Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup

Comparative genetic analysis between human and chimpanzee may detect genetic divergences responsible for human-specific characteristics. Previous studies have identified a series of genes that potentially underwent Darwinian positive selection during human evolution. However, without a closely related species as outgroup, it is difficult to identify human-lineage-specific changes, which is critical in delineating the biological uniqueness of humans. In this study, we conducted phylogeny-based analyses of 2633 human brain-expressed genes using rhesus macaque as the outgroup. We identified 47 candidate genes showing strong evidence of positive selection in the human lineage. Genes with maximal expression in the brain showed a higher evolutionary rate in human than in chimpanzee. We observed that many immune-defense-related genes were under strong positive selection, and this trend was more prominent in chimpanzee than in human. We also demonstrated that rhesus macaque performed much better than mouse as an outgroup in identifying lineage-specific selection in humans.     

Chimpanzees as an outgroup for the examination of human dental evolution

In the assessment of human origins, chimpanzees (Pan troglodytes, henceforth called Pan) represent the best hominoid outgroup for comparisons. Such an outgroup roots the "anatomically modern" human population cluster, or continuum. This study incorporates chimpanzees into a worldwide modern human database of quantified complete tooth variables (approximately 30 per tooth; e.g., root, pulp, enamel) in an attempt to develop a more accurate phylogeny of the hominoid continuum, with only intervening extinct hominids missing. Canonical discriminate analysis was performed mainly among Liberian common chimpanzees and global samples of humans. The first canonical variable explained 70% of the total variance and showed a tight cluster of humans, with chimpanzees as a distant outgroup. Within the human community, first non-San Bushman, sub-Saharan Africans and Andamanese, and then, close in, Australian aborigines were positioned towards Pan. Their relative orientation suggested an African human origin with the first branch within sub-Saharan Africa: sub-Saharan Africans and San Bushmen. Next, Andamanese Negritos, and then Australian aborigines, formed the early first surviving modern human lineage to leave Africa. Thin enamel and big teeth with relatively large roots characterized Pan nonmolar teeth. Humans showed a generalized sexual dimorphism for all teeth, with males having bigger teeth, bigger relative roots, and thinner enamel than females, while only Pan canines had significant and impressive sexual dimorphism. Interestingly, Pan molars were not larger than human molars. The data suggest that although hominids underwent two dental macroevolutionary events, the lineage leading to modern humans only experienced anterior tooth-size reduction. The suggested evolutionary significance of the observed total tooth variation is discussed.     

Zebrafish as outgroup model to study evolution of scavenger receptor class B type I functions

Background and aimsScavenger receptor class B1 (SCARB1) - also known as the high-density lipoprotein (HDL) receptor - is a multi-ligand scavenger receptor that is primarily expressed in liver and steroidogenic organs. This receptor is known for its function in reverse cholesterol transport (RCT) in mammals and hence disruption leads to a massive increase in HDL cholesterol in these species. The extracellular domain of SCARB1 - which is important for cholesterol handling - is highly conserved across multiple vertebrates, except in zebrafish. Methods: To examine the functional conservation of SCARB1 among vertebrates, two stable scarb1 knockout zebrafish lines, scarb1 715delA (scarb1 −1 nt) and scarb1 715_716insGG (scarb1 +2 nt), were created using CRISPR-Cas9 technology.ResultsWe demonstrate that, in zebrafish, SCARB1 deficiency leads to disruption of carotenoid-based pigmentation, reduced fertility, and a decreased larvae survival rate, whereas steroidogenesis was unaltered. The observed reduced fertility is driven by defects in female fertility (−50 %, p < 0.001). Importantly, these alterations were independent of changes in free (wild-type 2.4 ± 0.2 μg/μl versus scarb1^−/− 2.0 ± 0.1 μg/μl) as well as total (wild-type 4.2 ± 0.4 μg/μl versus scarb1^−/− 4.0 ± 0.3 μg/μl) plasma cholesterol levels. Uptake of HDL in the liver of scarb1^−/− zebrafish larvae was reduced (−86.7 %, p < 0.001), but this coincided with reduced perfusion of the liver. No effect was observed on lipoprotein uptake in the caudal vein. SCARB1 deficient canaries, which also lack carotenoids in their plumage, similarly as scarb1^−/− zebrafish, failed to show an increase in plasma free- and total cholesterol levels.ConclusionOur findings suggest that the specific function of SCARB1 in maintaining plasma cholesterol could be an evolutionary novelty that became prominent in mammals, while other known functions were already present earlier during vertebrate evolution.     

Genome reduction as the dominant mode of evolution

A common belief is that evolution generally proceeds towards greater complexity at both the organismal and the genomic level, numerous examples of reductive evolution of parasites and symbionts notwithstanding. However, recent evolutionary reconstructions challenge this notion. Two notable examples are the reconstruction of the complex archaeal ancestor and the intron‐rich ancestor of eukaryotes. In both cases, evolution in most of the lineages was apparently dominated by extensive loss of genes and introns, respectively. These and many other cases of reductive evolution are consistent with a general model composed of two distinct evolutionary phases: the short, explosive, innovation phase that leads to an abrupt increase in genome complexity, followed by a much longer reductive phase, which encompasses either a neutral ratchet of genetic material loss or adaptive genome streamlining. Quantitatively, the evolution of genomes appears to be dominated by reduction and simplification, punctuated by episodes of complexification.     

Retroposon insertions and the chronology of avian sex chromosome evolution

The vast majority of extant birds possess highly differentiated Z and W sex chromosomes. Nucleotide sequence data from gametologs (homologs on opposite sex chromosomes) suggest that this divergence occurred throughout early bird evolution via stepwise cessation of recombination between identical sex chromosomal regions. Here, we investigated avian sex chromosome differentiation from a novel perspective, using retroposon insertions and random insertions/deletions for the reconstruction of gametologous gene trees. Our data confirm that the CHD1Z/CHD1W genes differentiated in the ancestor of the neognaths, whereas the NIPBLZ/NIPBLW genes diverged in the neoavian ancestor and independently within Galloanserae. The divergence of the ATP5A1Z/ATP5A1W genes in galloanserans occurred independently in the chicken, the screamer, and the ancestor of duck-related birds. In Neoaves, this gene pair differentiated in each of the six sampled representatives, respectively. Additionally, three of our investigated loci can be utilized as universal, easy-to-use independent tools for molecular sexing of Neoaves or Neognathae.     

The role of parsimony,outgroup analysis,and theory of evolution in phylogenetic systematics

It is argued that both the principle of parsimony and the theory of evolution, especially that of natural selection, are essential analytical tools in phylogenetic systematics, whereas the widely used outgroup analysis is completely useless and may even be misleading. In any systematic analysis, two types of patterns of characters and character states must be discriminated which are referred to as completely and incompletely resolved. In the former, all known species are presented in which the characters and their states studied occur, whereas in the latter this is not the case. Dependent on its structure, a pattern of characters and their states may be explained by either a unique or by various conflicting, equally most parsimonious hypotheses of relationships. The so-called permutation method is introduced which facilitates finding the conflicting, equally most parsimonious hypotheses of relationships. The utility of the principle of parsimony is limited by the uncertainty as to whether its application in systematics must refer to the minimum number of steps needed to explain a pattern of characterts and their states most parsimoniously or to the minimum number of evolutionary events assumed to have caused these steps. Although these numbers may differ, the former is usually preferred for simplicity. The types of outgroup analysis are shown to exist which are termed parsimony analysis based on test samples and cladistic type of outgroup analysis. Essentially, the former is used for analysing incompletely resolved patterns of characters and their states, the latter for analysing completely resolved ones. Both types are shown to be completely useless for rejecting even one of various conflicting, equally most parsimonious hypotheses of relationships. According to contemporary knowledge, this task can be accomplished only by employing the theory of evolution (including the theory of natural selection). But even then, many phylogenetic-systematic problems will remain unsolved. In such cases, arbitrary algorithms like those offered by phenetics can at best offer pseudosolutions to open problems. Despite its limitations, phylogenetic systematics is superior to any kind of aphylogenetic systematics (transformed cladistics included) in approaching a (not: the) “general reference system” of organisms.     

Tempo and mode of hummingbird evolution

Lack of adequate historical data has hindered understanding of the evolutionary tempo and mode of many ecologically well-characterized avian radiations. DNA hybridization distances among 28 hummingbirds (Trochilidae) were used to establish a timescale for this family's radiation into more than 330 species. Under a variety of analytical assumptions, genetic distances calibrated with a fossil divergence date corrected for incompleteness in the geologic record indicated that all extant hummingbird lineages began to diverge in the Early Miocene, approximately 40 Myr (million years) after the Paleocene date estimated for the divergence of hummingbirds and swifts. The long period prior to the radiation of living forms provides ample time for divergent evolution to produce the large morphological gap that has tended to obscure the sister-relationship of hummingbirds and swifts. The Miocene radiation of extant hummingbird lineages itself began with the divergence of the hermit and nonhermit subfamilies approximately 17 Ma (million years ago), followed by the rapid divergence of two Andean and one principally Central and North American clade at approximately 12 Ma. Younger subsidiary lineages, including ones found mainly in the Andes or in North America, date to the later Miocene-earlier Pliocene, approximately 6 Ma. The DNA hybridization-based chronology thus indicates a protracted, rather than stricdy rapid, radiation. Evidence from a broader spectrum of organisms supports the general pattern that higher taxonomic structure within many extant continental families evolved in the Miocene, suggesting that a common environmental pacemaker initiated radiation in unrelated groups. Compared to those in the Pleistocene, radiations tracing to the Miocene may have depended less on rapid climate cycling than on creation of new habitats by major geologic and climatic upheavals. For extant hummingbirds, a principal cause for their Miocene diversification probably was the ability of the ecologically generalized subfamily of nonhermits to radiate in montane areas created by the Andean and other orogenies. Similar interactions between new habitats and their exploitation by ecological generalists may explain, at least in part, the contemporaneous radiation of Passeriformes, the most diverse avian order.     

Mitochondrial DNA sequences of primates: Tempo and mode of evolution

Summary We cloned and sequenced a segment of mitochondrial DNA from human, chimpanzee, gorilla, orangutan, and gibbon. This segment is 896 bp in length, contains the genes for three transfer RNAs and parts of two proteins, and is homologous in all 5 primates. The 5 sequences differ from one another by base substitutions at 283 positions and by a deletion of one base pair. The sequence differences range from 9 to 19% among species, in agreement with estimates from cleavage map comparisons, thus confirming that the rate of mtDNA evolution in primates is 5 to 10 times higher than in nuclear DNA. The most striking new finding to emerge from these comparisons is that transitions greatly outnumber transversions. Ninety-two percent of the differences among the most closely related species (human, chimpanzee, and gorilla) are transitions. For pairs of species with longer divergence times, the observed percentage of transitions falls until, in the case of comparisons between primates and non-primates, it reaches a value of 45. The time dependence is probably due to obliteration of the record of transitions by multiple substitutions at the same nucleotide site. This finding illustrates the importance of choosing closely related species for analysis of the evolutionary process. The remarkable bias toward transitions in mtDNA evolution necessitates the revision of equations that correct for multiple substitutions at the same site. With revised equations, we calculated the incidence of silent and replacement substitutions in the two protein-coding genes. The silent substitution rate is 4 to 6 times higher than the replacement rate, indicating strong functional constraints at replacement sites. Moreover, the silent rate for these two genes is about 10% per million years, a value 10 times higher than the silent rate for the nuclear genes studied so far. In addition, the mean substitution rate in the three mitochondrial tRNA genes is at least 100 times higher than in nuclear tRNA genes. Finally, genealogical analysis of the sequence differences supports the view that the human lineage branched off only slightly before the gorilla and chimpanzee lineages diverged and strengthens the hypothesis that humans are more related to gorillas and chimpanzees than is the orangutan.Abbreviations mtDNA mitochondrial DNA - bp base pair - URF unidentified reading frame     

The tempo and mode of barnacle evolution

Previous phylogenetic attempts at resolving barnacle evolutionary relationships are few and have relied on limited taxon sampling. Here we combine DNA sequences from three nuclear genes (18S, 28S and H3) and 44 morphological characters collected from 76 thoracican (ingroup) and 15 rhizocephalan (outgroup) species representing almost all the Thoracica families to assess the tempo and mode of barnacle evolution. Using phylogenetic methods of maximum parsimony, maximum likelihood, and Bayesian inference and 14 fossil calibrations, we found that: (1) Iblomorpha form a monophyletic group; (2) pedunculated barnacles without shell plates (Heteralepadomorpha) are not ancestral, but have evolved, at least twice, from plated forms; (3) the ontogenetic pattern with 5-->6-->8-->12+ plates does not reflect Thoracica shell evolution; (4) the traditional asymmetric barnacles (Verrucidae) and the Balanomorpha are each monophyletic and together they form a monophyletic group; (5) asymmetry and loss of a peduncle have evolved twice in the Thoracica, resulting in neither the Verrucomorpha nor the Sessilia forming monophyletic groups in their present definitions; (6) the Scalpellomorpha are not monophyletic; (7) the Thoracica suborders evolved since the Early Carboniferous (340mya) with the final radiation of the Sessilia in the Upper Jurassic (147mya). These results, therefore, reject many of the underlying hypotheses about character evolution in the Cirripedia Thoracica, stimulate a variety of new thoughts on thoracican radiation, and suggest the need for a major rearrangement in thoracican classification based on estimated phylogenetic relationships.     

Historical biogeography: Geography as evolution,evolution as geography

Abstract

Despite a number of advances in method in recent years, biogeography remains a field with a poorly developed philosophical core. As a result, its historical and ecological sides remain as isolated from one another as ever. In this essay I argue that a more unified approach to biogeographic studies will become possible only when workers realise that it is necessary to reject absolute space, “geography as handmaiden” approaches to distribution problems in favour of structuralist models compatible with both probabilistic spatial interaction and deterministic phylogenetic kinds of thinking. Pros and cons of regionalist, vicariance, and panbiogeographic approaches are weighed in this regard; it is shown that the primary objections of the latter schools to the approach of the former are vitiated when one dwells on second-order, rather than first-order, interpretations of regional faunal structure. This approach makes it possible to construct joint taxonomic/spatial models conducive to pattern analysis; the latter permits the genesis of hypotheses that can be tested through independently conceived theories of process (such as vicariance). An example of the kind of pattern study envisioned, involving generalised track depiction, is briefly described. A suggested cycle of research is thus laid out in which systematic revision becomes a function of a joint “natural” spatial and phylogenetic/historical approach to the subject.     

Carbon isotopes as indicators of elephant diets and African environments

Stable carbon isotope ratios have been successfully used to assess modern animal diets and to reconstruct prehistoric diets of animals and humans (Vogel & van der Merwe, 1977; van der Merwe & Vogel, 1978; Burleigh & Brothwell, 1978; Vogel, 1978a; DeNiro & Epstein, 1978; Tieszen et al., 1979; Tieszen & Imbamba, 1980; Chisholm, Nelson & Schwarcz, 1982; Tauber, 1981). We have used ¹³C/¹²C ratio measurements of bone collagen to study the diets of African elephants in twelve wildlife refuges. These represent most of the habitats in which elephants live, including such diverse plant communities as primary rain forest, savanna woodland and desert. The δ¹³C values were found to have a simple linear relationship with tree density in most cases. When translated into relative amounts of dietary browse (C₃ plants) and graze (C₄ plants), the grass content is seen to be systematically under-represented, presumably due to inefficient metabolism. This does not affect the relationship between elephant diet and tree density, which has implications for the study of elephant-woodland interactions, and for reconstructions of past African environments.     

Hydrogen evolution as a consumption mode of reducing equivalents in green algal fermentation

Dark anaerobic fermentation in the green algae Chlamydomonas MGA 161, Chlamydomonas reinhardtii, Chlorella pyrenoidosa, and Chlorococcum minutum was studied. Our isolate, Chlamydomonas MGA 161, was unusual in having high H₂ but almost no formate. The fermentation pattern in Chlamydomonas MGA 161 was altered by changes in the NaCl or NH₄Cl concentration. Glycerol formation increased at low (0.1%) and high (7%) NaCl concentrations; starch degradation, and formation of ethanol, H₂, and CO₂ increased with the addition of NH₄Cl to above 5 millimolar in N-deficient cells. C. reinhardtii and C. pyrenoidosa exhibited a very similar anaerobic metabolism, forming formate, acetate and ethanol in a ratio of about 2:2:1. C. minutum was also unusual in forming acetate, glycerol, and CO₂ as its main products, with H₂, formate, and ethanol being formed in negligible amounts. In the presence of CO, ethanol formation increased twofold in Chlamydomonas MGA 161 and C. reinhardtii, but the fermentation pattern in C. minutum did not change. An experiment with hypophosphite addition showed that dark H₂ evolution of the Escherichia coli type could be ruled out in Chlamydomonas MGA 161 and C. reinhardtii. Among the green algae investigated, three fermentation types were identified by the distribution pattern of the end products, which reflected the consumption mode of reducing equivalents in the cells.     

Molecular evolution of mammalian aquaporin-2: further evidence that elephant shrew and aardvark join the paenungulate clade

A 328-bp sequence from exon 1 of the gene for aquaporin-2 (AQP2) was compared in 12 mammalian species, representing as many eutherian orders. This sequence encodes the N-terminal half of this kidney- specific water channel protein. Most amino acid replacements, as well as an insertion, have occurred in extracellular loops connecting the transmembrane helices, in agreement with a lower functional importance of these loops. Phylogenetic analyses were performed with parsimony, distance, and maximum-likelihood methods. The AQP2 data set, alone as well as in combination with previously published alpha A-crystallin protein sequences, strongly supports a clade consisting of elephant, hyrax, aardvark, and elephant shrew, reaching bootstrap values of 99%. This finding fully agrees with the only other presently available sequence data sets that include these taxa, those of von Willebrand factor and interphotoreceptor retinoid-binding protein, and suggests that this extended paenungulate clade is one of the most conspicuous superordinal groupings in eutherian phylogeny. Some support was obtained for an artiodactyl/perissodactyl clade, while the grouping of pholidotes with edentates was contradicted.      

Common origin and evolution of glycosyltransferases using Dol-P-monosaccharides as donor substrate

On the basis of the analysis of 64 glycosyltransferases from 14 species we propose that several successive duplications of a common ancestral gene, followed by divergent evolution, have generated the mannosyltransferases and the glucosyltransferases involved in asparagine-linked glycosylation (ALG) and phosphatidyl-inositol glycan anchor (PIG or GPI), which use lipid-related donor and acceptor substrates. Long and short conserved peptide motifs were found in all enzymes. Conserved and identical amino acid positions were found for the alpha 2/6- and the alpha 3/4-mannosyltransferases and for the alpha 2/3-glucosyltransferases, suggesting unique ancestors for these three superfamilies. The three members of the alpha 2-mannosyltransferase family (ALG9, PIG-B, and SMP3) and the two members of the alpha 3-glucosyltransferase family (ALG6 and ALG8) shared 11 and 30 identical amino acid positions, respectively, suggesting that these enzymes have also originated by duplication and divergent evolution. This model predicts a common genetic origin for ALG and PIG enzymes using dolichyl-phospho-monosaccharide (Dol-P-monosaccharide) donors, which might be related to similar spatial orientation of the hydroxyl acceptors. On the basis of the multiple sequence analysis and the prediction of transmembrane topology we propose that the endoplasmic reticulum glycosyltransferases using Dol-P-monosaccharides as donor substrate have a multispan transmembrane topology with a first large luminal conserved loop containing the long motif and a small cytosolic conserved loop containing the short motif, different from the classical type II glycosyltransferases, which are anchored in the Golgi by a single transmembrane domain.     

The tempo and mode of evolution: body sizes of island mammals

The tempo and mode of body size evolution on islands are believed to be well known. It is thought that body size evolves relatively quickly on islands toward the mammalian modal value, thus generating extreme cases of size evolution and the island rule. Here, we tested both theories in a phylogenetically explicit context, by using two different species-level mammalian phylogenetic hypotheses limited to sister clades dichotomizing into an exclusively insular and an exclusively mainland daughter nodes. Taken as a whole, mammals were found to show a largely punctuational mode of size evolution. We found that, accounting for this, and regardless of the phylogeny used, size evolution on islands is no faster than on the continents. We compared different selection regimes using a set of Ornstein-Uhlenbeck models to examine the effects of insularity of the mode of evolution. The models strongly supported clade-specific selection regimes. Under this regime, however, an evolutionary model allowing insular species to evolve differently from their mainland relatives performs worse than a model that ignores insularity as a factor. Thus, insular taxa do not experience statistically different selection from their mainland relatives.     

The mode of pheromone evolution: evidence from bark beetles

Sex and aggregation pheromones consist of species-specific blends of chemicals. The way in which different species' blends have evolved has been the subject of some debate. Theoretical predictions suggest that differences between species have arisen not through the accruing of small changes, but through major shifts in chemical composition. Using data on the aggregation pheromones of 34 species of bark beetle from two genera, Dendroctonus and Ips, we investigated how the distributions of the chemical components of their pheromone blends mirror their phylogenetic relationships. We tested whether there were consistent patterns that could be used to help elucidate the mode of pheromone evolution. Although there were obvious differences in pheromone blends between the two genera, the differences between species within each genus followed a less clear phylogenetic pattern. In both genera, closely related species are just as different as more distantly related species. Within Dendroctonus, particularly, most chemical components were distributed randomly across the phylogeny. Indeed, for some chemicals, closely related species may actually be more different than would be expected from a random distribution of chemical components. This argues strongly against the idea of minor shifts in pheromone evolution. Instead, we suggest that, within certain phylogenetic constraints, pheromone evolution in bark beetles is characterized by large saltational shifts, resulting in sibling species being substantially phenotypically (i.e. pheromonally) different from one another, thus agreeing with theoretical predictions.