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Models have always been central to inferring molecular evolution and to reconstructing phylogenetic trees. Their use typically involves the development of a mechanistic framework reflecting our understanding of the underlying biological processes, such as nucleotide substitutions, and the estimation of model parameters by maximum likelihood or Bayesian inference. However, deriving and optimizing the likelihood of the data is not always possible under complex evolutionary scenarios or even tractable for large datasets, often leading to unrealistic simplifying assumptions in the fitted models. To overcome this issue, we coupled stochastic simulations of genome evolution with a new supervised deep-learning model to infer key parameters of molecular evolution. Our model is designed to directly analyze multiple sequence alignments and estimate per-site evolutionary rates and divergence without requiring a known phylogenetic tree. The accuracy of our predictions matched that of likelihood-based phylogenetic inference when rate heterogeneity followed a simple gamma distribution, but it strongly exceeded it under more complex patterns of rate variation, such as codon models. Our approach is highly scalable and can be efficiently applied to genomic data, as we showed on a dataset of 26 million nucleotides from the clownfish clade. Our simulations also showed that the integration of per-site rates obtained by deep learning within a Bayesian framework led to significantly more accurate phylogenetic inference, particularly with respect to the estimated branch lengths. We thus propose that future advancements in phylogenetic analysis will benefit from a semi-supervised learning approach that combines deep-learning estimation of substitution rates, which allows for more flexible models of rate variation, and probabilistic inference of the phylogenetic tree, which guarantees interpretability and a rigorous assessment of statistical support. [ABSTRACT FROM AUTHOR]

Abstract Background Independent origins of carnivory in multiple angiosperm families are fabulous examples of convergent evolution using a diverse array of life forms and habitats. Previous studies have indicated that carnivorous plants have distinct evolutionary trajectories of plastid genome (plastome) compared to their non-carnivorous relatives, yet the extent and general characteristics remain elusive. Results We compared plastomes from 9 out of 13 carnivorous families and their non-carnivorous relatives to assess carnivory-associated evolutionary patterns. We identified inversions in all sampled Droseraceae species and four species of Utricularia, Pinguicula, Darlingtonia and Triphyophyllum. A few carnivores showed distinct shifts in inverted repeat boundaries and the overall repeat contents. Many ndh genes, along with some other genes, were independently lost in several carnivorous lineages. We detected significant substitution rate variations in most sampled carnivorous lineages. A significant overall substitution rate acceleration characterizes the two largest carnivorous lineages of Droseraceae and Lentibulariaceae. We also observe moderate substitution rates acceleration in many genes of Cephalotus follicularis, Roridula gorgonias, and Drosophyllum lusitanicum. However, only a few genes exhibit significant relaxed selection. Conclusion Our results indicate that the carnivory of plants have different effects on plastome evolution across carnivorous lineages. The complex mechanism under carnivorous habitats may have resulted in distinctive plastome evolution with conserved plastome in the Brocchinia hechtioides to strongly reconfigured plastomes structures in Droseraceae. Organic carbon obtained from prey and the efficiency of utilizing prey-derived nutrients might constitute possible explanation.

Background: Independent origins of carnivory in multiple angiosperm families are fabulous examples of convergent evolution using a diverse array of life forms and habitats. Previous studies have indicated that carnivorous plants have distinct evolutionary trajectories of plastid genome (plastome) compared to their non-carnivorous relatives, yet the extent and general characteristics remain elusive. Results: We compared plastomes from 9 out of 13 carnivorous families and their non-carnivorous relatives to assess carnivory-associated evolutionary patterns. We identified inversions in all sampled Droseraceae species and four species of Utricularia, Pinguicula, Darlingtonia and Triphyophyllum. A few carnivores showed distinct shifts in inverted repeat boundaries and the overall repeat contents. Many ndh genes, along with some other genes, were independently lost in several carnivorous lineages. We detected significant substitution rate variations in most sampled carnivorous lineages. A significant overall substitution rate acceleration characterizes the two largest carnivorous lineages of Droseraceae and Lentibulariaceae. We also observe moderate substitution rates acceleration in many genes of Cephalotus follicularis, Roridula gorgonias, and Drosophyllum lusitanicum. However, only a few genes exhibit significant relaxed selection. Conclusion: Our results indicate that the carnivory of plants have different effects on plastome evolution across carnivorous lineages. The complex mechanism under carnivorous habitats may have resulted in distinctive plastome evolution with conserved plastome in the Brocchinia hechtioides to strongly reconfigured plastomes structures in Droseraceae. Organic carbon obtained from prey and the efficiency of utilizing prey-derived nutrients might constitute possible explanation. [ABSTRACT FROM AUTHOR]

Coding sequence evolution is influenced by both natural selection and neutral evolutionary forces. In many species, the effects of mutation bias, codon usage, and GC-biased gene conversion (gBGC) on gene sequence evolution have not been detailed. Quantification of how these forces shape substitution patterns is therefore necessary to understand the strength and direction of natural selection. Here, we used comparative genomics to investigate the association between base composition and codon usage bias on gene sequence evolution in butterflies and moths (Lepidoptera), including an in-depth analysis of underlying patterns and processes in one species, Leptidea sinapis. The data revealed significant G/C to A/T substitution bias at third codon position with some variation in the strength among different butterfly lineages. However, the substitution bias was lower than expected from previously estimated mutation rate ratios, partly due to the influence of gBGC. We found that A/T-ending codons were overrepresented in most species, but there was a positive association between the magnitude of codon usage bias and GC-content in third codon positions. In addition, the tRNA-gene population in L. sinapis showed higher GC-content at third codon positions compared to coding sequences in general and less overrepresentation of A/T-ending codons. There was an inverse relationship between synonymous substitutions and codon usage bias indicating selection on synonymous sites. We conclude that the evolutionary rate in Lepidoptera is affected by a complex interaction between underlying G/C -> A/T mutation bias and partly counteracting fixation biases, predominantly conferred by overall purifying selection, gBGC, and selection on codon usage. [ABSTRACT FROM AUTHOR]

Abstract Background Plastomes of heterotrophic plants have been greatly altered in structure and gene content, owing to the relaxation of selection on photosynthesis-related genes. The orchid tribe Gastrodieae is the largest and probably the oldest mycoheterotrophic clade of the extant family Orchidaceae. To characterize plastome evolution across members of this key important mycoheterotrophic lineage, we sequenced and analyzed the plastomes of eleven Gastrodieae members, including representative species of two genera, as well as members of the sister group Nervilieae. Results The plastomes of Gastrodieae members contain 20 protein-coding, four rRNA and five tRNA genes. Evolutionary analysis indicated that all rrn genes were transferred laterally and together, forming an rrn block in the plastomes of Gastrodieae. The plastome GC content of Gastrodia species ranged from 23.10% (G. flexistyla) to 25.79% (G. javanica). The plastome of Didymoplexis pallens contains two copies each of ycf1 and ycf2. The synonymous and nonsynonymous substitution rates were very high in the plastomes of Gastrodieae among mycoheterotrophic species in Orchidaceae and varied between genes. Conclusions The plastomes of Gastrodieae are greatly reduced and characterized by low GC content, rrn block formation, lineage-specific reconfiguration and gene content, which might be positively selected. Overall, the plastomes of Gastrodieae not only serve as an excellent model for illustrating the evolution of plastomes but also provide new insights into plastome evolution in parasitic plants.

Genome mergers between independently evolving lineages, via allopolyploidy, can potentially lead to instantaneous sympatric speciation. However, little is known about the consequences of allopolyploidy and the resultant "genome shock" on genome evolution and expression beyond the plant and fungal branches of the Tree of Life. The aim of this study was to compare substitution rates and gene expression patterns in two allopolyploid brown algae (Phaeophyceae and Heterokonta) and their progenitors in the genus Pelvetiopsis N. L. Gardner in the north-east Pacific, and to date their relationships. We used RNA-seq data, all potential orthologues, and putative single-copy loci for phylogenomic, divergence, and gene expression analyses. The multispecies coalescent placed the origin of allopolyploids in the late Pleistocene (0.35-0.05 Ma). Homoeologues displayed increased nonsynonymous divergence compared with parental orthologues, consistent with relaxed selective constraint following allopolyploidization, including for genes with no evidence of pseudogenization or neofunctionalization. Patterns of homoeologue-orthologue expression conservation and expression level dominance were largely shared with both natural plant and fungal allopolyploids. Our results provide further support for common cross-Kingdom patterns of allopolyploid genome evolution and transcriptional responses, here in the evolutionarily distinct marine heterokont brown algae.

Abstract Background An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing for numerous factors, such as life history and habitat, that are linked both to the molecular processes of mutation and fixation and to rates of macroevolutionary diversification. However, the most widely used methods rely on idealised models of rate variation, such as the uncorrelated and autocorrelated clocks, and molecular dating methods are rarely tested against complex models of rate change. One relationship that is not accounted for in molecular dating is the potential for interaction between molecular substitution rates and speciation, a relationship that has been supported by empirical studies in a growing number of taxa. If these relationships are as widespread as current evidence suggests, they may have a significant influence on molecular dates. Results We simulate phylogenies and molecular sequences under three different realistic rate variation models—one in which speciation rates and substitution rates both vary but are unlinked, one in which they covary continuously and one punctuated model in which molecular change is concentrated in speciation events, using empirical case studies to parameterise realistic simulations. We test three commonly used “relaxed clock” molecular dating methods against these realistic simulations to explore the degree of error in molecular dates under each model. We find average divergence time inference errors ranging from 12% of node age for the unlinked model when reconstructed under an uncorrelated rate prior using BEAST 2, to up to 91% when sequences evolved under the punctuated model are reconstructed under an autocorrelated prior using PAML. Conclusions We demonstrate the potential for substantial errors in molecular dates when both speciation rates and substitution rates vary between lineages. This study highlights the need for tests of molecular dating methods against realistic models of rate variation generated from empirical parameters and known relationships.

In this study, we examined the ribosomal DNA internal transcribed spacers and mtDNA markers for their use in the prospecting of 480 ladybird species belonging to 14 tribes to assess the evolutionary topology and substitution rates. Substitution patterns of the respective markers were estimated using a cascade of algorithms such as pairwise sequence comparisons, maximum likelihood estimates of the substitution matrix, transitions/transversions (ti/tv) and gamma parameters with a suitable substitution model. Maximum likelihood (ML) estimates showed that COI (R = 1.16) and COII (R = 1.36) were more biased towards transitions. COI has a higher ti/tv ratio indicating more substitutions and less divergence among the species in the phylogenetic tree, though it had moderate bootstrap support. ML and Bayesian analysis were used to construct the morphology character matrix and molecular datasets in order to establish the evolutionary relationship. All the characters of male and female genitalia supported mophyletic topology. The phylogenetic results of molecular datasets suggest that most of the taxa significantly support monophyly. Phylogenetic analysis depict COI consists of more substitution as it shows less divergence among species. [ABSTRACT FROM AUTHOR]

Do the properties of amino acids affect their rates of substitution? The neutral theory predicts that greater selective constraint leads to slower rates of evolution; similarly, we expect amino acids that are more different from each other to have lower rates of exchange because such changes are most likely to affect protein structure and function. Here we test these predictions, using substitution rates estimated from empirical amino acid exchangeability matrices. To measure degree of amino acid difference, we focussed on two physicochemical properties, hydrophobicity and molecular weight, uncorrelated metrics that are known to have important implications for protein structure and function. We find that for both hydrophobicity and molecular weight, amino acid pairs with large differences had lower rates of substitution. We also found that amino acids that differed in both properties had the lowest rates of substitution, suggesting that both physicochemical properties are under selective constraint. Mutation properties, such as the number of mutations or the number of transitions as opposed to transversions separating amino acid pairs, were also important predictors of substitution rates. The relationship between amino acid substitution rates and differences in their physiochemical properties holds across several taxonomically restricted datasets. This finding suggests that purifying selection affects amino acid substitution rates in a similar manner across taxonomic groups with different effective population sizes., (© The Author(s) 2025. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Background: Plastomes of heterotrophic plants have been greatly altered in structure and gene content, owing to the relaxation of selection on photosynthesis-related genes. The orchid tribe Gastrodieae is the largest and probably the oldest mycoheterotrophic clade of the extant family Orchidaceae. To characterize plastome evolution across members of this key important mycoheterotrophic lineage, we sequenced and analyzed the plastomes of eleven Gastrodieae members, including representative species of two genera, as well as members of the sister group Nervilieae. Results: The plastomes of Gastrodieae members contain 20 protein-coding, four rRNA and five tRNA genes. Evolutionary analysis indicated that all rrn genes were transferred laterally and together, forming an rrn block in the plastomes of Gastrodieae. The plastome GC content of Gastrodia species ranged from 23.10% (G. flexistyla) to 25.79% (G. javanica). The plastome of Didymoplexis pallens contains two copies each of ycf1 and ycf2. The synonymous and nonsynonymous substitution rates were very high in the plastomes of Gastrodieae among mycoheterotrophic species in Orchidaceae and varied between genes. Conclusions: The plastomes of Gastrodieae are greatly reduced and characterized by low GC content, rrn block formation, lineage-specific reconfiguration and gene content, which might be positively selected. Overall, the plastomes of Gastrodieae not only serve as an excellent model for illustrating the evolution of plastomes but also provide new insights into plastome evolution in parasitic plants. [ABSTRACT FROM AUTHOR]

Considering the phylogenetic differences in the taxonomic framework of the Chaetophorales as determined by the use of nuclear molecular markers or chloroplast genes, the current study was the first to use phylotranscriptomic analyses comparing the transcriptomes of 12 Chaetophorales algal species. The results showed that a total of 240,133 gene families and 143 single-copy orthogroups were identified. Based on the single-copy orthogroups, supergene analysis and the coalescent-based approach were adopted to perform phylotranscriptomic analysis of the Chaetophorales. The phylogenetic relationships of most species were consistent with those of phylogenetic analyses based on the chloroplast genome data rather than nuclear molecular markers. The Schizomeriaceae and the Aphanochaetaceae clustered into a well-resolved basal clade in the Chaetophorales by either strategy. Evolutionary analyses of divergence time and substitution rate also revealed that the closest relationships existed between the Schizomeriaceae and Aphanochaetaceae. All species in the Chaetophorales exhibited a large number of expanded and contracted gene families, in particular the common ancestor of the Schizomeriaceae and Aphanochaetaceae. The only terrestrial alga, Fritschiella tuberosa, had the greatest number of expanded gene families, which were associated with increased fatty acid biosynthesis. Phylotranscriptomic and evolutionary analyses all robustly identified the unique taxonomic relationship of Chaetophorales consistent with chloroplast genome data, proving the advantages of high-throughput data in phylogeny. [ABSTRACT FROM AUTHOR]

The faster-X/Z effect hypothesis states that genes linked to X/Z chromosomes should accumulate mutations faster than autosomal genes. Although faster evolution of X/Z-linked genes has been reported in several plant and animal lineages, conflicting results have been reported in others. We examined the faster-Z effect in chameleons of the genus Furcifer, a lineage with differentiated ZZ/ZW chromosomes for at least 20 million years. We sequenced the genomes of four species of Furcifer chameleons in the Illumina platform and compared the substitution rates of synonymous and non-synonymous mutations and their ratios among autosomal, Z-specific, and pseudoautosomal protein-coding genes. The inclusion of two chameleon outgroups lacking the differentiated ZZ/ZW sex chromosomes allowed us to control for gene-specific evolutionary rates that might confound the testing of the faster-X/Z effect. Significant differences in evolutionary rates were found between autosomal, Z-specific, and pseudoautosomal genes of Furcifer chameleons. However, the inclusion of the outgroups with different sex chromosomes suggests that these genes had different evolutionary rates prior to their incorporation into the differentiated ZZ/ZW sex chromosomes of the Furcifer genus. The results highlight the need to control for differences in the evolutionary rates of individual genes when testing for the faster X/Z effect., (© The Author(s) 2024. Published by Oxford University Press on behalf of The American Genetic Association. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Mitochondrial DNA (mtDNA) is a popular resource used for the study of evolutionary processes in birds, especially to infer divergence times between lineages. In many cases, due to the scarcity of fossils with which to constrain the age of nodes on a phylogenetic topology, dating relies on mtDNA substitution rates that, ideally, are specific to the taxa being studied. As such values are often unavailable, many studies use fixed‐rate values from other studies, such as the 'standard molecular clock'. The validity of this universal rate across all bird lineages and for the different mtDNA loci has been questioned by multiple authors. We here performed the most comprehensive calibration of the mtDNA molecular clock in birds, with the inclusion of complete mitochondrial genomes for 622 bird species and 25 reliable fossil calibrations. The results show variation in the rates among lineages and among markers, confirming the lack of universality of the standard molecular clock. Moreover, we provide specific rates for every mtDNA marker (except D‐loop) in each of the sampled avian orders, a valuable tool for molecular clock analyses in the absence of fossil calibrations. [ABSTRACT FROM AUTHOR]

Abstract Background Parasitic plants rely on their host to cover their nutritional requirements either for their entire life or a smaller part of it. Depending on the level of parasitism, a proportional reduction on the plastid genome has been found. However, knowledge on gene loss and evolution of the mitogenome of parasitic plants is only available for four hemiparasitic Viscum species (Viscaceae), which lack many of the mitochondrial genes, while the remaining genes exhibit very fast molecular evolution rates. In this study, we include another genus, Phoradendron, from the Viscaceae, as well as 10 other hemiparasitic or holoparasitic taxa from across the phylogeny of the angiosperms to investigate how fast molecular evolution works on their mitogenomes, and the extent of gene loss. Results Our observations from Viscum were replicated in Phoradendron liga, whereas the remaining parasitic plants in the study have a complete set of the core mitochondrial genes and exhibit moderate or only slightly raised substitution rates compared to most autotrophic taxa, without any statistically significant difference between the different groups (autotrophs, hemiparasites and holoparasites). Additionally, further evidence is provided for the placement of Balanophoraceae within the order Santalales, while the exact placement of Cynomoriaceae still remains elusive. Conclusions We examine the mitochondrial gene content of 11 hemiparasitic and holoparasitic plants and confirm previous observations in Viscaceae. We show that the remaining parasitic plants do not have significantly higher substitution rates than autotrophic plants in their mitochondrial genes. We provide further evidence for the placement of Balanophoraceae in the Santalales.

The strength and microstructural analysis of recycled geopolymer are presented in this paper. Five kinds of geopolymers containing 0%, 20%, 50%, 80% and 100 % of recycled geopolymer powder were prepared using metakaolin as the source material. The alkali activator solution was a mixture of sodium silicate (Na2SiO3) and 12 M sodium hydroxide (NaOH). The change laws of compressive and flexural strength of recycled geopolymer specimens were investigated. And the microscopic characteristics were carried out by SEM, XRD and FTIR to observe the internal morphology and analyze changes in components of recycled geopolymers at different substitution rates. The results show that, with the increase of substitution rate of recycled geopolymer powder, the mechanical properties of recycled geopolymers degenerate and the looser structure are formed. When the substitution rate is less than 50%, the recycled geopolymer specimen meets the use requirements of heavy traffic load class. And the specimen with 80% of substitution rate satisfies the requirements of plastering mortar. [ABSTRACT FROM AUTHOR]

To examine the compressive dynamic performance of rubber concrete, a uniaxial compression experimental study on rubber concrete was carried out using a hydraulic servo based on five different rubber substitution rates under eight different earthquake magnitude loading strain rates. The compressive failure modes and stress-strain curves of rubber concrete were obtained. By comparatively analyzing the mechanical characteristics of rubber concrete under different loading conditions, the following conclusions are drawn: with the increase in rubber substitution rate, the integrity of concrete upon compressive failure is gradually improved, and rubber particles exhibit an evident modification effect on cement mortar at the concrete interface. Under the influence of loading strain rate, the patterns of compressive failure mode of rubber concrete with different substitution rates are similar to that of ordinary concrete. Under the same loading strain rate, with the increase in rubber substitution rate, the compressive strength of rubber concrete gradually decreases while the plastic deformation capacity gradually increases. For the same rubber substitution rate, the compressive strength and elastic modulus of rubber concrete gradually increases with the increase in loading strain rate. The increase in rubber substitution rate gradually reduces the increasing amplitude of compressive strength and elastic modulus of rubber concrete under the influence of loading strain rate. Meanwhile, an equation was proposed to describe the coupling effect of rubber substitution rate and strain rate on the compressive strength dynamic increase factor of rubber concrete, and the underlying stress mechanism was further discussed. These results have significance in promoting the application of rubber concrete in engineering practice.

The article is aimed at researching the factors of economic growth in the education sphere of Ukraine. It is determined that the result of activities in the sphere of education, provision of educational services at the macro-economic level can be the volumes of gross added value of education, and factors of economic growth can be the number of employees and the amount of capital investments in the researched sphere. The use of the mentioned indicators is substantiated taking into account the modern system of providing information by the State Statistics Service of Ukraine. Tendencies of changes in the factors of economic growth for 2007–2016 are analyzed. The model of economic growth in education with exogenous inclusion of the factor of scientific-technological progress is built. The indicators of efficiency are calculated by correlation of factors of the economic growth function in the sphere of education. The necessity to increase the volume of capital investments in the sphere of education for modernization of material and technical base, use of the newest software, forms and methods of training is substantiated.

The typical chloroplast genome consists of two inverted repeat (IR) and two single-copy (SC) regions. Each region has its own pattern of molecular evolution. Many studies have shown that the IR region has a low substitution rate. The plastid rps12 gene encodes ribosomal protein small subunit 12, which is composed of 5′-rps12 (exon 1) and 3′-rps12 (exon 2–3); 3′-rps12 is near the IR region and enters or leaves the IR region as it expands and contracts, enabling study of the variation in its substitution rate. We analyzed the evolutionary rate and adaptive evolution of the rps12 genes of 118 ferns and 2 lycophytes in a phylogenetic context using the maximum likelihood method. We found that the substitution rate of exon 2–3 was significantly lower in the IR region than in the LSC (1–11 times higher in the LSC), and also lower than that of exon 1 in the LSC region (1.9–6.7 times higher for exon 1). In addition, there was more GC content at the third codon position, and the rps12 gene encoded 123 amino acids, with 107 negative selection sites and 4 positive selection sites. These results prove that the substitution rate decreases after the sequence fragments enter the IR region and demonstrate the highly conserved nature of the rps12 gene. [ABSTRACT FROM AUTHOR]

Despite many qualitative discussions about the benefits of free-floating bike-sharing systems (FFBS), high-resolution and quantitative assessments about the economic benefits of FFBS for users are absent. This study proposes an innovative trip-level inference approach for quantifying the economic benefits of FFBS, leveraging massive FFBS transaction data, the emerging multimodal routing Application Programming Interface from online navigators and travel choice modeling. The proposed approach is able to analyze the economic benefit for every single bike-sharing trip and investigate the spatiotemporal heterogeneity in the economic benefits from FFBS. An empirical analysis in Shanghai is conducted using the proposed approach. The estimated saved travel time, cost, and economic benefit due to using FFBS per trip are estimated to be 9.95 min, 3.64 CNY, and 8.68 CNY-eq, respectively. The annual saved travel time, cost, and economic benefits from FFBS in Shanghai are estimated to be 17.665 billion min, 6.463 billion CNY, and 15.410 billion CNY-eq, respectively. The relationships between economic benefits from FFBS and built environment factors in different urban contexts are quantitatively examined using Multiple Linear Regression to explain the spatial heterogeneity in the economic benefits of FFBS. The outcomes provide a useful tool for evaluating the benefits of shared mobility systems, insights into the users' economic benefit from using FFBS from per-trip, aggregated and spatial perspective, as well as its influencing factors. The results could efficiently support the scientific planning, operation and policy making concerning FFBS in different urban contexts. [ABSTRACT FROM AUTHOR]

Cyanophora is the glaucophyte model taxon. Following the sequencing of the nuclear genome of C. paradoxa, studies based on single organelle and nuclear molecular markers revealed previously unrecognized species diversity within this glaucophyte genus. Here, we present the complete plastid (ptDNA) and mitochondrial (mtDNA) genomes of C. kugrensii, C. sudae, and C. biloba. The respective sizes and coding capacities of both ptDNAs and mtDNAs are conserved among Cyanophora species with only minor differences due to specific gene duplications. Organelle phylogenomic analyses consistently recover the species C. kugrensii and C. paradoxa as a clade and C. sudae and C. biloba as a separate group. The phylogenetic affiliations of the four Cyanophora species are consistent with architectural similarities shared at the organelle genomic level. Genetic distance estimations from both organelle sequences are also consistent with phylogenetic and architecture evidence. Comparative analyses confirm that the Cyanophora mitochondrial genes accumulate substitutions at 3‐fold higher rates than plastid counterparts, suggesting that mtDNA markers are more appropriate to investigate glaucophyte diversity and evolutionary events that occur at a population level. The study of complete organelle genomes is becoming the standard for species delimitation and is particularly relevant to study cryptic diversity in microbial groups. [ABSTRACT FROM AUTHOR]

This study is the first to determine the transcriptomes of eight colonial volvocine algae: Pandorina morum, P. colemaniae, Volvulina compacta, Eudorina elegans, E. cylindrica, Yamagishiella unicocca, Colemanosphaera charkowiensis and C. angeleri. By analysing these data together with the whole-genome data of Chlamydomonas reinhardtii and other colonial volvocine algae, we determined 26 979 gene families and 105 single-copy orthogroups. Using the single-copy orthogroups, we adopted a supermatrix and coalescent-based approach to perform phylotranscriptomic analysis of colonial volvocine algae. The phylogenetic relationships of most species were consistent with those of a previous study, and the results showed paraphyly of the genus Pandorina. Then, we analysed gene family expansion and contraction in colonial volvocine algae and found that they exhibited a large number of expanded and contracted gene families. In particular, the common ancestor of the Volvocaceae had the largest number of expanded gene families, which may be associated with the increased volume of extracellular matrix. Finally, using the ML method to analyse the substitution rates among colonial volvocine algae based on single-copy orthogroups, we showed a significantly higher non-synonymous substitution (dN) rate in Tetrabaena socialis. By analysing the differences in the dN/dS ratio, we found that more orthogroups exhibited a significantly higher dN/dS in T. socialis; we speculate that the higher dN/dS could indicate relaxed selection pressure and that this lower constraint allows the accumulation of more non-synonymous mutations in T. socialis. [ABSTRACT FROM AUTHOR]

A previous study detected mixing of two deeply split mtDNA clades (Clade I and Clade II) for Atlantic and Mediterranean populations of the medusozoan Pelagia noctiluca. The north hemisphere glaciations and the Messinian salinity crisis have been proposed as the two main biogeographic events related to the isolation between the Atlantic Ocean and the Mediterranean Sea. We tested if the splitting time between Clade I and Clade II of P. noctiluca was associated with one of these geological events. Our study was based on DNA sequence data of mitochondrial (COI and 16S ribosomal RNA) and nuclear (18S ribosomal RNA, internal transcribed spacer 1 and 5.8S ribosomal RNA) genes from populations of the Atlantic and Pacific Ocean and the Mediterranean Sea. The rise of the Isthmus of Panama was used to calibrate substitution rates for COI. This calibration was based on the detection of a shallow but significant genetic structure between P. noctiluca populations from the Pacific and the Atlantic Oceans. Considering our calibration for COI, we refute a possible origin of Clades I and II during the Messinian salinity crisis. Our estimates suggest the origin for a putative common ancestor of Clades I and II around 2.57 Ma (with 95% 2.91–2.22 HPD), roughly corresponding to the Gelasian stage of the early Pleistocene. These alterations include changes in the sea level and oceanic currents at the Strait of Gibraltar and other regions of the Mediterranean basin, and could explain the origin of the two P. noctiluca clades. [ABSTRACT FROM AUTHOR]

• All the five genera of the Daphniidae were included in this study. • A highly supported phylogenies of the Daphniidae was obtained using 636 nuclear single-copy genes. • Some discrepancies between nuclear and mtDNA based trees were observed at deeper nodes. • A new candidate sister lineage for Daphnia magna was identified. • We dated the Daphniidae phylogeny using both fossil records and substitution rates. In the post-genomic era, much of phylogenetic analyses still relies on mitochondrial DNA, either alone or in combination with few nuclear genes. Although this approach often makes it possible to construct well-supported trees, it is limited because mtDNA describes the history of a single locus, and nuclear phylogenies based on a few loci may be biased, leading to inaccurate tree topologies and biased estimations of species divergence time. In this study, we perform a phylogenomic analysis of the Daphniidae family (Crustacea: Branchiopoda: Anomopoda) including some of the most frequently studied model organisms (Daphnia magna and D. pulex) whose phylogenetic relationships have been based primarily on an assessment of a few mtDNA genes. Using high-throughput sequencing, we were able to assemble 38 whole mitochondrial genomes and draft nuclear genomes for 18 species, including at least one species for each known genus of the family Daphniidae. Here we present phylogenies based on 636 nuclear single-copy genes shared among all sampled taxa and based on whole mtDNA genomes. The phylogenies we obtained were highly supported and showed some discrepancies between nuclear and mtDNA based trees at deeper nodes. We also identified a new candidate sister lineage of Daphnia magna. Our time-calibrated genomic trees, which we constructed using both fossil records and substitution rates, yielded very different estimates of branching event times compared to those based on mtDNA. By providing multi-locus, fossil-calibrated trees of the Daphniidae, our study contributes to an improved phylogenetic framework for ecological and evolutionary studies that use water fleas as a model system. [ABSTRACT FROM AUTHOR]

Crangonyctidae is a speciose and almost exclusively freshwater Holarctic family of amphipod crustaceans. Its members inhabit groundwater as well as epigean biotopes with groundwater connections, and often exhibit endemic, relict distributions. Therefore, it has been proposed that this poorly dispersing, yet intercontinentally distributed family must have ancient Mesozoic origins. Here, we test the hypothesis that Crangonyctidae originated before the final break-up of Laurasia at the end of the Cretaceous. We used molecular phylogenetic analyses based on mitochondrial and nuclear markers and incorporated six out of the seven recognized genera. We calculated divergence times using a novel calibration scheme based exclusively on fossils and, for comparison, also applied substitution rates previously inferred for other arthropods. Our results indicate that crangonyctids originated during the Early Cretaceous in a northerly temperate area comprising nowadays North America and Europe, supporting the Laurasian origin hypothesis. Moreover, high latitude lineages were found to be generally older than the ones at lower latitudes, further supporting the boreal origin of the group and its relict biogeography. The estimated substitution rate of 1.773% Ma−1 for the COI marker agrees well with other arthropod rates, making it appropriate for dating divergences at various phylogenetic levels within the Amphipoda. Furthermore, our extensive phylogeny reinforces the polyphyly of the intercontinental genera Crangonyx, Stygobromus, and Synurella, supports the monophyly of Bactrurus, and elucidates the position of Lyurella. We conclude that crangonyctids are an ideal model for testing continental-level vicariance hypotheses and should be in the focus of future phylogenomic studies. [ABSTRACT FROM AUTHOR]

The mitochondrion is a pivotal organelle for energy production, and includes components encoded by both the mitochondrial and nuclear genomes. Functional and evolutionary interactions are expected between the nuclear- and mitochondrial-encoded components. The topic is of broad interest in biology, with implications to genetics, evolution, and medicine. Here, we compare the evolutionary rates of mitochondrial proteins and ribosomal RNAs to rates of mitochondria-associated nuclear-encoded proteins, across the major orders of holometabolous insects. There are significant evolutionary rate correlations (ERCs) between mitochondrial-encoded and mitochondria-associated nuclear-encoded proteins, which are likely driven by different rates of mitochondrial sequence evolution and correlated changes in the interacting nuclear-encoded proteins. The pattern holds after correction for phylogenetic relationships and considering protein conservation levels. Correlations are stronger for both nuclear-encoded OXPHOS proteins that are in contact with mitochondrial OXPHOS proteins and for nuclear-encoded mitochondrial ribosomal amino acids directly contacting the mitochondrial rRNAs. We find that ERC between mitochondrial- and nuclear-encoded proteins is a strong predictor of nuclear-encoded proteins known to interact with mitochondria, and ERC shows promise for identifying new candidate proteins with mitochondrial function. Twenty-three additional candidate nuclear-encoded proteins warrant further study for mitochondrial function based on this approach, including proteins in the minichromosome maintenance helicase complex. [ABSTRACT FROM AUTHOR]

The number of amino acids that occupy a given protein site during evolution reflects the selective constraints operating on the site. This evolutionary variability is strongly influenced by the structural properties of the site in the native structure, and it is quantified either through sequence entropy or through substitution rates. However, while the sequence entropy only depends on the equilibrium frequencies of the amino acids, the substitution rate also depends on the exchangeability matrix that describes mutations in the mathematical model of the substitution process. Here we apply two variants of a mathematical model of protein evolution with selection for protein stability, both against unfolding and against misfolding. Exploiting the approximation of independent sites, these models allow computing site-specific substitution processes that satisfy global constraints on folding stability. We find that site-specific substitution rates do not depend only on the selective constraints acting on the site, quantified through its sequence entropy. In fact, polar sites evolve faster than hydrophobic sites even for equal sequence entropy, as a consequence of the fact that polar amino acids are characterized by higher mutational exchangeability than hydrophobic ones. Accordingly, the model predicts that more polar proteins tend to evolve faster. Nevertheless, these results change if we compare proteins that evolve under different mutation biases, such as orthologous proteins in different bacterial genomes. In this case, the substitution rates are faster in genomes that evolve under mutational bias that favor hydrophobic amino acids by preferentially incorporating the nucleotide Thymine that is more frequent in hydrophobic codons. This appearingly contradictory result arises because buried sites occupied by hydrophobic amino acids are characterized by larger selective factors that largely amplify the substitution rate between hydrophobic amino acids, while the selective factors of exposed sites have a weaker effect. Thus, changes in the mutational bias produce deep effects on the biophysical properties of the protein (hydrophobicity) and on its evolutionary properties (sequence entropy and substitution rate) at the same time. The program Prot_evol that implements the two site-specific substitution processes is freely available at https://ub.cbm.uam.es/prot_fold_evol/prot_fold_evol_soft_main.php#Prot_Evol.

The plastid accD gene encodes a subunit of the acetyl-CoA carboxylase (ACCase) enzyme. The length of accD gene has been supposed to expand in Cryptomeria japonica, Taiwania cryptomerioides, Cephalotaxus, Taxus chinensis, and Podocarpus lambertii, and the main reason for this phenomenon was the existence of tandemly repeated sequences. However, it is still unknown whether the accD gene length in other cupressophytes has expanded. Here, in order to investigate how widespread this phenomenon was, 18 accD sequences and its surrounding regions of cupressophyte were sequenced and analyzed. Together with 39 GenBank sequence data, our taxon sampling covered all the extant gymnosperm orders. The repetitive elements and substitution rates of accD among 57 gymnosperm species were analyzed, the results show: (1) Reading frame length of accD gene in 18 cupressophytes species has also expanded. (2) Many repetitive elements were identified in accD gene of cupressophyte lineages. (3) The synonymous and non-synonymous substitution rates of accD were accelerated in cupressophytes. (4) accD was located in rearrangement endpoints. These results suggested that repetitive elements may mediate the chloroplast genome rearrangement and accelerated the substitution rates.

The number of amino acids that occupy a given protein site during evolution reflects the selective constraints operating on the site. This evolutionary variability is strongly influenced by the structural properties of the site in the native structure, and it is quantified either through sequence entropy or through substitution rates. However, while the sequence entropy only depends on the equilibrium frequencies of the amino acids, the substitution rate also depends on the exchangeability matrix that describes mutations in the mathematical model of the substitution process. Here we apply two variants of a mathematical model of protein evolution with selection for protein stability, both against unfolding and against misfolding. Exploiting the approximation of independent sites, these models allow computing site-specific substitution processes that satisfy global constraints on folding stability. We find that site-specific substitution rates do not depend only on the selective constraints acting on the site, quantified through its sequence entropy. In fact, polar sites evolve faster than hydrophobic sites even for equal sequence entropy, as a consequence of the fact that polar amino acids are characterized by higher mutational exchangeability than hydrophobic ones. Accordingly, the model predicts that more polar proteins tend to evolve faster. Nevertheless, these results change if we compare proteins that evolve under different mutation biases, such as orthologous proteins in different bacterial genomes. In this case, the substitution rates are faster in genomes that evolve under mutational bias that favor hydrophobic amino acids by preferentially incorporating the nucleotide Thymine that is more frequent in hydrophobic codons. This appearingly contradictory result arises because buried sites occupied by hydrophobic amino acids are characterized by larger selective factors that largely amplify the substitution rate between hydrophobic amino acids, while the selective factors of exposed sites have a weaker effect. Thus, changes in the mutational bias produce deep effects on the biophysical properties of the protein (hydrophobicity) and on its evolutionary properties (sequence entropy and substitution rate) at the same time. The program Prot_evol that implements the two site-specific substitution processes is freely available at https://ub.cbm.uam.es/prot_fold_evol/prot_fold_evol_soft_main.php#Prot_Evol. [ABSTRACT FROM AUTHOR]

The plastid accD gene encodes a subunit of the acetyl-CoA carboxylase (ACCase) enzyme. The length of accD gene has been supposed to expand in Cryptomeria japonica, Taiwania cryptomerioides, Cephalotaxus, Taxus chinensis, and Podocarpus lambertii, and the main reason for this phenomenon was the existence of tandemly repeated sequences. However, it is still unknown whether the accD gene length in other cupressophytes has expanded. Here, in order to investigate how widespread this phenomenon was, 18 accD sequences and its surrounding regions of cupressophyte were sequenced and analyzed. Together with 39 GenBank sequence data, our taxon sampling covered all the extant gymnosperm orders. The repetitive elements and substitution rates of accD among 57 gymnosperm species were analyzed, the results show: (1) Reading frame length of accD gene in 18 cupressophytes species has also expanded. (2) Many repetitive elements were identified in accD gene of cupressophyte lineages. (3) The synonymous and non-synonymous substitution rates of accD were accelerated in cupressophytes. (4) accD was located in rearrangement endpoints. These results suggested that repetitive elements may mediate the chloroplast genome rearrangement and accelerated the substitution rates. [ABSTRACT FROM AUTHOR]

Apostasioideae, consists of only two genera, Apostasia and Neuwiedia, which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of Apostasia wallichii and Neuwiedia singapureana were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids. Unlike many orchid plastomes (e.g., Paphiopedilum and Vanilla), the plastomes of Apostasioideae contain a full set of 11 functional NADH dehydrogenase (ndh) genes. The distribution of repeat sequences and simple sequence repeat elements enhanced the view that the mutation rate of non-coding regions was higher than that of coding regions. The 10 loci—ndhA intron, matK-5′trnK, clpP-psbB, rps8-rpl14, trnT-trnL, 3′trnK-matK, clpP intron, psbK-trnK, trnS-psbC, and ndhF-rpl32—that had the highest degrees of sequence variability were identified as mutational hotspots for the Apostasia plastome. Furthermore, our results revealed that plastid genes exhibited a variable evolution rate within and among different orchid genus. Considering the diversified evolution of both coding and non-coding regions, we suggested that the plastome-wide evolution of orchid species was disproportional. Additionally, the sequences flanking the inverted repeat/small single copy (IR/SSC) junctions of photosynthetic orchid plastomes were categorized into three types according to the presence/absence of ndh genes. Different evolutionary dynamics for each of the three IR/SSC types of photosynthetic orchid plastomes were also proposed.

Objectives: Hepatitis A virus (HAV), transmitted mainly through the fecal-oral route, is one of the major causes of acute viral hepatitis worldwide. HAV is endemic in China. This study performed genetic and evolutionary analysis of HAV isolates circulated in the country. Methods: Clinical samples were collected and HAV nucleotide and deduced amino acid sequences were analyzed. 70 representative sequences of HAV VP3-VP1-2A regions sampled from 1988 to 2014 were compared and characterized using the Bayesian Markov Chain Monte Carlo approach (BEAST software, Version1.7.5). Results: All isolates from China in this study belonged to genotype I, with most of the samples clustering in subgenotype IA, while several unique amino acid variants were observed. The estimated mean substitution rate was 5.56×10-4 substitutions / site / year, the time to the most recent common ancestor of genotype I isolates in China was calculated to be around 180 years ago. Skyline plots showed the incidence of HAV went down gradually from the mid-1990s. Conclusions: The evolution estimations were consistent with the laboratory and epidemiological results. Several isolates from China showed amino acid changes close to the immunodominant sites, which needs to be further analyzed. The study results have indicated the effectiveness of improving economic and sanitation levels together with HAV vaccination to control HAV-related infections in China.

Protein structures strongly influencemolecular evolution. In particular, the evolutionary rate of a protein site depends on the number of its native contacts. Stability-constrained models of protein evolution consider this influence of protein structure on evolution by predicting the effect of mutations on the stability of the native state, but they currently neglect how mutations affect the protein structure. These models predict that buried protein sites with more native contacts are more constrained by natural selection and less variable, as observed. Nevertheless, previous work did not consider the stability against compact misfolded conformations, although it is known that the negative design that destabilizes these misfolded conformations influences protein evolution significantly. Here, we show that stability-constrained models that consider misfolding predict that site-specific sequence entropy and substitution rate peak at amphiphilic sites with an intermediate number of contacts, as these sites are less constrained than exposed sites with few contacts whose hydrophobicity must be limited. This result holds both for amean-field model with independent sites and for a pairwisemodel that takes as a reference the wild-type sequence, but it contrasts with the observations that indicate that the entropy and the substitution rate decrease monotonically with the number of contacts. Our work suggests that stability-constrained models overestimate the tolerance of amphiphilic sites against mutations, either because of the limits of the free energy function or, more importantly in our opinion, because they do not consider how mutations perturb the native protein structure. [ABSTRACT FROM AUTHOR]

Squamates include all lizards and snakes, and display some of the most diverse and extreme morphological adaptations among vertebrates. However, compared with birds and mammals, relatively few resources exist for comparative genomic analyses of squamates, hampering efforts to understand the molecular bases of phenotypic diversification in such a speciose clade. In particular, the ~400 species of anole lizard represent an extensive squamate radiation. Here, we sequence and assemble the draft genomes of three anole species--Anolis frenatus, Anolis auratus, and Anolis apletophallus--for comparison with the available reference genome of Anolis carolinensis. Comparative analyses reveal a rapid background rate of molecular evolution consistent with a model of punctuated equilibrium, and strong purifying selection on functional genomic elements in anoles. We find evidence for accelerated evolution in genes involved in behavior, sensory perception, and reproduction, as well as in genes regulating limb bud development and hindlimb specification. Morphometric analyses of anole fore and hindlimbs corroborated these findings. We detect signatures of positive selection across several genes related to the development and regulation of the forebrain, hormones, and the iguanian lizard dewlap, suggesting molecular changes underlying behavioral adaptations known to reinforce species boundaries were a key component in the diversification of anole lizards. [ABSTRACT FROM AUTHOR]

Haemosporidians are a diverse group of vector-borne parasitic protozoa that includes the agents of human malaria; however, most of the described species are found in birds and reptiles. Although our understanding of these parasites' diversity has expanded by analyses of their mitochondrial genes, there is limited information on these genes' evolutionary rates. Here, 114 mitochondrial genomes (mtDNA) were studied from species belonging to four genera: Leucocytozoon, Haemoproteus, Hepatocystis, and Plasmodium. Contrary to previous assertions, the mtDNA is phylogenetically informative. The inferred phylogeny showed that, like the genus Plasmodium, the Leucocytozoon and Haemoproteus genera are not monophyletic groups. Although sensitive to the assumptions of the molecular dating method used, the estimated times indicate that the diversification of the avian haemosporidian subgenera/genera took place after the Cretaceous-Paleogene boundary following the radiation of modern birds. Furthermore, parasite clade differences in mtDNA substitution rates and strength of negative selection were detected. These differences may affect the biological interpretation of mtDNA gene lineages used as a proxy to species in ecological and parasitological investigations. Given that the mitochondria are critically important in the parasite life cycle stages that take place in the vector and that the transmission of parasites belonging to particular clades has been linked to specific insect families/subfamilies, this study suggests that differences in vectors have affected the mode of evolution of haemosporidian mtDNA genes. The observed patterns also suggest that the radiation of haemosporidian parasites may be the result of community-level evolutionary processes between their vertebrate and invertebrate hosts. [ABSTRACT FROM AUTHOR]

Heterotrophic carbon acquisition is the most unusual lifestyle in plants, whereby the heterotrophs obtain water, nutrients, and macromolecules from either another plant or a fungus. Besides numerous morphological changes that accompany the transition to a fully heterotrophic lifestyle in plants, the so-called parasitic reduction syndrome manifests at the molecular level, especially in the plastid genome. Here, we provide an overview of the sizes, architectures, and coding capacity of plastid genomes in heterotrophic land plants, with a major focus on flowering plants. Our compilation of plastomes of over 75 taxa covering 15 lineages of haustorial parasites and mycoheterotrophs reveals novel insights into the order of housekeeping gene losses, where apparently several plastid tRNA gene deletions precede the loss of ribosomal subunits. A comparison of the three major conceptual models of plastome degradation en route to heterotrophy in plants shows that plastid evolutionary trajectories are essentially convergent across lineages--independent of the feeding type. However, several questions regarding the series and timing of functional and physical gene losses remain unclear, in part because functional data are widely lacking. Nevertheless, the currently available evolutionary models of reductive plastome evolution provide excellent starting points for leaving the paths of descriptive science towards hypothesis-driven research. [ABSTRACT FROM AUTHOR]

A number of plant groups have been proposed as ideal systems to explore plastid inheritance, plastome evolution and plastome-nuclear genome coevolution. Quick generation times and a compact nuclear genome in Arabidopsis thaliana, the relative ease of plastid isolation from Spinacia oleracea and the tractability of plastid transformation in Nicotiana tabacum are all desirable attributes in a model system; however, these and most other groups all lack novelty in terms of plastome structure and nucleotide sequence evolution. Contemporary sequencing and assembly technologies have facilitated analyses of atypical plastomes and, as predicted by early investigations, Geraniaceae plastomes have experienced unprecedented rearrangements relative to the canonical structure and exhibit remarkably high rates of synonymous and nonsynonymous nucleotide substitutions. While not the only lineage with unusual plastome features, likely no other group represents the array of aberrant phenomena recorded for the family. In this chapter, Geraniaceae plastomes will be discussed and, where possible, compared with other taxa. [ABSTRACT FROM AUTHOR]

The molecular clock hypothesis is an important concept in biology. Deviations from a constant rate of nucleotide substitution have been found widely among lineages, genomes, genes and individual sites. Phylogenetic research can accommodate for these differences in applying specific models of evolution. Lineage-specific rate heterogeneity however can generate bi- or multimodal distributions of substitution rates across the branches of a tree and this may mislead phylogenetic inferences with currently available models. The plant family Annonaceae is an excellent case to study lineage-specific rate heterogeneity. The two major sister subfamilies, Annonoideae and Malmeoideae, have shown great discrepancies in branch lengths. We used high-throughput sequencing data of 72 genes, 99 spacers and 16 introns from 24 chloroplast genomes and nuclear ribosomal DNA of 23 species to study the molecular rate of evolution in Annonaceae. In all analyses, longer branch lengths and/or higher substitution rates were found for the Annonoideae compared to the Malmeoideae. The Annonaceae had wide variability in chloroplast length, ranging from minimal 175,684 bp to 201,723 for Annonoideae and minimal 152,357 to 170,985 bp in Malmeoideae, mostly reflecting variation in inverted-repeat length. The Annonoideae showed a higher GC-content in the conserved parts of the chloroplast genome and higher omega ( d N / d S )-ratios than the Malmeoideae, which could indicate less stringent purifying selection, a pattern that has been found in groups with small population sizes. This study generates new insights into the processes causing lineage-specific rate heterogeneity, which could lead to improved phylogenetic methods. [ABSTRACT FROM AUTHOR]

In many species, spermatogenesis involves more cell divisions than oogenesis, and the male germline, therefore, accumulates more DNA replication errors, a phenomenon known as male mutation bias. The extent of male mutation bias (α) is estimated by comparing substitution rates of the X, Y, and autosomal chromosomes, as these chromosomes spend different proportions of their time in the germlines of the two sexes. Malemutation bias has been characterized in placental and marsupial mammals as well as birds, but analyses in monotremes failed to detect any such bias. Monotremes are an ancient lineage of egg-laying mammals with distinct biological properties, which include unique germline features. Here, we sought to assess the presence and potential characteristics of male mutation bias in platypus and the short-beaked echidna based on substitution rate analyses of X, Y, and autosomes. We established the presence of moderate male mutation bias in monotremes, corresponding to an α value of 2.12-3.69. Given that it has been unclear what proportion of the variation in substitution rates on the different chromosomal classes is really due to differential number of replications, we analyzed the influence of other confounding forces (selection, replication-timing, etc.) and found that male mutation bias is the main force explaining the between-chromosome classes differences in substitution rates. Finally, we estimated the proportion of variation at the gene level in substitution rates that is owing to replication effects and found that this phenomenon can explain>68%of these variations in monotremes, and in control species, rodents, and primates. [ABSTRACT FROM AUTHOR]

Mitochondrial DNA (mtDNA) sequences are becoming increasingly important in the study of human population history. Here, we explore the differences in the amount of information of different mtDNA regions and their utility for the reconstruction of South American population history. We analyzed six data sets comprising 259 mtDNA sequences from South America: Complete mtDNA, Coding, Control, hypervariable region I (HVRI), Control plus cytochrome b (cytb), and cytb plus 12S plus 16S. The amount of information in each data set was estimated employing several site-by-site and haplotype-based statistics, distances among sequences, neighbor-joining trees, distances among the estimated trees, Bayesian skyline plots, and phylogenetic informativeness profiles. The different mtDNA data sets have different amounts of information to reconstruct demographic events and phylogenetic trees with confidence. Whereas HVRI is not suitable for phylogenetic reconstruction of ancient clades, this region, as well as the Control data set, displays information for the demographic reconstruction during the Holocene period, probably because of the high rate of mutation of these regions. As expected, the Complete mtDNA and Coding data sets, displaying slower rates of mutation, present suitable information to estimate the founding subhaplogroups that populated South America and for the reconstruction of ancient demographic events. Our results point out the importance of evaluating the utility of different DNA regions to respond to different questions and problems in the human population studies, mainly considering the time scale of the phenomenon and the informativeness of the molecular region in a particular geographical area. [ABSTRACT FROM AUTHOR]

The majority of variation in rates of molecular evolution among seed plants remains both unexplored and unexplained. Although some attention has been given to flowering plants, reports of molecular evolutionary rates for their sister plant clade (gymnosperms) are scarce, and to our knowledge differences in molecular evolution among seed plant clades have never been tested in a phylogenetic framework. Angiosperms and gymnosperms differ in a number of features, of which contrasting reproductive biology, life spans, and population sizes are the most prominent. The highly conserved morphology of gymnosperms evidenced by similarity of extant species to fossil records and the high levels of macrosynteny at the genomic level have led scientists to believe that gymnosperms are slow-evolving plants, although some studies have offered contradictory results. Here, we used 31,968 nucleotide sites obtained from orthologous genes across a wide taxonomic sampling that includes representatives of most conifers, cycads, ginkgo, and many angiosperms with a sequenced genome. Our results suggest that angiosperms and gymnosperms differ considerably in their rates of molecular evolution per unit time, with gymnosperm rates being, on average, seven times lower than angiosperm species. Longer generation times and larger genome sizes are some of the factors explaining the slow rates of molecular evolution found in gymnosperms. In contrast to their slow rates of molecular evolution, gymnosperms possess higher substitution rate ratios than angiosperm taxa. Finally, our study suggests stronger and more efficient purifying and diversifying selection in gymnosperm than in angiosperm species, probably in relation to larger effective population sizes. [ABSTRACT FROM AUTHOR]

We assembled the plastome of the temperate, Southern Hemisphere liana Muehlenbeckia australis from high throughput sequencing data (paired-end Illumina reads) generated from total genomic DNA sequencing libraries. M. australis’ chloroplast genome sequence (GenBank: MG604297) is 163,484 bp in length and composed of long single copy (LSC; 88,166 bp) and short single copy (SSC; 13,486 bp) regions flanked by inverted repeats (IR; 30,916 bp each) typical for angiosperms. The plastome includes 131 genes comprising 83 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes, two possible pseudogenes, psbL and rpl23 with internal stop codons, and truncated repeats of ndhF and rps19 at IR boundaries.

Observed Variability (OV) and Tree Independent Generation of Evolutionary Rates (TIGER) are quick and easy-to-apply tree-independent methods that have been proposed to provide unbiased estimates of each character’s rate of evolution and serve as the basis for excluding rapidly evolving characters. Both methods have been applied to multiple phylogenomic datasets, and in many cases the authors considered their trees inferred from the OV- and TIGER-delimited sub-matrices to be better estimates of the phylogeny than their trees based on all characters. In this study we use four sets of simulations and an empirical phylogenomic example to demonstrate that both methods share a systematic bias against characters with more symmetric distributions of character states, against characters with greater observed character-state space, and against large clades in the context of character conflict. As a result these methods can favor convergences and reversals over synapomorphy, exacerbate long-branch attraction, and produce mutually exclusive phylogenetic inferences that are dependent upon differential taxon sampling. We assert that neither OV nor TIGER should be relied upon to increase the ratio of phylogenetic to non-phylogenetic signal in a data matrix. We also assert that skepticism is warranted for empirical phylogenetic results that are based on OV- and/or TIGER-based character deletion wherein a small clade is supported after deletion of characters, yet is contradicted by a larger clade when the entire data matrix was analyzed. [ABSTRACT FROM AUTHOR]

Substitution rates are known to be variable among genes, chromosomes, species, and lineages due to multifarious biological processes. Here, we consider another source of substitution rate variation due to a technical bias associated with gene tree discordance. Discordance has been found to be rampant in genome-wide data sets, often due to incomplete lineage sorting (ILS). This apparent substitution rate variation is caused when substitutions that occur on discordant gene trees are analyzed in the context of a single, fixed species tree. Such substitutions have to be resolved by proposing multiple substitutions on the species tree, and we therefore refer to this phenomenon as Substitutions Produced by ILS (SPILS). We use simulations to demonstrate that SPILS has a larger effect with increasing levels of ILS, and on trees with larger numbers of taxa. Specific branches of the species trees are consistently, but erroneously, inferred to be longer or shorter, and we show that these branches can be predicted based on discordant tree topologies. Moreover, we observe that fixing a species tree topology when performing tests of positive selection increases the false positive rate, particularly for genes whose discordant topologies are most affected by SPILS. Finally, we use data from multiple Drosophila species to show that SPILS can be detected in nature. Although the effects of SPILS are modest per gene, it has the potential to affect substitution rate variation whenever high levels of ILS are present, particularly in rapid radiations. The problems outlined here have implications for character mapping of any type of trait, and for any biological process that causes discordance. We discuss possible solutions to these problems, and areas in which they are likely to have caused faulty inferences of convergence and accelerated evolution. [ABSTRACT FROM AUTHOR]

The use of amino acid substitution matrices to model protein evolution has yielded important insights into both the evolutionary process and the properties of specific protein families. In order to make these models tractable, standard substitution matrices represent the average results of the evolutionary process rather than the underlying molecular biophysics and population genetics, treating proteins as a set of independently evolving sites rather than as an integrated biomolecular entity. With advances in computing and the increasing availability of sequence data, we now have an opportunity to move beyond current substitution matrices to more interpretable mechanistic models with greater fidelity to the evolutionary process of mutation and selection and the holistic nature of the selective constraints. As part of this endeavour, we consider how epistatic interactions induce spatial and temporal rate heterogeneity, and demonstrate how these generally ignored factors can reconcile standard substitution rate matrices and the underlying biology, allowing us to better understand the meaning of these substitution rates. Using computational simulations of protein evolution, we can demonstrate the importance of both spatial and temporal heterogeneity in modelling protein evolution. [ABSTRACT FROM AUTHOR]

Mitochondrial genomes (mitogenomes) of flowering plants are well known for their extreme diversity in size, structure, gene content, and rates of sequence evolution and recombination. In contrast, little is known about mitogenomic diversity and evolution within gymnosperms. Only a single complete genome sequence is available, from the cycad Cycas taitungensis, while limited information is available for the one draft sequence, from Norway spruce (Picea abies). To examine mitogenomic evolution in gymnosperms, we generated complete genome sequences for the ginkgo tree (Ginkgo biloba) and a gnetophyte (Welwitschia mirabilis). There is great disparity in size, sequence conservation, levels of shared DNA, and functional content among gymnosperm mitogenomes. The Cycas and Ginkgo mitogenomes are relatively small, have low substitution rates, and possess numerous genes, introns, and edit sites; we infer that these properties were present in the ancestral seed plant. By contrast, the Welwitschia mitogenome has an expanded size coupled with accelerated substitution rates and extensive loss of these functional features. The Picea genome has expanded further, to more than 4Mb. With regard to structural evolution, the Cycas and Ginkgo mitogenomes share a remarkable amount of intergenic DNA, which may be related to the limited recombinational activity detected at repeats in Ginkgo. Conversely, the Welwitschia mitogenome shares almost no intergenic DNA with any other seed plant. By conducting the first measurements of rates of DNA turnover in seed plant mitogenomes, we discovered that turnover rates vary by orders of magnitude among species. [ABSTRACT FROM AUTHOR]