The developmental evolution of avian digit homology: An update

The identity of avian digits has been unresolved since the beginning of evolutionary morphology in the mid-19th century, i.e. as soon as questions of phylogenetic homology have been raised. The main source of concern is the persistent discrepancy between anatomical/paleontological and embryological evidence over the identity of avian digits. In this paper, recent evidence pertaining to the question of avian digit homology is reviewed and the various ideas of how to resolve the disagreement among developmental and phylogenetic evidence are evaluated. Paleontological evidence unequivocally supports the hypothesis that the fully formed digits of maniraptoran theropods are digits DI, DII, and DIII, because the phylogenetic position of Herrerasaurus is resolved, even when hand characters are excluded from the analysis. Regarding the developmental origin of the three digits of the avian hand the discovery of an anterior digit condensation in the limb bud of chickens and ostriches conclusively shows that these three digits are developing from condensations CII, CIII, and CIV. The existence of this additional anterior condensation has been confirmed in four different labs, using four different methods: Alcian blue staining, PNA affinity histochemistry, micro-capillary regression and Sox9 expression. Finally, recent evidence shows that the digit developing from condensation CII has a Hox gene expression pattern that is found in digit DI of mice forelimb and chick hind limbs. The sum of these data supports the idea that digit identity has shifted relative to the location of condensations, known as Frame Shift Hypothesis, such that condensation CII develops into digit DI and condensation CIII develops into digit DII, etc. A review of the literature on the digit identity of the Italian Three-toed Skink or Luscengola (Chalcides chalcides), shows that digit identity frame shifts may not be limited to the bird hand but may be characteristic of “adaptive” digit reduction in amniotes (sensu Steiner, H., Anders, G., 1946. Zur Frage der Entstehung von Rudimenten. Die Reduktion der Gliedmassen von Chalcides tridactylus Laur. Rev. Suisse Zool. 53, 537–546) in general. In this mode of evolution two digits are lost, in the course of the adaptation of the three anterior digits to a function that does not require the two posterior digits. This evidence suggests that the evolution of digits in tetrapods can proceed at least on two distinct levels of integration, the level of digit condensations and that of adult digits.     

Intrachromosomal rearrangements in avian genome evolution: evidence for regions prone to breakpoints

It is generally believed that the organization of avian genomes remains highly conserved in evolution as chromosome number is constant and comparative chromosome painting demonstrated there to be very few interchromosomal rearrangements. The recent sequencing of the zebra finch (Taeniopygia guttata) genome allowed an assessment of the number of intrachromosomal rearrangements between it and the chicken (Gallus gallus) genome, revealing a surprisingly high number of intrachromosomal rearrangements. With the publication of the turkey (Meleagris gallopavo) genome it has become possible to describe intrachromosomal rearrangements between these three important avian species, gain insight into the direction of evolutionary change and assess whether breakpoint regions are reused in birds. To this end, we aligned entire chromosomes between chicken, turkey and zebra finch, identifying syntenic blocks of at least 250 kb. Potential optimal pathways of rearrangements between each of the three genomes were determined, as was a potential Galliform ancestral organization. From this, our data suggest that around one-third of chromosomal breakpoint regions may recur during avian evolution, with 10% of breakpoints apparently recurring in different lineages. This agrees with our previous hypothesis that mechanisms of genome evolution are driven by hotspots of non-allelic homologous recombination.     

冬季森林鸟类对林窗的响应分析

林窗主要指由森林中老龄树死亡或其他偶然因素导致的成熟阶段优势树种死亡,从而造成在林冠层形成空隙的现象。2011年11月—2012年2月,于广西防城金花茶国家级自然保护区,采用定点观察法,就北热带季雨林冬季鸟类对林窗的响应特征及鸟类在林窗和非林窗的分布特征等进行了研究。在林窗记录到鸟类45种,占所有鸟类的84.9%,平均种数为9.6种;在非林窗记录到鸟类39种,占所有鸟类的73.6%,平均种数为5.3种。多元回归表明林窗面积、林窗外10m乔木平均高度、林窗外10m乔木数量、林窗外10m灌木数量、林窗外1m草本平均盖度和裸地比例是林窗影响鸟类多样性的关键因子。总体上,林窗鸟类多样性大于非林窗。另外,林窗对鸟类空间分布影响主要表现在:鸟类的垂直分布以林窗中层和林冠层为主,水平分布以近离和较近离为主,而这种空间分布格局主要是由鸟类取食生态位分化所造成。     

Influences of population size and woodland area on bird species distributions in small woods

Distributions of individual bird species in 151 small woods (size range 0.02–30 ha) were investigated in 3 consecutive years during which the abundance of certain species varied markedly. Relationships between the probabilities of certain bird species breeding and woodland area were described using incidence functions derived from logistic regression analysis. In general, for species which were largely dependent on woodland and seldom occurred in other habitats (such as hedgerows and gardens), the probability of breeding approached 100% only for woods of 10 ha and more, whereas species with less stringent habitat requirements occurred in the majority of woods, including those of 1 ha and less. The sensitivity of incidence functions to changes in regional abundance and the size distribution of the study woods was examined. For some species, distribution patterns could not be distinguished from those expected if pairs had been distributed in proportion to woodland area (random placement), but the majority did not conform to random placement in at least 1 of the 3 years. This nonconformity was consistent across all 3 years for some species, such as wren (Troglodytes troglodytes), despite substantial fluctuations in population sizes between years, while for others, such as robin (Erithacus rubecula), distribution patterns changed with changes in regional abundance. The results suggested that some species, such as wren and blackbird (Turdus merula), preferred small woods, while other species, such as chiffchaff (Phylloscopus collybita), preferred large woods. For several other species, including robin, great tit (Parus major), long-tailed tit (Aegithalos caudatus) and marsh tit (P. palustris), small woods appeared to be sub-optimal under at least some conditions.     

Nested bird and micro-habitat assemblages in a peatland archipelago

Biotic assemblages of insular habitats are nested when poor assemblages are subsets of richer ones. Nestedness of species assemblages is frequent and may result from selective extinction or frequent colonization in insular habitats. It may also be created by a nested distribution of habitats among islands or by sampling bias. We sampled 67 isolated peatlands (7–843 ha) in southern Quebec, Canada, to measure nestedness of bird species assemblages among peatlands and assess the habitat nestedness hypothesis. Species and microhabitat assemblages were both strongly nested among peatlands. Whether sites were ranked by species richness, microhabitat richness or peatland area had no effect on nestedness. However, microhabitat nestedness was significantly reduced when sites were sorted by area rather than by microhabitat richness. As expected, if bird-microhabitat associations are responsible for the nested pattern of distribution, we found a positive correlation between the contributions of bird species and microhabitats to individual site nestedness. Nevertheless, microhabitat assemblages were significantly less nested than bird species assemblages, possibly because of frequent recolonization by birds or uneven sampling among sites. Received: 12 June 1998 / Accepted: 20 September 1998     

Process in the evolution of bird migration and pattern in avian ecogeography

Current ideas about the evolution of bird migration equate its origin with the first appearance of fully migratory populations, and attribute its evolution to a selective advantage generated by increased breeding success, gained through temporary emigration from resident populations to breed in under-exploited seasonal areas. I propose an alternative hypothesis in which migration first appears as a temporary directional shift away from the breeding site outside the reproductive period, in response to seasonal variation in the direction and/or severity of environmental gradients. Fully migratory populations then appear through either extinction of sedentary phenotypes, or colonisation of vacant seasonal areas by migrants. Where colonisation occurs, resident ancestral populations can be driven to extinction by competition from migrants which invade their range outside the breeding season, resulting in fully migratory species. An analogous process drives the evolution of migration between high latitudes and the tropics, since extension of breeding range into higher latitudes may drive low latitude populations to extinction, resulting in an overall shift of breeding range. This process can explain reverse latitudinal gradients in avian diversity in the temperate zone, since the breeding ranges of migratory species concentrate in latitudes where they enjoy the highest breeding success. Near absence of forest-dwelling species among Palaearctic-African migrants is attributable to the lack of forest in northern Africa for much of the Tertiary, which has precluded selection both for southward extension of migration by west Palaearctic forest species, and northward breeding colonisation by African forest species.     

The evolution of avian migration

The study of avian migration has reached sophisticated levels in many areas, including ecology, behaviour, and physiology. Traditional discussions of the evolution of migration, however, have been compromised for several reasons. Previous ideas concerning the ancestral home of migrant species, southern or northern, and whether a partially migratory stage always precedes a fully migratory stage, were not expressed as testable hypotheses. Plotting migratory behaviour on phylogenetic trees has become commonplace and allows tests of traditional hypotheses. Some of these studies are reviewed, lending some support for almost all of the previous ideas. Although phylogenetic mapping helps to frame questions about the evolution of migration in a testable framework, there are two serious issues. First, experimental and observational studies reveal that the expression of migratory behaviour can change rapidly within a lineage, which can violate assumptions of character mapping. In addition, a species distribution model is used to show that current conditions for obligate migratory populations of the chipping sparrow were much restricted at the Last Glacial Maximum, and that the species might have been considered a partial migrant at that time. The expression of migratory behaviour in an extant species might be an artefact of the current inter‐glacial period. Only if the rate of gains and losses of migratory behaviour can be incorporated into a phylogenetic mapping exercise will the actual evolutionary pattern of migration be revealed. For example, reconstruction of the ancestral area and the evolutionary history of migratory categories in a clade of New World warblers depended on the assumptions of character state transitions. A second concern is that the trait ‘migratory’ is too broad for evolutionary analysis and that, if possible, the expression of hyperphagia, Zugunruhe, and navigation could be mapped individually. Loss or suppression of any of these components can lead to sedentary populations, revealing how migratory behaviour can appear and disappear rapidly. A report of low levels of Zugunruhe in a sedentary bird, Saxicola torquata, is reconstructed as derived in a clade of otherwise migratory populations, suggesting that the loss of migration was a result of suppression (but not elimination) of Zugunruhe. When researchers mention the independent origin of migration in a clade, they are most likely referring to the gain or loss of the expression of the ancestral migratory programme, not the de novo evolution of migration per se. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 237–250.     

A robust tool highlights the influence of bird migration on influenza A virus evolution

One of the fundamental unknowns in the field of influenza biology is a panoramic understanding of the role wild birds play in the global maintenance and spread of influenza A viruses. Wild aquatic birds are considered a reservoir host for all lowly pathogenic avian influenza A viruses (AIV) and thus serve as a potential source of zoonotic AIV, such as Australasian‐origin H5N1 responsible for morbidity and mortality in both poultry and humans, as well as genes that may contribute to the emergence of pandemic viruses. Years of broad, in‐depth wild bird AIV surveillance have helped to decipher key observations and ideas regarding AIV evolution and viral ecology including the trending of viral lineages, patterns of gene flow within and between migratory flyways and the role of geographic boundaries in shaping viral evolution (Bahl et al. 2009 ; Lam et al. 2012 ). While these generally ‘virus‐centric’ studies have ultimately advanced our broader understanding of AIV dynamics, recent studies have been more host‐focused, directed at determining the potential impact of host behaviour on AIV, specifically, the influence of bird migration upon AIV maintenance and transmission. A large number of surveillance studies have taken place in Alaska, United States—a region where several global flyways overlap—with the aim of detecting the introduction of novel, Australasian‐origin highly pathogenic H5N1 AIV into North America. By targeting bird species with known migration habits, long‐distance migrators were determined to be involved in the intercontinental movement of individual AIV gene segments, but not entire viruses, between the Australasian and North American flyways (Koehler et al. 2008 ; Pearce et al. 2010 ). Yet, bird movement is not solely limited to long‐distance migration, and the relationship of resident or nonmigratory and intermediate‐distance migrant populations with AIV ecology has only recently been explored by Hill et al. ( 2012 ) in this issue of Molecular Ecology. Applying a uniquely refined, multidimensional approach, Hill et al. validate the innovative use of stable isotope assays for qualifying migration status of wild mallards within the Pacific flyway. The authors reveal that AIV prevalence and diversity did not differ in wintering mallard ducks with different migration strategies, and while migrant mallards do indeed introduce AIV, these viruses do not circulate as the predominant viruses in resident birds. On the other hand, resident mallards from more temperate regions act as reservoirs, possibly contributing to the unseasonal circulation and extended transmission period of AIV. This study highlights the impact of animal behaviour on shaping viral evolution, and the unique observations made will help inform prospective AIV surveillance efforts in wild birds.     

Fire regime shifts affect bird species distributions

Aim Fire is a major driver of ecosystem structure and process, and shifts in fire regimes are implicated in the decline of many species. Shifting fire regimes have been documented around the world, and fire frequency and extent is predicted to increase in many areas because of changes in both climate and land management. Here, we evaluate how predicted increases in fire frequency are likely to impact on species distributions. Location The tropical savannas of northern Australia. Methods We developed distribution models for 44 bird species using the modelling algorithm Maxent. Our models incorporated bird locality records and environmental variables including climate, total fire frequency and the subset of fire frequency occurring late in the dry season. We investigated the effect of increasing total fire frequency and increasing fire late in the dry season, on species distributions by projecting species model algorithms onto scenarios of incrementally increased total fire frequency. Results The probability of presence for most species was higher when fire frequency late in the dry season was low. Species showed a mixed response to an overall increase in total fire frequency, with one‐third predicted to increase in distribution. However, almost all species (98%) showed a decrease in predicted range with increased late‐dry season fire, and species distribution area was generally negatively correlated with an increase in late‐dry season fire. Main conclusions Our study highlighted the array of responses of species to increasing fire frequency and suggested that increased fire frequency late in the dry season is detrimental to most savanna‐restricted bird species. The understanding of individual species’ preferences for particular fire frequencies is important for informed conservation planning.     

Biotic interactions improve prediction of boreal bird distributions at macro-scales

Aim The role of biotic interactions in influencing species distributions at macro‐scales remains poorly understood. Here we test whether predictions of distributions for four boreal owl species at two macro‐scales (10 × 10 km and 40 × 40 km grid resolutions) are improved by incorporating interactions with woodpeckers into climate envelope models. Location Finland, northern Europe. Methods Distribution data for four owl and six woodpecker species, along with data for six land cover and three climatic variables, were collated from 2861 10 × 10 km grid cells. Generalized additive models were calibrated using a 50% random sample of the species data from western Finland, and by repeating this procedure 20 times for each of the four owl species. Models were fitted using three sets of explanatory variables: (1) climate only; (2) climate and land cover; and (3) climate, land cover and two woodpecker interaction variables. Models were evaluated using three approaches: (1) examination of explained deviance; (2) four‐fold cross‐validation using the model calibration data; and (3) comparison of predicted and observed values for independent grid cells in eastern Finland. The model accuracy for approaches (2) and (3) was measured using the area under the curve of a receiver operating characteristic plot. Results At 10‐km resolution, inclusion of the distribution of woodpeckers as a predictor variable significantly improved the explanatory power, cross‐validation statistics and the predictive accuracy of the models. Inclusion of land cover led to similar improvements at 10‐km resolution, although these improvements were less apparent at 40‐km resolution for both land cover and biotic interactions. Main conclusions Predictions of species distributions at macro‐scales may be significantly improved by incorporating biotic interactions and land cover variables into models. Our results are important for models used to predict the impacts of climate change, and emphasize the need for comprehensive evaluation of the reliability of species–climate impact models.     

Note on the glide of a bird with wings bent downwards

This note considers the influence of the bending down of the wings of a bird on the performance of its glide. The induced drag of bent wings is compared with the induced drag of a corresponding straight wing. Numerical results are given.     

Temporal turnover of common species in avian assemblages in North America

Aim We examine patterns of temporal turnover of common species in avian assemblages in North America to test the hypothesis that changes in avian diversity structure observed in these assemblages were associated with the colonization of common species. Location The contiguous United States and southern Canada. Methods We measured temporal turnover from 1968 to 2003 for 547 avian species at 1673 North American Breeding Bird Survey (BBS) routes. We used the Euclidian distance between expected and observed presence/absence vectors and randomization tests to place species into two categories, common and not‐common, and into three categories for common species: (1) always common, (2) common and colonizing, and (3) common and extirpated. We used these categories to identify species experiencing extreme colonization and extirpation events and to examine changes in species composition at BBS routes. We also determined how these patterns were associated with changes in species richness and changes in similarity in species composition. Results Nine of the 547 species represented outliers, where the number of BBS routes colonized greatly exceeded the number extirpated; no species showed extreme values for extirpation. The nine species colonized BBS routes primarily in the upper Midwest and north‐eastern United States. Presence of the nine species at BBS routes was correlated with increasing net gain in common species (difference between common colonized and common extirpated), higher levels of species richness and increasing species richness over time, more similar species compositions and increasing similarity over time, and a greater prevalence of common species over not‐common species. The literature indicates that all nine species experienced some form of geographical range expansion during the time of the survey involving four elements: (1) introduction and invasion; (2) the ability to use human‐altered environments, including habitats associated with agricultural, suburban, or urban areas; (3) intensive management activities, including habitat improvements and reintroductions and (4) the ability to use habitats formed through forest regeneration. These factors in combination point to anthropogenic activities and related land use histories as the primary drivers of change. One of the nine species colonized regions well outside its historic geographical range and the remaining eight species were native within the regions they colonized. Main conclusions Our results suggest that a combination of anthropogenic activities promoted, within certain regions of North America, the geographical expansion of a limited number of common species that were native to those regions. These colonization events were correlated with changes in diversity structure, implying that large‐scale diversity patterns were being influenced by anthropogenic activities. These changes can be characterized primarily by gains in species richness, an increased prevalence of common species, and more similar species compositions. Thus, using simple large‐scale measures of diversity could be problematic if recent biogeographical patterns of species diversity are not considered. Specifically, using species richness or an indicator species to assess diversity could bias assessments towards common species whose populations have recently benefited through anthropogenic activities.     

A fossil brain from the Cretaceous of European Russia and avian sensory evolution

Fossils preserving traces of soft anatomy are rare in the fossil record; even rarer is evidence bearing on the size and shape of sense organs that provide us with insights into mode of life. Here, we describe unique fossil preservation of an avian brain from the Volgograd region of European Russia. The brain of this Melovatka bird is similar in shape and morphology to those of known fossil ornithurines (the lineage that includes living birds), such as the marine diving birds Hesperornis and Enaliornis, but documents a new stage in avian sensory evolution: acute nocturnal vision coupled with well-developed hearing and smell, developed by the Late Cretaceous (ca 90Myr ago). This fossil also provides insights into previous 'bird-like' brain reconstructions for the most basal avian Archaeopteryx--reduction of olfactory lobes (sense of smell) and enlargement of the hindbrain (cerebellum) occurred subsequent to Archaeopteryx in avian evolution, closer to the ornithurine lineage that comprises living birds. The Melovatka bird also suggests that brain enlargement in early avians was not correlated with the evolution of powered flight.     

The primary feather lengths of early birds with respect to avian wing shape evolution

We examine the relationships between primary feather length (f(prim)) and total arm length (ta) (sum of humerus, ulna and manus lengths) in Mesozoic fossil birds to address one aspect of avian wing shape evolution. Analyses show that there are significant differences in the composition of the wing between the known lineages of basal birds and that mean f(prim) (relative to ta length) is significantly shorter in Archaeopteryx and enantiornithines than it is in Confuciusornithidae and in living birds. Based on outgroup comparisons with nonavian theropods that preserve forelimb primary feathers, we show that the possession of a relatively shorter f(prim) (relative to ta length) must be the primitive condition for Aves. There is also a clear phylogenetic trend in relative primary feather length throughout bird evolution: our analyses demonstrate that the f(prim)/ta ratio increases among successive lineages of Mesozoic birds towards the crown of the tree ('modern birds'; Neornithes). Variance in this ratio also coincides with the enormous evolutionary radiation at the base of Neornithes. Because the f(prim)/ta ratio is linked to flight mode and performance in living birds, further comparisons of wing proportions among Mesozoic avians will prove informative and certainly imply that the aerial locomotion of the Early Cretaceous Confuciusornis was very different to other extinct and living birds.