Two Novel Closure Rules for Constructing Phylogenetic Super-Networks

A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection ℘ of partial trees (leaf-labeled trees whose leaves are bijectively labeled by species or, more generally, taxa, each supported by, e.g., a gene) into an overall parental structure that displays all trees in ℘. This already difficult problem is complicated by the fact that the trees in ℘ regularly support conflicting phylogenetic relationships and are not on the same but only overlapping taxa sets. A desirable requirement on the sought after parental structure, therefore, is that it can accommodate the observed conflicts. Phylogenetic networks are a popular tool capable of doing precisely this. However, not much is known about how to construct such networks from partial trees, a notable exception being the Z-closure super-network approach, which is based on the Z-closure rule, and the Q-imputation approach. Although attractive approaches, they both suffer from the fact that the generated networks tend to be multidimensional making it necessary to apply some kind of filter to reduce their complexity. To avoid having to resort to a filter, we follow a different line of attack in this paper and develop closure rules for generating circular phylogenetic networks which have the attractive property that they can be represented in the plane. In particular, we introduce the novel Y-(closure) rule and show that this rule on its own or in combination with one of Meacham’s closure rules (which we call the M-rule) has some very desirable theoretical properties. In addition, we present a case study based on Rivera et al. “ring of life” to explore the reconstructive power of the M- and Y-rule and also reanalyze an Arabidopsis thaliana data set.     

Rapoport's bathymetric rule and the latitudinal species diversity gradient for Northeast Pacific fishes and Northwest Atlantic gastropods: evidence against a causal link

Aim Few studies have explicitly considered the recurrent pattern of declining species diversity and increasing geographical range size that exists for numerous taxa across a variety of physical gradients. We extend Stevens’ [ Stevens, G.C. (1996) Journal of Biogeography, 23 , 149] work on Rapoport's bathymetric rule, using a more complete latitudinal assemblage of Northeast Pacific fishes and new data from Northwest Atlantic gastropods, to show that bathymetrical range size and species diversity are not causally linked. Location Fishes from the Northeast Pacific (0°–60° N) and gastropods from the Northwest Atlantic (0°–74° N) distributed from the surface to depths greater than 200 m. Methods Species pools were divided into three bathymetrical subgroups: (1) species restricted to shallow waters, between the surface and 200 m, (2) species that occurred in waters, both shallow and deep of 200 m, and (3) species restricted to waters deeper than 200 m. Median bathymetrical range size and total number of species were plotted against latitude (2° bins) using Stevens’ method, for the entire species pool and individual bathymetrical groups. Results For both fishes and gastropods, the apparent link between extratropical diversity and bathymetrical range size is an artefact resulting from the disproportionately high number of shallow restricted species in tropical latitudes, and the loss of these species in temperate latitudes. Furthermore, the extratropical gradient in gastropod diversity and bathymetrical range size are decoupled by approximately 15°, and while the latitudinal pattern for diversity is consistent across bathymetrical groups, median bathymetrical range size is highly irregular. Main conclusions These results suggests that functional groups can contribute disproportionately to patterns apparent at larger scales and that analysis of ecographical patterns by subregion is a novel approach that can help resolve debates over causality when patterns are seemingly coincident.     

Local Competition Between Foraging Relatives: Growth and Survival of Bruchid Beetle Larvae

Kin selection theory states that when resources are limited and all else is equal, individuals will direct competition away from kin. However, when competition between relatives is completely local, as is the case in granivorous insects whose larval stages spend their lives within a single seed, this can reduce or even negate the kin-selected benefits. Instead, an increase in competition may have the same detrimental effects on individuals that forage with kin as those that forage with non-kin. In a factorial experiment we assessed the effects of relatedness and competition over food on the survival and on fitness-related traits of the bruchid beetle Callosobruchus maculatus. Relatedness of competitors did not affect the survival of larvae. Larval survival substantially decreased with increasing larval density, and we found evidence that beetles maturing at a larger size were more adversely affected by competition, resulting in lower survival rates. Furthermore, females showed a reduction in their growth rate with increasing larval density, emerging smaller after the same development time. Males increased their growth rate, emerging earlier but at a similar size when food was more limited. Our results add to the growing number of studies that fail to show a relationship between relatedness and a reduction in competition between relatives in closed systems, and emphasize the importance of the scale at which competition between relatives occurs.     

Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection

High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared with its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low, because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation.     

Rapid evolution of great kiskadees on Bermuda: an assessment of the ability of the island rule to predict the direction of contemporary evolution in exotic vertebrates

Aim To determine whether an exotic bird species, the great kiskadee (Pitangus sulphuratus), has diverged in morphology from its native source population, and, if so, has done so in a manner predicted by the island rule. The island rule predicts that insular vertebrates will tend towards dwarfism or gigantism when isolated on islands, depending on their body size. For birds, the island rule predicts that species with body sizes below 70–120 g should increase in size. The great kiskadee has a mean mass of c. 60 g in its native range, therefore we predicted that it would increase in size within the exotic, and more insular, Bermudan range. Location The islands of Bermuda (exotic population) and Trinidad (native source population). Methods We took eight morphological measurements on 84 individuals captured in the exotic (Bermudan) population and 62 individuals captured in the native source (Trinidadian) population. We compared morphological metrics between populations using univariate and principal components analyses. We assessed whether the effects of genetic drift could explain observed differences in morphology. We calculated divergence rates in haldanes and darwins for comparison with published examples of contemporary evolution. Finally, we used mark–recapture analysis to determine the effects of the measured morphological characters on survivorship within the exotic Bermudan population. Results Individuals in the exotic Bermudan population have larger morphological dimensions than individuals in the native source population on Trinidad. The degree of divergence in body mass (g) and bill width (mm) is probably not due to genetic drift. This rate of divergence is nearly equal to that observed amongst well‐documented examples of contemporary bird evolution, and is within the mid‐range of rates reported across taxa. There is no clear effect of body size on survivorship as only one character (bill width) was found to have an influence on individual survivorship. Main conclusions Exotic species provide useful systems for examining evolutionary predictions over contemporary time‐scales. We found that divergence between the exotic and native populations of this bird species occurred over c. 17 generations, and was in the direction predicted by the island rule, a principle based on the study of native species.     

Ultrasound mediated efficient synthesis of new 4-oxoquinazolin-3(4H)-yl)furan-2-carboxamides as potent tyrosinase inhibitors: Mechanistic approach through chemoinformatics and molecular docking studies

We have carried out the synthesis of new 4-oxoquinazolin-3(4H)-yl)furan-2-carboxamide derivatives by the reaction between isatoic anhydride, 2-furoic hydrazide and substituted salicylaldehydes in ethanol: water (5:5 v/v) solvent system using p-TSA as a catalyst under ultrasound irradiation at room temperature. The structures of newly synthesized compounds were confirmed through spectral techniques such as IR, ¹H NMR, ¹³C NMR, and LCMS. The important features of this protocol include simple and easy workup procedure, reaction carried out at ambient temperature, use of ultrasound and high yield of oxoquinazolin-3(4H)-yl)furan-2-carboxamides in short reaction time. The synthesized compounds 4a–4j were screened against tyrosinase enzyme and all these compounds found to be potent inhibitors with much lower IC₅₀ value of 0.028 ± 0.016 to 1.775 ± 0.947 µM than the standard kojic acid (16.832 ± 1.162 µM). The kinetics mechanism for compound 4e was analyzed by Lineweaver-Burk plots which revealed that compound inhibited tyrosinase non-competitively by forming an enzyme-inhibitor complex. Along with this all the synthesized compounds (4a–4j) were scanned for their DPPH free radical scavenging ability. The outputs received through in vitro and in silico analysis are coherent to the each other with good binding energy values (kcal/mol) posed by synthesized ligands.     

Structural basis for the N‐degron specificity of ClpS1 from Arabidopsis thaliana

The N‐degron pathway determines the half‐life of proteins in both prokaryotes and eukaryotes by precisely recognizing the N‐terminal residue (N‐degron) of substrates. ClpS proteins from bacteria bind to substrates containing hydrophobic N‐degrons (Leu, Phe, Tyr, and Trp) and deliver them to the caseinolytic protease system ClpAP. This mechanism is preserved in organelles such as mitochondria and chloroplasts. Bacterial ClpS adaptors bind preferentially to Leu and Phe N‐degrons; however, ClpS1 from Arabidopsis thaliana (AtClpS1) shows a difference in that it binds strongly to Phe and Trp N‐degrons and only weakly to Leu. This difference in behavior cannot be explained without structural information due to the high sequence homology between bacterial and plant ClpS proteins. Here, we report the structure of AtClpS1 at 2.0 Å resolution in the presence of a bound N‐degron. The key determinants for α‐amino group recognition are conserved among all ClpS proteins, but the α3‐helix of eukaryotic AtClpS1 is significantly shortened, and consequently, a loop forming a pocket for the N‐degron is moved slightly outward to enlarge the pocket. In addition, amino acid replacement from Val to Ala causes a reduction in hydrophobic interactions with Leu N‐degron. A combination of the fine‐tuned hydrophobic residues in the pocket and the basic gatekeeper at the entrance of the pocket controls the N‐degron selectivity of the plant ClpS protein.