A supertree of early tetrapods

A genus-level supertree for early tetrapods is built using a matrix representation of 50 source trees. The analysis of all combined trees delivers a long-stemmed topology in which most taxonomic groups are assigned to the tetrapod stem. A second analysis, which excludes source trees superseded by more comprehensive studies, supports a deep phylogenetic split between lissamphibian and amniote total groups. Instances of spurious groups are rare in both analyses. The results of the pruned second analysis are mostly comparable with those of a recent, character-based and large-scale phylogeny of Palaeozoic tetrapods. Outstanding areas of disagreement include the branching sequence of lepospondyls and the content of the amniote crown group, in particular the placement of diadectomorphs as stem diapsids. Supertrees are unsurpassed in their ability to summarize relationship patterns from multiple independent topologies. Therefore, they might be used as a simple test of the degree of corroboration of nodes in the contributory analyses. However, we urge caution in using them as a replacement for character-based cladograms and for inferring macroevolutionary patterns.     

Differential evolution of voltage-gated sodium channels in tetrapods and teleost fishes

The voltage-gated sodium channel (SCN) alpha subunits are large proteins with central roles in the generation of action potentials. They consist of approximately 2,000 amino acids encoded by 24-27 exons. Previous evolutionary studies have been unable to reconcile the proposed gene duplication schemes with the species distribution and molecular phylogeny of the genes. We have carefully annotated the complete SCN gene sequences, correcting numerous database errors, for a broad range of vertebrate species and analyzed their phylogenetic relationships. We have also compared the chromosomal positions of the SCN genes relative to adjacent gene families. Our studies show that the ancestor of the vertebrates probably had a single sodium channel gene with two characteristic AT-AC introns, the second of which is unique to vertebrate SCN genes. This ancestral gene, located close to a HOX gene cluster, was quadrupled along with HOX in the two rounds of basal vertebrate tetraploidizations to generate the ancestors of the four channels SCN1A, SCN4A, SCN5A, and SCN8A. The third tetraploidization in the teleost fish ancestor doubled this set of genes and all eight are still present in at least three of four investigated teleost fish genomes. In tetrapods, the gene family expanded by local duplications before the radiation of amniotes, generating the cluster SCN5A, SCN10A, and SCN11A on one chromosome and the cluster SCN1A, SCN2A, SCN3A, and SCN9A on a different chromosome. In eutherian mammals, a tenth gene, SCN7A, arose in a local duplication in the SCN1A gene cluster. The SCN7A gene has undergone rapid evolution and has lost the ability to cause action potentials-instead, it functions as a sodium sensor. The three genes in the SCN5A cluster were translocated from the HOX-bearing chromosome in a mammalian ancestor along with several adjacent genes. This evolutionary scenario is supported by the adjacent TGF-β receptor superfamily (comprised of five distinct families) and the cysteine-serine-rich nuclear protein gene family as well as the HOX clusters. The independent expansions of the SCN repertoires in tetrapods and teleosts suggest that the functional diversification may differ between the two lineages.     

Biogeography of Triassic tetrapods: evidence for provincialism and driven sympatric cladogenesis in the early evolution of modern tetrapod lineages

Triassic tetrapods are of key importance in understanding their evolutionary history, because several tetrapod clades, including most of their modern lineages, first appeared or experienced their initial evolutionary radiation during this Period. In order to test previous palaeobiogeographical hypotheses of Triassic tetrapod faunas, tree reconciliation analyses (TRA) were performed with the aim of recovering biogeographical patterns based on phylogenetic signals provided by a composite tree of Middle and Late Triassic tetrapods. The TRA found significant evidence for the presence of different palaeobiogeographical patterns during the analysed time spans. First, a Pangaean distribution is observed during the Middle Triassic, in which several cosmopolitan tetrapod groups are found. During the early Late Triassic a strongly palaeolatitudinally influenced pattern is recovered, with some tetrapod lineages restricted to palaeolatitudinal belts. During the latest Triassic, Gondwanan territories were more closely related to each other than to Laurasian ones, with a distinct tetrapod fauna at low palaeolatitudes. Finally, more than 75 per cent of the cladogenetic events recorded in the tetrapod phylogeny occurred as sympatric splits or within-area vicariance, indicating that evolutionary processes at the regional level were the main drivers in the radiation of Middle and Late Triassic tetrapods and the early evolution of several modern tetrapod lineages.     

On the evolution of arterial vascular patterns of tetrapods

The factors that explain the diverse arrangement of the major arteries of tetrapods are not known. Here, I aim to illuminate some of the underpinnings of these patterns. I review the variation in the sauropsid left, right, and dorsal aortae regarding the origin of the gastrointestinal blood vessels and the relative diameters of left and right aortae where they join together to form the dorsal aorta. I focus on these features because the quality of blood that flows through these aortae can vary depending on the state of cardiac shunting and the size of the vessel can provide insight into the quantity of blood borne by the vessels. I then place the information in a phyletic, historical, and ecological context. The plesiomorphic pattern is for the gastrointestinal vessels to arise as segmental arteries from the dorsal aorta, which is formed from the confluence of left and right aortae with similar diameters. The pattern is well conserved with only two major variations. First, in several clades of reptiles (testudines, crocodilians, lizards of the genera Varanus and Hydrosaurus) a substantial portion of the gastrointestinal arteries arises from the left aorta, leaving the diameter of the left aorta smaller than the right at their confluence. I hypothesize that this vascular arrangement facilitates growth by allowing more alkaline blood to flow to the somatic (body wall) and appendicular circulations, which may promote bone deposition and inhibit resorption, whereas hypercapnic, acidic blood flows to the digestive viscera, which may provide CO₂ as a substrate for the synthesis of gastric acid, bicarbonate, fatty acids, glutamine, purine rings, as well as glucose from lactate. Second, in some snakes and lizards with snake‐like body forms, such as Amphisbaenidae, the diameters of left and right aortae are asymmetrical at their confluence with the left aorta exceeding the right, but in members of the amphibian order Gymnophiona the right generally exceeds the left. This condition is associated with asymmetrical development of the lungs. J. Morphol. 2011. © 2011 Wiley‐Liss, Inc.     

The stapes of the Goal Measures embolomere Pholiderpeton scutigerum Huxley (Amphibia: Anthracosauria) and otic evolution in early tetrapods

Middle ear structure has been of interest for a long time in studies of the origins and relationships of early tetrapod groups. The model of a dorsally-directed, rod-like stapes with a tympanum, thought common to labyrinthodont amphibians, was taken to be primitive for tetrapods. The stapes of embolomeres and other early anthracosaurs were assumed to be of this form, but difficulties resulted if the middle ear structure of fossil and living reptiles was considered ultimately derived from this source.
The embolomere stapes has been identified and does not conform to the predicted model. It most closely resembles that of Greererpeton , an early notchless temnospondyl. The stapes is compared with those of other tetrapods in terms of the theoretical five processes. An interpretation is put forward in which all but the opercular are seen as potentially present. The embolomere stapes is compared with that of Greererpeton in terms of recent theories of mechanical function and is seen to weaken them. They are then compared as part of a possible acoustic mechanism. The embolomere middle ear structure is reinterpreted as a receiver for low-frequency sound and the 'otic notch' is not considered to have housed a tympanum.
The resemblance between the stapes of these two animals seems best explained by their closeness to the plesiomorphic condition for tetrapods, a conclusion which forces the abandonment of the concept of a 'labyrinthodont middle ear'. The middle ear structure of later groups can be interpreted as having evolved from one similar to that seen in these two animals. The conclusion supports those reached in other recent papers that tympana were not primitive for tetrapods but have been independently derived in several groups.     

Origins and evolution of biological novelty

Understanding the origins and impacts of novel traits has been a perennial interest in many realms of ecology and evolutionary biology. Here, we build on previous evolutionary and philosophical treatments of this subject to encompass novelties across biological scales and eco-evolutionary perspectives. By defining novelties as new features at one biological scale that have emergent effects at other biological scales, we incorporate many forms of novelty that have previously been treated in isolation (such as novelty from genetic mutations, new developmental pathways, new morphological features, and new species). Our perspective is based on the fundamental idea that the emergence of a novelty, at any biological scale, depends on its environmental and genetic context. Through this lens, we outline a broad array of generative mechanisms underlying novelty and highlight how genomic tools are transforming our understanding of the origins of novelty. Lastly, we present several case studies to illustrate how novelties across biological scales and systems can be understood based on common mechanisms of change and their environmental and genetic contexts. Specifically, we highlight how gene duplication contributes to the evolution of new complex structures in visual systems; how genetic exchange in symbiosis alters functions of both host and symbiont, resulting in a novel organism; and how hybridisation between species can generate new species with new niches.     

Intercentrum versus pleurocentrum growth in early tetrapods: A paleohistological approach

A variety of vertebral centrum morphologies have evolved within early tetrapods which range from multipartite centra consisting of intercentra and pleurocentra in stem‐tetrapods, temnospondyls, seymouriamorphs, and anthracosaurs up to monospondylous centra in lepospondyls. With the present study, we aim to determine the formation of both intercentrum and pleurocentrum and asked whether these can be homologized based on their bone histology. Both intercentra and pleurocentra ossified endochondrally and periosteal bone was subsequently deposited on the outer surface of the centra. Our observations indicate low histological variation between intercentrum and pleurocentrum in microstructural organization and growth which inhibits the determination of homologies. However, intercentrum and pleurocentrum development differs during ontogeny. As previously assumed, the intercentrum arises from ventrally located and initially paired ossification centers that fuse ventromedially to form the typical, crescentic, rhachitomous intercentrum. In contrast, presacral pleurocentra may be ancestrally represented by four ossification centers: a ventral and a dorsal pair. Subsequently, two divergent developmental patterns are observed: In stem‐tetrapods and temnospondyls, the pleurocentrum evolves from the two dorsally located ossification centers which may occasionally fuse to form a dorsal crescent. In some dvinosaurian temnospondyls, the pleurocentrum may even ossify to full rings. In comparison, the pleurocentrum of stem‐amniotes (anthracosaurs, chroniosuchids, seymouriamorphs, and lepospondyls) arises from the two ventrally located ossification centers whereby the ossification pattern is almost identical to that of temnospondyls but mirror‐inverted. Thus, the ring‐shaped pleurocentrum of Discosauriscus ossifies from ventral to dorsal. We also propose that the ossified portions of the intercentrum and pleurocentrum continued as cartilaginous rings or discs that surrounded the notochord in the living animals.     

Origins and evolution of eukaryotic RNA interference

Small interfering RNAs (siRNAs) and genome-encoded microRNAs (miRNAs) silence genes via complementary interactions with mRNAs. With thousands of miRNA genes identified and genome sequences of diverse eukaryotes available for comparison, the opportunity emerges for insights into the origin and evolution of RNA interference (RNAi). The miRNA repertoires of plants and animals appear to have evolved independently. However, conservation of the key proteins involved in RNAi suggests that the last common ancestor of modern eukaryotes possessed siRNA-based mechanisms. Prokaryotes have an RNAi-like defense system that is functionally analogous but not homologous to eukaryotic RNAi. The protein machinery of eukaryotic RNAi seems to have been pieced together from ancestral archaeal, bacterial and phage proteins that are involved in DNA repair and RNA processing.     

Origins and evolution of cell phenotypes in breast tumors

This study presents a stochastic model that correlates genomic instability with tumor formation. The model describes the time- and space-variant volumetric concentrations of cancer cells of various phenotypes in a breast tumor. The cells of epithelial origin in the cancerous breast tissue are classified into four different phenotypes, normal epithelial cells and the grade 1, grade 2 and grade 3 cancer cell types with increasing potential for growth and invasion. Equations governing the time course of volumetric concentrations of cell phenotypes are derived by using the principle of conservation of mass. Cell migration into and from the stroma is taken into account. The transformations between cell phenotypes are due to genetic inheritance and chromosome aberrations. These transformations are assumed to be stochastic functions of the local cell concentration. The simulations of the model for planar geometry replicate the shapes of human breast tumors and capture the time history of tumor growth in animal models. Simulations point to transformation of tumor cell population from heterogeneous compositions to a single phenotype at advanced stages of invasive tumors. Systematic variations of model parameters in the computations indicate the important roles the migration capacity, proliferation rate, and phenotype transition probability play in tumor growth. The model developed provides realistic simulations for standard breast cancer therapies and can be used in the optimization studies of chemotherapy, radiotherapy, hormone therapy and emerging individualized therapies for cancer.     

Origins and evolution of antigenic diversity in malaria parasites

Each year, malaria parasites cause more than 500 million infections and 0.5-3 million deaths worldwide, mostly among children under five living in sub-Saharan Africa. In contrast with several viral and bacterial pathogens, which elicit long-lived immunity after a primary infection, these parasites require several years of continuous exposure to confer partial, usually non-sterilizing immune protection. One of the main obstacles to the acquisition of antimalarial immunity is the high degree of antigenic diversity in potential target antigens, which enables parasites to evade immune responses elicited by past exposure to variant forms of the same antigen. Allelic polymorphism, the existence of genetically stable alternative forms of antigen-coding genes, originates from nucleotide replacement mutations and intragenic recombination. In addition, malaria parasites display antigenic variation, whereby a clonal lineage of parasites expresses successively alternate forms of an antigen without changes in genotype. This review focuses on molecular and evolutionary processes that promote allelic polymorphism and antigenic variation in natural malaria parasite populations and their implications for naturally acquired immunity and vaccine development.     

Origins and evolution of isoprenoid lipid biosynthesis in archaea

A characteristic feature of the domain archaea are the lipids forming the hydrophobic core of their cell membrane. These unique lipids are composed of isoprenoid side-chains stereospecifically ether linked to sn-glycerol-1-phosphate. Recently, considerable progress has been made in characterizing the enzymes responsible for the synthesis of archaeal lipids. However, little is known about their evolution. To better understand how this unique biosynthetic apparatus came to be, large-scale database surveys and phylogenetic analyses were performed. All characterized enzymes involved in the biosynthesis of isoprenoid side-chains and the glycerol phosphate backbone along with their assembly in ether lipids were included in these analyses. The sequence data available in public databases was complemented by an in-depth sampling of isoprenoid lipid biosynthesis genes from multiple genera of the archaeal order Halobacteriales, allowing us to look at the evolution of these enzymes on a smaller phylogenetic scale. This investigation of the isoprenoid biosynthesis apparatus of archaea on small and large phylogenetic scales reveals that it evolved through a combination of evolutionary processes, including the co-option of ancestral enzymes, modification of enzymatic specificity, orthologous and non-orthologous gene displacement, integration of components from eukaryotes and bacteria and lateral gene transfer within and between archaeal orders.     

Disease, parasitism and herbivory: Multidimensional challenges in plant evolution

Plants provide feeding sites for a broad range of parasites, commensals and symbionts. In the process, they can be subjected to selection whenever feeding choices are based upon heritable traits of the plants and the feeding affects plant fitness. The outcome of such selection depends on the correlation between choices made by various taxa. Recent work suggests that this multispecies selection, although common in natural communities, now needs to be incorporated more fully into ecological and evolutionary perspectives.     

Genome: Origins and evolution of the term

The appearance of a new scientific term is a significant event in the human cognitive process and the result of the realization of the separateness of an object or a phenomenon. Our article concentrates on the origins of basic genetic terms, such as genetics, gene, genotype, genome, gene pool, and genomics. We propose using the term karyogenomics for the special direction of genomics related to the study of the organization and evolution of eukaryotic genomes by means of modern chromosome analysis, as well as by full genome sequencing.     

3 Origins and evolution of the translation machinery

The protein synthesis machinery largely evolved prior to the last common ancestor and hence its study can provide insight to early events in the origin of life, including the transition from the hypothetical RNA world to living systems as we know them. By utilizing information from primary sequences, atomic resolution structures, and functional properties of the various components, it is possible to identify timing relationships (Hsiao et al., 2009; Fox, 2010). Taken together, these timing events are used to develop a preliminary time line for major evolutionary events leading to the modern protein synthesis machinery. It has been argued that a key initial event was the hybridization of two or more RNAs that created the peptidyl transferase center, (PTC), of the ribosome (Agmon et al. 2005). The PTC, left side of figure, contains a characteristic cavity/pore that serves as the entrance to the exit tunnel and is thought to be essential to the catalysis (Fox et al., 2012). This cavity is distinct from typical RNA pores (right side of figure) in that the nitrogenous bases face towards the lumen of the pore and thus are available for hydrogen bonding interactions. In typical RNA pores, the bases carefully avoid the lumen region. In support of Agmon et al. 2005), it is argued that this key difference reflects the fact the pore was created by an early hybridization event rather than normal RNA folding.     

Origins of variance in seed number and mass: interaction of sex expression and herbivory in Lomatium salmoniflorum

Summary As in many plant species, Lomatium salmoniflorum (Umbelliferae) individuals produce many flowers, only a subset of which produce mature seeds that escape seed parasitism and enter the seed bank. The interrelationships between the timing and number of flowers produced, sex expression, seed set, and seed parasitism were studied for their direct and indirect effects on the numbers and masses of viable seeds produced by individual plants. In a sample population of 369 plants that produced 161 386 flowers, 76% of the plants produced some hermaphroditic flowers. The percentage of hermaphroditic flowers increased significantly with the total number of flowers produced by a plant. Seed set was 65–90% in plants producing >600 flowers, but was highly variable in plants producing fewer flowers. Hand-pollinated plants showed the same pattern of seed set, suggesting that variable seed set in small plants may result from insufficient resources for seed development. The majority of schizocarps was produced by only 12% of the plants. Parasites killed 24.5% of the seeds prior to dispersal. Another 14.5% of the seeds lacked endosperm. Hence, the initial 161 386 flowers, which included 25874 hermaphroditic flowers each capable of producing two seeds, produced 42 468 seeds of which an estimated 25906 entered the seed bank as undamaged seeds with fully developed endosperm. Path analysis indicated that the number of hermaphroditic flowers on a plant and the percentage of seeds attacked by seed parasites had the greatest direct effects on the number of viable seeds entering the seed bank. The date at which a plant began flowering and the percentage of flowers setting seed had smaller or only indirect effects on viable seed production. Mean seed mass for plants was not significantly related to any of the factors that affected seed number, but little of the variance in seed mass occurred among plants. Masses of intact seeds in the population ranged 9-fold in both 1987 and 1988. Thirty-five percent of the variance was among seeds within umbels, 46% was among umbels within plants, and only 19% was among plants. The large variation among umbels within plants resulted from a seasonal pattern in which seeds from umbels produced late in the spring had lower mean seed masses than seeds from umbels produced early in the spring. Overall, the results indicate that both direct and indirect interactions between number of flowers, the date of initiation of flowering, seed set, and seed parasitism affect the number of viable seeds entering the seed bank. These interactions strongly bias viable seed output to a small minority of plants that produce many seeds with a wide range of masses over the growing season.