Molecular evolutionary genomics of birds

Insight into the molecular evolution of birds has been offered by the steady accumulation of avian DNA sequence data, recently culminating in the first draft sequence of an avian genome, that of chicken. By studying avian molecular evolution we can learn about adaptations and phenotypic evolution in birds, and also gain an understanding of the similarities and differences between mammalian and avian genomes. In both these lineages, there is pronounced isochore structure with highly variable GC content. However, while mammalian isochores are decaying, they are maintained in the chicken lineage, which is consistent with a biased gene conversion model where the high and variable recombination rate of birds reinforces heterogeneity in GC. In Galliformes, GC is positively correlated with the rate of nucleotide substitution; the mean neutral mutation rate is 0.12-0.15% at each site per million years but this estimate comes with significant local variation in the rate of mutation. Comparative genomics reveals lower d(N)/d(S) ratios on micro- compared to macrochromosomes, possibly due to population genetic effects or a non-random distribution of genes with respect to chromosome size. A non-random genomic distribution is shown by genes with sex-biased expression, with male-biased genes over-represented and female-biased genes under-represented on the Z chromosome. A strong effect of selection is evident on the non-recombining W chromosome with high d(N)/d(S) ratios and limited polymorphism. Nucleotide diversity in chicken is estimated at 4-5 x 10(-3) which might be seen as surprisingly high given presumed bottlenecks during domestication, but is lower than that recently observed in several natural populations of other species. Several important aspects of the molecular evolutionary process of birds remain to be understood and it can be anticipated that the upcoming genome sequence of a second bird species, the zebra finch, as well as the integration of data on gene expression, shall further advance our knowledge of avian evolution.     

DNA evolutionary rates in nine-primaried passerine birds

Differences in single-copy nuclear-DNA sequences among 13 species of passerine birds were measured using DNA-DNA hybridization. A matrix of pairwise dissimilarity values (delta mode distances) was constructed from analysis of fitted thermal dissociation curves. A least-squares method of phylogenetic estimation was used to construct two topologies from the distance matrix, one constraining branch lengths of sister taxa to be equal and the other permitting such lengths to vary. These topologies were identical in the pattern of branching of taxa, and the difference in their sums of squares was not statistically significant, suggesting that rates of DNA evolution in sister groups of nine- primaried oscines are equal. A nonparametric test for nonrandom variation in distances of sister groups to outgroup taxa revealed no statistically significant deviation from random variation that would be expected as a result of measurement error. However, the level of measurement error was such that rates of DNA evolution in sister taxa could vary by as much as 10% without being detected with the statistical methods used here.      

Geographic range size and evolutionary age in birds

Together with patterns of speciation and extinction, post-speciation transformations in the range sizes of individual species determine the form of contemporary species range-size distributions. However, the methodological problems associated with tracking the dynamics of a species' range size over evolutionary time have precluded direct study of such range-size transformations, although indirect evidence has led to several models being proposed describing the form that they might take. Here, we use independently derived molecular data to estimate ages of species in six monophyletic groups of birds, and examine the relationship between species age and global geographic range size. We present strong evidence that avian range sizes are not static over evolutionary time. In addition, it seems that, with the regular exception of certain taxa (for example island endemics and some threatened species), range-size transformations are non-random in birds. In general, range sizes appear to expand relatively rapidly post speciation; subsequently; and perhaps more gradually, they then decline as species age. We discuss these results with reference to the various models of range-size dynamics that have been proposed.     

Sex,long life and the evolutionary transition to cooperative breeding in birds

Long life is a typical feature of individuals living in cooperative societies. One explanation is that group living lowers mortality, which selects for longer life. Alternatively, long life may make the evolution of cooperation more likely by ensuring a long breeding tenure, making helping behaviour and queuing for breeding positions worthwhile. The benefit of queuing will, however, depend on whether individuals gain indirect fitness benefits while helping, which is determined by female promiscuity. Where promiscuity is high and therefore the indirect fitness benefits of helping are low, cooperation can still be favoured by an even longer life span. We present the results of comparative analyses designed to test the likelihood of a causal relationship between longevity and cooperative breeding by reconstructing ancestral states of cooperative breeding across birds, and by examining the effect of female promiscuity on the relationship between these two traits. We found that long life makes the evolution of cooperation more likely and that promiscuous cooperative species are exceptionally long lived. These results make sense of promiscuity in cooperative breeders and clarify the importance of life-history traits in the evolution of cooperative breeding, illustrating that cooperation can evolve via the combination of indirect and direct fitness benefits.     

Independent evolutionary reductions of the phallus in basal birds

Despite a long history of anatomical studies in birds, the genitalia of most avian species remain undescribed. Birds are the only vertebrate taxon with internal fertilization where an intromittent phallus has been lost in most species. Studying the anatomical transitions of the avian phallus in those species where it is still present, allows us to test evolutionary hypotheses of why the phallus was lost in the ancestor of modern birds. As part of an anatomical survey of the evolution of avian phallus morphology, we have examined some avian species whose genitalia have not been described. Previously, there were only two known events of phallus reduction in birds: one transition from intromittent to non‐intromittent in the Galliformes, and a complete loss of phallic structures in the ancestor of Neoaves. Here we report three additional cases of phallus reduction in birds: a transition from intromittent to non‐intromittent phallus in Tinamiformes (Crypturellus, Tinamidae), the presence of a non‐intromittent phallus in Alectura (Megapodidae), and a complete loss of the phallus in Leipoa (Megapodidae). In addition, we report on the unique morphology of the Crypturellus non‐intromittent phallus. These new records of phallus reduction highlight the dynamic nature of phallus evolution in birds. Our findings provide evidence against the hypothesis that the phallus in birds is maintained to insure paternity in taxa with exclusive male parental care, since both groups where we report phallus reduction provide predominately male‐only care.     

Functional and evolutionary consequences of cranial fenestration in birds

Ostrich‐like birds (Palaeognathae) show very little taxonomic diversity while their sister taxon (Neognathae) contains roughly 10,000 species. The main anatomical differences between the two taxa are in the crania. Palaeognaths lack an element in the bill called the lateral bar that is present in both ancestral theropods and modern neognaths, and have thin zones in the bones of the bill, and robust bony elements on the ventral surface of their crania. Here we use a combination of modeling and developmental experiments to investigate the processes that might have led to these differences. Engineering‐based finite element analyses indicate that removing the lateral bars from a neognath increases mechanical stress in the upper bill and the ventral elements of the skull, regions that are either more robust or more flexible in palaeognaths. Surgically removing the lateral bar from neognath hatchlings led to similar changes. These results indicate that the lateral bar is load‐bearing and suggest that this function was transferred to other bony elements when it was lost in palaeognaths. It is possible that the loss of the load‐bearing lateral bar might have constrained diversification of skull morphology in palaeognaths and thus limited taxonomic diversity within the group.     

副突变及其发生机制和演化意义

上世纪50年代科学家首次在玉米中发现副突变（paramutation）,后来陆续在其他生物体中也发现了这种现象。副突变是一种不符合孟德尔遗传法则的遗传模式。近来运用现代分子生物学技术研究表明,RNA是副突变发生的基础机制,涉及表观遗传（epigenetic inheritance）调控及染色体结构的动态变化。副突变的演化有着重要的生物学意义,了解副突变将有助于农作物的改良及人类遗传疾病的治疗。本文综述了副突变的研究进展,以期为相关的教学和研究整理资料。     

Ecological,evolutionary, and conservation implications of incubation temperature‐dependent phenotypes in birds

Incubation is a vital component of reproduction and parental care in birds. Maintaining temperatures within a narrow range is necessary for embryonic development and hatching of young, and exposure to both high and low temperatures can be lethal to embryos. Although it is widely recognized that temperature is important for hatching success, little is known about how variation in incubation temperature influences the post‐hatching phenotypes of avian offspring. However, among reptiles it is well known that incubation temperature affects many phenotypic traits of offspring with implications for their future survival and reproduction. Although most birds, unlike reptiles, physically incubate their eggs, and thus behaviourally control nest temperatures, variation in temperature that influences embryonic development still occurs among nests within a population. Recent research in birds has primarily been limited to populations of megapodes and waterfowl; in each group, incubation temperature has substantial effects on hatchling phenotypic traits important for future development, survival, and reproduction. Such observations suggest that incubation temperature (and incubation behaviours of parents) is an important but underappreciated parental effect in birds and may represent a selective force instrumental in shaping avian reproductive ecology and life‐history traits. However, much more research is needed to understand how pervasive phenotypic effects of incubation temperature are among birds, the sources of variation in incubation temperature, and how effects on phenotype arise. Such insights will not only provide foundational information regarding avian evolution and ecology, but also contribute to avian conservation.     

Distinct evolutionary patterns of morphometric sperm traits in passerine birds

The striking diversity of sperm shape across the animal kingdom is still poorly understood. Postcopulatory sexual selection is an important factor driving the evolution of sperm size and shape. Interestingly, morphometric sperm traits, such as the length of the head, midpiece and flagellum, exhibit a strong positive phenotypic correlation across species. Here we used recently developed comparative methods to investigate how such phenotypic correlations between morphometric sperm traits may evolve. We compare allometric relationships and evolutionary trajectories of three morphometric sperm traits (length of head, midpiece and flagellum) in passerine birds. We show that these traits exhibit strong phenotypic correlations but that allometry varies across families. In addition, the evolutionary trajectories of the midpiece and flagellum are similar while the trajectory for head length differs. We discuss our findings in the light of three scenarios accounting for correlated trait evolution: (i) genetic correlation; (ii) concerted response to selection acting simultaneously on different traits; and (iii) phenotypic correlation between traits driven by mechanistic constraints owing to selection on sperm performance. Our results suggest that concerted response to selection is the most likely explanation for the phenotypic correlation between morphometric sperm traits.     

The evolutionary relationship among beak shape,mechanical advantage,and feeding ecology in modern birds*

Extensive research on avian adaptive radiations has led to a presumption that beak morphology predicts feeding ecology in birds. However, this ecomorphological relationship has only been quantified in a handful of avian lineages, where associations are of variable strength, and never at a broad macroevolutionary scale. Here, we used shape analysis and phylogenetic comparative methods to quantify the relationships among beak shape, mechanical advantage, and two measures of feeding ecology (feeding behavior and semiquantitative dietary preferences) in a broad sample of modern birds, comprising most living orders. We found a complex relationship, with most variables showing a significant relationship with feeding ecology but little explanatory power. For example, diet accounts for less than 12% of beak shape variation. Similar beak shapes are associated with disparate dietary regimes, even when accounting for diet‐feeding behavior relationships and phylogeny. Very few lineages optimize for stronger bite forces, with most birds exhibiting relatively fast, weak bites, even in large predatory taxa. The extreme morphological and behavioral flexibility of the beak in birds suggests that, far from being an exemplary feeding adaptation, avian beak diversification may have been largely contingent on trade‐offs and constraints.     

Life history patterns in birds and mammals and their evolutionary interpretation

Summary It is argued that allometric principles account for most of the observed variation in the life history patterns amongst birds. To test this contention it is shown that traits such as incubation time, growth rates, age at first reproduction, lifespan, clutch weight and egg weight all scale to body weight with exponents similar to those found for analogous traits in mammals. It is then shown that most of the variation amongst bird taxa and between birds and mammals based on body weight allometry can be explained by variations in brain size, body temperature and metabolic rate, consistent with theories of growth and ageing derived from mammalian studies. Finally, it is suggested that the evidence for life histostory allometry is sufficiently strong that it argues for a more epigenetic view of life history patterns and their evolution than is generally conceded in most adaptation theories.     

Variations in the hypotarsus morphology of birds and their evolutionary significance

Crown group (neornithine birds) exhibit a great variation in the morphology of the hypotarsus, a structure on the proximal end of the tarsometatarsus, which guides the tendons of the flexor muscles of the toes. Hypotarsus morphology is of significance for the identification of fossil taxa, and several extant groups show characteristic patterns that are of phylogenetic interest. So far, however, the diversity of hypotarsus morphologies has been little studied, and there are no comprehensive studies across all neornithine birds. In particular, the identities of the involved canals and sulci remain elusive, and some confusion exists about their correct homologies. In this study, hypotarsus morphologies are for the first time surveyed among all extant birds, and basic patterns are characterized. Instances are identified, in which particular hypotarsus morphologies are correlated with certain locomotion types, inferences are made about possible ancestral morphologies, and some patterns of phylogenetic interest are discussed.     

The evolutionary transition to coloniality promotes higher blood parasitism in birds

Parasitism has been argued as one of the major costs of breeding sociality in birds. However, there is no clear evidence for an increased parasite pressure associated with the evolutionary transition from solitary to colonial breeding. I used the pairwise comparative method to test whether colonial bird species incur in a greater risk of infection and if they must to face with a greater diversity of blood parasites (Haematozoa), by comparing pairs of congeners that included one solitary and one colonial breeding species. The richness, both in terms of number of species and number of genera, as well as the prevalence of blood parasites resulted higher in colonial species than in their solitary breeding sisters, while controlling for differences in research effort and other potentially confounding effects. These results point towards higher transmission rates of blood parasites among colonial hosts. Given the detrimental effects of blood parasites on their host fitness, the higher risk of infection and the exposition to a more diverse parasite fauna may have imposed an important cost associated to the evolution of avian coloniality. This may help to explain why colonial species have larger immune system organs, as well as to explore differences in other host life history traits potentially shaped by blood parasites.     

Ecological and evolutionary physiology of desert birds: a progress report

The adaptive significance of mechanisms of energy and water conservation among species of desert rodents, which avoid temperature extremes by remaining within a burrow during the day, is well established. Conventional wisdom holds that arid-zone birds, diurnal organisms that endure the brunt of their environment, occupy these desert climates because of the possession of physiological design features common to all within the class Aves. We review studies that show that desert birds may have evolved specific features to deal with hot desert conditions including: a reduced basal metabolic rate (BMR) and field metabolic rate (FMR), and lower total evaporative water loss (TEWL) and water turnover (WTO).Previous work on the comparative physiology of desert birds relied primarily on information gathered on species from the deserts of the southwestern U.S., which are semi-arid habitats of recent geologic origin. We include data on species from Old World deserts, which are geologically older than those in the New World, and place physiological responses along an aridity axis that includes mesic, semi-arid, arid, and hyperarid environments.The physiological differences between desert and mesic birds that we have identified using the comparative method could arise as a result of acclimation to different environments, of genetic change mediated by selection, or both. We present data on the flexibility of BMR and TEWL in Hoopoe Larks that suggest that phenotypic adjustments in these variables can be substantial. Finally, we suggest that linkages between the physiology of individual organism and its life-history are fundamental to the understanding of life-history evolution.     

Degenerative joint disease in African great apes: an evolutionary perspective

Degenerative joint disease is investigated in the spine and major peripheral joints (shoulder, elbow, hip and knee) in samples of chimpanzees (Pan troglodytes schweinfurthii; P. troglodytes troglodytes), lowland gorillas (Gorilla gorilla gorilla), and bonobos (P. paniscus). The P. troglodytes schweinfurthii sample comes from Gombe National Park, Tanzania, while the other samples are derived from museum materials originally collected in west/central Africa. Total data for African ape samples include 5807 surfaces for ascertainment of vertebral osteophytosis, 12,479 surfaces for determination of spinal osteoarthritis, and 1211 joints for evaluation of peripheral joint osteoarthritis. All apes display significantly less spinal disease than in a comparable human sample, and these differences are most likely a consequence of human biomechanical adaptations for bipedal locomotion. Apes are also generally less involved in the major peripheral joints than are humans, but human groups are themselves highly variable in prevalence of peripheral osteoarthritis. These data agree with other findings of low prevalence of degenerative joint prevalence in free-ranging apes, but contrast markedly with evidence derived from colony-reared Old World monkeys.     

Information and its use by animals in evolutionary ecology

Information is a crucial currency for animals from both a behavioural and evolutionary perspective. Adaptive behaviour relies upon accurate estimation of relevant ecological parameters; the better informed an individual, the better it can develop and adjust its behaviour to meet the demands of a variable world. Here, we focus on the burgeoning interest in the impact of ecological uncertainty on adaptation, and the means by which it can be reduced by gathering information, from both 'passive' and 'responsive' sources. Our overview demonstrates the value of adopting an explicitly informational approach, and highlights the components that one needs to develop useful approaches to studying information use by animals. We propose a quantitative framework, based on statistical decision theory, for analysing animal information use in evolutionary ecology. Our purpose is to promote an integrative approach to studying information use by animals, which is itself integral to adaptive animal behaviour and organismal biology.