Transcriptomic Analysis Pipeline (TAP) for quality control and functional assessment of transcriptomes.

Background: RNA-sequencing (RNA-seq) has revolutionized the exploration of biological mechanisms, shedding light on the roles of non-coding RNAs, including long non-coding RNAs (lncRNAs), across various biological processes, including stress responses. Despite these advancements, there remains a gap in our understanding of the implications of different RNA-seq library protocols on comprehensive lncRNA expression analysis, particularly in non-mammalian organisms.

Results: In this study, we sought to bridge this knowledge gap by investigating lncRNA expression patterns in under thermal stress conditions.

Population genomics supports multiple hybrid zone origins of socially hybridogenetic lineages of Pogonomyrmex harvester ants.

Reproductive division of labor in the social insects is typically determined by environmental cues; however, genetic effects on caste have been discovered in a growing set of ant taxa. An extreme form of genetic caste determination is "social hybridogenesis," in which co-occurring genetic lineages obligately interbreed to produce workers, whereas daughter queens are of pure-lineage ancestry. In this study, we tested the hypothesis that social hybridogenesis in the genus Pogonomyrmex resulted from one or more interspecific hybridization events, and if so, whether individual lineages were of hybrid ancestry.

Insights from a comprehensive study of Trypanosoma cruzi: A new mitochondrial clade restricted to North and Central America and genetic structure of TcI in the region.

More than 100 years since the first description of Chagas Disease and with over 29,000 new cases annually due to vector transmission (in 2010), American Trypanosomiasis remains a Neglected Tropical Disease (NTD). This study presents the most comprehensive Trypanosoma cruzi sampling in terms of geographic locations and triatomine species analyzed to date and includes both nuclear and mitochondrial genomes. This addresses the gap of information from North and Central America.

Integrating GWAS and Transcriptomics to Identify the Molecular Underpinnings of Thermal Stress Responses in .

Thermal tolerance of an organism depends on both the ability to dynamically adjust to a thermal stress and preparatory developmental processes that enhance thermal resistance. However, the extent to which standing genetic variation in thermal tolerance alleles influence dynamic stress responses vs. preparatory processes is unknown.

Trade-Offs in Cold Resistance at the Northern Range Edge of the Common Woodland Ant (Formicidae).

Geographic variation in low temperatures at poleward range margins of terrestrial species often mirrors population variation in cold resistance, suggesting that range boundaries may be set by evolutionary constraints on cold physiology. The northeastern woodland ant occurs up to approximately 45°N in central Maine. We combined presence/absence surveys with classification tree analysis to characterize its northern range limit and assayed two measures of cold resistance operating on different timescales to determine whether and how marginal populations adapt to environmental extremes.

Residual survival and local dispersal drive reinfestation by Triatoma dimidiata following insecticide application in Guatemala.

Chagas disease is caused by the protozoan parasite Trypanosoma cruzi and transmitted by triatomine insect vectors. In Guatemala, insecticide spraying is an integral part of management of the main vector, Triatoma dimidiata. Spraying typically has low efficacy, which may be due to incomplete elimination from infested houses, within-village dispersal, or influx from other villages or sylvan environments.

Correction: A single Danio rerio hars gene encodes both cytoplasmic and mitochondrial histidyl-tRNA synthetases.

[This corrects the article DOI: 10.1371/journal.pone.

Vectors of diversity: Genome wide diversity across the geographic range of the Chagas disease vector Triatoma dimidiata sensu lato (Hemiptera: Reduviidae).

To date, the phylogeny of Triatoma dimidiata sensu lato (s. l.) (Hemiptera: Reduviidae: Triatominae), the epidemiologically most important Chagas disease vector in Central America and a secondary vector in Mexico and northern South America, has only been investigated by one multi-copy nuclear gene (Internal Transcribed Spacer - 2) and a few mitochondrial genes.

A single Danio rerio hars gene encodes both cytoplasmic and mitochondrial histidyl-tRNA synthetases.

Histidyl tRNA Synthetase (HARS) is a member of the aminoacyl tRNA synthetase (ARS) family of enzymes. This family of 20 enzymes is responsible for attaching specific amino acids to their cognate tRNA molecules, a critical step in protein synthesis. However, recent work highlighting a growing number of associations between ARS genes and diverse human diseases raises the possibility of new and unexpected functions in this ancient enzyme family.

Heat tolerance predicts the importance of species interaction effects as the climate changes.

Few studies have quantified the relative importance of direct effects of climate change on communities versus indirect effects that are mediated thorough species interactions, and the limited evidence is conflicting. Trait-based approaches have been popular in studies of climate change, but can they be used to estimate direct versus indirect effects? At the species level, thermal tolerance is a trait that is often used to predict winners and losers under scenarios of climate change. But thermal tolerance might also inform when species interactions are likely to be important because only subsets of species will be able to exploit the available warmer climatic niche space, and competition may intensify in the remaining, compressed cooler climatic niche space.

Effects of desiccation and starvation on thermal tolerance and the heat-shock response in forest ants.

Temperature increases associated with global climate change are likely to be accompanied by additional environmental stressors such as desiccation and food limitation, which may alter how temperature impacts organismal performance. To investigate how interactions between stressors influence thermal tolerance in the common forest ant, Aphaenogaster picea, we compared the thermal resistance of workers to heat shock with and without pre-exposure to desiccation or starvation stress. Knockdown (KD) time at 40.

Climatic warming destabilizes forest ant communities.

How will ecological communities change in response to climate warming? Direct effects of temperature and indirect cascading effects of species interactions are already altering the structure of local communities, but the dynamics of community change are still poorly understood. We explore the cumulative effects of warming on the dynamics and turnover of forest ant communities that were warmed as part of a 5-year climate manipulation experiment at two sites in eastern North America. At the community level, warming consistently increased occupancy of nests and decreased extinction and nest abandonment.

Thermal reactionomes reveal divergent responses to thermal extremes in warm and cool-climate ant species.

Background: The distributions of species and their responses to climate change are in part determined by their thermal tolerances. However, little is known about how thermal tolerance evolves. To test whether evolutionary extension of thermal limits is accomplished through enhanced cellular stress response (enhanced response), constitutively elevated expression of protective genes (genetic assimilation) or a shift from damage resistance to passive mechanisms of thermal stability (tolerance), we conducted an analysis of the reactionome: the reaction norm for all genes in an organism's transcriptome measured across an experimental gradient.

The evolution of heat shock protein sequences, cis-regulatory elements, and expression profiles in the eusocial Hymenoptera.

Background: The eusocial Hymenoptera have radiated across a wide range of thermal environments, exposing them to significant physiological stressors. We reconstructed the evolutionary history of three families of Heat Shock Proteins (Hsp90, Hsp70, Hsp40), the primary molecular chaperones protecting against thermal damage, across 12 Hymenopteran species and four other insect orders. We also predicted and tested for thermal inducibility of eight Hsps from the presence of cis-regulatory heat shock elements (HSEs).

Inter-genomic sexual conflict drives antagonistic coevolution in harvester ants.

The reproductive interests of males and females are not always aligned, leading to sexual conflict over parental investment, rate of reproduction and mate choice. Traits that increase the genetic interests of one sex often occur at the expense of the other, selecting for counter-adaptations leading to antagonistic coevolution. Reproductive conflict is not limited to intraspecific interactions; interspecific hybridization can produce pronounced sexual conflict between males and females of different species, but it is unclear whether such conflict can drive sexually antagonistic coevolution between reproductively isolated genomes.

A novel family of terminal-repeat retrotransposon in miniature (TRIM) in the genome of the red harvester ant, Pogonomyrmex barbatus.

We report the first described non-plant family of TRIMs (terminal-repeat retrotransposons in miniature), which are small nonautonomous LTR retrotransposons, from the whole-genome sequence of the red harvester ant, Pogonomyrmex barbatus (Hymenoptera: Myrmicinae). Members of this retrotransposon family, named PbTRIM, have typical features of plant TRIMs in length and structure, although they share no overall sequence similarity. PbTRIM elements and their solo-LTRs are abundant in the host genome and exhibit an uneven distribution pattern.

Intergenerational effect of juvenile hormone on offspring in Pogonomyrmex harvester ants.

Parents can influence the phenotypes of their offspring via a number of mechanisms. In harvester ants, whether female progeny develop into workers or daughter queens is strongly influenced by the age and temperature conditions experienced by their mother, which is associated with variation in maternal ecdysteroid deposition in fertilized eggs. In many insects, juvenile hormone (JH) is antagonistic to ecdysteroid release, suggesting that seasonal and age-based variation in maternal JH titers may explain maternal effects on offspring size and reproductive caste.

Mechanisms of reproductive isolation between an ant species of hybrid origin and one of its parents.

The establishment of new species by hybridization is difficult because it requires the development of reproductive isolation (RI) in sympatry to escape the homogenizing effects of gene flow from the parental species. Here we investigated the role of two pre- and two postzygotic mechanisms of RI in a system comprising two interdependent Pogonomyrmex harvester ant lineages (the H1 and H2 lineages) of hybrid origin and one of their parental species (P. rugosus).

Two alternate mechanisms contribute to the persistence of interdependent lineages in Pogonomyrmex harvester ants.

Some populations of Pogonomyrmex harvester ants comprise pairs of highly differentiated lineages with queens mating at random with several males of their own and of the alternate lineage. These queens produce two types of diploid offspring, those fertilized by males of the queens' lineage which develop into new queens and those fertilized by males of the other lineage which mostly develop into functionally sterile workers. This unusual mode of genetic caste determination has been found in 26 populations and a total of four lineage pairs (F(1)-F(2), G(1)-G(2), H(1)-H(2) and J(1)-J(2)) have been described in these populations.

Characterization and distribution of Pogonomyrmex harvester ant lineages with genetic caste determination.

Genetic caste determination has been described in two populations of Pogonomyrmex harvester ants, each comprising a pair of interbreeding lineages. Queens mate with males of their own and of the alternate lineage and produce two types of diploid offspring, those fertilized by males of the queens' lineage which develop into queens and those fertilized by males of the other lineage which develop into workers. Each of the lineages has been shown to be itself of hybrid origin between the species Pogonomyrmex barbatus and Pogonomyrmex rugosus, which both have typical, environmentally determined caste differentiation.

Behavioral differences between Pogonomyrmex rugosus and dependent lineage (H1/H2) harvester ants.

The discovery of genetic caste determination (GCD) in populations of Pogonomyrmex harvester ants raises many questions about the evolution and persistence of such populations. The genetic caste determination arises from the existence of two distinct, but mutually dependent, genetic lineages within a population. Workers always develop from a combination of the two lineages, but their sister queens develop from within-lineage matings.

Reproductive isolation between Pogonomyrmex rugosus and two lineages with genetic caste determination.

Hybrid speciation occurs when combination of two interspecific genomes results in individuals that are of high fitness but reproductively incompatible with the parental species. Although hybrid speciation is a relatively common source of new species in plants, it appears to be a much rarer occurrence in animal taxa. Here we report on reproductive isolation and range overlap between the rough harvester ant Pogonomyrmex rugosus and two lineages with hybrid genotypes (H 1 and H2).

Loss of phenotypic plasticity generates genotype-caste association in harvester ants.

Caste differentiation and reproductive division of labor are the hallmarks of insect societies. In ants and other social Hymenoptera, development of female larvae into queens or workers generally results from environmentally induced differences in gene expression. However, several cases in which certain gene combinations may determine reproductive status have been described in bees and ants.

An hypothesis-driven, molecular phylogenetics exercise for college biology students.

This hypothesis-driven laboratory exercise teaches how DNA evidence can be used to investigate an organism's evolutionary history while providing practical modeling of the fundamental processes of gene transcription and translation. We used an inquiry-based approach to construct a laboratory around a nontrivial, open-ended evolutionary question about the relationship of five species of Drosophila. In the course of answering this question, students at the early college biology level learn how the information in DNA can be extracted and used by both the cell and scientists.