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The Arabidopsis thaliana population has been exposed to unexperienced biotic and abiotic stresses as a result of range expansion or environmental change. To obtain a global picture of the genetic adaptations in the population history of A. thaliana, we constructed a database of the phenotypic-adaptations (p-adaptations) and gene expression-adaptations (e-adaptations). We analysed the dynamics of the allele frequencies at the 23,880 QTLs of 174 traits and 8,618 eQTLs of 1,829 genes with respect to the total SNPs in the genomes, and identified 650 p-adaptations and 3,925 e-adaptations (FDR=0.05). The population underwent large scale p-adaptations and e-adaptations along four lineages, the eastward migration to Central Asia and South Siberia, Russia, the northward migration to Sweden, the migration to Azerbaijan, and the migration of the German population to the United States. Extremely cold winters and short summers prolonged seed dormancy, and expanded the root system architecture. Low temperatures prolonged the growing season and low light intensity required the increased chloroplast activity. The subtropical and humid environment enhanced phytohormone signaling pathways in response to the biotic and abiotic stresses. Exposure to heavy metals selected for alleles underlying low heavy metal uptake from soil, lower growth rate, lower resistance to bacteria, and higher expression of photosynthetic genes were selected. The database of p-adaptations and e-adaptations, which complements studies focusing on specific aspects of adaptation, may be useful for future studies to understand the biological adaptations of A. thaliana throughout its population history.

It is unknown what determines genetic diversity and how genetic diversity is associated with various biological traits. In this work, we provide insight into these issues. By comparing genetic variation of 14,671 mammalian gene trees with thousands of individual human, chimpanzee, gorilla, mouse, and dog/wolf genomes, we found that intraspecific genetic diversity can be predicted by long-term molecular evolutionary rates rather than de novo mutation rates. This relationship was established during the early stage of mammalian evolution. Moreover, we developed a method to detect fluctuations of species-specific selection on genes based on the deviations of intraspecific genetic diversity predicted from long-term rates. We showed that the evolution of epithelial cells, rather than connective tissue, mainly contributed to morphological evolution of different species. For humans, evolution of the immune system and selective sweeps caused by infectious diseases are the most representative examples of adaptive evolution.

During the process of range expansion, populations encounter a variety of environments. They respond to the local environments by modifying their mutually interacting traits. Common approaches of landscape analysis include first focusing on the genes that undergo diversifying selection or directional selection in response to environmental variation. To understand the whole history of populations, it is ideal to capture the history of their range expansion with reference to the series of surrounding environments and to infer the multitrait coadaptation. To this end, we propose a complementary approach; it is an exploratory analysis using up-to-date methods that integrate population genetic features and features of selection on multiple traits. First, we conduct correspondence analysis of site frequency spectra, traits, and environments with auxiliary information of population-specific fixation index (FST). This visualizes the structure and the ages of populations and helps infer the history of range expansion, encountered environmental changes, and selection on multiple traits. Next, we further investigate the inferred history using an admixture graph that describes the population split and admixture. Finally, principal component analysis of the selection on edge-by-trait (SET) matrix identifies multitrait coadaptation and the associated edges of the admixture graph. We introduce a newly defined factor loadings of environmental variables in order to identify the environmental factors that caused the coadaptation. A numerical simulation of one-dimensional stepping-stone population expansion showed that the exploratory analysis reconstructed the pattern of the environmental selection that was missed by analysis of individual traits. Analysis of a public dataset of natural populations of black cottonwood in northwestern America identified the first principal component (PC) coadaptation of photosynthesis- vs growth-related traits responding to the geographical clines of temperature and day length. The second PC coadaptation of volume-related traits suggested that soil condition was a limiting factor for aboveground environmental selection.

During the history of range expansion, the populations encounter with variety of environments. They respond to the local environments by modifying the mutually interacting traits. Therefore, to understand the whole life history of the populations, it is ideal to capture the history of their range expansion with reference to the series of surrounding environments and to infer the coadaptation of the multiple traits. Toward this end, we provide an exploratory analysis based on the features of populations: site frequency spectra of populations, population-specific FST, association between genes and environments, positive selections on traits mapped on the admixture graph, and GWAS results. Correspondence analysis of genes, environments, and traits provides a bird’s-eye view of the history of population differentiation and range expansion and various types of environmental selections at the times. Principal component analysis of the estimated trait-specific polygenic adaptations mapped on the admixture graph enables to understand the coadaptation of multiple traits. The potential usefulness was confirmed by analyzing a public dataset of wild poplar in northwestern America. In response to the northern cold temperature and longer daylength, the populations increased the photosynthetic activity and nutrient use efficiency at the expense of the risk of pathogen invasion, and in response to warm temperature, they increased the growth. At higher altitude, they shifted the maximum activity to earlier period in spring to reduce the activity in dry summer. The R codes for our representation method and simulations of population colonization used in this study are available as supplementary script.

A recommendation of: Meline Saubin, Stephane De Mita, Xujia Zhu, Bruno Sudret, Fabien Halkett Impact of ploidy and pathogen life cycle on resistance durability https://doi.org/10.1101/2021.05.28.446112

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.

Phylogenetic trees based on multiple genomic loci enable us to estimate the evolution of functional constraints that operate on genes based on lineage-specific fluctuation of the evolutionary rate at particular gene loci, “gene–branch interactions”. Using this information as predictors, our previous work inferred that the common ancestor of placental mammals was nocturnal, insectivorous, solitary, and bred seasonally. Here, we added seven new continuous traits including lifespan, bodyweight, and five reproduction-related traits and inferred the coevolution network of 14 core life history traits for 89 mammals. In this network, bodyweight and lifespan are not directly connected to each other, instead, their correlation is due to both of them coevolving with gestation period. Diurnal mammals are more likely to be monogamous than nocturnal mammals, while arboreal mammals tend to have a smaller litter size than terrestrial mammals. Coevolution between diet and the seasonal breeding behavior test shows that year-round breeding preceded the dietary change to omnivory, while seasonal breeding preceded the dietary change to carnivory. We also discuss the evolution of reproductive strategy of mammals. Genes selected as predictors were identified as well, for example, genes function as tumor suppressor were selected as predictors of weaning age.

Background: Random forest (RF) captures complex feature patterns that differentiate groups of samples and is rapidly being adopted in microbiome studies. However, a major challenge is the high dimensionality of microbiome datasets. They include thousands of species or molecular functions of particular biological interest. This high dimensionality significantly reduces the power of random forest approaches for identifying true differences. The widely used Boruta algorithm iteratively removes features that are proved by a statistical test to be less relevant than random probes. Result: We developed a massively parallel forward variable selection algorithm and coupled it with the RF classifier to maximize the predictive performance. The forward variable selection algorithm adds new variable to a set of selected variables as far as the prespecified criterion of predictive power is improved. At each step, the parameters of random forest are optimized. We demonstrated the performance of the proposed approach, which we named RF-FVS, by analyzing two published datasets from large-scale case-control studies: (i) 16S rRNA gene amplicon data for Clostridioides difficile infection (CDI) and (ii) shotgun metagenomics data for human colorectal cancer (CRC). The RF-FVS approach further screened the variables that the Boruta algorithm left and improved the accuracy of the random forest classifier from 81% to 99.01% for CDI and from 75.14% to 90.17% for CRC. Conclusion: Valid variable selection is essential for the analysis of high-dimensional microbiota data. By adopting the Boruta algorithm for pre-screening of the variables, our proposed RF-FVS approach improves the accuracy of random forest significantly with minimum increase of computational burden. The procedure can be used to identify the functional profiles that differentiate samples between different conditions.

As one of the most successful categories of organisms, mammals occupy a variety of niches on earth as a result of macroevolution. Transcription factors (TFs), the basic regulators of gene expression, may also evolve during mammalian phenotypic diversification and macroevolution. 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 mammals experienced an upsurge in TF losses around 100 million years ago and also near the K–Pg boundary, thus implying a relationship with the divergence of placental animals. From approximately 100 million years ago to the present, losses dominated TF events without a significant change in TF gains. To quantify the effects of this TF pruning on mammalian macroevolution, we analyzed rates of molecular evolution and expression profiles of regulated target genes. Surprisingly, TF loss decelerated, rather than accelerated, molecular evolutionary rates of their target genes, suggesting increased functional constraints. Furthermore, an association study revealed that massive TF losses are significantly positively correlated with solitary behavior, nocturnality, reproductive-seasonality and insectivory life history traits, possibly through rewiring of regulatory networks.

BackgroundRandom forest (RF) captures complex feature patterns that differentiate groups of samples and is rapidly being adopted in microbiome studies. However, a major challenge is the high dimensionality of microbiome datasets. They include thousands of species or molecular functions of particular biological interest. This high dimensionality significantly reduces the power of random forest approaches for identifying true differences. The widely used Boruta algorithm iteratively removes features that are proved by a statistical test to be less relevant than random probes.ResultWe developed a massively parallel forward variable selection algorithm and coupled it with the RF classifier to maximize the predictive performance. The forward variable selection algorithm adds new variable to a set of selected variables as far as the prespecified criterion of predictive power is improved. At each step, the parameters of random forest are optimized. We demonstrated the performance of the proposed approach, which we named RF-FVS, by analyzing two published datasets from large-scale case-control studies: (i) 16S rRNA gene amplicon data for Clostridioides difficile infection (CDI) and (ii) shotgun metagenomics data for human colorectal cancer (CRC). The RF-FVS approach further screened the variables that the Boruta algorithm left and improved the accuracy of the random forest classifier from 81% to 99.01% for CDI and from 75.14% to 90.17% for CRC.ConclusionValid variable selection is essential for the analysis of high-dimensional microbiota data. By adopting the Boruta algorithm for pre-screening of the variables, our proposed RF-FVS approach improves the accuracy of random forest significantly with minimum increase of computational burden. The procedure can be used to identify the functional profiles that differentiate samples between different conditions.

The Japanese archipelago is located at the periphery of the continent of Asia. Rivers in the Japanese archipelago, separated from the continent of Asia about 17 Ma, have experienced an intermittent exchange of freshwater fish taxa through a narrow land bridge generated by lowered sea level. As the Korean Peninsula and Japanese archipelago were not covered by an ice sheet during glacial periods, phylogeographical analyses in this region can trace the history of biota for a long time beyond the last glacial maximum. In this study, we analyzed the phylogeography of four freshwater fish taxa,Hemibarbus longirostris, dark chubNipponocypris temminckii, Tanakiassp. andCarassiusssp., whose distributions include both the Korean Peninsula and western Japan. We found for each taxon that a small component of diverse Korean clades of freshwater fishes migrated in waves into the Japanese archipelago to form the current phylogeographic structure of biota. Indigenous populations were replaced by succeeding migrants. We refer to this phenomenon as “waves out of the Korean Peninsula,” with parallels to “out of Africa” in humans.

Notwithstanding the rapid developments in sequencing techniques, Y and W sex chromosomes have still been mostly excluded from whole genome sequencing projects due to their high repetitive DNA content. Therefore, Y and W chromosomes are poorly described in most species despite their biological importance. Several methods were developed for identifying Y or W-linked sequences among unmapped scaffolds. However, it is not enough to discover functional regions from short unmapped scaffolds. Here, we provide a new and simple strategy based on k-mer comparison for comprehensive analysis of the W chromosome in Bombyx mori. Using this novel method, we effectively assembled de novo 1281 W-derived genome contigs (totaling 1.9 Mbp), and identified 156 W-linked transcript RNAs and 345 W-linked small RNAs. This method will help in the elucidation of mechanisms of sexual development and exploration of W chromosome biological functions, and provide insights into the evolution of sex chromosomes. Moreover, we showed this method can be employed in identifying heterogametic sex chromosomes (W and Y chromosomes) in many other species where genomic information is still scarce.

Most lepidopteran species are herbivores, and interaction with host plants affects their gene expression and behavior as well as their genome evolution. Gustatory receptors (Grs) are expected to mediate host plant selection, feeding, oviposition and courtship behavior. However, due to their high diversity, sequence divergence and extremely low level of expression it has been difficult to identify precisely a complete set of Grs in Lepidoptera. By manual annotation and BAC sequencing, we improved annotation of 43 gene sequences compared with previously reported Grs in the most studied lepidopteran model, the silkworm, Bombyx mori, and identified 7 new tandem copies of BmGr30 on chromosome 7, bringing the total number of BmGrs to 76. Among these, we mapped 68 genes to chromosomes in a newly constructed chromosome distribution map and 8 genes to scaffolds; we also found new evidence for large clusters of BmGrs, especially from the bitter receptor family. RNA-seq analysis of diverse BmGr expression patterns in chemosensory organs of larvae and adults enabled us to draw a precise organ specific map of BmGr expression. Interestingly, most of the clustered genes were expressed in the same tissues and more than half of the genes were expressed in larval maxillae, larval thoracic legs and adult legs. For example, BmGr63 showed high expression levels in all organs in both larval and adult stages. By contrast, some genes showed expression limited to specific developmental stages or organs and tissues. BmGr19 was highly expressed in larval chemosensory organs (especially antennae and thoracic legs), the single exon genes BmGr53 and BmGr67 were expressed exclusively in larval tissues, the BmGr27-BmGr31 gene cluster on chr7 displayed a high expression level limited to adult legs and the candidate CO2 receptor BmGr2 was highly expressed in adult antennae, where few other Grs were expressed. Transcriptional analysis of the Grs in B. mori provides a valuable new reference for finding genes involved in plant-insect interactions in Lepidoptera and establishing correlations between these genes and vital insect behaviors like host plant selection and courtship for mating. (C) 2017 The Author(s). Published by Elsevier Ltd.

Populations are shaped by their history. It is crucial to interpret population structure in an evolutionary context. PairwiseFSTmeasures population structure, whereas population-specificFSTmeasures deviation from the ancestral population. To understand the current population structure and a population’s history of range expansion, we propose a representation method that overlays population-specificFSTestimates on a sampling location map, and on an unrooted neighbor-joining tree and a multi-dimensional scaling plot inferred from a pairwiseFSTdistance matrix. We examined the usefulness of our procedure using simulations that mimicked population colonization from an ancestral population and by analyzing published human, Atlantic cod, and wild poplar data. Our results demonstrated that population-specificFSTvalues identify the source population and trace the evolutionary history of its derived populations. Conversely, pairwiseFSTvalues represent the current population structure. By integrating the results of both estimators, we obtained a new picture of the population structure that incorporates evolutionary history. The generalized least squares of genome-wide population-specificFSTindicated that the wild poplar population expanded its distribution to the north, where daylight hours are long in summer, to seashores with abundant rainfall, and to the south with dry summers. Genomic data highlight the power of the bias-corrected moment estimators ofFST, whether global, pairwise, or population-specific, that provide unbiased estimates ofFST. AllFSTmoment estimators described in this paper have reasonable process times and are useful in population genomics studies. The R codes for our method and simulations are available in the Supplemental Material.

What determines genetic diversity and how it connects to the various biological traits is unknown. In this work, we offer answers to these questions. By comparing genetic variation of 14,671 mammalian gene trees with thousands of individual genomes of human, chimpanzee, gorilla, mouse and dog/wolf, we found that intraspecific genetic diversity is determined by long-term molecular evolutionary rates, rather thande novomutation rates. This relationship was established during the early stage of mammalian evolution. Expanding this new finding, we developed a method to detect fluctuations of species-specific selection on genes as the deviations of intra-species genetic diversity predicted from long-term rates. We show that the evolution of epithelial cells, rather than of connective tissue, mainly contributes to morphological evolution of different species. For humans, evolution of the immune system and selective sweeps subjected by infectious diseases are most representative of adaptive evolution.

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.

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.

Summary The Palaeognathae comprise the flightless ratites and the volant tinamous, and together with the Neognathae constitute the extant members of class Aves. It is commonly believed that Palaeognathae originated in Gondwana since most of the living species are found in the Southern Hemisphere [1–3]. However, this hypothesis has been questioned because the fossil paleognaths are mostly from the Northern Hemisphere in their earliest time (Paleocene) and possessed many putative ancestral characters [4]. Uncertainties regarding the origin and evolution of Palaeognathae stem from the difficulty in estimating their divergence times [1, 2] and their remarkable morphological convergence. Here, we recovered nuclear genome fragments from extinct elephant birds, which enabled us to reconstruct a reliable phylogenomic time tree for the Palaeognathae. Based on the tree, we identified homoplasies in morphological traits of paleognaths and reconstructed their morphology-based phylogeny including fossil species without molecular data. In contrast to the prevailing theories, the fossil paleognaths from the Northern Hemisphere were placed as the basal lineages. Combined with our stable divergence time estimates that enabled a valid argument regarding the correlation with geological events, we propose a new evolutionary scenario that contradicts the traditional view. The ancestral Palaeognathae were volant, as estimated from their molecular evolutionary rates, and originated during the Late Cretaceous in the Northern Hemisphere. They migrated to the Southern Hemisphere and speciated explosively around the Cretaceous-Paleogene boundary. They then extended their distribution to the Gondwana-derived landmasses, such as New Zealand and Madagascar, by overseas dispersal. Gigantism subsequently occurred independently on each landmass.

Conformance proportion is a useful index in agricultural, biological, and environmental applications, which is defined as the proportion that a characteristic of interest falls in an acceptance region of a specification. In practice, however, the acceptance region may not be available when employing the regular conformance proportion. In this article, we propose a new index in which the acceptance region is obtained from a reference population. Furthermore, we develop approaches to constructing confidence limits for the proposed conformance proportion using the concept of a fiducial generalized pivotal quantity. We first consider the simple situation that the characteristic is assumed to be a univariate normal random variable. Then we extend it to the one-way random effects model. The proposed method is evaluated through simulation study and real data analysis. It is shown that our proposed new index and its statistical inference are easy to implement and reasonably satisfactory for most applications. Supplementary materials accompanying this paper appear on-line.

Mammals have variable numbers (1300&ndash, 2000) of transcription factors (TFs), but the reasons for this large variation are unclear. To investigate general TF patterns, we de novo identified 156,906 TFs from 96 mammalian species. We identified more than 500 human isolated TFs that are rarely reported in human TF-to-TF networks. Mutations in the genes of these TFs were less lethal than those of connected TFs. Consequently, these isolated TFs are more tolerant of changes and have become unique during speciation. They may also serve as a source of variation for TF evolution. Reconciliation of TF-family phylogenetic trees with a mammalian species tree revealed an average of 37.8% TF gains and 15.0% TF losses over 177 million years, which implies that isolated TFs are pervasive in mammals. Compared with non-TF interacting genes, TF-interacting genes have unique TF profiles and have higher expression levels in mice than in humans. Different expression levels of the same TF-interacting gene contribute to species-specific phenotypes. Formation and loss of isolated TFs enabling unique TF profiles may provide variable switches that adjust divergent expression profiles of target genes to generate species-specific phenotypes, thereby making species unique.

Reconstructing phylogenies has become a common task in comparative biology. It is however difficult to construct fully reliable phylogenies: trees estimated from different loci may differ and different genetic characters may support different phylogenies. Validation and robustness assessment are therefore critical. Here, we review sources of errors and uncertainties and introduce support values used to characterize weak and strong parts of the tree. We also show to construct robust consensus trees from a robust and how to detect outliers at either the loci or species level. Finally, we show how continuous distances on a tree space can be used to frame validation in a statistical setting.

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.

The giant rhinoceros beetles (Dynastini, Scarabaeidae, Coleoptera) are distributed in tropical and temperate regions in Asia, America and Africa. Recent molecular phylogenetic studies have revealed that the giant rhinoceros beetles can be divided into three clades representing Asia, America and Africa. Although a correlation between their evolution and the continental drift during the Pangean breakup was suggested, there is no accurate divergence time estimation among the three clades based on molecular data. Moreover, there is a long chronological gap between the timing of the Pangean breakup (Cretaceous: 110-148 Ma) and the emergence of the oldest fossil record (Oligocene: 33 Ma). In this study, we estimated their divergence times based on molecular data, using several combinations of fossil calibration sets, and obtained robust estimates. The inter-continental divergence events among the clades were estimated to have occurred about 99 Ma (Asian clade and others) and 78 Ma (American clade and African clade), both of which are after the Pangean breakup. These estimates suggest their inter-continental divergences occurred by overseas sweepstakes dispersal, rather than by vicariances of the population caused by the Pangean breakup.

The diversity of marine communities is in striking contrast with the diversity of terrestrial communities. In all oceans, species richness is low in tropical areas and high at latitudes between 20 and 40°. While species richness is a primary metric used in conservation and management strategies, it is important to take into account the complex phylogenetic patterns of species compositions within communities. We measured the phylogenetic skew and diversity of shark communities throughout the world. We found that shark communities in tropical seas were highly phylogenetically skewed, whereas temperate sea communities had phylogenetically diversified species compositions. Interestingly, although geographically distant from one another, tropical sea communities were all highly skewed toward requiem sharks (Carcharhinidae), hammerhead sharks (Sphyrnidae), and whale sharks (Rhincodon typus). Worldwide, the greatest phylogenetic evenness in terms of clades was found in the North Sea and coastal regions of countries in temperate zones, such as the United Kingdom, Ireland, southern Australia, and Chile. This study is the first to examine patterns of phylogenetic diversity of shark communities on a global scale. Our findings suggest that when establishing conservation activities, it is important to take full account of phylogenetic patterns of species composition and not solely use species richness as a target. Protecting areas of high phylogenetic diversity in sharks, which were identified in this study, could form a broader strategy for protecting other threatened marine species.

To assess the extent of improvement of rainfed rice production by using a participatory approach, we compared research project participants and non-participants (total of 206 rice-growing households) with regard to yield variability and their perspective on climate change at seven sites in Northeast Thailand. The participants were characterized by membership in local groups, an active learning attitude, and confidence in their farming. Compared to non-participants, the participants produced crops with higher yield and had more knowledge about the Intergovernmental Panel on Climate Change (IPCC) message and advanced farming technologies. Both groups had similar reactions to past climatic damage experiences, but the participants tended to have a more positive attitude about adaptation to climate change and mitigation by refraining from residual straw burning than the non-participants. The farmers’ attitude about adaptation to climate change was positively associated with their active learning and close relationship with researchers. There was a large yield gap between the bottom 10 percentile farmers (0.63 t/ha) and the top 10 percentile farmers (4.05 t/ha), with an average yield of 2.18 t/ha. Yield was associated with the level of market orientation, with the market-oriented farmers attaining higher yield, including yield from broadcast seeding (2.71 t/ha), than the subsistence farmers (1.66 t/ha). Our findings suggest that technical improvement of rice production in the region by using the participatory approach could be enhanced by selecting participants who are linked with local groups, tend to be market orientated, and are willing to learn with researchers.

Multidimensional diagnosis plays a central role in infant developmental care, which leads to the prediction of future disabilities. Information consolidated from objective and subjective, early and late, central and peripheral data may reveal neuro-pathological mechanisms and realize earlier and more precise preventive intervention. In the current study, we retrospectively searched correlating factors to the following neurological and behavioral development of 'Head Control' and 'Roll Over' using multivariate correlation analysis of differ-ent diagnostic domains over age, subject/object information of the patients who were previously admitted in our neonatal intensive care unit (NICU) and could be developmentally followed up in our outpatient clinic. Based on the hematologic and biochemical data, MRI brain anatomy during NICU hospitalization, we characterized all the acquired data distribution from 31 infants with either 'appeared neurologically normal (ANN, n = 21)’ or 'appeared neurologically abnormal (ANA, n = 10)’ pro tempore, with a physician's clinical judgment before discharge. Besides single factor comparisons between ANN and ANA, we examined their development difference by using the multidimensional information processing, principal component analysis (PCA). The diagnostic predictors of neuro-behavioral development were selected by regression analysis with variable selection. It resulted that hematological and brain anatomical factors seemed correlated to both ‘Head Control’ and ‘Roll Over’. This report suggested certain possibility of the cross-domain translational approach between subjective and objective developmental information through multivariate analyses, with candidate markers preliminarily to be evaluated in further studies.

Tooth agenesis is one of the most common congenital anomalies in humans. However, the etiology of tooth agenesis remains largely unclear, as well as evidence base useful for genetic counseling. Therefore, we estimated the prevalence and sibling recurrence risk, and investigated agenetic patterns systematically. Tooth agenesis was classified into two subtypes: hypodontia (one to five missing teeth) and oligodontia (six or more missing teeth). The prevalence of these two subtypes were 6.8% [95% confidence interval (CI): 6.1-7.7%] and 0.1% (95% CI: 0.04-0.3%), respectively, and sibling recurrence risk of these were 24.5% (95% CI: 13.8-38.3%) and 43.8% (95% CI: 26.4-62.3%), respectively. This result suggests that the severe phenotype, oligodontia, might be mostly transmitted in a dominant fashion. Using a simple statistical modeling approach, our data were found to be consistent with a bilateral symmetry model, meaning that there was equal probability of missing teeth from the right and left sides.

Recently, deep drilling into the seafloor has revealed that there are vast sedimentary ecosystems of diverse microorganisms, particularly archaea, in subsurface areas. We investigated the β diversity patterns of archaeal communities in sediment layers under the seafloor and their determinants. This study was accomplished by analyzing large environmental samples of 16S ribosomal RNA gene sequences and various geochemical data collected from a sediment core of 365.3 m, obtained by drilling into the seafloor off the east coast of the Shimokita Peninsula. To extract the maximum amount of information from these environmental samples, we first developed a method for measuring β diversity using sequence data by applying probability theory on a set of strings developed by two of the authors in a previous publication. We introduced an index of β diversity between sequence populations from which the sequence data were sampled. We then constructed an estimator of the β diversity index based on the sequence data and demonstrated that it converges to the β diversity index between sequence populations with probability of 1 as the number of sampled sequences increases. Next, we applied this new method to quantify β diversities between archaeal sequence populations under the seafloor and constructed a quantitative model of the estimated β diversity patterns. Nearly 90% of the variation in the archaeal β diversity was explained by a model that included as variables the differences in the abundances of chlorine, iodine, and carbon between the sediment layers.

A recommendation of: Anouk Willemsen, Marta Felez-Sanchez, and Ignacio G. Bravo Genome plasticity in Papillomaviruses and de novo emergence of E5 oncogenes 10.1101/337477

We comprehensively compared all available questionnaires for measuring quantitative autistic traits (QATs) in terms of reliability and construct validity in 3,147 non-clinical and 60 clinical subjects with normal intelligence. We examined four full-length forms, the Subthreshold Autism Trait Questionnaire (SATQ), the Broader Autism Phenotype Questionnaire, the Social Responsiveness Scale2-Adult Self report (SRS2-AS), and the Autism-Spectrum Quotient (AQ). The SRS2-AS and the AQ each had several short forms that we also examined, bringing the total to 11 forms. Though all QAT questionnaires showed acceptable levels of test-retest reliability, the AQ and SRS2-AS, including their short forms, exhibited poor internal consistency and discriminant validity, respectively. The SATQ excelled in terms of classical test theory and due to its short length.

In this study, we developed a method of fractional parentage analysis using microsatellite markers. We propose a method for calculating parentage probability, which considers missing data and genotyping errors due to null alleles and other causes, by regarding observed alleles as realizations of random variables which take values in the set of alleles at the locus and developing a method for simultaneously estimating the true and null allele frequencies of all alleles at each locus. We then applied our proposed method to a large sample collected from a wild population of brown trout (Salmo trutta). On analyzing the data using our method, we found that the reproductive success of brown trout obeyed a power law, indicating that when the parent-offspring relationship is regarded as a link, the reproductive system of brown trout is a scale-free network. Characteristics of the reproductive network of brown trout include individuals with large bodies as hubs in the network and different power exponents of degree distributions between males and females.

Marine aquaculture and stock enhancement are major causes of the introduction of alien species. A good example of such an introduction is the Japanese shortneck clam Ruditapes philippinarum, one of the most important fishery resources in the world. To meet the domestic shortage of R. philippinarum caused by depleted catches, clams were imported to Japan from China and the Korean peninsula. The imported clam is an alien species that has a very similar morphology, and was misidentified as R. philippinarum (hereafter, Ruditapes form). We genotyped 1,186 clams of R. philippinarum and R. form at four microsatellite loci, sequenced mitochondrial DNA (COI gene fragment) of 485 clams, 34 of which were R. variegatus, and measured morphometric and meristic characters of 754 clams from 12 populations in Japan and China, including the Ariake Sea and Tokyo Bay, where large numbers of R. form were released. Our analyses confirmed that R. form was from the genus Ruditapes, and the genetic differentiation between R. philippinarum and R. form was distinct, but small, compared with five bivalve outgroups. However, R. form had distinct shell morphology, especially larger numbers of radial ribs on the shell surface, suggesting that R. form might be a new Ruditapes species or a variation of R. philippinarum that originated from southern China. A genetic affinity of the sample from the Ariake Sea to R. form was found with the intermediate shell morphology and number of radial ribs, and the hybrid proportion was estimated at 51.3 ± 4.6 % in the Ariake Sea.

The tobacco cutworm, Spodoptera litura, is among the most widespread and destructive agricultural pests, feeding on over 100 crops throughout tropical and subtropical Asia. By genome sequencing, physical mapping and transcriptome analysis, we found that the gene families encoding receptors for bitter or toxic substances and detoxification enzymes, such as cytochrome P450, carboxylesterase and glutathione-S-transferase, were massively expanded in this polyphagous species, enabling its extraordinary ability to detect and detoxify many plant secondary compounds. Larval exposure to insecticidal toxins induced expression of detoxification genes, and knockdown of representative genes using short interfering RNA (siRNA) reduced larval survival, consistent with their contribution to the insect’s natural pesticide tolerance. A population genetics study indicated that this species expanded throughout southeast Asia by migrating along a South India–South China–Japan axis, adapting to wide-ranging ecological conditions with diverse host plants and insecticides, surviving and adapting with the aid of its expanded detoxification systems. The findings of this study will enable the development of new pest management strategies for the control of major agricultural pests such as S. litura.