Differences In Evolutionary Rates Research Articles

Eukaryotic nuclear structure explains the evolutionary rate difference of ribosome export factors

Because the nucleus is the cellular structure essentially differentiating eukaryotes from prokaryotes, the formation of the nuclear membrane should have been a key event in eukaryotic evolution. Although an evolutionary cause of formation of the nucleus such as symbiosis has been speculated but still not clarified, evolutionary establishment of the transport system across the nuclear membrane must have been prerequisite for survival of the then-emerging eukaryotes. In particular, export of ribosomes, one of the largest complexes in a eukaryotic cell, from the nucleus to the cytoplasm must have been crucial for retaining the translation system of proteins. As discovered in recent years, kinetic steps in this nucleocytoplasmic transport pathway are stimulated by proteins called ribosome export factors (REFs). Hence, evolution of REFs is of particular interest, and description of the evolutionary features of REFs is of immediate value. However, even the evolutionary rates of REFs are still poorly understood compared with those of ribosomal components. With the aim of understanding the evolutionary features of REFs, we estimated the rates of amino acid substitutions of REFs for two related species of yeast, Saccharomyces cerevisiae and Saccharomyces paradoxus, and compared them with those of ribosomal components. We found that the average rate of amino acid substitutions for REFs was somewhat higher than that of ribosomal components, although the former was much lower than the grand average of other 5527 proteins. Moreover, we also found that the REFs were clearly classified into two classes; the slowly evolving REFs and the rapidly evolving REFs. Interestingly, we found that the slowly and rapidly evolving REFs correspond to the membranous REFs (mREFs) and the non-membranous REFs (non-mREFs), respectively. Further analyses with 112 REFs from 16 eukaryotic species also showed clear differences in the evolutionary rates between these two classes. Because the non-mREFs are involved in non-membranous transport from the nucleolus to nucleoplasm and the mREFs are committed to membranous transport from the nucleoplasm to the cytoplasm, the mREFs appear to have much stronger functional constraints than the non-mREFs. Thus, we conclude that the evolutionary appearance of mREFs may be one of the crucial factors for ensuring the transport from the nucleus to the cytoplasm when the nucleus was formed in the process of eukaryotic evolution.

Genetic diversity and purifying selection in West Nile virus populations are maintained during host switching

To investigate differential evolutionary rates and selective forces of WNV in hosts and vectors, we measured the genetic diversity that arose during alternating passage in mosquitoes and birds. Within-host genetic diversity was monitored in each of three experimentally passed replicates, and the complete genome sequence of each WNV strain was determined after passage. The intrahost genetic diversity that arose during alternating passage was significantly greater than the diversity generated during chicken-only passage and similar to mosquito-only passage. d N / d S ratios suggested purifying selection similar to chick-passed virus, but not to mosquito-passed virus. Thus, the abundant genetic variation contributed to WNV populations through infection of mosquitoes and the strong purifying selection contributed by infection of birds may be maintained despite frequent host switching.

Unequal Rates of Y Chromosome Gene Divergence during Speciation of the Family Ursidae

Evolution of the bear family Ursidae is well investigated in terms of morphological, paleontological, and genetic features. However, several phylogenetic ambiguities occur within the subfamily Ursinae (the family Ursidae excluding the giant panda and spectacled bear), which may correlate with behavioral traits of female philopatry and male-biased dispersal which form the basis of the observed matriarchal population structure in these species. In the process of bear evolution, we investigate the premise that such behavioral traits may be reflected in patterns of variation among genes with different modes of inheritance: matrilineal mitochondrial DNA (mtDNA), patrilineal Y chromosome, biparentally inherited autosomes, and the X chromosome. In the present study, we sequenced 3 Y-linked genes (3,453 bp) and 4 X-linked genes (4,960 bp) and reanalyzed previously published sequences from autosome genes (2,347 bp) in ursid species to investigate differences in evolutionary rates associated with patterns of inheritance. The results describe topological incongruence between sex-linked genes and autosome genes and between nuclear DNA and mtDNA. In more ancestral branches within the bear phylogeny, Y-linked genes evolved faster than autosome and X-linked genes, consistent with expectations based on male-driven evolution. However, this pattern changes among branches leading to each species within the lineage of Ursinae whereby the evolutionary rates of Y-linked genes have fewer than expected substitutions. This inconsistency between more recent nodes of the bear phylogeny with more ancestral nodes may reflect the influences of sex-biased dispersal as well as molecular evolutionary characteristics of the Y chromosome, and stochastic events in species natural history, and phylogeography unique to ursine bears.

Contrasting the Efficacy of Selection on the X and Autosomes in Drosophila

To investigate the relative efficacy of both positive and purifying natural selection on the X chromosome and the autosomes in Drosophila, we compared rates and patterns of molecular evolution between these chromosome sets using the newly available alignments of orthologous genes from 12 species. Parameters that may influence the relative X versus autosomal substitution rates include the relative effective population sizes, the male and female germline mutation rates, the distribution of allelic effects on fitness, and the degree of dominance of novel mutations. Our analysis reveals that codon usage bias is consistently greater for X-linked genes, suggesting that purifying selection consistently has greater efficacy on the X chromosome than on the autosomes across the Drosophila phylogeny. However, our results are less consistent with respect to the efficacy of positive selection, with only some lineages showing a higher substitution rate on the X chromosome. This suggests that either the distribution of selective effects of mutations or other relevant parameters are sufficiently variable across species to tip the balance in different ways in individual lineages. These data suggest that rates of substitution are not solely governed by adaptive evolution. This genome-wide analysis provides a clear picture that the efficacy of selection varies intragenomically and that this effect is markedly more consistent across the phylogeny in the case of purifying selection. Our results also suggest that simple models that predict systematic differences in rates of evolution between the X and the autosomes can only be made to be compatible with these Drosophila data if the relevant population genetic parameters that drive substitution rates differ among species and chromosomal contexts.

Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

BackgroundDespite a large agreement between ribosomal RNA and concatenated protein phylogenies, the phylogenetic tree of the bacterial domain remains uncertain in its deepest nodes. For instance, the position of the hyperthermophilic Aquificales is debated, as their commonly observed position close to Thermotogales may proceed from horizontal gene transfers, long branch attraction or compositional biases, and may not represent vertical descent. Indeed, another view, based on the analysis of rare genomic changes, places Aquificales close to epsilon-Proteobacteria.ResultsTo get a whole genome view of Aquifex relationships, all trees containing sequences from Aquifex in the HOGENOM database were surveyed. This study revealed that Aquifex is most often found as a neighbour to Thermotogales. Moreover, informational genes, which appeared to be less often transferred to the Aquifex lineage than non-informational genes, most often placed Aquificales close to Thermotogales. To ensure these results did not come from long branch attraction or compositional artefacts, a subset of carefully chosen proteins from a wide range of bacterial species was selected for further scrutiny. Among these genes, two phylogenetic hypotheses were found to be significantly more likely than the others: the most likely hypothesis placed Aquificales as a neighbour to Thermotogales, and the second one with epsilon-Proteobacteria. We characterized the genes that supported each of these two hypotheses, and found that differences in rates of evolution or in amino-acid compositions could not explain the presence of two incongruent phylogenetic signals in the alignment. Instead, evidence for a large Horizontal Gene Transfer between Aquificales and epsilon-Proteobacteria was found.ConclusionMethods based on concatenated informational proteins and methods based on character cladistics led to different conclusions regarding the position of Aquificales because this lineage has undergone many horizontal gene transfers. However, if a tree of vertical descent can be reconstructed for Bacteria, our results suggest Aquificales should be placed close to Thermotogales.

PATTERNS OF REPRODUCTIVE ISOLATION IN MEDITERRANEAN DECEPTIVE ORCHIDS

The evolution of reproductive isolation is of central interest in evolutionary biology. In plants, this is typically achieved by a combination of pre- and postpollination mechanisms that prevent, or limit, the amount of interspecific gene flow. Here, we investigated and compared two ecologically defined groups of Mediterranean orchids that differ in pollination biology and pollinator specificity: sexually deceptive orchids versus food-deceptive orchids. We used experimental crosses to assess the strength of postmating prezygotic, and postzygotic reproductive isolation, and a phylogenetic framework to determine their relative rates of evolution. We found quantitative and qualitative differences between the two groups. Food-deceptive orchids have weak premating isolation but strong postmating isolation, whereas the converse situation characterizes sexually deceptive orchids. Only postzygotic reproductive isolation among food-deceptive orchids was found to evolve in a clock-like manner. Comparison of evolutionary rates, within a common interval of genetic distance, showed that the contribution of postmating barriers was more relevant in the food-deceptive species than in the sexually deceptive species. Asymmetry in prezygotic isolation was found among food-deceptive species. Our results indicate that postmating barriers are most important for reproductive isolation in food-deceptive orchids, whereas premating barriers are most important in sexually deceptive orchids. The different rate of evolution of reproductive isolation and the relative strength of pre- and postmating barriers may have implication for speciation processes in the two orchid groups.

Positive Selection and Gene Conversion in SPP120, a Fertilization-Related Gene, during the East African Cichlid Fish Radiation

The ability to infer historical natural selection from sequence data aides in finding genes that might be important in adaptation and the formation of new species. As the fastest evolving and largest known vertebrate radiation, the cichlid fish of the African Great Lakes exhibit a wide range of recent morphological diversification. We used DNA databases, mostly of expressed sequence tags, to find candidate orthologous coding sequences from 2 tribes of cichlids and, using an automated procedure, scanned these sequence pairs for high dN/dS, the signal of positive selection and protein adaptation. The results included vertebrate genes commonly found to be under selection (e.g., major histocompatibility complex [MHC] loci) as well as genes known to be important specifically in the cichlid radiation (e.g., long-wave-sensitive opsins). Further investigation focused on a gene encoding a fertilization-related protein, SPP120, which was previously known only from cichlids. Using maximum likelihood analysis on novel SPP120 cDNA sequences from a range of African cichlids, we demonstrate the influence of positive selection in a specific subregion of the protein. We also show that SPP120 is a tandemly arranged, multicopy gene evolving with occasional interlocus gene conversion. A search of the Medaka genome database also revealed a tandem arrangement of multiple SPP120 copies and evolutionary rate differences between Medaka gene subregions mirroring those found for cichlids. Combined, these results suggest that SPP120 has been under repeated diversifying selection for over 100 Myr.

Comparative infructescence morphology in Altingia (Altingiaceae) and discordance between morphological and molecular phylogenies

Altingia (Altingiaceae) is a tropical to subtropical Asian genus of lowland trees for which 5-15 species have been recognized. Morphological diversity, particularly of the mature infructescence, has been poorly known, especially for species with relatively localized and narrow distributions, and our understanding of Altingia has lagged behind that of its close temperate relative Liquidambar (sweet gum). In this contribution, mature infructescence structure, at the levels of anatomy, morphology, and micromorphology, and some distinctive inflorescence features, are described for five recognized species of Altingia, some for the first time. In the phylogenetic framework of both morphology and molecules, characters of Altingia contrast with those of Liquidambar and suggest that character evolution within Altingiaceae is at least partly related to geographic and climatic distribution. Differences in rates of evolution and morphological convergence suggest complex patterns of diversification in Altingiaceae at several different phylogenetic levels: (1) at the deep nodes, characters of the stem lineage fossil Microaltingia persist into crown group Altingiaceae, morphological stasis; (2) at the generic level, convergence within both Liquidambar and Altingia toward their respective habitats; (3) at the infrageneric level, morphological divergence in species diversification within Altingia, in response to diverse habitats of the eastern Asian subtropics; and (4) within the intercontinental disjunct species pair L. orientalis-L. styraciflua, morphological stasis.

Still Stratus Not Altocumulus: Further Evidence against the Date/Party Hub Distinction

Using a small dataset of protein–protein interactions [1], it was proposed that the yeast protein interaction network is made up of two sorts of hubs, party and date, and that these define modularity in the yeast protein interaction network. We found [2], by using several larger high-confidence datasets and appropriate statistical analyses, that we could not support these conclusions. Bertin et al. now invite analysis of a further dataset of protein-protein interactions, which they argue support the party/date distinction. The claimed properties of party and date hubs are not, however, present in this dataset either. In particular, when controlling for important covariables where necessary, there is no evidence for (1) bimodality in partner co-expression, (2) enrichment for similarly localized proteins that physically interact with party hubs, (3) a lower rate of evolution of party hubs, (4) differences in the effects of deletion of date and party hubs, or (5) higher genetic connectivity of date hubs. In sum, all of our prior conclusions remain robust and there is no evidence for distinctive classes of network hubs. It was suggested [1] that some hub proteins operate at the same intracellular place and time with their multiple interactants (as if at a party) while others operate on a one-by-one basis with their numerous partners (as if on a date). Is this distinction informative? Originally, four features were used to the draw a partition between date and party hubs: expression bimodality, localization entropy, network fragmentation, and genetic connectivity [1]. A subsequent analysis suggested a fifth distinction, namely different rates of evolution after control for covariables [3]. Given the small size of the original dataset and the absence of statistical support for some of the assertions, we asked [2] whether these claims were robust. In both the original dataset and in new high-confidence interaction datasets [2], we found we could not support any of the five points of evidence. Bertin et al. now nominate a new dataset, which they argue supports three of the five points of evidence. Bertin et al. first note a curation issue with one of our many datasets, called HC, which inadvertently contains interactions that were, owing to an ambiguity in the literature, supported by a single analysis. We certainly agree that inclusion of the data from [4] and [5] as independent validations was in error, as the data in [5] indeed fully encompasses that of [4] (A-C Gavin, personal communication). However, approximately half of the interactions reported in [4] remain multi-validated by other means. An updated high-confidence dataset that removes this duplication and incorporates more recent interaction data is available here (Dataset S1) and as a download from the BioGRID database (see http://www.thebiogrid.org). Importantly, however, our dataset HCm is unaffected by the above concern as we required validation of an interaction by multiple different methods. The new build of Bertin et al. (called “filtered-HC”) mimics HCm by excluding interactions not multivalidated with different methods. As the results of HCm confirmed those of our other datasets [2], we were surprised by the claim that the date/party distinction is still supported in filtered-HC. Because this dataset provides the most robustly defendable set of interactions, here we re-analyse the filtered-HC network to ask whether it substantiates the date/party distinction.

Evolutionary proteomics identifies amino acids essential for ligand-binding of the cytokinin receptor CHASE domain

BackgroundIn plants the hormone cytokinin is perceived by members of a small cytokinin receptor family, which are hybrid sensor histidine kinases. While the immediate downstream signaling pathway is well characterized, the domain of the receptor responsible for ligand binding and which residues are involved in this process has not been determined experimentally.ResultsUsing a live cell hormone-binding assay, we show that cytokinin is bound by a receptor domain predicted to be extracellular, the so called CHASE (cyclases, histidine kinase associated sensory extracellular) domain. The CHASE domain occurs not only in plant cytokinin receptors but also in numerous orphan receptors in lower eukaryotes and bacteria. Taking advantage of this fact, we used an evolutionary proteomics approach to identify amino acids important for cytokinin binding by looking for residues conserved in cytokinin receptors, but not in other receptors. By comparing differences in evolutionary rates, we predicted five amino acids within the plant CHASE domains to be crucial for cytokinin binding. Mutagenesis of the predicted sites and subsequent binding assays confirmed the relevance of four of the selected amino acids, showing the biological significance of site-specific evolutionary rate differences.ConclusionThis work demonstrates the use of a bioinformatic analysis to mine the huge set of genomic data from different taxa in order to generate a testable hypothesis. We verified the hypothesis experimentally and identified four amino acids which are to a different degree required for ligand-binding of a plant hormone receptor.

Molecular evolution of the neurotrophin family members and their Trk receptors

Neurotrophins are structurally related proteins regulating brain development and function. Molecular evolution studies of neurotrophins and their receptors are essential for understanding the mechanisms underlying the coevolution processes of these gene families and how they correlate with the increased complexity of the vertebrate nervous system. In order to improve our current knowledge of the molecular evolution of neurotrophins and receptors, we have collected all information available in the literature and analyzed the genome database for each of them. Statistical analysis of aminoacid and nucleotide sequences of the neurotrophin and Trk family genes was applied to both complete genes and mature sequences, and different phylogenetic methods were used to compare aminoacid and nucleotide sequences variability among the different species. All collected data favor a model in which several rounds of genome duplications might have facilitated the generation of the many different neurotrophins and the acquisition of specific different functions correlated with the increased complexity of the vertebrate nervous system during evolution. We report findings that refine the structure of the evolutionary trees for neurotrophins and Trk receptors families, indicate different rates of evolution for each member of the two families, and newly demonstrate that the NGF-like genes found in Fowlpox and Canarypox viruses are closely related to reptile NGF.

Multilocus perspectives on the monophyly and phylogeny of the order Charadriiformes (Aves)

BackgroundThe phylogeny of shorebirds (Aves: Charadriiformes) and their putative sister groups was reconstructed using approximately 5 kilobases of data from three nuclear loci and two mitochondrial genes, and compared to that based on two other nuclear loci.ResultsCharadriiformes represent a monophyletic group that consists of three monophyletic suborders Lari (i.e., Laridae [including Sternidae and Rynchopidae], Stercorariidae, Alcidae, Glareolidae, Dromadidae, and Turnicidae), Scolopaci (i.e., Scolopacidae [including Phalaropidae], Jacanidae, Rostratulidae, Thinocoridae, Pedionomidae), and Charadrii (i.e., Burhinidae, Chionididae, Charadriidae, Haematopodidae, Recurvirostridae, and presumably Ibidorhynchidae). The position of purported "gruiform" buttonquails within Charadriiformes is confirmed. Skimmers are most likely sister to terns alone, and plovers may be paraphyletic with respect to oystercatchers and stilts. The Egyptian Plover is not a member of the Glareolidae, but is instead relatively basal among Charadrii. None of the putative sisters of Charadriiformes were recovered as such.ConclusionHypotheses of non-monophyly and sister relationships of shorebirds are tested by multilocus analysis. The monophyly of and interfamilial relationships among shorebirds are confirmed and refined. Lineage-specific differences in evolutionary rates are more consistent across loci in shorebirds than other birds and may contribute to the congruence of locus-specific phylogenetic estimates in shorebirds.

Islands Spark Accelerated Evolution

The notion of islands as natural testbeds for evolutionary study is nearly as old as the theory of evolution itself. The restricted scale, isolation, and sharp boundaries of islands create unique selective pressures, often to dramatic effect. Following what’s known as the “island rule,” small animals evolve into outsize versions of their continental counterparts while large animals shrink. Once restricted to islands, small animals often lacked predators and the competition between species that constrained the growth of their relatives on the mainland. Large mammals, on the other hand, no longer had access to vast grasslands and other abundant food sources and grew smaller to survive. Giant tortoises and iguanas still inhabit the Galapagos and a few other remote islands today, but only fossils remain of the dwarf hippopotami, elephants, and deer that once lived on islands in Indonesia, the Mediterranean, and the Pacific Ocean. The fossil record suggests that these size changes (as well as other morphological changes) occur rapidly after species become isolated on islands, but this assumption has never been empirically examined in a systematic manner. In a new study, Virginie Millien puts this longstanding hypothesis to the test by analyzing the fossil record and data from living species. Comparing the rates of evolutionary change between island and mainland populations for 88 species at intervals ranging from 21 years to 12 million years, Millien confirmed that island species undergo accelerated evolutionary changes over relatively short time frames, between decades and several thousand years. (One can imagine rats of horror movie proportions if such rates persisted for millions of years.) Measuring rates of evolutionary change has proven difficult because the fossil record rarely captures every morphological shift in a lineage, precise dating isn’t always possible, and it’s often not clear when the ancestral form first appeared on the island. To get a robust sample of island and mainland mammalian species, Millien collected data from text, figures, and tables in an extensive survey of the published literature. From these datasets, she calculated a total of 826 evolutionary rates for 170 populations representing the 88 species. (Rates of evolutionary change are measured in units called, appropriately enough, “darwins.”) Evolution rates, she found, decreased over time intervals for both island and mainland species, with a slower rate of decrease for island species. The differences in evolutionary rates between island and mainland pairs also decreased over time, becoming statistically insignificant for intervals over 45,000 years. Overall, island species evolved faster than mainland species—a phenomenon that was most pronounced for intervals between 21 years through 20,000 years. Island evolution theory predicts that the most extreme effects of isolation will be seen on the smallest, most far-flung islands. In keeping with theory, Millien found that evolutionary rates for different populations of the same species varied with island locale. Thus, the rate of evolution does not appear to be an evolutionarily conserved trait, like metabolic rate or whiskers. Because rodents make up nearly half of the world’s mammalian species—and over 70% of taxa on some islands in this study—Millien repeated her analysis on a subset of the data with equal numbers of rodent and non-rodent taxa. The overrepresentation of rodents had no effect on the results, which still revealed significant differences between island and mainland evolution rates for the same species or populations. The finding that mammals evolve faster on islands, Millien argues, comports with the island evolution theory prediction that mammals respond to their new island homes with rapid morphological and size adaptations. The brisk pace of these changes may explain why the fossil record harbors few examples of intermediate forms between the mainland ancestor and island descendant. Millien’s results also conform with the hypothesis that evolution rates for island species slow down after the initial period of accelerated change, approaching rates on the mainland. If island species can evolve quickly, Millien argues, it stands to reason that mainland species retain a similar capacity. As habitat destruction continues to pose the number one threat to biodiversity, many mainland habitats are beginning to resemble islands, with isolated pockets of wildlife separated by degraded or developed lands. Thus, island species may serve as a model for understanding how mainland species will adapt to the rapidly changing environmental conditions brought on by habitat destruction and global warming. It appears that some mainland species are already responding like island species: a 1989 study followed the island rule in linking fragmented habitat to body size changes in 25 European mammals over the past 200 years. How long animals can continue to evolve in the face of these changes, however, remains to be seen.

Differential evolutionary rates of duplicated genes in protein interaction network

In the network of protein–protein interactions (PPIs), a loss and gain of the partnering proteins can cause drastic changes of network formation during evolution. With the aim of examining the evolutionary effects of the loss and gain of the partnering proteins on PPIs, we examined a relationship between evolutionary rates and losses and/or gains of PPIs for duplicated gene pairs encoding proteins involved in the PPI network. For duplicated pairs, which provided us with a unique opportunity of making fair comparisons of the genes with the same initial condition, we found that the evolutionary rate of the protein with more PPI partners is much slower than that of the other with fewer PPI partners. Moreover, when the ratio of evolutionary rates (faster rate/slower rate) was computed for each of the duplicated pairs, the ratio for the duplicated pair sharing any PPI partners was significantly lower than that for the pair sharing no PPI partners. These results indicate that the duplicated gene pairs differentiate through the losses and/or gains of the PPI partners, resulting in a change in their evolutionary rates. In particular, we point out that the PPI losses for the duplicated gene products that are involved in the functional classes of ‘transcription’ and ‘protein fate’ have an impact on their evolutionary rates more than the PPI losses for others.

Protein Evolution Is Faster Outside the Cell

Some proteins are highly conserved across all species, whereas others diverge significantly even between closely related species. Attempts have been made to correlate the rate of protein evolution to amino acid composition, protein dispensability, and the number of protein-protein interactions, but in all cases, conflicting studies have shown that the theories are hard to confirm experimentally. The only correlation that is undisputed so far is that highly/broadly expressed proteins seem to evolve at a lower rate. Consequently, it has been suggested that correlations between evolution rate and factors like protein dispensability or the number of protein-protein interactions could be just secondary effects due to differences in expression. The purpose of this study was to analyze mammalian proteins/genes with known subcellular location for variations in evolution rates. We show that proteins that are exported (extracellular proteins) evolve faster than proteins that reside inside the cell (intracellular proteins). We find weak, but significant, correlations between evolution rates and expression levels, percentage of tissues in which the proteins are expressed (expression broadness), and the number of protein interaction partners. More important, we show that the observed difference in evolution rate between extra- and intracellular proteins is largely independent of expression levels, expression broadness, and the number of protein-protein interactions. We also find that the difference is not caused by an overrepresentation of immunological proteins or disulfide bridge-containing proteins among the extracellular data set. We conclude that the subcellular location of a mammalian protein has a larger effect on its evolution rate than any of the other factors studied in this paper, including expression levels/patterns. We observe a difference in evolution rates between extracellular and intracellular proteins for a yeast data set as well and again show that it is completely independent of expression levels.

Reconciling Extreme Branch Length Differences: Decoupling Time and Rate through the Evolutionary History of Filmy Ferns

The rate of molecular evolution is not constant across the Tree of Life. Characterizing rate discrepancies and evaluating the relative roles of time and rate along branches through the past are both critical to a full understanding of evolutionary history. In this study, we explore the interactions of time and rate in filmy ferns (Hymenophyllaceae), a lineage with extreme branch length differences between the two major clades. We test for the presence of significant rate discrepancies within and between these clades, and we separate time and rate across the filmy fern phylogeny to simultaneously yield an evolutionary time scale of filmy fern diversification and reconstructions of ancestral rates of molecular evolution. Our results indicate that the branch length disparity observed between the major lineages of filmy ferns is indeed due to a significant difference in molecular evolutionary rate. The estimation of divergence times reveals that the timing of crown group diversification was not concurrent for the two lineages, and the reconstruction of ancestral rates of molecular evolution points to a substantial rate deceleration in one of the clades. Further analysis suggests that this may be due to a genome-wide deceleration in the rate of nucleotide substitution.

Inferring the Root of <I>Isoëtes</I>: Exploring Alternatives in the Absence of an Acceptable Outgroup

The ancient divergence between the lycopsid genus Isoetes and its closest living relative (Selaginella) has resulted in considerable morphological and genetic disparity, yet within Isoetes there is remarkable morphological and genetic uniformity. This has made it difficult to identify the phylogenetic root of the genus. In this study, we addressed this problem and characterized the early branching patterns within Isoetes using an expanded set of taxa and three molecular markers. We assessed the saturation in the molecular data sets, tested for differences in evolutionary rate, determined the stability of the ingroup topology, and evaluated the applicability of the molecular clock. We then explored three alternative rooting approaches: outgroup, midpoint, and maximum likelihood under the assumption of a molecular clock. Attempts to infer the root of Isoetes using the outgroup approach were severely hindered by the effects of saturation, but the results from midpoint rooting and the enforcement of the molecular clock were highly consistent among the data sets. We identify the root of Isoetes to be located among three major, highly supported clades.

Snakes as agents of evolutionary change in primate brains

Current hypotheses that use visually guided reaching and grasping to explain orbital convergence, visual specialization, and brain expansion in primates are open to question now that neurological evidence reveals no correlation between orbital convergence and the visual pathway in the brain that is associated with reaching and grasping. An alternative hypothesis proposed here posits that snakes were ultimately responsible for these defining primate characteristics. Snakes have a long, shared evolutionary existence with crown-group placental mammals and were likely to have been their first predators. Mammals are conservative in the structures of the brain that are involved in vigilance, fear, and learning and memory associated with fearful stimuli, e.g., predators. Some of these areas have expanded in primates and are more strongly connected to visual systems. However, primates vary in the extent of brain expansion. This variation is coincident with variation in evolutionary co-existence with the more recently evolved venomous snakes. Malagasy prosimians have never co-existed with venomous snakes, New World monkeys (platyrrhines) have had interrupted co-existence with venomous snakes, and Old World monkeys and apes (catarrhines) have had continuous co-existence with venomous snakes. The koniocellular visual pathway, arising from the retina and connecting to the lateral geniculate nucleus, the superior colliculus, and the pulvinar, has expanded along with the parvocellular pathway, a visual pathway that is involved with color and object recognition. I suggest that expansion of these pathways co-occurred, with the koniocellular pathway being crucially involved (among other tasks) in pre-attentional visual detection of fearful stimuli, including snakes, and the parvocellular pathway being involved (among other tasks) in protecting the brain from increasingly greater metabolic demands to evolve the neural capacity to detect such stimuli quickly. A diet that included fruits or nectar (though not to the exclusion of arthropods), which provided sugars as a neuroprotectant, may have been a required preadaptation for the expansion of such metabolically active brains. Taxonomic differences in evolutionary exposure to venomous snakes are associated with similar taxonomic differences in rates of evolution in cytochrome oxidase genes and in the metabolic activity of cytochrome oxidase proteins in at least some visual areas in the brains of primates. Raptors that specialize in eating snakes have larger eyes and greater binocularity than more generalized raptors, and provide non-mammalian models for snakes as a selective pressure on primate visual systems. These models, along with evidence from paleobiogeography, neuroscience, ecology, behavior, and immunology, suggest that the evolutionary arms race begun by constrictors early in mammalian evolution continued with venomous snakes. Whereas other mammals responded by evolving physiological resistance to snake venoms, anthropoids responded by enhancing their ability to detect snakes visually before the strike.

The testis-specific apoptosis related gene TTL.6 underwent adaptive evolution in the lineage leading to humans

The TTL.6 gene is a member of the tubulin-tyrosine ligase (TTL) family involved in apoptosis and preferentially expressed in the testis. We sequenced the coding region and part of the introns of TTL.6 in world wide human populations and five representative nonhuman primate species covering great apes, lesser ape and Old World monkey. The sequence substitution patterns of TTL.6 in primates demonstrated a sharp difference in evolutionary rates among different primate lineages. Our results indicated an accelerated evolution of TTL.6 in the human lineage, which was caused by Darwinian positive selection. Further analysis on sequence variations in human populations demonstrated an excess of derived common alleles, which was likely caused by genetic hitchhiking, an implication of recent positive selection on TTL.6 in human populations.

Studies of morphological and molecular phylogenetic divergence in spiders (Araneae: Homalonychus) from the American southwest, including divergence along the Baja California Peninsula

Comparative phylogenetic and phylogeographic analyses have revealed a pervasive midpeninsular divergence in the mitochondrial genealogies of numerous vertebrate taxa distributed on the Baja California Peninsula. In this study, we extend the investigation of regional vicariance in Baja California to an arthropod taxon by examining patterns of phylogenetic and morphological divergence in the spider genus Homalonychus (Araneae, Homalonychidae). We analyzed data from two mtDNA genes (16S rRNA and NADH dehydrogenase subunit (1) and a nuclear gene (28S rRNA) using maximum parsimony and Bayesian phylogenetic analyses, and also conducted geometric morphometric analyses employing landmark data on male and female genitalia. Genes and morphology both reveal a deep split across the Colorado River and Gulf of California, separating Homalonychus selenopoides on the east side of river from its congener Homalonychus theologus on the west side of the river, including the Baja California Peninsula. Along the north–south axis of the Baja Peninsula, an apparently more recent midpeninsular phylogenetic break is evident within H. theologus in the mitochondrial genome and in female genitalia. However, there is no measurable divergence between northern and southern populations in either nuclear DNA or male genitalia. We suggest that this discordance between datasets reflects either a difference in rates of evolution between male versus female systems, or that male-based nuclear gene flow is obscuring a phylogenetic split that is fixed in the female-based systems. Our findings provide additional support for a midpeninsular Baja divergence event, although the timing and geological evidence for such an event remain elusive.