Comparative Phylogenetic Analysis Research Articles

Degree of anisogamy is unrelated to the intensity of sexual selection

Males and females often display different behaviours and, in the context of reproduction, these behaviours are labelled sex roles. The Darwin–Bateman paradigm argues that the root of these differences is anisogamy (i.e., differences in size and/or function of gametes between the sexes) that leads to biased sexual selection, and sex differences in parental care and body size. This evolutionary cascade, however, is contentious since some of the underpinning assumptions have been questioned. Here we investigate the relationships between anisogamy, sexual size dimorphism, sex difference in parental care and intensity of sexual selection using phylogenetic comparative analyses of 64 species from a wide range of animal taxa. The results question the first step of the Darwin–Bateman paradigm, as the extent of anisogamy does not appear to predict the intensity of sexual selection. The only significant predictor of sexual selection is the relative inputs of males and females into the care of offspring. We propose that ecological factors, life-history and demography have more substantial impacts on contemporary sex roles than the differences of gametic investments between the sexes.

Interspecific variation in bristle number on forewings of tiny insects does not influence clap-and-fling aerodynamics.

Miniature insects must overcome significant viscous resistance in order to fly. They typically possess wings with long bristles on the fringes and use a clap-and-fling mechanism to augment lift. These unique solutions to the extreme conditions of flight at tiny sizes (<2 mm body length) suggest that natural selection has optimized wing design for better aerodynamic performance. However, species vary in wingspan, number of bristles (n) and bristle gap (G) to diameter (D) ratio (G/D). How this variation relates to body length (BL) and its effects on aerodynamics remain unknown. We measured forewing images of 38 species of thrips and 21 species of fairyflies. Our phylogenetic comparative analyses showed that n and wingspan scaled positively and similarly with BL across both groups, whereas G/D decreased with BL, with a sharper decline in thrips. We next measured aerodynamic forces and visualized flow on physical models of bristled wings performing clap-and-fling kinematics at a chord-based Reynolds number of 10 using a dynamically scaled robotic platform. We examined the effects of dimensional (G, D, wingspan) and non-dimensional (n, G/D) geometric variables on dimensionless lift and drag. We found that: (1) increasing G reduced drag more than decreasing D; (2) changing n had minimal impact on lift generation; and (3) varying G/D minimally affected aerodynamic forces. These aerodynamic results suggest little pressure to functionally optimize n and G/D. Combined with the scaling relationships between wing variables and BL, much wing variation in tiny flying insects might be best explained by underlying shared growth factors.

Convergent flight morphology among Müllerian mimic mutualists.

Müllerian mimicry involves a signal mutualism between prey species, shaped by visually hunting predators, and recent work has emphasized the importance of color pattern. Predators respond to more than color pattern, however, and other traits are much less studied. This article examines the hypothesis of convergent evolution in flight-related morphology among eight mimicry complexes composed of 51 butterfly species (Nymphalidae, Danainae, Ithomiini) from a single community in Ecuador. Phylogenetic comparative analyses of 14 variables indicated strong morphological differences between mimicry complexes belonging to three clusters of morphological space ("large yellow transparent," "tiger," and "transparent"), not the eight predicted based on color pattern alone. Analyses found convergence within mimicry complexes, convergence between mimicry complexes within morphospace clusters, and divergence between mimicry complexes from different morphospace clusters. These three clusters differed in size, and body and wing shape, predicting that flight biomechanics also converge (i.e., locomotor mimicry). Potential constraints on evolution of morphological mimicry related to predator discrimination, and evolutionary rates, likely e xplain why flight-related morphology differences were limited to three clusters of morphological space. Finally, the added complexity that flight-related morphology brings to signals between predator and prey indicates that evolutionary switches in color pattern are not all equally likely, potentially limiting the evolution of color patterns if they do not match morphology.

Comparing ITS‐2 and COI as DNA barcode markers for the most common cyathostomin species based on comparative phylogenetic analysis

Comparing ITS‐2 and COI as DNA barcode markers for the most common cyathostomin species based on comparative phylogenetic analysis

Identification and Full Characterisation of Two Novel Crustacean Infecting Members of the Family Nudiviridae Provides Support for Two Subfamilies.

Multiple enveloped viruses with rod-shaped nucleocapsids have been described, infecting the epithelial cell nuclei within the hepatopancreas tubules of crustaceans. These bacilliform viruses share the ultrastructural characteristics of nudiviruses, a specific clade of viruses infecting arthropods. Using histology, electron microscopy and high throughput sequencing, we characterise two further bacilliform viruses from aquatic hosts, the brown shrimp (Crangon crangon) and the European shore crab (Carcinus maenas). We assembled the full double stranded, circular DNA genome sequences of these viruses (~113 and 132 kbp, respectively). Comparative genomics and phylogenetic analyses confirm that both belong within the family Nudiviridae but in separate clades representing nudiviruses found in freshwater and marine environments. We show that the three thymidine kinase (tk) genes present in all sequenced nudivirus genomes, thus far, were absent in the Crangon crangon nudivirus, suggesting there are twenty-eight core genes shared by all nudiviruses. Furthermore, the phylogenetic data no longer support the subdivision of the family Nudiviridae into four genera (Alphanudivirus to Deltanudivirus), as recently adopted by the International Committee on Taxonomy of Viruses (ICTV), but rather shows two main branches of the family that are further subdivided. Our data support a recent proposal to create two subfamilies within the family Nudiviridae, each subdivided into several genera.

Proteome Analysis of Condensed Barley Mitotic Chromosomes.

Proteins play a major role in the three-dimensional organization of nuclear genome and its function. While histones arrange DNA into a nucleosome fiber, other proteins contribute to higher-order chromatin structures in interphase nuclei, and mitotic/meiotic chromosomes. Despite the key role of proteins in maintaining genome integrity and transferring hereditary information to daughter cells and progenies, the knowledge about their function remains fragmentary. This is particularly true for the proteins of condensed chromosomes and, in particular, chromosomes of plants. Here, we purified barley mitotic metaphase chromosomes by a flow cytometric sorting and characterized their proteins. Peptides from tryptic protein digests were fractionated either on a cation exchanger or reversed-phase microgradient system before liquid chromatography coupled to tandem mass spectrometry. Chromosomal proteins comprising almost 900 identifications were classified based on a combination of software prediction, available database localization information, sequence homology, and domain representation. A biological context evaluation indicated the presence of several groups of abundant proteins including histones, topoisomerase 2, POLYMERASE 2, condensin subunits, and many proteins with chromatin-related functions. Proteins involved in processes related to DNA replication, transcription, and repair as well as nucleolar proteins were found. We have experimentally validated the presence of FIBRILLARIN 1, one of the nucleolar proteins, on metaphase chromosomes, suggesting that plant chromosomes are coated with proteins during mitosis, similar to those of human and animals. These results improve significantly the knowledge of plant chromosomal proteins and provide a basis for their functional characterization and comparative phylogenetic analyses.

Conformity to Bergmann's rule in birds depends on nest design and migration.

Ecogeographical rules attempt to explain large‐scale spatial patterns in biological traits. One of the most enduring examples is Bergmann's rule, which states that species should be larger in colder climates due to the thermoregulatory advantages of larger body size. Support for Bergmann's rule, however, is not consistent across taxonomic groups, raising questions about what factors may moderate its effect. Behavior may play a crucial, yet so far underexplored, role in mediating the extent to which species are subject to environmental selection pressures in colder climates. Here, we tested the hypothesis that nest design and migration influence conformity to Bergmann's rule in a phylogenetic comparative analysis of the birds of the Western Palearctic, a group encompassing dramatic variation in both climate and body mass. We predicted that migratory species and those with more protected nest designs would conform less to the rule than sedentary species and those with more exposed nests. We find that sedentary, but not short‐ or long‐distance migrating, species are larger in colder climates. Among sedentary species, conformity to Bergmann's rule depends, further, on nest design: Species with open nests, in which parents and offspring are most exposed to adverse climatic conditions during breeding, conform most strongly to the rule. Our findings suggest that enclosed nests and migration enable small birds to breed in colder environments than their body size would otherwise allow. Therefore, we conclude that behavior can substantially modify species’ responses to environmental selection pressures.

Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum

BackgroundThe identification and functional analysis of genes that improve tolerance to low potassium stress in S. spontaneum is crucial for breeding sugarcane cultivars with efficient potassium utilization. Calcineurin B-like (CBL) protein is a calcium sensor that interacts with specific CBL-interacting protein kinases (CIPKs) upon plants’ exposure to various abiotic stresses.ResultsIn this study, nine CBL genes were identified from S. spontaneum. Phylogenetic analysis of 113 CBLs from 13 representative plants showed gene expansion and strong purifying selection in the CBL family. Analysis of CBL expression patterns revealed that SsCBL01 was the most commonly expressed gene in various tissues at different developmental stages. Expression analysis of SsCBLs under low K+ stress indicated that potassium deficiency moderately altered the transcription of SsCBLs. Subcellular localization showed that SsCBL01 is a plasma membrane protein and heterologous expression in yeast suggested that, while SsCBL01 alone could not absorb K+, it positively regulated K+ absorption mediated by the potassium transporter SsHAK1.ConclusionsThis study provided insights into the evolution of the CBL gene family and preliminarily demonstrated that the plasma membrane protein SsCBL01 was involved in the response to low K+ stress in S. spontaneum.

Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer.

Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot on foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onions. Our recent host range evaluation study identified two pathovars; P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. that are pathogenic on onions and millets or on millets only, respectively. In the current study, we developed a pan-genome using the whole genome sequencing of newly identified/classified Psi strains from both pathovars [pv. cepacicola (n = 4) and pv. setariae (n = 13)]. The full spectrum of the pan-genome contained 7030 genes. Among these, 3546 (present in genomes of all 17 strains) were the core genes that were a subset of 3682 soft-core genes (present in ≥16 strains). The accessory genome included 1308 shell genes and 2040 cloud genes (present in ≤2 strains). The pan-genome showed a clear linear progression with >6000 genes, suggesting that the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison with core genome SNPs-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study using Psi strains from both pathovars along with strains from other Pantoea species, namely, P. stewartii subsp. stewartii LMG 2715T, P. ananatis LMG 2665T, P. agglomerans LMG L15, and P. allii LMG 24248T. A total of 317 HGT events among four Pantoea species were identified with most gene transfer events occurring between Psi pv. cepacicola and Psi pv. setariae. Pan-GWAS analysis predicted a total of 154 genes, including seven gene-clusters, which were associated with the pathogenicity phenotype (necrosis on seedling) on onions. One of the gene-clusters contained 11 genes with known functions and was found to be chromosomally located.

Pathological analysis and genetic characterization of the first outbreak H5N8 subtype avian influenza virus isolated from wild swan in Shandong, China.

In January 2021, an outbreak of H5N8 subtype avian influenza was identified from wild mute swans (Cygnus olor) in an overwintering site located within Yellow River Delta Nature Reserve in Shandong, China, for the first time. We sequenced the hemagglutinin (HA) and neuraminidase (NA) genome segments of the virus, named A/mute swan/Shandong/1/2021 (H5N8), and explored the genetic characterization and comparative phylogenetic analysis to track its origin. The wild swans prior to death showed nervous signs accompanied by a twisted neck. The major pathological changes of the heart, lung, trachea, kidney, spleen, and glandular stomach were hemorrhage, and extensive necrotic lesions in the liver and pancreas were also observed. Further analysis of the HA and NA phylogenetic trees generated by H5N8 strains isolated worldwide revealed that the isolate has a close genetic relationship with the H5N8 subtype avian influenza virus (AIV) recently isolated in Korea and Japan from 2020 to 2021, suggesting the potential role of mute swans in the global dissemination of the H5N8 subtype AIVs along the migration routes. Therefore, enhanced active surveillance in wild and domestic birds is required to monitor the introduction and spread of the H5N8 subtype AIV by migratory birds in order to decrease the risk of H5N8 outbreaks.

Evolution of Renal-Disease Factor APOL1 Results in Cis and Trans Orientations at the Endoplasmic Reticulum That Both Show Cytotoxic Effects.

The recent and exclusively in humans and a few other higher primates expressed APOL1 (apolipoprotein L1) gene is linked to African human trypanosomiasis (also known as African sleeping sickness) as well as to different forms of kidney diseases. Whereas APOL1’s role as a trypanolytic factor is well established, pathobiological mechanisms explaining its cytotoxicity in renal cells remain unclear. In this study, we compared the APOL family members using a combination of evolutionary studies and cell biological experiments to detect unique features causal for APOL1 nephrotoxic effects.We investigated available primate and mouse genome and transcriptome data to apply comparative phylogenetic and maximum likelihood selection analyses. We suggest that the APOL gene family evolved early in vertebrates and initial splitting occurred in ancestral mammals. Diversification and differentiation of functional domains continued in primates, including developing the two members APOL1 and APOL2. Their close relationship could be diagnosed by sequence similarity and a shared ancestral insertion of an AluY transposable element. Live-cell imaging analyses showed that both expressed proteins show a strong preference to localize at the endoplasmic reticulum (ER). However, glycosylation and secretion assays revealed that—unlike APOL2—APOL1 membrane insertion or association occurs in different orientations at the ER, with the disease-associated mutants facing either the luminal (cis) or cytoplasmic (trans) side of the ER. The various pools of APOL1 at the ER offer a novel perspective in explaining the broad spectrum of its observed toxic effects.

Sexual size dimorphism in lizards: Rensch's rule, reproductive mode, clutch size, and line fitting method effects.

Rensch's rule relates to a pattern whereby sexual size dimorphism is more female-biased in small-sized species and more male-biased in large-sized ones. We collected literature and museum data on the body size of males and females belonging to 4032 lizard species, as well as data on their reproductive modes and clutch sizes. We used phylogenetic comparative analyses, and general linear mixed models, to test Rensch's rule and examined how reproductive mode and clutch size affect sexual size dimorphism. Sexual size dimorphism was independent of clutch size in lizard species with variable clutch sizes and in oviparous lizards. Large litters were associated with female-biased sexual dimorphism in viviparous and in scincomorph lizards. Inference regarding Rensch's rule depended on the analytical method used to identify it. The widely used, but less conservative, reduced major axis regression usually support Rensch's rule while ordinary least squares regressions mostly show isometric relationships. The rule tended to apply more to oviparous than to viviparous lizards. We infer that Rensch's rule is, at best, a weak pattern in lizards. This is especially true in viviparous lineages where females reproduce infrequently and therefore evolve large sizes to maximise fecundity, resulting in female-biased dimorphism.

Comparative Chloroplast Genomes of Four Lycoris Species (Amaryllidaceae) Provides New Insight into Interspecific Relationship and Phylogeny.

Simple SummaryThe genus Lycoris (Amaryllidaceae) comprises about 20 species with high ornamental and medicinal value. However, germplasm identification is still difficult due to frequent interspecific hybridization and intraspecific morphological variation within this genus. Plastid genome sequencing has been proven to be a useful tool to identify closely related species and is widely used in the field of plant evolution and phylogeny. In the present study, we provided four chloroplast genomes of Lycoris and retrieved seven published species in the genus for comparative genomics and phylogenetic analyses. All these chloroplast genomes possess the typical quadripartite structure with conserved genome arrangement and gene content, yet their lengths varied due to expansion/contraction of the IR/SC boundaries. Phylogenetic relationships within Lycoris were resolved with high resolution using complete cp genome sequences. These results could not only offer a genome-scale platform for identification and utilization of Lycoris but also provide a phylogenomic framework for future studies in this genus.The genus Lycoris (Amaryllidaceae) consists of about 20 species, which is endemic to East Asia. Although the Lycoris species is of great horticultural and medical importance, challenges in accurate species identification persist due to frequent natural hybridization and large-scale intraspecific variation. In this study, we sequenced chloroplast genomes of four Lycoris species and retrieved seven published chloroplast (cp) genome sequences in this genus for comparative genomic and phylogenetic analyses. The cp genomes of these four newly sequenced species were found to be 158,405–158,498 bp with the same GC content of 37.8%. The structure of the genomes exhibited the typical quadripartite structure with conserved gene order and content. A total of 113 genes (20 duplicated) were identified, including 79 protein-coding genes (PCGs), 30 tRNAs, and 4 rRNAs. Phylogenetic analysis showed that the 11 species were clustered into three main groups, and L. sprengeri locate at the base of Lycoriss. The L. radiata was suggested to be the female donor of the L. incarnata, L. shaanxiensis, and L. squamigera. The L. straminea and L. houdyshelii may be derived from L. anhuiensis, L. chinensis, or L. longituba. These results could not only offer a genome-scale platform for identification and utilization of Lycoris but also provide a phylogenomic framework for future studies in this genus.

Sex-specific contributions to nest building in birds

Abstract The causes and consequences of interspecific variation in sex-specific contributions to animal parental care are relatively well understood during pregnancy or incubation and during offspring provisioning, but comparative patterns of sex-biased investment during nest-, den-, or other shelter-building have been almost completely overlooked. This is surprising because birthing shelters’ protective properties have important fitness consequences for both parents and offspring. Here, we address this gap in our knowledge by testing predictions concerning sex-specific contributions to avian nest building in more than 500 species of Western Palearctic birds in relation to the time available to breed and sex-specific reproductive effort, while also examining correlates with nesting site and nest structure. Using multivariate phylogenetic comparative and path analysis approaches, we found that, opposite to what had been predicted, species in which females build nests alone have shorter breeding seasons and breed at higher latitudes. In addition, species in which females lay larger clutch sizes and incubate eggs alone are more likely to have nests built by females alone, again countering predictions that reproductive contributions are not traded-off between the sexes. Finally, however, sex-specific nest building contributions were predictably related to nest site and structure, as species in which females built nests alone were more likely to have open cup nests relative to enclosed, domed nests of species in which both parents build. Our study provides important new insights, and generates several new questions for experimental research into the adaptive dynamics of sex-specific contributions prior or at the onset of parental care.

The Genome Analysis of the Human Lung-Associated Streptomyces sp. TR1341 Revealed the Presence of Beneficial Genes for Opportunistic Colonization of Human Tissues.

Streptomyces sp. TR1341 was isolated from the sputum of a man with a history of lung and kidney tuberculosis, recurrent respiratory infections, and COPD. It produces secondary metabolites associated with cytotoxicity and immune response modulation. In this study, we complement our previous results by identifying the genetic features associated with the production of these secondary metabolites and other characteristics that could benefit the strain during its colonization of human tissues (virulence factors, modification of the host immune response, or the production of siderophores). We performed a comparative phylogenetic analysis to identify the genetic features that are shared by environmental isolates and human respiratory pathogens. The results showed a high genomic similarity of Streptomyces sp. TR1341 to the plant-associated Streptomyces sp. endophyte_N2, inferring a soil origin of the strain. Putative virulence genes, such as mammalian cell entry (mce) genes were not detected in the TR1341’s genome. The presence of a type VII secretion system, distinct from the ones found in Mycobacterium species, suggests a different colonization strategy than the one used by other actinomycete lung pathogens. We identified a higher diversity of genes related to iron acquisition and demonstrated that the strain produces ferrioxamine B in vitro. These results indicate that TR1341 may have an advantage in colonizing environments that are low in iron, such as human tissue.

A New Enterobacter cloacae Bacteriophage EC151 Encodes the Deazaguanine DNA Modification Pathway and Represents a New Genus within the Siphoviridae Family

A novel Enterobacter cloacae phage, EC151, was isolated and characterized. Electron microscopy revealed that EC151 has a siphovirus-like virion morphology. The EC151 nucleotide sequence shows limited similarity to other phage genomes deposited in the NCBI GenBank database. The size of the EC151 genome is 60,753 bp and contains 58 putative genes. Thirty-nine of them encode proteins of predicted function, 18 are defined as hypothetical proteins, and one ORF identifies as the tRNA-Ser-GCT-encoding gene. Six ORFs were predicted to be members of the deazaguanine DNA modification pathway, including the preQ0 transporter. Comparative proteomic phylogenetic analysis revealed that phage EC151 represents a distinct branch within a group of sequences containing clades formed by members of the Seuratvirus, Nonagvirus, and Vidquintavirus genera. In addition, the EC151 genome showed gene synteny typical of the Seuratvirus, Nonagvirus, and Nipunavirus phages. The average genetic distances of EC151/Seuratvirus, EC151/Nonagvirus, and EC151/Vidquintavirus are approximately equal to those between the Seuratvirus, Nonagvirus, and Vidquintavirus genera (~0.7 substitutions per site). Therefore, EC151 may represent a novel genus within the Siphoviridae family. The origin of the deazaguanine DNA modification pathway in the EC151 genome can be traced to Escherichia phages from the Seuratvirus genus.

FGF gene family characterization provides insights into its adaptive evolution in Carnivora.

Fibroblast growth factors (FGFs) encoded by the FGF gene family can regulate development and physiology in animals. However, their evolutionary characteristics in Carnivora are largely unknown. In this study, we identified 660 sequences of three types of FGF genes from 30 unannotated genomes of Carnivora animals (before 7th May 2020), and the FGF genes from 52 Carnivora species were analyzed through the method of comparative genomics. Phylogenetic and selective pressure analyses were carried out based on the FGF genes of these 52 Carnivora species. The phylogenetic analysis results demonstrated that the FGF gene family was divided into 10 subfamilies and that FGF5 formed one clade rather than belonging to the subfamilies of FGF4 and FGF6. The evolutionary analysis results showed that the FGF genes were prominently subjected to purifying selection and were highly conserved in the process of Carnivora evolution. We also carried out phylogenetic comparative analyses, which indicated that the habitat was one of the factors that shaped the evolution of Carnivora FGF genes. The FGF1 and FGF6 genes were positively selected in the Carnivora animals, and positive selection signals were detected for the FGF19 gene in semiaquatic Carnivora animals. In summary, we clarified the phylogenetic and evolutionary characteristics of Carnivora FGF genes and provided valuable data for future studies on evolutionary characterization of Carnivora animals.

The Evolutionary Patterns of Genome Size in Ensifera (Insecta: Orthoptera).

Genomic size variation has long been a focus for biologists. However, due to the lack of genome size data, the mechanisms behind this variation and the biological significance of insect genome size are rarely studied systematically. The detailed taxonomy and phylogeny of the Ensifera, as well as the extensive documentation concerning their morphological, ecological, behavioral, and distributional characteristics, make them a strong model for studying the important scientific problem of genome size variation. However, data on the genome size of Ensifera are rather sparse. In our study, we used flow cytometry to determine the genome size of 32 species of Ensifera, the smallest one being only 1C = 0.952 pg with the largest species up to 1C = 19.135 pg, representing a 20-fold range. This provides a broader blueprint for the genome size variation of Orthoptera than was previously available. We also completed the assembly of nine mitochondrial genomes and combined mitochondrial genome data from public databases to construct phylogenetic trees containing 32 species of Ensifera and three outgroups. Based on these inferred phylogenetic trees, we detected the phylogenetic signal of genome size variation in Ensifera and found that it was strong in both males and females. Phylogenetic comparative analyses revealed that there were no correlations between genome size and body size or flight ability in Tettigoniidae. Reconstruction of ancestral genome size revealed that the genome size of Ensifera evolved in a complex pattern, in which the genome size of the grylloid clade tended to decrease while that of the non-grylloid clade expanded significantly albeit with fluctuations. However, the evolutionary mechanisms underlying variation of genome size in Ensifera are still unknown.

Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence

BackgroundDuplicated gene pairs produced by ancient polyploidy maintain high sequence similarity over a long period of time and may result from illegitimate recombination between homeologous chromosomes. The genomes of Asian cultivated rice Oryza sativa ssp. indica (XI) and Oryza sativa ssp. japonica (GJ) have recently been updated, providing new opportunities for investigating ongoing gene conversion events and their impact on genome evolution.ResultsUsing comparative genomics and phylogenetic analyses, we evaluated gene conversion rates between duplicated genes produced by polyploidization 100 million years ago (mya) in GJ and XI. At least 5.19–5.77% of genes duplicated across the three rice genomes were affected by whole-gene conversion after the divergence of GJ and XI at ~ 0.4 mya, with more (7.77–9.53%) showing conversion of only portions of genes. Independently converted duplicates surviving in the genomes of different subspecies often use the same donor genes. The ongoing gene conversion frequency was higher near chromosome termini, with a single pair of homoeologous chromosomes, 11 and 12, in each rice genome being most affected. Notably, ongoing gene conversion has maintained similarity between very ancient duplicates, provided opportunities for further gene conversion, and accelerated rice divergence. Chromosome rearrangements after polyploidization are associated with ongoing gene conversion events, and they directly restrict recombination and inhibit duplicated gene conversion between homeologous regions. Furthermore, we found that the converted genes tended to have more similar expression patterns than nonconverted duplicates. Gene conversion affects biological functions associated with multiple genes, such as catalytic activity, implying opportunities for interaction among members of large gene families, such as NBS-LRR disease-resistance genes, contributing to the occurrence of the gene conversion.ConclusionDuplicated genes in rice subspecies generated by grass polyploidization ~ 100 mya remain affected by gene conversion at high frequency, with important implications for the divergence of rice subspecies.

Evolution of large males is associated with female-skewed adult sex ratios in amniotes.

Body size often differs between the sexes (leading to sexual size dimorphism, SSD), as a consequence of differential responses by males and females to selection pressures. Adult sex ratio (ASR, the proportion of males in the adult population) should influence SSD because ASR relates to both the number of competitors and available mates, which shape the intensity of mating competition and thereby promotes SSD evolution. However, whether ASR correlates with SSD variation among species has not been yet tested across a broad range of taxa. Using phylogenetic comparative analyses of 462 amniotes (i.e., reptiles, birds, and mammals), we fill this knowledge gap by showing that male bias in SSD increases with increasingly female-skewed ASRs in both mammals and birds. This relationship is not explained by the higher mortality of the larger sex because SSD is not associated with sex differences in either juvenile or adult mortality. Phylogenetic path analysis indicates that higher mortality in one sex leads to skewed ASR, which in turn may generate selection for SSD biased toward the rare sex. Taken together, our findings provide evidence that skewed ASRs in amniote populations can result in the rarer sex evolving large size to capitalize on enhanced mating opportunities.