ON THE RATIONALE AND UTILITY OF WEIGHTING NUCLEOTIDE SEQUENCE DATA

The phylogenetic history of Selaginellaceae based on DNA sequences from the plastid and nucleus: extreme substitution rates and rate heterogeneity

Molecular phylogenetic research on Selaginellaceae has focused on the plastid gene rbcL, which in this family has unusually high substitution rates. Here we develop a molecular data set from the nuclear 26S ribosomal DNA gene with the aim of evaluating and extending the results of previous phylogenetic research. The 26S rDNA and the rbcL regions were sequenced for a sample of 23 species, which represent the main elements of species diversity in the family. The data were analysed independently and in combination using both maximum parsimony and Bayesian inference. Although several between genome differences were found, the general pattern of relationships uncovered by all analyses was very similar. Results corroborate the previous study supporting new groupings not previously recognised on morphological grounds. Substitution rates in the 26S rDNA were also found to be high (26% informative) for the region analysed, but lower than for rbcL (37% informative). These data indicate that high substitution rates might be widespread in all three genomes (i.e., plastid, mitochondrion, and nucleus).

On combining protein sequences and nucleic acid sequences in phylogenetic analysis: the homeobox protein case

Amino acid encoding genes contain character state information that may be useful for phylogenetic analysis on at least two levels. The nucleotide sequence and the translated amino acid sequences have both been employed separately as character states for cladistic studies of various taxa, including studies of the genealogy of genes in multigene families. In essence, amino acid sequences and nucleic acid sequences are two different ways of character coding the information in a gene. Silent positions in the nucleotide sequence (first or third positions in codons that can accrue change without changing the identity of the amino acid that the triplet codes for) may accrue change relatively rapidly and become saturated, losing the pattern of historical divergence. On the other hand, non-silent nucleotide alterations and their accompanying amino acid changes may evolve too slowly to reveal relationships among closely related taxa. In general, the dynamics of sequence change in silent and non-silent positions in protein coding genes result in homoplasy and lack of resolution, respectively. We suggest that the combination of nucleic acid and the translated amino acid coded character states into the same data matrix for phylogenetic analysis addresses some of the problems caused by the rapid change of silent nucleotide positions and overall slow rate of change of non-silent nucleotide positions and slowly changing amino acid positions. One major theoretical problem with this approach is the apparent non-independence of the two sources of characters. However, there are at least three possible outcomes when comparing protein coding nucleic acid sequences with their translated amino acids in a phylogenetic context on a codon by codon basis. First, the two character sets for a codon may be entirely congruent with respect to the information they convey about the relationships of a certain set of taxa. Second, one character set may display no information concerning a phylogenetic hypothesis while the other character set may impact information to a hypothesis. These two possibilities are cases of non-independence, however, we argue that congruence in such cases can be thought of as increasing the weight of the particular phylogenetic hypothesis that is supported by those characters. In the third case, the two sources of character information for a particular codon may be entirely incongruent with respect to phylogenetic hypotheses concerning the taxa examined. In this last case the two character sets are independent in that information from neither can predict the character states of the other. Examples of these possibilities are discussed and the general applicability of combining these two sources of information for protein coding genes is presented using sequences from the homeobox region of 46 homeobox genes from Drosophila melanogaster to develop a hypothesis of genealogical relationship of these genes in this large multigene family.

Increasing fidelity in parsimony analysis of dorid nudibranchs by differential weighting, or a tale of two genes

Phylogenetic analyses of 22 dorid nudibranch species and 2 outgroup (dendronotacean and notaspidean) species were performed using sequences from two different mitochondrial genes (16S rRNA and COI). Several methods of differential weighting (positional, transformational, and combined) were explored using character congruence between the linked data sets as an optimality criterion. Most weighting schemes gave an increase in congruence as well as phylogenetic signal. The optimal weighting scheme according to the criterion was successive weighting of each character (positional weighting) with 1/(number of steps) in combination with LN weighting of character changes (transformational weighting). The cladogram from the optimal weighting scheme was, in general, congruent with existing classifications. One exception is the genus Goniodoris, which was paraphyletic if Okenia aspersa was not also included.

The impact of parsimony weighting schemes on inferred relationships among toucans and neotropical barbets (Aves: piciformes)

The development of new schemes for weighting DNA sequence data for phylogenetic analysis continues to outpace the development of consensus on the most appropriate weights. The present study is an exploration of the similarities and differences between results from 22 character weighting schemes when applied to a study of barbet and toucan (traditional avian families Capitonidae and Ramphastidae) phylogenetic relationships. The dataset comprises cytochrome b sequences for representatives of all toucan and Neotropical barbet genera, as well as for several genera of Paleotropical barbets. The 22 weighting schemes produced conflicting patterns of relationship among taxa, often with conflicting patterns each receiving strong bootstrap support. Use of multiple weighting schemes helped to identify the source within the dataset (codon position, transitions, transversions) of the various putative phylogenetic signals. Importantly, some phylogenetic hypotheses were consistently supported despite the wide range of weights employed. The use of phylogenetic frameworks to summarize the results of these multiple analyses proved very informative. Relationships among barbets and toucans inferred from these data support the paraphyly of the traditional Capitonidae. Additionally, these data support paraphyly of Neotropical barbets, but rather than indicating a relationship between Semnornis and toucans, as previously suggested by morphological data, most analyses indicate a basal position of Semnornis within the Neotropical radiation. The cytochrome b data also allow inference of relationships among toucans. Supported hypotheses include Ramphastos as the sister to all other toucans, a close relationship of Baillonius and Pteroglossus with these two genera as the sister group to an (Andigena, Selenidera) clade, and the latter four genera as a sister group to Aulacorhynchus.

Nuclear genes resolve mesozoic-aged divergences in the insect order Lepidoptera

Compared to the number of genes available for study of both younger and older divergences, few genes have yet been identified that can strongly resolve phylogenetic splits of Mesozoic age ( approximately 65-250 mya). Thus, reconstruction of Mesozoic-age phylogenies, exemplified by basal divergences within the major orders of holometabolous insects, is likely to be especially dependent on combining multiple lines of evidence. This study tests the potential of the 18S ribosomal RNA gene for reconstructing Mesozoic-aged divergences within the insect order Lepidoptera and its ability when combined with a second, previously analyzed nuclear gene (phosphoenolpyruvate carboxykinase, PEPCK) to strongly resolve these relationships. 18S sequences were obtained for 21 taxa, representing major clades of Lepidoptera plus outgroups from the other "panorpoid orders. A well-corroborated morphology-based "test phylogeny was used to evaluate the effects of partitioning the 18S gene according to variable versus conserved domains, paired versus unpaired sites in the secondary structure, and transition versus transversion substitutions. Likelihood and unweighted parsimony analyses of the 18S data recover the "test phylogeny" almost completely, with no improvement of agreement or support provided by any form of weighting or partitioning. No conflict in signal between 18S and PEPCK was detected by the partition homogeneity test. Combined parsimony analysis yielded strong bootstrap support for nearly all relationships, much higher than for either gene alone, thereby also providing strong evidence on several hypotheses about the early evolution of lepidopteran-plant interactions. These genes in combination may be widely useful for resolving insect divergences of comparable age.

Molecular phylogeny and biogeography of tribe anthemideae (Asteraceae), based on chloroplast gene ndhF

Anthemideae (Asteraceae) is primarily a north temperate, Old World tribe of 109 genera and approximately 1740 species. We sequenced a 1200-bp portion of chloroplast gene ndhF for representative genera and subtribes and constructed a phylogeny for the tribe. There is support for monophyly of subtribes Chrysantheminae and Gonosperminae and for portions of some subtribes. However, our molecular phylogeny differs significantly from traditional classifications and from previously published morphological phylogenies of the tribe. Many South African genera from several different subtribes form a basal grade, indicating multiple, relictual lineages. Eurasian genera form a recently derived clade that includes the Mediterranean genera of the Iberian Peninsula and North Africa. There is little resolution or support for the placement of eastern Asian genera. Apparently, the tribe originated in the Southern Hemisphere, presumably in Africa, with the Eurasian and Mediterranean members being derived from a common ancestor.

Phylogenetic relationships in the mushroom genus Coprinus and dark-spored allies based on sequence data from the nuclear gene coding for the large ribosomal subunit RNA: divergent domains, outgroups, and monophyly

Phylogenetic relationships were investigated in the mushroom genus Coprinus based on sequence data from the nuclear encoded large-subunit rDNA gene. Forty-seven species of Coprinus and 19 additional species from the families Coprinaceae, Strophariaceae, Bolbitiaceae, Agaricaceae, Podaxaceae, and Montagneaceae were studied. A total of 1360 sites was sequenced across seven divergent domains and intervening sequences. A total of 302 phylogenetically informative characters was found. Ninety-eight percent of the average divergence between taxa was located within the divergent domains, with domains D2 and D8 being most divergent and domains D7 and D10 the least divergent. An empirical test of phylogenetic signal among divergent domains also showed that domains D2 and D3 had the lowest levels of homoplasy. Two equally most parsimonious trees were resolved using Wagner parsimony. A character-state weighted analysis produced 12 equally most parsimonious trees similar to those generated by Wagner parsimony. Phylogenetic analyses employing topological constraints suggest that none of the major taxonomic systems proposed for subgeneric classification is able to completely reflect phylogenetic relationships in Coprinus. A strict consensus integration of the two Wagner trees demonstrates the problematic nature of choosing outgroups within dark-spored mushrooms. The genus Coprinus is found to be polyphyletic and is separated into three distinct clades. Most Coprinus taxa belong to the first two clades, which together form a larger monophyletic group with Lacrymaria and Psathyrella in basal positions. A third clade contains members of Coprinus section Comati as well as the genus Leucocoprinus, Podaxis pistillaris, Montagnea arenaria, and Agaricus pocillator. This third clade is separated from the other species of Coprinus by members of the families Strophariaceae and Bolbitiaceae and the genus Panaeolus.

Phylogenetic relationships of the liverworts (Hepaticae), a basal embryophyte lineage, inferred from nucleotide sequence data of the chloroplast gene rbcL

Sequence data from the chloroplast-encoded gene rbcL were obtained for 24 liverworts, a basal group of embryophytes. Maximum likelihood and parsimony analyses of these data, along with data from other major green plant lineages, confirm hypotheses based on morphological data, such as the paraphyly of bryophytes, and the basal position of liverworts. Molecular data corroborate the deep separation between the complex thalloid and leafy/simple thalloid liverworts implied by morphological data, but the monophyly of liverworts could not be rejected. The effects of accounting for site-to-site rate heterogeneity in these data were examined using maximum likelihood methods. Comparison of trees obtained with and without rate heterogeneity showed that simply allowing for heterogeneity had a greater improvement on likelihood score than optimization of transition/transversion bias. Incorporation of site-to-site rate heterogeneity in the larger analysis, however, did not necessarily change which topology was favored. Properties of rbcL sequences from the two liverwort groups were compared. Significantly different substitution rates were found between leafy/simple thalloid and complex thalloid liverwort taxa, with rates of rbcL sequence evolution in leafy/simple thalloid taxa being higher and more indicative of those of vascular plants, and with those of complex thalloid taxa (such as Marchantia) being slower. Codon usage in rbcL in complex thalloid liverworts was biased toward NNU and NNA, compared to the leafy/simple thalloid liverworts. Although base composition and relative substitution rates differed between the two groups, no significant differences were detected within each of the two groups of liverworts. The signal present in first and second codon sites versus third codon sites was compared. While the third codon positions in rbcL across this taxon sampling are highly variable (with only 15 constant sites of 439), the trees obtained were in general agreement with trees from the entire data set and with trees obtained from independent sources of data. The presence of signal in third codon positions across greater than 400 MY of plant evolution means that definitions of saturation based on pair-wise comparisons of sequences inadequately assess phylogenetic signal.

Cladistic analysis of molecular and morphological data

Considerable progress has been made recently in phylogenetic reconstruction in a number of groups of organisms. This progress coincides with two major advances in systematics: new sources have been found for potentially informative characters (i.e., molecular data) and (more importantly) new approaches have been developed for extracting historical information from old or new characters (i.e., Hennigian phylogenetic systematics or cladistics). The basic assumptions of cladistics (the existence and splitting of lineages marked by discrete, heritable, and independent characters, transformation of which occurs at a rate slower than divergence of lineages) are discussed and defended. Molecular characters are potentially greater in quantity than (and usually independent of) more traditional morphological characters, yet their great simplicity (i.e., fewer potential character states; problems with determining homology), and difficulty of sufficient sampling (particularly from fossils) can lead to special difficulties. Expectations of the phylogenetic behavior of different types of data are investigated from a theoretical standpoint, based primarily on variation in the central parameter lambda (branch length in terms of expected number of character changes per segment of a tree), which also leads to possibilities for character and character state weighting. Also considered are prospects for representing diverse yet clearly monophyletic clades in larger-scale cladistic analyses, e.g., the exemplar method vs. "compartmentalization" (a new approach involving substituting an inferred "archetype" for a large clade accepted as monophyletic based on previous analyses). It is concluded that parsimony is to be preferred for synthetic, "total evidence" analyses because it appears to be a robust method, is applicable to all types of data, and has an explicit and interpretable evolutionary basis.

Phylogenetic studies of ribosomal RNA variation in higher moths and butterflies (Lepidoptera: Ditrysia)

The selection of exemplars has been shown both theoretically and empirically to affect tree topology, but the importance of the number and nature of taxa used to represent higher taxonomic lineages in molecular studies is rarely stressed. In our rRNA study of higher moths and butterflies (Lepidoptera: Ditrysia), the selection of different exemplars and outgroups caused major tree rearrangements. We also examined the effectiveness with which conserved rRNA regions track the diversification of Lepidoptera. Homoplasy is as prevalent at the few variable sites of conserved regions (18E, 18J, 28F) as at the many variable sites of a more rapidly evolving region (28B). Finally, 28B sequence variation differs qualitatively among lepidopteran superfamilies of presumed comparable age, the Papilionoidea (true butterflies) and Noctuoidea (cutworm moths and relatives).