Much like neighboring nations, living in close proximity can often lead to conflict over limited resources for social insect colonies. As with warring nations, conflicts among insect societies can also result in one colony attempting to invade the other. Though emigrations are common and well understood in social insects, the process of emigration in the context of conflict is not known. During emigrations of the ant Temnothorax rugatulus, colonies first employ the use of scouts, who search for new nest locations. These scouts then recruit naïve workers to these nests resulting in a ‘voting’ process through which colonies can collectively choose the best nest site. Once the decision is made, the selected nest is rapidly populated by workers who physically carry the queen(s), brood, and remaining naïve ants to the new nest. Invasions occurring during inter-colony conflicts bear a striking resemblance to this process. The state of the final nest suggested merged colonies, and statistical models were used to test for the likelihood of this. Here we test whether colonies of T. rugatulus use the same mechanisms during invasions as those used in emigrations by observing conflicts between colonies of T. rugatulus ants and tracking instances of scouting and recruitment, transport and changes in populations in each nest. Our results support the predicted order of behaviors starting with scouting, followed by recruitment and transport last. In addition, presence of the quorum rule, which determines the switch from recruitment to transport, is confirmed. Furthermore, evidence showed that the colonies were merged at the time of transport. While ant emigration patterns are well understood, there is a gap in understanding conflict driven emigrations/invasions. Our results serve to better understand conflict in social insects by further understanding the mechanisms used during conflicts.

Agassiz’s desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex.

Data Availability: All genomic and transcriptomic sequence files are available from the NIH-NCBI BioProject database (accession numbers PRJNA352725, PRJNA352726, and PRJNA281763). All genome assembly, transcriptome assembly, predicted protein, transcript, genome annotation, repeatmasker, phylogenetic trees, .vcf and GO enrichment files are available on Harvard Dataverse (doi:10.7910/DVN/EH2S9K).