models can be improved. Instead of focusing on estimating parameters, we concentrate on the population genetic implications of these models. Specifically, we obtain estimates of the product of effective population size and relative fitness difference of alleles. The approach is illustrated with two applications to protein-coding DNA. In the first, a codon-based evolutionary model yields a stationary distribution of sequences, which, when the sequences are translated, matches a variable-length Markov model trained on human proteins. In the second, we introduce an insertion–deletion model that describes selectively neutral evolutionary changes to DNA. We then show how to modify the neutral model so that its stationary distribution at the amino acid level can match a profile hidden Markov model, such as the one associated with the Pfam database.

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