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Regulation of gene expression relies on the activity of specialized genomic elements, enhancers or silencers, distributed over sometimes large distance from their target gene promoters. A significant part of vertebrate genomes consists in such regulatory elements, but their identification and that of their target genes remains challenging, due to the lack of clear signature at the nucleotide level. For many years the main hallmark used for identifying functional elements has been their sequence conservation between genomes of distant species, indicative of purifying selection. More recently, genome-wide biochemical assays have opened new avenues for detecting regulatory regions, shifting attention away from evolutionary constraints. Here, we review the respective contributions of comparative genomics and biochemical assays for the definition of regulatory elements and their targets and advocate that both sequence conservation and preserved synteny, taken as signature of functional constraint, remain essential tools in this task. [ABSTRACT FROM AUTHOR]

The protein titin plays a key role in vertebrate muscle where it acts like a giant molecular spring. Despite its importance and conservation over vertebrate evolution, a lack of high quality annotations in non-model species makes comparative evolutionary studies of titin challenging. The PEVK region of titin—named for its high proportion of Pro-Glu-Val-Lys amino acids—is particularly difficult to annotate due to its abundance of alternatively spliced isoforms and short, highly repetitive exons. To understand PEVK evolution across mammals, we developed a bioinformatics tool, PEVK_Finder, to annotate PEVK exons from genomic sequences of titin and applied it to a diverse set of mammals. PEVK_Finder consistently outperforms standard annotation tools across a broad range of conditions and improves annotations of the PEVK region in non-model mammalian species. We find that the PEVK region can be divided into two subregions (PEVK-N, PEVK-C) with distinct patterns of evolutionary constraint and divergence. The bipartite nature of the PEVK region has implications for titin diversification. In the PEVK-N region, certain exons are conserved and may be essential, but natural selection also acts on particular codons. In the PEVK-C, exons are more homogenous and length variation of the PEVK region may provide the raw material for evolutionary adaptation in titin function. The PEVK-C region can be further divided into a highly repetitive region (PEVK-CA) and one that is more variable (PEVK-CB). Taken together, we find that the very complexity that makes titin a challenge for annotation tools may also promote evolutionary adaptation. [ABSTRACT FROM AUTHOR]

Vertebrate estrogen receptors (ERs) perform numerous cell signaling and transcriptional regulatory functions. ERɑ (Esr1) and ERβ (Esr2) likely evolved from an ancestral receptor that duplicated and diverged at the protein and cis -regulatory levels, but the evolutionary history of ERs, including the timing of proposed duplications, remains unresolved. Here we report on identification of two distinct ERs in cartilaginous fishes and demonstrate their orthology to ERα and ERβ. Phylogenetic analyses place the ERα/ERβ duplication near the base of crown gnathostomes (jawed vertebrates). We find that ERα and ERβ from little skate (Leucoraja erinacea) and mammals share key subtype-specific residues, indicating conserved protein evolution. In contrast, jawless fishes have multiple non-orthologous Esr genes that arose by parallel duplications. Esr1 and Esr2 are expressed in subtype-specific and sexually dimorphic patterns in skate embryos, suggesting that ERs might have functioned in sexually dimorphic development before the divergence of cartilaginous and bony fishes. [ABSTRACT FROM AUTHOR]

Whole-genome duplication (WGD) has been a major evolutionary driver of increased genomic complexity in vertebrates. One such event occurred in the salmonid family ∼80 Ma (Ss4R) giving rise to a plethora of structural and regulatory duplicate-driven divergence, making salmonids an exemplary system to investigate the evolutionary consequences of WGD. Here, we present a draft genome assembly of European grayling (Thymallus thymallus) and use this in a comparative framework to study evolution of gene regulation following WGD. Among the Ss4R duplicates identified in European grayling and Atlantic salmon (Salmo salar), one-third reflect nonneutral tissue expression evolution, with strong purifying selection, maintained over ∼50 Myr. Of these, the majority reflect conserved tissue regulation under strong selective constraints related to brain and neural-related functions, as well as higher-order protein–protein interactions. A small subset of the duplicates have evolved tissue regulatory expression divergence in a common ancestor, which have been subsequently conserved in both lineages, suggestive of adaptive divergence following WGD. These candidates for adaptive tissue expression divergence have elevated rates of protein coding- and promoter-sequence evolution and are enriched for immune- and lipid metabolism ontology terms. Lastly, lineage-specific duplicate divergence points toward underlying differences in adaptive pressures on expression regulation in the nonanadromous grayling versus the anadromous Atlantic salmon. Our findings enhance our understanding of the role of WGD in genome evolution and highlight cases of regulatory divergence of Ss4R duplicates, possibly related to a niche shift in early salmonid evolution. [ABSTRACT FROM AUTHOR]

The globin gene superfamily has been well-characterized in vertebrates, however, there has been limited research in early-diverging lineages, such as phylum Cnidaria. This study aimed to identify globin genes in multiple cnidarian lineages, and use bioinformatic approaches to characterize the evolution, structure, and expression of these genes. Phylogenetic analyses and in silico protein predictions showed that all cnidarians have undergone an expansion of globin genes, which likely have a hexacoordinate protein structure. Our protein modeling has also revealed the possibility of a single pentacoordinate globin lineage in anthozoan species. Some cnidarian globin genes displayed tissue and development specific expression with very few orthologous genes similarly expressed across species. Our phylogenetic analyses also revealed that eumetazoan globin genes form a polyphyletic relationship with vertebrate globin genes. Overall, our analyses suggest that a Ngb-like and GbX-like gene were most likely present in the globin gene repertoire for the last common ancestor of eumetazoans. The identification of a large-scale expansion and subfunctionalization of globin genes in actiniarians provides an excellent starting point to further our understanding of the evolution and function of the globin gene superfamily in early-diverging lineages. [ABSTRACT FROM AUTHOR]

Heterostracans are a clade of extinct jawless fishes that were a large component of early vertebrate ecosystems. They are key members of the gnathostome stem, and as such they are central to our interpretation and understanding of early vertebrate evolution. Our knowledge of heterostracan inter-relationships is incomplete, with previous phylogenetic analyses focusing on the intra-relationships of individual clades. The two largest clades of heterostracans, Cyathaspididae and Pteraspidiformes, comprise Janvier's 'higher heterostracans' and have been interpreted as monophyletic sister groups. Here we present a new parsimony-based phylogeny for the Pteraspidiformes and Cyathaspididae including quantitative data. Our results indicate that Cyathaspididae are a paraphyletic assemblage with respect to a monophyletic Pteraspidiformes (which includes the Psammosteidae). Furthermore, we show that the Anchipteraspididae are sister group to Pteraspidiformes, when using pteraspid-type bauplan to interpret their anatomy. Application of stratigraphic range data and congruence measures was used to assess the performance of different treatments of phylogenetic data in terms of stratigraphic consistency; equal weighting of quantitative and qualitative characters was found to consistently outperform implied weighting. Our combined results indicate that inclusion of quantitative characters can greatly improve resolution of ostracoderm phylogenies and provide a framework to consider the intra- and inter-relationships of heterostracans more broadly. [ABSTRACT FROM AUTHOR]

Genetic diversity (GD) is largely determined by effective population size, which may vary dramatically for species that differ in key aspects of their biology such as vagility. To identify evolutionary patterns associated with animal distributions and movements, we examined relationships among GD (i.e. microsatellite heterozygosity and allelic richness), taxonomic class, biome and migratory behaviour. Linear regression revealed that migratory mammals, reptiles, amphibians and fishes had less GD compared to nonmigratory species, whereas migratory birds had more GD than their nonmigratory counterparts. We also found that the biome a species inhabits influences the GD of migratory and nonmigratory species differently. For example, migratory amphibians at low latitudes are more genetically diverse than migratory amphibians at higher latitudes. However, we found the reverse relationship (i.e. decreased GD in low-latitude migratory species compared to higher latitude migratory species) in mammals and fishes and no influence of biome on reptile GD. We suggest that these differences are a result of differences in vagility, the extent of philopatry among the classes and perhaps differential selection between terrestrial and aquatic species. We argue that these categorical disparities in GD reflect changes in effective population size driven at least partly by differences in habitat. [ABSTRACT FROM AUTHOR]

The independent acquisition of endothermy in synapsids and diapsids are major events in vertebrate evolution since they were the driving force of a suite of correlated changes in anatomical, physiological, behavioural and ecological traits. While avian endothermy is assumed to have occurred at the archosauriform node, the acquisition of mammalian endothermy is poorly constrained both temporally and phylogenetically. Among the many unequivocal anatomical correlates of endothermy in synapsids, the presence of insulative pelage or respiratory turbinates only allows discrete inferences of presence/absence of endothermy. The analysis of bone histology allows richer palaeobiological inferences. We described the osteohistology and growth patterns of Moghreberia nmachouensis and two related taxa (Lystrosaurus and Oudenodon) for comparative purposes. Our observations suggest increasing growth rates from Moghreberia [the presence of incipient fibrolamellar bone (FLB) in humerus and femur], to Lystrosaurus (the presence of well-developed FLB in the femur but the presence of incipient FLB in the humerus), to Oudenodon (the presence of well-developed FLB in humerus and femur). However, qualitative histology does not allow reliable inferences about the occurrence of endothermy. We performed the first quantitative inferences of resting metabolic rates on fossil synapsids (M. nmachouensis as a model and Lystrosaurus and Oudenodon for comparative purposes) using quantitative histology (size, shape and density of osteocyte lacunae) combined with phylogenetic eigenvector maps. Our inferences are consistent with our qualitative histological observations: the mass-independent resting metabolic rate inferred for M. nmachouensis (2.58 mLO2 h-1 g-0.67) is lower than the value inferred for Lystrosaurus (3.80 mLO2 h-1 g-0.67), which is lower than that inferred for Oudenodon (4.58 mLO2 h-1 g-0.67). Optimization of these inferences onto a phylogenetic tree of tetrapods using the parsimony method allowed us to better constrain the temporal (more than 260 Myr ago) and phylogenetic (Neotherapsida) frames of the acquisition of mammalian endothermy. [ABSTRACT FROM AUTHOR]

Although frequent in vertebrates (e.g. crocodylians, stem-tetrapods, turtles), the adaptive significance of bone ornamentation, that is the honeycomb-like pattern of pits and ridges that occur on the surface of dermal bones, remains poorly understood. In order to help assess the evolutionary history and ecological correlates of this character, ornamentation was quantified in 69 extant and extinct Pseudosuchia (taxa more closely related to crocodiles than to birds). This variable was related to the dominant habitat (terrestrial, amphibious, pelagic) of these taxa within a phylogenetic framework covering more than 250 Myr of evolution. The phylogenetic analyses reveal a significant correlation between the degree of bone ornamentation on the skull roof with lifestyle (terrestrial, amphibious, pelagic). A straightforward adaptive interpretation of these results is to be avoided because skull morphology has recently been shown to strongly influence local development of bone ornamentation in Crocodylia. Indeed, ornamentation in long-snouted amphibious forms scores low or nil values on the skull roof while scoring very high values on osteoderms. Our results also show that amphibious forms, whether marine or fluvial, have a high degree of ornamentation, whereas terrestrial and pelagic forms are either not ornamented or have a low level of ornamentation. It is hypothesized that the high development of ornamentation among semi-aquatic pseudosuchians has been positively selected because it improves basking efficiency in semi-aquatic ambush (i.e. poorly active) predators. This process would have occurred at the Triassic-Jurassic boundary. [ABSTRACT FROM AUTHOR]

Parenting strategies can be flexible within a species and may have varying fitness effects. Understanding this flexibility and its fitness consequences is important for understanding why parenting strategies evolve. In the present study, we investigate the fitness consequences of flexible parenting in the burying beetle Nicrophorus orbicollis, a species known for its advanced provisioning behaviour of regurgitated vertebrate carrion to offspring by both sexes. We show that, even when a parent is freely allowed to abandon the carcass at any point in time, biparental post-hatching care is the most common pattern of care adopted in N. orbicollis. Furthermore, two parents together raised more offspring than single parents of either sex, showing that the presence of the male can directly influence parental fitness even in the absence of competitors. This contrasts with studies in other species of burying beetle, where biparental families do not differ in offspring number. This may explain why biparental care is more common in N. orbicollis than in other burying beetles. We suggest how the fitness benefits of two parents may play a role in the evolution and maintenance of flexible biparental care in N. orbicollis. [ABSTRACT FROM AUTHOR]

In vertebrate hosts, malaria parasites face a tradeoff between replicating and the production of transmission stages that can be passed onto mosquitoes. This tradeoff is analogous to growth-reproduction tradeoffs in multicellular organisms. We use a mathematical model tailored to the life cycle and dynamics of malaria parasites to identify allocation strategies that maximize cumulative transmission potential to mosquitoes. We show that plastic strategies can substantially outperform fixed allocation because parasites can achieve greater fitness by investing in proliferation early and delaying the production of transmission stages. Parasites should further benefit from restraining transmission investment later in infection, because such a strategy can help maintain parasite numbers in the face of resource depletion. Early allocation decisions are predicted to have the greatest impact on parasite fitness. If the immune response saturates as parasite numbers increase, parasites should benefit from even longer delays prior to transmission investment. The presence of a competing strain selects for consistently lower levels of transmission investment and dramatically increased exploitation of the red blood cell resource. While we provide a detailed analysis of tradeoffs pertaining to malaria life history, our approach for identifying optimal plastic allocation strategies may be broadly applicable. [ABSTRACT FROM AUTHOR]

Vertebrates, as most animal phyla, originated >500 million years ago during the Cambrian explosion, and progressively radiated into the extant classes. Inferring the evolutionary history of the group requires understanding the architecture of the developmental programs that constrain the vertebrate anatomy. Here, I review recent comparative genomic and epigenomic studies, based on ChIP-seq and chromatin accessibility, which focus on the identification of functionally equivalent cis-regulatory modules among species. This pioneer work, primarily centered in the mammalian lineage, has set the groundwork for further studies in representative vertebrate and chordate species. Mapping of active regulatory regions across lineages will shed new light on the evolutionary forces stabilizing ancestral developmental programs, as well as allowing their variation to sustain morphological adaptations on the inherited vertebrate body plan. [ABSTRACT FROM AUTHOR]

Morphological cladograms of vertebrates are often inferred from greater numbers of characters describing the skull and teeth than from postcranial characters. This is either because the skull is believed to yield characters with a stronger phylogenetic signal (i.e., contain less homoplasy), because morphological variation therein is more readily atomized, or because craniodental material is more widely available (particularly in the palaeontological case). An analysis of 85 vertebrate datasets published between 2000 and 2013 confirms that craniodental characters are significantly more numerous than postcranial characters, but finds no evidence that levels of homoplasy differ in the two partitions. However, a new partition test, based on tree-to-tree distances (as measured by the Robinson Foulds metric) rather than tree length, reveals that relationships inferred from the partitions are significantly different about one time in three, much more often than expected. Such differences may reflect divergent selective pressures in different body regions, resulting in different localized patterns of homoplasy. Most systematists attempt to sample characters broadly across body regions, but this is not always possible. We conclude that trees inferred largely from either craniodental or postcranial characters in isolation may differ significantly from those that would result from a more holistic approach. We urge the latter. [ABSTRACT FROM AUTHOR]

Teleosaurids were a clade of marine crocodylomorphs that were globally distributed during the Jurassic Period. They evolved a wide range of body sizes, from small (∼2-3 m) to very large (> 9 m). Until now, the largest known Middle Jurassic teleosaurid was ' Steneosaurus' obtusidens, from the Oxford Clay Formation of the UK. Here, we re-examine a very large Oxford Clay specimen (ilium, ischium, and femur) that had been tentatively attributed to ' S.' obtusidens. Based on comparative anatomical study with the ' S.' obtusidens holotype and referred specimens of Steneosaurus edwardsi and Steneosaurus leedsi, we conclude that this very large individual actually pertains to S. edwardsi. Based on comparisons with the Machimosaurus mosae neotype (which has a complete femur and skeleton), we estimate a total length in excess of 7 m for this large S. edwardsi individual, making it the largest known Middle Jurassic teleosaurid. Therefore, along with the closely related genus Machimosaurus, this clade of large-bodied Middle- Late Jurassic teleosaurids were the largest species during the first 100 million years of crocodylomorph evolution. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, ●●, ●●-●●. [ABSTRACT FROM AUTHOR]

The occurrence of contemporary ecotype formation through adaptive divergence of populations within the range of an invasive species typically requires standing genetic variation but can be facilitated by phenotypic plasticity. The relative contributions of both of these to adaptive trait differentiation have rarely been simultaneously quantified in recently diverging vertebrate populations. Here we study a case of intraspecific divergence into distinct lake and stream ecotypes of threespine stickleback that evolved in the past 140 years within the invasive range in Switzerland. Using a controlled laboratory experiment with full-sib crosses and treatments mimicking a key feature of ecotypic niche divergence, we test if the phenotypic divergence that we observe in the wild results from phenotypic plasticity or divergent genetic predisposition. Our experimental groups show qualitatively similar phenotypic divergence as those observed among wild adults. The relative contribution of plasticity and divergent genetic predisposition differs among the traits studied, with traits related to the biomechanics of feeding showing a stronger genetic predisposition, whereas traits related to locomotion are mainly plastic. These results implicate that phenotypic plasticity and standing genetic variation interacted during contemporary ecotype formation in this case. [ABSTRACT FROM AUTHOR]

Sharks occupy marine habitats ranging from shallow, inshore environments to pelagic, and deepwaters, and thus provide a model system for testing how gross habitat differences have shaped vertebrate macroevolution. Palaeontological studies have shown that onshore lineages diversify more quickly than offshore taxa. Among onshore habitats, coral reef-association has been shown to increase speciation rates in several groups of fishes and invertebrates. In this study, we investigated whether speciation rates are habitat dependent by generating the first comprehensive molecular timescale for shark divergence. Using phylogenetic comparative methods, we rejected the hypothesis that shelf (i.e. onshore) lineages have higher speciation rates compared to those occupying deepwater and oceanic (i.e. offshore) habitats. Our results, however, support the hypothesis of increased speciation rates in coral reef-associated lineages within the Carcharhinidae. Our new timetree suggests that the two major shark lineages leading to the extant shark diversity began diversifying mostly after the end-Permian mass extinction: the squalimorphs into deepwater and the galeomorphs into shelf habitats. We suggest that the breakdown of the onshore-offshore speciation rate pattern in sharks is mediated by success in deepwater environments through ecological partitioning, and in some cases, the evolution of morphological novelty. [ABSTRACT FROM AUTHOR]

Evolutionary transitions between sex-determining mechanisms ( SDMs) are an enigma. Among vertebrates, individual sex (male or female) is primarily determined by either genes (genotypic sex determination, GSD) or embryonic incubation temperature (temperature-dependent sex determination, TSD), and these mechanisms have undergone repeated evolutionary transitions. Despite this evolutionary lability, transitions from GSD (i.e. from male heterogamety, XX/ XY, or female heterogamety, ZZ/ ZW) to TSD are an evolutionary conundrum, as they appear to require crossing a fitness valley arising from the production of genotypes with reduced viability owing to being homogametic for degenerated sex chromosomes ( YY or WW individuals). Moreover, it is unclear whether alternative (e.g. mixed) forms of sex determination can persist across evolutionary time. It has previously been suggested that transitions would be easy if temperature-dependent sex reversal (e.g. XX male or XY female) was asymmetrical, occurring only in the homogametic sex. However, only recently has a mechanistic model of sex determination emerged that may allow such asymmetrical sex reversal. We demonstrate that selection for TSD in a realistic sex-determining system can readily drive evolutionary transitions from GSD to TSD that do not require the production of YY or WW individuals. In XX/ XY systems, sex reversal (female to male) occurs in a portion of the XX individuals only, leading to the loss of the Y allele (or chromosome) from the population as XX individuals mate with each other. The outcome is a population of XX individuals whose sex is determined by incubation temperature ( TSD). Moreover, our model reveals a novel evolutionarily stable state representing a mixed-mechanism system that has not been revealed by previous approaches. This study solves two long-standing puzzles of the evolution of sex-determining mechanisms by illuminating the evolutionary pathways and endpoints. [ABSTRACT FROM AUTHOR]

The invasion of land was a pivotal event in vertebrate evolution that was associated with major appendicular modifications. Although fossils indicate that the evolution of fundamentally limb-like appendages likely occurred in aquatic environments, the functional consequences of using early digited limbs, rather than fins, for terrestrial propulsion have had little empirical investigation. Paleontological and experimental analyses both have led to the proposal of an early origin of “hind limb-driven” locomotion among tetrapods or their ancestors. However, the retention of a pectoral appendage that had already developed terrestrial adaptations has been proposed for some taxa, and few data are available from extant functional models that can provide a foundation for evaluating the relative contributions of pectoral and pelvic appendages to terrestrial support among early stem tetrapods. To examine these aspects of vertebrate locomotor evolution during the invasion of land, we measured three-dimensional ground reaction forces (GRFs) produced by isolated pectoral fins of mudskipper fishes (Periophthalmus barbarus) during terrestrial crutching, and compared these to isolated walking footfalls by the forelimbs and hind limbs of tiger salamanders (Ambystoma tigrinum), a species with subequally-sized limbs that facilitate comparisons to early tetrapods. Pectoral appendages of salamanders and mudskippers exhibited numerous differences in GRFs. Compared with salamander forelimbs, isolated fins of mudskippers bear lower vertical magnitudes of GRFs (as a proportion of body weight), and had GRFs that were oriented more medially. Comparing the salamanders’ forelimbs and hind limbs, although the peak net GRF occurs later in stance for the forelimb, both limbs experience nearly identical mediolateral and vertical components of GRF, suggesting comparable contributions to support. Thus, forelimbs could also have played a significant locomotor role among basal tetrapods that had limbs of sub-equal size. However, the salamander hind limb and mudskipper pectoral fin had a greater acceleratory role than did the salamander forelimb. Together, data from these extant taxa help to clarify how structural change may have influenced locomotor function through the evolutionary invasion of land by vertebrates. [ABSTRACT FROM AUTHOR]

Natural selection is considered a major force shaping brain size evolution in vertebrates, whereas the influence of sexual selection remains controversial. On one hand, sexual selection could promote brain enlargement by enhancing cognitive skills needed to compete for mates. On the other hand, sexual selection could favour brain size reduction due to trade-offs between investing in brain tissue and in sexually selected traits. These opposed predictions are mirrored in contradictory relationships between sexual selection proxies and brain size relative to body size. Here, we report a phylogenetic comparative analysis that highlights potential flaws in interpreting relative brain size-mating system associations as effects of sexual selection on brain size in shorebirds ( Charadriiformes), a taxonomic group with an outstanding diversity in breeding systems. Considering many ecological effects, relative brain size was not significantly correlated with testis size. In polyandrous species, however, relative brain sizes of males and females were smaller than in monogamous species, and females had smaller brain size than males. Although these findings are consistent with sexual selection reducing brain size, they could also be due to females deserting parental care, which is a common feature of polyandrous species. Furthermore, our analyses suggested that body size evolved faster than brain size, and thus the evolution of body size may be confounding the effect of the mating system on relative brain size. The brain size-mating system association in shorebirds is thus not only due to sexual selection on brain size but rather, to body size evolution and other multiple simultaneous effects. [ABSTRACT FROM AUTHOR]

The tooth is a major component of the vertebrate feeding apparatus and plays a crucial role in species survival, thus subjecting tooth developmental programs to strong selective constraints. However, irrespective of their functional importance, teeth have been lost in multiple lineages of tetrapod vertebrates independently. To understand both the generality and the diversity of developmental mechanisms that cause tooth agenesis in tetrapods, we investigated expression patterns of a series of tooth developmental genes in the lower jaw of toothless turtles and compared them to that of toothed crocodiles and the chicken as a representative of toothless modern birds. In turtle embryos, we found impairment of Shh signaling in the oral epithelium and early-stage arrest of odontoblast development caused by termination of Msx2 expression in the dental mesenchyme. Our data indicate that such changes underlie tooth agenesis in turtles and suggest that the mechanism that leads to early-stage odontogenic arrest differs between birds and turtles. Our results demonstrate that the cellular and molecular mechanisms that regulate early-stage arrest of tooth development are diverse in tetrapod lineages, and odontogenic developmental programs may respond to changes in upstream molecules similarly thereby evolving convergently with feeding morphology. [ABSTRACT FROM AUTHOR]

Splicing regulatory elements (SREs) are sequences bound by proteins that influence splicing of nearby splice sites. Constitutively spliced introns have evolved to utilize many different splicing factors. The evolutionary processes that influenced which splicing factors are used for splicing of individual introns are generally unclear. We demonstrate that in the lineage that gave rise to mammals, many introns lost U-rich sequences and gained G-rich sequences, both of which resemble known SREs. The apparent conversion of U-rich to G-rich SREs suggests that the associated splicing factors are functionally equivalent. In support of this we demonstrated that U-rich and G-rich SREs are both capable of promoting splicing of an SRE-dependent splicing reporter. Furthermore, we demonstrate, using the heterologous MS2 tethering system (bacterial MS2 coat fusion-protein and its RNA stem-loop binding site), that both the U-rich SRE-binding protein (TIA1) and the G-rich SRE-binding protein (HNRNPF) can promote splicing of the same intron. We also observed that gain of G-rich SREs is significantly associated with G/C-rich genomic isochores, suggesting that gain or loss of SREs was driven by the same processes that ultimately resulted in the formation of mammalian genomic isochores. We propose the following model for the gain and loss of mammalian SREs. Ancestral U-rich SREs located in genomic regions that were experiencing high rates of A/T to G/C conversion would have suffered frequent deleterious mutations. However, this same process resulted in increased formation of functionally equivalent G-rich SREs, and acquisition of new G-rich SREs decreased purifying selection on the U-rich SREs, which were then free to decay. [ABSTRACT FROM AUTHOR]

The diversity and abundance of non–long terminal repeat (LTR) retrotransposons (nLTR-RT) differ drastically among vertebrate genomes. At one extreme, the genome of placental mammals is littered with hundreds of thousands of copies resulting from the activity of a single clade of nLTR-RT, the L1 clade. In contrast, fish genomes contain a much more diverse repertoire of nLTR-RT, represented by numerous active clades and families. Yet, the number of nLTR-RT copies in teleostean fish is two orders of magnitude smaller than in mammals. The vast majority of insertions appear to be very recent, suggesting that nLTR-RT do not accumulate in fish genomes. This pattern had previously been explained by a high rate of turnover, in which the insertion of new elements is offset by the selective loss of deleterious inserts. The turnover model was proposed because of the similarity between fish and Drosophila genomes with regard to their nLTR-RT profile. However, it is unclear if this model applies to fish. In fact, a previous study performed on the puffer fish suggested that transposable element insertions behave as neutral alleles. Here we examined the dynamics of amplification of nLTR-RT in the three-spine stickleback (Gasterosteus aculeatus). In this species, the vast majority of nLTR-RT insertions are relatively young, as suggested by their low level of divergence. Contrary to expectations, a majority of these insertions are fixed in lake and oceanic populations; thus, nLTR-RT do indeed accumulate in the genome of their fish host. This is not to say that nLTR-RTs are fully neutral, as the lack of fixed long elements in this genome suggests a deleterious effect related to their length. This analysis does not support the turnover model and strongly suggests that a much higher rate of DNA loss in fish than in mammals is responsible for the relatively small number of nLTR-RT copies and for the scarcity of ancient elements in fish genomes. We further demonstrate that nLTR-RT decay in fish occurs mostly through large deletions and not by the accumulation of small deletions. [ABSTRACT FROM AUTHOR]

Sialic acid, a common terminal substitution of glycoconjugates, has been so far consistently identified in all vertebrates as well as in a growing number of bacterial species. It is assumed to be widely distributed among animal species of the deuterostome phylum, based on its identification in few echinoderm and all vertebrate species. However, whole sections of deuterostome, especially those intermediate species between invertebrates and vertebrates including cephalochordates, urochordates and hemichordates, are still unexplored in term of sialylation capacities. The discovery of functional sialic acid machinery in some of these species may shed new light onto the evolution of glycosylation capacities in deuterostome lineage. In a first approach, we investigated the sialylation pattern of a cephalocordate species, Branchiostoma belcheri, which occupies a strategic phylogenetic position to understand the transition of invertebrates toward vertebrates. Structural analysis of B. belcheri glycoconjugates established that this organism synthesizes large quantities of various sialic acids, some of which present rare or novel structures such as methylated sialic acids. These sialic acids were shown to be mainly associated with mono- and disialylated core 1-type O-glycans. Moreover, screening of the animal organs revealed the existence of exquisite tissue specificity in the distribution of sialic acids. Description of sialylation profiles was then correlated with the expression patterns of key enzymes involved in the biosynthesis of major forms of sialic acids, which provides the first complete overview of the sialylation patterns in cephalochordates. [ABSTRACT FROM PUBLISHER]

Alternative splicing (AS) has the potential to greatly expand the functional repertoire of mammalian transcriptomes. However, few variant transcripts have been characterized functionally, making it difficult to assess the contribution of AS to the generation of phenotypic complexity and to study the evolution of splicing patterns. We have compared the AS of 309 protein-coding genes in the human ENCODE pilot regions against their mouse orthologs in unprecedented detail, utilizing traditional transcriptomic and RNAseq data. The conservation status of every transcript has been investigated, and each functionally categorized as coding (separated into coding sequence [CDS] or nonsense-mediated decay [NMD] linked) or noncoding. In total, 36.7% of human and 19.3% of mouse coding transcripts are species specific, and we observe a 3.6 times excess of human NMD transcripts compared with mouse; in contrast to previous studies, the majority of species-specific AS is unlinked to transposable elements. We observe one conserved CDS variant and one conserved NMD variant per 2.3 and 11.4 genes, respectively. Subsequently, we identify and characterize equivalent AS patterns for 22.9% of these CDS or NMD-linked events in nonmammalian vertebrate genomes, and our data indicate that functional NMD-linked AS is more widespread and ancient than previously thought. Furthermore, although we observe an association between conserved AS and elevated sequence conservation, as previously reported, we emphasize that 30% of conserved AS exons display sequence conservation below the average score for constitutive exons. In conclusion, we demonstrate the value of detailed comparative annotation in generating a comprehensive set of AS transcripts, increasing our understanding of AS evolution in vertebrates. Our data supports a model whereby the acquisition of functional AS has occurred throughout vertebrate evolution and is considered alongside amino acid change as a key mechanism in gene evolution. [ABSTRACT FROM PUBLISHER]

Although much progress has been achieved in understanding the genetic basis of adaptation, the drivers of genome evolution remain obscure. For instance, extensive variation among reptilian genomes continues largely unexplained, yet reptiles hold critical clues about vertebrate evolution. Turtles posses diverse chromosome numbers (2 N= 28-66) derived from extensive genomic rearrangements, plus varied sex-determining mechanisms (genotypic and temperature-dependent). Here, we show that rates of evolution in turtle chromosome number are ∼20-fold higher along phylogenetic branches where transitions between sex-determining mechanisms also occur, revealing a strong coevolution of these traits and making drift a less likely driver. Directional tests indicate that both traits evolved effectively in synchrony. These events occurred near global extremes in temperature shifts over the last 200 million years, although the role of climate change remains unknown at this point. Two alternative testable explanations for these patterns are proposed. First, selection for sex determination turnover may co-opt mechanisms (e.g., chromatin remodeling) favoring genomic rearrangements. Alternatively, chromosomal rearrangements underlying diploid number evolution may alter gene regulation enabling transitions in sex-determining mechanisms. Our data indicate that the evolution of sex determination is intimately linked to profound genomic changes underlying diploid number evolution, the ecological context of which remains intriguing. [ABSTRACT FROM AUTHOR]

The cellular energy produced by mitochondria is a fundamental currency of life. However, the extent to which mitochondrial (mt) performance (power and endurance) is adapted to habitats and life strategies of vertebrates is not well understood. A global analysis of mt genomes revealed that hydrophobicity (HYD) of mt membrane proteins (MMPs) is much lower in terrestrial vertebrates than in fishes and shows a strong negative correlation with serine/threonine composition (STC). Here, we present evidence that this systematic feature of MMPs was crucial for the evolution of large terrestrial vertebrates with high aerobic capacity. An Arrhenius-type equation gave positive correlations between STC and maximum life span (MLS) in terrestrial vertebrates (with a few exceptions relating to the lifestyle of small animals with a high resting metabolic rate [RMR]) and negative correlations in secondary marine vertebrates, such as cetaceans and alligators (which returned from land to water, utilizing buoyancy with increased body size). In particular, marked STC increases in primates (especially hominoids) among placentals were associated with very high MLS values. We connected these STC increases in MMPs with greater stability of respiratory complexes by estimating the degradation of the Arrhenius plot given by accelerating mtRMR up to mt maximum metabolic rate. Both mtRMR and HYD in terrestrial vertebrates decreased with increasing body mass. Decreases in mtRMR raise MMP stability when high mobility is not required, whereas decreased HYD may weaken this stability under the hydrophobic environment of lipid bilayer. High maximal metabolic rates (5–10 RMR), which we postulate require high MMP mobility, presumably render MMPs more unstable. A marked rise in STC may therefore be essential to stabilize MMPs, perhaps as dynamic supercomplexes, via hydrogen bonds associated with serine/threonine motifs. [ABSTRACT FROM AUTHOR]

Functional divergence between homologous proteins is expected to affect amino acid sequences in two main ways, which can be considered as proxies of biochemical divergence: a “covarion-like” pattern of correlated changes in evolutionary rates, and switches in conserved residues (“conserved but different”). Although these patterns have been used in case studies, a large-scale analysis is needed to estimate their frequency and distribution. We use a phylogenomic framework of animal genes to answer three questions: 1) What is the prevalence of such patterns? 2) Can we link such patterns at the amino acid level with selection inferred at the codon level? 3) Are patterns different between paralogs and orthologs? We find that covarion-like patterns are more frequently detected than “constant but different,” but that only the latter are correlated with signal for positive selection. Finally, there is no obvious difference in patterns between orthologs and paralogs. [ABSTRACT FROM PUBLISHER]

In dissecting the transition from invertebrates to vertebrates at the molecular level, whole-genome duplications are recognized as a key event. This gave rise to more copies of genes in jawed vertebrates (gnathostomes), such as the four Hox clusters in the human, compared to the single ancestral cluster in invertebrates. To date, as the most early-branching lineages in vertebrates, cyclostomes (hagfishes and lampreys) have been used for comparative analyses of gene regulations and functions. However, assignment of orthology/paralogy for cyclostomes’ genes is not unambiguously demonstrated. Thus, there is a high degree of incongruence in tree topologies between gene families, although whole genome duplications postulate uniform patterns in gene phylogeny. In this review, we demonstrate how expansion of an ancient genome before the cyclostome–gnathostome split, followed by reciprocal gene loss, can cause this incongruence. This is sometimes referred to as ‘hidden paralogy’. [ABSTRACT FROM PUBLISHER]

Whilst coding sequences are readily recognised in vertebrate genomes using computational approaches, the identification of non-coding regulatory sequences has traditionally been much more difficult, due to their small size and, as a general rule, low sequence homology between genomes. Nevertheless, a small proportion of non-coding sequence is very highly conserved across the entire vertebrate radiation. This review will look at the specific properties of these sequences, how they have been identified and assayed functionally, and current progress in the quest to identify and understand the underlying language and grammar encoded within them. I will also discuss the evolution of these elements, and examine their emerging and likely roles in disease. Together these analyses are starting to unravel how conserved non-coding regions function at the molecular level. [ABSTRACT FROM AUTHOR]

Although pterosaurs are a well-known lineage of Mesozoic flying reptiles, their fossil record and evolutionary dynamics have never been adequately quantified. On the basis of a comprehensive data set of fossil occurrences correlated with taxon-specific limb measurements, we show that the geological ages of pterosaur specimens closely approximate hypothesized patterns of phylogenetic divergence. Although the fossil record has expanded greatly in recent years, collectorship still approximates a sigmoid curve over time as many more specimens (and thus taxa) still remain undiscovered, yet our data suggest that the pterosaur fossil record is unbiased by sites of exceptional preservation (lagerstätte). This is because as new species are discovered the number of known formations and sites yielding pterosaur fossils has also increased – this would not be expected if the bulk of the record came from just a few exceptional faunas. Pterosaur morphological diversification is, however, strongly age biased: rarefaction analysis shows that peaks of diversity occur in the Late Jurassic and Early Cretaceous correlated with periods of increased limb disparity. In this respect, pterosaurs appear unique amongst flying vertebrates in that their disparity seems to have peaked relatively late in clade history. Comparative analyses also show that there is little evidence that the evolutionary diversification of pterosaurs was in any way constrained by the appearance and radiation of birds. [ABSTRACT FROM AUTHOR]

Whole-genome duplications (WGDs) have occurred repeatedly in the vertebrate lineage, but their evolutionary significance for phenotypic evolution remains elusive. Here, we have investigated the impact of the fish-specific genome duplication (FSGD) on the evolution of pigmentation pathways in teleost fishes. Pigmentation and color patterning are among the most diverse traits in teleosts, and their pigmentary system is the most complex of all vertebrate groups. [ABSTRACT FROM PUBLISHER]

Because of its basal position on the phylogenetic tree of vertebrates, the lamprey embryo would be expected to exhibit segmental head mesoderm. Recent observations, however, show that the lamprey does not have any somite-like segments in the head. Coelomic head cavities that are most conspicuous in elasmobranch embryos, do not appear to represent universal vertebrate traits. From the perspective of generative constraint, segmental structures in the vertebrate body can be classified into primary segments, which arise as segmental embryonic primordia such as somites and pharyngeal pouches, and secondary segments whose patterns are determined by the presence of primary segments. Secondary segments include neural crest derivatives and epibranchial placodes that are not initially segmented. The head mesoderm of vertebrates is secondarily regionalized into several domains that do not impose any secondary segmental patterns on other structures. Thus, the vertebrate head is characterized by a lack of segmental generative constraint in its mesoderm. Classical segmental theories are now refuted because they attempted to equate the vertebrate head with that of the amphioxus, whose rostral somites are considered primary segments, which are absent from vertebrates. [ABSTRACT FROM AUTHOR]

Whether or not the vertebrate head is fundamentally segmented has been controversial for over 150 years. Beginning in the late 19th century, segmentalist theories proposed that the vertebrate head evolved from an amphioxus-like ancestor in which mesodermal somites extended the full length of the body with remnants of segmentation persisting as the mesodermal head cavities of sharks and lampreys. Antisegmentalists generally argued either that the vertebrate ancestors never had any mesodermal segmentation anteriorly or that they lost it before the origin of the vertebrates; in either case, the earliest vertebrates had an unsegmented head and the embryonic cranial mesoderm of vertebrates is at best pseudo-segmented, evolving independently of any pre-vertebrate segmental pattern. Recent morphologic studies have generally confirmed the accuracy of the major classical studies of head development in lampreys and sharks, yet disagree with their theoretical conclusions regarding the evolution of head segmentation. Studies of developmental genes in amphioxus and vertebrates, which have demonstrated conservation of the mechanisms of anterior-posterior patterning in the two groups, have shed new light on this controversy. Most pertinently, some homologs of genes expressed in the anterior amphioxus somites, which form as outpocketings of the gut, are also expressed in the walls of the head cavities of lampreys, which form similarly, and in their major derivatives (the velar muscles) as well as in the eye and jaw muscles of bony gnathostomes, which derive from unsegmented head mesoderm. These muscles share gene expression with the corresponding muscles of the shark, which derive from the walls of head cavities that form, not as outpocketings of the gut, but as secondary cavities within solid blocks of tissue. While molecular data that can be compared across all the relevant taxa remain limited, they are consistent with an evolutionary scenario in which the cranial paraxial mesoderm of the lamprey and shark evolved from the anterior somites of an amphioxus-like ancestor. Although, bony vertebrates have lost the mesodermal head segments present in the shark and lamprey, their remnants persist in the muscles of the eye and jaw. [ABSTRACT FROM AUTHOR]

The fossil record has been an invaluable aid for reconstructing the major events of vertebrate evolution. There is no comparable record for protochordates, however, which severely limits our knowledge of their ancestral morphology, habits, and mode of life. The alternative is inference based on an interpretation of living protochordates but this is fraught with problems, not least being our own biases of what we think an ancestral chordate ought to look like. Relevant to the present symposium is the problem of head/trunk relationships and whether or not the myotomes of the trunk originally extended into the head in vertebrates. I will review what is currently known of patterns of innervation in tunicates and amphioxus in relation to Romer's somaticovisceral concept of the vertebrate body to show how little progress has been made in resolving this problem. There are, in contrast, surprisingly good prospects for solving some other puzzles concerning chordate origins. Dorsoventral inversion provides a good example. A consensus is now emerging, based largely on molecular data from hemichordates that casts new light on the asymmetry of the head in amphioxus. Specifically, the morphogenetic growth process that reestablishes symmetry in late-stage larvae can now be seen, at least in part, as a recapitulation of past evolutionary events, and this has important implications for the origin and basic organization of the brain. [ABSTRACT FROM AUTHOR]

It is difficult for terrestrial vertebrates to invade the sea, and little is known about the transitional evolutionary processes that produce secondarily marine animals. The utilization of marine resources in the intertidal zone is likely to be an important first step for invasion. An example of this step is marine scavenging by the Florida cottonmouth snakes (Agkistrodon piscivorus conanti) that inhabit Gulf Coast islands. These snakes principally consume dead fish that are dropped from colonial nesting bird rookeries, but they also scavenge beaches for intertidal carrion, consuming dead fish and marine plants, and occasionally enter seawater. Thus, allochthonous marine productivity supports the insular cottonmouth population through two pathways, and one of these pathways connects the snakes directly to the sea. The trophic ecology and behaviors of this unusual snake population suggest a requisite evolutionary scenario for the successful transition of vertebrates from a terrestrial to a marine existence. [ABSTRACT FROM AUTHOR]

The diversification of the tetrapod stem group occurred during the late Middle through the Late Devonian, that is from the Givetian to Famennian stages about 385-365 million years ago. The relationships between the known taxa representing this radiation have currently reached a reasonable consensus so that interpretations of the order of appearance of tetrapod characters is possible. The immediate fish relatives of the earliest limbed tetrapods show what is interpreted as a progressive increase in the spiracular chamber and its opening to the outside. Here, this is inferred to be associated with an increased capacity for air-breathing. Lungs are thought to have been present in most early bony fishes, and were most likely ventilated by air-gulping. This could have brought about a facultative capacity for air-breathing, which the tetrapod stem group exploited to the greatest degree. These adaptations are shown not only in freshwater forms but also in estuarine and marginal marine forms. Estimates of oxygen levels during this period suggest that they were unprecedentedly low during the Givetian and Frasnian periods. At the same time, plant diversification was at its most rapid, changing the character of the landscape and contributing, via soils, soluble nutrients, and decaying plant matter, to anoxia in all water systems. The co-occurrence of these global events may explain the evolution of air-breathing adaptations in at least two lobe-finned groups, contributing directly to the rise of the tetrapod stem group. In contrast to recent studies, low atmospheric oxygen is not considered to be a causal factor in the lack of fossils documenting the evolution of Early Carboniferous tetrapods. [ABSTRACT FROM AUTHOR]

The chordates include vertebrates plus two groups of invertebrates (the cephalochordates and tunicates). Previous embryonic fate maps of the cephalochordate amphioxus (Branchiostoma) were influenced by preconceptions that early development in amphioxus and ascidian tunicates should be fundamentally the same and that the early amphioxus embryo, like that of amphibians, should have ventral mesoderm. Although detailed cell lineage tracing in amphioxus has not been done because of limited availability of the embryos and because cleavage is radial and holoblastic with the blastomeres nearly equal in size and not tightly adherent until the mid-blastula stage, a compilation of data from gene expression and function, blastomere isolation and dye labeling allows a more realistic fate map to be drawn. The revised fate map is substantially different from that of ascidians. It shows (1) that the anterior pole of the amphioxus embryo is offset dorsally from the animal pole only by about 20°, (2) that the ectoderm/mesendoderm boundary (the future rim of the blastopore) is at the equator of the blastula, which approximately coincides with the 3rd cleavage plane, and (3) that there is no ventral mesoderm during the gastrula stage. Involution or ingression of cells over the blastopore lip is negligible, and the blastopore, which is posterior, closes centripetally as if by a purse string. During the gastrula stage, the animal pole shifts ventrally, coming to lie about 20° ventral to the anterior tip of the late gastrula/early neurula. Comparisons of the embryos of amphioxus and vertebrates indicate that in spite of large differences in the mechanics of cleavage and gastrulation, anterior/posterior and dorsal/ventral patterning occur by homologous genetic mechanisms. Therefore, the small, nonyolky embryo of amphioxus is probably a reasonable approximation of the basal chordate embryo before the evolution of determinate cleavage in the tunicates and the evolution large amounts of yolk in basal vertebrates. [ABSTRACT FROM AUTHOR]

Modern agnathans include only two groups, the lampreys and the hagfish, that collectively comprise the group Cyclostomata. Although accumulating molecular data support the cyclostomes as a monophyletic group, there remain some unsettled questions regarding the evolutionary relationships of these animals in that they differ greatly in anatomical and developmental patterns and in their life histories. In this review, we summarize recent developmental data on the lamprey and discuss some questions related to vertebrate evolutionary development raised by the limited information available on hagfish embryos. Comparison of the lamprey and gnathostome developmental patterns suggests some plesiomorphic traits of vertebrates that would have already been established in the most recent common ancestor of the vertebrates. Understanding hagfish development will further clarify the, as yet, unrecognized ancestral characters that either the lampreys or hagfishes may have lost. We stress the immediate importance of hagfish embryology in the determination of the most plausible scenario for the early history of vertebrate evolution, by addressing questions about the origins of the neural crest, thyroid, and adenohypophysis as examples. [ABSTRACT FROM AUTHOR]

Cranial placodes give rise to many evolutionary novelties of the vertebrate head, such as its specialized paired sense organs and cranial ganglia. There is an increasing evidence that all placodes originate from a common primordium located around the anterior neural plate and defined by the expression of transcription factors of the Six1/2, Six4/5, and Eya families. These transcription factors continue to be expressed in the different placodes and appear to control similar developmental processes (e.g., proliferation, cell shape changes, and neurogenesis) in the different placodes suggesting that they play a central role for generic placodal development. Elucidating the central role of Six and Eya genes for placodal development requires an understanding of (1) how these genes are induced in the pre-placodal ectoderm at the right place and time and (2) how they subsequently affect and promote placodal development. The first part of this review gives a brief overview of what is currently known about these upstream and downstream regulatory linkages of Six and Eya genes. The second part of the review then discusses the distribution and function of Six and Eya genes in other deuterostomes in order to infer changes of upstream and downstream linkages in the course of deuterostome evolution by which Six and Eya genes adopted their new role in vertebrate placode development. It is argued that these genes were probably recruited to the neural plate border in the ancestor of urochordates and vertebrates, and adopted novel roles in the regulation of neuronal differentiation and possibly other pathways of cytodifferentiation as well in the vertebrate lineage. [ABSTRACT FROM AUTHOR]

Genes of the major histocompatibility complex (MHC) are indispensable for pathogen defence in vertebrates. With wild-caught three-spined sticklebacks ( Gasterosteus aculeatus) we conducted the first study to relate individual reproductive parameters to both MHC class I and II diversities. An optimal MHC class II B diversity was found for male nest quality. However, male breeding colouration was most intense at a maximal MHC class I diversity. One MHC class I allele was associated with male redness. Similarly, one MHC class II B allele was associated with continuous rather than early female reproduction, possibly extending the reproductive period. Both alleles occurred more frequently with increasing individual allele diversity. We suggest that if an allele is currently not part of the optimum, it had not been propagated by choosy females. The parasite against which this allele provides resistance is therefore unlikely to have been predominant the previous year – a step to negative frequency-dependent selection. [ABSTRACT FROM AUTHOR]

Abstract Elucidating how natural selection promotes local adaptation in interaction with migration, genetic drift and mutation is a central aim of evolutionary biology. While several conceptual and practical limitations are still restraining our ability to study these processes at the DNA level, genes of the major histocompatibility complex (MHC) offer several assets that make them unique candidates for this purpose. Yet, it is unclear what general conclusions can be drawn after 15 years of empirical research that documented MHC diversity in the wild. The general objective of this review is to complement earlier literature syntheses on this topic by focusing on MHC studies other than humans and mice. This review first revealed a strong taxonomic bias, whereby many more studies of MHC diversity in natural populations have dealt with mammals than all other vertebrate classes combined. Secondly, it confirmed that positive selection has a determinant role in shaping patterns of nucleotide diversity in MHC genes in all vertebrates studied. Yet, future tests of positive selection would greatly benefit from making better use of the increasing number of models potentially offering more statistical rigour and higher resolution in detecting the effect and form of selection. Thirdly, studies that compared patterns of MHC diversity within and among natural populations with neutral expectations have reported higher population differentiation at MHC than expected either under neutrality or simple models of balancing selection. Fourthly, several studies showed that MHC-dependent mate preference and kin recognition may provide selective factors maintaining polymorphism in wild outbred populations. However, they also showed that such reproductive mechanisms are complex and context-based. Fifthly, several studies provided evidence that MHC may significantly influence fitness, either by affecting reproductive success or progeny survival to pathogens infections. Overall, the evidence is compelling that the MHC currently represents the best system available in vertebrates to investigate how natural selection can promote local adaptation at the gene level despite the counteracting actions of migration and genetic drift. We conclude this review by proposing several directions where future research is needed. [ABSTRACT FROM AUTHOR]

Presents a study that demonstrated the generality of the phenomenon of sequence block shuffling by showing that blocks within the β-globin promoter have been continually rearranged during vertebrate evolution. Comparison of promoter sequences of the paraloguos human globin genes; Discussion on the evolutionary conservation of transcriptional initiation sites in growth hormone gene promoter orthologues; Information on the complexity analysis.

Presents a study which analyzed published data from AC microsatellite loci in several vertebrate classes to address some questions about microsatellite evolution. Methods; Results; Discussion.

Investigates the evolution of red-gree color vision in vertebrates by inferring the amino acid sequences of the ancestral pigments of 11 selected visual pigments. Introduction of necessary mutations into contemporary pigments; Mutations of MWS and LWS pigments; Molecular basis of pigments during vertebrate evolution.

Presents an analysis of the evolution of vertebrate Hox genes and clusters, with emphasis on the differences between the Hox A clusters of fish and tetrapod lineages. Discussion of the Hox case for a teleost-specific genome duplication; Insights from variation in Hox-cluster A; Cladistic reconstruction of the evolution of Hox A clusters in invertebrates.

Presents information on a study which reviewed the evolution of vertebrate axial muscles. Convergent features of the musculoskeletal system of cretaceans and tunas; Morphology of axial muscles and pattern of force transmission in scombrid fishes; Reinforcement of the peripheral body as a retinaculum.

Presents information on a study which examined the role of retinoid signalling and metabolism in vertebrate evolution. Components of the retinoid signalling system; Biological effects of vitamin A; Results and discussion.

Focuses on methanogenetic bacteria in relation to the evolution of vertebrates. Relation of feeding habits to intestinal differences and the composition of microbial biota in the intestinal tracts; Lack of methanogens in some species; Sharing of competence for intestinal methanogenic bacteria by related species and higher taxa; Importance of methanogenic bacteria to the evolution of amniotes.

Presents a hypothesis on the origin of vertebrates. Question of origin from the sea or fresh water; Fossil record of early vertebrates; Osmoregulatory physiology of living fishes; Construction of alternate hypotheses that attempt to explain how vertebrates evolved from photochordates; Marine scenarios; Anadromous scenario.