Complete mitochondrial genomes from four subspecies of common chaffinch (Fringilla coelebs): New inferences about mitochondrial rate heterogeneity,neutral theory,and phylogenetic relationships within the order Passeriformes

We describe whole mitochondrial genome sequences from four subspecies of the common chaffinch (Fringilla coelebs), and compare them to 31 publicly available mitochondrial genome sequences from other Passeriformes. Rates and patterns of mitochondrial gene evolution are analyzed at different taxonomic levels within this avian order, and evidence is adduced for and against the nearly neutral theory of molecular evolution and the role of positive selection in shaping genetic variation of this small but critical genome. We find evidence of mitochondrial rate heterogeneity in birds as in other vertebrates, likely due to differences in mutational pressure across the genome. Unlike in gadine fish and some of the human mitochondrial work we do not observe strong support for the nearly neutral theory of molecular evolution; instead evidence from molecular clocks, distribution of dN/dS ratios at different levels of the taxonomic hierarchy and in different lineages, McDonald–Kreitman tests within Fringillidae, and site-specific tests of selection within Passeriformes, all point to a role for positive selection, especially for the complex I NADH dehydrogenase genes. The protein-coding mitogenome phylogeny of the order Passeriformes is broadly consistent with previously-reported molecular findings, but provides support for a sister relationship between the superfamilies Muscicapoidea and Passeroidea on a short basal internode of the Passerida where relationships have been difficult to resolve. An unexpected placement of the Paridae (represented by Hume's groundpecker) within the Muscicapoidea was observed. Consistent with other molecular studies the mtDNA phylogeny reveals paraphyly within the Muscicapoidea and a sister relationship of Fringilla with Carduelis rather than Emberiza.     

Phylogeny and Divergence Times of Gymnosperms Inferred from Single-Copy Nuclear Genes

Phylogenetic reconstruction is fundamental to study evolutionary biology and historical biogeography. However, there was not a molecular phylogeny of gymnosperms represented by extensive sampling at the genus level, and most published phylogenies of this group were constructed based on cytoplasmic DNA markers and/or the multi-copy nuclear ribosomal DNA. In this study, we use LFY and NLY, two single-copy nuclear genes that originated from an ancient gene duplication in the ancestor of seed plants, to reconstruct the phylogeny and estimate divergence times of gymnosperms based on a complete sampling of extant genera. The results indicate that the combined LFY and NLY coding sequences can resolve interfamilial relationships of gymnosperms and intergeneric relationships of most families. Moreover, the addition of intron sequences can improve the resolution in Podocarpaceae but not in cycads, although divergence times of the cycad genera are similar to or longer than those of the Podocarpaceae genera. Our study strongly supports cycads as the basal-most lineage of gymnosperms rather than sister to Ginkgoaceae, and a sister relationship between Podocarpaceae and Araucariaceae and between Cephalotaxaceae-Taxaceae and Cupressaceae. In addition, intergeneric relationships of some families that were controversial, and the relationships between Taxaceae and Cephalotaxaceae and between conifers and Gnetales are discussed based on the nuclear gene evidence. The molecular dating analysis suggests that drastic extinctions occurred in the early evolution of gymnosperms, and extant coniferous genera in the Northern Hemisphere are older than those in the Southern Hemisphere on average. This study provides an evolutionary framework for future studies on gymnosperms.     

Self-sterility in flowering plants: preventing self-fertilization increases family diversification rates

Background and Scope

New data are presented on the distribution and frequency of self-sterility (SS) – predominantly pre-zygotic self-incompatibility (SI) systems – in flowering plants and the hypothesis is tested that families with self-sterile taxa have higher net diversification rates (DRs) than those with exclusively self-compatible taxa using both absolute and relative rate tests.

Key Results

Three major forms of SI systems (where pollen is rejected at the stigmatic, stylar or ovarian interface) are found to occur in the oldest families of flowering plants, with times of divergence >100 million years before the present (mybp), while post-fertilization SS and heterostyly appear in families with crown ages of 81 and 87 mybp, respectively. It is also founnd that many (22) angiosperm families exhibit >1 SI phenotype and that the distribution of different types of SS does not show strong phylogenetic clustering, collectively suggesting that SS and SI systems have evolved repeatedly de novo in angiosperm history. Families bearing self-sterile taxa have higher absolute DRs using all available calibrations of the angiosperm tree, and this affect is caused mostly by the high DR of families with homomorphic SI systems (in particular stigmatic SI) or those in which multiple SS/SI phenotypes have been observed (polymorphic). Lastly, using sister comparisons, it is further demonstrated that in 29 of 38 sister pairs (including 95 families), the self-sterile sister group had higher species richness and DR than its self-compatible sister based on either the total number of taxa in the clade with SS or only the estimated fraction to harbour SS based on literature surveys.

Conclusions

Collectively, these analyses point to the importance of SS, particularly pre-zygotic SI in the evolution of flowering plants.     

Disparity and Evolutionary Rate Do Not Explain Diversity Patterns in Muroid Rodents (Rodentia: Muroidea)

A positive correlation between diversity and disparity/evolutionary rate is predicted by multiple evolutionary theories. However, recent empirical studies in various taxa do not always find such an association. Similarly, we find no correlation between these two levels of variation, based on cranial morphometric data and molecular phylogenetic data from 317 muroid rodent species and dipodoid outgroups, analyzed using three-dimensional geometric morphometrics. This disassociation was found using both phylogenetic and non-phylogenetic approaches, indicating that an increase in clade richness is not necessarily followed by an increase in morphological divergence and vice versa. Furthermore, the distribution of muroid families in morphospace is highly overlapping suggesting greater variation within than between clades. Taken together with the observation that families with the most distinctive cranial morphologies (nesomyids, dipodids, and spalacids) are the least diverse, indicates that evolution of new cranial morphologies may not play an important role in the diversification of muroid rodents.     

Molecular systematics of aphids and their primary endosymbionts

Aphids constitute a monophyletic group within the order Homoptera (i.e., superfamily Aphidoidea). The Aphidoidea originated in the Jurassic about 150 my ago from some aphidiform ancestor whose origin can be traced back to about 250 my ago. They exhibit a mutualistic association with intracellular bacteria (Buchnera sp.) related to Escherichia coli. Buchnera is usually considered the aphids' primary endosymbiont. The association is obligate for both partners. The 16S rDNA-based phylogeny of Buchnera from four aphid families showed complete concordance with the morphology-based phylogeny of their aphid hosts, which pointed to a single original infection in a common ancestor of aphids some 100-250 my ago followed by cospeciation of aphids and Buchnera. This study concentrated on the molecular phylogeny of both the aphids and their primary endosymbionts of five aphid families including for the first time representatives of the family Lachnidae. We discuss results based on two Buchnera genes (16S rDNA and the beta subunit of the F-ATPase complex) and on one host mitochondrial gene (the subunit 6 of the F-ATPase complex). Although our data do not allow definitive evolutionary relationships to be established among the different aphid families, some traditionally accepted groupings are put into question from both bacterial and insect data. In particular, the Lachnidae and the Aphididae, which from morphological data are considered recently evolved sister groups, do not seem to be as closely related as is usually accepted. Finally, we discuss our results in the light of the proposed parallel evolution of aphids and their endosymbionts.     

The effects of sex-biased gene expression and X-linkage on rates of adaptive protein sequence evolution in Drosophila

A faster rate of adaptive evolution of X-linked genes compared with autosomal genes may be caused by the fixation of new recessive or partially recessive advantageous mutations (the Faster-X effect). This effect is expected to be largest for mutations that affect only male fitness and absent for mutations that affect only female fitness. We tested these predictions in Drosophila melanogaster by using genes with different levels of sex-biased expression and by estimating the extent of adaptive evolution of non-synonymous mutations from polymorphism and divergence data. We detected both a Faster-X effect and an effect of male-biased gene expression. There was no evidence for a strong association between the two effects—modest levels of male-biased gene expression increased the rate of adaptive evolution on both the autosomes and the X chromosome, but a Faster-X effect occurred for both unbiased genes and female-biased genes. The rate of genetic recombination did not influence the magnitude of the Faster-X effect, ruling out the possibility that it reflects less Hill–Robertson interference for X-linked genes.     

Comparative analysis of complete genomes reveals gene loss, acquisition and acceleration of evolutionary rates in Metazoa, suggests a prevalence of evolution via gene acquisition and indicates that the evolutionary rates in animals tend to be conserved

In this study we systematically examined the differences between the proteomes of Metazoa and other eukaryotes. Metazoans (Homo sapiens, Ceanorhabditis elegans and Drosophila melanogaster) were compared with a plant (Arabidopsis thaliana), fungi (Saccharomyces cerevisiae and Schizosaccaromyces pombe) and Encephalitozoan cuniculi. We identified 159 gene families that were probably lost in the Metazoan branch and 1263 orthologous families that were specific to Metazoa and were likely to have originated in their last common ancestor (LCA). We analyzed the evolutionary rates of pan-eukaryotic protein families and identified those with higher rates in animals. The acceleration was shown to occur in: (i) the LCA of Metazoa or (ii) independently in the Metazoan phyla. A high proportion of the accelerated Metazoan protein families was found to participate in translation and ribosome biogenesis, particularly mitochondrial. By functional analysis we show that no metabolic pathway in animals evolved faster than in other organisms. We conclude that evolution in the LCA of Metazoa was extensive and proceeded largely by gene duplication and/or invention rather than by modification of extant proteins. Finally, we show that the rate of evolution of a gene family in animals has a clear, but not absolute, tendency to be conserved.     

A supermatrix approach provides a comprehensive genus-level phylogeny for Gentianales

Gentianales consist of Apocynaceae, Gelsemiaceae, Gentianaceae, Loganiaceae, and Rubiaceae, of which the majority are woody plants in tropical and subtropical areas. Despite extensive efforts in reconstructing the phylogeny of Gentianales based on molecular data, some interfamily and intrafamily relationships remain uncertain. We reconstructed the genus-level phylogeny of Gentianales based on the supermatrix of eight plastid markers (rbcL, matK, atpB, ndhF, rpl16, rps16, thetrnL-trnF region, and atpB-rbcL spacer) and one mitochondrial gene (matR) using maximum likelihood. The major clades and their relationships retrieved in the present study concur with those of previous studies. All of the five families of Gentianales are monophyletic with strong support. We resolved Rubiaceae as sister to the remaining families in Gentianales and showed support for the sister relationship between Loganiaceae and Apocynaceae. Our results provide new insights into relationships among intrafamilial clades. For example, within Rubiaceae we found that Craterispermeae were sister to Morindeae + (Palicoureeae + Psychotrieae) and that Theligoneae were sister to Putorieae. Within Gentianaceae, our phylogeny revealed that Gentianeae were sister to Helieae and Potalieae, and subtribe Lisianthiinae were sister to Potaliinae and Faroinae. Within Loganiaceae, we found Neuburgia as sister to Spigelieae. Within Apocynaceae, our results supported Amsonieae as sister to Melodineae, and Hunterieae as sister to a clade comprising Plumerieae + (Carisseae + APSA). We also confirmed the monophyly of Perplocoideae and the relationships among Baisseeae + (Secamonoideae + Asclepiadoideae).     

The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers

The Brassicaceae, including Arabidopsis thaliana and Brassica crops, is unmatched among plants in its wealth of genomic and functional molecular data and has long served as a model for understanding gene, genome, and trait evolution. However, genome information from a phylogenetic outgroup that is essential for inferring directionality of evolutionary change has been lacking. We therefore sequenced the genome of the spider flower (Tarenaya hassleriana) from the Brassicaceae sister family, the Cleomaceae. By comparative analysis of the two lineages, we show that genome evolution following ancient polyploidy and gene duplication events affect reproductively important traits. We found an ancient genome triplication in Tarenaya (Th-α) that is independent of the Brassicaceae-specific duplication (At-α) and nested Brassica (Br-α) triplication. To showcase the potential of sister lineage genome analysis, we investigated the state of floral developmental genes and show Brassica retains twice as many floral MADS (for MINICHROMOSOME MAINTENANCE1, AGAMOUS, DEFICIENS and SERUM RESPONSE FACTOR) genes as Tarenaya that likely contribute to morphological diversity in Brassica. We also performed synteny analysis of gene families that confer self-incompatibility in Brassicaceae and found that the critical SERINE RECEPTOR KINASE receptor gene is derived from a lineage-specific tandem duplication. The T. hassleriana genome will facilitate future research toward elucidating the evolutionary history of Brassicaceae genomes.     

The Ancestral Carnivore Karyotype As Substantiated by Comparative Chromosome Painting of Three Pinnipeds,the Walrus,the Steller Sea Lion and the Baikal Seal (Pinnipedia,Carnivora)

Karyotype evolution in Carnivora is thoroughly studied by classical and molecular cytogenetics and supplemented by reconstructions of Ancestral Carnivora Karyotype (ACK). However chromosome painting information from two pinniped families (Odobenidae and Otariidae) is noticeably missing. We report on the construction of the comparative chromosome map for species from each of the three pinniped families: the walrus (Odobenus rosmarus, Odobenidae–monotypic family), near threatened Steller sea lion (Eumetopias jubatus, Otariidae) and the endemic Baikal seal (Pusa sibirica, Phocidae) using combination of human, domestic dog and stone marten whole-chromosome painting probes. The earliest karyological studies of Pinnipedia showed that pinnipeds were characterized by a pronounced karyological conservatism that is confirmed here with species from Phocidae, Otariidae and Odobenidae sharing same low number of conserved human autosomal segments (32). Chromosome painting in Pinnipedia and comparison with non-pinniped carnivore karyotypes provide strong support for refined structure of ACK with 2n = 38. Constructed comparative chromosome maps show that pinniped karyotype evolution was characterized by few tandem fusions, seemingly absent inversions and slow rate of genome rearrangements (less then one rearrangement per 10 million years). Integrative comparative analyses with published chromosome painting of Phoca vitulina revealed common cytogenetic signature for Phoca/Pusa branch and supports Phocidae and Otaroidea (Otariidae/Odobenidae) as sister groups. We revealed rearrangements specific for walrus karyotype and found the chromosomal signature linking together families Otariidae and Odobenidae. The Steller sea lion karyotype is the most conserved among three studied species and differs from the ACK by single fusion. The study underlined the strikingly slow karyotype evolution of the Pinnipedia in general and the Otariidae in particular.     

Molecular phylogenetic relationships and the coevolution of placentotrophy and superfetation in Poecilia (Poeciliidae: Cyprinodontiformes)

Members of Poeciliidae are used as model organisms for experimental studies on natural and sexual selection, and comparative studies of life-history evolution. The latter have demonstrated multiple origins of both superfetation and placentotrophy within Poeciliidae. Most recently, placentotrophy has been described in five species of Poecilia (Pamphorichthys), but only one of these (P.hasemani) shows evidence of superfetation. Here, we use a molecular phylogeny based on concatenated nuclear and mitochondrial gene sequences to test hypotheses of correlated evolution between superfetation and placentotrophy in Poecilia. Taxon sampling included all species in the subgenera Micropoecilia and Pamphorichthys for which the presence or absence of placentotrophy and superfetation have been determined, as well as representatives of all other Poecilia subgenera (Acanthophacelus, Limia, Mollienesia, Poecilia, Pseudolimia). Phylogenetic analyses were performed with maximum parsimony, maximum likelihood, and Bayesian methods; ancestral states for life-history characters were reconstructed with parsimony and SIMMAP; correlation analyses were performed with SIMMAP; and divergence times were estimated using a relaxed molecular clock. All subgenera in Poecilia were recovered as monophyletic. The basal split in Poecilia is between P. (Acanthophacelus)+P. (Micropoecilia) and the other five subgenera. In the latter clade, P. (Poecilia) is the sister-group to the remaining four subgenera. Within P. (Pamphorichthys), all analyses with the combined data set recovered P. (Pamphorichthys) araguaiensis as the sister taxon to P. (Pamphorichthys) hollandi, and P. (Pamphorichthys) scalpridens as the sister taxon to P. (Pamphorichthys) minor. P. (Pamphorichthys) hasemani was either the sister taxon to P. (Pamphorichthys) hollandi+P. (Pamphorichthys) minor (maximum likelihood, Bayesian) or the sister taxon to all other Pamphorichthys species (maximum parsimony). Ancestral state reconstructions suggest that placentotrophy and superfetation evolved on the same branch in P. (Micropoecilia), whereas placentotrophy evolved before superfetation in P. (Pamphorichthys). SIMMAP analyses indicate a statistically significant association between placentotrophy and superfetation. Within P. (Micropoecilia) both placentotrophy and superfetation evolved in ≤4 million years. Within P. (Pamphorichthys), superfetation evolved in ≤9 million years on the P. (Pamphorichthys) hasemani branch, and placentotrophy evolved in ≤10 million years in the common ancestor of this subgenus.     

Sperm competition and sperm midpiece size: no consistent pattern in passerine birds

Sperm competition is thought to be a major force driving the evolution of sperm shape and function. However, previous studies investigating the relationship between the risk of sperm competition and sperm morphometry revealed inconclusive results and marked differences between taxonomic groups. In a comparative study of two families of passerines (Fringillidae and Sylviidae) and also across species belonging to different passerine families, we investigated the relative importance of the phylogenetic background on the relationship between sperm morphometry and the risk of sperm competition. The risk of sperm competition was inferred from relative testis mass as an indicator of investment in sperm production. We found: (i) a significant positive association between both midpiece length and flagellum length and relative testis mass in the Fringillidae, (ii) a significant negative association between sperm trait dimensions and relative testis mass in the Sylviidae, and (iii) no association across all species. Despite the striking difference in the patterns shown by the Sylviidae and the Fringillidae, the relationship between midpiece length and flagellum length was positive in both families and across all species with positive allometry. Reasons for the differences and similarities between passerine families are discussed.     

Adaptive protein evolution and regulatory divergence in Drosophila

Two recent studies demonstrated a positive correlation between divergence in gene expression and protein sequence in Drosophila. This correlation could be driven by positive selection or variation in functional constraint. To distinguish between these alternatives, we compared patterns of molecular evolution for 1,862 genes with two previously reported estimates of expression divergence in Drosophila. We found a slight negative trend (nonsignificant) between positive selection on protein sequence and divergence in expression levels between Drosophila melanogaster and Drosophila simulans. Conversely, shifts in expression patterns during Drosophila development showed a positive association with adaptive protein evolution, though as before the relationship was weak and not significant. Overall, we found no strong evidence for an increase in the incidence of positive selection on protein-coding regions in genes with divergent expression in Drosophila, suggesting that the previously reported positive association between protein and regulatory divergence primarily reflects variation in functional constraint.     

High resolution synteny maps allowing direct comparisons between the coffee and tomato genomes

Tomato (Solanum lycopersicum) and coffee (Coffea canephora) belong to the sister families Solanaceae and Rubiaceae, respectively. We report herein the mapping of a common set of 257 Conserved Ortholog Set II genes in the genomes of both species. The mapped markers are well distributed across both genomes allowing the first syntenic comparison between species from these two families. The majority (75%) of the synteny blocks are short (<4 cM); however, some extend up to 50 cM. In an effort to further characterize the synteny between these two genomes, we took advantage of the available sequence for the tomato genome to show that tomato chromosome 7 is syntenic to half of the two coffee linkage groups E and F with the putative break point in tomato localized to the boundary of the heterochromatin and euchromatin on the long arm. In addition to the new insight on genome conservation and evolution between the plant families Solanaceae and Rubiaceae, the comparative maps presented herein provide a translational tool by which coffee researchers may take benefit of DNA sequence and genetic information from tomato and vice versa. It is thus expected that these comparative genome information will help to facilitate and expedite genetic and genomic research in coffee.     

Fast molecular evolution associated with high active metabolic rates in poison frogs

Molecular evolution is simultaneously paced by mutation rate, genetic drift, and natural selection. Life history traits also affect the speed of accumulation of nucleotide changes. For instance, small body size, rapid generation time, production of reactive oxygen species (ROS), and high resting metabolic rate (RMR) are suggested to be associated with faster rates of molecular evolution. However, phylogenetic correlation analyses failed to support a relationship between RMR and molecular evolution in ectotherms. In addition, RMR might underestimate the metabolic budget (e.g., digestion, reproduction, or escaping predation). An alternative is to test other metabolic rates, such as active metabolic rate (AMR), and their association with molecular evolution. Here, I present comparative analyses of the associations between life history traits (i.e., AMR, RMR, body mass, and fecundity) with rates of molecular evolution of and mitochondrial loci from a large ectotherm clade, the poison frogs (Dendrobatidae). My results support a strong positive association between mass-specific AMR and rates of molecular evolution for both mitochondrial and nuclear loci. In addition, I found weaker and genome-specific covariates such as body mass and fecundity for mitochondrial and nuclear loci, respectively. No direct association was found between mass-specific RMR and rates of molecular evolution. Thus, I provide a mechanistic hypothesis of the link between AMRs and the rate of molecular evolution based on an increase in ROS within germ line cells during periodic bouts of hypoxia/hyperoxia related to aerobic exercise. Finally, I propose a multifactorial model that includes AMR as a predictor of the rate of molecular evolution in ectothermic lineages.     

Accelerated rate of gene gain and loss in primates

The molecular changes responsible for the evolution of modern humans have primarily been discussed in terms of individual nucleotide substitutions in regulatory or protein coding sequences. However, rates of nucleotide substitution are slowed in primates, and thus humans and chimpanzees are highly similar at the nucleotide level. We find that a third source of molecular evolution, gene gain and loss, is accelerated in primates relative to other mammals. Using a novel method that allows estimation of rate heterogeneity among lineages, we find that the rate of gene turnover in humans is more than 2.5 times faster than in other mammals and may be due to both mutational and selective forces. By reconciling the gene trees for all of the gene families included in the analysis, we are able to independently verify the numbers of inferred duplications. We also use two methods based on the genome assembly of rhesus macaque to further verify our results. Our analyses identify several gene families that have expanded or contracted more rapidly than is expected even after accounting for an overall rate acceleration in primates, including brain-related families that have more than doubled in size in humans. Many of the families showing large expansions also show evidence for positive selection on their nucleotide sequences, suggesting that selection has been important in shaping copy-number differences among mammals. These findings may help explain why humans and chimpanzees show high similarity between orthologous nucleotides yet great morphological and behavioral differences.     

Phylogenetic analysis of the Metastrongyloidea (Nematoda: Strongylida) inferred from ribosomal RNA gene sequences

Phylogenetic relationships among nematodes of the strongylid superfamily Metastrongyloidea were analyzed using partial sequences from the large-subunit ribosomal RNA (LSU rRNA) and small-subunit ribosomal RNA (SSU rRNA) genes. Regions of nuclear ribosomal DNA (rDNA) were amplified by polymerase chain reaction, directly sequenced, aligned, and phylogenies inferred using maximum parsimony. Phylogenetic hypotheses inferred from the SSU rRNA gene supported the monophyly of representative taxa from each of the 7 currently accepted metastrongyloid families. Metastrongyloid taxa formed the sister group to representative trichostrongyloid sequences based on SSU data. Sequences from either the SSU or LSU RNA regions alone provided poor resolution for relationships within the Metastrongyloidea. However, a combined analysis using sequences from all rDNA regions yielded 3 equally parsimonious trees that represented the abursate Filaroididae as polyphyletic, Parafilaroides decorus as the sister species to the monophyletic Pseudaliidae, and a sister group relationship between Oslerus osleri and Metastrongylus salmi. Relationships among 3 members of the Crenosomatidae, and 1 representative of the Skrjabingylidae (Skrjabingylus chitwoodorum) were not resolved by these combined data. However, members of both these groups were consistently resolved as the sister group to the other metastrongyloid families. These relationships are inconsistent with traditional classifications of the Metastrongyloidea and existing hypotheses for their evolution.     

Numbers of genes in the NBS and RLK families vary by more than four-fold within a plant species and are regulated by multiple factors

Many genes exist in the form of families; however, little is known about their size variation, evolution and biology. Here, we present the size variation and evolution of the nucleotide-binding site (NBS)-encoding gene family and receptor-like kinase (RLK) gene family in Oryza, Glycine and Gossypium. The sizes of both families vary by numeral fold, not only among species, surprisingly, also within a species. The size variations of the gene families are shown to correlate with each other, indicating their interactions, and driven by natural selection, artificial selection and genome size variation, but likely not by polyploidization. The numbers of genes in the families in a polyploid species are similar to those of one of its diploid donors, suggesting that polyploidization plays little roles in the expansion of the gene families and that organisms tend not to maintain their ‘surplus’ genes in the course of evolution. Furthermore, it is found that the size variations of both gene families are associated with organisms’ phylogeny, suggesting their roles in speciation and evolution. Since both selection and speciation act on organism’s morphological, physiological and biological variation, our results indicate that the variation of gene family size provides a source of genetic variation and evolution.