Phylogeographic relationships in the polypore fungus Pycnoporus inferred from molecular data

The genus Pycnoporus forms a group of four species known especially for producing high redox potential laccases suitable for white biotechnology. A sample of 36 Pycnoporus strains originating from different geographical areas was studied to seek informative molecular markers for the typing of new strains in laboratory culture conditions and to analyse the phylogeographic relationships in this cosmopolitan group. ITS1-5.8S-ITS2 ribosomal DNA and partial regions of β-tubulin and laccase lac3-1 gene were sequenced. Phylogenetic trees inferred from these sequences clearly differentiated the group of Pycnoporus cinnabarinus strains from the group of Pycnoporus puniceus strains into strongly supported clades (100% bootstrap value). Molecular clustering based on lac 3-1 sequences enabled the distribution of Pycnoporus sanguineus and Pycnoporus coccineus through four distinct, well supported clades and sub-clades. A neotropical sub-clade, grouping the P. sanguineus strains from French Guiana and Venezuela, corresponded to P. sanguineus sensu stricto. A paleotropical sub-clade, clustering the strains from Madagascar, Vietnam and New Caledonia, was defined as Pycnoporus cf. sanguineus. The Australian clade corresponded to P. coccineus sensu stricto. The Eastern Asian region clade, clustering the strains from China and Japan, formed a P. coccineus-like group. Laccase gene (lac 3-1) analysis within the Pycnoporus species can highlight enzyme functional diversity associated with biogeographical origin.     

Molecular dating and phylogenetic relationships among Teiidae (Squamata) inferred by molecular and morphological data

We present a phylogenetic analysis of teiid lizards based on partitioned and combined analyses of 12S and 16S mitochondrial DNA sequences, and morphological and ultrastructural characters. There were some divergences between 12S and 16S cladograms, but phylogenetic analyses of the combined molecular data corroborated the monophyly of Tupinambinae, Teiinae, and "cnemidophorines", with high support values. The total combined analysis (molecules+morphology) produced similar results, with well-supported Teiinae and "cnemidophorines". We present an evolutionary scenario for the evolution of Teiidae, based on molecular dating of evolutionary events using Bayesian methods, ancestral areas analysis, the fossil record, the geographic distribution of genera, and environmental and geologic changes during the Tertiary. According to this scenario, (1) all current teiid genera, except Aspidoscelis, originated in isolation in South America; (2) most teiid genera originated during the Eocene, a period characterized by savanna expansion in South America; and (3) Cnemidophorus originated in South America, after which some populations dispersed to Central America during the Late Miocene.     

Consistency of SINE insertion topology and flanking sequence tree: quantifying relationships among cetartiodactyls

Short interspersed nuclear elements (SINEs) have been used to generate unambiguous phylogenetic topologies relating eukaryotic taxa. The irreversible nature of SINE retroposition is supported by a large body of comparative genome data and is a fundamental assumption inherent in the value of this qualitative method of inference. Here, we assess the key assumption of unidirectional SINE insertion by comparing the SINE insertion-derived topology and the phylogenetic tree based on seven independent loci of five taxa in the order Cetartiodactyla (Cetacea + Artiodactyla). The data sets and analyses were largely independent, but the loci were, by definition, linked, and thus their consistency supported an irreversible pattern of SINE retroposition. Moreover, our analyses of the flanking sequences provided estimates of divergence times among cetartiodactyl lineages unavailable from SINE insertion analysis alone. Unexpected rate heterogeneity among sites of SINE-flanking sequences and other noncoding DNA sequences were observed. Sequence simulations suggest that this rate heterogeneity may be an artifact resulting from the inaccuracies of the substitution model used.     

Phylogenetic relationships among species of Prunus as inferred by isozyme markers

Summary An isozyme survey of 34 species of Prunus representing subgenera Prunus, Amygdalus, Cerasus, and Lithocerasus detected 110 presumptive alleles at 11 isozyme loci. Principal component analysis was conducted on the covariance matrix derived from allelic frequencies calculated for each species. Cluster analysis was performed on the first 30 principal components. Results generally support traditional classification of Prunus at the subgeneric level, except for members of subgenus Lithocerasus and two members of subgenus Amygdalus. Prunus glandulosa Thunb., P. japonica Thunb., and P. tomentosa Thunb. of subgenus Lithocerasus and P. triloba Lindl. of subgenus Amygdalus appear to represent primitive species. P. besseyi Bailey and P. pumila L. of subgenus Lithocerasus and P. andersonii of subgenus Amygdalus should be assigned to subgenus Prunus. Placement of its members indicates that subgenus Lithocerasus is an artificial grouping of species that are very different genetically although similar phenotypically.Paper No. 12529 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh, NC 27695-7643, USA     

Phylogenetic relationships within Serpulidae (Sabellida, Annelida) inferred from molecular and morphological data

We assessed phylogenetic relationships within Serpulidae (including Spirorbinae) using parsimony and Bayesian analyses of 18S rDNA, the D1 and D9−D10 regions of 28S rDNA, and 38 morphological characters. In total, 857 parsimony informative characters were used for 31 terminals, 29 serpulids and sabellid and sabellariid outgroups. Following ILD assessment the two sequence partitions and morphology were analysed separately and in combination. The morphological parsimony analysis was congruent with the results of the 2003 preliminary analysis by Kupriyanova in suggesting that a monophyletic Serpulinae and Spirorbinae form a clade, while the remaining serpulids form a basal grade comprising what are normally regarded as Filograninae. Bremer support values were, however, quite low throughout. In contrast, the combined analyses of molecular and morphological data sets provided highly resolved and well-supported trees, though with some conflict when compared to the morphology-only analysis. Spirorbinae was recovered as a sister group to a monophyletic group comprising both 'filogranin' taxa ( Salmacina , Filograna , Protis , and Protula ) and 'serpulin' taxa such as Chitinopoma , Metavermilia , and Vermiliopsis . Thus the traditionally formulated subfamilies Serpulinae and Filograninae are not monophyletic. This indicates that a major revision of serpulid taxonomy is needed at the more inclusive taxonomic levels. We refrain from doing so based on the present analyses since we feel that further taxon sampling and molecular sequencing are required. The evolution of features such as the operculum and larval development are discussed.     

Phylogenetic relationships of thorny catfishes (Siluriformes: Doradidae) inferred from molecular and morphological data

Doradidae is a putatively monophyletic group of South American freshwater catfishes containing 30 extant genera and 72 valid species. Only one study to date has attempted to estimate phylogenetic relationships among doradids. This morphological analysis partitioned species into two basal genera ( Wertheimeria and Francisodoras ) and a crown group of three subfamilies (Platydoradinae, Astrodoradinae and Doradinae) whose relationships were unresolved. No subsequent work has been done to resolve the subfamilial trichotomy or to assess whether postulated intergeneric relationships are accurate. We address this problem with complete sequences (2.5 kilobases, kb) of mitochondrial 12S and 16S rRNA genes and partial (1.3 kb) sequences of the nuclear elongation factor-1 alpha (EF1α) gene from representatives of 23 doradid genera (43 species) and 13 outgroups from additional siluriform families. Phylogenetic analysis of these data yields strong support for the monophyly of Doradidae and Astrodoradinae (as well as other relationships), but otherwise shows significant conflict with morphological results. A partial re-examination of published morphological data indicates that many characters may have been incorrectly polarized and many taxa have incorrect state assignments. Our results provide a framework for ongoing efforts to describe the species-level diversity of this poorly understood neotropical family.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 140 , 551–575.     

Genetic relationships of Aglaonema species and cultivars inferred from AFLP markers

BACKGROUND AND AIMS: Aglaonema is an important ornamental foliage plant genus, but genetic relationships among its species and cultivars have not been reported. This study analysed genetic relatedness of 54 cultivars derived from nine species using amplified fragment length polymorphism (AFLP) markers. METHODS: Initially, 48 EcoRI + 2/MseI + 3 primer set combinations were screened, from which six primer sets that showed clear scoreable and highly polymorphic fragments were selected and used for AFLP reactions. AFLP fragments were scored and entered into a binary data matrix as discrete variables. Jaccard's coefficient of similarity was calculated for all pair-wise comparisons among the 54 cultivars, and a dendrogram was constructed by the unweighted pair-group method using the arithmetic average (UPGMA). KEY RESULTS: The number of AFLP fragments generated per primer set ranged from 59 to 112 with fragment sizes varying from 50 to 565 bp. A total of 449 AFLP fragments was detected, of which 314 were polymorphic (70 %). All cultivars were clearly differentiated by their AFLP fingerprints. The 54 cultivars were divided into seven clusters; cultivars within each cluster generally share similar morphological characteristics. Cluster I contains 35 cultivars, most of them are interspecific hybrids developed mainly from A. commutatum, A. crispum or A. nitidum. However, Jaccard's similarity coefficients among these hybrids are 0.84 or higher, suggesting that these popular hybrid cultivars are genetically much closer than previously thought. This genetic similarity may imply that A. nitidum and A. crispum are likely progenitors of A. commutatum. CONCLUSIONS: Results of this study demonstrate the efficiency and ease of using AFLP markers for investigating genetic relationships of ornamental foliage plants, a group usually propagated vegetatively. The AFLP markers developed will help future Aglaonema cultivar identification, germplasm conservation and new cultivar development.     

Phylogenetic relationships within the New World endemic Zeltnera (Gentianaceae-Chironiinae) inferred from molecular and karyological data

The New World endemic genus Zeltnera consists of 25 species mainly distributed in the western part of the United States and Mexico. Chromosome counts performed on 113 populations (24 species) reveal extensive congruence between chromosomal groups and the assemblages obtained from analyses of nuclear ribosomal DNA (ITS) and chloroplast DNA (trnL intron and trnL-F intergenic spacer) sequences. Karyological and molecular data sets support three main biogeographic groups for Zeltnera. A first and mainly unresolved cluster (n = 17 and n = 20) occurs in California, whereas two other clades are centered in the Texas region (n = 20 and n = 21) and in Mexico (n = 21 and n = 22). Under the assumption of a molecular clock, and using both dispersal and vicariance explanations for the current distribution of the respective species, the genus is thought to have a North American origin with considerable diversification in the early Pliocene (ca. 5 million years ago). Geological events, such as desert formation and mountain orogenies, have created insuperable barriers that today separate the three major and likely vicariant groups.     

Phylogenetic relationships and evolution of Crassulaceae inferred from matK sequence data

Chloroplast gene matK sequence data were used to estimate the phylogeny of 112 species of Crassulaceae sampled from 33 genera and all six recognized subfamilies. Our analyses suggest that five of six subfamilies recognized in the most recent comprehensive classification of the family are not monophyletic. Instead, we recovered a basal split in Crassulaceae between the southern African CRASSULA: clade (Crassuloideae) and the rest of the family (Sedoideae). These results are compatible with recent studies of cpDNA restriction site analyses. Within Sedoideae, four subclades were also recovered: KALANCHOE:, Leucosedum, Acre, and AEONIUM:; evidence also exists for a TELEPHIUM: clade and SEMPERVIVUM: clade. The genus SEDUM: is highly polyphyletic with representatives spread throughout the large Sedoideae clade. Sympetaly and polymerous flowers have arisen multiple times in Crassulaceae and thus are not appropriate characters upon which to base subfamilial limits, as has been done in the past. One floral character, haplostemy, appears to be confined to the well-supported CRASSULA: clade. Our analyses suggest a southern African origin of the family, with subsequent dispersal northward into the Mediterranean region. From there, the family spread to Asia/eastern Europe and northern Europe; two separate lineages of European Crassulaceae subsequently dispersed to North America and underwent substantial diversification. Our analyses also suggest that the original base chromosome number in Crassulaceae is x = 8 and that polyploidy has played an important role in seven clades. Three of these clades are exclusively polyploid (SEMPERVIVUM: clade and two subclades within the KALANCHOE: and AEONIUM: clades), whereas four (Crassula, Telephium, Leucosedum, and ACRE: clades) comprise both diploid and polyploid taxa. Polyploidy is particularly rampant and cytological evolution especially complex in the ACRE: clade.     

Phylogenetic relationships of Gagea Salisb. (Liliaceae) in Italy, inferred from molecular and morphological data matrices

All known Italian Gagea species (23) representing seven out of 14 sections were included in this study. Morphological, molecular and combined data support the basal position of G. trinervia (Anthericoides). According to the molecular data, the sections Anthericoides, Lloydia, Gagea, Minimae and Spathaceae are very well supported; representatives of the sections Didymobulbos and Fistulosae clustered together in the same clade. In this clade, several near-related species groups (series) were recognised. According to 35 morpho-anatomical, ontogenetic and karyological data the section Gagea forms a well-defined monophyletic clade. Within this clade G. tisoniana, G. pusilla and G. cfr. paczoskii are near related. The position of the critical putative hybrid taxa G. luberonensis and G. polidorii is discussed. New series Solenarium (Dulac) Peruzzi and Tison, Occidentales (A. Terracc.) Peruzzi and Tison and Saxatiles (A. Terracc.) Peruzzi and Tison are proposed.     

Heritability of phenolics in Quercus laevis inferred using molecular markers.

Studies of quantitative inheritance of phenotypes do not generally encompass the range of environmental conditions to which a population may be exposed in a natural setting and are rarely conducted on long-lived species due to the time required for traditional crossing experiments. We used a marker-based method to estimate relatedness with microsatellite markers in a natural population of a long-lived oak, then used this inferred relatedness to examine quantitative genetic variation in the concentration of foliar phenolics. Estimating heritability using this method requires both significant relatedness and variance in relatedness over distance. However, this population did not show significant variance of relatedness, so only the presence of heritability, and its ranking among traits and environments, could be estimated. Seven foliar phenolics showed a significant relationship between phenotypic similarity and relatedness. The significance of this relationship varied among individual phenolic compounds, as well as by season. Genetic factors appeared to have a more measurable influence on the production of secondary compounds early in the season. After leaf expansion, covariance of relatedness and phenotypic variance appear to become less significant. Therefore heritability may vary seasonally for these traits.     

Morphology and biogeography of Apiaceae subfamily Saniculoideae as inferred by phylogenetic analysis of molecular data

The phylogenetic placements of several African endemic genera at the base of Apiaceae subfamilies Saniculoideae and Apioideae have revolutionized ideas of relationships that affect hypotheses of character evolution and biogeography. Using an explicit phylogeny of subfamily Saniculoideae, we reconstructed the evolutionary history of phenotypic characters traditionally important in classification, identified those characters most useful in supporting relationships, and inferred historical biogeography. The 23 characters examined include those of life history, vegetative morphology, inflorescences, and fruit morphology and anatomy. These characters were optimized over trees derived from maximum parsimony analysis of chloroplast DNA trnQ-trnK sequences from 94 accessions of Apiaceae. The results revealed that many of these characters have undergone considerable modification and that traditional assumptions regarding character-state polarity are often incorrect. Infrasubfamilial relationships inferred by molecular data are supported by one to five morphological characters. However, none of these morphological characters support the monophyly of subfamilies Saniculoideae or Apioideae, the clade of Petagnaea, Eryngium and Sanicula, or the sister-group relationship between Eryngium and Sanicula . Southern African origins of Saniculoideae and of its tribes Steganotaenieae and Saniculeae are supported based on dispersal-vicariance analysis.     

Phylogenetic relationships of the Aurantioideae inferred from chloroplast DNA sequence data

The tribes and subtribes of Aurantioideae, an economically important subfamily of the Rutaceae, have a controversial taxonomic history because of the lack of a phylogenetic framework. The rps16 and trnL-trnF sequences of the chloroplast were analyzed phylogenetically to construct an evolutionary history and evaluate the most recent classification system of Swingle and Reece (The Citrus Industry, volume 1 [1967]). Taxa representing tribes Citreae and Clauseneae and five of the six subtribes were sampled. Conflicts in the positions of some taxa between the rps16 and trnL-trnF trees are poorly supported. In all analyses, the Aurantioideae are monophyletic. The strict consensus tree of the combined analysis indicates that the two tribes along with the subtribes sampled are not monophyletic. The combined topology is not congruent with the widely used classification of Aurantioideae by Swingle and Reece. The tribes and subtribes are in need of revision.     

Intra- and inter-specific variations in Lens revealed by RAPD markers

Randomly amplified polymorphic DNA (RAPD) markers were used to estimate intra- and interspecific variations in the genus Lens (lentil). Twenty cultivars of L. culinaris ssp. culinaris, including 11 microsperma (small-seeded) and nine macrosperma (large-seeded) types, and 16 wild relatives (four accessions each of L. culinaris ssp. orientalis, L. odemensis, L. nigricans and L. ervoides), were evaluated for genetic variability using a set of 40 random 10-mer primers. Fifty reproducibly scorable DNA bands were observed from ten of the primers, 90% of which were polymorphic. Genetic distances between each of the accessions were calculated from simple matching coefficients. A dendrogram showing genetic relationships between them was constructed by an unweighted pair-group method with arithmetical averages (UPGMA). This study revealed that (1) expect for L. ervoides, the level of intraspecific variation in cultivated lentil is lower than that in wild species, (2) L. culinaris ssp. orientalis is the most likely candidate for a progenitor of the cultivated species, and (3) microsperma and macrosperma cultivars were indistinguishable by the RAPD markers identified here.     

Molecular phylogeny of North American long-eared bats (Vespertilionidae: Corynorhinus); inter- and intraspecific relationships inferred from mitochondrial and nuclear DNA sequences

The taxonomy of the North American big-eared bats, genus Corynorhinus, was revised by Handley [Handley, C.O., 1959. A revision of the American bats of the genera Euderma and Plecotus. Proc. U.S. Nat. Mus. 110, 95-246] using a morphological systematics approach. Handley employed 17 morphological characters and identified only four characters that reliably differentiated the three species he recognized, C. townsendii, C. rafinesquii, and C. mexicanus. All three species have been shown to lead relatively sedentary lives and have a wing morphology that limits long-distance dispersal. Further, populations of two species, C. townsendii and C. rafinesquii, are considered to be declining. Handley [Handley, C.O., 1959. A revision of the American bats of the genera Euderma and Plecotus. Proc. U.S. Nat. Mus. 110, 95-246] recognized five subspecies of C. townsendii (C. t. australis, C. t. ingens, C. t. pallescens, C. t. townsendii, and C. t. virginianus) and two of C. rafinesquii (C. r. rafinesquii and C. r. macrotis). Two C. townsendii subspecies, C. t. ingens and C. t. virginianus, are listed as endangered under the Endangered Species Act. These facts and the lack of a thorough molecular systematic examination of this genus were the impetus for this study. Using mitochondrial and nuclear intron DNA sequences, a molecular phylogeny was inferred. The combined DNA phylogeny supports Handley's [Handley, C.O., 1959. A revision of the American bats of the genera Euderma and Plecotus. Proc. U. S. Nat. Mus. 110, 95-246] designation of three species. Further the endangered subspecies, C. t. ingens and C. t. virginianus are corroborated, as were the monophyly of the other subspecies. However, the geographical ranges of two of these subspecies, C. t. pallescens and C. t. townsendii, are revised based on biogeographic distributions as understood from our results. Estimates of timing of divergences indicate that the three species, C. townsendii, C. rafinesquii, and C. mexicanus may have diverged before Pleistocene climatic oscillations began, and therefore their cladogenesis was not the result of those processes. However, subspecific divergences within C. townsendii appear to have occurred during and been driven largely by the climatic processes of the Pleistocene Epoch. We propose new hypotheses of dispersal scenarios that may have led to the current biogeography of these lineages.     

Interordinal relationships and timescale of eutherian evolution as inferred from mitochondrial genome data

Extensive phylogenetic analyses of the updated sequence data of mammalian mitochondrial genomes were carried out using the maximum likelihood method in order to resolve deep branchings in eutherian evolution. The divergence times in the mammalian tree were estimated by a relaxed molecular clock of the mitochondrial proteins calibrated with multiple references. A Chiroptera/Eulipotyphla (i.e. bat/mole) clade and a close relationship of this clade to Fereuungulata (Carnivora+Perissodactyla+Cetartiodactyla) were reconfirmed with high statistical significance. However, a support for a monophyly of Fereuungulata relative to the Chiroptera/Eulipotyphla clade was fragile, and we suggest that the three branchings among Carnivora, Perissodactyla, Cetartiodactyla and Chiroptera/Eulipotyphla occurred successively in a short time period, estimated to be approximately 77Myr BP. The Chiroptera/Eulipotyphla divergence was estimated to roughly coincide with the Cretaceous-Tertiary boundary (65Myr BP). The monophyly of Rodentia, the Lagomorpha/Rodentia clade (traditionally called Glires), and the Afrotheria/Xenarthra clade were preferred over alternative relationships, but the supports of these clades were not strong enough to exclude other possibilities. Although several super-order taxa of eutherians were strongly supported by the analyses of the mitochondrial genome data, the branching order in the deepest part of the eutherian tree remained ambiguous from the data presently available.