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Many lizard species face extinction due to worldwide climate change. The Guatemalan Beaded Lizard, Heloderma charlesbogerti, is a member of the Family Helodermatidae that may be particularly imperiled; fewer than 600 mature individuals are believed to persist in the wild. In addition, H. charlesbogerti lizards are phenotypically remarkable. They are large in size, charismatically patterned, and possess a venomous bite. Here, we report the draft genome of the Guatemalan Beaded Lizard using DNA from a wild-caught individual. The assembled genome totals 2.31 Gb in length, similar in size to the genomes of related species. Single-copy orthologs were used to produce a novel molecular phylogeny, revealing that the Guatemalan Beaded Lizard falls into a clade with the Asian Glass Lizard (Anguidae) and in close association with the Komodo Dragon (Varanidae) and the Chinese Crocodile Lizard (Shinisauridae). In addition, we identified 31,411 protein-coding genes within the genome. Of the genes identified, we found 504 that evolved with a differential constraint on the branch leading to the Guatemalan Beaded Lizard. Lastly, we identified a decline in the effective population size of the Guatemalan Beaded Lizard approximately 400,000 years ago, followed by a stabilization before starting to dwindle again 60,000 years ago. The results presented here provide important information regarding a highly endangered, venomous reptile that can be used in future conservation, functional genetic, and phylogenetic analyses.

 

Ants are millimetres in scale yet collectively create metre-scale nests in diverse substrates. To discover principles by which ant collectives self-organize to excavate crowded, narrow tunnels, we studied incipient excavation in small groups of fire ants in quasi-two-dimensional arenas. Excavation rates displayed three stages: initially excavation occurred at a constant rate, followed by a rapid decay, and finally a slower decay scaling in time as t −1/2 . We used a cellular automata model to understand such scaling and motivate how rate modulation emerges without global control. In the model, ants estimated their collision frequency with other ants, but otherwise did not communicate. To capture early excavation rates, we introduced the concept of ‘agitation’—a tendency of individuals to avoid rest if collisions are frequent. The model reproduced the observed multi-stage excavation dynamics; analysis revealed how parameters affected features of multi-stage progression. Moreover, a scaling argument without ant–ant interactions captures tunnel growth power-law at long times. Our study demonstrates how individual ants may use local collisional cues to achieve functional global self-organization. Such contact-based decisions could be leveraged by other living and non-living collectives to perform tasks in confined and crowded environments. 

Social organisms which construct nests consisting of tunnels and chambers necessarily navigate confined and crowded conditions. Unlike low density collectives like bird flocks and insect swarms in which hydrodynamic and statistical phenomena dominate, the physics of glasses and supercooled fluids is important to understand clogging behaviors in high density collectives. Our previous work revealed that fire ants flowing in confined tunnels utilize diverse behaviors like unequal workload distributions, spontaneous direction reversals and limited interaction times to mitigate clogging and jamming and thus maintain functional flow; implementation of similar rules in a small robophysical swarm led to high performance through spontaneous dissolution of clogs and clusters. However, how the insects learn such behaviors and how we can develop “task capable” active matter in such regimes remains a challenge in part because interaction dynamics are dominated by local, potentially time-consuming collisions and no single agent can survey and guide the entire collective. Here, hypothesizing that effective flow and clog mitigation could be generated purely by collisional learning dynamics, we challenged small groups of robots to transport pellets through a narrow tunnel, and allowed them to modify their excavation probabilities over time. Robots began excavation with equal probabilities to excavate and without probability modification, clogs and clusters were common. Allowing the robots to perform a “reversal” and exit the tunnel when they encountered another robot which prevented forward progress improved performance. When robots were allowed to change their reversal probabilities via both a collision and a self-measured (and noisy) estimate of tunnel length, unequal workload distributions comparable to our previous work emerged and excavation performance improved. Our robophysical study of an excavating swarm shows that despite the seeming complexity and difficulty of the task, simple learning rules can mitigate or leverage unavoidable features in task capable dense active matter, leading to hypotheses for dense biological and robotic swarms. 

Eusociality represents an extreme form of social behavior characterized by a reproductive division of labor. Eusociality necessarily evolved through kin selection, which requires interactions among related individuals. However, many eusocial taxa also show cooperation between non-kin groups, challenging the idea that cooperative actions should only occur among relatives. This review explores the causes and consequences of non-kin cooperation in ants. Ants display a diversity of behaviors that lead to non-kin cooperation within and between species. These interactions occur among both reproductive and non-reproductive individuals. The proximate and ultimate mechanisms leading to non-kin cooperative interactions differ substantially depending on the biotic and abiotic environment. We end this review with directions for future research and suggest that the investigation of non-kin cooperative actions provides insight into processes leading to social evolution. 

Abstract 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. 

Epigenetic information affects gene function by interacting with chromatin, while not changing the DNA sequence itself. However, it has become apparent that the interactions between epigenetic information and chromatin can, in fact, indirectly lead to DNA mutations and ultimately influence genome evolution. This review evaluates the ways in which epigenetic information affects genome sequence and evolution. We discuss how DNA methylation has strong and pervasive effects on DNA sequence evolution in eukaryotic organisms. We also review how the physical interactions arising from the connections between histone proteins and DNA affect DNA mutation and repair. We then discuss how a variety of epigenetic mechanisms exert substantial effects on genome evolution by suppressing the movement of transposable elements. Finally, we examine how genome expansion through gene duplication is also partially controlled by epigenetic information. Overall, we conclude that epigenetic information has widespread indirect effects on DNA sequences in eukaryotes and represents a potent cause and constraint of genome evolution. This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’