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PubMed1999

A phylogenetic approach to RNA structure prediction.

Methods based on the Mutual Information statistic (MI methods) predict structure by looking for statistical correlations between sequence positions in a set of aligned sequences. Although MI methods are often quite effective, these methods ignore the underlying phylogenetic relationships of the sequences they analyze. Thus, they cannot distinguish between correlations due to structural interactions, and spurious correlations resulting from phylogenetic history. In this paper, we introduce a method analogous to MI that incorporates phylogenetic information. We show that this method accurately recovers the structures of well-known RNA molecules. We also demonstrate, with both real and simulated data, that this phylogenetically-based method outperforms standard MI methods, and improves the ability to distinguish interacting from non-interacting positions in RNA. This method is flexible, and may be applied to the prediction of protein structure given the appropriate evolutionary model. Because this method incorporates phylogenetic data, it also has the potential to be improved with the addition of more accurate phylogenetic information, although we show that even approximate phylogenies are helpful.

Computer Simulation↗

PubMed2000

Exploring the Phylogenetic Structure of Ecological Communities: An Example for Rain Forest Trees.

Because of the correlation expected between the phylogenetic relatedness of two taxa and their net ecological similarity, a measure of the overall phylogenetic relatedness of a community of interacting organisms can be used to investigate the contemporary ecological processes that structure community composition. I describe two indices that use the number of nodes that separate taxa on a phylogeny as a measure of their phylogenetic relatedness. As an example of the use of these indices in community analysis, I compared the mean observed net relatedness of trees (≥10 cm diameter at breast height) in each of 28 plots (each 0.16 ha) in a Bornean rain forest with the net relatedness expected if species were drawn randomly from the species pool (of the 324 species in the 28 plots), using a supertree that I assembled from published sources. I found that the species in plots were more phylogenetically related than expected by chance, a result that was insensitive to various modifications to the basic methodology. I tentatively infer that variation in habitat among plots causes ecologically more similar species to co-occur within plots. Finally, I suggest a range of applications for phylogenetic relatedness measures in community analysis.

net ecological similarity↗

PubMed2025

Phylogenetic Methods Meet Deep Learning.

Deep learning (DL) has been widely used in various scientific fields, but its integration into phylogenetics has been slower, primarily due to the complex nature of phylogenetic data. The studies that apply DL to sequencing data often limit analyses to four-taxon trees. Many of these studies serve as "proof of principle" and perform similarly to traditional phylogeny reconstruction methods. New ways of using training data, such as encoding with compact bijective ladderized vectors or transformers, enable the handling of much larger trees and genomic data sets. This short perspective focuses on the application of DL in phylogenetics, introducing prevalent DL architectures. We highlight potential problems in the field by discussing the risks of using simulation-based training data and emphasize the importance of reproducibility and robustness in computational estimates. Finally, we explore promising research areas, including the combination of phylogenetics and population genetics in DL, the analysis of neighbor dependencies, and the potential to significantly reduce computational cost compared to traditional methods. This perspective illustrates the potential of DL in complementing traditional phylogeny reconstruction methods and aiding the advancement of phylogenetic analysis, especially in performing computationally demanding tasks such as model selection or estimating branch support values.

Humans↗

PubMed1997

Phylogenetic relationships of entomopathogenic nematodes (Heterorhabditidae and Steinernematidae) inferred from partial 18S rRNA gene sequences.

Aligned 265-bp sequences of partial 18S rRNA gene were used to infer phylogenetic relationships among entomopathogenic nematodes by using maximum parsimony and likelihood methods. Phylogenetic analyses support Heterorhabditidae and Steinernematidae belonging to different monophylies. There was more sequence divergence in Steinernema species than in Heterorhabditis species. These results are congruent with the phylogenies based on morphological, life cycle, and distributional evidence. Examination of all trees within 1% of the length of the most parsimonious trees and bootstrap analyses support most relationships among Steinernema species but the relationships among Heterorhabditis species were not supported. We suggest that the partial 18S rRNA gene sequences may be too conserved for phylogenetic inference among Heterorhabditis species, but are well suited for phylogenetic inference within and among closely related families and genera of entomopathogenic nematodes and for inferring phylogenetic relationships among Steinernema species.

Animals↗

PubMed1997

The utility of DNA sequences of an intron from the beta-fibrinogen gene in phylogenetic analysis of woodpeckers (Aves: Picidae).

Estimating phylogenies from DNA sequence data has become the major methodology of molecular phylogenetics. To date, molecular phylogenetics of the vertebrates has been very dependent on mtDNA, but studies involving mtDNA are limited because the several genes comprising the mt-genome are inherited as a single linkage group. The only apparent solution to this problem is to sequence additional genes, each representing a distinct linkage group, so that the resultant gene trees provide independent estimates of the species tree. There exists the need to find novel gene sequences which contain enough phylogenetic information to resolve relationships between closely related species. A possible source is the nuclear-encoded introns, because they evolve more rapidly than exons. We designed primers to amplify and sequence the 7 intron from the beta-fibrinogen gene for a recently evolved group, the woodpeckers. We sequenced the entire intron for 10 specimens representing five species. Nucleotide substitutions are randomly distributed along the length of the intron, suggesting selective neutrality. A preliminary analysis indicates that the phylogenetic signal in the intron is as strong as that in the mitochondrial encoded cytochrome b (cyt b) gene. The topology of the beta-fibrinogen tree is identical to that of the cyt b tree. This analysis demonstrates the ability of the 7 intron of beta-fibrinogen to provide well resolved, independent gene trees for recently evolved groups and establishes it as a source of sequences to be used in other phylogenetic studies.

Animals↗

PubMed1998

C-mos, a nuclear marker useful for squamate phylogenetic analysis.

Phylogenetic reconstruction in molecular systematics has largely been achieved using mitochondrial gene sequences and less frequently sequences of nuclear ribosomal RNA genes. At present few other nuclear genes have been identified that could be used to test these phylogenies. C-mos, a single-copy nuclear oncogene, has been identified as a candidate nuclear marker. Data are presented on the usefulness of c-mos sequences in the phylogenetic analysis of squamate reptile families. We obtained partial sequences of c-mos from 13 squamate reptile families and outgroup representatives from the orders Rhynchocephalia, Chelonia, and Crocodylia. Phylogenetic analysis reveals a high degree of phylogenetic information contained within the sequence for both the synonymous and nonsynonymous substitutions. Phylogenetic resolution was present at both the deepest and shallower divergences but relationships among the major squamate lineages were not resolved, possibly because rapid cladogenesis may have led to the diversification of these lineages.

Animals↗

PubMed1998

The eastern Asian and eastern and western North American floristic disjunction: congruent phylogenetic patterns in seven diverse genera.

One of the most remarkable examples of intercontinental disjunction of the North Temperate Flora involves eastern Asia and eastern and western North America. Although there has been considerable interest in this phytogeographic pattern for over 150 years (e.g., Gray, 1859; Li, 1952; Graham, 1972; Boufford and Spongberg, 1983; Wu, 1983; Tiffney, 1985a, 1985b), relationships among taxa displaying the disjunction remain obscure. Understanding phylogenetic relationships is, however, a prerequisite for historical biogeographic analyses of this distributional pattern. To understand better the relationships of taxa displaying this intercontinental disjunction, phylogenetic analyses were conducted using a variety of DNA data sets for species of four genera (Cornus, Boykinia, Tiarella, and Trautvetteria) that occur in eastern Asia, eastern North America, and western North America. An area cladogram was constructed for each of the four genera, all of which show a similar pattern of relationship: the eastern Asian species are sister to all North American species. An identical phylogenetic pattern is also found in three other taxa exhibiting this disjunction (Aralia sect. Aralia, Calycanthus, and Adiantum pedatum). The congruent phylogenetic pattern found in these seven diverse genera raises the possibility of a common origin of the eastern Asia, eastern and western North America disjunction. The data are in agreement with the long-standing hypothesis that this well-known floristic disjunction represents the fragmentation of a once continuous Mixed Mesophytic forest community and suggest that the disjunction may have involved only two major vicariance events: an initial split between Eurasia and North America, followed by the isolation of floras between eastern and western North America. However, congruence between phylogenies and geographic distributions does not necessarily indicate an identical phytogeographic history. Taxa exhibiting the same phylogenetic pattern may have originated at different geological times. Analysis of divergence times using the molecular clock indicates that species of Cornus, Boykinia, and Calycanthus may have diverged at different geological times, suggesting that the floristic disjunction involving eastern Asia and North America may not be simple; it may have involved multiple historical events at very different geological times in different genera.

Asia, Eastern↗

PubMed1998

Molecular phylogenetics of the avian genus Pipilo and a biogeographic argument for taxonomic uncertainty.

We sequenced 1709 base pairs (bp) of mitochondrial DNA including parts of cytochrome b, ND 2, and the control region (CR I, II) for seven members of the avian genus Pipilo (towhees), Melozone kieneri (rusty-crowned ground-sparrow), and Arremonops rufivirgatus (olive sparrow). A total of 457 bp was variable and 257 bp were potentially phylogenetically informative. All gene regions were similarly variable (20.2 to 28.4%) except for CR II (38.4%); third position transitions were as common as substitutions in the CR. Tree topology was sensitive to choice of outgroup(s) and individual sequences used as exemplars. Six trees were considered viable phylogenetic hypotheses based on maximum parsimony and maximum likelihood analyses. These trees generally supported two groups of towhees (rufous-sided group, brown towhee group), a sister taxon relationship for P. aberti and P. crissalis, and a sister taxon relationship for P. ocai and P. maculatus. The occurrence of M. kiernei within Pipilo in three trees challenges the monophyly of the latter; the other species of Melozone and other outgroups require study to resolve Pipilo monophyly. The relationships of P. albicollis and P. fuscus were ambiguous, as they were with previous data sets (allozymes, mtDNA restriction sites); they could be sister species or either one could be the basal species in the brown towhee group. We suggest that this taxonomic uncertainty obtains from the contemporaneous origin of P. fuscus, P. albicollis, and the ancestor of P. aberti/P. crissalis. We favor a "star" phylogeny because species in unrelated lineages found in the same region as P. albicollis are similarly difficult to resolve phylogenetically. Synapomorphies from coding genes and the CR did not preferentially support basal and terminal nodes, and hence did not provide different windows of taxonomic resolution, which might be expected from the apparent rapid rate of CR evolution. Phylogenetic trees inferred from allozymes, restriction sites, and mtDNA sequences were congruent, suggesting that each is a useful source of phylogenetic information.

Animals↗

PubMed1998

Phylogenetic analysis of southern hemisphere flat oysters based on partial mitochondrial 16S rDNA gene sequences.

Oysters are among the most familiar, best studied, and morphologically variable of all marine invertebrate taxa. However, our knowledge of oyster phylogeny and systematics is rudimentary, especially for the subfamily Ostreinae (flat oysters). It is unclear, for instance, whether the predominant flat oysters occurring between latitudes 35 and 50 degrees S constitute a single circumglobal species, or multiple, phylogenetically distinct, regional taxa. We have performed the first DNA molecular phylogenetic analysis of ostreinid taxa to distinguish among competing phylogenetic and systematic hypotheses for Southern Hemisphere Ostreinae. An approximately 450-nucleotide fragment of the mitochondrial large ribosomal subunit (16S) was sequenced for 41 individual oysters, representing 14 taxa of brooding oysters: 5 Southern Hemisphere Ostreinae, 5 Northern Hemisphere Ostreinae, and 4 outgroup species of the subfamily Lophinae. Phylogenetic analyses of the resulting data set yielded consensus tree topologies that are comprehensively incongruent with prevailing morphologically based interpretations of systematic relationships among the Ostreinae. Three ostreinid mitochondrial clades were evident, each containing representatives of Southern Hemisphere regional ostreinid taxa, some of which robustly cocluster with Northern Hemisphere taxa. These three clades represent the first well-supported phylogenetic framework for this ecologically prominent and commercially important oyster subfamily.

Animals↗

PubMed1998

Molecular tests of phylogenetic taxonomies: a general procedure and example using four subfamilies of the lizard family Iguanidae.

A general procedure is described for examining when results of molecular phylogenetic analyses warrant formal revision of taxonomies constructed using morphological characters. We illustrate this procedure with tests of monophyly for four subfamilies in the lizard family Iguanidae using 1561 aligned base positions (838 phylogenetically informative) of mitochondrial DNA sequences, representing coding regions for eight tRNAs, ND2, and portions of ND1 and COI. Ten new sequences ranging in length from 1732 to 1751 bases are compared with 12 previously reported sequences and 67 morphological characters (54 phylogenetically informative) from the literature. New morphological character states are provided for Sator. Phylogenies derived from the molecular and combined data are in agreement but both conflict with phylogenetic inferences from the morphological data alone. Strong support is found for the monophyly of the subfamilies Crotaphytinae and Phrynosomatinae. Monophyly of the Iguaninae is weakly supported in each analysis. All analyses suggest that the Tropidurinae is not monophyletic but the hypothesis of monophyly cannot be rejected. A phylogenetic taxonomy is proposed in which the Tropidurinae* is maintained as a metataxon (denoted with an asterisk), for which monophyly has not been demonstrated. Within the Phrynosomatinae, the close relationship of Sator and Sceloporus is questioned and an alternative hypothesis in which Sator is the sister taxon to a clade comprising Petrosaurus, Sceloporus, and Urosaurus is presented. Statistical tests of monophyly provide a powerful way to evaluate support for taxonomic groupings. Use of the metataxon prevents premature taxonomic rearrangements where support is lacking.

Animals↗

PubMed1998

Phylogenetic relationships of the Acanthocephala inferred from 18S ribosomal DNA sequences.

Phylogenetic relationships within the Acanthocephala have remained unresolved. Past systematic efforts have focused on creating classifications with little consideration of phylogenetic methods. The Acanthocephala are currently divided into three major taxonomic groups: Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala. These groups are characterized by structural features in addition to the taxonomy and habitat of hosts parasitized. In this study the phylogenetic relationships of 11 acanthocephalan species are examined with 18S rDNA sequences. Maximum parsimony, minimum evolution, and maximum likelihood methods are used to estimate phylogenetic relationships. Within the context of sampled taxa, all phylogenetic analyses are consistent with monophyly of the major taxonomic groups of the Acanthocephala, suggesting that the current higher order classification is natural. The molecular phylogeny is used to examine patterns of character evolution for various structural and ecological characteristics of the Acanthocephala. Arthropod intermediate host distributions, when mapped on the phylogeny, are consistent with monophyletic groups of acanthocephalans. Vertebrate definitive host distributions among the Acanthocephala display independent radiations into similar hosts. Levels of uncorrected sequence divergence among acanthocephalans are high; however, relative-rate tests indicate significant departure from rate uniformity among acanthocephalans, arthropods, and vertebrates. This precludes comparison of 18S divergence levels to assess the relative age of the Acanthocephala. However, other evidence suggests an ancient origin of the acanthocephalan-arthropod parasitic association.

Acanthocephala↗

PubMed1999

Molecular phylogenetics, tRNA evolution, and historical biogeography in anguid lizards and related taxonomic families.

Phylogenetic relationships among lizards of the families Anguidae, Anniellidae, Xenosauridae, and Shinisauridae are investigated using 2001 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNA(Ile), tRNA(Gln), tRNA(Met), ND2, tRNA(Trp), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr), and COI (subunit I of cytochrome c oxidase), plus the origin for light-strand replication (O(L)) between the tRNA(Asn) and the tRNA(Cys) genes. The aligned sequences contain 1013 phylogenetically informative characters. A well-resolved phylogenetic hypothesis is obtained. Because monophyly of the family Xenosauridae (Shinisaurus and Xenosaurus) is statistically rejected, we recommend placing Shinisaurus in a separate family, the Shinisauridae. The family Anniellidae and the anguid subfamilies Gerrhonotinae and Anguinae each form monophyletic groups receiving statistical support. The Diploglossinae*, which appears monophyletic, is retained as a metataxon (denoted with an asterisk) because its monophyly is statistically neither supported nor rejected. The family Anguidae appears monophyletic in analyses of the DNA sequence data, and statistical support for its monophyly is provided by reanalysis of previously published allozymic data. Anguid lizards appear to have had a northern origin in Laurasia. Taxa currently located on Gondwanan plates arrived there by dispersal from the north in two separate events, one from the West Indies to South America and another from a Laurasian plate to Morocco. Because basal anguine lineages are located in western Eurasia and Morocco, formation of the Atlantic Ocean (late Eocene) is implicated in the separation of the Anguinae from its North American sister taxon, the Gerrhonotinae. Subsequent dispersal of anguine lizards to East Asia and North America appears to have followed the Oligocene drying of the Turgai Sea. The alternative hypothesis, that anguine lizards originated in North America and dispersed to Asia via the Bering land bridge with subsequent colonization of Europe and Morocco, requires a phylogenetic tree seven steps longer than the most parsimonious hypothesis. North African, European, and West Asian anguines were isolated from others by the rapid uplift of Tibet in the late Oligocene to Miocene. Phylogenetic analysis of evolutionary changes in the gene encoding tRNA(Cys) suggests gradual reduction of dihydrouridine (D) stems by successive deletion of bases in some lineages. This evolutionary pattern contrasts with the one observed for parallel elimination of the D-stem in mitochondrial tRNAs of eight other reptile groups, in which replication slippage produces direct repeats. An unusual, enlarged TpsiC (T) stem is inferred for tRNA(Cys) in most species.

Animals↗

PubMed1999

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.

Coprinus↗

PubMed2001

Phylogenetic relationships within the cyst-forming nematodes (Nematoda, Heteroderidae) based on analysis of sequences from the ITS regions of ribosomal DNA.

The ITS1, ITS2, and 5.8S gene sequences of nuclear ribosomal DNA from 40 taxa of the family Heteroderidae (including the genera Afenestrata, Cactodera, Heterodera, Globodera, Punctodera, Meloidodera, Cryphodera, and Thecavermiculatus) were sequenced and analyzed. The ITS regions displayed high levels of sequence divergence within Heteroderinae and compared to outgroup taxa. Unlike recent findings in root knot nematodes, ITS sequence polymorphism does not appear to complicate phylogenetic analysis of cyst nematodes. Phylogenetic analyses with maximum-parsimony, minimum-evolution, and maximum-likelihood methods were performed with a range of computer alignments, including elision and culled alignments. All multiple alignments and phylogenetic methods yielded similar basic structure for phylogenetic relationships of Heteroderidae. The cyst-forming nematodes are represented by six main clades corresponding to morphological characters and host specialization, with certain clades assuming different positions depending on alignment procedure and/or method of phylogenetic inference. Hypotheses of monophyly of Punctoderinae and Heteroderinae are, respectively, strongly and moderately supported by the ITS data across most alignments. Close relationships were revealed between the Avenae and the Sacchari groups and between the Humuli group and the species H. salixophila within Heteroderinae. The Goettingiana group occupies a basal position within this subfamily. The validity of the genera Afenestrata and Bidera was tested and is discussed based on molecular data. We conclude that ITS sequence data are appropriate for studies of relationships within the different species groups and less so for recovery of more ancient speciations within Heteroderidae.

Animals↗

PubMed2001

Phylogenetic inferences from molecular sequences: review and critique.

Conflicting results often accompany phylogenetic analyses of RNA, DNA, or protein sequences across diverse species. Causes contributing to these conflicts relate to ambiguities in identifying homologous characters of alignments, sensitivity of tree-making methods to unequal evolutionary rates, biases in species sampling, unrecognized paralogy, functional differentiation, loss of phylogenetic informational content due to long branches or fast evolution, and difficulties with the assumptions and approximations used to infer phylogenetic relationships. Attempts to surmount these conflicts by averaging over many proteins are problematic due to inherent biases of selected families, lack of signal in others, and events of lateral transfer, fusion, and/or chimerism. The process of assessing reliability of the results using the bootstrap method is strewn with obstacles because of lack of independence and inhomogeneity in the molecular data. Problems inherent to the three major procedures for developing phylogenetic trees--parsimony, likelihood, distance--are reviewed. Special attention is given to the problem of inferring evolutionary distances from patterns of similarity among sequences. The difficulties encountered by methods of phylogenetic reconstructions based on the analysis of divergent sequence families make new methods based on the analysis of complete genomes reasonable alternatives. Several of these are considered, including the signature sequences of Gupta and associates, the study of genome profiles, and the genomic signature set forth by Karlin and colleagues.

Animals↗

PubMed1996

Usefulness and limitation of phylogenetic analysis for hepatitis C virus core region: application to isolates from Egyptian and Yemeni patients.

We report here the nucleotide sequences of the core region of HCV isolates from Egyptian and Yemeni patients and the method for classifying these HCV isolates by phylogenetic analysis. Sequence comparison suggested that the genotypes of these isolates were the same. Preliminary phylogenetic analysis of the HCV core region indicated that the genotypes of both isolates were 1c. However, an additional phylogenetic tree of the HCV core region constructed using a greater number of HCV isolates than that used in the preliminary analysis and on the basis of alignment of nucleotide sequences in an appropriate length indicated that the genotypes of these isolates were 4 and not 1c. For a more detailed analysis, the nucleotide sequences of the HCV E1 region as well as the core region for the same Yemeni patient were determined. A phylogenetic tree of the E1 region confirmed that the genotype of the HCV isolate from the Yemeni patient was 4. These data indicate that even when classifying HCV isolates using phylogenetic analysis, the misclassification would occur if care is not taken regarding the number and sequence lengths of the isolates included in the analysis.

Base Sequence↗

PubMed1983

Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data.

The accuracies and efficiencies of three different methods of making phylogenetic trees from gene frequency data were examined by using computer simulation. The methods examined are UPGMA, Farris' (1972) method, and Tateno et al.'s (1982) modified Farris method. In the computer simulation eight species (or populations) were assumed to evolve according to a given model tree, and the evolutionary changes of allele frequencies were followed by using the infinite-allele model. At the end of the simulated evolution five genetic distance measures (Nei's standard and minimum distances, Rogers' distance, Cavalli-Sforza's f theta, and the modified Cavalli-Sforza distance) were computed for all pairs of species, and the distance matrix obtained for each distance measure was used for reconstructing a phylogenetic tree. The phylogenetic tree obtained was then compared with the model tree. The results obtained indicate that in all tree-making methods examined the accuracies of both the topology and branch lengths of a reconstructed tree (rooted tree) are very low when the number of loci used is less than 20 but gradually increase with increasing number of loci. When the expected number of gene substitutions (M) for the shortest branch is 0.1 or more per locus and 30 or more loci are used, the topological error as measured by the distortion index (dT) is not great, but the probability of obtaining the correct topology (P) is less than 0.5 even with 60 loci. When M is as small as 0.004, P is substantially lower. In obtaining a good topology (small dT and high P) UPGMA and the modified Farris method generally show a better performance than the Farris method. The poor performance of the Farris method is observed even when Rogers' distance which obeys the triangle inequality is used. The main reason for this seems to be that the Farris method often gives overestimates of branch lengths. For estimating the expected branch lengths of the true tree UPGMA shows the best performance. For this purpose Nei's standard distance gives a better result than the others because of its linear relationship with the number of gene substitutions. Rogers' or Cavalli-Sforza's distance gives a phylogenetic tree in which the parts near the root are condensed and the other parts are elongated. It is recommended that more than 30 loci, including both polymorphic and monomorphic loci, be used for making phylogenetic trees. The conclusions from this study seem to apply also to data on nucleotide differences obtained by the restriction enzyme techniques.

Algorithms↗

PubMed1999

Phylogenetic studies of complete mitochondrial DNA molecules place cartilaginous fishes within the tree of bony fishes.

It is commonly acknowledged that cartilaginous fishes, Chondrichthyes, have a basal position among the Gnathostomata (jawed vertebrates). In order to explore this relationship we have sequenced the complete mitochondrial genome of the spiny dogfish, Squalus acanthias, and included it in a phylogenetic analysis together with a number of bony fishes and amniotes. The phylogenetic reconstructions placed the dogfish among the bony fishes. Thus, and contrary to the common view, the analyses have shown that the position of the sharks is not basal among the gnathostomes. The presently recognized phylogenetic position of the dogfish was identified irrespective of the outgroup used, echinoderms or agnathan fishes. The lungfish was the most basal gnathostome fish, while the teleosteans had an apical position in the piscine tree. A basal position of the dogfish among the gnathostomes was statistically rejected, but the phylogenetic relationship among the coelacanth, spiny dogfish, and teleosts was not conclusively resolved. The findings challenge the current theory that sharks and other chondrichthyans, if monophyletic, are the sister group to all other extant gnathostomes. The results open to question the status of several morphological characters commonly used in piscine phylogenetic reconstruction, most notably the presence versus absence of endochondral bone in the endoskeleton, the macromeric versus micromeric structure of the exoskeleton, and the presence/absence of swimbladder and/or lung. The study also confirmed recent findings demonstrating that the origin of the amniotes is deeper than the diversification of extant bony fishes.

Animals↗