Macey et al. (98-14)
Abstract. -- A phylogenetic tree for acrodont lizards (Chamaeleonidae and Agamidae) is established based on 1434 bases (1041 informative) of aligned DNA positions from a 1685-1778 base-pair region of the mitochondrial genome. Sequences from three protein-coding genes (ND1, ND2, and COI) are combined with sequences from eight intervening tRNA genes for samples of 70 acrodont taxa and two outgroups. Parsimony analysis of nucleotide sequences identifies seven major clades in the Acrodonta. Most agamid lizards are placed into three distinct clades. One clade is composed of all taxa occurring in Australia and New Guinea. Physignathus cocincinus from southeast Asia is the sister taxon to the Australia/New Guinea clade. A second clade is composed of taxa occurring from Tibet and the Indian Subcontinent east through south and east Asia. A third clade is composed of taxa occurring from Africa east through Arabia and West Asia to Tibet and the Indian Subcontinent. These three clades contain all agamid lizards except Uromastyx, Leiolepis, and Hydrosaurus, which represent three additional clades of the Agamidae. The Chamaeleonidae forms another clade weakly supported as the sister taxon to the Agamidae. All seven clades of the Acrodonta contain members occurring on land masses derived from Gondwanaland. A hypothesis of agamid lizards rafting with Gondwanan plates is examined statistically. This hypothesis suggests that the African/West Asian clade is of African or Indian origin, and the South Asian clade is either of Indian or southeast Asian origin. The shortest tree suggests a possible African origin for the former and an Indian origin for the latter, but this result is not statistically robust. The Australia/New Guinea clade rafted with the Australia-New Guinea plate and forms the sister group to a southeast-Asian taxon that occurs on plates that broke from northern Australia-New Guinea. Other acrodont taxa are inferred to be associated with the plates of Afro-Arabia and Madagascar (Chamaeleonidae), India (Uromastyx), or southeast Asia (Hydrosaurus and Leiolepis). Introduction of different biotic elements to Asia via separate Gondwanan plates may be a major theme of Asian biogeography. Three historical events may be responsible for the sharp faunal barrier between southeast Asia and Australia-New Guinea known as Wallaces line: (1) primary vicariance cause by plate separations, (2) secondary contact of southeast Asian plates with Eurasia leading to dispersal from Eurasia into southeast Asia, and (3) dispersal of the Indian fauna (following collision of that subcontinent) to southeast Asia. Acrodont lizards show the first and third of these biogeographic patterns and anguid lizards exhibit the second pattern. Modern faunal diversity may be influenced primarily by historical events such as tectonic collisions and land bridge connections, which are expected to promote episodic turnover of continental faunas by introducing new faunal elements into an area. Repeated tectonic collisions may be one of the most important phenomena promoting continental biodiversity. Phylogenetics is a powerful method for investigating these processes. [Reptilia, Sauria, Iguania, Acrodonta, Agamidae, Chamaeleonidae, Plate Tectonics, Mitochondrial DNA, Phylogenetics]
Macey et al. (99-59)
Abstract. -- DNA sequences from 195 squamate reptiles indicate that mitochondrial gene order is the most reliable phylogenetic character establishing monophyly of acrodont lizards, and of the snake families Boidae, Colubridae and Viperidae. Gene order shows no evidence of evolutionary parallelisms or reversals in these taxa. Derived secondary structures of mitochondrial tRNAs also prove to be useful phylogenetic characters showing no reversals. Parallelisms for secondary structures of tRNAs are restricted to deep lineages that are separated by at least 200 million years of independent evolution. Presence of a stem-and-loop structure between the genes encoding tRNA(Asn) and tRNA(Cys), where the replication origin for light-strand synthesis is typically located in vertebrate mitochondrial genomes, is found to undergo at least three and possibly up to seven evolutionary shifts, most likely parallel losses. This character is therefore a less desirable phylogenetic marker than the other structural changes examined. Sequencing multi-genic regions that include tRNA genes may be preferable to the common practice of obtaining single-gene fragments for phylogenetic inference because it permits observation of major structural changes in the mitochondrial genome. Such characters occasionally may provide phylogenetic information on relatively short internal branches for which base substitutional changes are expected to be relatively uninformative. [Reptilia, Acrodonta, Gene Organization, Mitochondrial DNA, tRNA, Replication, Phylogenetics.]
Mitchell et al.
Abstract.A central question concerning data collection strategy for molecular phylogenies has been: is it better to increase the number of characters or the number of taxa sampled to improve the robustness of a phylogeny estimate? A recent simulation study concluded that increasing the number of taxa sampled is preferable to increasing the number of nucleotide characters if taxa are chosen specifically to break up long branches. We explore this hypothesis using empirical data from noctuoid moths, one of the largest superfamilies of insects. Separate studies of two nuclear genes, elongation factor-1a (EF-1a) and dopa decarboxylase (DDC), have yielded similar gene trees and high concordance with morphological groupings for 49 exemplar species. However support levels were quite low for nodes deeper than the subfamily level. We tested the effects on phylogenetic signal of (1) increasing the taxon sampling by nearly 60%, to 77 species, and (2) combining data from the two genes in a single analysis. Surprisingly, the increased taxon sampling, although designed to break up long branches, generated significantly greater disagreement between the two gene data sets and decreased support levels for deeper nodes. We appear to have inadvertently introduced new long branches, and breaking these up may require a yet larger taxon sample. Sampling additional characters (combining data) greatly inceased phylogenetic signal. To contrast the potential effect of combining data from independent genes with collection of the same total number of characters from a single gene, we simulated the latter by bootstrap augmentation of the single gene data sets. Support levels for combined data were at least as high as those for the bootstrap-augmented data set for DDC, and much higher than those for the augmented EF-1a data set. This supports the view that in obtaining additional sequence data to solve a refractory systematic problem, it is prudent to take them from an independent gene. [Keywords: taxon sampling, independent genes, combining data, Noctuoidea, Noctuidae]
Moncalvo et al.
Abstract.- Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene (nLSU-rDNA) were sequenced for 154 selected taxa representing most families within the Agaricales. Several phylogenetic methods were used, including weighted and equally weighted parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The starting tree for branch swapping in the ML analyses was the tree with the highest ML score among previously produced MP and NJ trees. A high degree of consensus was observed between phylogenetic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used, however, all NJ trees still supported most of the same terminal groupings as MP and ML trees. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, using both parsimony and likelihood tests. Our analyses suggest that weighted parsimony and ML provide the best estimates of Agaricales phylogeny. Similar support was observed between bootstrapping and jackknifing methods for evaluation of tree robustness. Phylogenetic analyses revealed many groups of agaricoid fungi that are supported by moderate to high bootstrap or jackknife levels or are consistent with morphology-based classification schemes. Analyzes also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singer). Examples of monophyletic groups include the families Amanitaceae, Coprinaceae (excluding Coprinus comatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the mycorrhizal species of Tricholoma (including Leucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and Lyophyllum; and Pleurotus with Hohenbuehelia. Several nonmonophyletic groups revealed by these data include the families Tricholomataceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular data sets. [Fungal evolution; higher phylogeny; homobasidiomycete; large scale molecular phylogeny; tree support.]
Savolainen et al.
Abstract --Following (1) the large scale molecular phylogeny of seed plants based on plastid rbcL gene sequences (published in 1993 by Chase et al., Ann. Missouri Bot. Gard. 80: 528-580) and (2) the 18S nuclear phylogeny of flowering plants (published in 1997 by Soltis et al., Ann. Missouri Bot. Gard. 84: 1-49), we present a phylogenetic analysis of flowering plants based upon a second plastid gene, atpB, analyzed separately and in combination with rbcL sequences for 357 taxa. Despite some discrepancies, the atpB-based phylogenetic trees were highly congruent with those derived from the analysis of rbcL and 18S rDNA, and the combination of atpB and rbcL DNA sequences (comprising ca. 3000 base pairs) produced increased bootstrap support for many major sets of taxa. The angiosperms are divided into two major groups: noneudicots with inaperturate or uniaperturate pollen (monocots plus Laurales, Magnoliales, Piperales, Ceratophyllales, and Amborellaceae-Nymphaeaceae-Illiciaceae) and the eudicots with triaperturate pollen (particularly asterids and rosids). Based on rbcL alone and atpB/rbcL combined, the noneudicots (excluding Ceratophyllum) are monophyletic, whereas they form a grade in the atpB trees. Ceratophyllum is sister to the rest of angiosperms whith rbcL alone and in the combined atpB/rbcL analysis, whereas with atpB alone, Amborellaceae, Nymphaeaceae, and Illiciaceae/Schisandraceae form a grade at the base of the angiosperms. The phylogenetic information at each codon position and the different types of substitutions (observed transitions and transversions in the trees versus pairwise comparisons) were examined; taking into account their respective consistency and retention indices, we demonstrate that third codon positions and transitions are the most useful characters in these phylogenetic reconstructions. This study further demonstrates that phylogenetic analysis of large matrices is feasible. [angiosperm, large molecular datasets, complex phylogenies, atpB, rbcL]
Steel et al.
Abstract --Phylogenetic inference is well known to be problematic if both long and short branches occur together in the underlying tree. With biological data, correcting for this problem may require simultaneous consideration for both substitution biases and rate heterogeneity between lineages and across sequence positions. A particular form of the latter is the presence of invariable sites, which are well known to mislead estimation of genetic divergences. Here we describe a capture-recapture method to estimate the proportion of invariable sites in an alignment of amino acids or nucleotides. We use it to investigate phylogenetic signals in 18S ribosomal DNA sequences from Holometabolus insects. Our results suggest that, as taxa diverged, their 18S rDNA sequences have altered in both their distribution of sites that can vary as well as in their base compositions. [invariable sites, LogDet, sites free to vary, covariotide evolution]
Thornton and DeSalle
Abstract --When a data set is partitioned, the resulting subsets may contain phylogenetically conflicting signals if they have different evolutionary histories. In a data set with many taxa, a single taxon that contains multiple phylogenetic histories may result in significant global incongruence, but no methods are available in a parsimony framework to localize incongruence to specific clades in a phylogeny and test the significance of incongruence on a local scale. Here we present a new method to quantify the conflict between data partitions for any clade in a phylogeny and to test the statistical significance of that conflict using a metric called the local incongruence length difference. We apply this method to the evolutionary history of the nuclear receptor superfamily, a large group of transcriptional regulators that play essential roles in metazoan development and physiology. All nuclear receptors are composed of several discrete domains, including one that binds to DNA response elements on specific target genes and another that binds to the appropriate ligand. We have performed combined and separate phylogenetic analyses of these two domains and have tested the hypothesis that nuclear receptors have evolved by a simple process of lineage splitting and divergence, without domain shuffling or other forms of sequence transfer between proteins. Our analysis indicates that significant conflict exists between the partitioned domains at a limited number of nodes on the tree, suggesting that several groups of receptors are "hybrid proteins" formed by domain shuffling or other forms of sequence transfer between more ancient nuclear receptors.[Nuclear receptors, incongruence, gene family evolution, molecular evolution, exon shuffling, character partitions]