The systematic relationships of the snake genus Anomochilus

Phylogenetic analysis of 38 skeletal characters, 12 muscular characters and 15 visceral characters in 17 major snake clades plus Anomochilus suggests that Anomochilus is the sister taxon of all other living alethinophidian snakes. However, skeletal, muscular and visceral character sets analysed separately or in pairs give four groups of nonconcordant tree topologies. Based on the cladogram derived from the total evidence, two families are erected to prevent the existing family Uropeltidae from becoming paraphyletic: Anomochilidae, for the Malaysian and Indonesian genus Anomochilus , and Cylindrophiidae, for the Sri Lankan, Southeast Asian and Indonesian genus Cylindrophis and the Upper Eocene fossil Eoanilius.     

Using phylogeny to investigate the origins of the Cape flora: the importance of taxonomic, gene and genome sampling strategies

Phylogenetic methods hold great promise for the reconstruction of the transition from precursor to modern flora and the identification of underlying factors which drive the process. The phylogenetic methods presently used to address the question of the origin of the Cape flora of South Africa are considered here. The sampling requirements of each of these methods, which include dating of diversifications using calibrated molecular trees, sister pair comparisons, lineage through time plots and biogeographical optimizations, are reviewed. Sampling of genes, genomes and species are considered. Although increased higher-level studies and increased sampling are required for robust interpretation, it is clear that much progress is already made. It is argued that despite the remarkable richness of the flora, the Cape flora is a valuable model system to demonstrate the utility of phylogenetic methods in determining the history of a modern flora.     

Phylogenetic relationships, diversification and biogeography in Neotropical Brotogeris parakeets

Aim We present a molecular phylogenetic analysis of Brotogeris (Psittacidae) using several distinct and complementary approaches: we test the monophyly of the genus, delineate the basal taxa within it, uncover their phylogenetic relationships, and finally, based on these results, we perform temporal and spatial comparative analyses to help elucidate the historical biogeography of the Neotropical region. Location Neotropical lowlands, including dry and humid forests. Methods Phylogenetic relationships within Brotogeris were investigated using the complete sequences of the mitochondrial genes cyt b and ND2, and partial sequences of the nuclear intron 7 of the gene for Beta Fibrinogen for all eight species and 12 of the 17 taxa recognized within the genus (total of 63 individuals). In order to delinetae the basal taxa within the genus we used both molecular and plumage variation, the latter being based on the examination of 597 skin specimens. Dates of divergence and confidence intervals were estimated using penalized likelihood. Spatial and temporal comparative analyses were performed including several closely related parrot genera. Results Brotogeris was found to be a monophyletic genus, sister to Myiopsitta. The phylogenetic analyses recovered eight well‐supported clades representing the recognized biological species. Although some described subspecies are diagnosably distinct based on morphology, there was generally little intraspecific mtDNA variation. The Amazonian species had different phylogenetic affinities and did not group in a monophyletic clade. Brotogeris diversification took place during the last 6 Myr, the same time‐frame as previously found for Pionus and Pyrilia. Main conclusions The biogeographical history of Brotogeris implies a dynamic history for South American biomes since the Pliocene. It corroborates the idea that the geological evolution of Amazonia has been important in shaping its biodiversity, argues against the idea that the region has been environmentally stable during the Quaternary, and suggests dynamic interactions between wet and dry forest habitats in South America, with representatives of the Amazonian biota having several independent close relationships with taxa endemic to other biomes.     

A comparison of phenetic and phylogenetic methods applied to the systematics of Oligochaeta

A comparative study of naidid subfamilies shows that a combination of ordination, Jaccard/Average Linkage cluster analysis and Wagner parsimony provides a useful basis for a rational phylogeny but that this does not differ markedly from the original proposed by Sperber nearly four decades ago. Hennig rules, modified by Wiley, permit a preliminary phylogeny and classification of the Annelida to be made by hand. An error in earlier versions suggested that the Dorydrilidae lacked prostate glands, and this is corrected.     

Phylogeny of five Prosopium species with comparisons with other Coregonine fishes based on isozyme electrophoresis*

Phylogenetic relationships of Prosopium gemmifer, P. spilonotus, P. williamsoni, P. cylindraceum and P. coulteri species were determined based on variation at 37 allozyme loci, and compared with Stenodus and nine species of Coregonus. Of the three genera, Prosopium was the most distinct with Nei genetic distances to Coregonus of D=0·55—1·05 and to Stenodus of D=0·58—0·92. Stenodus and Coregonus were closely related but grouped as sister taxa with a mean genetic distance of 0·31 (range 0·22—0·40). These results agree with the degree of morphological differentiation among the genera as well as with observations concerning hybridization, e.g. many Coregonus species hybridize with Stenodus, but no natural hybrids are known between Prosopium and other coregonines. Within Prosopium, P. coulteri was the most divergent species branching out at D=0·51 from the others and followed by P. cylindraceum at D=0·28. The three remaining species are closely related. Among them P. williamsoni joins P. gemmifer and P. spilonotus at 0·04, and the distance between the two Bear Lake endemics is only 0·004. The distance between P. cylindraceum and the remaining Prosopium species is similar to distances between Stenodus and Coregonus. The small genetic distance between P. spilonotus and P. gemmifer suggests their recent divergence. Even though no fixed differences were found between them, diVerent alleles were present at two loci at large enough frequencies to indicate reproductive isolation. This confirms that P. gemmifer and P. spilonotus are good biological species as indicated by their distinct morphology and ecology.     

CLADISTICS OF THE BRYOPSIDALES: A PRELIMINARY ANALYSIS

The Bryopsidales contains some of the most species rich and ecologically dominant algae in tropical ecosystems. However, the evolutionary relationships among the 29 genera and several hundred species of this order remain poorly resolved. Because of a lack of known reproductive characters for many taxa, evolutionary hypotheses grouped genera by similarities in morphological characters. To apply standard cladistical analyses to further our understanding of this group, this study presents the first comprehensive compilation of reported morphological, reproductive, and subcellular characteristics for genera in the Bryopsidales. Computer-assisted cladistical analyses ultimately identified phylogenetically informative and uninformative characters. Although the topology of the trees generated in this study is expected to change as additional data are added to this matrix, many traditional groupings and recent groupings based on molecular data were supported.     

TESTS FOR ANCIENT SPECIES FLOCKS BASED ON MOLECULAR PHYLOGENETIC APPRAISALS OF SEBASTES ROCKFISHES AND OTHER MARINE FISHES

The concept of species flocks has been central to previous interpretations of patterns and processes of explosive species radiations within several groups of freshwater fishes. Here, molecular phytogenies of species-rich Sebastes rockfishes from the northeastern Pacific Ocean were used to test predictions of null theoretical models that assume random temporal placements of phylogenetic nodes. Similar appraisals were conducted using molecular data previously published for particular cichlid fishes in Africa that epitomize, by virtue of a rapid and recent radiation of species, the traditional concept of an intralacustrine “species flock.” As gauged by the magnitudes of genetic divergence in cytochrome b sequences from mitochondrial DNA, as well as in allozymes, most speciation events in the Sebastes complex were far more ancient than those in the cichlids. However, statistical tests of the nodal placements in the Sebastes phylogeny suggest that speciation events in the rockfishes were temporally nonrandom, with significant clustering of cladogenetic events in time. Similar conclusions also apply to an ancient complex of icefishes (within the Notothenioidei) analyzed in the same fashion. Thus, the rockfishes (and icefishes) may be interpreted as ancient species flocks in the marine realm. The analyses exemplified in this report introduce a conceptual and operational approach for extending the concept of species flocks to additional environmental settings and evolutionary timescales.     

A defence of the calcichordates

Peterson (1994, Short Courses in Paleontology 7, Pal. Soc. & Univ. Tennessee; 1995, Lethaia 28 ) has claimed that the calcichordate theory of the origin of chordates can be dismissed on purely methodological grounds, without evaluating the anatomy of the calcichordates. He claimed this on the basis of his finding that the interrelationships for extant deuterostomes obtained by a PAUP analysis were not altered by including calcichordate fossils in the analysis, allegedly coded according to the anatomical interpretations of the calcichordate theory. This result, however, was due (1) to acceptance of dubious homologies among extant deuterostomes, (2) to reliance, when asserting that the fossils made no difference, on a majority-rule tree based on 13 equal-shortest trees; and (3) to the use of numerous multi-state characters in coding, which had the effect of denying, a priori , many of the homologies claimed by the calcichordate theory between fossil and extant forms. When these errors are corrected, a new PAUP analysis yields a tree consistent with the calcichordate theory. Peterson's claim therefore fails.