Trends in the karyotype evolution of Loricariidae fish (Siluriformes)

Six species of Loricariidae belonging to the subfamilies Hypostominae (Hypostomus emarginatus, Rhinelepsis aspera, Pogonopoma wertheimeri), Ancistrinae (Panaque cf. nigrolineatus, Hemiancistrus sp.) and Loricariinae (Sturisoma cf. nigrirostrum) were studied cytogenetically. The results show that 2n = 54 represents the basal diploid number for this fish family. Different trends in the karyotypic evolution can be seen among the subfamilies: Hypostominae and Loricariinae species present diversified karyotypic macrostructures, while the Ancistrinae appear to show more conserved karyotypes. Among the Hypostominae, the genus Hypostomus had a wide karyotypic variation (2n = 52 to 80), where centric fissions seem to play an important role in this chromosomal divergence. The nucleolar organizing regions were diversified, and occurrence of multiple NORs was frequent. Heteromorphic chromosomes belonging to distinct sex chromosome systems can also occur infrequently among the Loricariidae.     

A new phylogenetic classification for the gymnophthalmid genera Cercosaura , Pantodactylus and Prionodactylus (Reptilia: Squamata)

Because of the poor state of knowledge of many of the gymnophthalmid genera, systematic revision is necessary to render the classification consistent with evolutionary history. To that end, I conducted a review of the species of three genera of the Cercosaurinae which appear to form a monophyletic group: Cercosaura , Pantodactylus , and Prionodactylus . Phylogenetic analysis of 61 morphological characters was conducted after specimens of all species were examined to evaluate the composition of each taxon. The phylogenetic reconstruction suggested that the genus Prionodactylus was paraphyletic. A new phylogenetic classification is proposed that synonymizes Pantodactylus and Prionodactylus with Cercosaura. Cercosaura is redefined to include 11 species and seven subspecies. A key is provided to distinguish among species.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society, 2003, 137 , 101−115.     

On the difference between mono-, holo-, and paraphyletic groups: a consistent distinction of process and pattern

About 50 years ago, the German entomologist Willi Hennig presented a new approach in biological systematics that he called a phylogenetic systematics. The main difference between his approach and traditional Linnean systematics was that he distinguished two new kinds of groups that he called mono- and paraphyletic groups, and whereof he considered only monophyletic groups to be natural groups. However, almost immediately after publication of his approach in English, some biological systematists commented that his monophyletic groups rather ought to be called holophyletic groups. The comment sparked a heated debate about the definition of the concept 'monophyletic groups', but the debate never reached consensus. In this paper, I claim that the controversy does not concern the definition of the concept monophyletic groups per se , but instead conceptualization of phylogenies (i.e. dichotomously branching processes) in a general sense. I discuss the relation between mono-, holo- and paraphyletic groups, and conclude that Hennig's conceptualization of phylogenies is both inconsistent and empirically wrong, whereas Linné's instead is consistent and correct.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 217–220.     

Mitochondrial phylogeny of Arvicolinae using comprehensive taxonomic sampling yields new insights

Comprehensive taxonomic sampling can vastly improve the accuracy of phylogenetic reconstruction. Here, we present the most inclusive phylogenetic analysis of Arvicolinae (Mammalia, Rodentia) to date, combining all published cytochrome  b gene sequences of greater than 1097 bp and new sequences from two monotypic genera. Overall, the phylogenetic relationships between 69 species of voles and lemmings, representing 18 genera and 10 tribes, were studied. By applying powerful modern approaches to phylogenetic reconstruction, such as maximum likelihood and Bayesian analysis, we provide new information on the early pulse of evolution within the Arvicolinae. While the position of two highly divergent lineages, Phenacomys and Ondatra , could not be resolved, the tribe Lemmini, appeared as the most basal group of voles. The collared lemmings (Dicrostonychini) grouped together with all of the remaining tribes. The two previously unstudied monotypic genera Dinaromys and Prometheomys form a moderately well-supported monophyletic clade, possibly a sister group to Ellobius (Ellobiusini). Furthermore, with one exception, all tribes ( sensu Musser & Carleton, 2005) proved to be monophyletic and can thus be regarded as meaningful evolutionary entities. Only the tribe Arvicolini emerged as paraphyletic in both analyses because of the unresolved phylogenetic position of Arvicola terrestris . Steppe voles of the genus Lagurus were solidly supported as a sister group to the Microtus and allies clade.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 825–835.     

A phylogenetic analysis of the genera of Lejeuneaceae (Hepaticae)

The Lejeuneaceae are the largest family of the liverworts (Hepaticae), with almost a thousand species in 91 currently accepted genera. We analysed phylogenetic relationships of 69 genera, representing all major subfamilies and tribes recognized in the family, by using 49 informative morphological characters (31 gametophytic, 18 sporophytic), one chemical character, and applying equal and successive weighting of characters and parsimony analysis. In all trees recovered, the Lejeuneaceae were monophyletic with Nipponolejeunea (subfam. Nipponolejeuneoideae) forming the basalmost lineage. The remaining genera clustered in two major groups, the monophyletic Lejeuneoideae (52 genera) and the paraphyletic Ptychanthoideae (16 genera). Within each, several multigeneric lineages corresponding in part to previously described taxa were recovered: the Acrolejeuneinae and Ptychanthinae clades in the Ptychanthoideae, and the Brachiolejeuneinae, Lejeuneeae and Tuyamaella–Cololejeunea clades in the Lejeuneoideae. Bryopteris , a genus sometimes treated as a separate family, was nested in the Ptychanthinae clade. The Tuyamaella–Cololejeunea lineage corresponded with three previously recognized subfamilies (Cololejeuneoideae, Myriocoleoideae and Tuyamaelloideae) and contained genera with neotenic features, in two subclades. These features seemed to have originated by multiple heterochronic events: single origins were detected for 'protonemal neoteny' and 'primary neoteny', whereas 'secondary neoteny' probably evolved twice. Relationships within the large Lejeuneeae clade (43 genera) remained largely unresolved, although several putative lineages were detected in majority rule trees. Additional characters such as DNA sequences may provide better phylogenetic resolution in this group.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 143 , 391–410.     

Phylogenetic analysis of Nymphaeales using fast-evolving and noncoding chloroplast markers

The Nymphaeales (water-lilies and relatives) represent one of the earliest branching lineages of angiosperms and comprise about 70 aquatic species. Here, we present a comprehensive study of phylogenetic relationships within the Nymphaeales from a dataset containing 24 representatives of the order, including all currently recognized genera and all subgenera of the genus Nymphaea , plus 5 outgroup taxa. Nine different regions of the chloroplast genome − comprising spacers, group II introns, a group I intron, and a protein coding gene − were analysed. This resulted in a character matrix of 6597 positions and an additional 369 characters obtained from coded length mutations. Maximum parsimony and Bayesian analyses of the complete dataset yielded congruent, fully resolved and well-supported trees. Our data confirm the monophyly of the Cabombaceae but do not provide convincing support for the monophyly of Nymphaeaceae with respect to Nuphar . Moreover, the genus Nymphaea is inferred to be paraphyletic with respect to Ondinea , Victoria and Euryale . In fact, the Australian endemic Ondinea forms a highly supported clade with members of the Australian Nymphaea subgenus Anecphya . In addition, Victoria and Euryale are inferred to be closely related to a clade comprising all night-blooming water-lilies ( Nymphaea subgenera Hydrocallis and Lotos ). An experimental approach showed taxon sampling to be of influence on the nodes reconstructed in core Nymphaeaceae. The results underscore that more diverse genera, if not clearly known to be monophyletic, should be represented by all major lineages.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 154 , 141–163.     

Okeanomyces, a new genus to accommodate Halosphaeria cucullata (Halosphaeriales, Ascomycota)

The taxonomic affinity of Halosphaeria cucullata to Halosphaeria is reassessed based on a recent collection of this fungus. Halosphaeria cucullata is characterized by immersed, darkly coloured ascomata, clavate asci which deliquesce very early in development, and cylindrical ascospores with or without a polar cap-like appendage at one end. In a phylogenetic analysis of the LSU rDNA sequences from members of the Halosphaeriaceae, H. cucullata did not form a monophyletic clade with H. appendiculata , the type species of the genus. These results suggest that H. cucullata should not be included in Halosphaeria . Okeanomyces gen. nov. is proposed to accommodate this fungus.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 146 , 223–229.     

Morphological perspective on the classification and evolution of Recent Pterioidea (Mollusca: Bivalvia)

The evolutionary relationships of the Recent Pterioidea are inferred from a phylogenetic analysis of representatives of all pterioidean genera based on original observations of anatomy and shell morphology, and an extensive survey of bivalve literature. The well-resolved cladogram supports monophyly for the superfamily, but renders all but one family (the monotypic Pulvinitidae) polyphyletic. In addition, these results reveal a considerable level of convergence and parallelisms through the Pterioidea. The branching order of pterioid genera in the morphological analysis is largely corroborated by the sequence of their appearance in the fossil record. The palaeontological evidence provides important information on dating lineage splitting events and transitional taxa. The proposed phylogeny integrates the cladistic analysis of the Recent Pterioidea with the fossil record and suggests that the crown-group pterioideans probably originated in the Triassic from the Bakevelliidae, an extinct paraphyletic stem group from which the Ostreoidea are also ultimately derived.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 148 , 253–312.     

Evolution of St Helena arborescent Astereae (Asteraceae): relationships of the genera Commidendrum and Melanodendron

The cladistic relationships of endemic Commidendrum (four species) and Melanodendron (one species) from St Helena were inferred from sequences of ITS1 and ITS2 of nuclear ribosomal DNA. Despite showing a range of morphological and ecological variation, the four species of Commidendrum , C. spurium , C. robustum , C. rotundifolium , and C. rugosum , form a closely related monophyletic group with percentage sequence divergence between 0.2 and 0.9%. Melanodendron integrifolium is sister to Commidendrum indicating that the two genera may have evolved from a common ancestor that arrived in St Helena via a single dispersal event. The closest relatives of Commidendrum and Melanodendron appear to be South African, in the predominantly shrubby genus Felicia , although further sampling of South African Astereae is required. We discuss the evolution and adaptive radiation of these rare and threatened species with particular reference to the possible role of heterochrony.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 144 , 69–83.     

Phylogenetic relationships among gekkotan lizards inferred from C-mos nuclear DNA sequences and a new classification of the Gekkota

A phylogeny of gekkotan lizards was derived from C- mos nuclear DNA sequence data. Forty-one currently recognized genera, representing all major gekkotan lineages, were included in the study. A total of 378 bp of partial C- mos gene sequences was obtained and aligned. Maximum parsimony (MP) and maximum likelihood (ML) trees were generated based on unweighted analysis using P AUP *; similar tree topologies were recovered by both methods. The Eublepharidae were monophyletic and its relationship to other major clades was poorly resolved. The Pygopodidae of Kluge (1987) was monophyletic, but relationships within this group differed from those retrieved by previous analyses. The Diplodactylini + padded carphodactylines were the sister group of pygopods + padless carphodactylines. The Gekkonidae were monophyletic, but we found no evidence in support of the Teratoscincinae, as Teratoscincus was embedded well within the gekkonids. Both MP and ML analyses supported the basal position of Sphaerodactylus within the gekkonids, in contrast to morphologically based hypotheses. We propose a new higher order classification of the Gekkota that reflect these results. Five gekkotan families: Eublepharidae, Gekkonidae, Pygopodidae, Diplodactylidae, and Carphodactylidae are recognized. The higher order status of the sphaerodactyls will require more intensive sampling of this group. Our results support the hypothesis that the early cladogenesis of the Gekkota was associated with the split of Eastern Gondwanaland from Western Gondwanaland. Divergences among living genera in the Eublepharidae and the Eastern Gondwanan lineages (Diplodactylidae, Pygopodidae and Carphodactylidae) may be older than those in the Gekkonidae.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 353–368.     

Multiple levels of allopatric divergence in the endemic Philippine fruit bat Haplonycteris fischeri (Pteropodidae)

As part of a larger comparative phylogeographical study of Philippine fruit bats, I used fragments of the mitochondrial genes cytochrome  b and ND2 to investigate phylogeography and diversification in Haplonycteris fischeri , a pteropodid bat endemic to the Philippines but widespread within the archipelago. Genetic diversity in H. fischeri was extremely high in these commonly studied genes, with 101 unique haplotypes in 123 sequenced individuals, although small, continuously isolated islands had less diversity than had large island complexes. Seven monophyletic groups and one paraphyletic group were restricted to individual islands, groups of islands, or parts of islands. Each Pleistocene island complex had a single resident monophyletic lineage; these five groups were separated by approximately 6–8% sequence divergence and apparently have been diverging for 4–6 Myr. Within island groups, monophyletic lineages on some individual islands suggest that current ocean channels have also been barriers to gene flow; in some cases, multiple allopatric clades were present on single islands. Basal divergence dates were estimated to be in the early Pliocene, and most diversification was apparently connected to the ongoing geological evolution of the Philippines. Geological history and current geography interact with ecology to cause substantial genetic differentiation within this primary forest-specialist species.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 329–349.     

Molecular phylogeny of the genus Philodendron (Araceae): delimitation and infrageneric classification

The genus Philodendron (Araceae) is a large neotropical group whose classification remains unclear. Previous classifications are based on morphological characters, mainly from the inflorescence, flower and leaf shape. The classification by Krause, with few modifications, is still the most commonly used system. To examine phylogenetic relationships in the genus, two ribosomal DNA nuclear markers, internal transcribed spacer (ITS) and external transcribed spacer (ETS), and the chloroplast intron rpl 16, were sequenced and analysed for more than 80 species of Philodendron and its close relative Homalomena . According to the resulting phylogeny, the genus Homalomena may be paraphyletic to the genus Philodendron . The inclusion of the American Homalomena species within the genus Philodendron might resolve this taxonomic problem. All three subgenera of Philodendron were revealed as monophyletic. Below the subgeneric level, the groups obtained in our phylogeny globally correspond to sections recognized in previous classifications. Among the morphological characters used by previous taxonomists to build their classifications, and which we optimized onto one of the most parsimonious trees, most characters were found to be homoplasious. However, leaf shape, characteristics of the sterile zone on the spadix and venation patterns are useful for delimiting subgenera and sections within the genus.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 156 , 13–27.     

Ecomorphological and genetic divergence between lowland and montane forms of the Pieris napi species complex (Pieridae, Lepidoptera)

The present study aimed to investigate the morphological and genetic differentiation of lowland and montane populations of the Pieris napi species complex in Norway and to make inferences about the subspecific status of Pieris napi adalwinda and Pieris napi napi . We measured 22 morphological characters on 228 individuals from eight populations in Central Norway (20–1100 m a.s.l.). In addition, lowland and mountain animals were reared at a high altitude locality. Half the animals from either locality were reared on mountain plant, and the other half on a lowland plant. Finally, a fragment of the mitochondrial cytochrome b gene was sequenced for individuals from Central and South-eastern Norway and Germany. Principal component analysis of morphological characters showed a zone of abrupt change from lowland to mountain morphological character states between populations at 506 m and 730 m a.s.l., respectively. The transplant experiment showed that the morphological differences have a genetic basis and that food plants have no impact on morphology. Limited, but significant, molecular genetic differentiation was found between lowland and mountain animals, but the phylogenetic analysis, however, showed that the lowland form ( P. n. napi ) is paraphyletic and the montane form ( P. n. adalwinda ) is monophyletic. Further study is required before taxonomic recognition can be applied.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 727–745.     

A review of the lower actinopterygian phylogeny

A review of lower actinopterygian phylogeny has led us to the conclusion that the Cladistia are the sister group of Recent actinopterygians (Actinopteri) and that the extinct Palaeonisciformes are a paraphyletic group, comprising stem-group actinopterygians (e.g. Cheirolepis ), stem-group actinopterans (e.g. Moythomasia ) and relatives of higher actinopterans such as Pteronisculus . Our analysis further concluded that the Acipenseriformes formed a clade together with Saurichthys and Birgeria , which was most parsimoniously resolved when the Acipenseriformes and Saurichthys were sister groups.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 511−525.     

Phylogeny and evolutionary history of the Aplodontoidea (Mammalia: Rodentia)

Athough over a hundred species of fossil aplodontoids have been described since the extant species, Aplodontia rufa (the mountain beaver), was first described by Rafinesque in 1817, a thorough survey of the relationships among all the species in this clade has not been undertaken since McGrew's study in 1941. Here, a complete phylogenetic analysis of all published species of aplodontoids is used to reconstruct the evolutionary relationships within the clade, and to present an updated classification of the Aplodontoidea. Several of the traditionally recognized subfamilies are found to be paraphyletic, namely the Prosciurinae, the Allomyinae, and the Meniscomyinae. Others, however, including the Aplodontinae and the Mylagaulidae, appear to be monophyletic. These latter two taxa, which include all of the hypsodont members of the aplodontoid clade, seem to be sister taxa. The history of the aplodontoid clade shows several episodes of rapid diversification in the Early Oligocene, the Late Oligocene, and the Early to Middle Miocene. The Ansomyinae and Aplodontinae show comparatively low speciation rates. The patterns of change in morphology and evolutionary rates suggest a need for a more detailed study of the causes of diversification, extinction, and ecological change in this lineage.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 153 , 769–838.     

The evolutionary pathway of light emission in myodocopid Ostracoda

The evolutionary history of bioluminescence and iridescence in myodocopid ostracods was estimated by phylogenetic analysis of mitochondrial 16S ribosomal RNA sequences. The inferred phylogeny of the myodocopids suggests that the common ancestor of Myodocopida evaluated in this study exhibits iridescence. This type of light emission was once lost and recaptured independently in the descendant lineages. Bioluminescent species also evolved from non-luminous ancestral species. In the suborder Myodocopina, all the bioluminescent species form a monophyletic group, suggesting that bioluminescence evolved only once. Structural differences between two bioluminescent groups in the order Myodocopida suggests independent origins for bioluminescence.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 449–455.     

Cymbonotus (Compositae: Arctotideae, Arctotidinae): an endemic Australian genus embedded in a southern African clade

The Compositae (Asteraceae) is the largest flowering plant family if described, accepted taxa are considered. Recent revisions in the taxonomy of the family have resulted in the recognition of ten subfamilies and 35 tribes. The tribe Arctotideae is one of the smallest, with around 200 species; it contains two subtribes and several hard-to-place taxa. Previous work has shown that the subtribe Arctotidinae is well defined and is restricted to southern Africa, except for the Australian genus Cymbonotus . Molecular data from internal transcribed spacer (ITS), ndh F, and trn L-F sequences were used (24 previously published sequences; 47 new sequences) to determine the patterns of relationships within the subtribe. Twenty-three samples from the ingroup, including members of all genera and all three species of Cymbonotus , were included in the analysis, together with two outgroup taxa. Cymbonotus is monophyletic and deeply embedded in the subtribe; Haplocarpha is paraphyletic and basal in position; all other genera are monophyletic; however, Arctotis has over 60 species and only eight were sampled for this study, so additional work may prove otherwise. Arctotis is nested high in the tree and has short branch lengths; this may reflect recent radiation. By contrast, the species of the paraphyletic and basal Haplocarpha have long branches, which may indicate an older radiation and a shared ancestry with the remainder of the subtribe. The presence of Cymbonotus in Australia is most probably the result of long-distance dispersal.  Journal compilation © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 153 , 1–8. No claim to original US government works