Uninode coding vs gene tree parsimony for phylogenetic reconstruction using duplicate genes

Two different methods of using paralogous genes for phylogenetic inference have been proposed: reconciled trees (or gene tree parsimony) and uninode coding. Gene tree parsimony suffers from 10 serious problems, including differential weighting of nucleotide and gap characters, undersampling which can be misinterpreted as synapomorphy, all of the characters not being allowed to interact, and conflict between gene trees being given equal weight, regardless of branch support. These problems are largely avoided by using uninode coding. The uninode coding method is elaborated to address multiple gene duplications within a single gene tree family and handle problems caused by lack of gene tree resolution. An example of vertebrate phylogeny inferred from nine genes is reanalyzed using uninode coding. We suggest that uninode coding be used instead of gene tree parsimony for phylogenetic inference from paralogous genes.     

THE PHYLOGENY OFLECANACTIS(OPEGRAPHACEAE)

The genusLecanactis, with 24 species, has been phylogenetically analysed using cladistic parsimony methods and support tests. Morphological, anatomical and chemical data were used, comprising 38 characters. Twelve equally most parsimonious trees were obtained. The successive approximations character weighting method gave one most parsimonious tree. The ingroup,Lecanactis, is supported as monophyletic. Although parsimony jackknifing and Bremer support indicate that the trees are poorly supported, some groups are wholly or partly distinguished in both the strict consensus tree, the successive weighting tree and the Jac tree.     

Drawbacks with the use of microsatellites in phylogeography: the song sparrow Melospiza melodia as a case study

Microsatellites are commonly used molecular markers in phylogeography, and many view them as superior to mitochondrial DNA (mtDNA) gene trees. Being based on frequencies of alleles, and not gene trees, microsatellites exhibit the same analytical drawbacks that resulted in the abandonment of allozymes in genetic studies of population history. I illustrate some these familiar drawbacks by reanalyzing microsatellite data on the song sparrow. Subspecies were previously evaluated with hierarchical analyses of molecular variance, suggesting that subspecies explain 8% of the total variance in microsatellite frequencies. However, this useful heuristic technique only evaluates a priori groupings, and the objective of the study ought to be to discover such groupings, not assume them. In fact, other arbitrary groupings of samples explained the same or greater amounts of variance, and I suggest that for testing subspecies limits, a gene tree is preferable. Grouping population samples by subspecies in the San Francisco Bay area accounts for 1.2% of the microsatellite variation, and despite claims that this informs conservation planning, the data do not support any particular population or subspecies as being genetically or evolutionarily significant. A distance phenogram was used to infer a sequential colonization of the Aleutian Islands, but because individuals were pooled into a priori groups and the phenogram was arbitrarily rooted, this conclusion is tenuous. A plot of heterozygosity vs number of alleles per sample showed that an equally parsimonious interpretation is that current genetic diversity tracks effective population size. Microsatellites should be replaced in nuclear-gene phylogeography by analyses of sequences, which will benefit the study of phylogeography, comparison of nuclear and mtDNA results, and aid in interpreting the results in a conservation context.     

The phylogeny and classification of Scaphopoda (Mollusca): an assessment of current resolution and cladistic reanalysis

The first cladistic analysis of phylogeny in the class Scaphopoda (Steiner 1992a,1996) examined relationships among family and selected sub-family taxa using morphological data. A preferred/ consensus tree of relationships illustrated monophyly of the orders Dentaliida and Gadilida, partial resolution among dentaliid families, and complete resolution among gadilid taxa. However, several alternative replications of the analysis, including use of a revised data matrix, did not produce the reported tree number or level of resolution; in all cases, monophyly of the Dentaliida was not supported by strict consensus of resultant parsimonious trees. Reanalysis, using unordered characters and outgroup rooting, only clearly resolves monophyly of the Gadilida and the sister relationship of the Entalinidae with the remaining gadilid families. These analyses emphasize the need for more comparative data and thorough parsimony analysis in scaphopod cladistic phylogenetics, as relationships in this class are still some way from resolution.     

Evaluating intraspecific "network" construction methods using simulated sequence data: do existing algorithms outperform the global maximum parsimony approach?

In intraspecific studies, reticulated graphs are valuable tools for visualization, within a single figure, of alternative genealogical pathways among haplotypes. As available software packages implementing the global maximum parsimony (MP) approach only give the possibility to merge resulting topologies into less-resolved consensus trees, MP has often been neglected as an alternative approach to purely algorithmic (i.e., methods defined solely on the basis of an algorithm) "network" construction methods. Here, we propose to search tree space using the MP criterion and present a new algorithm for uniting all equally most parsimonious trees into a single (possibly reticulated) graph. Using simulated sequence data, we compare our method with three purely algorithmic and widely used graph construction approaches (minimum-spanning network, statistical parsimony, and median-joining network). We demonstrate that the combination of MP trees into a single graph provides a good estimate of the true genealogy. Moreover, our analyses indicate that, when internal node haplotypes are not sampled, the median-joining and MP methods provide the best estimate of the true genealogy whereas the minimum-spanning algorithm shows very poor performances.     

Generic interrelationships within the Spionidae (Annelida: Polychaeta)

The phylogenetic relationships of spionid genera are estimated from parsimony analyses of morphological characters, with Trochochaetidae, Poecilochaetidae and Uncispionidae as outgroups. A first analysis of currendy recognised genera proved inconclusive and even exclusion of six of the most polymorphic genera resulted in 13 305 equally parsimonious trees and a fully collapsed consensus tree. A second analysis using only the type species of each genus, yielded four equally parsimonious trees; reduced to two after successive weighting. The topologies of these two trees indicated division of the family into four main groups: (1) Aonidella and Xandaros; (2) Prionospio (sensu fato)-complex, Laonice, Spiophanes and Aonides; (3) a large assemblage of genera, including Polydora-{senm late), Scolelepis, Malacoceros and Spio; (4) Atherospio, Pseudatherospio and Pygospiopsis. Earlier literature classifications of the group are evaluated and compared with die new results.     

Chloroplast DNA restriction site variation and phylogeny of the Berberidaceae

Comparative restriction site mapping of the chloroplast genome was performed to examine phylogenetic relationships among 27 species representing 16 genera of the Berberidaceae and two outgroups. Chloroplast genomes of the species included in this study showed no major structural rearrangements (i.e., they are collinear to tobacco cpDNA) except for the extension of the inverted repeat in species of Berberis and Mahonia. Excluding several regions that exhibited severe length variation, a total of 501 phylogenetically informative sites was mapped for ten restriction enzymes. The strict consensus tree of 14 equally parsimonious trees indicated that some berberidaceous genera (Berberis, Mahonia, Diphylleia) are not monophyletic. To explore phylogenetic utility of different parsimony methods phylogenetic trees were generated using Wagner, Dollo, and weighted parsimony for a reduced data set that included 18 species. One of the most significant results was the recognition of the four chromosomal groups, which were strongly supported regardless of the parsimony method used. The most notable difference among the trees produced by the three parsimony methods was the relationships among the four chromosomal groups. The cpDNA trees also strongly supported a close relationship of several generic pairs (e.g., Berberis-Mahonia, Epimedium-Vancouveria, etc.). Maximum likelihood values were computed for the four different tree topologies of the chromosomal groups, two Wagner, one Dollo, and one weighted topology. The results indicate that the weighted tree has the highest likelihood value. The lowest likelihood value was obtained for the Dollo tree, which had the highest bootstrap and decay values. Separate analyses using only the Inverted Repeat (IR) region resulted in a tree that is identical to the weighted tree. Poor resolution and/or support for the relationships among the four chromosomal lineages of the Berberidaceae indicate that they may have radiated from an ancestral stock in a relatively short evolutionary time.     

Comparison of the Cladograms Produced by Li's Method and Farris' Method

In order to avoid producing many equally most parsimonious trees, Li (1990) developed a new cladistic method, the Median Elimination Series (MES), to construct a single cladogram for a given data set. However, we found that Li's method can produce more than one tree if two or more taxa have the same advancement index (which is the total number of apomorphies for a taxon in a given data set), because there is no objective method to decide which taxon should be connected first and different orders of connection can produce different trees. Li claimed that the result produced by his method did not apply the principle of simplicity (parsimony). Nevertheless, Zhang (1991) recognised that Li's method actually accepted the principle of parsimony. Here we demonstrated that Li's method also can produce the minimum-length trees. We conclude that Li's method could produce more than one tree and the tree(s) may be the minimum-length possible. However, the length of tree(s) depends on the order of connection of the taxa. The major problems in using Li's methodare discussed.     

Trees and/or networks to display intraspecific DNA sequence variation?

Phylogenetic trees and networks are both used in the scientific literature to display DNA sequence variation at the intraspecific level. Should we rather use trees or networks? I argue that the process of inferring the most parsimonious genealogical relationships among a set of DNA sequences should be dissociated from the problem of displaying this information in a graph. A network graph is probably more appropriate than a strict consensus tree if many alternative, equally most parsimonious, genealogies are to be included. Within the maximum parsimony framework, current phylogenetic inference and network‐building algorithms are both unable to guarantee the finding of all most parsimonious (MP) connections. In fact, each approach can find MP connections that the other does not. Although it should be possible to improve at least the maximum parsimony approach, current implementations of these algorithms are such that it is advisable to use both approaches to increase the probability of finding all possible MP connections among a set of DNA sequences.     

Maximum Parsimony on Phylogenetic networks

Background

Phylogenetic networks are generalizations of phylogenetic trees, that are used to model evolutionary events in various contexts. Several different methods and criteria have been introduced for reconstructing phylogenetic trees. Maximum Parsimony is a character-based approach that infers a phylogenetic tree by minimizing the total number of evolutionary steps required to explain a given set of data assigned on the leaves. Exact solutions for optimizing parsimony scores on phylogenetic trees have been introduced in the past.

Results

In this paper, we define the parsimony score on networks as the sum of the substitution costs along all the edges of the network; and show that certain well-known algorithms that calculate the optimum parsimony score on trees, such as Sankoff and Fitch algorithms extend naturally for networks, barring conflicting assignments at the reticulate vertices. We provide heuristics for finding the optimum parsimony scores on networks. Our algorithms can be applied for any cost matrix that may contain unequal substitution costs of transforming between different characters along different edges of the network. We analyzed this for experimental data on 10 leaves or fewer with at most 2 reticulations and found that for almost all networks, the bounds returned by the heuristics matched with the exhaustively determined optimum parsimony scores.

Conclusion

The parsimony score we define here does not directly reflect the cost of the best tree in the network that displays the evolution of the character. However, when searching for the most parsimonious network that describes a collection of characters, it becomes necessary to add additional cost considerations to prefer simpler structures, such as trees over networks. The parsimony score on a network that we describe here takes into account the substitution costs along the additional edges incident on each reticulate vertex, in addition to the substitution costs along the other edges which are common to all the branching patterns introduced by the reticulate vertices. Thus the score contains an in-built cost for the number of reticulate vertices in the network, and would provide a criterion that is comparable among all networks. Although the problem of finding the parsimony score on the network is believed to be computationally hard to solve, heuristics such as the ones described here would be beneficial in our efforts to find a most parsimonious network.     

The phylogeny of the Asteridae sensu lato based on chloroplast ndhF gene sequences

A phylogenetic study of Asteridae sensu lato was conducted based on chloroplast ndhF gene sequences for 116 ingroup and 13 outgroup species. Prior molecular studies based on rbcL sequences identified terminal groups corresponding to families, but were unable to resolve relationships among them. These results are largely consistent with earlier rbcL studies, but provide much greater resolution and stronger bootstrap support throughout the tree. The parsimony analysis found eight equally parsimonious trees, all of which recognize four major clades with the following relationship: (Cornales (Ericales (Euasterids I, Euasterids II))). Euasterids I includes (Garryales ((Solanales, Boraginaceae) (Gentianales, Lamiales))), although with weak support for relationships among the named clades. Euasterids II includes (Aquifoliales (Asterales (Apiales, Dipsacales))) with strong support for these relationships. Relationships within Ericales are weakly supported and merit further attention.     

Coalescent methods for estimating phylogenetic trees

We review recent models to estimate phylogenetic trees under the multispecies coalescent. Although the distinction between gene trees and species trees has come to the fore of phylogenetics, only recently have methods been developed that explicitly estimate species trees. Of the several factors that can cause gene tree heterogeneity and discordance with the species tree, deep coalescence due to random genetic drift in branches of the species tree has been modeled most thoroughly. Bayesian approaches to estimating species trees utilizes two likelihood functions, one of which has been widely used in traditional phylogenetics and involves the model of nucleotide substitution, and the second of which is less familiar to phylogeneticists and involves the probability distribution of gene trees given a species tree. Other recent parametric and nonparametric methods for estimating species trees involve parsimony criteria, summary statistics, supertree and consensus methods. Species tree approaches are an appropriate goal for systematics, appear to work well in some cases where concatenation can be misleading, and suggest that sampling many independent loci will be paramount. Such methods can also be challenging to implement because of the complexity of the models and computational time. In addition, further elaboration of the simplest of coalescent models will be required to incorporate commonly known issues such as deviation from the molecular clock, gene flow and other genetic forces.     

CLADISTIC AND BIOGEOGRAPHIC ANALYSIS OF THE "BLUE ASH' EUCALYPTS

Abstract— A cladistic analysis of the "blue ash" eucalypts ( Eucalyptus , Myrtaceae) is presented. Five equally parsimonious trees were found, and a strict consensus tree constructed. A revised informal classification, recognizing five series ( Planchonianinae, Sphaerocarpinae, Piperitinae, Fraxininae and Haemastominae , informal subgenus Monocalyptus ) is based on the consensus cladogram. A biogeographic analysis applies a new implementation of Assumptions 0 and 1, coding data in the form of three-area statements and using parsimony analysis. These results are used to evaluate hand resolution of Assumption 2. In comparison, Brooks parsimony analysis did not produce area cladograms that best fit the data. Series and subseries were analysed separately for area relationships, which showed a repeated pattern across the blue ash clade; combining all the data in one analysis was seen as equivalent to confounding paralogy and orthology in molecular studies. A resolved area cladogram is presented for southeastern Australia.     

ANOTHER MONOPHYLY INDEX: REVISITING THE JACKKNIFE

Abstract — Randomization routines have quickly gained wide usage in phylogenetic systematies. Introduced a decade ago, the jackknife has rarely been applied in cladistic methodology. This data resampling technique was re-investigated here as a means to discover the effect that taxon removal may have on the stability of the results obtained from parsimony analyses. This study shows that the removal of even a single taxon in an analysis can cause a solution of relatively few multiple equally parsimonious trees in an inclusive matrix to result in hundreds of equally parsimonious trees with the single removal of a taxon. On the other hand, removal of other taxa can stabilize the results to fewer trees. An index of clade stability, the Jackknife Monophyly Index (JMI) is developed which, like the bootstrap, applies a value to each clade according to its frequency of occurrence in jackknife pseudoreplicates. Unlike the bootstrap and earlier application of the jackknife, alternative suboptimal hypotheses are not forwarded by this method. Only those clades in the most parsimonious tree(s) are given JMI values. The behaviour of this index is investigated both in relation to a hypothetical and a real data set, as well as how it performs in comparison to the bootstrap. The JMI is found to not be influenced by uninformative characters or relative synapomorphy number, unlike the bootstrap.     

A phylogenetic analysis of the monogenomic Triticeae (Poaceae) based on morphology

A cladistic analysis, primarily based on morphology, is presented from 40 diploid taxa representing the 24 monogenomic genera of the Triticeae. General problems related to the treatment of hybrids and supposedly allopolyploid heterogenomic taxa are highlighted. Special emphasis is given to taxa not traditionally included in Aegilops s.J. Most of the 33 characters used in the analysis are coded as binary. The only four multistate characters in the matrix are treated as unordered. Three diploid species of Bromus are used as outgroup. The number of equally parsimonious trees found is very large (approx. 170000; length = 107, ci = 0.36, ri = 0.75) and the strict consensus tree has an expectedly low level of resolution. However, most of the equally parsimonious trees owe their existence to an unresolved Aegilops clade. If this clade is replaced by its hypothetical ancestor, the number of equally parsimonious trees drops dramatically (48; length = 78, ci = 0.45, ri = 0.76). When trees for which more highly resolved compatible trees exist are excluded, only two trees remain. Bremer support is used as a measure of branch support. The trees based on morphology and on molecular data are largely incongruent.     

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.     

Phylogeny of frogs of the Physalaemus pustulosus species group,with an examination of data incongruence

Characters derived from advertisement calls, morphology, allozymes, and the sequences of the small subunit of the mitochondrial ribosomal gene (12S) and the cytochrome oxidase I (COI) mitochondrial gene were used to estimate the phylogeny of frogs of the Physalaemus pustulosus group (Leptodactylidae). The combinability of these data partitions was assessed in several ways: measures of phylogenetic signal, character support for trees, congruence of tree topologies, compatibility of data partitions with suboptimal trees, and homogeneity of data partitions. Combined parsimony analysis of all data equally weighted yielded the same tree as the 12S partition analyzed under parsimony and maximum likelihood. The COI, allozyme, and morphology partitions were generally congruent and compatible with the tree derived from combined data. The call data were significantly different from all other partitions, whether considered in terms of tree topology alone, partition homogeneity, or compatibility of data with trees derived from other partitions. The lack of effect of the call data on the topology of the combined tree is probably due to the small number of call characters. The general incongruence of the call data with other data partitions is consistent with the idea that the advertisement calls of this group of frogs are under strong sexual selection.     

Phylogeny of nereidids (Polychaeta, Nereididae) with paragnaths

A phylogenetic analysis was conducted of the Nereidinae — those members of the Nereididae (Polychaeta) with pharyngeal paragnaths. We had two objectives: to test the monophyly of currently accepted genera, subgenera and informal subgeneric groupings within the Nereidinae, and, if warranted, to propose a more natural classification of the Nereidinae. Parsimony analyses were undertaken, including 52 terminal taxa from all genera and informal groupings from the large heterogeneous genera Nereis , Ceratonereis , Neanthes and Perinereis . Analyses of a character set of 52 informative characters yielded more than 10 000 equally parsimonious trees with a length of 176 steps (consistency index [CI] = 0.34, retention index [RI] = 0.66). Reweighting three times resulted in 445 most parsimonious trees with length 54.62 (CI = 0.59, RI = 0.79). Many characters widely used in nereidid systematics were found to exhibit high levels of homoplasy. The most parsimonious trees could not be rooted such that the selected ingroup, 'Nereididae with paragnaths', was monophyletic, causing us to reject the monophyly of the Nereidinae as currently defined. The following genera were well supported by the parsimony analyses and are newly diagnosed: Alitta , Ceratonereis , Pseudonereis , Simplisetia , Solomononereis and Unanereis . Alitta succinea , Pseudonereis cortezi , Pseudonereis noodti and Pseudonereis pseudonoodti are proposed as new combinations. The parsimony analysis supported the monophyly of neither Composetia , Neanthes , Nereis and Perinereis nor of any new groupings of remaining species presently placed in those genera. It is these poorly supported genera that comprise most species of Nereididae.     

Inferring angiosperm phylogeny from EST data with widespread gene duplication

Background

Most studies inferring species phylogenies use sequences from single copy genes or sets of orthologs culled from gene families. For taxa such as plants, with very high levels of gene duplication in their nuclear genomes, this has limited the exploitation of nuclear sequences for phylogenetic studies, such as those available in large EST libraries. One rarely used method of inference, gene tree parsimony, can infer species trees from gene families undergoing duplication and loss, but its performance has not been evaluated at a phylogenomic scale for EST data in plants.

Results

A gene tree parsimony analysis based on EST data was undertaken for six angiosperm model species and Pinus, an outgroup. Although a large fraction of the tentative consensus sequences obtained from the TIGR database of ESTs was assembled into homologous clusters too small to be phylogenetically informative, some 557 clusters contained promising levels of information. Based on maximum likelihood estimates of the gene trees obtained from these clusters, gene tree parsimony correctly inferred the accepted species tree with strong statistical support. A slight variant of this species tree was obtained when maximum parsimony was used to infer the individual gene trees instead.

Conclusion

Despite the complexity of the EST data and the relatively small fraction eventually used in inferring a species tree, the gene tree parsimony method performed well in the face of very high apparent rates of duplication.