The pattern of molecular evolution varies among gene sites and genes in a genome. By taking into account the complex heterogeneity of evolutionary processes among sites in a genome, Bayesian infinite ...mixture models of genomic evolution enable robust phylogenetic inference. With large modern data sets, however, the computational burden of Markov chain Monte Carlo sampling techniques becomes prohibitive. Here, we have developed a variational Bayesian procedure to speed up the widely used PhyloBayes MPI program, which deals with the heterogeneity of amino acid profiles. Rather than sampling from the posterior distribution, the procedure approximates the (unknown) posterior distribution using a manageable distribution called the variational distribution. The parameters in the variational distribution are estimated by minimizing Kullback-Leibler divergence. To examine performance, we analyzed three empirical data sets consisting of mitochondrial, plastid-encoded, and nuclear proteins. Our variational method accurately approximated the Bayesian inference of phylogenetic tree, mixture proportions, and the amino acid propensity of each component of the mixture while using orders of magnitude less computational time.
Life history and behavioral traits are often difficult to discern from the fossil record, but evolutionary rates of genes and their changes over time can be inferred from extant genomic data. Under ...the neutral theory, molecular evolutionary rate is a product of mutation rate and the proportion of neutral mutations 1, 2. Mutation rates may be shared across the genome, whereas proportions of neutral mutations vary among genes because functional constraints vary. By analyzing evolutionary rates of 1,185 genes in a phylogeny of 89 mammals, we extracted historical profiles of functional constraints on these rates in the form of gene-branch interactions. By applying a novel statistical approach to these profiles, we reconstructed the history of ten discrete traits related to activity, diet, and social behaviors. Our results indicate that the ancestor of placental mammals was solitary, seasonally breeding, insectivorous, and likely nocturnal. The results suggest placental diversification began 10–20 million years before the K-Pg boundary (66 million years ago), with some ancestors of extant placental mammals becoming diurnal and adapted to different diets. However, from the Paleocene to the Eocene-Oligocene transition (EOT, 33.9 mya), we detect a post-K-Pg nocturnal bottleneck where all ancestral lineages of extant placentals were nocturnal. Although diurnal placentals may have existed during the elevated global temperatures of the Paleocene-Eocene thermal maximum 3, we hypothesize that diurnal placentals were selectively extirpated during or after the global cooling of the EOT, whereas some nocturnal lineages survived due to preadaptations to cold environments 4.
•Rates of molecular evolution enable reconstructing states of life history traits•The ancestor of placentals was solitary, seasonally breeding, and insectivorous•All ancestors of extant placentals underwent a post-K-Pg nocturnal bottleneck
Using a novel rate-based method of reconstructing ancestral states, Wu et al. find that the ancestor of placental mammals was solitary, seasonally breeding, insectivorous, and likely nocturnal. All ancestral lineages of extant placentals were nocturnal from the Paleocene to the Eocene-Oligocene transition (EOT, 33.9 mya).
The release of artificially produced juveniles is a popular tool in fishery management, with more than 26 billion seeds of 180 marine species released annually into the wild in more than 20 ...countries. Despite this, there is a lack of research on, and monitoring of, the effects of such stocking efforts in most programs. We aim to improve assessments of the effectiveness of marine stock enhancement and sea-ranching programs using a novel computer program to estimate stocking effectiveness based on a two-stage sampling strategy of fishery landings. We revisit our two-stage sampling method published in 1992 and briefly summarize the estimation procedure using standard literature notations. As an example, we estimate commercial landings of released Japanese flounder (Paralichthys olivaceus), the contribution of released seeds to total commercial landings, and their recapture rate. Contour lines of predicted standard errors of landings and the optimal number of days within survey budget constraints required to sample fish landings per market are estimated. Our method can be applied to any species and case involving two-stage sampling, where all released seeds are marked or tagged, including genetically marked individuals. If the number of individuals that have been released in a sample is known, the stocking effectiveness can be determined with an R script. This program can also be used to determine the optimal sampling strategy.
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•Surveying commercial landings at fish markets is the most reliable method to evaluate stocking effectiveness.•Two-stage sampling of fish markets and survey days is commonly used.•An R script is presented to operationalize two-stage sampling framework.•The method can be generally applied in any instance involving two-stage sampling.
Recent studies on evolutionarily distant viral groups have shown that the number of viral genomes that establish cell infection after cell-to-cell transmission is unexpectedly small (1-20 genomes). ...This aspect of viral infection appears to be important for the adaptation and survival of viruses. To clarify how the number of viral genomes that establish cell infection is determined, we developed a simulation model of cell infection for tomato mosaic virus (ToMV), a positive-strand RNA virus. The model showed that stochastic processes that govern the replication or degradation of individual genomes result in the infection by a small number of genomes, while a large number of infectious genomes are introduced in the cell. It also predicted two interesting characteristics regarding cell infection patterns: stochastic variation among cells in the number of viral genomes that establish infection and stochastic inequality in the accumulation of their progenies in each cell. Both characteristics were validated experimentally by inoculating tobacco cells with a library of nucleotide sequence-tagged ToMV and analyzing the viral genomes that accumulated in each cell using a high-throughput sequencer. An additional simulation model revealed that these two characteristics enhance selection during tissue infection. The cell infection model also predicted a mechanism that enhances selection at the cellular level: a small difference in the replication abilities of coinfected variants results in a large difference in individual accumulation via the multiple-round formation of the replication complex (i.e., the replication machinery). Importantly, this predicted effect was observed in vivo. The cell infection model was robust to changes in the parameter values, suggesting that other viruses could adopt similar adaptation mechanisms. Taken together, these data reveal a comprehensive picture of viral infection processes including replication, cell-to-cell transmission, and evolution, which are based on the stochastic behavior of the viral genome molecules in each cell.
Genetic stock identification (GSI) is a major management tool of Pacific salmon (Oncorhynchus Spp.) that has provided rich genetic baseline data of allozymes, microsatellites, and single‐nucleotide ...polymorphisms (SNPs) across the Pacific Rim. Here, we analyzed published data sets for adult chum salmon (Oncorhynchus keta), namely 10 microsatellites, 53 SNPs, and a mitochondrial DNA locus (mtDNA3, control region, and NADH‐3 combined) in samples from 495 locations in the same distribution range (n = 61,813). TreeMix analysis of the microsatellite loci identified the greatest convergence toward Japanese/Korean populations and suggested two admixture events from Japan/Korea to Russia and the Alaskan Peninsula. The SNPs had been purposively collected from rapidly evolving genes to increase the power of GSI. The largest expected heterozygosity was observed in Japanese/Korean populations for microsatellites, whereas it was largest in Western Alaskan populations for SNPs, reflecting the SNP discovery process. A regression of SNP population structures on those of microsatellites indicated the selection of the SNP loci according to deviations from the predicted structures. Specifically, we matched the sampling locations of the SNPs with those of the microsatellites and performed regression analyses of SNP allele frequencies on a 2‐dimensional scaling (MDS) of matched locations obtained from microsatellite pairwise FST values. The MDS first axis indicated a latitudinal cline in American and Russian populations, whereas the second axis showed differentiation of Japanese/Korean populations. The top five outlier SNPs included mtDNA3, U502241 (unknown), GnRH373, ras1362, and TCP178, which were identified by principal component analysis. We summarized the functions of 53 nuclear genes surrounding SNPs and the mtDNA3 locus by referring to a gene database system and propose how they may influence the fitness of chum salmon.
By regressing the SNP population structures on those of the microsatellites, we estimated the selection on the SNP loci according to deviations from the predicted structures. The top five outlier SNPs were mtDNA3 (control region and NADH‐3 combined), U502241 (unknown), GnRH373, ras1362, and TCP178, which significantly differentiated in Japanese/Korean populations. The functions of the outlier SNPs related to fitness, namely endurance exercise training, oxygen consumption, reproduction, and growth.
Release of captively-bred individuals into the wild is one of the most popular tools in fisheries, forestry, and wildlife management, and introgression of hatchery-reared animals into wild ...populations is of global concern. However, research and monitoring of impacts on wild populations are generally lacking, and the benefit of hatcheries for long-term fisheries and conservation goals is unclear. Using spatio-temporal genetic monitoring and a four-dacade time series of catch data, we quantified the effects on the size and genetic diversity of wild populations of one of the world's largest marine stock enhancement programs-the red sea bream (Pagrus major) in Kagoshima Bay, Japan. Our analyses found that the stock enhancement program reduced genetic diversity of the population, but the genetic effect diminished with increased size of the wild population. Increases to the seaweed communities and reduced fishing efforts were the primary factors associated with the wild population recovery; effects of aquaculture were much smaller. Our results represent crucial evidence that hatcheries for enhancement and conservation of populations cannot be successful over the long term unless sufficient efforts are also made to reduce harvest rates and rehabilitate natural habitats.
An empirical Bayes (EB) pairwise FST estimator was previously introduced and evaluated for its performance by numerical simulation. In this study, we conducted coalescent simulations and generated ...genetic population structure mechanistically, and compared the performance of the EBFST with Nei's GST, Nei and Chesser's bias‐corrected GST (GST_NC), Weir and Cockerham's θ (θWC) and θ with finite sample correction (θWC_F). We also introduced EB estimators for Hedrick’ G’ST and Jost’ D. We applied these estimators to publicly available SNP genotypes of Atlantic herring. We also examined the power to detect the environmental factors causing the population structure. Our coalescent simulations revealed that the finite sample correction of θWC is necessary to assess population structure using pairwise FST values. For microsatellite markers, EBFST performed the best among the present estimators regarding both bias and precision under high gene flow scenarios (FST≤0.032). For 300 SNPs, EBFST had the highest precision in all cases, but the bias was negative and greater than those for GST_NC and θWC_F in all cases. GST_NC and θWC_F performed very similarly at all levels of FST. As the number of loci increased up to 10 000, the precision of GST_NC and θWC_F became slightly better than for EBFST for cases with FST≥0.004, even though the size of the bias remained constant. The EB estimators described the fine‐scale population structure of the herring and revealed that ~56% of the genetic differentiation was caused by sea surface temperature and salinity. The R package finepop for implementing all estimators used here is available on CRAN.
The question of why we age and finally die has been a central subject in the life, medical, and health sciences. Many aging theories have proposed biomarkers that are related to aging. However, they ...do not have sufficient power to predict the aging process and longevity. We here propose a new biomarker of human aging based on the mass‐specific basal metabolic rate (msBMR). It is well known by the Harris–Benedict equation that the msBMR declines with age but varies among individual persons. We tried to renormalize the msBMR by primarily incorporating the body mass index into this equation. The renormalized msBMR (RmsBMR) which was derived in one cohort of American men (n = 25,425) was identified as one of the best biomarkers of aging, because it could well reproduce the observed respective American, Italian, and Japanese data on the mortality rate and survival curve. A recently observed plateau of the mortality rate in centenarians corresponded to the lowest value (threshold) of the RmsBMR, which stands for the final stage of human life. A universal decline of the RmsBMR with age was associated with the mitochondrial number decay, which was caused by a slight fluctuation of the dynamic fusion/fission system. This decay form was observed by the measurement in mice. Finally, the present approach explained the reason why the BMR in mammals is regulated by the empirical algometric scaling law.
This theory started with the age dependency of the mass‐specific basal metabolic rate (msBMR) given by the Harris–Benedict equation. We removed the msBMR variation among individuals with a same age and obtained a universal msBMR function F(T) to reproduce the observed mortality rate and survival curve. The function F(T) was based on an exponential decay of the mitochondrial number in the standard cell with age. The theory also gave a theoretical basis to the allometric scaling law in mammals.
As one of the most successful group of organisms, mammals occupy a variety of niches on Earth as a result of macroevolution. Transcription factors (TFs), the fundamental regulators of gene ...expression, may also have evolved. To examine the relationship between TFs and mammalian macroevolution, we analyzed 140,821 de novo-identified TFs and their birth and death histories from 96 mammalian species. Gene tree vs. species tree reconciliation revealed that placental mammals experienced an upsurge in TF losses around 100 million years ago (Mya) and also near the Cretaceous–Paleogene boundary (K–Pg boundary, 66 Mya). Early Euarchontoglires, Laurasiatheria and marsupials appeared between 100 and 95 Mya and underwent initial diversification. The K-Pg boundary was associated with the massive extinction of dinosaurs, which lead to adaptive radiation of mammals. Surprisingly, TF loss decelerated, rather than accelerated, molecular evolutionary rates of their target genes. As the rate of molecular evolution is affected by the mutation rate, the proportion of neutral mutations and the population size, the decrease in molecular evolution may reflect increased functional constraints to survive target genes.
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