Large-scale assignment of orthology: back to phylogenetics?

Reliable orthology prediction is central to comparative genomics. Although orthology is defined by phylogenetic criteria, most automated prediction methods are based on pairwise sequence comparisons. Recently, automated phylogeny-based orthology prediction has emerged as a feasible alternative for genome-wide studies.     

Unleashing the force of cladistics? Metazoan phylogenetics and hypothesis testing

The accumulation of multiple phylogenetic hypotheses for theMetazoa invites an evaluation of current progress in the field.I discuss three case studies from the recent literature to assesshow cladistic analyses of metazoan morphology have contributedto our understanding of animal evolution. The first case studyon cleavage cross patterns examines whether a decade of unanimouscharacter scoring across different cladistic studies can beconsidered a reliable indicator of accumulated wisdom. The tworemaining case studies illustrate how the unique strength ofcladistic analyses to arbitrate between competing hypothesescan be crippled when insufficient attention is directed towardsthe construction of the data matrix. The second case study discussesa recent morphological cladistic analysis aimed at providinginsight into the evolution of larval ciliary bands (prototrochs)in the Spiralia, and the third case study evaluates how foursubsequent morphological cladistic analyses have contributedto our understanding of the phylogenetic placement of a problematicum,the Myzostomida. I conclude that current phylogenetic analysesof the Metazoa have not fully exploited the power of cladisticsto test available alternative hypotheses. If our goal is togenerate genuine progress in understanding rather than stochasticvariation of opinions through time, we have to shift our attentionfrom using cladistics as an easy tool to generate "novel" hypothesesof metazoan relationships, towards employing cladistics morecritically as an effective instrument to test the relative meritof available multiple alternative hypotheses.     

Missing something? Codon aversion as a new character system in phylogenetics

Although many studies have documented codon usage bias in different species, the importance of codon usage in a phylogenetic framework remains largely unknown. We demonstrate that a phylogenetic signal is present in the codon usage and non‐usage biases of 17 717 orthologues evaluated across 72 tetrapod species using a simple parsimony analysis of a binary matrix of codon characters. Phylogenies estimated using stop codons were more congruent with previous hypotheses than phylogenies based on any other single codon or a combination of codons. Although each codon is present in every species, specific genes have different codon preferences and may or may not use every possible codon. This observation allowed us to map the pattern of codon usage and non‐usage across the topology. These results suggest that codon usage is phylogenetically conserved across shallow and deep levels within tetrapods.     

What can phylogenetics tell us about speciation in the Cape flora?

The spectacular diversity of the Cape flora has promoted wide speculation on the evolutionary processes behind its origins, but until recently these ideas could not be tested rigorously due to the almost complete absence of a fossil record for the region. Now, molecular phylogenetic approaches, combined with analyses of ecological and biogeographical information, offer the potential to test key hypotheses about speciation of so-called Cape clades of flowering plants. We outline the main theories and how they might be tested by phylogenetic approaches. One conclusion is that population level studies of particular species complexes are now needed to complement the growing volume of phylogenetic information for Cape clades and to provide better understanding of mechanisms of population divergence in the Cape. Another is that comparisons between Cape and non-Cape clades are needed to confirm whether speciation is indeed faster in the Cape region. An alternative possibility, that extinction rates are lower, should also be considered in these comparisons. By virtue of the ongoing, coordinated efforts by a global team of botanists, the Cape is now uniquely placed for exploring the origins and assembly of a regional assemblage or biome.     

Are monophyly and synapomorphy the same or different? Revisiting the role of morphology in phylogenetics

Species are groups of organisms, marked out by reproductive (replicative) properties. Monophyletic taxa are groups of species, marked out by synapomorphies. In Nelson’s analysis, monophyly and synapomorphy are identical relations. Monophyly and synapomorphy, however, are not equivalent relations. Monophyly is epistemically not accessible, whereas synapomorphy is epistemically accessible through character analysis. Monophyly originates with speciation, the two sister‐species that come into being through the splitting of the ancestral species lineage forming a monophyletic taxon at the lowest level of inclusiveness. Synapomorphy provides the empirical evidence for monophyly, inferred from character analysis in the context of a three‐taxon statement. If synapomorphy and monophyly were equivalent, phylogenetic systematists should find a single tree, instead of multiple equally parsimonious trees. Understanding synapomorphy as the relevant evidence for phylogenetic inference reveals a category mistake in contemporary phylogenetics: the treatment of morphological characters mapped onto molecular trees as synapomorphies and homoplasies. The mapping of morphological characters onto nodes of a molecular tree results in an empirically empty procedure for synapomorphy discovery. Morphological synapomorphies and homoplasies can only be discovered by morphological and combined analyses. The use of morphology in phylogenetic inference in general is defended by examples from Laurales and Squamata in particular. To make empirical evidence scientifically relevant in order to search for concordance, or dis‐concordance, of phylogenetic signal, is certainly more fruitful for phylogenetics than the uncritical mapping of morphological traits on a molecular scaffold. © The Willi Hennig Society 2010.     

When is enough,enough in phylogenetics? A case in point from Hordeum (Poaceae)

Direct optimization was used to reconstruct the phylogeny of the 26 diploid taxa included in the genus Hordeum. The total data set was composed of 16 nucleotide sequence regions from the nuclear as well as the plastid genome. The nine nuclear regions were from single‐copy, protein coding genes located on six of the seven chromosome pairs in the diploid H. vulgare genome. The seven plastid regions comprise protein coding genes as well as intergenic regions. Studies of character congruence between data partitions showed no correlation between chromosomal location and congruence among the nuclear sequences and a level of congruence among the plastid sequences comparable with the level among the nuclear sequences. Combined analysis of all data resolved the phylogeny completely with most clades being robust and well supported. However, due to incongruence among data partitions some relationships are still and likely to remain ambiguously inferred. Rather than adding still more genes to the phylogenetic analyses, patterns of incongruence may be better explored by adding data from multiple specimens per taxon. For some species relationships the plastid data appear positively misleading, emphasizing the need for caution if plastid data are the only or dominant type of data used for phylogenetic reconstruction and subsequent re‐classification.
© The Willi Hennig Society 2011.     

Parametric Maximum Parsimonious Reconstruction on Trees

We give a formal study of the relationships between the transition cost parameters and the generalized maximum parsimonious reconstructions of unknown (ancestral) binary character states {0,1}\{\mathtt{0},\mathtt{1}\} over a phylogenetic tree. As a main result, we show there are two thresholds l¹_n\lambda^{\mathtt{1}}_{n} and l⁰_n\lambda^{\mathtt{0}}_{n}, generally confounded, associated to each node n of the phylogenetic tree and such that there exists a maximum parsimonious reconstruction associating state 1\mathtt{1} to n (resp. state 0\mathtt{0} to n) if the ratio “10\mathtt{1}\mathtt{0}-cost”/“01\mathtt{0}\mathtt{1}-cost” is smaller than l¹_n\lambda^{\mathtt{1}}_{n} (resp. greater than l⁰_n\lambda^{\mathtt{0}}_{n}). We propose a dynamic programming algorithm computing these thresholds in a quadratic time with the size of tree.     

Molecular phylogenetics of Iberian wall lizards (Podarcis): is Podarcis hispanica a species complex?

Phylogenetic relationships between species and morphotypes of Podarcis wall lizards from the Iberian Peninsula and north Africa were estimated using partial 12S rRNA and cytochrome b mitochondrial DNA sequences. All species except Podarcis hispanica form monophyletic units. P. hispanica is paraphyletic, although all identified morphotypes are monophyletic. These morphotypes represent highly divergent lineages showing 10-15% pairwise sequence divergence with the cytochrome b gene. The data suggest that P. hispanica is a species complex. We recommend using P. hispanica* until additional sampling delimits the number and ranges of species currently referred to P. hispanica. P. carbonelli, which has recently been raised to species status, is confirmed as a genetically distinct form. P. atrata is genetically distinct, but much more closely related to some populations of P. hispanica than previously thought.     

Molecular and morphological phylogenetics of weevils (coleoptera,curculionoidea): do niche shifts accompany diversification?

The main goals of this study were to provide a robust phylogeny for the families of the superfamily Curculionoidea, to discover relationships and major natural groups within the family Curculionidae, and to clarify the evolution of larval habits and host-plant associations in weevils to analyze their role in weevil diversification. Phylogenetic relationships among the weevils (Curculionoidea) were inferred from analysis of nucleotide sequences of 18S ribosomal DNA (rDNA; approximately 2,000 bases) and 115 morphological characters of larval and adult stages. A worldwide sample of 100 species was compiled to maximize representation of weevil morphological and ecological diversity. All families and the main subfamilies of Curculionoidea were represented. The family Curculionidae sensu lato was represented by about 80 species in 30 "subfamilies" of traditional classifications. Phylogenetic reconstruction was accomplished by parsimony analysis of separate and combined molecular and morphological data matrices and Bayesian analysis of the molecular data; tree topology support was evaluated. Results of the combined analysis of 18S rDNA and morphological data indicate that monophyly of and relationships among each of the weevil families are well supported with the topology ((Nemonychidae, Anthribidae) (Belidae (Attelabidae (Caridae (Brentidae, Curculionidae))))). Within the clade Curculionidae sensu lato, the basal positions are occupied by mostly monocot-associated taxa with the primitive type of male genitalia followed by the Curculionidae sensu stricto, which is made up of groups with the derived type of male genitalia. High support values were found for the monophyly of some distinct curculionid groups such as Dryophthorinae (several tribes represented) and Platypodinae (Tesserocerini plus Platypodini), among others. However, the subfamilial relationships in Curculionidae are unresolved or weakly supported. The phylogeny estimate based on combined 18S rDNA and morphological data suggests that diversification in weevils was accompanied by niche shifts in host-plant associations and larval habits. Pronounced conservatism is evident in larval feeding habits, particularly in the host tissue consumed. Multiple shifts to use of angiosperms in Curculionoidea were identified, each time associated with increases in weevil diversity and subsequent shifts back to gymnosperms, particularly in the Curculionidae.     

Fission or fusion? Mitochondrial DNA phylogenetics of the chromosome races of Hemideina crassidens (Orthoptera: Anostostomatidae)

The weta Hemideina crassidens has two chromosomal races that differ by two centric fusions or fissions. The mitochondrial DNA of weta from both chromosomal races and a sister species were sequenced for a 750-bp region of the gene coding for cytochrome oxidase I. The average pairwise genetic distance among the 15 (XO)-chromosome race weta was almost four times greater than the average distance among the 19 (XO)-chromosome race weta. The weta from the 19-chromosome race formed a well-supported monophyletic clade in all shortest maximum parsimony trees. Maximum likelihood and neighbor-joining trees suggested that the 15-chromosome karyotype was paraphyletic with respect to the 19-chromosome karyotype, but this was not supported by maximum parsimony analyses. Although phylogenetic analysis could not exclude chromosome fusion as the rearrangement responsible for the karyotype differentiation, the level of sequence variation and pattern of distribution appear to implicate fission as the more likely event.     

Parametric analysis of the ratio-dependent predator–prey model

We present a complete parametric analysis of stability properties and dynamic regimes of an ODE model in which the functional response is a function of the ratio of prey and predator abundances. We show the existence of eight qualitatively different types of system behaviors realized for various parameter values. In particular, there exist areas of coexistence (which may be steady or oscillating), areas in which both populations become extinct, and areas of "conditional coexistence" depending on the initial values. One of the main mathematical features of ratio-dependent models, distinguishing this class from other predator-prey models, is that the Origin is a complicated equilibrium point, whose characteristics crucially determine the main properties of the model. This is the first demonstration of this phenomenon in an ecological model. The model is investigated with methods of the qualitative theory of ODEs and the theory of bifurcations. The biological relevance of the mathematical results is discussed both regarding conservation issues (for which coexistence is desired) and biological control (for which extinction is desired).     

Who is the closest extant cousin of humans? Total‐evidence approach to hominid phylogenetics via simultaneous optimization

J. R. Grehan & J. H. Schwartz (Journal of Biogeography, 2009, 36 , 1823–1844) argued that humans (Homo) are more closely related to orangutans (Pongo) than to chimpanzees (Pan), and used this scenario to draw biogeographical conclusions about human origins. They discussed a contradiction between phenotypical and molecular results that has led to a debate about the reliability of genetic versus phenotypic data. The main aim of our study is to test the conflicting phylogenetic hypotheses by a total‐evidence analysis based on simultaneous optimization of extensive phenotypic and molecular data sets. Our results supported the human–chimpanzee clade, without any phenotypical–molecular data conflict, as the same phylogeny emerged both from the total analysis and when the molecular and phenotypic data were analysed separately. Sensitivity analyses showed that the result was not dependent on the parameters chosen for character weighting.     

Molecular phylogenetics of the arboreal Australian gecko genus Oedura Gray 1842 (Gekkota: Diplodactylidae): another plesiomorphic grade?

The family Diplodactylidae is the most ecologically diverse and geographically widespread radiation of geckos within Australasia. Herein we present a first comprehensive phylogenetic analysis of relationships of diplodactylid geckos currently assigned to the genus Oedura, a group of relatively generalised arboreal Australian geckos. Maximum Likelihood, bayesian and Maximum Parsimony analyses of a combination of over two and a half kilobases of nuclear (PDC, Rag-1) and mitochondrial (ND2, ND4, tRNA) sequence data all identified four distinctive lineages within Oedura s.l. Based on their deep divergences and a suite of diagnostic morphological characters we recognise each of these four lineages as genera, two of which are monotypic and newly described herein. Our molecular data also suggest that Oedura s.l. is not monophyletic, but is instead a plesiomorphic grade restricted to islands of rocky or forested habitat around coastal and central Australia. In contrast, combined analysis of all data suggests the Australian arid zone is dominated by a single comparatively derived and relatively species rich clade including most other genera of Australian Diplodactylidae. Additional data are required to properly resolve basal divergence events within the Diplodactylidae, however the emerging pattern of relationships and divergence is consistent with the hypothesis that monsoonal and temperate lineages are ancestral to the arid zone fauna, but also indicate that arid zone lineages and radiations are relatively old, and potentially date back to the mid Miocene or earlier.