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PubMed2026

Comparative genomics and phylogenetic analysis of three Malvaceae species on the basis of chloroplast genomes.

INTRODUCTION: The Malvaceae family shows rich species diversity and has substantial economic and medicinal value. However, the frequent interspecific hybridization among members of this family has resulted in confused phylogenetic relationships among the groups, limiting the usefulness of traditional classification methods. METHODS: This study aimed to investigate the phylogenetic relationships among selected taxa of Malvaceae by evaluating 23 chloroplast (CP) genomes, including three newly assembled CP genomes. Among these three genomes, the CP genome of Hibiscus schizopetalus L. was reported for the first time, while the CP genomes of Alcea rosea L. and Hibiscus grewiifolius L., which have been deposited in NCBI, were re-analyzed here alongside newly generated data for comparative purposes. In addition, 20 downloaded CP genomes encompassing 13 genera were analyzed using SNPs in whole CP genomes data. RESULTS: The results showed that the genomes ranged from 160,403 to 161,978 base pairs in length and consisted of small single copies (SSCs) and large single copies (LSCs) separated by two inverted repeat sequences (IRs), forming a typical quadripartite circular structure. The entire genome sequence showed relative conservation across species in terms of structure, GC content, codon usage, and gene composition. The mutation sites were mainly located in the LSC and SSC regions, and the variability in the non-coding regions was higher than that in the coding regions. The nucleotide polymorphism (Pi) analysis identified the non-coding regions such as ndhF-rpl32 and psbZ-trnG as high variable hotspots. A maximum likelihood phylogenetic tree was constructed based on SNPs in whole CP genomes data. The phylogenetic analysis divided these 23 species into five highly supported clades. It also revealed a close sister-group relationship between Abelmoschus and Hibiscus species, suggesting that Hibiscus may have a separate lineage from okra species. DISCUSSION: In conclusion, the increasing availability of CP genome resources will enhance our understanding of the classification and evolutionary patterns of the Malvaceae family. The development of molecular markers will provide important molecular evidence for precise identification and classification revision of plants in this family.

Malvaceae↗

PubMed1991

What's old and new in molecular phylogenetics.

While it is fairly easy to devise a phylogenetic tree based on molecular data, it has proven difficult to tell how reliable any such tree is. Thus while the genetic inference that humans, chimpanzees, and gorillas cluster together is widely accepted, the genetic inference that the primary division among Old World human populations is between Asia and EurAfrica is not. A molecular phylogenetic inference linking humans and chimpanzees was proposed in the 1980s based on the technique of DNA hybridization. Despite several recent publications in primary and secondary source material, much confusion still exists surrounding the work. This paper tries to clarify issues that may still be confusing to physical anthropologists, and proposes criteria upon which to judge the robusticity of a phylogenetic inference based on DNA hybridization, in light of a recent published claim of replication. The claim of replication is considered critically. Interestingly, the original DNA hybridization data may actually show a chimp-gorilla link, in harmony with other phylogenetic results.

Animals↗

PubMed2005

Hierarchical phylogenetics as a quantitative analytical framework for evolutionary developmental biology.

Phylogenetics has inherent utility in evolutionary developmental biology (EDB) as it is an established methodology for estimating evolutionary relationships and for making comparisons between levels of biological organization. However, explicit phylogenetic methods generally have been limited to two levels of organization in EDB-the species and the gene. We demonstrate that phylogenetic methods can be applied broadly to other organizational levels, such as morphological structures or cell types, to identify evolutionary patterns. We present examples at and between different hierarchical levels of organization to address questions central to EDB. We argue that this application of "hierarchical phylogenetics" can be a unifying analytical approach to the field of EDB.

Animals↗

PubMed1979

DNA reassociation kinetics in diploid and phylogenetically tetraploid cyprinidae.

Four diploid and three phylogenetically tetraploid Cyprinidae (Ostariophysi) have been characterized as for nuclear DNA content, modal chromosome number and DNA reassociation kinetics (hydroxyapatite chromatography). Among the diploid species nuclear DNA content (10(-12) g DNA/2C) was 1.62 for Tinca tinca, 1.87 for Scardinius erythrophthalmus, 2.53 for Leuciscus cephalus and 2.75 for Alburnus alburnus, while the phylogenetically tetraploid species Carassius auratus, Barbus barbus and Cyprinus carpio attained 3.40, 3.66 and 3.80 respectively. Modal chromosome number was 2n = 48-50 for diploid individuals and 2n = 100-104 for phylogenetically tetraploid ones. In all the species 5--8% of the genome is represented by highly repetitive and foldback DNA. In DNA reassociation kinetics of phylogenetically tetraploid Cyprinidae a distinct plateau separates an intermediate reassociating sequence fraction (about 22% of the genome; with average repetition frequencies between 1,000 and 1,400) from a slow reassociating one (unique DNA; about 72% of the genome). These two genome fractions are not clearly distinguishable from each other in Cot curves of the diploid Cyprinidae, where a similar plateau is not evident. Since simple ploidy changes are not expected to affect DNA reassociation kinetics we suggest a different evolution in the genome organization of the two ploidy groups. Some possible hypotheses are discussed.

Animals↗

PubMed2005

Phylogenetic patterns of enamel microstructure in dinosaur teeth.

The tooth enamel microstructure of all the dinosaur taxa that are adequately represented in the American Museum of Natural History collections were analyzed using scanning electron microscopy. This study aims to determine whether or not better sampling within a major nonmammalian amniote (hereafter referred to descriptively as "reptile") clade will unearth phylogenetic patterns in enamel microstructure in addition to those dictated by tooth function. While interest in reptile enamel microstructure has increased in the past few years, intensive sampling focused on just one monophyletic reptile clade was not previously implemented. This study reveals that phylogenetic constraints play a larger role in shaping enamel microstructure in reptiles than previously thought. Within many monophyletic dinosaur clades the combination of enamel types and enamel features within a tooth-the schmelzmuster-is the same in all the taxa due to their common ancestry, and their schmelzmusters are diagnostic of their respective clades. While distantly related taxa with similar teeth and diets have similar schmelzmusters due to functional constraints, phylogenetic constraints keep those schmelzmusters distinct from one another. An interesting finding of this analysis is that the enamel complexity of a taxon does not necessarily coincide with the position of the taxon on a phylogenetic tree; more derived taxa do not necessarily have more derived enamel and more primitive taxa do not necessarily have more primitive enamel.

Animals↗

PubMed1995

Phylogenetic ordinal placement based on rDNA sequences of the freshwater genera Ophioceras and Pseudohalonectria.

The ordinal placement of two closely related freshwater genera, Ophioceras and Pseudohalonectria, was assessed by using phylogenetic analysis of morphological characters, partial sequences of the large subunit ribosomal DNA and restriction site variations in the internal transcribed spacer (ITS). The two genera have some morphological features that are used to define taxa in both the Sordariales and Diaporthales, and, hence, their phylogenetic relationships are unclear. Equally weighted analyses of thirty-eight morphological characters produced unresolved phylogenetic trees and unequivocal conclusions could not be drawn based on the morphological data. The polymerase chain reaction-amplified ITS region was variable in length between the two genera and restriction sites in the ITS region were determined. Analysis of variation in restriction sites in the ITS region placed Ophioceras and Pseudohalonectria in one clade with taxa sampled from Sordariales. About 350 basepairs of DNA sequence from the 5' end of the large subunit rDNA were also determined. In phylogenetic analysis of the sequence data with Hypocrea lutea and Nectria cinnabarina as outgroups, Ophioceras and Pseudohalonectria showed a closer relationship to Neurospora crassa, Schizothecium sp., and Sordaria fimicola of the Sordariales than to Cryphonectria parasitica and Endothia gyrosa of the Diaporthales.

Ascomycota↗

PubMed2002

Two issues in archaeological phylogenetics: taxon construction and outgroup selection.

Cladistics is widely used in biology and paleobiology to construct phylogenetic hypotheses, but rarely has it been applied outside those disciplines. There is, however, no reason to suppose that cladistics is not applicable to anything that evolves by cladogenesis and produces a nested hierarchy of taxa. This includes cultural phenomena such as languages and tools recovered from archaeological contexts. Two methodological issues assume primacy in attempts to extend cladistics to archaeological materials: the construction of analytical taxa and the selection of appropriate outgroups. In biology the species is the primary taxonomic unit used, irrespective of the debates that have arisen in phylogenetic theory over the nature of species. Also in biology the phylogenetic history of a group of taxa usually is well enough known that an appropriate taxon can be selected as an outgroup. No analytical unit parallel to the species exists in archaeology, and thus taxa have to be constructed specifically for phylogenetic analysis. One method of constructing taxa is paradigmatic classification, which defines classes (taxa) on the basis of co-occurring, unweighted character states. Once classes have been created, a form of occurrence seriation-an archaeological method based on the theory of cultural transmission and heritability-offers an objective basis for selecting an outgroup.

Archaeology↗

PubMed1993

The phylogenetic utility of cytochrome b: lessons from bufonid frogs.

The mitochondrial cytochrome b gene is widely used in systematic studies to resolve divergences of many different ages. To investigate phylogenetic relationships among frogs of the large family Bufonidae, and to explore the utility of cytochrome b for this purpose, approximately one-third of the gene was sequenced from representatives of this group. Samples were chosen to represent a range of divergence levels within Bufonidae: (1) deep (= old), among species from around the world; (2) middle, among North American species; and (3) shallow (= young), within a single species group (the Bufo boreas group). The inferred amino acid sequences of cytochrome b are highly similar in these frogs although most pairwise comparisons of the nucleotide sequences are 15-20% different. Consequently insufficient information is available to generate robust phylogenetic hypotheses for the older divergences; silent differences are saturated and yet almost no informative replacement differences exist. Among the younger divergences, silent differences are not saturated and some resolution is possible. These results show that (1) the amino acid sequence of cytochrome b evolves differently in Bufonidae than expected based on other vertebrates (2) it consequently provides surprisingly little information about old divergences in Bufonidae, and (3) phylogenetic studies applying particular genes to new groups should begin with preliminary surveys of exemplar taxa representing the range of divergence times within the group to estimate the likely phylogenetic utility of that gene in that group.

Amino Acid Sequence↗

PubMed1994

Characterization of random amplified polymorphic DNA (RAPD) products from Xanthomonas campestris and some comments on the use of RAPD products in phylogenetic analysis.

As part of our research to determine phylogenetic relationships of organisms within the phytobacterial species Xanthomonas campestris, we have examined the use of the random amplified polymorphic DNA (RAPD) technique. The objective of this aspect of our research was to determine if a valid cladistic character analysis could be carried out by direct comparison of RAPD products separated on ethidium bromide-stained agarose gels. RAPD products were amplified from 47 Xanthomonas campestris DNA templates using a single oligonucleotide primer. These RAPD products were compared and variation was characterized by Southern analysis of both RAPD products and genomic DNA of the 47 bacterial strains using two cloned RAPD products as probes. Analysis of the data set revealed that the RAPD products were not necessarily homologous or independent, crucial prerequisites for characters to be analyzed in a cladistic phylogenetic analysis. It has been commonly assumed that RAPD variation occurs due to insertion/deletion events or alterations in the primer binding site. Within our data set, we demonstrate absence phenotypes arising from the apparent absence of corresponding loci and also due to the preferred synthesis of alternative RAPD products from unrelated loci. These different types of variation are a reflection of different types of genotypic variation, and direct examination of RAPD products did not allow us to distinguish by which mechanism a particular absence phenotype arose. Although this may not be important for phenetic analyses, for analyses of homologous characters using a cladistic approach it is critical. We also detected unrelated, co-migrating RAPD products and multiple related RAPD products within reaction mixtures. These could both contribute to errors in estimates of similarity, important in any phylogenetic analysis. All of these characteristics of RAPD products should be taken into consideration when RAPD products are used for phylogenetic comparisons.

Blotting, Southern↗

PubMed1994

Why one-kilobase sequences from mitochondrial DNA fail to solve the Hoatzin phylogenetic enigma.

To address the suitability of mitochondrial DNA sequence data for higher avian systematics, cytochrome b sequences for nine species of Cuculiformes and Galliformes were gathered and compared to those of the Hoatzin, a specialized bird whose phylogenetic affinities have long puzzled ornithologists. Additional avian cytochrome b sequences from GenBank also were incorporated into the comparisons. Various phenetic and parsimony analyses applied to the molecular data coded in four formats (nucleotide sequences, purines versus pyrimidines, first and second positions of codons, and translated amino acid sequences) yielded several consistent phylogenetic arrangements, including the distinction of Galliformes from Cuculiformes, a clade composed of the Guira Cuckoo and Groove-billed Ani (Crotophagidae) to the exclusion of the other assayed cuculiforms (Cuculidae and Coccyzidae), and a clade composed of the New World quail (Odontophoridae, in the Sibley-Ahlquist classification) as a sister group to most or all Old World galliforms assayed (Phasianidae and Numididae). The latter result is of particular interest because it supports a controversial systematic realignment of the Galliformes based on DNA-DNA hybridization data. With regard to the phylogenetic position of the Hoatzin, the analysis differed in face-value outcome, although alternative clades were in all cases poorly supported by bootstrapping, and internodal distances were small relative to the range of genetic separations within either Cuculiformes or Galliformes. These uncertainties in phylogenetic resolution of the Hoatzin appear to be attributable to shallow slopes in the regressions relating cytochrome b sequence differences to evolutionary time, in conjunction with homoplasy in the data, sampling error in the estimation of genetic differences, and the relatively close temporal placements of relevant evolutionary nodes.

Animals↗

PubMed1995

Phylogenetic relationships among phrynosomatid lizards as inferred from mitochondrial ribosomal DNA sequences: substitutional bias and information content of transitions relative to transversions.

The phylogenetic relationships among 40 species, representing all genera, within the North American lizard family Phrynosomatidae were inferred from mitochondrial ribosomal RNA gene sequences. Cladistic analysis of the DNA sequence data (779 bp; 162 informative characters) supported the monophyly of the sand lizards (Callisaurus, Cophosaurus, Holbrookia, and Uma), Petrosaurus, Phrynosoma, Urosaurus, and Uta. All the species of Sceloporus, except S. variabilis and S. chrysostictus, formed a clade. Except for a sand lizard + Phrynosoma clade, the intergeneric relationships inferred from the mtDNA were largely incongruent with recent cladistic analyses based on morphology. Sceloporus group monophyly was not supported, with Petrosaurus being a member of a clade containing Sator, Sceloporus, and Urosaurus, to the exclusion of Uta. The phylogenetic placement of Uta was ambiguous. The substitutional bias in the phrynosomatid mitochondrial rDNA sequences was examined, as well as the phylogenetic information content of transitions relative to transversions. There appeared to be a lower transition bias than observed in other vertebrate sequences, with some classes of transversions occurring as frequently as G <-> A transitions. Transitions were no less informative for phylogeny reconstruction than transversions. Therefore, transitions should not be down-weighted in phylogenetic analysis, as is often done.

Animals↗

PubMed1996

Molecular phylogenetics of Puffinus shearwaters: preliminary evidence from mitochondrial cytochrome b gene sequences.

Puffinus shearwaters (Family Procellariidae) are a diverse genus of pelagic seabirds or petrels with a worldwide distribution. Five subgroups of species have been recognized on the basis of osteological and external morphological characters. However, phylogenetic relationships among extant taxa are poorly understood, and evolutionary scenarios to explain the current overlapping distribution of the species subgroups are speculative. Phylogenetic analyses of partial mitochondrial cytochrome b gene sequences were used to examine the relationships among 19 species and subspecies of Puffinus shearwaters. In general, the molecular data support previous morphologically based phylogenetic hypotheses. However, the subgroup Neonectris appears to be polyphyletic with Puffinus nativitatis more closely related to species in the subgroup Puffinus. In addition the molecular data revealed a phylogenetic split between the Puffinus subgroup, with a worldwide distribution, and the remaining four subgroups which have an essentially southern hemisphere distribution. This suggests an evolutionary history in which the Puffinus ancestor was split between two geographic regions, from which dispersal and vicariant events resulted in the evolution and distribution of extant taxa.

Animals↗

PubMed1996

A molecular and morphological perspective on the phylogenetic relationships of the otophysan fishes.

We examined the phylogenetic relationships among the major lineages of otophysan fishes (Cypriniformes, Characiformes, Siluroidei, and Gymnotoidei) using a combined analysis of molecular and morphological characters. The molecular characters comprised 160 phylogenetically informative sites from nuclear-encoded ribosomal RNA and 208 phylogenetically informative sites from the mitochondrial genes encoding ribosomal RNA and the valine transfer RNA for nine otophysan taxa and a gonorynchiform outgroup. The morphological data comprised 85 characters that were obtained from an earlier cladistic study. Congruence among molecular and morphological characters is generally high. The combined analysis supports a sister group relationship between the Gymnotoidei and Siluroidei, which together form a sister group to the Characiformes. The separation of the Cypriniformes from all other otophysans represents the earliest phylogenetic split within the Otophysi. Despire the generally high congruence among molecular and morphological characters, the molecular data analyzed separately produce a topology that differs from the analysis of the combined data. Sources of the taxonomic incongruence between the molecular and morphological data are examined.

Animals↗

PubMed1996

Phylogenetic utility of histone H3 intron sequences in the perennial relatives of soybean (Glycine: Leguminosae).

Histone H3 loci form a large multigene family in most plant species. In Glycine, some of these loci possess introns, whose sequences can provide characters for assessing phylogenetic relationships among species of the genus. Phylogenetic analyses of two closely related H3-B loci revealed a complex evolutionary pattern, producing trees from which species relationships could not be inferred readily. The single H3-D locus, in contrast, provided data suitable for the construction of gene trees whose topologies were sufficiently similar to other hypotheses of relationships within the subgenus Glycine to give confidence that evolution at this locus is tracking species phylogenies. H3-D topologies identified several of the same groupings found in previous phylogenetic studies using the chloroplast genome. However, histone H3-D and chloroplast genome data sets were in other respects incongruent, as revealed by both topological differences and numerical measures of congruence. The principal difference involved Glycine falcata, whose chloroplast genome belongs to one of the three strongly supported clades in the subgenus, but whose histone H3-D allele was sister to those of the remaining members of the subgenus. The H3-D topology is more in keeping with the morphologically, ecologically, and genetically divergent nature of this species. The H3-D locus appears to be a useful source of phylogenetic characters for interspecific studies in Glycine, providing resolution among taxa whose relationships were unresolved in previous studies.

Chloroplasts↗

PubMed1997

Phylogenetic analysis of the Triticeae (Poaceae) based on rpoA sequence data.

A phylogenetic analysis was conducted on 31 diploid species representing 21 of the 24 monogenomic genera of the Triticeae. The data used were derived from a 1343- to 1358-bp region of the plastid genome spanning the entire rpoA gene plus minor parts of the petD and rps11 genes and the two intergenic spacers surrounding rpoA. Bromus inermis (Bromeae) was used as an outgroup. A total of 68 variable sites, 25 of them phylogenetically informative, and seven length mutations were detected. The length mutations occurred in the noncoding regions. Phylogenetic analyses were performed on the whole data set and on various subsets. The analysis of the unweighted data resulted in 48 equally parsimonious trees (length 98, CI = 0.88, RI = 0.92, ti = 0.25). A parsimony jackknife analysis proved several clades to be well supported. The effect of transition/transversion weighting was also investigated. In general, congruence with other data sets was negatively effected by weighting. The preferred phylogenetic hypothesis is congruent with a phylogeny based on plastid RFLP data including the same taxa, but it is largely incongruent with phylogenies derived from nuclear rDNA and morphology.

Base Sequence↗

PubMed1997

Molecular evolution and phylogenetic utility of the chloroplast rpl16 intron in Chusquea and the Bambusoideae (Poaceae).

Phylogenetic relationships within Chusquea, a diverse genus of neotropical woody bamboos, and among selected members of the Bambusoideae were explored using rpl16 intron sequence data from the chloroplast genome. Mechanisms of mutation, including slipped-strand mispairing, secondary structure, minute inversions, and base substitutions, were examined within the rpl16 intron, and their effects on sequence alignment and phylogenetic analysis were investigated. Thirty-five bamboo sequences were generated and two separate matrices were analyzed using maximum parsimony. In the first, 23 sequences from Chusquea, 1 of Neurolepis, and 3 outgroups were included. Neurolepis was supported as sister to Chusquea, Chusquea was strongly supported as a monophyletic lineage, and three species of Chusquea subg. Rettbergia were resolved as the most basal clade within the genus. In the second analysis, 15 sequences, 14 from across the subfamily and 1 outgroup, were included. A Bambusoideae clade was recovered with the Olyreae/Parianeae (herbaceous bamboos) and the Bambuseae (woody bamboos) each supported as monophyletic. Two clades corresponding to temperate and tropical woody bamboos were derived within the Bambuseae and the tropical taxa were further split into New World and Old World clades. The rpl16 intron in bamboos was found to be susceptible to frequent length mutations of multiple origins, nonindependent character evolution, and regions of high mutability, all of which created difficulties in alignment and phylogenetic analysis; nonetheless the rpl16 intron is phylogenetically informative at the inter- and intrageneric levels in bamboos.

Chloroplasts↗

PubMed1997

Escaping from the Felsenstein zone by detecting long branches in phylogenetic data.

Long branches in a true phylogeny tend to disrupt hierarchical character covariation (phylogenetic signal) in the distribution of traits among organisms. The distortion of hierarchical structure in character-state matrices can lead to errors in the estimation of phylogenetic relationships and inconsistency of methods of phylogenetic inference. Examination of trees distorted by long-branch attraction will not reveal the identities of problematic taxa, in part because the distortion can mask long branches by reducing inferred branch lengths and through errors in branching order. Here we present a simple method for the detection of taxa whose placement in evolutionary trees is made difficult by the effects of long-branch attraction. The method is an extension of a tree-independent conceptual framework of phylogenetic data exploration (RASA). Taxa that are likely to attract are revealed because long branches leave distinct footprints in the distribution of character states among taxa, and these traces can be directly observed in the error structure of the RASA regression. Problematic taxa are identified using a new diagnostic plot called the taxon variance plot, in which the apparent cladistic and phenetic variances contributed by individual taxa are compared. The procedure for identifying long edges employs algorithms solved in polynomial time and can be applied to morphological, molecular, and mixed characters. The efficacy of the method is demonstrated using simulated evolution and empirical evidence of long branches in a set of recently published sequences. We show that the accuracy of evolutionary trees can be improved by detecting and combating the potentially misleading influences of long-branch taxa.

Classification↗

PubMed1998

Phylogenetic relationships among Agamid lizards of the Laudakia caucasia species group: testing hypotheses of biogeographic fragmentation and an area cladogram for the Iranian Plateau.

Phylogenetic relationships within the Laudakia caucasia species group on the Iranian Plateau were investigated using 1708 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNAGln, tRNAIle, tRNAMet, ND2, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, and COI (subunit I of cytochrome c oxidase). The aligned sequences contain 207 phylogenetically informative characters. Three hypotheses for historical fragmentation of Laudakia populations on the Iranian Plateau were tested. In two hypotheses, fragmentation of populations is suggested to have proceeded along continuous mountain belts that surround the Iranian Plateau. In another hypothesis, fragmentation is suggested to have resulted from a north-south split caused by uplifting of the Zagros Mountains in the late Miocene or early Pliocene [5-10 MYBP (million years before present)]. The shortest tree suggest the later hypothesis, and statistical tests reject the other two hypothesis. The phylogenetic tree is exceptional in that every branch is well supported. Geologic history provides dates for most branches of the tree. A plot of DNA substitutions against dates from geologic history refines the date for the north-south split across the Iranian Plateau to 9 MYBP (late Miocene). The rate of evolution for this segment of mtDNA is 0.65% (0.61-0.70%) change per lineage per million years. A hypothesis of area relationships for the biota of the Iranian Plateau is generated from the phylogenetic tree.

Animals↗