The importance of considering age when quantifying wild animals' welfare.

Wild animals experience different challenges and opportunities as they mature, and this variety of experiences can lead to different levels of welfare characterizing the day-to-day lives of individuals of different ages. At the same time, most wild animals who are born do not survive to adulthood. Individuals who die as juveniles do not simply experience a homogeneous fraction of the lifetimes of older members of their species; rather, their truncated lives may be characterized by very different levels of welfare. Here, I propose the concept of welfare expectancy as a framework for quantifying wild animal welfare at a population level, given individual-level data on average welfare with respect to age. This concept fits conveniently alongside methods of analysis already used in population ecology, such as demographic sensitivity analysis, and is applicable to evaluating the welfare consequences of human interventions and natural pressures that disproportionately affect individuals of different ages. In order to understand better and improve the state of wild animal welfare, more attention should be directed towards young animals and the particular challenges they face.

Assessing the evolutionary persistence of ecological relationships: A review and preview.

Species interactions, such as pollination, parasitism and predation, form the basis of functioning ecosystems. The origins and resilience of such interactions therefore merit attention. However, fossils only occasionally document ancient interactions, and phylogenetic methods are blind to recent interactions. Is there some other way to track shared species experiences? "Comparative demography" examines when pairs of species jointly thrived or declined. By forging links between ecology, epidemiology, and evolutionary biology, this method sheds light on biological adaptation, species resilience, and ecosystem health. Here, we describe how this method works, discuss examples, and suggest future directions in hopes of inspiring interest, imitators, and critics.

Comparative demography elucidates the longevity of parasitic and symbiotic relationships.

Parasitic and symbiotic relationships govern vast nutrient and energy flows, yet controversy surrounds their longevity. Enduring relationships may engender parallel phylogenies among hosts and parasites, but so may ephemeral relationships when parasites colonize related hosts. An understanding of whether symbiont and host populations have grown and contracted in concert would be useful when considering the temporal durability of these relationships. Here, we devised methods to compare demographic histories derived from genomic data. We compared the historical growth of the agent of severe human malaria, Plasmodium falciparum, and its mosquito vector, Anopheles gambiae, to human and primate histories, thereby discerning long-term parallels and anthropogenic population explosions. The growth history of Trichinella spiralis, a zoonotic parasite disseminated by swine, proved regionally specific, paralleling distinctive growth histories for wild boar in Asia and Europe. Parallel histories were inferred for an anemone and its algal symbiont (Exaiptasia pallida and Symbiodinium minutum). Concerted growth in potatoes and the agent of potato blight (Solanum tuberosum and Phytophthora infestans) did not commence until the age of potato domestication. Through these examples, we illustrate the utility of comparative historical demography as a new exploratory tool by which to interrogate the origins and durability of myriad ecological relationships. To facilitate future use of this approach, we introduce a tool called C-PSMC to align and evaluate the similarity of demographic history curves.

Hybridization is limited between two lineages of freeze-resistant Trichinella during coinfection in a mouse model.

Hybridization between two closely related but distinct genetic lineages may lead to homogenization of the two lineages with potentially novel phenotypes, or selective pressure to avoid hybridization if the two lineages are truly distinct. Trichinella nativa and Trichinella T6 are zoonotic nematode parasites which can be distinguished genetically despite occasional hybridization. Here, using an experimental murine model, we attempt to determine whether there are barriers to hybridization when sizeable numbers of each lineage are allowed to coinfect a host. Two mice were independently infected with equal numbers of T. nativa and T6. The offspring of these coinfections were genotyped at two microsatellite loci and one mitochondrial locus capable of distinguishing T. nativa from T6 genotypes. Among larvae in the F1 generation, offspring of every possible mating were encountered. Most larvae (63.6%) derived from T. nativa×T. nativa matings, while 21.1% of offspring were the product of T6×T6 matings, and only 15.3% were hybrid offspring of T. nativa×T6 crosses, differing markedly from null expectations. In this experimental model, T. nativa and Trichinella T6 were able to mate, but ratios of offspring indicated pre- or post-zygotic barriers to hybridization that may include assortative mating, genetic incompatibilities, and/or differences in the fitness of offspring. These barriers would limit gene flow between these two lineages in a natural setting, serving as a barrier to their homogenization and promoting their persistence as distinct and separate entities.

The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A*0201 and B*27.

In silico tools are employed to examine the evolutionary relationship to possible vaccine peptide candidates' development. This perspective sheds light on the proteomic changes affecting the creation of HLA specific T-cell stimulating peptide vaccines for HIV. Full-length sequences of the envelope protein of the HIV subtypes A, B, C and D were obtained through the NCBI Protein database were aligned using CLUSTALW. They were then analyzed using RANKPEP specific to Human Leukocyte Antigen A*02 and B*27. Geneious was used to catalogue the collected gp160 sequences and to construct a phylogenic tree. Mesquite was employed for ancestral state reconstruction to infer the order of amino acid substitutions in the epitopes examined. The results showed that consensus peptide identified SLAEKNITI had changes that indicated predicted escape mutation in strains of HIV responding to pressure exerted by CD8+ cells expressing HLA A*02. The predominating 9-mers IRIGPGQAF of gp120 are significantly less immunogenic toward HLA B*27 than to HLA A*02. The data confirms previous findings on the importance for efficacious binding, of an arginine residue at the 2(nd) position of the gag SL9 epitope, and extends this principle to other epitopes which interacts with HLA B*27. This study shows that the understanding of viral evolution relating T-cell peptide vaccine design is a development that has much relevance for the creation of personalized therapeutics for HIV treatment.