The complete mitochondrial genome of the intertidal spider (Desis jiaxiangi) provides novel insights into the adaptive evolution of the mitogenome and the evolution of spiders

Background Although almost all extant spider species live in terrestrial environments, a few species live fully submerged in freshwater or seawater. The intertidal spiders (genus Desis) built silk nests within coral crevices can survive submerged in high tides. The diving bell spider, Argyroneta aquatica, resides in a similar dynamic environment but exclusively in freshwater. Given the pivotal role played by mitochondria in supplying most energy for physiological activity via oxidative phosphorylation and the environment, herein we sequenced the complete mitogenome of Desis jiaxiangi to investigate the adaptive evolution of the aquatic spider mitogenomes and the evolution of spiders. Results We assembled a complete mitogenome of the intertidal spider Desis jiaxiangi and performed comparative mitochondrial analyses of data set comprising of Desis jiaxiangi and other 45 previously published spider mitogenome sequences, including that of Argyroneta aquatica. We found a unique transposition of trnL2 and trnN genes in Desis jiaxiangi. Our robust phylogenetic topology clearly deciphered the evolutionary relationships between Desis jiaxiangi and Argyroneta aquatica as well as other spiders. We dated the divergence of Desis jiaxiangi and Argyroneta aquatica to the late Cretaceous at ~ 98 Ma. Our selection analyses detected a positive selection signal in the nd4 gene of the aquatic branch comprising both Desis jiaxiangi and Argyroneta aquatica. Surprisingly, Pirata subpiraticus, Hypochilus thorelli, and Argyroneta aquatica each had a higher Ka/Ks value in the 13 PCGs dataset among 46 taxa with complete mitogenomes, and these three species also showed positive selection signal in the nd6 gene. Conclusions Our finding of the unique transposition of trnL2 and trnN genes indicates that these genes may have experienced rearrangements in the history of intertidal spider evolution. The positive selection signals in the nd4 and nd6 genes might enable a better understanding of the spider metabolic adaptations in relation to different environments. Our construction of a novel mitogenome for the intertidal spider thus sheds light on the evolutionary history of spiders and their mitogenomes.

Comparative genome and transcriptome integration studies reveal the mechanism of pectoral muscle development and function in pigeons

Background: Various morphological breeds of rock pigeons have emerged as a result of human domestication. Pigeon breed resources provide a genetic model for the study of phenomics. The pectoral muscles are play a key role for the meat production performance of the meat pigeon and the athletic ability of the High flyers. Euro-pigeons and Silver King are commercial varieties that exhibit good meat production performance. In contrast to the domestication direction of meat pigeons, the traditional Chinese ornamental pigeon breed, High flyers, has a small and light body. Here, we investigate the molecular mechanism of the pectoral muscle development and function of pigeons using whole-genome and RNA sequencing data Result: The selective sweep analysis (FST and log2 (θπ ratio)) revealed 293 and 403 positive selection genes in Euro-pigeons and Silver King, respectively, of which 65 genes were shared. With the Silver King and Euro-pigeon as the control group, the High flyers were selected for 427 and 566 genes respectively. There were 673 differentially expressed genes in the breast muscle transcriptome between the commercial meat pigeons and ornamental pigeons. Pigeon genome selection signal combined with the breast muscle transcriptome revealed that 6 genes from commercial varieties of pigeons and 5 genes from Chinese traditional ornamental pigeons were positively selected. These genes were involved in pathways related to muscle development and function. Conclusion: Integrated selection signal, transcriptome analysis, and functional annotation identified SYNE1 as a key gene enriched in the actin binding and muscle cell differentiation pathways. Moreover, SYNE1 gene mutations have been associated with human muscular dystrophy. The differential expression of this gene reveals that it has a negative regulatory role in the development and function of pigeon breast muscle.

The Population Structure and Selection Signal Analysis of Shenxian Pigs based on Genome Resequencing Technology

ABSTRACTShenxian pigs are the only local black pig of Hebei Province, and were listed in the Genetics of Livestock and Poultry Resources of China in 2016. This breed of pig is considered to be a valuable local pig germplasm genetic resource in China. In the present study, in order to understand the genetic variations of Shenxian pigs, identify selected regions related to superior traits, and accelerate the breeding processes of Shenxian pigs, the whole genome of the Shenxian pigs was resequenced and compared with that of large white pigs. The goal was to explore the germplasm characteristics of Shenxian pigs.The results obtained in this research investigation revealed that the genetic relationships of the Shenxian pig breed were complex, and that sub-populations could be identified within the general population. A total of 23M SNP sites were obtained by whole genome resequencing, and 1,509 selected sites were obtained via bioinformatics analyses. It was determined after annotation that a total of 19 genes were enriched in three items of bioengineering, molecular function, and cell composition.During this research investigation, the aforementioned 19 genes were subjected to GO and KEGG analyses. Subsequently, the candidate genes related to cell proliferation were obtained (DMTF1 and WDR5), which were considered to possibly be related to the slow growth and development of Shenxian pigs. In addition, the candidate genes related to lactation were obtained (CSN2 and CSN3).

Novel start codons introduce novel coding sequences in the human genomes

Start-gain mutations can introduce novel start codons and generate novel coding sequences that may affect the function of genes. In this study, we systematically investigated the novel start codons that were either polymorphic or fixed in the human genomes. 829 polymorphic start-gain SNVs were identified in the human populations, and the novel start codons introduced by these SNVs have significantly higher activity in translation initiation. Some of these start-gain SNVs were reported to be associated with phenotypes and diseases in previous studies. By comparative genomic analysis, we found 26 human-specific start codons that were fixed after the divergence between the human and chimpanzee, and high-level translation initiation activity was observed on them. The negative selection signal was detected in the novel coding sequences introduced by these human-specific start codons, indicating the important function of these novel coding sequences. This study reveals start-gain mutations are keeping appearing in the human genomes during the evolution and may be important sources altering the function of genes which may further affect the phenotypes or cause diseases.

Limited Evidence for Selection at the FADS Locus in Native American Populations

The FADS locus contains the genes FADS1 and FADS2 that encode enzymes involved in the synthesis of long-chain polyunsaturated fatty acids. This locus appears to have been a repeated target of selection in human evolution, likely because dietary input of long-chain polyunsaturated fatty acids varied over time depending on environment and subsistence strategy. Several recent studies have identified selection at the FADS locus in Native American populations, interpreted as evidence for adaptation during or subsequent to the passage through Beringia. Here, we show that these signals are confounded by independent selection—postdating the split from Native Americans—in the European and, possibly, the East Asian populations used in the population branch statistic test. This is supported by direct evidence from ancient DNA that one of the putatively selected haplotypes was already common in Northern Eurasia at the time of the separation of Native American ancestors. An explanation for the present-day distribution of the haplotype that is more consistent with the data is that Native Americans retain the ancestral state of Paleolithic Eurasians. Another haplotype at the locus may reflect a secondary selection signal, although its functional impact is unknown.

The effect of autopolyploidy on population genetic signals of hard sweeps

Searching for population genomic signals left behind by positive selection is a major focus of evolutionary biology, particularly as sequencing technologies develop and costs decline. The effect of the number of chromosome copies (i.e. ploidy) on the manifestation of these signals remains an outstanding question, despite a wide appreciation of ploidy being a fundamental parameter governing numerous biological processes. We clarify the principal forces governing the differential manifestation and persistence of the selection signal by separating the effects of polyploidy on the rates of fixation versus rates of diversity (i.e. mutation and recombination) using coalescent simulations. We explore the major consequences of polyploidy, finding a more localized signal, greater dependence on dominance and longer persistence of the signal following fixation, and discuss what this means for within- and across ploidy inference on the strength and prevalence of selective sweeps. As genomic advances continue to open doors for interrogating natural systems, simulations such as this aid our ability to interpret and compare data across ploidy levels.

Limited evidence for selection at the FADS locus in Native American populations

The FADS locus contains the genes FADS1 and FADS2 that encode enzymes involved in the synthesis of long-chain polyunsaturated fatty acids (LC-PUFA). This locus appears to have been a repeated target of selection in human evolution, likely because dietary input of LC-PUFA varied over time depending on environment and subsistence strategy. Several recent studies have identified selection at the FADS locus in Native American populations, interpreted as evidence for adaptation during or subsequent to the passage through Beringia. Here, we show that these signals of selection are confounded by the presence of parallel adaptation–postdating their split from Native Americans–in the European and East Asian populations used in the population branch statistic (PBS) test. This is supported by direct evidence from ancient DNA that one of the putatively selected haplotypes was already common in Northern Eurasia at the time of the separation of Native American ancestors. A more parsimonious explanation for the present-day distribution of the haplotype is that Native Americans retain the ancestral state of Paleolithic Eurasians. Another haplotype at the locus may reflect a secondary selection signal, although its functional impact is unknown.

Polygenic Selection, Polygenic Scores, Spatial Autocorrelation and Correlated Allele Frequencies. Can We Model Polygenic Selection on Intellectual Abilities?

The majority of polygenic selection signal of educational attainment GWAS hits is confined to a handful of SNPs within genomic regions replicated across GWAS publications. A polygenic score comprising 9 SNPs predicts population IQ (r=0.9), outperforming 99.9% of the polygenic scores obtained from sets of random SNPs. Its predictive power remains unaffected after controlling for spatial autocorrelation. Even random polygenic scores are moderate predictors of population IQ, and their predictive power increases logarithmically with the number of SNPs, indicating an exponential reduction in noise.Thus, the predictive power of polygenic scores has to be scaled in proportion to the number of SNPs composing them.