Diversification of body shape in Sebastes rockfishes of the north‐east Pacific

Body shape variation is integrally related to many aspects of fish ecology, including locomotion and foraging, and can indicate the functional diversity of fish assemblages. Few studies have thoroughly characterized body shape in a diverse marine fish clade, or investigated both temporal and spatial patterns of variation in body shape disparity. Here, I use digital photographs to measure geometric body shape in 66 species of north‐east Pacific rockfish (Sebastes spp.), including a correction for error introduced by arching of specimens. Different components of interspecific shape variation show associations with fish size, depth habitat, trophic niche and phylogenetic relationships. Overall, the accumulation of body shape disparity appears to have been near‐constant over time, and shows little variation across the latitudinal range of rockfish.     

Evolutionary dynamics of ecological niche in three Rhinogobio fishes from the upper Yangtze River inferred from morphological traits

In the past decades, it has been debated whether ecological niche should be conserved among closely related species (phylogenetic niche conservatism, PNC) or largely divergent (traditional ecological niche theory and ecological speciation) and whether niche specialist and generalist might remain in equilibrium or niche generalist could not appear. In this study, we employed morphological traits to describe ecological niche and test whether different niche dimensions exhibit disparate evolutionary patterns. We conducted our analysis on three Rhinogobio fish species (R. typus, R. cylindricus, and R. ventralis) from the upper Yangtze River, China. Among the 32 measured morphological traits except body length, PCA extracted the first four principal components with their loading scores >1.000. To find the PNC among species, Mantel tests were conducted with the Euclidean distances calculated from the four principal components (representing different niche dimensions) against the pairwise distances calculated from mitochondrial cytochrome b sequence variations. The results showed that the second and the third niche dimension, both related to swimming ability and behavior, exhibited phylogenetic conservatism. Further comparison on niche breadth among these three species revealed that the fourth dimension of R. typus showed the greatest width, indicating that this dimension exhibited niche generalism. In conclusion, our results suggested that different niche dimensions could show different evolutionary dynamic patterns: they may exhibit PNC or not, and some dimensions may evolve generalism.     

You stay,but I Hop: Host shifting near and far co‐dominated the evolution of Enchenopa treehoppers

The importance and prevalence of phylogenetic tracking between hosts and dependent organisms caused by co‐evolution and shifting between closely related host species have been debated for decades. Most studies of phylogenetic tracking among phytophagous insects and their host plants have been limited to insects feeding on a narrow range of host species. However, narrow host ranges can confound phylogenetic tracking (phylogenetic tracking hypothesis) with host shifting between hosts of intermediate relationship (intermediate hypothesis). Here, we investigated the evolutionary history of the Enchenopa binotata complex of treehoppers. Each species in this complex has high host fidelity, but the entire complex uses hosts across eight plant orders. The phylogenies of E. binotata were reconstructed to evaluate whether (1) tracking host phylogeny; or (2) shifting between intermediately related host plants better explains the evolutionary history of E. binotata. Our results suggest that E. binotata primarily shifted between both distant and intermediate host plants regardless of host phylogeny and less frequently tracked the phylogeny of their hosts. These findings indicate that phytophagous insects with high host fidelity, such as E. binotata, are capable of adaptation not only to closely related host plants but also to novel hosts, likely with diverse phenology and defense mechanisms.     

Phylogenetic dimension of tree communities reveals high conservation value of disturbed tropical rain forests

Aim

The conversion of old‐growth tropical forests into human‐modified landscapes threatens biodiversity worldwide, but its impact on the phylogenetic dimension of remaining communities is still poorly known. Negative and neutral responses of tree phylogenetic diversity to land use change have been reported at local and landscape scales. Here, we hypothesized that such variable responses to disturbance depend on the regional context, being stronger in more degraded rain forest regions with a longer history of land use.

Location

Six regions in Mexico and Brazil.

Methods

We used a large vegetation database (6,923 trees from 686 species) recorded in 98 50‐ha landscapes distributed across two Brazilian and four Mexican regions, which exhibit different degrees of disturbance. In each region, we assessed whether phylogenetic alpha and beta diversities were related to landscape‐scale forest loss, the percentage of shade‐intolerant species (a proxy of local disturbance) and/or the relatedness of decreasing (losers) and increasing (winners) taxa.

Results

Contrary to our expectations, the percentage of forest cover and shade‐intolerant species were weakly related to phylogenetic alpha and beta diversities in all but one region. Loser species were generally as dispersed across the phylogeny as winner species, allowing more degraded, deforested and species‐poorer forests to sustain relatively high levels of evolutionary (phylogenetic) diversity.

Main conclusion

Our findings support previous evidence indicating that traits related to high susceptibility to forest disturbances are convergent or have low phylogenetic signal. More importantly, they reveal that the evolutionary value of disturbed forests is (at least in a phylogenetic sense) much greater than previously thought.

     

Modeling and analysis of soybean (Glycine max. L) Cu/Zn,Mn and Fe superoxide dismutases

Superoxide dismutase (SOD, EC 1.15.1.1) is an important metal-containing antioxidant enzyme that provides the first line of defense against toxic superoxide radicals by catalyzing their dismutation to oxygen and hydrogen peroxide. SOD is classified into four metalloprotein isoforms, namely, Cu/Zn SOD, Mn SOD, Ni SOD and Fe SOD. The structural models of soybean SOD isoforms have not yet been solved. In this study, we describe structural models for soybean Cu/Zn SOD, Mn SOD and Fe SOD and provide insights into the molecular function of this metal-binding enzyme in improving tolerance to oxidative stress in plants.     

The first Tanyderidae (Diptera) from Lower Cretaceous Álava amber (Spain)

A new genus and species, Espanoderus barbarae gen. et sp. nov., belonging to the family Tanyderidae (Diptera, Nematocera), is described from Lower Cretaceous amber of Spain (Álava amber). The new genus is the smallest member of Tanyderinae and the first member of the family from the Álava amber. The position of the new genus in a phylogenetic tree of Tanyderidae is presented.

http://zoobank.org/urn:lsid:zoobank.org:pub:EC3284BA-C07F-48AC-8AF5-4F9D2EF4EA6C     

Leaf epidermal features of Rhododendron (Ericaceae)from China and their systematic significance

Rhododendron is the largest genus within the subfamily Rhododendroideae, which has about 1000 known species in the world and more than 500 species in China. Since the genus was established by Linnaeus, its infrageneric relationships have been well studied by many taxonomists on the basis of morphological characters and molecular data. In 1996, Chamberlain et al. proposed a new system of Rhododendron with eight subgenera, i.e., Azaleastrum, Candidastrum, Hymenanthes, Mumeazalea, Pentanthera, Rhododendron, Therorhodion, and Tsutsusi. In this paper, micromorphological characters of leaf epidermis in 4 varieties, 48 species, 6 subgenera of Rhododendron from China were examined using light microscopy (LM) and scanning electron microscopy (SEM). Leaf epidermal features are described and micromorphological types are distinguished here according to morphological characters such as scale, gland, foliar trichome and stomatal apparatus of leaf epidermis. It is shown that the leaf epidermal cells are usually irregular or polygonal in shape. The patterns of anticlinal walls are straight, arched or undulate. The stomatal apparatuses are anomocytic and are usually found on abaxial, not adaxial, epidermis. The results also show that: (1) the lepidote rhododendron (i.e., subgen. Rhododendron), which has both scales and papillae on leaf epidermis, differs distinctly from the elepidote rhododendron; (2) three types of leaf epidermis are identified in subgen. Hymenanthes (i.e., R. fortunei-type, R. chihsinianum-type and R. simiarum-type), whereas four in subgen. Tsutsusi (i.e., R. mariesii-type, R. simsii-type, R. mariae-type and R. flosculum-type); (3) except for R. westlandii and R. henryi, the species of subgen. Azaleastrum show similar morphological characters, i.e., dense stomatal apparatuses surrounded by ringed or discontinuous striates; (4) R. molle of subgen. Pentanthera differs from the species of other subgenera on morphological characters such as foliar trichomes, dense stomatal apparatuses with asymmetrical outer stomatal rims surrounded by undulate-striates, and no gland; (5) only R. redowskianum is found with distinct T-pieces at the polar region of guard cells in Rhododendron. The results support the conclusion inferred from molecular systematic studies that subgen. Therorhodion is the basal clade of Rhododendron. Finally, the relationships between the closely related species are also discussed on the basis of leaf epidermal features.     

Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence

Bayesian Markov chain Monte Carlo sampling has become increasingly popular in phylogenetics as a method for both estimating the maximum likelihood topology and for assessing nodal confidence. Despite the growing use of posterior probabilities, the relationship between the Bayesian measure of confidence and the most commonly used confidence measure in phylogenetics, the nonparametric bootstrap proportion, is poorly understood. We used computer simulation to investigate the behavior of three phylogenetic confidence methods: Bayesian posterior probabilities calculated via Markov chain Monte Carlo sampling (BMCMC-PP), maximum likelihood bootstrap proportion (ML-BP), and maximum parsimony bootstrap proportion (MP-BP). We simulated the evolution of DNA sequence on 17-taxon topologies under 18 evolutionary scenarios and examined the performance of these methods in assigning confidence to correct monophyletic and incorrect monophyletic groups, and we examined the effects of increasing character number on support value. BMCMC-PP and ML-BP were often strongly correlated with one another but could provide substantially different estimates of support on short internodes. In contrast, BMCMC-PP correlated poorly with MP-BP across most of the simulation conditions that we examined. For a given threshold value, more correct monophyletic groups were supported by BMCMC-PP than by either ML-BP or MP-BP. When threshold values were chosen that fixed the rate of accepting incorrect monophyletic relationship as true at 5%, all three methods recovered most of the correct relationships on the simulated topologies, although BMCMC-PP and ML-BP performed better than MP-BP. BMCMC-PP was usually a less biased predictor of phylogenetic accuracy than either bootstrapping method. BMCMC-PP provided high support values for correct topological bipartitions with fewer characters than was needed for nonparametric bootstrap.     

Molecular,genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana

Chromosomal inversions can provide windows onto the cytogenetic, molecular, evolutionary and demographic histories of a species. Here we investigate a paracentric 1.17‐Mb inversion on chromosome 4 of Arabidopsis thaliana with nucleotide precision of its borders. The inversion is created by Vandal transposon activity, splitting an F‐box and relocating a pericentric heterochromatin segment in juxtaposition with euchromatin without affecting the epigenetic landscape. Examination of the RegMap panel and the 1001 Arabidopsis genomes revealed more than 170 inversion accessions in Europe and North America. The SNP patterns revealed historical recombinations from which we infer diverse haplotype patterns, ancient introgression events and phylogenetic relationships. We find a robust association between the inversion and fecundity under drought. We also find linkage disequilibrium between the inverted region and the early flowering Col‐FRIGIDA allele. Finally, SNP analysis elucidates the origin of the inversion to South‐Eastern Europe approximately 5000 years ago and the FRI‐Col allele to North‐West Europe, and reveals the spreading of a single haplotype to North America during the 17th to 19th century. The ‘American haplotype’ was identified from several European localities, potentially due to return migration.