Bushes in the tree of life

Phylogenetic studies of sinipercid fish (Perciformes: Sinipercidae) based on multiple genes, with first application of an immune-related gene, the virus-induced protein (viperin) gene

The sinipercid fish represent a group of 12 species of freshwater percoid fish endemic to East Asia. To date published morphological and molecular phylogenetics hypotheses of sinipercid fish are part congruent, and there are some areas of significant disagreement with respect to species relationships. The present study used separate and combined methods to analyze 7307 bp of data from three mitochondrial genes (cyt b, CO1 and 16S rRNA; approximately 2312 bp) and three nuclear genes (viperin, the first two introns of S7 ribosomal protein gene; approximately 4995 bp) for the attempts to estimate the relationships among sinipercids and to assess the phylogenetic utility of these markers. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and partitioned Bayesian analyses. Despite the detection of significant heterogeneity of phylogenetic signal between the mitochondrial and nuclear partitions, the combined data analysis represented the best-supported topology of all data. The sinipercid fish form a monophyletic group with two distinct clades, one corresponding to the genus Siniperca and the other to Coreoperca. Coreoperca whiteheadi is the sister taxon to Coreoperca herzi plus Coreoperca kawamebari. In the Siniperca, Siniperca undulata is the sister taxon to the other members of Siniperca, within the subclade containing the other members of the genus, Siniperca chuatsi and Siniperca kneri are sister species, next joined by Siniperca obscura, Siniperca roulei, Sinipercascherzeri and finally by Siniperca fortis. The potential utilities of six different genes for phylogenetic resolution of closely related sinipercid species were also evaluated, with special interest in that of the novel virus-induced protein (viperin) gene.

Molecular evolution of the pDo500 satellite DNA family in Dolichopoda cave crickets (Rhaphidophoridae)

BACKGROUND

Non-coding satellite DNA (satDNA) usually has a high turn-over rate frequently leading to species specific patterns. However, some satDNA families evolve more slowly and can be found in several related species. Here, we analyzed the mode of evolution of the pDo500 satDNA family of Dolichopoda cave crickets. In addition, we discuss the potential of slowly evolving satDNAs as phylogenetic markers.

RESULTS

We sequenced 199 genomic or PCR amplified satDNA repeats of the pDo500 family from 12 Dolichopoda species. For the 38 populations under study, 39 pDo500 consensus sequences were deduced. Phylogenetic analyses using Bayesian, Maximum Parsimony, and Maximum Likelihood approaches yielded largely congruent tree topologies. The vast majority of pDo500 sequences grouped according to species designation. Scatter plots and statistical tests revealed a significant correlation between genetic distances for satDNA and mitochondrial DNA. Sliding window analyses showed species specific patterns of variable and conserved regions. The evolutionary rate of the pDo500 satDNA was estimated to be 1.63-1.78% per lineage per million years.

CONCLUSIONS

The pDo500 satDNA evolves gradually at a rate that is only slightly faster than previously published rates of insect mitochondrial COI sequences. The pDo500 phylogeny was basically congruent with the previously published mtDNA phylogenies. Accordingly, the slowly evolving pDo500 satDNA family is indeed informative as a phylogenetic marker.

The mitochondrial genome of the 'twisted-wing parasite' Mengenilla australiensis (Insecta, Strepsiptera): a comparative study

BACKGROUND

Strepsiptera are an unusual group of sexually dimorphic, entomophagous parasitoids whose evolutionary origins remain elusive. The lineage leading to Mengenilla australiensis (Family Mengenillidae) is the sister group to all remaining extant strepsipterans. It is unique in that members of this family have retained a less derived condition, where females are free-living from pupation onwards, and are structurally much less simplified. We sequenced almost the entire mitochondrial genome of M. australiensis as an important comparative data point to the already available genome of its distant relative Xenos vesparum (Family Xenidae). This study represents the first in-depth comparative mitochondrial genomic analysis of Strepsiptera.

RESULTS

The partial genome of M. australiensis is presented as a 13421 bp fragment, across which all 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes and 18 transfer RNA (tRNA) sequences are identified. Two tRNA translocations disrupt an otherwise ancestral insect mitochondrial genome order. A+T content is measured at 84.3%, C-content is also very skewed. Compared with M. australiensis, codon bias in X. vesparum is more balanced. Interestingly, the size of the protein coding genome is truncated in both strepsipterans, especially in X. vesparum which, uniquely, has 4.3% fewer amino acids than the average holometabolan complement. A revised assessment of mitochondrial rRNA secondary structure based on comparative structural considerations is presented for M. australiensis and X. vesparum.

CONCLUSIONS

The mitochondrial genome of X. vesparum has undergone a series of alterations which are probably related to an extremely derived lifestyle. Although M. australiensis shares some of these attributes; it has retained greater signal from the hypothetical most recent common ancestor (MRCA) of Strepsiptera, inviting the possibility that a shift in the mitochondrial selective environment might be related to the specialization accompanying the evolution of a small, morphologically simplified completely host-dependent lifestyle. These results provide useful insights into the nature of the evolutionary transitions that accompanied the emergence of Strepsiptera, but we emphasize the need for adequate sampling across the order in future investigations concerning the extraordinary developmental and evolutionary origins of this group.

Coevolution between a family of parasite virulence effectors and a class of LINE-1 retrotransposons

Parasites are able to evolve rapidly and overcome host defense mechanisms, but the molecular basis of this adaptation is poorly understood. Powdery mildew fungi (Erysiphales, Ascomycota) are obligate biotrophic parasites infecting nearly 10,000 plant genera. They obtain their nutrients from host plants through specialized feeding structures known as haustoria. We previously identified the AVR(k1) powdery mildew-specific gene family encoding effectors that contribute to the successful establishment of haustoria. Here, we report the extensive proliferation of the AVR(k1) gene family throughout the genome of B. graminis, with sequences diverging in formae speciales adapted to infect different hosts. Also, importantly, we have discovered that the effectors have coevolved with a particular family of LINE-1 retrotransposons, named TE1a. The coevolution of these two entities indicates a mutual benefit to the association, which could ultimately contribute to parasite adaptation and success. We propose that the association would benefit 1) the powdery mildew fungus, by providing a mechanism for amplifying and diversifying effectors and 2) the associated retrotransposons, by providing a basis for their maintenance through selection in the fungal genome.

Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions

Ten complete mammalian genome sequences were compared by using the "feature frequency profile" (FFP) method of alignment-free comparison. This comparison technique reveals that the whole nongenic portion of mammalian genomes contains evolutionary information that is similar to their genic counterparts--the intron and exon regions. We partitioned the complete genomes of mammals (such as human, chimp, horse, and mouse) into their constituent nongenic, intronic, and exonic components. Phylogenic species trees were constructed for each individual component class of genome sequence data as well as the whole genomes by using standard tree-building algorithms with FFP distances. The phylogenies of the whole genomes and each of the component classes (exonic, intronic, and nongenic regions) have similar topologies, within the optimal feature length range, and all agree well with the evolutionary phylogeny based on a recent large dataset, multispecies, and multigene-based alignment. In the strictest sense, the FFP-based trees are genome phylogenies, not species phylogenies. However, the species phylogeny is highly related to the whole-genome phylogeny. Furthermore, our results reveal that the footprints of evolutionary history are spread throughout the entire length of the whole genome of an organism and are not limited to genes, introns, or short, highly conserved, nongenic sequences that can be adversely affected by factors (such as a choice of sequences, homoplasy, and different mutation rates) resulting in inconsistent species phylogenies.

Sequence diversity, population genetics and potential recombination events in grapevine rupestris stem pitting-associated virus in Pacific North-West vineyards

Grapevine rupestris stem pitting-associated virus (GRSPaV; genus Foveavirus, family Flexiviridae) is present in many grape-growing regions of the world. A total of 84 full-length coat protein (CP) sequences and 57 sequences representing the helicase-encoding region (HR) of the RNA-dependent RNA polymerase were obtained from wine grape cultivars grown in the Pacific North-West (PNW) of the United States and their molecular diversity was compared with corresponding sequences previously reported from other grape-growing regions. In pairwise comparisons, the CP sequences from PNW isolates showed identities between 80 and 100% at the nucleotide level and the HR sequences showed identities between 79 and 100%. A global phylogenetic analysis of the CP and HR sequences revealed segregation of GRSPaV isolates into four major lineages with isolates from PNW distributed in all four lineages, indicating a lack of clustering by geographical origin. Scion cultivars grafted onto rootstock were found to contain mixtures of more genetic variants belonging to different lineages than own-rooted cultivars. Assessment of population genetic parameters found that the CP was more variable than the HR region. The discordant gene phylogenies obtained for some CP and HR sequences and the identification of potential recombination events involving parents from different lineages provided strong evolutionary evidence for genetic diversity among GRSPaV isolates. These results underscore the highly variable nature of the virus with implications for grapevine health status and distribution of virus-tested planting materials. This study also contributes to an increased understanding of molecular population genetics of viruses infecting deciduous woody perennials.

The phylogenetic forest and the quest for the elusive tree of life

Extensive horizontal gene transfer (HGT) among prokaryotes seems to undermine the tree of life (TOL) concept. However, the possibility remains that the TOL can be salvaged as a statistical central trend in the phylogenetic "forest of life" (FOL). A comprehensive comparative analysis of 6901 phylogenetic trees for prokaryotic genes revealed a signal of vertical inheritance that was particularly strong among the 102 nearly universal trees (NUTs), despite the high topological inconsistency among the trees in the FOL, most likely, caused by HGT. The topologies of the NUTs are similar to the topologies of numerous other trees in the FOL; although the NUTs cannot represent the FOL completely, they reflect a significant central trend. Thus, the original TOL concept becomes obsolete but the idea of a "weak" TOL as the dominant trend in the FOL merits further investigation. The totality of gene trees comprising the FOL appears to be a natural representation of the history of life given the inherent tree-like character of the replication process.

Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life

Horizontal gene transfer (HGT) is often considered to be a source of error in phylogenetic reconstruction, causing individual gene trees within an organismal lineage to be incongruent, obfuscating the 'true' evolutionary history. However, when identified as such, HGTs between divergent organismal lineages are useful, phylogenetically informative characters that can provide insight into evolutionary history. Here, we discuss several distinct HGT events involving all three domains of life, illustrating the selective advantages that can be conveyed via HGT, and the utility of HGT in aiding phylogenetic reconstruction and in dating the relative sequence of speciation events. We also discuss the role of HGT from extinct lineages, and its impact on our understanding of the evolution of life on Earth. Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life's history.

Search for a 'Tree of Life' in the thicket of the phylogenetic forest

BACKGROUND

Comparative genomics has revealed extensive horizontal gene transfer among prokaryotes, a development that is often considered to undermine the 'tree of life' concept. However, the possibility remains that a statistical central trend still exists in the phylogenetic 'forest of life'.

RESULTS

A comprehensive comparative analysis of a 'forest' of 6,901 phylogenetic trees for prokaryotic genes revealed a consistent phylogenetic signal, particularly among 102 nearly universal trees, despite high levels of topological inconsistency, probably due to horizontal gene transfer. Horizontal transfers seemed to be distributed randomly and did not obscure the central trend. The nearly universal trees were topologically similar to numerous other trees. Thus, the nearly universal trees might reflect a significant central tendency, although they cannot represent the forest completely. However, topological consistency was seen mostly at shallow tree depths and abruptly dropped at the level of the radiation of archaeal and bacterial phyla, suggesting that early phases of evolution could be non-tree-like (Biological Big Bang). Simulations of evolution under compressed cladogenesis or Biological Big Bang yielded a better fit to the observed dependence between tree inconsistency and phylogenetic depth for the compressed cladogenesis model.

CONCLUSIONS

Horizontal gene transfer is pervasive among prokaryotes: very few gene trees are fully consistent, making the original tree of life concept obsolete. A central trend that most probably represents vertical inheritance is discernible throughout the evolution of archaea and bacteria, although compressed cladogenesis complicates unambiguous resolution of the relationships between the major archaeal and bacterial clades.

Paleocene emergence of elephant relatives and the rapid radiation of African ungulates

Elephants are the only living representatives of the Proboscidea, a formerly diverse mammalian order whose history began with the 55-million years (mys) old Phosphatherium. Reported here is the discovery from the early late Paleocene of Morocco, ca. 60 mys, of the oldest and most primitive elephant relative, Eritherium azzouzorum n.g., n.sp., which is one of the earliest known representatives of modern placental orders. This well supported stem proboscidean is extraordinarily primitive and condylarth-like. It provides the first dental evidence of a resemblance between the proboscideans and African ungulates (paenungulates) on the one hand and the louisinines and early macroscelideans on the other. Eritherium illustrates the origin of the elephant order at a previously unknown primitive stage among paenungulates and "ungulates." The primitive morphology of Eritherium suggests a recent and rapid paenungulate radiation after the Cretaceous-Tertiary boundary, probably favoured by early endemic African paleoecosystems. At a broader scale, Eritherium provides a new old calibration point of the placental tree and supports an explosive placental radiation. The Ouled Abdoun basin, which yields the oldest known African placentals, is a key locality for elucidating phylogeny and early evolution of paenungulates and other related endemic African lineages.

The genetic code can cause systematic bias in simple phylogenetic models

Phylogenetic analysis depends on inferential methodology estimating accurately the degree of divergence between sequences. Inaccurate estimates can lead to misleading evolutionary inferences, including incorrect tree topology estimates and poor dating of historical species divergence. Protein coding sequences are ubiquitous in phylogenetic inference, but many of the standard methods commonly used to describe their evolution do not explicitly account for the dependencies between sites in a codon induced by the genetic code. This study evaluates the performance of several standard methods on datasets simulated under a simple substitution model, describing codon evolution under a range of different types of selective pressures. This approach also offers insights into the relative performance of different phylogenetic methods when there are dependencies acting between the sites in the data. Methods based on statistical models performed well when there was no or limited purifying selection in the simulated sequences (low degree of dependency between sites in a codon), although more biologically realistic models tended to outperform simpler models. Phylogenetic methods exhibited greater variability in performance for sequences simulated under strong purifying selection (high degree of the dependencies between sites in a codon). Simple models substantially underestimate the degree of divergence between sequences, and underestimation was more pronounced on the internal branches of the tree. This underestimation resulted in some statistical methods performing poorly and exhibiting evidence for systematic bias in tree inference. Amino acid-based and nucleotide models that contained generic descriptions of spatial and temporal heterogeneity, such as mixture and temporal hidden Markov models, coped notably better, producing more accurate estimates of evolutionary divergence and the tree topology.

Analysis of rare genomic changes does not support the unikont-bikont phylogeny and suggests cyanobacterial symbiosis as the point of primary radiation of eukaryotes

The deep phylogeny of eukaryotes is an important but extremely difficult problem of evolutionary biology. Five eukaryotic supergroups are relatively well established but the relationship between these supergroups remains elusive, and their divergence seems to best fit a “Big Bang” model. Attempts were made to root the tree of eukaryotes by using potential derived shared characters such as unique fusions of conserved genes. One popular model of eukaryotic evolution that emerged from this type of analysis is the unikont–bikont phylogeny: The unikont branch consists of Metazoa, Choanozoa, Fungi, and Amoebozoa, whereas bikonts include the rest of eukaryotes, namely, Plantae (green plants, Chlorophyta, and Rhodophyta), Chromalveolata, excavates, and Rhizaria. We reexamine the relationships between the eukaryotic supergroups using a genome-wide analysis of rare genomic changes (RGCs) associated with multiple, conserved amino acids (RGC_CAMs and RGC_CAs), to resolve trifurcations of major eukaryotic lineages. The results do not support the basal position of Chromalveolata with respect to Plantae and unikonts or the monophyly of the bikont group and appear to be best compatible with the monophyly of unikonts and Chromalveolata. Chromalveolata show a distinct, additional signal of affinity with Plantae, conceivably, owing to genes transferred from the secondary, red algal symbiont. Excavates are derived forms, with extremely long branches that complicate phylogenetic inference; nevertheless, the RGC analysis suggests that they are significantly more likely to cluster with the unikont–Chromalveolata assemblage than with the Plantae. Thus, the first split in eukaryotic evolution might lie between photosynthetic and nonphotosynthetic forms and so could have been triggered by the endosymbiosis between an ancestral unicellular eukaryote and a cyanobacterium that gave rise to the chloroplast.

Paleontology, genomics, and combined-data phylogenetics: can molecular data improve phylogeny estimation for fossil taxa?

The genomics revolution offers great promise for resolving the phylogeny of living taxa, but does it offer any benefits for reconstructing relationships among extinct (fossil) taxa? Superficially, the answer would seem to be "no," given that molecular data cannot be obtained for most fossil taxa. However, because fossil taxa often interdigitate among living taxa on the Tree of Life, molecular data may indirectly enhance phylogenetic accuracy for fossil taxa in the context of a combined analysis of morphological and molecular data for living and fossil taxa. Here, I use simulations to assess accuracy for fossil taxa in a mixed analysis of living and fossil taxa, before and after addition of molecular data to the living taxa. The results show conditions where the accuracy for fossil taxa is greatly increased by adding molecular data, sometimes by as much as 100%. In other cases, the increase is negligible, such as when fossil taxa greatly outnumber living taxa in the analysis. However, there were few cases where accuracy was significantly decreased by the addition of the molecular data, suggesting that this practice may range from highly beneficial to mostly harmless. Overall, the results suggest that improvements in molecular phylogenetics can potentially benefit phylogeny reconstruction for fossil taxa.

The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

The evolutionary rates of protein-coding genes in an organism span, approximately, 3 orders of magnitude and show a universal, approximately log-normal distribution in a broad variety of species from prokaryotes to mammals. This universal distribution implies a steady-state process, with identical distributions of evolutionary rates among genes that are gained and genes that are lost. A mathematical model of such process is developed under the single assumption of the constancy of the distributions of the propensities for gene loss (PGL). This model predicts that genes of different ages, that is, genes with homologs detectable at different phylogenetic depths, substantially differ in those variables that correlate with PGL. We computationally partition protein-coding genes from humans, flies, and Aspergillus fungus into age classes, and show that genes of different ages retain the universal log-normal distribution of evolutionary rates, with a shift toward higher rates in "younger" classes but also with a substantial overlap. The only exception involves human primate-specific genes that show a heavy tail of rapidly evolving genes, probably owing to gene annotation artifacts. As predicted, the gene age classes differ in characteristics correlated with PGL. Compared with "young" genes (e.g., mammal-specific human ones), "old" genes (e.g., eukaryote-specific), on average, are longer, are expressed at a higher level, possess a higher intron density, evolve slower on the short time scale, and are subject to stronger purifying selection. Thus, genome evolution fits a simple model with approximately uniform rates of gene gain and loss, without major bursts of genomic innovation.

Universal artifacts affect the branching of phylogenetic trees, not universal scaling laws

BACKGROUND

The superficial resemblance of phylogenetic trees to other branching structures allows searching for macroevolutionary patterns. However, such trees are just statistical inferences of particular historical events. Recent meta-analyses report finding regularities in the branching pattern of phylogenetic trees. But is this supported by evidence, or are such regularities just methodological artifacts? If so, is there any signal in a phylogeny?

METHODOLOGY

In order to evaluate the impact of polytomies and imbalance on tree shape, the distribution of all binary and polytomic trees of up to 7 taxa was assessed in tree-shape space. The relationship between the proportion of outgroups and the amount of imbalance introduced with them was assessed applying four different tree-building methods to 100 combinations from a set of 10 ingroup and 9 outgroup species, and performing covariance analyses. The relevance of this analysis was explored taking 61 published phylogenies, based on nucleic acid sequences and involving various taxa, taxonomic levels, and tree-building methods.

PRINCIPAL FINDINGS

All methods of phylogenetic inference are quite sensitive to the artifacts introduced by outgroups. However, published phylogenies appear to be subject to a rather effective, albeit rather intuitive control against such artifacts. The data and methods used to build phylogenetic trees are varied, so any meta-analysis is subject to pitfalls due to their uneven intrinsic merits, which translate into artifacts in tree shape. The binary branching pattern is an imposition of methods, and seldom reflects true relationships in intraspecific analyses, yielding artifactual polytomies in short trees. Above the species level, the departure of real trees from simplistic random models is caused at least by two natural factors--uneven speciation and extinction rates; and artifacts such as choice of taxa included in the analysis, and imbalance introduced by outgroups and basal paraphyletic taxa. This artifactual imbalance accounts for tree shape convergence of large trees.

SIGNIFICANCE

There is no evidence for any universal scaling in the tree of life. Instead, there is a need for improved methods of tree analysis that can be used to discriminate the noise due to outgroups from the phylogenetic signal within the taxon of interest, and to evaluate realistic models of evolution, correcting the retrospective perspective and explicitly recognizing extinction as a driving force. Artifacts are pervasive, and can only be overcome through understanding the structure and biological meaning of phylogenetic trees. Catalan Abstract in Translation S1.

Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis

For more than a century, the origin of metazoan animals has been debated. One aspect of this debate has been centered on what the hypothetical “urmetazoon” bauplan might have been. The morphologically most simply organized metazoan animal, the placozoan Trichoplax adhaerens, resembles an intriguing model for one of several “urmetazoon” hypotheses: the placula hypothesis. Clear support for a basal position of Placozoa would aid in resolving several key issues of metazoan-specific inventions (including, for example, head–foot axis, symmetry, and coelom) and would determine a root for unraveling their evolution. Unfortunately, the phylogenetic relationships at the base of Metazoa have been controversial because of conflicting phylogenetic scenarios generated while addressing the question. Here, we analyze the sum of morphological evidence, the secondary structure of mitochondrial ribosomal genes, and molecular sequence data from mitochondrial and nuclear genes that amass over 9,400 phylogenetically informative characters from 24 to 73 taxa. Together with mitochondrial DNA genome structure and sequence analyses and Hox-like gene expression patterns, these data (1) provide evidence that Placozoa are basal relative to all other diploblast phyla and (2) spark a modernized “urmetazoon” hypothesis.

Following one of the basic principles in evolutionary biology that complex life forms derive from more primitive ancestors, it has long been believed that the higher animals, the Bilateria, arose from simpler (diploblastic) organisms such as the cnidarians (corals, polyps, and jellyfishes). A large number of studies, using different datasets and different methods, have tried to determine the most ancestral animal group as well as the ancestor of the higher animals. Here, we use “total evidence” analysis, which incorporates all available data (including morphology, genome, and gene expression data) and come to a surprising conclusion. The Bilateria and Cnidaria (together with the other diploblastic animals) are in fact sister groups: that is, they evolved in parallel from a very simple common ancestor. We conclude that the higher animals (Bilateria) and lower animals (diploblasts), probably separated very early, at the very beginning of metazoan animal evolution and independently evolved their complex body plans, including body axes, nervous system, sensory organs, and other characteristics. The striking similarities in several complex characters (such as the eyes) resulted from both lineages using the same basic genetic tool kit, which was already present in the common ancestor. The study identifies Placozoa as the most basal diploblast group and thus a living fossil genome that nicely demonstrates, not only that complex genetic tool kits arise before morphological complexity, but also that these kits may form similar morphological structures in parallel.

Total evidence analyses reveal a surprise: Higher animals did not evolve from any known lower animal group.

Darwinian evolution in the light of genomics

Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.

The origins of multicellularity and the early history of the genetic toolkit for animal development

Multicellularity appeared early and repeatedly in life's history; its instantiations presumably required the confluence of environmental, ecological, and genetic factors. Comparisons of several independently evolved pairs of multicellular and unicellular relatives indicate that transitions to multicellularity are typically associated with increases in the numbers of genes involved in cell differentiation, cell-cell communication, and adhesion. Further examination of the DNA record suggests that these increases in gene complexity are the product of evolutionary innovation, tinkering, and expansion of genetic material. Arguably, the most decisive multicellular transition was the emergence of animals. Decades of developmental work have demarcated the genetic toolkit for animal multicellularity, a select set of a few hundred genes from a few dozen gene families involved in adhesion, communication, and differentiation. Examination of the DNA records of the earliest-branching animal phyla and their closest protist relatives has begun to shed light on the origins and assembly of this toolkit. Emerging data favor a model of gradual assembly, with components originating and diversifying at different time points prior to or shortly after the origin of animals.

Placozoa and the evolution of Metazoa and intrasomatic cell differentiation

The multicellular Metazoa evolved from single-celled organisms (Protozoa) and usually - but not necessarily - consist of more cells than Protozoa. In all cases, and thus by definition, Metazoa possess more than one somatic cell type, i.e. they show-in sharp contrast to protists-intrasomatic differentiation. Placozoa have the lowest degree of intrasomatic variation; the number of somatic cell types according to text books is four (but see also Jakob W, Sagasser S, Dellaporta S, Holland P, Kuhn K, and Schierwater B. The Trox-2 Hox/ParaHox gene of Trichoplax (Placozoa) marks an epithelial boundary. Dev Genes Evol 2004;214:170-5). For this and several other reasons Placozoa have been regarded by many as the most basal metazoan phylum. Thus, the morphologically most simply organized metazoan animal, the placozoan Trichoplax adhaerens, resembles a unique model system for cell differentiation studies and also an intriguing model for a prominent "urmetazoon" hypotheses-the placula hypothesis. A basal position of Placozoa would provide answers to several key issues of metazoan-specific inventions (including for example different lines of somatic cell differentiation leading to organ development and axis formation) and would determine a root for unraveling their evolution. However, the phylogenetic relationships at the base of Metazoa are controversial and a basal position of Placozoa is not generally accepted (e.g. Schierwater B, DeSalle R. Can we ever identify the Urmetazoan? Integr Comp Biol 2007;47:670-76; DeSalle R, Schierwater B. An even "newer" animal phylogeny. Bioessays 2008;30:1043-47). Here we review and discuss (i) long-standing morphological evidence for the simple placozoan bauplan resembling an ancestral metazoan stage, (ii) some rapidly changing alternative hypotheses derived from molecular analyses, (iii) the surprising idea that triploblasts (Bilateria) and diploblasts may be sister groups, and (iv) the presence of genes involved in cell differentiation and signaling pathways in the placozoan genome.

Frequent and widespread parallel evolution of protein sequences

Understanding the patterns and causes of protein sequence evolution is a major challenge in evolutionary biology. One of the critical unresolved issues is the relative contribution of selection and genetic drift to the fixation of amino acid sequence differences between species. Molecular homoplasy, the independent evolution of the same amino acids at orthologous sites in different taxa, is one potential signature of selection; however, relatively little is known about its prevalence in eukaryotic proteomes. To quantify the extent and type of homoplasy among evolving proteins, we used phylogenetic methodology to analyze 8 genome-scale data matrices from clades of different evolutionary depths that span the eukaryotic tree of life. We found that the frequency of homoplastic amino acid substitutions in eukaryotic proteins was more than 2-fold higher than expected under neutral models of protein evolution. The overwhelming majority of homoplastic substitutions were parallelisms that involved the most frequently exchanged amino acids with similar physicochemical properties and that could be reached by a single-mutational step. We conclude that the role of homoplasy in shaping the protein record is much larger than generally assumed, and we suggest that its high frequency can be explained by both weak positive selection for certain substitutions and purifying selection that constrains substitutions to a small number of functionally equivalent amino acids.

The deep archaeal roots of eukaryotes

The set of conserved eukaryotic protein-coding genes includes distinct subsets one of which appears to be most closely related to and, by inference, derived from archaea, whereas another one appears to be of bacterial, possibly, endosymbiotic origin. The “archaeal” genes of eukaryotes, primarily, encode components of information-processing systems, whereas the “bacterial” genes are predominantly operational. The precise nature of the archaeo–eukaryotic relationship remains uncertain, and it has been variously argued that eukaryotic informational genes evolved from the homologous genes of Euryarchaeota or Crenarchaeota (the major branches of extant archaea) or that the origin of eukaryotes lies outside the known diversity of archaea. We describe a comprehensive set of 355 eukaryotic genes of apparent archaeal origin identified through ortholog detection and phylogenetic analysis. Phylogenetic hypothesis testing using constrained trees, combined with a systematic search for shared derived characters in the form of homologous inserts in conserved proteins, indicate that, for the majority of these genes, the preferred tree topology is one with the eukaryotic branch placed outside the extant diversity of archaea although small subsets of genes show crenarchaeal and euryarchaeal affinities. Thus, the archaeal genes in eukaryotes appear to descend from a distinct, ancient, and otherwise uncharacterized archaeal lineage that acquired some euryarchaeal and crenarchaeal genes via early horizontal gene transfer.

Problematica old and new

Problematica are taxa that defy robust phylogenetic placement. Traditionally the term was restricted to fossil forms, but it is clear that extant taxa may be just as difficult to place, whether using morphological or molecular (nucleotide, gene or genomic) markers for phylogeny reconstruction. We discuss the kinds and causes of Problematica within the Metazoa, as well as criteria for their recognition and possible solutions. The inclusive set of Problematica changes depending upon the nature and quality of (homologous) data available, the methods of phylogeny reconstruction and the sister taxa inferred by their placement or displacement. We address Problematica in the context of pre-cladistic phylogenetics, numerical morphological cladistics and molecular phylogenetics, and focus on general biological and methodological implications of Problematica, rather than presenting a review of individual taxa. Rather than excluding Problematica from phylogeny reconstruction, as has often been preferred, we conclude that the study of Problematica is crucial for both the resolution of metazoan phylogeny and the proper inference of body plan evolution.

Back in time: a new systematic proposal for the Bilateria

Conventional wisdom suggests that bilateral organisms arose from ancestors that were radially, rather than bilaterally, symmetrical and, therefore, had a single body axis and no mesoderm. The two main hypotheses on how this transformation took place consider either a simple organism akin to the planula larva of extant cnidarians or the acoel Platyhelminthes (planuloid-acoeloid theory), or a rather complex organism bearing several or most features of advanced coelomate bilaterians (archicoelomate theory). We report phylogenetic analyses of bilaterian metazoans using quantitative (ribosomal, nuclear and expressed sequence tag sequences) and qualitative (HOX cluster genes and microRNA sets) markers. The phylogenetic trees obtained corroborate the position of acoel and nemertodermatid flatworms as the earliest branching extant members of the Bilateria. Moreover, some acoelomate and pseudocoelomate clades appear as early branching lophotrochozoans and deuterostomes. These results strengthen the view that stem bilaterians were small, acoelomate/pseudocoelomate, benthic organisms derived from planuloid-like organisms. Because morphological and recent gene expression data suggest that cnidarians are actually bilateral, the origin of the last common bilaterian ancestor has to be put back in time earlier than the cnidarian-bilaterian split in the form of a planuloid animal. A new systematic scheme for the Bilateria that includes the Cnidaria is suggested and its main implications discussed.

Stable isotope evidence for an amphibious phase in early proboscidean evolution

The order Proboscidea includes extant elephants and their extinct relatives and is closely related to the aquatic sirenians (manatees and dugongs) and terrestrial hyracoids (hyraxes). Some analyses of embryological, morphological, and paleontological data suggest that proboscideans and sirenians shared an aquatic or semiaquatic common ancestor, but independent tests of this hypothesis have proven elusive. Here we test the hypothesis of an aquatic ancestry for advanced proboscideans by measuring delta(18)O in tooth enamel of two late Eocene proboscidean genera, Barytherium and Moeritherium, which are sister taxa of Oligocene-to-Recent proboscideans. The combination of low delta(18)O values and low delta(18)O standard deviations in Barytherium and Moeritherium matches the isotopic pattern seen in aquatic and semiaquatic mammals, and differs from that of terrestrial mammals. delta(13)C values of these early proboscideans suggest that both genera are likely to have consumed freshwater plants, although a component of C(3) terrestrial vegetation cannot be ruled out. The simplest explanation for the combined evidence from isotopes, dental functional morphology, and depositional environments is that Barytherium and Moeritherium were at least semiaquatic and lived in freshwater swamp or riverine environments, where they grazed on freshwater vegetation. These results lend new support to the hypothesis that Oligocene-to-Recent proboscideans are derived from amphibious ancestors.

Analysis of 142 genes resolves the rapid diversification of the rice genus

BACKGROUND

The completion of rice genome sequencing has made rice and its wild relatives an attractive system for biological studies. Despite great efforts, phylogenetic relationships among genome types and species in the rice genus have not been fully resolved. To take full advantage of rice genome resources for biological research and rice breeding, we will benefit from the availability of a robust phylogeny of the rice genus.

RESULTS

Through screening rice genome sequences, we sampled and sequenced 142 single-copy genes to clarify the relationships among all diploid genome types of the rice genus. The analysis identified two short internal branches around which most previous phylogenetic inconsistency emerged. These represent two episodes of rapid speciation that occurred approximately 5 and 10 million years ago (Mya) and gave rise to almost the entire diversity of the genus. The known chromosomal distribution of the sampled genes allowed the documentation of whole-genome sorting of ancestral alleles during the rapid speciation, which was responsible primarily for extensive incongruence between gene phylogenies and persisting phylogenetic ambiguity in the genus. Random sample analysis showed that 120 genes with an average length of 874 bp were needed to resolve both short branches with 95% confidence.

CONCLUSION

Our phylogenomic analysis successfully resolved the phylogeny of rice genome types, which lays a solid foundation for comparative and functional genomic studies of rice and its relatives. This study also highlights that organismal genomes might be mosaics of conflicting genealogies because of rapid speciation and demonstrates the power of phylogenomics in the reconstruction of rapid diversification.

The human phylome

The human phylome, which includes evolutionary relationships of all human proteins and their homologs among thirty-nine fully sequenced eukaryotes, is reconstructed.

Background:

Phylogenomics analyses serve to establish evolutionary relationships among organisms and their genes. A phylome, the complete collection of all gene phylogenies in a genome, constitutes a valuable source of information, but its use in large genomes still constitutes a technical challenge. The use of phylomes also requires the development of new methods that help us to interpret them.

Results:

We reconstruct here the human phylome, which includes the evolutionary relationships of all human proteins and their homologs among 39 fully sequenced eukaryotes. Phylogenetic techniques used include alignment trimming, branch length optimization, evolutionary model testing and maximum likelihood and Bayesian methods. Although differences with alternative topologies are minor, most of the trees support the Coelomata and Unikont hypotheses as well as the grouping of primates with laurasatheria to the exclusion of rodents. We assess the extent of gene duplication events and their relationship with the functional roles of the protein families involved. We find support for at least one, and probably two, rounds of whole genome duplications before vertebrate radiation. Using a novel algorithm that is independent from a species phylogeny, we derive orthology and paralogy relationships of human proteins among eukaryotic genomes.

Conclusion:

Topological variations among phylogenies for different genes are to be expected, highlighting the danger of gene-sampling effects in phylogenomic analyses. Several links can be established between the functions of gene families duplicated at certain phylogenetic splits and major evolutionary transitions in those lineages. The pipeline implemented here can be easily adapted for use in other organisms.

Topological variation in single-gene phylogenetic trees

A large-scale phylogenetic study of the human lineage dramatically points up the problems of using single genes to build phylogenetic trees.

A recent large-scale phylogenomic study has shown the great degree of topological variation that can be found among eukaryotic phylogenetic trees constructed from single genes, highlighting the problems that can be associated with gene sampling in phylogenetic studies.

Ancient rapid radiations of insects: challenges for phylogenetic analysis

Phylogenies of major groups of insects based on both morphological and molecular data have sometimes been contentious, often lacking the data to distinguish between alternative views of relationships. This paucity of data is often due to real biological and historical causes, such as shortness of time spans between divergences for evolution to occur and long time spans after divergences for subsequent evolutionary changes to obscure the earlier ones. Another reason for difficulty in resolving some of the relationships using molecular data is the limited spectrum of genes so far developed for phylogeny estimation. For this latter issue, there is cause for current optimism owing to rapid increases in our knowledge of comparative genomics. At least some historical patterns of divergence may, however, continue to defy our attempts to completely reconstruct them with confidence, at least using current strategies.

A new estimate of afrotherian phylogeny based on simultaneous analysis of genomic, morphological, and fossil evidence

BACKGROUND

The placental mammalian clade Afrotheria is now supported by diverse forms of genomic data, but interordinal relationships within, and morphological support for, the group remains elusive. As a means for addressing these outstanding problems, competing hypotheses of afrotherian interordinal relationships were tested through simultaneous parsimony analysis of a large data set (> 4,590 parsimony informative characters) containing genomic data (> 17 kb of nucleotide data, chromosomal associations, and retroposons) and 400 morphological characters scored across 16 extant and 35 extinct afrotherians.

RESULTS

Parsimony analysis of extant taxa alone recovered the interordinal topology (Afrosoricida, ((Macroscelidea, Tubulidentata), (Hyracoidea, (Proboscidea, Sirenia)))). Analysis following addition of extinct taxa instead supported Afroinsectivora (Afrosoricida + Macroscelidea) and Pseudoungulata (Tubulidentata + Paenungulata), as well as Tethytheria (Proboscidea + Sirenia). This latter topology is, however, sensitive to taxon deletion and different placements of the placental root, and numerous alternative interordinal arrangements within Afrotheria could not be statistically rejected. Relationships among extinct stem members of each afrotherian clade were more stable, but one alleged stem macroscelidean (Herodotius) never grouped with that clade and instead consistently joined pseudoungulates or paenungulates. When character transformations were optimized onto a less resolved afrotherian tree that reflects uncertainty about the group's interordinal phylogeny, a total of 21 morphological features were identified as possible synapomorphies of crown Afrotheria, 9 of which optimized unambiguously across all character treatments and optimization methods.

CONCLUSION

Instability in afrotherian interordinal phylogeny presumably reflects rapid divergences during two pulses of cladogenesis - the first in the Late Cretaceous, at and just after the origin of crown Afrotheria, and the second in the early Cenozoic, with the origin of crown Paenungulata. Morphological evidence for divergences during these two pulses either never existed or has largely been "erased" by subsequent evolution along long ordinal branches. There may, nevertheless, be more morphological character support for crown Afrotheria than is currently assumed; the features identified here as possible afrotherian synapomorphies can be further scrutinized through future phylogenetic analyses with broader taxon sampling, as well as recovery of primitive fossil afrotherians from the Afro-Arabian landmass, where the group is likely to have first diversified.

Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid speciation

Background

Despite the small number of ursid species, bear phylogeny has long been a focus of study due to their conservation value, as all bear genera have been classified as endangered at either the species or subspecies level. The Ursidae family represents a typical example of rapid evolutionary radiation. Previous analyses with a single mitochondrial (mt) gene or a small number of mt genes either provide weak support or a large unresolved polytomy for ursids. We revisit the contentious relationships within Ursidae by analyzing complete mt genome sequences and evaluating the performance of both entire mt genomes and constituent mtDNA genes in recovering a phylogeny of extremely recent speciation events.

Results

This mitochondrial genome-based phylogeny provides strong evidence that the spectacled bear diverged first, while within the genus Ursus, the sloth bear is the sister taxon of all the other five ursines. The latter group is divided into the brown bear/polar bear and the two black bears/sun bear assemblages. These findings resolve the previous conflicts between trees using partial mt genes. The ability of different categories of mt protein coding genes to recover the correct phylogeny is concordant with previous analyses for taxa with deep divergence times. This study provides a robust Ursidae phylogenetic framework for future validation by additional independent evidence, and also has significant implications for assisting in the resolution of other similarly difficult phylogenetic investigations.

Conclusion

Identification of base composition bias and utilization of the combined data of whole mitochondrial genome sequences has allowed recovery of a strongly supported phylogeny that is upheld when using multiple alternative outgroups for the Ursidae, a mammalian family that underwent a rapid radiation since the mid- to late Pliocene. It remains to be seen if the reliability of mt genome analysis will hold up in studies of other difficult phylogenetic issues. Although the whole mitochondrial DNA sequence based phylogeny is robust, it remains in conflict with phylogenetic relationships suggested by analysis of limited nuclear-encoded data, a situation that will require gathering more nuclear DNA sequence information.

The Biological Big Bang model for the major transitions in evolution

BACKGROUND

Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable. Usually, this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal.

HYPOTHESIS

I propose that most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on. This biphasic model of evolution incorporates the previously developed concepts of the emergence of protein folds by recombination of small structural units and origin of viruses and cells from a pre-cellular compartmentalized pool of recombining genetic elements. The model is extended to encompass other major transitions. It is proposed that bacterial and archaeal phyla emerged independently from two distinct populations of primordial cells that, originally, possessed leaky membranes, which made the cells prone to rampant gene exchange; and that the eukaryotic supergroups emerged through distinct, secondary endosymbiotic events (as opposed to the primary, mitochondrial endosymbiosis). This biphasic model of evolution is substantially analogous to the scenario of the origin of universes in the eternal inflation version of modern cosmology. Under this model, universes like ours emerge in the infinite multiverse when the eternal process of exponential expansion, known as inflation, ceases in a particular region as a result of false vacuum decay, a first order phase transition process. The result is the nucleation of a new universe, which is traditionally denoted Big Bang, although this scenario is radically different from the Big Bang of the traditional model of an expanding universe. Hence I denote the phase transitions at the end of each inflationary epoch in the history of life Biological Big Bangs (BBB).

CONCLUSION

A Biological Big Bang (BBB) model is proposed for the major transitions in life's evolution. According to this model, each transition is a BBB such that new classes of biological entities emerge at the end of a rapid phase of evolution (inflation) that is characterized by extensive exchange of genetic information which takes distinct forms for different BBBs. The major types of new forms emerge independently, via a sampling process, from the pool of recombining entities of the preceding generation. This process is envisaged as being qualitatively different from tree-pattern cladogenesis.

Deciphering ancient rapid radiations

A deeper phylogenetic understanding of ancient patterns of diversification would contribute to solving many problems in evolutionary biology, yet many of these phylogenies remain poorly resolved. Ancient rapid radiations pose a major challenge for phylogenetic analysis for two main reasons. First, the pattern to be deciphered, the order of divergence among lineages, tends to be supported by small amounts of data. Second, the time since divergence is large and, thus, the potential for misinterpreting phylogenetic information is great. Here, we review the underlying causes of difficulty in determining the branching patterns of diversification in ancient rapid radiations, and review novel data exploration tools that can facilitate understanding of these radiations.

Using genomic data to unravel the root of the placental mammal phylogeny

The phylogeny of placental mammals is a critical framework for choosing future genome sequencing targets and for resolving the ancestral mammalian genome at the nucleotide level. Despite considerable recent progress defining superordinal relationships, several branches remain poorly resolved, including the root of the placental tree. Here we analyzed the genome sequence assemblies of human, armadillo, elephant, and opossum to identify informative coding indels that would serve as rare genomic changes to infer early events in placental mammal phylogeny. We also expanded our species sampling by including sequence data from >30 ongoing genome projects, followed by PCR and sequencing validation of each indel in additional taxa. Our data provide support for a sister-group relationship between Afrotheria and Xenarthra (the Atlantogenata hypothesis), which is in turn the sister-taxon to Boreoeutheria. We failed to recover any indels in support of a basal position for Xenarthra (Epitheria), which is suggested by morphology and a recent retroposon analysis, or a hypothesis with Afrotheria basal (Exafricoplacentalia), which is favored by phylogenetic analysis of large nuclear gene data sets. In addition, we identified two retroposon insertions that also support Atlantogenata and none for the alternative hypotheses. A revised molecular timescale based on these phylogenetic inferences suggests Afrotheria and Xenarthra diverged from other placental mammals approximately 103 (95-114) million years ago. We discuss the impacts of this topology on earlier phylogenetic reconstructions and repeat-based inferences of phylogeny.

The choice of model organisms in evo-devo

Study of the model organisms of developmental biology was crucial in establishing evo-devo as a new discipline. However, it has been claimed that this limited sample of organisms paints a biased picture of the role of development in evolution. Consequently, judicious choice of new model organisms is necessary to provide a more balanced picture. The challenge is to determine the best criteria for choosing new model organisms, given limited resources.