Genetic Correlations in Mutation Processes

We study the role of phylogenetic trees on correlations in mutation processes. Generally, correlations decay exponentially with the generation number. We find that two distinct regimes of behavior exist. For mutation rates smaller than a critical rate, the underlying tree morphology is almost irrelevant, while mutation rates higher than this critical rate lead to strong tree-dependent correlations. We show analytically that identical critical behavior underlies all multiple point correlations. This behavior generally characterizes branching processes undergoing mutation.Comment: revtex, 8 pages, 2 fig

Phylogenetic and phenotypic divergence of an insular radiation of birds

Evolutionary divergence of lineages is one of the key mechanisms underpinning large scale patterns in biogeography and biodiversity. Island systems have been highly influential in shaping theories of evolutionary diversification and here I use the insular Zosteropidae of the south west Pacific to investigate the roles of ecology and biogeography in promoting evolutionary divergence. Initially I build a phylogenetic tree of the study group and use it to reveal the pattern of colonisation and diversification. My results suggest a complex history of dispersal with the observed pattern most likely a result of repeated bouts of colonisation and extinction. I then use the new phylogeny to quantify the diversification rates of the Zosteropidae. I find a very high rate of lineage divergence and suggest the most likely explanation relates to extensive niche availability in the south west Pacific. I also find evidence for an overall slowdown in diversification combined with repeated bursts of accelerated speciation, consistent with a model of taxon cycles. I do not find evidence for sympatric speciation, however. Finally I combine morphological and phylogenetic data to investigate the mode of evolution, evidence for character displacement and influence of biogeography on trait evolution. I find little support for the traditional theory of character displacement in sympatric species. I do, however, find some support for biogeographic theories. Taken together my results do not support traditional theories on the ecological and biogeographical basis of divergence, even in those cases where Zosterops have been used as exemplars. This appears to be because those theories assume rather simple patterns of colonisation and a static ecological system. Instead, my results suggest that evolutionary diversification is dominated by recurrent waves of colonisation and extinction, which, viewed at any particular moment, tend to obscure any underlying ecological rules

The radiation of cynodonts and the ground plan of mammalian morphological diversity

Cynodont therapsids diversified extensively after the Permo-Triassic mass extinction event, and gave rise to mammals in the Jurassic. We use an enlarged and revised dataset of discrete skeletal characters to build a new phylogeny for all main cynodont clades from the Late Permian to the Early Jurassic, and we analyse models of morphological diversification in the group. Basal taxa and epicynodonts are paraphyletic relative to eucynodonts, and the latter are divided into cynognathians and probainognathians, with tritylodonts and mammals forming sister groups. Disparity analyses reveal a heterogeneous distribution of cynodonts in a morphospace derived from cladistic characters. Pairwise morphological distances are weakly correlated with phylogenetic distances. Comparisons of disparity by groups and through time are non-significant, especially after the data are rarefied. A disparity peak occurs in the Early/Middle Triassic, after which period the mean disparity fluctuates little. Cynognathians were characterized by high evolutionary rates and high diversity early in their history, whereas probainognathian rates were low. Community structure may have been instrumental in imposing different rates on the two clades

Group size, Grooming and Social Cohesion in Primates

Most primates live in social groups in which affiliative bonds exist between individuals. Because these bonds need to be maintained through social interactions (grooming in most primates), sociality will be limited by time constraints. It has previously been shown that the time primates invest in grooming increases with group size. However, when groups become too large, individuals will not have enough time available to service all possible social relationships and group cohesion is expected to decrease. In this study, we used data from previously published studies to determine how large groups compromise on their grooming time and how ecological, phylogenetic and life history variables affect time invested in grooming (across species as well as within taxa). We used path analysis to analyse direct and indirect (via group size) effects on grooming. We showed that not only is grooming time determined by group size, but it is also affected by dispersal patterns and sex ratio. Furthermore, we found that grooming time is asymptotic when group size exceeds 40 individuals, indicating that time constraints resulting from ecological pressure force individuals to compromise on their grooming time. This was true across species, but a similar effect was also found within taxa. Cognitive constraints and predation pressure strongly affect group sizes and thereby have an indirect effect on primate grooming time. Primates that were found to live in groups larger than predicted by their neocortex size usually suffered from greater predation risk. However, most populations in our analysis were placed well within what we define as their eco-cognitive niche. © 2007 The Association for the Study of Animal Behaviour

Convergence and divergence in the evolution of cat skulls: temporal and spatial patterns of morphological diversity

Background: Studies of biological shape evolution are greatly enhanced when framed in a phylogenetic perspective. Inclusion of fossils amplifies the scope of macroevolutionary research, offers a deep-time perspective on tempo and mode of radiations, and elucidates life-trait changes. We explore the evolution of skull shape in felids (cats) through morphometric analyses of linear variables, phylogenetic comparative methods, and a new cladistic study of saber-toothed cats. Methodology/Principal Findings: A new phylogenetic analysis supports the monophyly of saber-toothed cats (Machairodontinae) exclusive of Felinae and some basal felids, but does not support the monophyly of various sabertoothed tribes and genera. We quantified skull shape variation in 34 extant and 18 extinct species using size-adjusted linear variables. These distinguish taxonomic group membership with high accuracy. Patterns of morphospace occupation are consistent with previous analyses, for example, in showing a size gradient along the primary axis of shape variation and a separation between large and small-medium cats. By combining the new phylogeny with a molecular tree of extant Felinae, we built a chronophylomorphospace (a phylogeny superimposed onto a two-dimensional morphospace through time). The evolutionary history of cats was characterized by two major episodes of morphological divergence, one marking the separation between saber-toothed and modern cats, the other marking the split between large and small-medium cats. Conclusions/Significance: Ancestors of large cats in the ‘Panthera’ lineage tend to occupy, at a much later stage, morphospace regions previously occupied by saber-toothed cats. The latter radiated out into new morphospace regions peripheral to those of extant large cats. The separation between large and small-medium cats was marked by considerable morphologically divergent trajectories early in feline evolution. A chronophylomorphospace has wider applications in reconstructing temporal transitions across two-dimensional trait spaces, can be used in ecophenotypical and functional diversity studies, and may reveal novel patterns of morphospace occupation

Metabolic flexibility as a major predictor of spatial distribution in microbial communities

A better understand the ecology of microbes and their role in the global ecosystem could be achieved if traditional ecological theories can be applied to microbes. In ecology organisms are defined as specialists or generalists according to the breadth of their niche. Spatial distribution is often used as a proxy measure of niche breadth; generalists have broad niches and a wide spatial distribution and specialists a narrow niche and spatial distribution. Previous studies suggest that microbial distribution patterns are contrary to this idea; a microbial generalist genus (Desulfobulbus) has a limited spatial distribution while a specialist genus (Methanosaeta) has a cosmopolitan distribution. Therefore, we hypothesise that this counter-intuitive distribution within generalist and specialist microbial genera is a common microbial characteristic. Using molecular fingerprinting the distribution of four microbial genera, two generalists, Desulfobulbus and the methanogenic archaea Methanosarcina, and two specialists, Methanosaeta and the sulfate-reducing bacteria Desulfobacter were analysed in sediment samples from along a UK estuary. Detected genotypes of both generalist genera showed a distinct spatial distribution, significantly correlated with geographic distance between sites. Genotypes of both specialist genera showed no significant differential spatial distribution. These data support the hypothesis that the spatial distribution of specialist and generalist microbes does not match that seen with specialist and generalist large organisms. It may be that generalist microbes, while having a wider potential niche, are constrained, possibly by intrageneric competition, to exploit only a small part of that potential niche while specialists, with far fewer constraints to their niche, are more capable of filling their potential niche more effectively, perhaps by avoiding intrageneric competition. We suggest that these counter-intuitive distribution patterns may be a common feature of microbes in general and represent a distinct microbial principle in ecology, which is a real challenge if we are to develop a truly inclusive ecology

A phylogenetic comparative analysis on the evolution of sequential hermaphroditism in seabreams (Teleostei : Sparidae)

The Sparids are an ideal group of fish in which to study the evolution of sexual systems since they exhibit a great sexual diversity, from gonochorism (separate sexes) to protandrous (male-first) and protogynous (female-first) sequential hermaphroditism (sex-change). According to the size-advantage model (SAM), selection should favour sex change when the second sex achieves greater reproductive success at a larger body size than the first sex. Using phylogenetic comparative methods and a sample of 68 sparid species, we show that protogyny and protandry evolve from gonochorism but evolutionary transitions between these two forms of sequential hermaphroditism are unlikely to happen. Using male gonadosomatic index (GSI) as a measure of investment in gametes and proxy for sperm competition, we find that, while gonochoristic and protogynous species support the predictions of SAM, protandrous species do not, as they exhibit higher GSI values than expected even after considering mating systems and spawning modes. We suggest that small males of protandrous species have to invest disproportionally more in sperm production than predicted not only when spawning in aggregations with high levels of sperm competition, but also when spawning in pairs due to the need to fertilize highly fecund females, much larger than themselves. We propose that this compensatory mechanism, together with Bateman’s principles in sequential hermaphrodites, should be formally incorporated in the SAM