Comparative Genomics Identifies Putative Signatures of Sociality in Spiders

CALANGO: A phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species

Living species vary significantly in phenotype and genomic content. Sophisticated statistical methods linking genes with phenotypes within a species have led to breakthroughs in complex genetic diseases and genetic breeding. Despite the abundance of genomic and phenotypic data available for thousands of species, finding genotype-phenotype associations across species is challenging due to the non-independence of species data resulting from common ancestry. To address this, we present CALANGO (comparative analysis with annotation-based genomic components), a phylogeny-aware comparative genomics tool to find homologous regions and biological roles associated with quantitative phenotypes across species. In two case studies, CALANGO identified both known and previously unidentified genotype-phenotype associations. The first study revealed unknown aspects of the ecological interaction between Escherichia coli, its integrated bacteriophages, and the pathogenicity phenotype. The second identified an association between maximum height in angiosperms and the expansion of a reproductive mechanism that prevents inbreeding and increases genetic diversity, with implications for conservation biology and agriculture.

Genomic signatures of recent convergent transitions to social life in spiders

The transition from solitary to social life is a major phenotypic innovation, but its genetic underpinnings are largely unknown. To identify genomic changes associated with this transition, we compare the genomes of 22 spider species representing eight recent and independent origins of sociality. Hundreds of genes tend to experience shifts in selection during the repeated transition to social life. These genes are associated with several key functions, such as neurogenesis, behavior, and metabolism, and include genes that previously have been implicated in animal social behavior and human behavioral disorders. In addition, social species have elevated genome-wide rates of molecular evolution associated with relaxed selection caused by reduced effective population size. Altogether, our study provides unprecedented insights into the genomic signatures of social evolution and the specific genetic changes that repeatedly underpin the evolution of sociality. Our study also highlights the heretofore unappreciated potential of transcriptomics using ethanol-preserved specimens for comparative genomics and phylotranscriptomics.

Social complexity and brain evolution: insights from ant neuroarchitecture and genomics

Brain evolution is hypothesized to be driven by requirements to adaptively respond to environmental cues and social signals. Diverse models describe how sociality may have influenced eusocial insect-brain evolution, but specific impacts of social organization and other selective forces on brain architecture have been difficult to distinguish. Here, we evaluate predictions derived from and/or inferences made by models of social organization concerning the effects of individual and collective behavior on brain size, structure, and function using results of neuroanatomical and genomic studies. In contrast to the predictions of some models, we find that worker brains in socially complex species have great behavioral and cognitive capacity. We also find that colony size, the evolution of worker physical castes, and task specialization affect brain size and mosaicism, supporting the idea that sensory, processing and motor requirements for behavioral performance select for adaptive allometries of functionally specialized brain centers. We review available transcriptomic and comparative genomic studies seeking to elucidate the molecular pathways functionally associated with social life and the genetic changes that occurred during the evolution of social complexity. We discuss ways forward, using comparative neuroanatomy, transcriptomics, and comparative genomics, to distinguish among multiple alternative explanations for the relationship between the evolution of neural systems and social complexity.

Kin selection for cooperation in natural bacterial populations

Bacteria secrete many molecules outside the cell, where they provide benefits to other cells. One potential reason for producing these “public goods” is that they benefit closely related cells that share the gene for cooperation (kin selection). While many laboratory studies have supported this hypothesis, there is a lack of evidence that kin selection favors cooperation in natural populations. We examined bacterial genomes from the environment and used population genetics theory to analyze the DNA sequences. Our analyses suggest that public goods cooperation has indeed been favored by kin selection in natural populations.

Bacteria produce a range of molecules that are secreted from the cell and can provide a benefit to the local population of cells. Laboratory experiments have suggested that these “public goods” molecules represent a form of cooperation, favored because they benefit closely related cells (kin selection). However, there is a relative lack of data demonstrating kin selection for cooperation in natural populations of bacteria. We used molecular population genetics to test for signatures of kin selection at the genomic level in natural populations of the opportunistic pathogen Pseudomonas aeruginosa. We found consistent evidence from multiple traits that genes controlling putatively cooperative traits have higher polymorphism and greater divergence and are more likely to harbor deleterious mutations relative to genes controlling putatively private traits, which are expressed at similar rates. These patterns suggest that cooperative traits are controlled by kin selection, and we estimate that the relatedness for social interactions in P. aeruginosa is r = 0.84. More generally, our results demonstrate how molecular population genetics can be used to study the evolution of cooperation in natural populations.

Temporal Analysis of Effective Population Size and Mating System in a Social Wasp

Highly social species are successful because they cooperate in obligately integrated societies. We examined temporal genetic variation in the eusocial wasp Vespula maculifrons to gain a greater understanding of evolution in highly social taxa. First, we wished to test if effective population sizes of eusocial species were relatively low due to the reproductive division of labor that characterizes eusocial taxa. We thus estimated the effective population size of V. maculifrons by examining temporal changes in population allele frequencies. We sampled the genetic composition of a V. maculifrons population at 3 separate timepoints spanning a 13-year period. We found that effective population size ranged in the hundreds of individuals, which is similar to estimates in other, non-eusocial taxa. Second, we estimated levels of polyandry in V. maculifrons in different years to determine if queen mating system varied over time. We found no significant change in the number or skew of males mated to queens. In addition, mating skew was not significant within V. maculifrons colonies. Therefore, our data suggest that queen mate number may be subject to stabilizing selection in this taxon. Overall, our study provides novel insight into the selective processes operating in eusocial species by analyzing temporal genetic changes within populations.

Venom and Social Behavior: The Potential of Using Spiders to Evaluate the Evolution of Sociality under High Risk

Risks of sociality, including competition and conspecific aggression, are particularly pronounced in venomous invertebrates such as arachnids. Spiders show a wide range of sociality, with differing levels of cannibalism and other types of social aggression. To have the greatest chance of surviving interactions with conspecifics, spiders must learn to assess and respond to risk. One of the major ways risk assessment is studied in spiders is via venom metering, in which spiders choose how much venom to use based on prey and predator characteristics. While venom metering in response to prey acquisition and predator defense is well-studied, less is known about its use in conspecific interactions. Here we argue that due to the wide range of both sociality and venom found in spiders, they are poised to be an excellent system for testing questions regarding whether and how venom use relates to the evolution of social behavior and, in return, whether social behavior influences venom use and evolution. We focus primarily on the widow spiders, Latrodectus, as a strong model for testing these hypotheses. Given that successful responses to risk are vital for maintaining sociality, comparative analysis of spider taxa in which venom metering and sociality vary can provide valuable insights into the evolution and maintenance of social behavior under risk.

Genomic Signature of Shifts in Selection and Alkaline Adaptation in Highland Fish

Understanding how organisms adapt to aquatic life at high altitude is fundamental in evolutionary biology. This objective has been addressed primarily related to hypoxia adaptation by recent comparative studies, whereas highland fish has also long suffered extreme alkaline environment, insight into the genomic basis of alkaline adaptation has rarely been provided. Here, we compared the genomes or transcriptomes of 15 fish species, including two alkaline tolerant highland fish species and their six alkaline intolerant relatives, three alkaline tolerant lowland fish species, and four alkaline intolerant species. We found putatively consistent patterns of molecular evolution in alkaline tolerant species in a large number of shared orthologs within highland and lowland fish taxa. Remarkably, we identified consistent signatures of accelerated evolution and positive selection in a set of shared genes associated with ion transport, apoptosis, immune response, and energy metabolisms in alkaline tolerant species within both highland and lowland fish taxa. This is one of the first comparative studies that began to elucidate the consistent genomic signature of alkaline adaptation shared by highland and lowland fish. This finding also highlights the adaptive molecular evolution changes that support fish adapting to extreme environments at high altitude.

Comparative transcriptomics highlights convergent evolution of energy metabolic pathways in group-living spiders

Although widely thought to be aggressive, solitary, and potentially cannibalistic, some spider species have evolved group-living behaviors. The distinct transition provides the framework to uncover group-living evolution. Here, we conducted a comparative transcriptomic study and examined patterns of molecular evolution in two independently evolved group-living spiders and twelve solitary species. We report that positively selected genes among group-living spider lineages are significantly enriched in nutrient metabolism and autophagy pathways. We also show that nutrient-related genes of group-living spiders convergently experience amino acid substitutions and accelerated relative evolutionary rates. These results indicate adaptive convergence of nutrient metabolism that may ensure energy supply in group-living spiders. The decelerated evolutionary rate of autophagy-related genes in group-living lineages is consistent with an increased constraint on energy homeostasis as would be required in a group-living environment. Together, the results show that energy metabolic pathways play an important role in the transition to group-living in spiders.