Character space restrictions and boundary conditions in the evolution of quantitative multistate characters

The effects of restrictions of available character space on the mean morphological distance between living members of evolutionary phylads are examined by Monte Carlo simulation. The approach involves specifying the degree to which ancestor-descendant species may differ and limiting the range of attainable character states within a phylad. Morphological evolution is modeled as a Markovian process involving quantitative multistate characters. States for a given character are allowed to evolve at time-dependent or speciation-dependent rates.The final distributions of morphological distance for a given trait among members of a phylad depend on the number of species in the phylad, the rate and pattern of evolution of new character states, and the existence of boundary conditions indicating possible selective constraints on the trait. When morphological change is proportional to time, increasing restrictions on character evolution tend to (a) lower mean distance between species and (b) leave the ratio of mean distances ($\text{D}{}_{\mathrm{R}}\text{D}{}_{\mathrm{p}}$) in species-rich vs. species-poor phylads of comparable evolutionary age near one. When change is proportional to rate of speciation, similar restrictions tend to (a) limit mean distance only in phylads in which the number of speciations exceeds the range of attainable character states and (b) permit $\text{D}{}_{\mathrm{R}}\text{D}{}_{\mathrm{p}}$ to be considerably greater than one, except in extreme cases. Implications of these results for the current phyletic gradualism-rectangular evolution controversy are considered.     

Genetic Change and Rates of Cladogenesis

Models are introduced which predict ratios of mean levels of genetic divergence in species-rich versus species-poor phylads under two competing assumptions: (1) genetic differentiation is a function of time, unrelated to the number of cladogenetic events and (2) genetic differentiation is proportional to the number of speciation events in the group. The models are simple, general, and biologically real, but not precise. They lead to qualitatively distinct predictions about levels of genetic divergence depending upon the relationship between rates of speciation and amount of genetic change. When genetic distance between species is a function of time, mean genetic distances in speciose and depauperate phylads of equal evolutionary age are very similar. On the contrary, when genetic distance is a function of the number of speciations in the history of a phylad, the ratio of mean genetic distances separating species in speciose versus depauperate phylads is greater than one, and increases rapidly as the frequency of speciations in one group relative to the other increases. The models may be tested with data from natural populations to assess (1) possible correlations between rates of anagenesis and cladogenesis and (2) the amount of genetic differentiation accompanying the speciation process. The data collected in electrophoretic surveys and other kinds of studies can be used to test the predictions of the models. For this purpose genetic distances need to be measured in speciose and depauperate phylads of equal evolutionary age. The limited information presently available agrees better with the model predicting that genetic change is primarily a function of time, and is not correlated with rates of speciation. Further testing of the models is, however, required before firm conclusions can be drawn.     

Divergent patterns of diversification in courtship and genitalic characters of Timema walking‐sticks

Understanding the patterns of diversification in sexual traits and the selection underlying such diversification represents a major unresolved question in evolutionary biology. We examined the phylogenetic diversification for courtship and external genitalic characters across ten species of Timema walking‐sticks, to infer the tempos and modes of character change in these sexual traits and to draw inferences regarding the selective pressures underlying speciation and diversification in this clade. Rates of inferred change in male courtship behaviours were proportional to speciation events, but male external genitalic structures showed a pattern of continuous change across evolutionary time, with divergence proportional to branch lengths. These findings suggest that diversification of courtship behaviour is mediated by processes that occur in association with speciation, whereas diversification of genitalia occurs more or less continuously, most likely driven by forces of sexual selection.     

Heterozygosity and hybrid performance in larch

Random Amplified Polymorphic DNAs (RAPD) were used for estimating genetic distances between 12 European larches (Larix decidua) and 12 Japanese larches (L. kaempferi) that were the parents in a factorial mating design. One hundred and eleven fragments were used for establishing genetic distances based on Jaccard's coefficient between parents. Thirteen fragments differentiated the larch species. The genetic distance between individuals of the same species (D _J =0.39 in the Japanese larch and 0.45 in the European larch) was lower than the genetic distance between species (D _J =0.72). A UPGMA dendrogram based on genetic distances clearly clustered each larch species, confirming the speciation at a molecular level. Correlations between genetic distances of the parents and performances of the hybrid families were established for various quantitative traits. Significant values were found for growth characters and branch insertion angle, which suggested an effect of general heterozygosity level on hybrid traits. These correlations also evolved with tree age: the maximal correlation was noticed on 6-year-old trees for height. The lack of correlation between parental genetic distances and hybrid performances for the other quantitative traits suggested that these characters were controlled by fewer genes. The results of this study show that crosses between genetically distant parents produce hybrids with excellent growth performances; this represents a potential selection criterion of the genitors.     

Distances that perfectly mislead

Given a collection of discrete characters (e.g., aligned DNA sites, gene adjacencies), a common measure of distance between taxa is the proportion of characters for which taxa have different character states. Tree reconstruction based on these (uncorrected) distances can be statistically inconsistent and can lead to trees different from those obtained using character-based methods such as maximum likelihood or maximum parsimony. However, in these cases the distance data often reveal their unreliability by some deviation from additivity, as indicated by conflicting support for more than one tree. We describe two results that show how uncorrected (and miscorrected) distance data can be simultaneously perfectly additive and misleading. First, multistate character data can be perfectly compatible and define one tree, and yet the uncorrected distances derived from these characters are perfectly treelike (and obey a molecular clock), only for a completely different tree. Second, under a Markov model of character evolution a similar phenomenon can occur; not only is there statistical inconsistency using uncorrected distances, but there is no evidence of this inconsistency because the distances look perfectly treelike (this does not occur in the classic two-parameter Felsenstein zone). We characterize precisely when uncorrected distances are additive on the true (and on a false) tree for four taxa. We also extend this result to a more general setting that applies to distances corrected according to an incorrect model.     

SELECTION FOR NATIVE CHARACTERS IN HYBRIDS BETWEEN TWO LOCALLY ADAPTED PLANT SUBSPECIES

Gene exchange between locally adapted plant populations can have significant evolutionary consequences, including changes in genetic diversity, introduction of adaptive or maladaptive traits, disruptive of coadaptive gene complexes, and the creation of new ecotypes or even species. The potential for introgression between divergent populations will depend on the strength of selection against nonnative characters. Morphologically variable F₂ hybrids of two Gilia capitata subspecies were used to evaluate the strength of phenotypic selection and the response to selection in the home habitats of each subspecies. At both sites, traits diagnostic of the subspecies were subject to significant phenotypic selection, probably mediated by direct selection on unmeasured correlated characters. Phenotypic selection favored native morphologies in all but a single case; leaf shape of one subspecies was favored in both habitats. The strength of selection varied between sites, with one site selecting more strongly against nonnative characters. Offspring of the F₂ hybrids showed a significant evolutionary response to selection when grown in a common environment. Evolution was in the direction of similarity with the subspecies native to the site where selection was imposed. This result reveals that native character states are adaptive and suggests that selection will maintain native morphologies even after a substantial influx of genes from an ecologically and morphologically distinct, and locally adapted subspecies.     

THE EFFECT OF ORDERED CHARACTERS ON PHYLOGENETIC RECONSTRUCTION

Abstract Morphological structures are likely to undergo more than a single change during the course of evolution. As a result, multistate characters are common in systematic studies and must be dealt with. Particularly interesting is the question of whether or not multistate characters should be treated as ordered (additive) or unordered (non-additive). In accepting a particular hypothesis of order, numerous others are necessarily rejected. We review some of the criteria often used to order character states and the underlying assumptions inherent in these criteria.
The effects that ordered multistate characters can have on phylogenetic reconstruction are examined using 27 data sets. It has been suggested that hypotheses of character state order are more informative then hypotheses of unorder and may restrict the number of equally parsimonious trees as well as increase tree resolution. Our results indicate that ordered characters can produce more, equal or less equally parsimonious trees and can increase, decrease or have no effect on tree resolution. The effect on tree resolution can be a simple gain in resolution or a dramatic change in sister-taxa relationships. In cases where several outgroups are included in the data matrix, hypotheses of order can change character polarities by altering outgroup topology. Ordered characters result in a different topology from unordered characters only when the hierarchy of the cladogram disagrees with the investigator's a priori hypothesis of order. If the best criterion for assessing character evolution is congruence with other characters, the practice of ordering multistate characters is inappropriate.     

Sympatric divergence and clinal variation in multiple coloration traits of Ficedula flycatchers

Geographic variation in phenotypes plays a key role in fundamental evolutionary processes such as local adaptation, population differentiation and speciation, but the selective forces behind it are rarely known. We found support for the hypothesis that geographic variation in plumage traits of the pied flycatcher Ficedula hypoleuca is explained by character displacement with the collared flycatcher Ficedula albicollis in the contact zone. The plumage traits of the pied flycatcher differed strongly from the more conspicuous collared flycatcher in a sympatric area but increased in conspicuousness with increasing distance to there. Phenotypic differentiation (P_ST) was higher than that in neutral genetic markers (F_ST), and the effect of geographic distance remained when statistically controlling for neutral genetic differentiation. This suggests that a cline created by character displacement and gene flow explains phenotypic variation across the distribution of this species. The different plumage traits of the pied flycatcher are strongly to moderately correlated, indicating that they evolve non‐independently from each other. The flycatchers provide an example of plumage patterns diverging in two species that differ in several aspects of appearance. The divergence in sympatry and convergence in allopatry in these birds provide a possibility to study the evolutionary mechanisms behind the highly divergent avian plumage patterns.     

A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference

AFLPs (and to a lesser extent ISSRs and RAPDs) are increasingly being used for phylogenetic inference among closely related species. Presence/absence characters for each AFLP allele treat all absences as homologous to one another. With three or more alleles, terminals are grouped by their shared absence of alleles in character-based phylogenetic-inference methods in a manner that is not redundant with their shared presence of an alternative allele. We conducted simulations to quantify how severe the negative effect of using presence/absence characters of individual bands is for phylogenetic inference relative to standard multistate characters. We examined alternative tree topologies, relative branch lengths, numbers of characters, rates of evolution, and numbers of alternative alleles, using both parsimony and Nei-and-Li distance analyses. Multistate parsimony generally outperformed presence/absence parsimony, which in turn outperformed Nei-and-Li distance. Increasing the character-state space (i.e., the number of alternative character states available) was found to be advantageous for all three methods of analysis examined, but was most advantageous for multistate parsimony. However, the advantage of multistate parsimony relative to Nei-and-Li distance decreased when applied to more divergent characters. More parsimony-informative variation generally alleviated the problem associated with scoring multistate characters as presence/absence characters. The ensemble consistency index was lower for presence/absence characters relative to multistate characters.     

A NOVEL METHOD FOR ECONOMICAL DIAGNOSIS OF CLADOGRAMS UNDER SANKOFF OPTIMIZATION

Abstract— A method is proposed to recode certain phylogenetic cost matrices in order to lessen the computational burden involved in the search for parsimonious cladograms. Multistate characters with complex costs among character states are converted to unordered multistate and binary variables with differential weights. These new variables can be optimized efficiently. The method has applications in cases where character states are distributed hierarchically and symmetrically. Cases of "inapplicable" states in morphology, and transition-transversion weighting in molecular sequence data are discussed this light.     

Supervised Lowess normalization of comparative genome hybridization data – application to lactococcal strain comparisons

Background

Visualising the evolutionary history of a set of sequences is a challenge for molecular phylogenetics. One approach is to use undirected graphs, such as median networks, to visualise phylogenies where reticulate relationships such as recombination or homoplasy are displayed as cycles. Median networks contain binary representations of sequences as nodes, with edges connecting those sequences differing at one character; hypothetical ancestral nodes are invoked to generate a connected network which contains all most parsimonious trees. Quasi-median networks are a generalisation of median networks which are not restricted to binary data, although phylogenetic information contained within the multistate positions can be lost during the preprocessing of data. Where the history of a set of samples contain frequent homoplasies or recombination events quasi-median networks will have a complex topology. Graph reduction or pruning methods have been used to reduce network complexity but some of these methods are inapplicable to datasets in which recombination has occurred and others are procedurally complex and/or result in disconnected networks.

Results

We address the problems inherent in construction and reduction of quasi-median networks. We describe a novel method of generating quasi-median networks that uses all characters, both binary and multistate, without imposing an arbitrary ordering of the multistate partitions. We also describe a pruning mechanism which maintains at least one shortest path between observed sequences, displaying the underlying relations between all pairs of sequences while maintaining a connected graph.

Conclusion

Application of this approach to 5S rDNA sequence data from sea beet produced a pruned network within which genetic isolation between populations by distance was evident, demonstrating the value of this approach for exploration of evolutionary relationships.     

Evolution of male tail development in rhabditid nematodes related to Caenorhabditis elegans

The evolutionary pathway that has led to male tails of diverse morphology among species of the nematode family Rhabditidae was reconstructed. This family includes the well-studied model species Caenorhabditis elegans. By relating the steps of male tail morphological evolution to the phenotypic changes brought about by developmental mutations induced experimentally in C. elegans, the goal is to identify genes responsible for morphological evolution. The varying morphological characters of the male tails of several rhabiditid species have been described previously (Fitch and Emmons, 1995, Dev. Biol. 170:564-582). The developmental events preceding differentiation of the adult structures have also been analyzed; in many cases the origins of varying adult morphological characters were traced to differences during ontogeny. In the present work, the evolutionary changes producing these differences were reconstructed in the context of the four possible phylogenies supported independently by sequences of 18S ribosomal RNA genes (rDNA). Two or more alternative states were defined for 36 developmental and adult morphological characters. These characters alone do not provide sufficient data to resolve most species relationships; however, when combined with the rDNA characters, they provide stronger support for one of the four rDNA phylogenies. Assuming a model of ordered transformations for multistate developmental characters generally results in greater resolution. Transformations between character states can be assigned unequivocally by parsimony to unambiguous branches for most of the characters. Correlations are thereby revealed for some of the developmental characters, indicating a probability of a shared developmental or genetic regulatory pathway. Four of the unequivocal character state changes on unambiguously supported branches closely resemble the phenotypic changes brought about by known mutations in C. elegans. These mutations define genes that are known to act in genetic regulatory hierarchies controlling pattern formation, differentiation, and morphogenesis. Although these studies are still at an early stage, these results strongly suggest that parallel studies of developmental mutants in C. elegans and of morphological and developmental evolution among related nematodes will help define genetic changes underlying the evolution of form.     

DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood

Background

The study of discrete characters is crucial for the understanding of evolutionary processes. Even though great advances have been made in the analysis of nucleotide sequences, computer programs for non-DNA discrete characters are often dedicated to specific analyses and lack flexibility. Discrete characters often have different transition rate matrices, variable rates among sites and sometimes contain unobservable states. To obtain the ability to accurately estimate a variety of discrete characters, programs with sophisticated methodologies and flexible settings are desired.

Results

DiscML performs maximum likelihood estimation for evolutionary rates of discrete characters on a provided phylogeny with the options that correct for unobservable data, rate variations, and unknown prior root probabilities from the empirical data. It gives users options to customize the instantaneous transition rate matrices, or to choose pre-determined matrices from models such as birth-and-death (BD), birth-death-and-innovation (BDI), equal rates (ER), symmetric (SYM), general time-reversible (GTR) and all rates different (ARD). Moreover, we show application examples of DiscML on gene family data and on intron presence/absence data.

Conclusion

DiscML was developed as a unified R program for estimating evolutionary rates of discrete characters with no restriction on the number of character states, and with flexibility to use different transition models. DiscML is ideal for the analyses of binary (1s/0s) patterns, multi-gene families, and multistate discrete morphological characteristics.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-320) contains supplementary material, which is available to authorized users.     

Speciational Evolution: a Phylogenetic Test With Allozymes in Sceloporus (Reptilia)

Abstract— The potential role of speciation in accelerating evolutionary divergence remains controversial. Earlier tests based on genetic and morphologic distances which indicated an absence of speciational evolution rely on problematic assumptions. We provide a phylogenetic test in which amounts of discrete character change relative to an outgroup are compared between sister taxa. Although this test is constrained by a need to assume similar extinction rates in groups compared, it provides conceptual improvements regarding monophyly, equal age of taxa, and distribution of homoplasy. Based on analysis of 68 informative allozyme characters for 19 lizard species in the genus Sceloporus , significant speciational evolution and punctuational change is, at least, a viable explanation for the distribution of observed character changes.     

Character combinations, convergence and diversification in ectoparasitic arthropods

Different lineages of organisms diversify over time at different rates, in part as a consequence of the characteristics of the species in these lineages. Certain suites of traits possessed by species within a clade may determine rates of diversification, with some particular combinations of characters acting synergistically to either limit or promote diversification; the most successful combinations may also emerge repeatedly in different clades via convergent evolution. Here, the association between species characters and diversification is investigated amongst 21 independent lineages of arthropods ectoparasitic on vertebrate hosts. Using nine characters (each with two to four states) that capture general life history strategy, transmission mode and host-parasite interaction, each lineage was described by the set of character states it possesses. The results show, firstly, that most possible pair-wise combinations of character states have been adopted at least once, sometimes several times independently by different lineages; thus, ectoparasitic arthropods have explored most of the life history character space available to them. Secondly, lineages possessing commonly observed combinations of character states are not necessarily the ones that have experienced the highest rates of diversification (measured as a clade’s species-per-genus ratio). Thirdly, some specific traits are associated with higher rates of diversification. Using more than one host per generation, laying eggs away from the host and intermediate levels of fecundity are features that appear to have promoted diversification. These findings indicate that particular species characters may be evolutionary drivers of diversity, whose effects could also apply in other taxa.     

Molecular phylogeny reveals the repeated evolution of complex male genital traits in the New Zealand moth genus Izatha (Lepidoptera: Xyloryctidae)

Male genitalia are among the most rapidly evolving and divergent morphological structures and sexual selection is known to drive this phenomenon in many taxa. Because of their diversity, even within a single genus, genital characters are frequently used to infer relationships among closely‐related species. Moths within the genus Izatha (Xyloryctidae) are ideal candidates for investigating the phylogenetic patterns of genital evolution as they display great variation in male genital structure and complexity. We determined the evolutionary relationships among 31 species of Izatha by constructing a molecular phylogeny of the genus based on the mitochondrial cytochrome oxidase subunit I gene and the isocitrate dehydrogenase and carbamoylphosphate synthase domain protein nuclear genes. This allowed estimations of ancestral male genital character states and patterns of male genital diversification using maximum‐likelihood models. The genus is divided into two well‐supported clades and two poorly supported clades at the root of the phylogeny with incomplete phylogenetic resolution within two species groups, likely due to rapid speciation. Izatha display a number of apomorphic phallic traits including cornuti (sclerotized spines) which are either discharged into the female during copulation (deciduous cornuti) or fixed to the male phallus (compound and fish‐hook cornuti). Within the genus, there is a reduction of secondary genital characters – the uncus and gnathos – but an elaboration of another grasping structure, the juxta; the potential origin and functionality of these male genital traits are discussed. Overall, some male genital characters provided a good indication of species relationships; however, several parts of the complex male genitalia of Izatha show evidence of homoplasy and convergence highlighting the problems of using these traits in determining species relationships. Additionally, this convergence has highlighted that complex genital structures may evolve repeatedly and independently within a lineage.     

The ancestral distance test: what relatedness can reveal about correlated evolution in large lineages with missing character data and incomplete phylogenies

The ancestral distance test is introduced to detect correlated evolution between two binary traits in large phylogenies that may lack resolved subclades, branch lengths, and/or comparative data. We define the ancestral distance as the time separating a randomly sampled taxon from its most recent ancestor (MRA) with extant descendants that have an independent trait. The sampled taxon either has (target sample) or lacks (nontarget sample) a dependent trait. Modeled as a Markov process, we show that the distribution of ancestral distances for the target sample is identical to that of the nontarget sample when characters are uncorrelated, whereas ancestral distances are smaller on average for the target sample when characters are correlated. Simulations suggest that the ancestral distance can be estimated using the time, total branch length, taxonomic rank, or number of speciation events between a sampled taxon and the MRA. These results are shown to be robust to deviations from Markov assumptions. A Monte Carlo technique estimates P-values when fully resolved phylogenies with branch lengths are available, and we evaluate the Monte Carlo approach using a data set with known correlation. Measures of relatedness were found to provide a robust means to test hypotheses of correlated character evolution.     

Co‐evolutionary patterns in congeneric monogeneans: a review of Dactylogyrus species and their cyprinid hosts

Patterns associated with the evolution of parasite diversity, speciation and diversification were analysed using Dactylogyrus species (gill monogeneans) and their cyprinid hosts as a model. The aim of this study was to use this highly specific host–parasite systems to review: (1) the diversity and distribution of Dactylogyrus species, (2) the patterns of organization and structure of Dactylogyrus communities, (3) the evolution and determinants of host specificity and (4) the mode of Dactylogyrus speciation and co‐evolutionary patterns in this Dactylogyrus–cyprinid systems. Dactylogyrus are a highly diverse group of parasites, with their biogeography and distribution clearly linked to the evolutionary history of their cyprinid hosts. The coexistence of several Dactylogyrus species on one host is facilitated by increasing niche distances and the differing morphology of their reproductive organs. The positive interspecific and intraspecific interactions seem to be the most important factors determining the structure of Dactylogyrus communities. Host specificity is partially constrained by parasite phylogeny. Being a strict specialist is an ancestral character for Dactylogyrus, being the intermediate specialists or generalists are the derived characters. The evolution of attachment organ morphology is associated with both parasite phylogeny and host specificity. Considering larger and long‐lived hosts or hosts with several ecological characters as the measures of resource predictability, specialists with larger anchors occurred on larger or longer‐living fish species. Intra‐host speciation, a mode of speciation not often recorded in parasites, was observed in Dactylogyrus infecting sympatric cyprinids. Sister parasite species coexisting on the same host occupied niches that differed in at least one niche variable. Intra‐host speciation, however, was not observed in Dactylogyrus species of congeneric hosts from geographically isolated areas, which suggested association by descent and host‐switching events.     

Morphological stasis in the Eurytemora affinis species complex (Copepoda: Temoridae)

Morphological stasis has long been regarded as one of the most challenging problems in evolutionary biology. This study focused on the copepod species complex, Eurytemora affinis, as a model system to determine pattern and degree of morphological stasis. This study revealed discordant rates of morphological differentiation, molecular evolution, and reproductive isolation, where speciation was accompanied by lack of morphological differentiation in secondary sex characters. Comparisons were made among phylogenies based on morphometrics, nuclear (allozyme) loci, and mitochondrial DNA (mtDNA) sequences from cytochrome oxidase I, for a total of 43 populations within the complex. These systematic relationships were also compared to patterns of reproductive isolation. In addition, genetic subdivision of nuclear molecular (allozyme) markers (G _ST) and quantitative (morphological) characters (Q _ST) were determined to infer evolutionary forces driving morphological differentiation. The morphometric phylogeny revealed that all clades, excluding the European clade, were morphologically undifferentiated and formed a polytomy (multifurcation). Morphometric distances were not correlated with mtDNA distances, or with patterns of reproductive isolation. In contrast, nuclear and mtDNA phylogenies were mostly congruent. Reproductive isolation proved to be the most sensitive indicator of speciation, given that two genetically and morphologically proximate populations showed evidence of hybrid breakdown. Quantitative genetic (morphological) subdivision (Q _ST = 0.162) was lower than nuclear genetic subdivision (G _ST = 0.617) for four laboratory-reared North American populations, indicating retarded evolution of morphological characters. This result contrasts with most other species, where Q _ST typically exceeds G _ST as a result of directional selection. Thus, in all but the European populations, evolution of the secondary sex characters was marked by morphological stasis, even between reproductively-isolated populations.