Are you my mother? Bayesian phylogenetic inference of recombination among putative parental strains

Reconstructing evolutionary relationships using Bayesian inference has become increasingly popular due to the ability of Bayesian inference to handle complex models of evolution. In this review we concentrate on inference of recombination events between strains of viruses when these events are sporadic, ie rare relative to point mutations. Bayesian inference is especially attractive in the detection of recombination events because it allows for simultaneous inferences about the presence, number and location of crossover points and the identification of parental sequences. Current frequentist recombination identification falls into a sequential testing trap. The most likely parental sequences and crossover points are identified using the data and then the certainty of recombination is assessed conditional on this identification. After briefly outlining basic phylogenetic models, Bayesian inference and Markov chain Monte Carlo (MCMC) computation, we summarise three different approaches to recombination detection and discuss current challenges in applying Bayesian phylogenetic inference of recombination.     

Kin or self‐recognition? Colonial fusibility of the bryozoan Celleporella hyalina

We estimated fusion frequency with respect to coancestry in the bryozoan Celleporella hyalina, whose briefly planktonic sexually produced larvae settle on algal substrata and proceed to form encrusting colonies by iterative budding. Frequency of fusion between paired colonies growing on an artificial substratum was positively correlated with coefficient of relatedness, with allorecognition ability increasing during the early stages of colonial growth after larval settlement. Parents repressed the growth of F1 progeny with which they had fused. The results are concordant with the Feldgarden-Yund model of selection for self-recognition, which regards fusion with kin as an inevitable source of error whose cost diminishes with increasing relatedness. Contrary to fusion compatibility, gametic compatibility is negatively correlated with coancestry, indicating a need for further research on the possibility of common or linked genetic control that has opposite effect at somatic and gametic levels.     

Kin selection in disguise?

In a recent article E.O. Wilson and B. H?lldobler (2005) describe an heuristic model for the evolution of eusociality. They present their model as an alternative to the standard model of kin selection, and describe the evolution of eusociality in terms of changes in frequency to an hypothetical eusocial allele. Here I build on sentiments of Foster et al. (2006) to suggest that the proposed model is not a clear alternative to the standard model, but appears to represent a special case of kin selection involving preferential interactions among individuals sharing the same altruistic gene. The model proposed by Wilson and H?lldobler is consistent with the ‘greenbeard’ model of kin selection, first proposed by W.D. Hamilton. Received 23 May 2006; revised 27 June 2006; accepted 5 July 2006.     

Are you my mother? Phylogenetic analysis reveals orphan hybrid stick insect genus is part of a monophyletic New Zealand clade

The hybrid stick insect genus Acanthoxyla Uvarov 1944 is unusual for an obligate parthenogen, in the extreme morphological diversity it exhibits that has led to eight species being recognised. The New Zealand sexual species Clitarchus hookeri [White, A. 1846. The zoology of the Voyage of H.M.S. Erebus and Terror. In: 1 Insects of New Zealand. E.W. Janson, London.] is the putative parental species in the hybridization that gave rise to the hybrid lineage Acanthoxyla. In an effort to identify the maternal ancestor of Acanthoxyla we sequenced nuclear 28S rDNA and/or mtDNA COI & COII of all nine endemic New Zealand stick insect genera, representing 17 of the 22 described species. We also sequenced 28S from eight non-New Zealand stick insects to supplement published 28S sequence data that provided a taxonomically and geographically broad sampling of the phasmids. We applied a novel search algorithm (SeqSSi=Sequence Similarity Sieve) to assist in selection of outgroup taxa for phylogenetic analysis prior to alignment. Phylogenetic reconstructions resolved an exclusively New Zealand clade to which the maternal lineage of Acanthoxyla belonged, but did not support existing higher level taxonomy of stick insects. We did not find a sexual maternal species for Acanthoxyla but phylogenetic relationships indicate that this species lived in New Zealand and could be classified among the New Zealand Phasmatinae. Among the available taxa, the nearest evolutionary neighbours to the New Zealand phasmid fauna as a whole were predominantly from the New Zealand region (Fiji, Australia, New Guinea, New Caledonia and South America). As it appears to be an orphan, it is interesting to speculate that a combination of parthenogenetic reproduction and/or hybrid vigour in Acanthoxyla may have contributed to the extinction of its mother.     

Are ant supercolonies crucibles of a new major transition in evolution?

The biological hierarchy of genes, cells, organisms and societies is a fundamental reality in the living world. This hierarchy of entities did not arise ex nihilo at the origin of life, but rather has been serially generated by a succession of critical events known as ‘evolutionary transitions in individuality’ (ETIs). Given the sequential nature of ETIs, it is natural to look for candidates to form the next hierarchical tier. We analyse claims that these candidates are found among ‘supercolonies’, ant populations in which discrete nests cooperate as part of a wider collective, in ways redolent of cells in a multicellular organism. Examining earlier empirical work and new data within the recently proposed ‘Darwinian space’ framework, we offer a novel analysis of the evolutionary status of supercolonies and show how certain key conditions might be satisfied in any future process transforming these collaborative networks into true Darwinian individuals.     

A comparison of mark–release–recapture methods for estimating colony size in the wood ant Formica lugubris

Colony size can be considered the analogue of the body size of a superorganism. Just as body size is important to the physiology of an individual animal, colony size correlates with the life-history and ecology of social insects. Although nest excavation and counting all individuals is the most accurate method for estimating colony size (or nest size), it has the major drawback of being destructive. Alternatively, mark–release–recapture (MRR) can be used repeatedly to measure the size of the same colony or nest. We compared the accuracy and feasibility of four MRR methods and a Mound-Volume method with complete counts from nest excavation for estimating the nest size of F. lugubris, a mound-building wood ant of the Formica rufa group, during the early spring in Scotland. We found that our After-Disturbing method, in which we performed marking and recapturing after gentle disturbance to the top of nest mound, has the best balance between accuracy, non-destructiveness, and time required. We also found that mound volume can be an index of ant nest size under certain conditions. Both non-destructive methods can be used on the same colony or nest repeatedly to monitor nest dynamics.     

Are we stuck in the standards?

To avoid duplication of effort, slow adoption and inefficiency in development, those developing biological standards need to communicate more with each other, attract help from experts in the ontology/standards communities and keep focused on needs of users.     

Kin selection and reciprocity in flight formation?

The reasons for conspicuous "V" and other flight formationsin birds are debated. Theory and recent empirical advances showthat energy saving is one important function of flight formations,but some aspects remain poorly understood. Combining theoriesof animal flight and sociality, we suggest that some of thevariation in flight formations has its base in kin selectionand reciprocation. The bird leading an acute V formation savesless energy than does the trailing participants. The disadvantageof leading is reduced in more obtuse formations, and when thelongitudinal distance between neighbors is small, the leadingbird can save about as much energy as others. Therefore, acuteV formations are predicted to occur mainly in circumstancesconducive to kin selection or reciprocity. These mechanismsseem possible, for example, in small flocks of adults with offspring,such as in swans, geese, and cranes. Inclusive fitness advantagesmay then favor an energetically expensive leader role for adults.In small groups, reciprocity is also possible among unrelatedadults that recognize each other and take turns leading theV formation. In contrast, obtuse formations are expected inlarge flocks of unrelated individuals, such as spring flocksof waders migrating long distances. Possibilities for testingthese ideas are discussed.     

Stay or drift? Queen acceptance in the ant <Emphasis Type="Italic">Formica paralugubris</Emphasis>

The acceptance of new queens in ant colonies has profound effects on colony kin structure and inclusive fitness of workers. Therefore, it is important to study the recognition and discrimination behaviour of workers towards reproductive individuals entering established colonies. We examined the acceptance rate of queens in populations of the highly polygynous ant F. paralugubris, where the genetic differentiation among nests and discrimination ability among workers suggest that workers might reject foreign queens. We experimentally introduced young queens in their natal nest and in foreign nests. Surprisingly, the survival rate of mated queens did not differ significantly when introduced in a foreign male-producing nest, a foreign female-producing nest, or the natal nest. Moreover, the survival of virgin queens in their natal nest was twice the one of mated queens, suggesting that mating status plays an important role for acceptance. The results indicate that other factors than queen discrimination by workers are implicated in the limited longdistance gene flow between nests in these populations. Received 8 April 2008; revised 16 June 2008; accepted 1 July 2008.