ALBERT

Description: Transposable elements, once described by Barbara McClintock as controlling genetic units, not only occupy the largest part of our genome but are also a prominent moving force of genomic plasticity and innovation. They usually replicate and reintegrate into genomes silently, sometimes causing malfunctions or misregulations, but occasionally millions of years later, a few may evolve into new functional units. Retrotransposons make their way into the genome following reverse transcription of RNA molecules and chromosomal insertion. In therian mammals, long interspersed elements 1 (LINE1s) self-propagate but also coretropose many RNAs, including mRNAs and small RNAs that usually exhibit an oligo(A) tail. The revitalization of specific LINE1 elements in the mammalian lineage about 150 Ma parallels the rise of many other nonautonomous mobilized genomic elements. We previously identified and described hundreds of tRNA-derived retropseudogenes missing characteristic oligo(A) tails consequently termed tailless retropseudogenes. Additional analyses now revealed hundreds of thousands of tailless retropseudogenes derived from nearly all types of RNAs. We extracted 2,402 perfect tailless sequences (with discernible flanking target site duplications) originating from tRNAs, spliceosomal RNAs, 5S rRNAs, 7SK RNAs, mRNAs, and others. Interestingly, all are truncated at one or more defined positions that coincide with internal single-stranded regions. 5S ribosomal and U2 spliceosomal RNAs were analyzed in the context of mammalian phylogeny to discern the origin of the therian LINE1 retropositional system that evolved in our 150-Myr-old ancestor.

Description: Presence/absence patterns of retroposon insertions at orthologous genomic loci constitute straightforward markers for phylogenetic or population genetic studies. In birds, the convenient identification and utility of these markers has so far been mainly restricted to the lineages leading to model birds (i.e., chicken and zebra finch). We present an easy-to-use, rapid, and cost-effective method for the experimental isolation of chicken repeat 1 (CR1) insertions from virtually any bird genome and potentially nonavian genomes. The application of our method to the little grebe genome yielded insertions belonging to new CR1 subfamilies that are scattered all across the phylogenetic tree of avian CR1s. Furthermore, presence/absence analysis of these insertions provides the first retroposon evidence grouping flamingos + grebes as Mirandornithes and several markers for all subsequent branching events within grebes (Podicipediformes). Five markers appear to be species-specific insertions, including the hitherto first evidence in birds for biallelic CR1 insertions that could be useful in future population genetic studies.

Description: The Australian numbat, Myrmecobius fasciatus , is the only marsupial that feeds almost exclusively on termites and that has a life following the diurnally restricted and dynamic geographical distribution of termites. The millions of years of this adaptation led to unique morphological and anatomical features, especially basicranial and dental characteristics, that make it difficult to identify a clear phylogenetic affiliation to other marsupials. From DNA sequence analyses, the family Myrmecobiidae is placed within the dasyuromorph marsupials, but the exact position varies from study to study, and support values are mostly rather modest. Here, we report the recovery and analysis of approximately 110,000 quasifossilized traces of mobile element insertions into the genome of a dasyurid marsupial (Tasmanian devil), 25 of which are phylogenetically informative for early dasyuromorphial evolution. Fourteen of these ancient retroposon insertions are shared by the 16 Dasyuromorphia species analyzed, including the numbat, but are absent in the outgroups. An additional 11 other insertions are present in all Dasyuridae but are absent in the numbat. These findings place numbats as the sister group to all living Dasyuridae and show that the investigated Dasyuromorphia, including the Myrmecobiidae, constitutes a monophyletic group that is separated from Peramelemorphia, Notoryctemorphia, and other marsupials.

Description: Understanding the impacts of invasive species requires placing invasion within a full community context. Plant invaders are often considered in the context of herbivores that may drive invasion by avoiding invaders while consuming natives (enemy escape), or inhibit invasion by consuming invaders (biotic resistance). However, predators that attack those herbivores are rarely considered as major players in invasion. Invasive plants often promote predators, generally by providing improved habitat. Here, we show that predator-promoting invaders may initiate a negative feedback loop that inhibits invasion. By enabling top-down control of herbivores, predator-promoting invaders lose any advantage gained through enemy escape, indirectly favoring natives. In cases where palatable invaders encounter biotic resistance, predator promotion may allow an invader to persist, but not dominate. Overall, results indicate that placing invaders in a full community context may reveal reduced impacts of invaders compared to expectations based on simple plant–plant or plant–herbivore subsystems. Understanding the impacts of invasive species requires placing invasion within a full community context. Invasive plants often promote predators, generally by providing improved habitat. Here, we show that predator-promoting invaders may initiate a negative feedback loop that inhibits invasion.

Description: Prey at risk of predation may experience stress and respond physiologically by altering their metabolic rates. Theory predicts that such physiological changes should alter prey nutrient demands from N-rich to C-rich macronutrients and shift the balance between maintenance and growth/reproduction. Theory further suggests that for ectotherms, temperature stands to exacerbate this stress. Yet, the interactive effects of predation stress and temperature stress on diet, metabolism, and survival of ectotherms are not well known. This knowledge gap was addressed with a laboratory study in which wild juvenile grasshoppers were collected, assigned to one of three groups, and raised at three different temperatures. All grasshoppers had access to equal quantities of two diets composed of opposite carbohydrate:protein ratios. Half of the individuals in each temperature group were exposed to predation risk cues from spider predators, while the other half were kept in risk free conditions. Grasshoppers consumed more carbohydrates when exposed to predation risk, but consumption favored greater protein intake as temperature increased. Moreover, the difference in carbohydrate intake between risk cue and risk free treatments diminished as temperature increased. Furthermore, variability between individual consumption patterns both within and between treatments decreased markedly as temperature increased, suggesting that higher temperatures promote more consistent individual consumption behaviors. Grasshoppers grew faster and larger as temperature increased, which translated into higher survival rates at higher temperatures. Warmer grasshoppers also did not alter their metabolic rates in response to predation risk cues, in contrast to colder grasshoppers. Digestive efficiency increased with temperature as well, further indicating that lower temperatures were much more stressful than higher temperatures for grasshoppers. The study shows that physiological responses of ectothermic herbivores to predation stress are highly plastic and temperature dependent, with higher temperatures promoting increased protein intake, growth, development, survival, and digestive efficiency relative to colder temperatures. These findings help to reconcile why dietary responses (proportion of protein vs. carbohydrate intake) to predation stress may vary among different prey taxa studied previously. This article is protected by copyright. All rights reserved.

Description: Climate change is expected to cause geographic redistributions of species. To the extent that species within assemblages have different niche requirements, assemblages may no longer remain intact and dis- and reassemble at current or new geographic locations. We explored how climate change projected by 2100 may transform the world's avian assemblages (characterized at a 110 km spatial grain) by modelling environmental niche-based changes to their dietary guild structure under 0 km, 500 km, and 2000 km dispersal distances. We examined guild structure changes at coarse (primary, high-level, and mixed consumers) and fine (frugivores, nectarivores, insectivores, herbivores, granivores, scavengers, omnivores, and carnivores) ecological resolutions to determine whether or not geographic co-occurrence patterns among guilds were associated with the magnitude to which guilds are functionally resolved. Dietary guilds vary considerably in their global geographic prevalence, and under broad-scale niche-based redistribution of species, these are projected to change very heterogeneously. A non-dispersal assumption results in the smallest projected changes to guild assemblages, but with significant losses for some regions and guilds, such as South American insectivores. Longer dispersal distances are projected to cause greater degrees of disassembly, and lead to greater homogenization of guild composition, especially in northern Asia and Africa. This arises because projected range gains and losses result in geographically heterogeneous patterns of guild compensation. Projected decreases especially of primary and mixed consumers most often are compensated by increases in high-level consumers, with increasing uncertainty about these outcomes as dispersal distance and degree of guild functional resolution increases. Further exploration into the consequences of these significant broad-scale ecological functional changes at the community or ecosystem level should be increasingly on the agenda for conservation science. This article is protected by copyright. All rights reserved.

Description: Testing for conserved and novel mechanisms underlying phenotypic evolution requires a diversity of genomes available for comparison spanning multiple independent lineages. For example, complex social behavior in insects has been investigated primarily with eusocial lineages, nearly all of which are Hymenoptera. If conserved genomic influences on sociality do exist, we need data from a wider range of taxa that also vary in their levels of sociality. Here, we present the assembled and annotated genome of the subsocial beetle Nicrophorus vespilloides , a species long used to investigate evolutionary questions of complex social behavior. We used this genome to address two questions. First, do aspects of life history, such as using a carcass to breed, predict overlap in gene models more strongly than phylogeny? We found that the overlap in gene models was similar between N. vespilloides and all other insect groups regardless of life history. Second, like other insects with highly developed social behavior but unlike other beetles, does N. vespilloides have DNA methylation? We found strong evidence for an active DNA methylation system. The distribution of methylation was similar to other insects with exons having the most methylated CpGs. Methylation status appears highly conserved; 85% of the methylated genes in N. vespilloides are also methylated in the hymentopteran Nasonia vitripennis . The addition of this genome adds a coleopteran resource to answer questions about the evolution and mechanistic basis of sociality and to address questions about the potential role of methylation in social behavior.

Description: Ecology, Volume 99, Issue 10, Page 2412-2413, October 2018. 〈br/〉