Universal Sharing Patterns in Proteomes and Evolution of Protein Fold Architecture and Life

Protein evolution is imprinted in both the sequence and the structure of evolutionary building blocks known as protein domains. These domains share a common ancestry and can be unified into a comparatively small set of folding architectures, the protein folds. We have traced the distribution of protein folds between and within proteomes belonging to Eukarya, Archaea, and Bacteria along the branches of a universal phylogeny of protein architecture. This tree was reconstructed from global fold-usage statistics derived from a structural census of proteomes. We found that folds shared by the three organismal domains were placed almost exclusively at the base of the rooted tree and that there were marked heterogeneities in fold distribution and clear evolutionary patterns related to protein architecture and organismal diversification. These include a relative timing for the emergence of prokaryotes, congruent episodes of architectural loss and diversification in Archaea and Bacteria, and a late and quite massive rise of architectural novelties in Eukarya perhaps linked to multicellularity.Reviewing Editor : Dr. David Pollock     

Evolution of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases

The AID/APOBEC family (comprising AID, APOBEC1, APOBEC2, and APOBEC3 subgroups) contains members that can deaminate cytidine in RNA and/or DNA and exhibit diverse physiological functions (AID and APOBEC3 deaminating DNA to trigger pathways in adaptive and innate immunity; APOBEC1 mediating apolipoprotein B RNA editing). The founder member APOBEC1, which has been used as a paradigm, is an RNA-editing enzyme with proposed antecedents in yeast. Here, we have undertaken phylogenetic analysis to glean insight into the primary physiological function of the AID/APOBEC family. We find that although the family forms part of a larger superfamily of deaminases distributed throughout the biological world, the AID/APOBEC family itself is restricted to vertebrates with homologs of AID (a DNA deaminase that triggers antibody gene diversification) and of APOBEC2 (unknown function) identifiable in sequence databases from bony fish, birds, amphibians, and mammals. The cloning of an AID homolog from dogfish reveals that AID extends at least as far back as cartilaginous fish. Like mammalian AID, the pufferfish AID homolog can trigger deoxycytidine deamination in DNA but, consistent with its cold-blooded origin, is thermolabile. The fine specificity of its mutator activity and the biased codon usage in pufferfish IgV genes appear broadly similar to that of their mammalian counterparts, consistent with a coevolution of the antibody mutator and its substrate for the optimal targeting of somatic mutation during antibody maturation. By contrast, APOBEC1 and APOBEC3 are later evolutionary arrivals with orthologs not found in pufferfish (although synteny with mammals is maintained in respect of the flanking loci). We conclude that AID and APOBEC2 are likely to be the ancestral members of the AID/APOBEC family (going back to the beginning of vertebrate speciation) with both APOBEC1 and APOBEC3 being mammal-specific derivatives of AID and a complex set of domain shuffling underpinning the expansion and evolution of the primate APOBEC3s.     

Habitat structural complexity and morphological diversity of fish assemblages in a Neotropical floodplain river

High species richness and evenness in structurally complex habitats has been hypothesized to be associated with niche partitioning. To test this idea, relationships between habitat structural complexity in river littoral-zone habitats and morphological diversity of tropical fishes were examined in the Cinaruco River, Venezuela. Six habitat attributes were quantified in 45 sites spanning a range of structural complexity. Fishes were collected during day and night to estimate species density and relative abundances at each site. Twenty-two morphological variables were measured for each species. Principal components analysis (PCA) of physical habitat data yielded two axes that modeled >80% of variation across sites. The first two axes from PCA of fish morphological variables modeled >70% of variation. Species density during both day and night was negatively associated with flow velocity and positively associated with habitat complexity. Similarity of day and night samples from the same site was significantly greater for sites with high habitat complexity and low flow. In general, mean local assemblage morphological PC scores were not significantly associated with habitat PC scores. Average, maximum, and standard deviation of morphological Euclidean distances of local assemblages revealed positive associations with structural complexity and negative associations with flow. These relationships held even when the positive relationship of species density was statistically removed from assemblage morphological patterns. Findings suggest that both species niche compression and assemblage niche space increase when habitat complexity is greater and flow velocity is lower in this tropical lowland river.Electronic Supplementary Material Supplementary material is available for this article at     

Recent approach to Buchia biostratigraphy from the Tethyan Himalaya area, China

Recent collections from six sections in Lanongla area, Tethyan Himalaya allow the establishment of four buchia assemblages. In ascending order, they are Buchia-Buchia spitiensis, Buchia masquensis-Buchia rugasa, Buchia blanfordiana, Buchia piochii and Buchia subokensis assemblages. These Buchia assemblages first demonstrate that not only the Upper Jurassic strata but also the highest Buchia assemblage-Buchia subokensis, which appeared in Lower Cretaceous strata all over the world are present in Lanongla area. This first records the highest Buchia assemblage in Lanongla area. __________ Translated from Acta Scientiarum Naturalium Universitatis Pekinensis, 2005, 41 (4) [译自: 北京大学学报( 自然科学版), 2005,41(4)]     

Diversity dynamics of Miocene mammals in relation to the history of tectonism and climate

Continental biodiversity gradients result not only from ecological processes, but also from evolutionary and geohistorical processes involving biotic turnover in landscape and climatic history over millions of years. Here, we investigate the evolutionary and historical contributions to the gradient of increasing species richness with topographic complexity. We analysed a dataset of 418 fossil rodent species from western North America spanning 25 to 5 Ma. We compared diversification histories between tectonically active (Intermontane West) and quiescent (Great Plains) regions. Although diversification histories differed between the two regions, species richness, origination rate and extinction rate per million years were not systematically different over the 20 Myr interval. In the tectonically active region, the greatest increase in originations coincided with a Middle Miocene episode of intensified tectonic activity and global warming. During subsequent global cooling, species richness declined in the montane region and increased on the Great Plains. These results suggest that interactions between tectonic activity and climate change stimulate diversification in mammals. The elevational diversity gradient characteristic of modern mammalian faunas was not a persistent feature over geologic time. Rather, the Miocene rodent record suggests that the elevational diversity gradient is a transient feature arising during particular episodes of Earth''s history.     

Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna

Understanding the evolutionary history of the species in a particular region provides insights into how that fauna was formed. Of particular interest to biogeographers is examining the impact a geographical barrier had in generating temporal genetic diversity among codistributed species. We examined the impact a major New World barrier, the Isthmus of Tehuantepec (IT) in southern Mexico, had on a regional bird fauna. Specifically, genetic data from 10 montane-forest bird taxa were analysed using approximate Bayesian computation (ABC) to test the hypothesis of simultaneous intraspecific diversification at the IT. Because effective population size (N_e) has the greatest impact on coalescent times, thereby affecting tests of divergence among codistributed taxa, we chose priors for both current and ancestral N_e using empirical estimates of theta. The ABC method detected two discrete diversification events. Subsequent analysis with the number of diversification events constrained to two suggests that four taxa diverged in an older event, with the remaining six diverging more recently. Application of a range of mutation rates from 2.0 to 5.0% Myr⁻¹ places both events within the Pleistocene or Late Pliocene, suggesting that fluctuations in montane habitat induced by climate cycles and a late Pliocene seaway may have fractured this montane bird fauna. The results presented here suggest this avian fauna responded in a relatively concerted fashion over the last several million years.     

A new Lower Cretaceous bird from China and tooth reduction in early avian evolution

A new avian genus and species, Zhongjianornis yangi gen. et sp. nov., is reported from the Lower Cretaceous lacustrine deposits of the Jiufotang Formation in Liaoning, northeast China. The new taxon is characterized by possessing the following combination of features: upper and lower jaws toothless, snout pointed, humerus with large and robust deltopectoral crest, second phalanx of the major manual digit longer than the first phalanx, unguals of the alular and major digits of similar length and significantly shorter than the corresponding penultimate phalanges, tibiotarsus slender and more than twice the length of the tarsometatarsus, and metatarsal IV longer than the other metatarsals. Phylogenetic analysis indicates that Zhongjianornis is phylogenetically basal to Confuciusornis and the dominant Mesozoic avian groups, Enantiornithes and Ornithurae, and therefore provides significant new information regarding the diversification of birds in the Early Cretaceous. It also represents the most basal bird that completely lacks teeth, suggesting that tooth loss was more common than expected in early avian evolution and that the avian beak appeared independently in several avian lineages, most probably as a response to selective pressure for weight reduction. Finally, the presence of a significantly enlarged humeral deltopectoral crest suggests that Zhongjianornis shares with other basal birds such as Jeholornis, Sapeornis and Confuciusornis a distinctive mode of adaptation for flight contrasting with that seen in more advanced birds, which instead possess an elongated sternum and a prominent keel.     

Large-scale patterns of diversification in the widespread legume genus Senna and the evolutionary role of extrafloral nectaries

Unraveling the diversification history of old, species-rich and widespread clades is difficult because of extinction, undersampling, and taxonomic uncertainty. In the context of these challenges, we investigated the timing and mode of lineage diversification in Senna (Leguminosae) to gain insights into the evolutionary role of extrafloral nectaries (EFNs). EFNs secrete nectar, attracting ants and forming ecologically important ant-plant mutualisms. In Senna, EFNs characterize one large clade (EFN clade), including 80% of its 350 species. Taxonomic accounts make Senna the largest caesalpinioid genus, but quantitative comparisons to other taxa require inferences about rates. Molecular dating analyses suggest that Senna originated in the early Eocene, and its major lineages appeared during early/mid Eocene to early Oligocene. EFNs evolved in the late Eocene, after the main radiation of ants. The EFN clade diversified faster, becoming significantly more species-rich than non-EFN clades. The shift in diversification rates associated with EFN evolution supports the hypothesis that EFNs represent a (relatively old) key innovation in Senna. EFNs may have promoted the colonization of new habitats appearing with the early uplift of the Andes. This would explain the distinctive geographic concentration of the EFN clade in South America.     

DISCOVERING EXCEPTIONAL DIVERSIFICATIONS AT CONTINENTAL SCALES: THE CASE OF THE ENDEMIC FAMILIES OF NEOTROPICAL SUBOSCINE PASSERINES

The study of continental adaptive radiations has lagged behind research on their island counterparts in part because the mere identification of adaptive radiations is more challenging at continental scales. Here, I demonstrate a new method based on simulations for discovering clades that show exceptionally high phenotypic diversity. The method does not require a phylogeny but accounts for differences in age and species richness among clades and incorporates effects of the phylogenetic structure of data. In addition, I developed a new multivariate measure of phenotypic diversity, which has the advantage over other measures of disparity in that it takes covariation into account. I applied these methods to a clade of endemic Neotropical suboscine passerines, within which the family Furnariidae has been considered an adaptive radiation. I found that the families Thamnophilidae, Furnariidae, and Dendrocolaptidae have experienced a higher rate of cladogenesis than have other clades. Although Thamnophilidae is exceptionally diverse in body size, only Furnariidae and Dendrocolaptidae are exceptionally diverse in shape. The combination of high rates of cladogenesis and high morphometric diversity in traits related to feeding and locomotion suggest that the clade Furnariidae‐Dendrocolaptidae represent an authentic continental adaptive radiation.     

Liaoxia Cao et S.Q. Wu (Gnetales): ephedroids from the Early Cretaceous Yixian Formation in Liaoning, northeastern China

Gnetalean compression-impression fossils are described from the Early Cretaceous Yixian Formation, Liaoning Province, north-eastern China, and assigned to six species of Liaoxia Cao et S.Q. Wu. The fossils have opposite-decussate phyllotaxis and cones comprising 2–12 pairs of bracts. Ovulate cones have seeds typically in a distal position. The species differ from each other and from previously described fossils in the absence or presence of leaves, shape of cones and seeds, and shape and position of cone bracts. The species of Liaoxia are probably close relatives of extant species of Ephedra L., but diagnostic reproductive details that could confirm this hypothesis are not preserved. The restricted information in the fossils and the poorly understood morphological diversity of extant Ephedra, prevent assignment of the fossils to any particular subgroup of Ephedra, as well as an explicit exclusion of them from the extant genus.