Phylogenetic relationships of New Zealand Asteraceae inferred from ITS sequences

Forty-five sequences from members of all genera of Asteraceae indigenous to New Zealand and 50 published sequences representing the tribal diversity in the family were analyzed to assess the utility of ITS sequences to resolve phylogenetic relationships. Previous studies using chloroplast DNA sequences and morphology provided support for several clades in the Asteraceae, yet the relationships among some of these were uncertain. The results from ITS analysis were largely consistent with these earlier studies. The New Zealand species are included in at least six clades, most of these corresponding to recognized tribes. Our results have also clarified the tribal affinities of a few anomalous genera. Haastia, previously aligned with the Gnaphalieae or the Astereae, is nested in the Senecioneae. Centipeda, previously included in the Astereae or Anthemideae, emerges near the Heliantheae. The relationships of Abrotanella remain unresolved. Received August 8, 2001 Accepted November 6, 2001     

Phylogenetic relationships within the New Zealand frog genus Leiopelma — immunological evidence

Abstract

Albumin evolution is examined within the anuran genus Leiopelma using the quantitative immunological technique of micro-complement fixation (MC'F). The albumins of L. archeyi and L. hamiltoni are relatively similar to each other, yet both differ greatly from the albumin of L. hochstetteri. Using albumin as a molecular clock, we estimate that L. hochstetteri diverged from the lineage leading to L. archeyi and L. hamiltoni during the Miocene, about 15 million years ago. The divergence of L. archeyi and L. hamiltoni appears to have been a Pliocene event (about 3 million years ago).     

Phylogenetic relationships of Australian and New Zealand feral pigs assessed by mitochondrial control region sequence and nuclear GPIP genotype

Pigs were introduced into Australia and New Zealand in the 18th and 19th centuries, with some establishing feral populations. With few records of pig introductions into these two countries, molecular phylogenetic analysis was used to assess their origins. Mitochondrial (mt) control region sequence and nuclear glucosephosphate isomerase pseudogene (GPIP) restriction fragments were used, as distinct European and Asian domestic pig and Wild Boar control region clades and GPIP genotypes can be recognised. Feral pig control region sequences clustered with either European or Asian domestic pig sequences and both Asian and European GPIP alleles were segregating. It was not possible to distinguish direct importation of Asian domestic animals into Australia and New Zealand from indirect introgression of Asian domestic sequences via Europe. However, the clustering of three feral control region sequences of pigs from northern Australia with Asian Wild Boar implies unrecorded introduction of Wild Boar or crossbred animals into Australia. However, two of these feral pigs had European GPIP alleles. In combination, analyses of control region and GPIP markers suggest that both European and Asian pigs have contributed in similar frequencies to the origins of Australian feral pigs.     

Phylogenetic relationships of theJuglandaceae

A cladistic analysis of molecular data from the chloroplast generbcL was used to examine the taxonomic relationships of the walnut family (Juglandaceae). In addition, chemical and morphological data from a previous study byHufford (1992) were incorporated, expanded, and analyzed independently and in combination with the molecular data. The results of these analyses suggest that theJuglandaceae are more closely related to theFagaceae, Betulaceae, Casuarinaceae, andUrticaceae and their relatives (sensuCronquist 1981) than they are to theAnacardiaceae (sensuThorne 1983). However, sequence data fromrbcL also suggest a relationship between the higherHamamelidae and certain families in theRosidae sensuCronquist 1981 (such asRosaceae andRhamnaceae), an outcome which would add credence to the widely accepted view of the polyphyletic nature of theHamamelidae.     

Climatic relationships of some New Zealand forest tree species

Abstract. A dataset of some 10 000 plots was used to describe the climatic relationships of 33 widespread New Zealand tree species. Estimates of mean annual temperature, temperature seasonality, mean annual solar radiation, and moisture balance were derived from mathematical surfaces fitted to climate station data. Plots were also categorized into five lithological classes and three drainage classes. Generalized additive models were used to examine species/environment relationships. Mean annual temperature and mean annual solar radiation are most strongly correlated with current tree distributions, followed by moisture balance, temperature seasonality, lithology, and drainage. Most broad-leaved tree species other than Nothofagus spp. reach their greatest levels of occurrence in warm, moist environments with high solar radiation. In contrast, Nothofagus spp. generally reach their greatest levels of occurrence in cooler and/or lower insolation environments, and all have lower levels of occurrence on rhyolitic substrates which have resulted from large-scale geomorphic disturbance, mostly over the past few thousand years. Although coniferous species have widely differing climatic optima, many are biased towards lithological classes characterized either by large-scale geomorphic disturbance or harsh edaphic conditions. The relevance of these results to particular synecological questions is briefly discussed. Continuing adjustments in the range of slow-dispersing Nothofagus spp. are strongly suggested, and the climatic suitability of extensive rhyolitic basins in the central North Island, from which these species are largely absent, is confirmed.     

Phylogenetic relationships and character evolution in New Zealand and selected Australian Gnaphalieae (Compositae) inferred from morphological and anatomical data

Most of the estimated 70–80 species of New Zealand Gnaphalieae are endemic. Those of Anaphalioides , Ewartia , Helichrysum , Leucogenes , Rachelia and Raoulia belong to a putatively monophyletic group which is supported by analysis of nuclear ITS DNA sequences and is virtually confined to New Zealand. All species of Craspedia , Euchiton , Ozothamnus and Pseudognaphalium are excluded from this group. A phylogenetic analysis of 42 species of Gnaphalieae, using 57 morphological, anatomical and palynological characters, was conducted to test the monophyly of this group and to seek evidence of generic relationships. The analysis does not resolve basal relationships among the Gnaphalieae studied here. The putative monophyletic New Zealand group is not retrieved. Monophyly is supported for each of Euchiton , Leucogenes , the whipcord species of Helichrysum , the pulvinate species of Raoulia , and Raoulia subg. Raoulia (excluding the aberrant R. cinerea ), but not for Anaphalioides or Raoulia s.l. There are these two distinct groups in Raoulia s.l. but also a substantial number of isolated species. The sole New Zealand species of Ewartia is not a sister species to Australian Ewartia . The Australian species Ewartia planchonii is the sister species to Euchiton rather than to the other Australian species of Ewartia .  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 141 , 183–203.     

Phylogenetic Diversity of New Zealand Gelidiales as Revealed by rbcL Sequence Data

Diversity and phylogenetic relationships of New Zealand representatives of the red algal order Gelidiales have been examined using rbcL sequence data. Extensive field collections have been made from throughout the New Zealand region. Six genera have been reported previously from New Zealand (Capreolia, Gelidium, Pterocladia, Pterocladiella, Pterocladiastrum, Ptilophora). This research has revealed species with very restricted local distributions, as well as the discovery of several undescribed, cryptic taxa. The common and widespread Gelidium caulacantheum is confirmed to be more closely related to Capreolia than to other species of Gelidium. The generic concept of Capreolia, based on life history characters, will need to be modified to accommodate additional species possessing “Gelidium” life histories. A species endemic to New Zealand, Gelidium ceramoides, has been found to differ significantly from all other members of the Gelidiales and requires reclassification in another genus and order. Examination of field collections and herbarium specimens in addition to molecular sequence data have led us to conclude that specimens previously placed in the genera Ptilophora and Pterocladiastrum belong within Pterocladia lucida.     

Phylogenetic relationships within Colchicaceae

Three plastid regions-the rps16 intron, the atpB-rbcL intergenic spacer, and the trnL-F region-in 73 taxa representing all the genera of Colchicaceae except Kuntheria were sequenced to investigate the intrafamilial relationships of the family. In total, the three gene regions, comprising 3830 characters, were analyzed both separately and in a combined matrix. The results did not support the division of the family into two subfamilies, but they did support a core clade of mainly African genera and a grade of Australian, North American, and Asian taxa. One of the four tribes, Iphigenieae, was grossly paraphyletic, and, unexpectedly, Colchicum was nested within Androcymbium. Further, taxa of Gloriosa and Littonia were intermixed.     

Phylogenetic relationships of cyphelloid homobasidiomycetes

The homobasidiomycetes includes the mushroom-forming fungi. Members of the homobasidiomycetes produce the largest, most complex fruiting bodies in the fungi, such as gilled mushrooms ("agarics"), boletes, polypores, and puffballs. The homobasidiomycetes also includes species that produce minute, cup- or tube-shaped "cyphelloid" fruiting bodies, that rarely exceed 1-2 mm diameter. The goal of this study was to estimate the phylogenetic placements of cyphelloid fungi within the homobasidiomycetes. Sequences from the nuclear large subunit (nuc-lsu) ribosomal DNA (rDNA), 5.8S rDNA, and internal transcribed spacers (ITS) 1 and 2 were obtained for 31 samples of cyphelloid fungi and 16 samples of other homobasidiomycetes, and combined with published sequences. In total, 71 sequences of cyphelloid fungi were included, representing 16 genera. Preliminary phylogenetic analyses of a 1477-sequence data set and BLAST searches using sequences of cyphelloid forms as queries were used to identify taxa that could be close relatives of cyphelloid forms. Subsequent phylogenetic analyses of one data set with 209 samples represented by nuc-lsu rDNA sequences (analyzed with parsimony) and another with 38 samples represented by nuc-lsu and 5.8S rDNA sequences (analyzed with parsimony and maximum likelihood) indicated that cyphelloid forms represent a polyphyletic assemblage of reduced agarics (euagarics clade, Agaricales). Unconstrained tree topologies suggest that there have been about 10-12 origins of cyphelloid forms, but evaluation of constrained topologies with the Shimodaira-Hasegawa test suggests that somewhat more parsimonious scenarios cannot be rejected. Whatever their number, the multiple independent origins of cyphelloid forms represent striking cases of parallel evolutionary reduction of complex fungal morphology.     

Chlorophyll-nutrient relationships in North Island lakes (New Zealand)

A model for the prediction of chlorophyll a in the near surface waters (1 m) of North Island lakes was developed using data from the literature and our own study of 12 North Island lakes. Annual geometric mean concentrations of chlorophyll a, total nitrogen and total phosphorus were used since no distinct growing season was discernable. Annual mean ratios of total nitrogen to total phosphorus in the near surface waters ranged between 10 and 59 (by weight). Strong correlations were obtained between log-transformed values of chlorophyll a and total nitrogen (r² = 0.53, n = 16), chlorophyll a and total phosphorus (r² = 0.71, n = 21), and between total nitrogen and total phosphorus (r² = 0.69, n = 16). However, after correcting for the high interdependency between total nitrogen and total phosphorus, only total phosphorus was found to be important in predicting chlorophyll concentrations. Much of the variance in the chlorophyll-phosphorus relation was attributable to differences in mean lake depth. Lakes with mean depths less than 11 m had significantly more chlorophyll a per unit of total phosphorus ( = 0.54 µg · µg^–1, SE = 0.05, n = 6) than lakes of greater mean depth ( = 0.17 µg · µg^–1, SE = 0.02, n = 14). When the effect of mean depth was taken into account, 89% of the variance in chlorophyll a was explained compared with 71% for the simple linear regression on total phosphorus alone.     

Phylogenetic relationships among superfamilies of Hymenoptera

The first comprehensive analysis of higher‐level phylogeny of the order Hymenoptera is presented. The analysis includes representatives of all extant superfamilies, scored for 392 morphological characters, and sequence data for four loci (18S, 28S, COI and EF‐1α). Including three outgroup taxa, 111 terminals were analyzed. Relationships within symphytans (sawflies) and Apocrita are mostly resolved. Well supported relationships include: Xyeloidea is monophyletic, Cephoidea is the sister group of Siricoidea + [Xiphydrioidea + (Orussoidea + Apocrita)]; Anaxyelidae is included in the Siricoidea, and together they are the sister group of Xiphydrioidea + (Orussoidea + Apocrita); Orussoidea is the sister group of Apocrita, Apocrita is monophyletic; Evanioidea is monophyletic; Aculeata is the sister group of Evanioidea; Proctotrupomorpha is monophyletic; Ichneumonoidea is the sister group of Proctotrupomorpha; Platygastroidea is sister group to Cynipoidea, and together they are sister group to the remaining Proctotrupomorpha; Proctotrupoidea s. str. is monophyletic; Mymarommatoidea is the sister group of Chalcidoidea; Mymarommatoidea + Chalcidoidea + Diaprioidea is monophyletic. Weakly supported relationships include: Stephanoidea is the sister group of the remaining Apocrita; Diaprioidea is monophyletic; Ceraphronoidea is the sister group of Megalyroidea, which together form the sister group of [Trigonaloidea (Aculeata + Evanioidea)]. Aside from paraphyly of Vespoidea within Aculeata, all currently recognized superfamilies are supported as monophyletic. The diapriid subfamily Ismarinae is raised to family status, Ismaridae stat. nov. © The Will Henning Society 2011.     

Phylogenetic relationships of dasyuromorphian marsupials revisited

We reassessed the phylogenetic relationships of dasyuromorphians using a large molecular database comprising previously published and new sequences for both nuclear (nDNA) and mitochondrial (mtDNA) genes from the numbat (Myrmecobius fasciatus), most living species of Dasyuridae, and the recently extinct marsupial wolf, Thylacinus cynocephalus. Our molecular tree suggests that Thylacinidae is sister to Myrmecobiidae + Dasyuridae. We show robust support for the dasyurid intrafamilial classification proposed by Krajewski & Westerman as well as for placement of most dasyurid genera, which suggests substantial homoplasy amongst craniodental characters presently used to generate morphology‐based taxonomies. Molecular dating with relaxed molecular clocks suggests that dasyuromorphian cladogenesis began in the Eocene, and that all three dasyuromorphian families originated prior to the end of this epoch. Radiation within Thylacinidae and Dasyuridae had occurred by the middle to late Oligocene, consistent with recognition of primitive thylacinids (e.g. Badjcinus turnbulli) in the later Oligocene and of putative dasyurids (e.g. Barinya wangala) by the early Miocene. We propose that all four extant dasyurid tribes were in existence by the early Miocene and that most modern dasyurid genera/species were established before the later Miocene. This is in marked contrast to the popularly accepted advocation of their origins in the latest Miocene–early Pliocene. © 2015 The Linnean Society of London     

Phylogenetic relationships of sugarcane rust fungi

The phylogenetic positions of Puccinia spp. infecting sugarcane (a complex hybrid of Saccharum spp.) were determined using 38 newly generated rust sequences and 26 sequences from GenBank. Rust specimens on sugarcane were collected from 164 locations in 23 countries and identified based on light microscopy. The morphology for all samples matched that of Puccinia kuehnii or P. melanocephala, the orange and brown rust pathogens of sugarcane, respectively. Nuclear ribosomal DNA sequences (rDNA) including portions of the 5.8S rDNA, the complete internal transcribed spacer 2 (ITS2) and 5′ region of the large subunit (nLSU) rDNA were obtained for each species along with 36 additional rust taxa. Despite a shared host, the two Puccinia spp. on sugarcane are not closely related within the Pucciniales. Phylogenetic analyses place P. melanocephala most closely to P. miscanthi, P. nakanishikii, and P. rufipes infecting Miscanthus sinensis, Cymbopogon citratus, and Imperata cylindrica, respectively. Puccinia kuehnii is basal to a clade of Poaceae-infecting rusts including P. agrophila, P. polysora, P. substriata, and Uromyces setariae-italicae infecting Schizachyrium spp., Zea mays, Digitaria spp., and Urochloa mosambicensis, respectively. Light and scanning electron microscopy images highlight morphological differences distinguishing the two sugarcane-infecting species. This study confirms the separation of rust species infecting Poaceae from Cyperaceae- and Juncaceae-infecting rusts and also provides support for the presence of an additional group that includes P. kuehnii and other grass-infecting relatives.     

Phylogenetic topology and timing of New Zealand olive shells are consistent with punctuated equilibrium

The olive shells of the genus Amalda comprises readily recognized species of marine neogastropod mollusks found around the world. The New Zealand Amalda fauna has particular notoriety as providing one of the best demonstrations of evolutionary morphological stasis, a prerequisite for punctuated equilibrium theory. An excellent fossil record includes representation of three extant endemic Amalda species used to explore patterns of form change. However, the phylogenetic relationship of the New Zealand Amalda species and the timing of their lineage splitting have not been studied, even though these would provide valuable evidence to test predictions of punctuated equilibrium. Here, we use entire mitogenome and long nuclear rRNA gene cassette data from 11 Amalda species, selected from New Zealand and around the world in light of high rates of endemicity among extant and fossil Amalda. Our inferred phylogenies do not refute the hypothesis that New Zealand Amalda are a natural monophyletic group and therefore an appropriate example of morphological stasis. Furthermore, estimates of the timing of cladogenesis from the molecular data for the New Zealand group are compatible with the fossil record for extant species and consistent with expectations of punctuated equilibrium.     

Length–weight relationships of 33 fish species from New Zealand

Length–weight relationships are presented for 33 fish species from New Zealand. The parameters a and b of the equation W = aL^b were estimated. Parameter b ranged from 2.51 (Pseudocaranx dentex) to 3.51 (Alepocephalus antipodianus) with a mean of 3.12 ± 0.24. Most of these estimates (90.9%) were between 2.8 and 3.4. Maximum lengths and depths of catch are updated for nine species.     

The feeding relationships of two invertebrate predators in a New Zealand river

The size frequency distributions and foods of the larvae of Archichauliodes diversus (Megaloptera: Corydalidae) and Stenoperla prasina (Plecoptera: Eustheniidae) were studied for a year in the Glentui River, South Island, New Zealand. These two species are the largest invertebrate predators inhabiting streams and rivers in New Zealand, where they are the only carnivorous members of their respective orders. Both species occupied the same habitat with A. diversus being slightly more abundant in most months. Many small larvae occurred within the sediments of the stream bed, whereas more larger larvae were found on stones lying on the surface. A wide size range of larvae was present throughout the year and the median size (in terms of head width) of both species was similar in most months. Larval growth could not be determined from field data and the life cycles of both species can be described as non-seasonal. Quantitative sampling in 5 months provided estimates of population densities. These were maximal in December when values of 136/m² for A. diversus and 114/m² for S. prasina were obtained. Larval Chironomidae and mayflies of the genus Deleatidium were the most frequently taken prey of both predators in all months, and no strong relationship between size or species of predator and size of prey was found. Caseless trichopteran larvae formed a less important component of the diets of both species and detritus was ingested by some individuals. No instances of cannibalism and only one example of cross-predation by each predator was seen. Diel sampling in November showed that large Deleatidium larvae were relatively more abundant in the guts of insect predators and in nocturnal drift samples than in the benthos. This suggests that their greater activity at night may increase their susceptibility to predation by nocturnal feeders. No clear ecological segregation of the two species with respect to habitat or prey utilization was found and there was no obvious interspecific competition for food, which appeared to be abundant at all times. Finally, the prevalence of non-seasonal life cycles in New Zealand aquatic insects is discussed in relation to the low degree of speciation in several groups.     

Phylogenetic relationships among various helical bacteria

Helical bacteria from the generaSpirillum, Oceanospirillum, Aquaspirillum, andAzospirillum—as well asSerpens flexibilis—were characterized by oligonucleotide cataloging of 16S rRNA in order to establish their phylogenetic relationships to one another and to Gramnegative bacteria in general. The various genera of helical bacteria are not specifically related to one another (to the exclusion of nonhelical bacteria) and, where tested, the individual genera as presently constituted are not phylogenetically coherent (with the possible exception ofOceanospirillum, which may form a deep grouping).     

Phylogenetic relationships among Spanish goats breeds

We partially sequenced the mitochondrial hypervariable region 1 (HVR1) in 60 goats belonging to six Spanish breeds. The analysis of these and previously published sequences reveals a weak phylogeographical structure in the Iberian Peninsula breeds. Individuals from a single breed did not group into a single cluster. Furthermore, individuals from different breeds often shared single phylogenetic tree branches after UPGMA analysis. This could reflect the non-existence of breed isolation because of traditional seasonal pastoralism and annual long-distance migrations. Three goats belonging to the C maternal lineage were found, demonstrating a wider than previously thought distribution for this lineage.     

Phylogenetic analysis of higher-level relationships of Odonata

Abstract. This is the most comprehensive analysis of higher‐level relationships in Odonata conducted thus far. The analysis was based on a detailed study of the skeletal morphology and wing venation of adults, complemented with a few larval characters, resulting in 122 phylogenetically informative characters. Eighty‐five genera from forty‐five currently recognized families and subfamilies were examined. In most cases, several species were chosen to serve as exemplars for a given genus. The seven fossil outgroup taxa included were exemplar genera from five successively more distant odonatoid orders and suborders: Tarsophlebiidae (the closest sister group of Odonata, previously placed as a family within ‘Anisozygoptera’), Archizygoptera, Protanisoptera, Protodonata and Geroptera. Parsimony analysis of the data, in which characters were treated both under equal weights and implied weighting, produced cladograms that were highly congruent, and in spite of considerable homoplasy in the odonate data, many groupings in the most parsimonious cladograms were well supported in all analyses, as indicated by Bremer support. The analyses supported the monophyly of both Anisoptera and Zygoptera, contrary to the well known hypothesis of zygopteran paraphyly. Within Zygoptera, two large sister clades were indicated, one comprised of the classical (Selysian) Calopterygoidea, except that Amphipterygidae, which have traditionally been placed as a calopterygoid family, nested within the other large zygopteran clade comprised of Fraser's ‘Lestinoidea’ plus ‘Coenagrionoidea’ (both of which were shown to be paraphyletic as currently defined). Philoganga alone appeared as the sister group to the rest of the Zygoptera in unweighted cladograms, whereas Philoganga + Diphlebia comprised the sister group to the remaining Zygoptera in all weighted cladograms. ‘Anisozygoptera’ was confirmed as a paraphyletic assemblage that forms a ‘grade’ towards the true Anisoptera, with Epiophlebia as the most basal taxon. Within Anisoptera, Petaluridae appeared as the sister group to other dragonflies.