C.C.M. Baker, D.J. Martins, J.N. Pelaez, J.P.J. Billen, A. Pringle, M.E. Frederickson, and N.E. Pierce. 2017. “Distinctive fungal communities in an obligate African ant plant mutualism.” Proceedings of the Royal Society B, 284, Pp. 20162501. Publisher's VersionAbstract
Three ant species nest obligately in the swollen-thorn domatia of the African ant-plant Vachellia (Acaciadrepanolobium, a model system for the study of ant-defence mutualisms and species coexistence. Here we report on the characteristic fungal communities generated by these ant species in their domatia. First, we describe behavioural differences between the ant species when presented with a cultured fungal isolate in the laboratory. Second, we use DNA metabarcoding to show that each ant species has a distinctive fungal community in its domatia, and that these communities remain characteristic of the ant species over two Kenyan sampling locations separated by 190 km. Third, we find that DNA extracted from female alates of Tetraponera penzigi and Crematogaster nigriceps contained matches for most of the fungal metabarcodes from those ant species' domatia, respectively. Fungal hyphae and other debris are also visible in sections of these alates' infrabuccal pockets. Collectively, our results indicate that domatium fungal communities are associated with the ant species occupying the tree. To the best of our knowledge, this is the first record of such ant-specific fungal community-level differences on the same myrmecophytic host species. These differences may be shaped by ant behaviour in the domatia, and by ants vectoring fungi when they disperse to establish new colonies. The roles of the fungi with respect to the ants and their host plant remain to be determined.
C.C.M. Baker, L.S. Bittleston, J.G. Sanders, and N.E. Pierce. 2016. “Dissecting host-associated communities with DNA barcodes.” Philosophical Transactions of the Royal Society B, 371, Pp. 20150328. Publisher's VersionAbstract
DNA barcoding and metabarcoding methods have been invaluable in the study of interactions between host organisms and their symbiotic communities. Barcodes can help identify individual symbionts that are difficult to distinguish using morphological characters, and provide a way to classify undescribed species. Entire symbiont communities can be characterized rapidly using barcoding and especially metabarcoding methods, which is often crucial for isolating ecological signal from the substantial variation among individual hosts. Furthermore, barcodes allow the evolutionary histories of symbionts and their hosts to be assessed simultaneously and in reference to one another. Here, we describe three projects illustrating the utility of barcodes for studying symbiotic interactions: first, we consider communities of arthropods found in the ant-occupied domatia of the East African ant-plant Vachellia (Acaciadrepanolobium; second, we examine communities of arthropod and protozoan inquilines in three species of Nepenthes pitcher plant in South East Asia; third, we investigate communities of gut bacteria of South American ants in the genus Cephalotes. Advances in sequencing and computation, and greater database connectivity, will continue to expand the utility of barcoding methods for the study of species interactions, especially if barcoding can be approached flexibly by making use of alternative genetic loci, metagenomes and whole-genome data.
L.S. Bittleston, C.C.M. Baker, L.B. Strominger, A. Pringle, and N.E. Pierce. 2016. “Metabarcoding as a tool for investigating arthropod diversity in Nepenthes pitcher plants.” Austral Ecology, 41, 2, Pp. 120-132.Abstract
The biodiversity of tropical forests consists primarily of small organisms that are difficult to detect and characterize. Next-generation sequencing (NGS) methods can facilitate analyses of these arthropod and microbial communities, leading to a better understanding of existing diversity and factors influencing community assembly. The pitchers of carnivorous pitcher plants often house surprisingly discrete communities and provide ideal systems for analysis using an NGS approach. The plants digest insects in order to access essential nutrients while growing in poor soils; however, the pitchers are also home to communities of living organisms, called inquilines. Certain arthropods appear to have coevolved with their pitcher plant hosts and are not found in other environments. We used Illumina amplicon sequencing of 18S rDNA to characterize the eukaryotes in three species of Nepenthes (Nepenthaceae) pitcher plants – N. gracilisN. rafflesiana and N. ampullaria – in each of three different parks in Singapore. The data reveal an unexpected diversity of eukaryotes, significant differences in community diversity among host species, variation in host specificity of inquilines and the presence of gregarine parasites. Counts of whole inquiline arthropods from the first collection year were roughly correlated with scaled 18S sequence abundances, indicating that amplicon sequencing is an effective means of gauging community structure. We barcoded a subset of the dipteran larvae using COI primers, and the resulting phylogenetic tree is mostly congruent with that found using the 18S locus, with the exception of one of five morphospecies. For many 18S and COI sequences, the best BLASTn matches showed low sequence identity, illustrating the need for better databases of Southeast Asian dipterans. Finally, networks of core arthropods and their host species were used to investigate degree of host specificity across multiple hosts, and this revealed significant specialization of certain arthropod fauna. 
PDF supplement
C.C.M. Baker, S. R. X. Dall, and D. J. Rankin. 2012. “Kin selection and the evolution of social information use in animal conflict.” PLoS ONE, 7, 2, Pp. e31664.Abstract
Animals often use social information about conspecifics in making decisions about cooperation and conflict. While the importance of kin selection in the evolution of intraspecific cooperation and conflict is widely acknowledged, few studies have examined how relatedness influences the evolution of social information use. Here we specifically examine how relatedness affects the evolution of a stylised form of social information use known as eavesdropping. Eavesdropping involves individuals escalating conflicts with rivals observed to have lost their last encounter and avoiding fights with those seen to have won. We use a game theoretical model to examine how relatedness affects the evolution of eavesdropping, both when strategies are discrete and when they are continuous or mixed. We show that relatedness influences the evolution of eavesdropping, such that information use peaks at intermediate relatedness. Our study highlights the importance of considering kin selection when exploring the evolution of complex forms of information use.
PDF supplement
A.A. Mushegian, C.N. Peterson, C.C.M. Baker, and A. Pringle. 2011. “Bacterial diversity across individual lichens.” Applied and Environmental Microbiology, 77, 12, Pp. 4249-4252.Abstract
Symbioses are unique habitats for bacteria. We surveyed the spatial diversity of bacterial communities across multiple individuals of closely related lichens using terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing. Centers of lichens house richer, more consistent assemblages than species-poor and compositionally disparate lichen edges, suggesting that ecological succession plays a role in structuring these communities.
PDF supplement