Molecular systematics

Journal of Molecular Evolution -     

Fruit differentiation, palynology, and systematics in theScabiosa group of genera andPseudoscabiosa (Dipsacaceae)

Fruits ofDipsacaceae are single-seeded, have bristle-shaped calyx segments and are tightly enclosed by four fused bracts forming an epicalyx. Comparative morphological and anatomical studies reveal a great diversity of epicalyx and calyx, often relevant to fruit dispersal. The present contribution deals with theScabiosa group of genera, the core of theScabioseae tribe. Most of its taxa develop a diaphragma from a meristem on the inside of the epicalyx. This diaphragma, together with the lower part of the epicalyx encloses the fruit proper, whereas the upper parts form a so-called epi-diaphragma (ed) and a ± hyaline corona. Differences of the epicalyx with respect to the size and position of the ed, elaboration of the corona, origin of pits (=foveoles) and other morphological and anatomical specializations can be demonstrated. Together with palynological and karyological data these new facts support an improved concept of relationships and systematics for the taxa studied:Scabiosa sect.Scabiosa and sect.Cyrtostemma are closely related and should be united to form the genusScabiosa s. str.;Pycnocomon can be maintained as an independent genus, sister toScabiosa sect.Trochocephalus which then has to be treated as a genus,Lomelosia. In contrast, the following genera have to be included inLomelosia:Tremastelma asLomelosia sect.Callistemma, andScabiosiopsis as part ofLomelosia sect.Lomelosia. Pseudoscabiosa deviates in so many features that it has to be excluded from the redefinedScabioseae s. str.     

A comparative chemotaxonomic study of eight taxa of the Dipsacaceae family

ABSTRACT

Eight taxa of the Dipsacaceae family were examined for their fatty acid and sterol composition. Separation and identification of the lipid fraction was achieved by gas chromatography and gas chromatography-mass spectrometry. The phenotypic differences among taxa were established by cluster analysis. Correlation coefficients were obtained to investigate numerical relationships among constituents of the fatty acids. The results showed many significant correlations between different constituents, as well as four clusters of taxa using two linkage types of clustering.     

Molecular systematics of Lachancea yeasts

This work presents the results of molecular-genetic investigation of a new yeast genus, Lachancea Kurtzman (2003). Analysis of rRNA sequences and molecular karyotyping have shown genetic homogeneity of the genus Lachancea. Yeasts of this genus have an identical haploid number of chromosomes equal to eight, whereas limiting chromosome sizes significantly differ in various species. The largest range of chromosome bands was registered in L. cidri strains (400-2800 kb), while the smallest was found in L. waltii (1400-2800 kb). The intra- and interspecies polymorphism of Lachancea chromosomes is discussed.     

Molecular systematics of the Canidae

Despite numerous systematic studies, the relationships among many species within the dog family, Canidae, remain unresolved. Two problems of broad evolutionary significance are the origins of the taxonomically rich canidae fauna of South America and the development in three species of the trenchant heel, a unique meat-cutting blade on the lower first molar. The first problem is of interest because the fossil record provides little evidence for the origins of divergent South American species such as the maned wolf and the bush dog. The second issue is problematic because the trenchant heel, although complex in form, may have evolved independently to assist in the processing of meat. We attempted to resolve these two issues and five other specific taxonomic controversies by phylogenetic analysis of 2,001 base pairs of mitochondrial DNA (mtDNA) sequence data from 23 canidae species. The mtDNA tree topology, coupled with data from the fossil record, and estimates of rates of DNA sequence divergence suggest at least three and possibly four North American invasions of South America. This result implies that an important chapter in the evolution of modern canids remains to be discovered in the fossil record and that the South American canidae endemism is as much the result of extinction outside of South America as it is due to speciation within South America. The origin of the trenchant heel is not well resolved by our data, although the maximum parsimony tree is weakly consistent with a single origin followed by multiple losses of the character in several extant species. A combined analysis of the mtDNA data and published morphological data provides unexpected support for a monophyletic South American canidae clade. However, the homogeneity partition tests indicate significant heterogeneity between the two data sets.     

Molecular systematics of the Cactaceae

Bayesian, maximum‐likelihood, and maximum‐parsimony phylogenies, constructed using nucleotide sequences from the plastid gene region trnK‐matK, are employed to investigate relationships within the Cactaceae. These phylogenies sample 666 plants representing 532 of the 1438 species recognized in the family. All four subfamilies, all nine tribes, and 69% of currently recognized genera of Cactaceae are sampled. We found strong support for three of the four currently recognized subfamilies, although relationships between subfamilies were not well defined. Major clades recovered within the largest subfamilies, Opuntioideae and Cactoideae, are reviewed; only three of the nine currently accepted tribes delimited within these subfamilies, the Cacteae, Rhipsalideae, and Opuntieae, are monophyletic, although the Opuntieae were recovered in only the Bayesian and maximum‐likelihood analyses, not in the maximum‐parsimony analysis, and more data are needed to reveal the status of the Cylindropuntieae, which may yet be monophyletic. Of the 42 genera with more than one exemplar in our study, only 17 were monophyletic; 14 of these genera were from subfamily Cactoideae and three from subfamily Opuntioideae. We present a synopsis of the status of the currently recognized genera.
© The Willi Hennig Society 2011.     

Molecular systematics of Goniodidae (Insecta: Phthiraptera)

The higher level phylogenetic relationships within the avian feather lice (Insecta: Phthiraptera: Ischnocera) are extremely problematic. Here we investigate the relationships of 1 family (Goniodidae), sometimes recognized as distinct within Ischnocera, using parsimony and likelihood analyses of nuclear and mitochondrial DNA sequences. These data support monophyly for a restricted definition of traditional Goniodidae, but recognition of this family would result in paraphyly of the large heterogeneous family Philopteridae. We show that the New World Chelopistes is not related to other members of Goniodidae, despite similarities in morphology, but rather is the sister taxon to Oxylipeurus. Within Goniodidae, genera are divided into those occurring on Galliformes (the Goniodes complex) and those occurring on Columbiformes (the Coloceras complex). Within the well-sampled Coloceras complex, or Physconelloidinae, several groups are identified. However, traditionally recognized genera such as Coloceras and Phvsconelloides appear to be paraphyletic. Whereas the phylogeny of Goniodidae reflects some aspects of host relationships, biogeography also influences coevolutionary history.     

Molecular systematics of citrus-associated Alternaria species

The causal agents of Alternaria brown spot of tangerines and tangerine hybrids, Alternaria leaf spot of rough lemon and Alternaria black rot of citrus historically have been referred to as Alternaria citri or A. alternata. Ten species of Alternaria recently were described among a set of isolates from leaf lesions on rough lemon (Citrus jambhiri) and tangelo (C. paradisi × C. reticulata), and none of these isolates was considered representative of A. alternata or A. citri. To test the hypothesis that these newly described morphological species are congruent with phylogenetic species, selected Alternaria brown spot and leaf spot isolates, citrus black rot isolates (post-harvest pathogens), isolates associated with healthy citrus tissue and reference species of Alternaria from noncitrus hosts were scored for sequence variation at five genomic regions and used to estimate phylogenies. These data included 432 bp from the 5' end of the mitochondrial ribosomal large subunit (mtLSU), 365 bp from the 5' end of the beta-tubulin gene, 464 bp of an endopolygalacturonase gene (endoPG) and 559 and 571 bp, respectively, of two anonymous genomic regions (OPA1-3 and OPA2-1). The mtLSU and beta-tubulin phylogenies clearly differentiated A. limicola, a large-spored species causing leaf spot of Mexican lime, from the small-spored isolates associated with citrus but were insufficiently variable to resolve evolutionary relationships among the small-spored isolates from citrus and other hosts. Sequence analysis of translation elongation factor alpha, calmodulin, actin, chitin synthase and 1, 3, 8-trihydroxynaphthalene reductase genes similarly failed to uncover significant variation among the small-spored isolates. Phylogenies estimated independently from endoPG, OPA1-3 and OPA2-1 data were congruent, and analysis of the combined data from these regions revealed nine clades, eight of which contained small-spored, citrus-associated isolates. Lineages inferred from analysis of the combined dataset were in general agreement with described morphospecies, however, three clades contained more than one morphological species and one morphospecies (A. citrimacularis) was polyphyletic. Citrus black rot isolates also were found to be members of more than a single lineage. The number of morphospecies associated with citrus exceeded that which could be supported under a phylogenetic species concept, and isolates in only five of nine phylogenetic lineages consistently were correlated with a specific host, disease or ecological niche on citrus. We advocate collapsing all small-spored, citrus-associated isolates of Alternaria into a single phylogenetic species, A. alternata.     

Fruit differentiation, palynology, and systematics in Pterocephalus Adanson and Pterocephalodes, gem now (Dipsacaceae)

The single-seeded fruits of the Dipsacaceae are enclosed by four fused bracts forming an epicalyx. A detailed study of the epicalyx morphology and anatomy of nearly all of the approximately 30 species of Pterocephalus s.L, together with other floral, palynological and karyological data, suggest only loose relationships and convergent similarities (homoplasies) between the core of the taxa (Pterocephalus s.s.), ranging from south-west and central Asia (P gedrosiacus, P. afghanicus) to Macaronesia (e.g. P. dumetorum) east Africa (P. frutescens) and southeast Asia (P. hookeri, P. bretschneideri and P. siamensis). The latter are separated as a new genus: Pterocephalodes. Pterocephalus S.S. lacks floral bracts, has numerous feathery calyx bristles and 5-merous corollas, and is apparently monophyletic. Its species demonstrate the gradual development of a hyalie corona, a diaphragma and other specialized epicalyx structures. These and other features allows the recognition of a relatively plesiornorphic, very widespread and paraphyletic basal group of perennial species (epicalyx type I), two more apomorphic perennial groups (epicalyx types II and III), and two most advanced groups (epicalyx types IV and V) with one perennial and two annual species. Pterocephalodes has floral bracts and 4-merous corollas, also appears to be monophyletic, and is limited to the eastern Himalaya and south-west China. It shares with Pseudoscabiosa the lack of a diaphragma in some of its species as well as the origin of a feathery pappus and of a corona. Thus, all three genera allow an insight into the evolutionary processes of fruit differentiation in the Dipsacaceae family.     

Molecular systematics of the genus Neotoma

DNA sequences from the mitochondrial DNA cytochrome-b gene were used to infer the systematic relationships of 13 species of wood rats (genus Neotoma). Parsimony, likelihood, and neighbor-joining analyses produced similar topologies in most cases and produced six systematic conclusions. First, results of previous studies were supported in the recognition of N. floridana magister as distinct species (N. magister). Second, evidence was provided for the recognition of cryptic species within N. albigula (N. albigula and N. leucodon) and N. mexicana (N. mexicana, N. isthmica, and N. picta). Third, the subgenus Neotoma is composed of four species groups (floridana, lepida, mexicana, and micropus). Fourth, support was provided for placement of N. stephensi within the lepida species group. Fifth, support was provided for the recognition of Hodomys as a separate genus, sister to Xenomys. Sixth, support for the elevation of the subgenus Teonoma to generic status is discussed.     

Molecular systematics of Saxifragaceae sensu stricto

To circumscribe Saxifragaceae sensu stricto better, as well as to elucidate generic relationships within this group, we sequenced the chloroplast gene rbcL and its 3' flanking region (yielding 1,471 bp) from 19 genera considered to represent core members of Saxifragaceae. In addition, we conducted a restriction site analysis of chloroplast DNA (cpDNA) for 21 core genera using 23 restriction endonucleases. Phylogenetic analyses using both data sets corroborate the results obtained from surveying the distribution of the loss of the intron in the chloroplast gene rp/2 in delimiting a well-defined Saxifragaceae sensu stricto. Within the Saxifragaceae s.s. clade, a number of poorly resolved, basal phylogenetic branches supports the hypothesis that Saxifragaceae s.s. radiated rapidly very early in its evolutionary history. Molecular data also indicate the presence of several strongly supported groups of genera, such as the Boykinia group (Boykinia, Suksdorfia, Bolandra, Sullivantia, Jepsonia, and Telesonix), the Heuchera group (Heuchera, Bensoniella, Conimitella, Eìmera, Lithophragma, Mitella, Tellima, Tiarelia, and Tolmiea) the Leptarrhena/Tanakaea group, and the Darmera group (Darmera, Astilboides, Mukdenia, Bergenia, and Rodgersia). Significantly, molecular data suggest that the very large, taxonomically complex genus Saxifraga may not be monophyletic. DNA data have also helped to resolve the generic relationships of problematic taxa, indicating, for example, that Telesonix and the enigmatic Jepsonia are sister taxa. In addition to its phylogenetic implications, this study provides insight into basic trends in morphological, chemical, and cytological evolution within Saxifragaceae s.s. The molecular-based phylogenies suggest multiple origins and/or losses of several classes of flavonoid compounds, as well as several independent instances of reduction in stamen and petal number, hypanthium-ovary fusion, and aneuploidy. This study also illustrates the ability of rbcL sequence data to resolve generic-level relationships in some taxonomic groups.     

Molecular systematics: A synthesis of the common methods and the state of knowledge

The comparative and evolutionary analysis of molecular data has allowed researchers to tackle biological questions that have long remained unresolved. The evolution of DNA and amino acid sequences can now be modeled accurately enough that the information conveyed can be used to reconstruct the past. The methods to infer phylogeny (the pattern of historical relationships among lineages of organisms and/or sequences) range from the simplest, based on parsimony, to more sophisticated and highly parametric ones based on likelihood and Bayesian approaches. In general, molecular systematics provides a powerful statistical framework for hypothesis testing and the estimation of evolutionary processes, including the estimation of divergence times among taxa. The field of molecular systematics has experienced a revolution in recent years, and, although there are still methodological problems and pitfalls, it has become an essential tool for the study of evolutionary patterns and processes at different levels of biological organization. This review aims to present a brief synthesis of the approaches and methodologies that are most widely used in the field of molecular systematics today, as well as indications of future trends and state-of-the-art approaches.     

Molecular systematics of pitvipers: paraphyly of the Bothrops complex

Phylogenetic relationships among pitvipers are inferred from a parsimony analysis using cytochrome b DNA sequences: 396 bp in the 5'end of the gene were sequenced in eight species of pitvipers (Agkistrodon blomhoffi, Agkistrodon contortrix, Bodiriechis schlegelii, Bothriopsis bilineata, Bothrops atrox, Crotalus atrox, Lachesis muta and Trimeresurus stejnegeri) and in four taxa used as outgroups (Atractaspis micropholis, Boa constrictor, Cerastes cerastes and Elapsoidea semiannulata). The monophyly of pitvipers and that of the group formed by the genera Atractaspis and Elapsoidea are confirmed. Among pitvipers, the genus Agkistrodon is paraphyletic. The Bothrops complex is polyphyletic, since the Central American genus Bothriechis is the sister group of the genus Crotalus and not clustered with the South American genera Bothriopsis and Bothrops.     

Molecular phylogeny and systematics of oligochaeta: Pro et contra

The systematics of oligochaete worms was discussed by experts for the entire 20th century. The development of computing and molecular techniques hold promise for the construction of a phylogenetically reasonable system. However, the eliminating of some paraphyletic lineages did not result in unanimous approval among a wide range of biologists (mainly morphologists and ecologists). Molecular systematics has helped clear up the position of many controversial species and genera, while causing doubts about the classification of higher rank taxa, which seemed to be logical and stable until recently.     

Molecular systematics of the Atlanto-Mediterranean Solea species

Within the genus Solea , four sister lineages have been evolved that actually correspond to the species S. vulgaris, S. senegalensis, S. kleini and S. lascaris . The existence of S. aegyptiaca and S. impar is not supported and these species can be synonymized under S. vulgaris and S. lascaris , respectively. This pattern of taxonomy agrees fully with that proposed by Ben-Tuvia (1990; Journal of Fish Biology 36, 947–960) based on morphological features. In addition, mtDNA data contradict the widely accepted relatedness between S. kleini and S. lascaris based on the shared enlarged forenostril on the blind side. A sample of soles clearly related to S. senegalensis was caught in the Gulf of Taranto (Ionian Sea), representing the most western finding of this species in the Mediterranean Sea.