Hominoid cytogenetics and evolution

Much of the literature on the chromosomes of the Hominoidea exists in virtual isolation from both evolutionary theory and physical anthropology. Several unjustified speculations about hominoid affinities in the literature of cytogenetics may be attributed to the effects of this isolation. In this paper, the literature of comparative hominoid cytogenetics is reviewed, and that on chromosomal band patterns and repetitive DNA distributions relative to current evolutionary theory is discussed. These data are critically analyzed and shown to be more consistent with an orthodox hominoid phylogeny than with heterodox phylogenies. Rates and modes of karyotypic evolution are also discussed in an attempt to begin to assimilate the study of hominoid chromosomes within the framework of physical anthropology.     

Systematics and evolution of syllids (Annelida,Syllidae)

A large, combined phylogenetic analysis (including morphological and molecular data from 18S rDNA, 16S rDNA and cytochrome c oxidase subunit I), with the highest number of species and genera of Syllidae studied to date (213 terminals), is examined. The data were explored with different parameters and optimality criteria (parsimony, likelihood, and bayesian inference). The monophyly of Syllidae and most of the traditional subfamilies is supported. The subfamily Eusyllinae is polyphyletic, as currently delineated, but it is herein reorganized and its diagnosis modified to be a valid group. Additional well supported clades arise. The phylogenetic relationships of the well known and established genera, as well as several enigmatic genera (e.g. Anguillosyllis, Paraopisthosyllis and Parahaplosyllis), the position of which in syllid taxonomy was uncertain or dubious to date, are clarified. The results corroborate previous hypotheses about the evolution of the reproductive and brooding modes. Within Syllinae, the nature of the stolon is phylogenetically informative. The classification of the whole family is revised and discussed on the basis of this phylogenetic hypothesis. © The Willi Hennig Society 2011.     

Fifty years of cytogenetics: a parallel view of the evolution of cytogenetics and genotoxicology

A parallelism exists between human cytogenetics and cytogenetic toxicology. The breakthroughs, mostly coming from and used in clinical genetics, are widely used in genetic toxicology. The birth of human cytogenetics occurred in 1956 when it was published that the diploid number of chromosomes in humans is 46. The first stage in chromosome-induced mutagenesis began in 1938 when Sax published the effects of X-rays on the chromosomes of Drosophila. In 1959, the cytogenetic anomalies for Down, Klinefelter, and Turner syndromes were described, and parallelly in 1960, the first publication on chromosomal aberrations in man caused by ionizing radiation appeared. The cytogenetic analysis of chromosomal aberrations in cell cultures is considered one of the primary methods to evaluate induced mutagenesis. At the end of the 1960s, banding techniques allowed chromosomes to be individually identified, in parallel, the sister chromatid exchange analysis technology was described. Another milestone in the history of induced mutagenesis was the discovery that mutagenic agents were able to alter chromosomal division and segregation in gonads inducing meiotic nondisjunction. Here we review new approaches and applications such as biological dosimetry, translocation scoring using FISH, and micronucleus test. Chromosomal aberrations and micronucleus test are now effective cytogenetic biomarkers of early effect used as cancer predictors. Human cytogenetics has proven to be effective over its 50-year lifespan and, although each new technique that has appeared seemed to announce its end, the fact is that the current state of cytogenetics is in reality a collection of techniques that, while common, are cheap, fast, and wide-ranging. Therefore, in genotoxicology, they continue to be useful to identify mutagenic agents as well as to evaluate and analyze exposed populations.     

Systematics and evolution of the subfamily Gerbillinae (Mammalia, Rodentia, Muridae)

Although they represent a quarter of the mammalian species, the evolutionary relationships among as well as within, the main murid lineages are still controversial. The subfamily Gerbillinae is no exception as previous studies based on morphological, karyotypical, and allozyme characters are highly incongruent. Here, we present the first molecular phylogeny for gerbils based on cytochrome b and 12S rRNA mitochondrial genes. Results are largely congruent between the two genes as well as with the concatenated data set with most of the nodes being well-supported. Based on the topologies retrieved here, we (1) propose the identification of three main clades, (2) support the split of Tatera genus into an Asian and an African group, the latter including Gerbillurus species, and (3) provide some evidence towards the inaccuracy of subgeneric divisions within both Gerbillus and Meriones. In addition, the sharp contrast between the genetic characters and morphological data sets suggest high levels of convergence, probably as a result of strong environmental constraints imposed on these rodents adapted to arid and semi-arid regions. Finally, molecular datings for the various cladogenetic events are in good agreement with the known gerbilline fossil record and support an African origin with subsequent migrations to Asia.     

Systematics and evolution within theCompositae,seen with the eyes of a chemist

The broad knowledge of the chemistry of theCompositae allows the discussion of its relevance for the systematics and evolution within the family. Furthermore a separation into subfamilies can be supported by the observed differences in the distribution of the main constituents in the tribes.     

Karyotype and DNA-content evolution in ten species of Crepis (Asteraceae) distributed in Bulgaria

Ten Crepis species from Bulgaria—five perennials (C. viscidula, C. paludosa, C. coryzaefolia, C. bilhynica, C. schochtii) four annuals (C. pulchra, C. sancta, C. setosa, C. zacintha) and one biennial (C. biennis)—were analysed karyologically using haematoxyh staining, Feulgen cytophotometry (scanning densitometry and video-based image analysis), and DNA flow cytometry with propidium iodide. All taxa but the biennial are diploids with descending basic chromosome numbers, x=6, 5, 4, 3. Significant positive correlations were found between nuclear DNA content and karyotype length and nuclear DNA content and karyotypic asymmetry. Together with the results of previous authors our data suggest that evolutionary advancement could be correlated with more symmetrical karyotypes. Negative significant correlations were established between presumably advanced growth habit (from rhizomatous and tap-rooted perennials towards highly specialized annuals) and chromosome number and karyotype length. Nuclear DNA 1C-values on average were higher in perennials than in annuals, but the ranges were overlapping and the differences not significant. Crepis biennis (2n=c. 40, presumably 10x) had the highest DNA quantity, but calculated at its x-level ranked relatively low in the species sample.     

Systematics and evolution of the genus Clathrobaculus Cossmann, 1912 (Gastropoda, Mathildidae)

The morphology and ontogeny of Jurassic gastropods those have been included in the genera Clathrobaculus Cossmann, 1912 and Gordenella Gründel, 1990 are discussed. Based on the ontogenetic research of their shells, several types of ontogeny are established in the species of these genera. The suggestion is made that the genus Gordenella should be considered as a junior synonym of Clathrobaculus within the family Mathildidae. The protoconchs of Clathrobaculus species are studied to reveal their morphological variability and a number of distinguishing characters in which they differ from the protoconchs of other mathildid genera. Four species of Clathrobaculus, of which two are new (C. medidilatatus and C. inconstantiplicatus), are described from the Jurassic deposits of the European part of Russia. The composition of C. fahrenkohli (Rouillier, 1846) and C. krantzi (Rouillier, 1849) is emended, and the protoconchs of these species and of the species C. inconstantiplicatus are described for the first time.     

Genome size shifts: karyotype evolution in Crepis section Neglectoides (Asteraceae)

Plant genome size evolution is a very dynamic process: the ancestral genome of angiosperms was initially most likely small, which led to a tendency towards genome increase during evolution. However, findings in several angiosperm lineages demonstrate mechanisms that also led to genome size contraction. Recent molecular investigations on the Asteraceae genus Crepis suggest that several genomic reduction events have occurred during the evolution of the genus. This study focuses on the Mediterranean Crepis sect. Neglectoides, which includes three species with some of the smallest genomes within the whole genus. Crepis neglecta has the largest genome in sect. Neglectoides, approximately twice the size of the two species Crepis cretica and Crepis hellenica. Whereas C. cretica and C. hellencia are more closely related to each other than to C. neglecta the karyotypes of the latter species and C. cretica are similar, while that of C. hellenica differs considerably. Here, the karyotypic organisation of the three species is investigated with fluorescence in‐situ hybridisation and studied in a molecular phylogenetic framework based on the nuclear markers Actin, CHR12, CPN60B, GPCR1 and XTH23. Our findings further corroborate the occurrence of genome size contraction in Crepis, and suggest that the difference in genome size between C. neglecta and C. cretica is mostly due to elimination of dispersed repetitive elements, whereas chromosomal reorganisation was involved in the karyotype formation of C. hellenica.     

Systematics of Fraxinus (Oleaceae) and evolution of dioecy

Phylogenetic relationships among 40 of the 43 recognized species of Fraxinus L. (Oleaceae) were estimated on the basis of 106 nuclear ribosomal ITS sequences. ITS trees resulting from maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) are congruent and identify six distinct lineages. These clades allow establishing sections with high molecular and morphological support. The basal resolution generally has low ML bootstrap and MP jackknife support, but the Bayesian posterior probabilities are high for certain relationships. An independent data set of combined sequences from the chloroplast rps16 and trnL-F regions contains few informative sites but corroborate most of the relationships in the ITS tree. The molecular phylogeny is discussed in the light of morphological and other data and a revised infrageneric classification with six sections are presented. The subgenera and subsections are abandoned and the section Pauciflorae is a new combination. Fraxinus quadrangulata and Fraxinus anomala are united with Fraxinus dipetala in the section Dipetalae and Fraxinus platypoda is transferred to the section Fraxinus. Fraxinus chiisanensis, Fraxinus spaethiana and Fraxinus cuspidata are treated as incertae sedis. A sectional key is given, together with a systematic list of the 43 recognized species, with common synonyms and distribution. Breeding system and other traits mapped on the phylogeny show that dioecy has three separate origins, and in each case followed after the transition from insect to wind pollination. In one instance dioecy evolved from hermaphroditism via androdioecy and twice via polygamy.     

Systematics and evolution of the Pan‐Alcidae (Aves,Charadriiformes)

Puffins, auks and their allies in the wing‐propelled diving seabird clade Pan‐Alcidae (Charadriiformes) have been proposed to be key pelagic indicators of faunal shifts in Northern Hemisphere oceans. However, most previous phylogenetic analyses of the clade have focused only on the 23 extant alcid species. Here we undertake a combined phylogenetic analysis of all previously published molecular sequence data (～ 12 kb) and morphological data (n = 353 characters) with dense species level sampling that also includes 28 extinct taxa. We present a new estimate of the patterns of diversification in the clade based on divergence time estimates that include a previously vetted set of twelve fossil calibrations. The resultant time trees are also used in the evaluation of previously hypothesized paleoclimatic drivers of pan‐alcid evolution. Our divergence dating results estimate the split of Alcidae from its sister taxon Stercorariidae during the late Eocene (～ 35 Ma), an evolutionary hypothesis for clade origination that agrees with the fossil record and that does not require the inference of extensive ghost lineages. The extant dovekie Alle alle is identified as the sole extant member of a clade including four extinct Miocene species. Furthermore, whereas an Uria + Alle clade has been previously recovered from molecular analyses, the extinct diversity of closely related Miocepphus species yields morphological support for this clade. Our results suggest that extant alcid diversity is a function of Miocene diversification and differential extinction at the Pliocene–Pleistocene boundary. The relative timing of the Middle Miocene climatic optimum and the Pliocene–Pleistocene climatic transition and major diversification and extinction events in Pan‐Alcidae, respectively, are consistent with a potential link between major paleoclimatic events and pan‐alcid cladogenesis.     

Systematics and evolution of ruminal species of the genus Prevotella

Bacterial species of the genusPrevotella represent a numerically dominant microbial population in the rumen of cattle. They belong to the phylogenetic divisionCytophaga-Flexibacter-Bacteroides (CFB) which is a large group of ecologically diverse bacteria with only a few shared traits. The phylogenetic descent from a common ancestor seems to be unquestionable, however, as judged from the small subunit ribosomal RNA analysis. Only 4 ruminalPrevotella species have been described to date, even though the sequence analysis of directly retrieved 16S rRNA genes indicates a large genetic diversity within this group of rumen bacteria. The closest relatives of ruminalPrevotella spp. are not surprisingly other species of the genusPrevotella, typically inhabiting the gastrointestinal tract, oral cavity and genital areas of other animals and man. The previous phylogenetic analysis showed that species of the genusPrevotella can be split into two groups or superclusters, the “ruminal” and the “non-ruminal prevotellas”. One of 4 currently described ruminalPrevotella spp.,i.e. P. albensis, has been placed outside the supercluster containing ruminalPrevotella spp. and within the supercluster containing the non-ruminalPrevotella spp. However, the number of available small subunit rRNA sequences from this species represents only a fraction of all known ruminalPrevotella sequences.     

Systematics and evolution of the Disa draconis complex (Orchidaceae)

The systematic status of Disa draconis (L.f.) Sw. is revised following extensive field studies of population variation in the Western Cape, South Africa. Principal component and cluster analyses revealed clear distinctions between populations from sandplain, semi-arid and montane environments. Diagnostic characters were found in each of the population clusters indicating the existence of a species complex, rather than a single taxon as in the current taxonomy. We propose, therefore, that the name D. draconis (L.f.) Sw. be restricted to the individuals of the sandplain populations from which the type was collected. We reinstate an earlier name, Disa harveiana Lindl., to describe the montane populations which possess several autapomorphic characters. We also show that the geographical variation in spur length and flowering time within this species can be partitioned into two geographically distinct subspecies: D. harveiana subsp. harveiana and D. harveiana subsp. longicalcarata Johnson & Linder. The populations from the semi-arid Karoo region were recognized as a distinct new species, Disa karooica Johnson & Linder, on the basis of their peculiar petal structure. A cladistic analysis indicated that the three species forming the D. draconis complex form a monophyletic and relatively specialized lineage within Disa sect. Coryphaea. The revised classification also has important conservation implications as D. draconis , previously considered a common species, is now restricted to a few highly threatened populations on the west coast near Cape Town.     

Systematics, biogeography, and evolution of the Neotropical peacock basses Cichla (Perciformes: Cichlidae)

To investigate forces influencing diversification in Neotropical fishes, the phylogenetic relationships among species and populations of the cichlid genus Cichla were examined. Mitochondrial DNA was sequenced for 454 individuals of the 5 nominal Cichla species and several putative undescribed species. Phylogenetic analyses support the distinction of two major clades of Cichla. Clade A includes C. temensis and two undescribed species from the lower Amazonas and Xingu Rivers. Clade B includes C. orinocensis, C. monoculus, C. ocellaris. C, intermedia, and an undescribed species from the upper Madeira River. Species boundaries were relatively well-circumscribed for clade B, while incomplete lineage sorting was inferred for clade A. Three probable instances of introgression were observed, including a regional population of C. orinocensis from the Negro River that shows a history of introgression. Biogeographic patterns from Cichla are partially congruent with those seen in several other Neotropical fish clades, and the diversification of Cichla species is inferred to result from both vicariance and sympatric divergence.