Investigating ontogenetic space with developmental cell lineages

Development plays a significant role in biological evolution, and is likely to prove an effective route to overcoming the limitations of direct genotype-phenotype mappings in artificial evolution. Nonetheless, the relationship between development and evolution is complex and still poorly understood. One question of current interest concerns the possible role that developmental processes may play in orienting evolution. A first step towards exploring this issue from a theoretical perspective is understanding the structure of ontogenetic space: the space of possible genotype-phenotype mappings. Using a quantitative model of development that enables ontogenetic space to be characterised in terms of complexity, we show that ontogenetic landscapes have a characteristic structure that varies with genotypic properties.

Evolution of plant water relations research in Australia

Ecophysiological research in Australia has focussed, at different times, on the fundamental similarities in function between all plant species, and on the peculiarity of Australian species with respect to their survival in stressful environments. Early work on plant water relations emphasised the differences between species, and indicated that diverse structural and functional attributes occurred in species from the same water-limited environment. Most recent research has emphasised processes that optimise rates of carbon dioxide exchange, but the understanding of functioning in plants with different morphological arrangements is incomplete. Variation in functions between individual plants and geographic populations in wild species has been examined to a lesser extent. The great variety within and between populations of wild plant species warrants further study for both understanding and more effective management of this biological resource.

Evolution of polydnaviruses as insect immune suppressors

Polydnaviruses (PDVs) are endogenous particles that are used by some endoparasitic hymenoptera to disrupt host immunity and development. Recent analyses of encapsidated PDV genes have increased the number of known PDV gene families, which are often closely related to insect genes. Several PDV proteins inactivate host haemocytes by damaging their actin cytoskeleton. These proteins share no significant sequence homology and occur in polyphyletic PDV genera, possibly indicating that convergent evolution has produced functionally similar immune-suppressive molecules causing a haemocyte phenotype characterised by damaged cytoskeleton and inactivation. These phenomena provide further insights into the immune-suppressive activity of PDVs and raise interesting questions about PDV evolution, a topic that has puzzled researchers ever since the discovery of PDVs.

Chic chicks: the evolution of chick ornamentation in rails

Competition over access to food has led to the evolution of a variety of exaggerated visual and vocal displays in altricial nestling birds. Precocial chicks that are fed by their parents also vary widely in appearance ranging from those with inconspicuous coloration to those with brightly colored bills, fleshy parts, and plumes. These ornaments are lost by the end of the period of parental dependence, suggesting they function in competition over parental care. We use a comparative approach to evaluate which ecological or life-history variables may have favored the evolution of conspicuous ornamentation in precocial chicks. We compiled data on chick morphology, ecology, and social organization of species in the Family Rallidae, a group with highly variable downy chicks. Chick ornamentation in the form of brightly colored bills, fleshy patches, or plumes is observed in 36 of 97 species for which downy chicks are described. Phylogenetic reconstructions suggest that nonornamentation is the ancestral state. Chick ornamentation has evolved multiple times within the Rallidae and is significantly associated with large clutch sizes and polygamous mating systems. Chick ornamentation was also weakly associated with adult ornamentation and adult dimorphism. We argue that these results support the hypothesis that lineages with higher levels of sibling competition are more likely to evolve ornamented chicks.

Evolution of the regular zone of histone H1 in Fabaceae plants

An analysis of the historic H1 subtype, H1-1, in eight legumes belonging to four genera of the tribe Vicieae (Pisum, Lathyrus, Lens, and Vicia), revealed an extended region consisting of the tandemly repeated AKPAAK motifs. We named this region the Regular zone (RZ). The AKPAAK motifs are organized into two blocks separated by a short (two or six amino acids) intervening sequence (IS). The distal block contains six AKPAAK motifs, while the number of repeats in the proximal block varies from six in V. faba to seven in the other species. In V. hirsuta, the first two repeated units of the proximal block are octapeptides AKAKPAAK. The apparent rate of synonymous substitutions in the blocks of RZ is much higher than in the rest of the gene. This can be explained by repeat shuffling within each block. In the C-domain of the orthologous H1 subtype froth Medicago truncatula (tribe Trifolieae), a region corresponding to the RZ of Vicieae species was found. It also consists of two blocks of AKPAAK motifs (four and three repeats in the proximal and distal blocks, respectively). These blocks are separated by a 20-amino acid IS. The first 20 amino acids of the Medicago RZ are not part of AKPAAK repeats. We hypothesise that the RZ has most probably evolved as a result of an expansion of AKPAAK repeats from two separate sites in the C-domain. This process started tens of millions of years ago and was most likely directed by positive selection.

Evidence for endothermic ancestors of crocodiles at the stem of archosaur evolution

Physiological, anatomical, and developmental features of the crocodilian heart support the paleontological evidence that the ancestors of living crocodilians were active and endothermic, but the lineage reverted to ectothermy when it invaded the aquatic, ambush predator niche. In endotherms, there is a functional nexus between high metabolic rates, high blood flow rates, and complete separation of high systemic blood pressure from low pulmonary blood pressure in a four-chambered heart. Ectotherms generally lack all of these characteristics, but crocodilians retain a four-chambered heart. However, crocodilians have a neurally controlled, pulmonary bypass shunt that is functional in diving. Shunting occurs outside of the heart and involves the left aortic arch that originates from the right ventricle, the foramen of Panizza between the left and right aortic arches, and the cog-tooth valve at the base of the pulmonary artery. Developmental studies show that all of these uniquely crocodilian features are secondarily derived, indicating a shift from the complete separation of blood flow of endotherms to the controlled shunting of ectotherms. We present other evidence for endothermy in stem archosaurs and suggest that some dinosaurs may have inherited the trait.

The origin and evolution of the surfactant system in fish: Insights into the evolution of lungs and swim bladders

Several times throughout their radiation fish have evolved either lungs or swim bladders as gas-holding structures. Lungs and swim bladders have different ontogenetic origins and can be used either for buoyancy or as an accessory respiratory organ. Therefore, the presence of air-filled bladders or lungs in different groups of fishes is an example of convergent evolution. We propose that air breathing could not occur without the presence of a surfactant system and suggest that this system may have originated in epithelial cells lining the pharynx. Here we present new data on the surfactant system in swim bladders of three teleost fish ( the air-breathing pirarucu Arapaima gigas and tarpon Megalops cyprinoides and the non-air-breathing New Zealand snapper Pagrus auratus). We determined the presence of surfactant using biochemical, biophysical, and morphological analyses and determined homology using immunohistochemical analysis of the surfactant proteins (SPs). We relate the presence and structure of the surfactant system to those previously described in the swim bladders of another teleost, the goldfish, and those of the air-breathing organs of the other members of the Osteichthyes, the more primitive air-breathing Actinopterygii and the Sarcopterygii. Snapper and tarpon swim bladders are lined with squamous and cuboidal epithelial cells, respectively, containing membrane-bound lamellar bodies. Phosphatidylcholine dominates the phospholipid (PL) profile of lavage material from all fish analyzed to date. The presence of the characteristic surfactant lipids in pirarucu and tarpon, lamellar bodies in tarpon and snapper, SP-B in tarpon and pirarucu lavage, and SPs ( A, B, and D) in swim bladder tissue of the tarpon provide strong evidence that the surfactant system of teleosts is homologous with that of other fish and of tetrapods. This study is the first demonstration of the presence of SP-D in the air-breathing organs of nonmammalian species and SP-B in actinopterygian fishes. The extremely high cholesterol/disaturated PL and cholesterol/PL ratios of surfactant extracted from tarpon and pirarucu bladders and the poor surface activity of tarpon surfactant are characteristics of the surfactant system in other fishes. Despite the paraphyletic phylogeny of the Osteichthyes, their surfactant is uniform in composition and may represent the vertebrate protosurfactant.

How primatology can inform us about the evolution of the humand mind

Humans are primates. We have evolved from common ancestors and the evolution of the human body is becoming increasingly clear as the archeological record expands. But for most people the gap between humans and animals lies in the mind, not in the body. And minds do not fossilise. To reconstruct the evolution of mind, scholars have thus increasingly looked to our closest relatives for clues. Here I discuss four ways in which the study of primates may inform such reconstruction: fact-finding, phylogenetic reconstruction, analogy, and regression models. Knowledge about primates can help us bridge the gap. Extinction of our closest relatives, on the other hand, would not only deplete that source of information but also increase the apparent differences between animal and human minds. It is likely that we have a long history of displacing closely related species, including the other hominids, leading us to appear ever more unique.

Functional promoter analysis using an approach based on an in vitro evolution strategy

In vitro evolution imitates the natural evolution of genes and has been very successfully applied to the modification of coding sequences, but it has not yet been applied to promoter sequences. We propose an alternative method for functional promoter analysis by applying an in vitro evolution scheme consisting of rounds of error-prone PCR, followed by DNA shuffling and selection of mutant promoter activities. We modified the activity in embryogenic sugarcane cells of the promoter region of the Goldfinger isolate of banana streak virus and obtained mutant promoter sequences that showed an average mutation rate of 2.5% after applying one round of error-prone PCR and DNA shuffling. Selection and sequencing of promoter sequences with decreased or unaltered activity allowed us to rapidly map the position of one cis-acting element that influenced promoter activity in embryogenic sugarcane cells and to discover neutral mutations that did not affect promoter Junction. The selective-shotgun approach of this promoter analysis method immediately after the promoter boundaries have been defined by 5' deletion analysis dramatically reduces the labor associated with traditional linker-scanning deletion analysis to reveal the position of functional promoter domains. Furthermore, this method allows the entire promoter to be investigated at once, rather than selected domains or nucleotides, increasing the, prospect of identifying interacting promoter regions.

Parallel evolution of sexual isolation in sticklebacks

Mechanisms of speciation are not well understood, despite decades of study. Recent work has focused on how natural and sexual selection cause sexual isolation. Here, we investigate the roles of divergent natural and sexual selection in the evolution of sexual isolation between sympatric species of threespine sticklebacks. We test the importance of morphological and behavioral traits in conferring sexual isolation and examine to what extent these traits have diverged in parallel between multiple, independently evolved species pairs. We use the patterns of evolution in ecological and mating traits to infer the likely nature of selection on sexual isolation. Strong parallel evolution implicates ecologically based divergent natural and/or sexual selection, whereas arbitrary directionality implicates nonecological sexual selection or drift. In multiple pairs we find that sexual isolation arises in the same way: assortative mating on body size and asymmetric isolation due to male nuptial color. Body size and color have diverged in a strongly parallel manner, similar to ecological traits. The data implicate ecologically based divergent natural and sexual selection as engines of speciation in this group.

And the beak shall inherit - evolution in response to invasion

The increased demographic performance of biological invaders may often depend on their escape from specifically adapted enemies. Here we report that native taxa in colonized regions may swiftly evolve to exploit such emancipated exotic species because of selection caused by invaders. A native Australian true bug has expanded it host range to include a vine imported from tropical America that has become a serious environmental weed. Based on field comparisons and historical museum specimens, we show that over the past 30-40 years, seed feeding soapberry bugs have evolved 5-10% longer mouthparts, better suited to attack the forest-invading balloon vines, which have large fruits. Laboratory experiments show that these differences are genetically based, and result in a near-doubling of the rate at which seeds are attacked. Thus a native biota that initially permits invasion may rapidly respond in ways that ultimately facilitate control.

Opsins: Evolution in waiting

Complete vertebrate genome sequencing has revealed a remarkable stability and uniformity in the protein-coding gene set, which at first glance might suggest that gene duplication events are relatively rare. This may be a red herring, or at least a red cichlid, as the Lake Malawi cichlid fishes show rapid and extensive duplication and diversification of their retinal cone photoreceptor opsin genes.