Tree shape‐based approaches for the comparative study of cophylogeny

Cophylogeny is the congruence of phylogenetic relationships between two different groups of organisms due to their long‐term interaction. We investigated the use of tree shape distance measures to quantify the degree of cophylogeny. We implemented a reverse‐time simulation model of pathogen phylogenies within a fixed host tree, given cospeciation probability, host switching, and pathogen speciation rates. We used this model to evaluate 18 distance measures between host and pathogen trees including two kernel distances that we developed for labeled and unlabeled trees, which use branch lengths and accommodate different size trees. Finally, we used these measures to revisit published cophylogenetic studies, where authors described the observed associations as representing a high or low degree of cophylogeny. Our simulations demonstrated that some measures are more informative than others with respect to specific coevolution parameters especially when these did not assume extreme values. For real datasets, trees’ associations projection revealed clustering of high concordance studies suggesting that investigators are describing it in a consistent way. Our results support the hypothesis that measures can be useful for quantifying cophylogeny. This motivates their usage in the field of coevolution and supports the development of simulation‐based methods, i.e., approximate Bayesian computation, to estimate the underlying coevolutionary parameters.     

Heme binding properties of heterologously expressed spinach cytochrome b(6): implications for transmembrane b-type cytochrome formation

In vivo and in vitro requirements for the formation of cytochrome b(6) were examined to analyze the mechanisms of transmembrane b-type cytochrome formation. After heterologous expression of spinach cytochrome b(6), formation of the holo-cytochrome was observed within the E. coli inner membrane. The transmembrane orientation of cytochrome b(6) appeared not to be critical for heme binding and holo-cytochrome formation. Furthermore, in vitro reconstitution of cytochrome b(6) was possible under oxidizing as well as under reducing conditions. Taken together these observations strongly indicate that transmembrane b-type cytochromes can spontaneously assemble in vitro as well as in a membrane.     

Linking increasing drought stress to Scots pine mortality and bark beetle infestations

In the dry Swiss Rhone Valley, Scots pine forests have experienced increased mortality in recent years. It has commonly been assumed that drought events and bark beetles fostered the decline, however, whether bark beetle outbreaks increased in recent years and whether they can be linked to drought stress or increasing temperature has never been studied. In our study, we correlated time series of drought indices from long-term climate stations, 11-year mortality trends from a long-term research plot, and mortality probabilities modeled from tree rings (as an indicator of tree vitality) with documented occurrences of various bark beetle species and a buprestid beetle, using regional Forest Service reports from 1902 to 2003 and advisory cases of the Swiss Forest Protection Service (SFPS) from 1984 to 2005. We compared the historical findings with measured beetle emergence from a 4-year tree felling and breeding chamber experiment. The documented beetle-related pine mortality cases increased dramatically in the 1990s, both in the forest reports and the advisory cases. The incidents of beetle-related pine mortality correlated positively with spring and summer temperature, and with the tree-ring based mortality index, but not with the drought index. The number of advisory cases, on the other hand, correlated slightly with summer drought index and temperature, but very highly with tree-ring-based mortality index. The tree-ring-based mortality index and observed tree mortality increased in years following drought. This was confirmed by the beetle emergences from felled trees. Following dry summers, more than twice as many trees were colonized by beetles than following wet summers. We conclude that increased temperatures in the Swiss Rhone Valley have likely weakened Scots pines and favored phloeophagous beetle population growth. Beetles contributed to the increased pine mortality following summer drought. Among the factors not addressed in this study, changed forest use may have also contributed to increased beetle populations and Scots pine mortality, whereas air pollution seems to be of lesser importance.     

Recalculating route: dispersal constraints will drive the redistribution of Amazon primates in the Anthropocene

Climate change will redistribute the global biodiversity in the Anthropocene. As climates change, species might move from one place to another, due to local extinctions and colonization of new environments. However, the existence of permeable migratory routes precedes faunal migrations in fragmented landscapes. Here, we investigate how dispersal will affect the outcome of climate change on the distribution of Amazon's primate species. We modeled the distribution of 80 Amazon primate species, using ecological niche models, and projected their potential distribution on scenarios of climate change. Then, we imposed landscape restrictions to primate dispersal, derived from a natural biogeographical barrier to primates (the main tributaries of the Amazon river) and an anthropogenic constraint to the migration of many canopy‐dependent animals (deforested areas). We also highlighted potential conflict zones, i.e. regions of high migration potential but predicted to be deforested. Species response to climate change varied across dispersal limitation scenarios. If species could occupy all newly suitable climate, almost 70% of species could expand ranges. Including dispersal barriers (natural and anthropogenic), however, led to range expansion in only less than 20% of the studied species. When species were not allowed to migrate, all of them lost an average of 90% of the suitable area, suggesting that climate may become unsuitable within their present distributions. All Amazon primate species may need to move as climate changes to avoid deleterious effects of exposure to non‐analog climates. The effect of climate change on the distribution of Amazon primates will ultimately depend on whether landscape permeability will allow climate‐driven faunal migrations. The network of protected areas in the Amazon could work as ‘stepping stones’ but most are outside important migratory routes. Therefore, protecting important dispersal corridors is foremost to allow effective migrations of the Amazon fauna in face of climate change and deforestation.     

Haplotypes of single cancer driver genes and their local ancestry in a highly admixed long-lived population of Northeast Brazil

Admixed populations have not been examined in detail in cancer genetic studies. Here, we inferred the local ancestry of cancer-associated single nucleotide polymorphisms (SNPs) and haplotypes of a highly admixed Brazilian population. SNP array was used to genotype 73 unrelated individuals aged 80-102 years. Local ancestry inference was performed by merging genotyped regions with phase three data from the 1000 Genomes Project Consortium using RFmix. The average ancestry tract length was 9.12-81.71 megabases. Strong linkage disequilibrium was detected in 48 haplotypes containing 35 SNPs in 10 cancer driver genes. All together, 19 risk and eight protective alleles were identified in 23 out of 48 haplotypes. Homozygous individuals were mainly of European ancestry, whereas heterozygotes had at least one Native American and one African ancestry tract. Native-American ancestry for homozygous individuals with risk alleles for HNF1B, CDH1, and BRCA1 was inferred for the first time. Results indicated that analysis of SNP polymorphism in the present admixed population has a high potential to identify new ancestry-associated alleles and haplotypes that modify cancer susceptibility differentially in distinct human populations. Future case-control studies with populations with a complex history of admixture could help elucidate ancestry-associated biological differences in cancer incidence and therapeutic outcomes.     

Interference between Proteins Hap46 and Hop/p60, Which Bind to Different Domains of the Molecular Chaperone hsp70/hsc70

Several structurally divergent proteins associate with molecular chaperones of the 70-kDa heat shock protein (hsp70) family and modulate their activities. We investigated the cofactors Hap46 and Hop/p60 and the effects of their binding to mammalian hsp70 and the cognate form hsc70. Hap46 associates with the amino-terminal ATP binding domain and stimulates ATP binding two- to threefold but inhibits binding of misfolded protein substrate to hsc70 and reactivation of thermally denatured luciferase in an hsc70-dependent refolding system. By contrast, Hop/p60 interacts with a portion of the carboxy-terminal domain of hsp70s, which is distinct from that involved in the binding of misfolded proteins. Thus, Hop/p60 and substrate proteins can form ternary complexes with hsc70. Hop/p60 exerts no effect on ATP and substrate binding but nevertheless interferes with protein refolding. Even though there is no direct interaction between these accessory proteins, Hap46 inhibits the binding of Hop/p60 to hsc70 but Hop/p60 does not inhibit the binding of Hap46 to hsc70. As judged from respective deletions, the amino-terminal portions of Hap46 and Hop/p60 are involved in this interference. These data suggest steric hindrance between Hap46 and Hop/p60 during interaction with distantly located binding sites on hsp70s. Thus, not only do the major domains of hsp70 chaperones communicate with each other, but cofactors interacting with these domains affect each other as well.     

Habitat Use and Diet of Baird's Tapirs (Tapirus bairdii) in a Montane Cloud Forest of the Cordillera de Talamanca, Costa Rica1

Results from 24 transects showed that tapirs were less abundant in areas with higher human presence. They also preferred less steep areas, especially as browsing sites. An analysis of feces showed that fibers were the largest component (40–55%) followed by leaves (10–30%) and twigs (15%). Bamboo (Chusquea spp.) was found in all samples and probably accounts for the high proportion of fibers. Twenty‐seven plant species were identified to be eaten by tapirs.