COMPONENT ANALYSIS: A VALIANT FAILURE?

A broadscale analysis of host-symbiont cophylogeny reveals the drivers of phylogenetic congruence

Symbioses exert substantial biological influence, with great evolutionary and ecological relevance for disease, major evolutionary transitions, and the structure and function of ecological communities. Yet, much remains unknown about the patterns and processes that characterise symbioses. A major unanswered question is the extent to which symbiont phylogenies mirror those of their hosts and if patterns differ for parasites and mutualists. Addressing this question offers fundamental insights into evolutionary processes, such as whether symbionts typically codiverge with their hosts or if diversity is generated via host switches. Here, we perform a meta-analysis of host-symbiont phylogenetic congruence, encompassing 212 host-symbiont cophylogenetic studies that include ~10,000 species. Our analysis supersedes previous qualitative assessments by utilising a quantitative framework. We show that symbiont phylogeny broadly reflects host phylogeny across biodiversity and life-history, demonstrating a general pattern of phylogenetic congruence in host-symbiont interactions. We reveal two key aspects of symbiont life-history that promote closer ties between hosts and symbionts: vertical transmission and mutualism. Mode of symbiosis and mode of transmission are intimately interlinked, but vertical transmission is the dominant factor. Given the pervasiveness of symbioses, these findings provide important insights into the processes responsible for generating and maintaining the Earth's rich biodiversity.

Biogeography of Amazonian fishes: deconstructing river basins as biogeographic units

ABSTRACT Biogeography of Amazonian fishes (2,500 species in vastly disjunct lineages) is complex and has so far been approached only partially. Here, we tackle the problem on the basis of the largest database yet on geographical distribution and phylogenetic relationships of Amazonian fishes, including all information available. Distributions of 4,095 species (both Amazonian and outgroups) and 84 phylogenetic hypotheses (comprising 549 phylogenetically-informative nodes) were compiled, qualified and plotted onto 46 areas (29 Amazonian and 17 non-Amazonian). The database was analyzed with PAE, CADE, BPA and BPA0, yielding largely congruent results and indicating that biogeographic signal is detectable on multiple dimensions of fish distribution, from single species ranges to cladistic congruence. Agreement is especially pronounced in deeper components, such as Trans-Andean, Cis-Andean, Western Amazon and Orinoco basins. Results show that all major Amazonian tributaries, as well as the Amazon basin itself, are non-monophyletic and constitute hybrid sets of heterogeneous biotic partitions. Amazonian drainages should not be assumed a priori as historically cohesive areas, contrary to widespread practice. Our hypothesis allows re-evaluation of broader issues in historical biogeography, such as the predictive power of biogeographic hypotheses, the vicariant/dispersal duality, the significance of widely distributed taxa, and the need for temporal dimension in biogeographic patterns.

PENGUINS, PETRELS, AND PARSIMONY: DOES CLADISTIC ANALYSIS OF BEHAVIOR REFLECT SEABIRD PHYLOGENY?

Whether or not behavior accurately reflects evolutionary relationships (phylogeny) has been hotly debated by ethologists and comparative psychologists. Previous studies attempting to resolve this question have generally lacked a quantitative, phylogenetic approach. In this study we used behavior and life-history (BLH) information (72 characters) to generate phylogenetic trees for 18 seabird species (albatrosses, petrels, and penguins). We compared these trees with trees obtained from isozyme electrophoretic analysis of blood proteins (15 loci and 98 electromorphs) and partial mitochondrial 12S ribosomal DNA sequences (381 base pairs). Cladistic analysis of the BLH data set generated three MP trees (tree length = 243, CI = 0.52, RI = 0.57) with significant cladistic structure. The BLH characters were classified into four types (foraging, agonistic, reproductive, and life history) and levels of homoplasy for each type were measured. No significant differences were found among these categories. The BLH trees were shown to be significantly more congruent with the electrophoretic and 12S sequence trees than expected by chance. This indicates that seabird BLH data contains phylogenetic signal. Areas of incongruence between BLH trees and a phylogeny generated by combining the data sets were predicted to result from ecological constraints that did not covary with phylogeny. These predictions were supported by the results of a concentrated changes test. This study found that this BLH data set was no more homoplasious than molecular data and that BLH trees were significantly congruent with molecular trees.

PHYLOGENETIC ESTIMATION OF PLASMID EXCHANGE IN BACTERIA

The existence of differential horizontal gene transfer may be assessed by comparing the phylogenetic trees derived from two different genes. We use this concept to estimate quantitatively the amount of plasmid exchange that has occurred in a bacterial population. By means of computer simulations we studied the effect of gene transfer on the topological distortion between two phylogenetic trees: one obtained from an euchromosomal gene and another from a plasmid-borne sequence, which may be subjected to horizontal transfer. The basic assumptions of our simulations were (a) that plasmid exchange had occurred recently (after the last population split); and (b) that either the amount of chromosomal horizontal exchange was negligible or that it was only a fraction of the amount of plasmid exchange in which case we will be estimating relative amounts of plasmid transfer. We found that the topological difference between two such trees is a function of the number of plasmid exchange events that have occurred. It can be explained by a logistic model that relates the average distortion index between two trees (d_T ) to the number of transfer events (x). The behavior remains the same under different conditions that were tested (symmetry of the topology, number of taxa in the tree, effect of reconstruction errors, mutation after plasmid transfer). We have also tried our method on empirical data from the literature and estimated the amount of gene transfer that may have occurred among Sym plasmids in agricultural field populations of Rhizobium leguminosarum biovar phaseoli. We found that between 15.77 to 29.98% of all genetic types in these populations have been either the source or the target of a plasmid transfer event. When the comparisons were made among trees derived exclusively from plasmid probes this value dropped to 2.00%. Phylogenetic trees derived from symbiotic and nonsymbiotic sequences were also used to infer the number of gene transfer events among 11 isolates from R. galegae. The estimated number of transfer events of symbiotic sequences was 10.515 (although we do not know out of how many genetic types). We concluded that intraspecific transfer of symbiotic sequences is widespread in these two species of the genus Rhizobium.

Phylogenetic framework for coevolutionary studies: a compass for exploring jungles of tangled trees

Phylogenetics is used to detect past evolutionary events, from how species originated to how their ecological interactions with other species arose, which can mirror cophylogenetic patterns. Cophylogenetic reconstructions uncover past ecological relationships between taxa through inferred coevolutionary events on trees, for example, codivergence, duplication, host-switching, and loss. These events can be detected by cophylogenetic analyses based on nodes and the length and branching pattern of the phylogenetic trees of symbiotic associations, for example, host-parasite. In the past 2 decades, algorithms have been developed for cophylogetenic analyses and implemented in different software, for example, statistical congruence index and event-based methods. Based on the combination of these approaches, it is possible to integrate temporal information into cophylogenetical inference, such as estimates of lineage divergence times between 2 taxa, for example, hosts and parasites. Additionally, the advances in phylogenetic biogeography applying methods based on parametric process models and combined Bayesian approaches, can be useful for interpreting coevolutionary histories in a scenario of biogeographical area connectivity through time. This article briefly reviews the basics of parasitology and provides an overview of software packages in cophylogenetic methods. Thus, the objective here is to present a phylogenetic framework for coevolutionary studies, with special emphasis on groups of parasitic organisms. Researchers wishing to undertake phylogeny-based coevolutionary studies can use this review as a "compass" when "walking" through jungles of tangled phylogenetic trees.

Towards sub-quadratic time and space complexity solutions for the dated tree reconciliation problem

BACKGROUND

Recent coevolutionary analysis has considered tree topology as a means to reduce the asymptotic complexity associated with inferring the complex coevolutionary interrelationships that arise between phylogenetic trees. Targeted algorithmic design for specific tree topologies has to date been highly successful, with one recent formulation providing a logarithmic space complexity reduction for the dated tree reconciliation problem.

METHODS

In this work we build on this prior analysis providing a further asymptotic space reduction, by providing a new formulation for the dynamic programming table used by a number of popular coevolutionary analysis techniques. This model gives rise to a sub quadratic running time solution for the dated tree reconciliation problem for selected tree topologies, and is shown to be, in practice, the fastest method for solving the dated tree reconciliation problem for expected evolutionary trees. This result is achieved through the analysis of not only the topology of the trees considered for coevolutionary analysis, but also the underlying structure of the dynamic programming algorithms that are traditionally applied to such analysis.

CONCLUSION

The newly inferred theoretical complexity bounds introduced herein are then validated using a combination of synthetic and biological data sets, where the proposed model is shown to provide an [Formula: see text] space saving, while it is observed to run in half the time compared to the fastest known algorithm for solving the dated tree reconciliation problem. What is even more significant is that the algorithm derived herein is able to guarantee the optimality of its inferred solution, something that algorithms of comparable speed have to date been unable to achieve.

Behavioural evolution in penguins does not reflect phylogeny

Over the past two decades, behavioural biologists and ecologists have made effective use of the comparative method, but have often stopped short of adopting an explicitly phylogenetic approach. We examined 68 behaviour and life history (BLH) traits of 15 penguin species to: (i) infer penguin phylogeny, (ii) assess homology of behavioural characters, and (iii) evaluate hypotheses about character evolution and ancestral states. Parsimony analysis of the BLH dataset found either two shortest trees (characters coded as unordered) or a single shortest tree (characters coded as a combination of unordered and Dollo). The BLH data had significant structure. Kishino-Hasegawa tests indicated that BLH trees were significantly different from most previous estimates of penguin phylogeny. The BLH phylogeny generated from Dollo characters appeared to be less accurate than the tree derived from the completely unordered dataset. Dividing BLH data into display and non-display traits resulted in no significant differences in level of homoplasy and no difference in the accuracy of phylogeny. Tests for homology of BLH traits were performed by mapping the characters onto a molecular tree. Assuming that independent gains are less likely than losses of character states, 65 of the 68 characters were likely to be homologous across taxa, and at least several characters appeared to have been stable since the origin of modern penguins around 30 Myr. Finally, the likely BLH traits of the most recent common ancestor of extant penguins were reconstructed from character states along the internal branch leading to the penguins. This analysis suggested that the "proto-penguin" probably had a similar life history to current temperate penguins but few ritualized behaviours. A southern, cool-temperate origin of penguins is suggested.

Phylogenetic analysis of symbionts in feather-feeding lice of the genus Columbicola: evidence for repeated symbiont replacements

BACKGROUND

Many groups of insects have obligate bacterial symbionts that are vertically transmitted. Such associations are typically characterized by the presence of a monophyletic group of bacteria living in a well-defined host clade. In addition the phylogeny of the symbiotic bacteria is typically congruent with that of the host, signifying co-speciation. Here we show that bacteria living in a single genus of feather lice, Columbicola (Insecta: Phthiraptera), present an exception to this typical pattern.

RESULTS

The phylogeny of Columbicola spp. symbionts revealed the presence of three candidate clades, with the most species-rich clade having a comb-like topology with very short internodes and long terminal branches. Evolutionary simulations indicate that this topology is characteristic of a process of repeated symbiont replacement over a brief time period. The two remaining candidate clades in our study exhibit high levels of nucleotide substitution, suggesting accelerated molecular evolution due to relaxed purifying selection or smaller effective population size, which is typical of many vertically transmitted insect symbionts. Representatives of the fast-evolving and slow-evolving symbiont lineages exhibit the same localization, migration, and transmission patterns in their hosts, implying direct replacement.

CONCLUSIONS

Our findings suggest that repeated, independent symbiont replacements have taken place over the course of the relatively recent radiation of Columbicola spp. These results are compatible with the notion that lice and other insects have the capability to acquire novel symbionts through the domestication of progenitor strains residing in their local environment.

Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution

Hosts and their symbionts are involved in intimate physiological and ecological interactions. The impact of these interactions on the evolution of each partner depends on the time-scale considered. Short-term dynamics - 'coevolution' in the narrow sense - has been reviewed elsewhere. We focus here on the long-term evolutionary dynamics of cospeciation and speciation following host shifts. Whether hosts and their symbionts speciate in parallel, by cospeciation, or through host shifts, is a key issue in host-symbiont evolution. In this review, we first outline approaches to compare divergence between pairwise associated groups of species, their advantages and pitfalls. We then consider recent insights into the long-term evolution of host-parasite and host-mutualist associations by critically reviewing the literature. We show that convincing cases of cospeciation are rare (7%) and that cophylogenetic methods overestimate the occurrence of such events. Finally, we examine the relationships between short-term coevolutionary dynamics and long-term patterns of diversification in host-symbiont associations. We review theoretical and experimental studies showing that short-term dynamics can foster parasite specialization, but that these events can occur following host shifts and do not necessarily involve cospeciation. Overall, there is now substantial evidence to suggest that coevolutionary dynamics of hosts and parasites do not favor long-term cospeciation.

Bacterial symbiont and salivary peptide evolution in the context of leech phylogeny

The evolutionary history of leeches is employed as a general framework for understanding more than merely the systematics of this charismatic group of annelid worms, and serves as a basis for understanding blood-feeding related correlates ranging from the specifics of gut-associated bacterial symbionts to salivary anticoagulant peptides. A variety of medicinal leech families were examined for intraluminal crop bacterial symbionts. Species of Aeromonas and Bacteroidetes were characterized with DNA gyrase B and 16S rDNA. Bacteroidetes isolates were found to be much more phylogenetically diverse and suggested stronger evidence of phylogenetic correlation than the gammaproteobacteria. Patterns that look like co-speciation with limited taxon sampling do not in the full context of phylogeny. Bioactive compounds that are expressed as gene products, like those in leech salivary glands, have 'passed the test' of evolutionary selection. We produced and bioinformatically mined salivary gland EST libraries across medicinal leech lineages to experimentally and statistically evaluate whether evolutionary selection on peptides can identify structure-function activities of known therapeutically relevant bioactive compounds like antithrombin, hirudin and antistasin. The combined information content of a well corroborated leech phylogeny and broad taxonomic coverage of expressed proteins leads to a rich understanding of evolution and function in leech history.

Analysis of parasite host-switching: limitations on the use of phylogenies

Even the most generalist parasites usually occur in only a subset of potential host species, a tendency which reflects overriding environmental constraints on their distributions in nature. The periodic shifting of these limitations represented by host-switches may have been an important process in the evolution of many host-parasite assemblages. To study such events, however, it must first be established where and when they have occurred. Past host-switches within a group of parasites are usually inferred from a comparison of the parasite phylogeny with that of the hosts. Congruence between the phylogenies is often attributed to a history of association by descent with cospeciation, and incongruence to host-switching or extinction in ‘duplicated’ parasite lineages (which diverged without a corresponding branching of the host tree). The inference of host-switching from incongrucnt patterns is discussed. Difficulties arise because incongruence can frequently be explained by different combinations of biologically distinct events whose relative probabilities are uncertain. Also, the models of host parasite relationships implicit in historical reconstructions may often not allow for plausible sources of incongruence other than host-switching or duplication/extinction, or for the possibility that colonization could, in some circumstances, be disguised by ‘false’ congruence.

A permutation test of host-parasite cospeciation

We introduce a statistical method that explores host-parasite coevolution by testing the null hypothesis that hosts and their associated parasites evolved independently. This test is simple and intuitive and involves only suitable randomization of the observed data. It is not even necessary to construct host and parasite phylogenetic trees, as the test can be performed directly on distance matrices. Statistical power of the test was evaluated using simulated data consistent with the alternative hypothesis of cospeciation. Results were compared with the method of Mantel (1967) and the ParaFit method of Legendre et al. (2002). We observed that our method has greater power overall and thus a higher ability to detect cospeciation in closely related host-parasite systems. Our test was also successful when applied to the pocket gopher and chewing lice system.

Phylogenetic tests of distribution patterns in South Asia: towards an integrative approach

The last four decades have seen an increasing integration of phylogenetics and biogeography. However, a dearth of phylogenetic studies has precluded such biogeographic analyses in South Asia until recently. Noting the increase in phylogenetic research and interest in phylogenetic biogeography in the region, we outline an integrative framework for studying taxon distribution patterns. While doing so, we pay particular attention to challenges posed by the complex geological and ecological history of the region, and the differences in distribution across taxonomic groups. We outline and compare three widely used phylogenetic biogeographic approaches: topology-based methods (TBMs), pattern-based methods (PBMs) and event-based methods (EBMs). TBMs lack a quantitative framework and utilize only part of the available phylogenetic information. Hence, they are mainly suited for preliminary enquiries. Both PBMs and EBMs have a quantitative framework, but we consider the latter to be particularly suited to the South Asian context since they consider multiple biogeographic processes explicitly, and can accommodate a reticulated history of areas. As an illustration, we present a biogeographic analysis of endemic Sri Lankan agamid lizards. The results provide insights into the relative importance of multiple processes and specific zones in the radiation of two speciose lizard clades.