Phylogeny,natural groups and nemertean classification

Contemporary practice in the classification of nemerteans (phylum Nemertea) is critically discussed. It is argued that basing higher taxa on the existence of a unique combination of characters in a species (or genus) is unlikely to lead to monophyletic taxa, and that this approach should be abandoned in favour of a classification based on explicit hypotheses of phylogeny. These hypotheses should be based on all available characters and characters should not be excluded before the analysis. The classification should be based on a reconstruction of the phylogeny and reflect this phylogeny in an unambiquous way.     

Phylogeny reconstruction in the neogene bryozoan metrarabdotos: A paleontologic evaluation of methodology

An adequate stratigraphic record can not only aid in both cladistic and stratophenetic reconstruction of phytogenies, but can also serve in estimating the temporal consistency of the resulting phylogenetic trees. For hypothetical data sets, cladistically constructed trees can be as consistent with the temporal distribution of sampled populations or species as those constructed stratophenetically. Empirical testing in taxonomic groups with sufficiently dense fossil records is needed to show whether, and under what conditions, this potential can be realized. A stratophenetic tree and cladistic trees based on several approaches to character weighting were constructed for Caribbean Neogene species of the bryozoan Metrarabdotos with multiple‐character data from closely spaced sequential populations. The modular morphology and highly punctuated evolutionary pattern of these species blur the distinction between continuous and discrete characters, so that all available characters are potentially of equal significance in establishing phytogenies, rather than just those with discrete states conventionally used in cladistic analysis. However, only the cladistic trees generated with all characters weighted to emphasize contribution to species discrimination have temporal consistencies that are clearly significant statistically and approach that of the stratophenetic tree in magnitude. These results provide a start toward establishing general guidelines for cladistic analysis of taxa with stratigraphie records too sparse for stratophenetic reconstruction.     

Phylogeny and biogeography of Crinum L. (Amaryllidaceae) inferred from nuclear and limited plastid non-coding DNA sequences

The genus Crinum L. is the only pantropical genus of the Amaryllidaceae. Phylogenetic and biogeographical analyses of nrDNA ITS and plastid trnL-F sequences for all continental groups of the genus Crinum and related African genera are presented, with the genus Amaryllis used as outgroup. ITS indicates that C. baumii is more closely related to Ammocharis and Cybistetes than to Crinum sensu stricto . Three clades are resolved in Crinum s.s. One unites a monophyletic American group with tropical and North African species. The second includes all southern African species and the Australian endemic C. flaccidum . The third includes monophyletic Madagascar, Australasian and Sino-Himalayan clades, with southern African species. The trnL-F phylogeny resolves an American and an Asian/Madagscar clade, and confirms the relationship of C. flaccidum with species endemic to southern Africa. The salverform, actinomorphic perianths of subg. Crinum appear to have evolved several times in the genus from ancestors with zygomorphic perianths (subg. Codonocrinum ), thus neither subgenus is monophyletic. Biogeographical analyses place the origin of Crinum in southern Africa, as the region is optimized at all ancestral nodes in the tree topology, and in basal interior nodes of all but one of the major clades. The genus underwent three major waves of radiation corresponding to the three main clades resolved in our trees. Two entries into Australia for the genus are indicated, as are separate Sino-Himalayan and Australasian dispersal events.  © 2003 The Linnean Society of London, Botanical Journal of the Linnean Society , 2003, 141 , 349–363.     

Phylogeny of Australian species of flatheads (Teleostei, Platycephalidae) as determined by allozyme electrophoresis

Phylogenetic relationships of 24 taxa of Platycephalid fish were examined for up to 40 loci using starch and polyacrylarnide gel electrophoresis. Over 400 different enzyme mobilities were scored. The extent of homoplasy was estimated to be between 5 and 12%. Polymorphism at the 1% level was observed at 26 of the 40 loci. The importance of shared polymorphic alleles in cladistic analysis was endorsed by the different results obtained from multistate and binary coding of alleles. Many loci were shown to contain phylogenetically informative ancestral alleles which appear irregularly in extant species. The polymorphism parsimony method provided the most informative results. Genetic similarities between endemic Australian species from each family stem provide the basis for a major revision of subfamilies and genera within the family.     

The taxonomy and biogeography of the Cladocera

For a variety of reasons, including the analysis of a number of taxa having the same names on different continents, we have concluded overwhelmingly that the chydorid Cladocera are not cosmopolitan in distribution but instead are restricted to smaller regions by their specific ecological requirements for habitat type and also by long-term events in earth history. Recent study ofChydorus faviformis and species resembling it indicates there has been no effective exchange of genetic material between North America and South America, nor between Australia and Asia, nor even between China, Malaysia, and India in southern Asia. Moreover, the patterns of distribution are even narrower than this, as in North America, for example, taxa having the same names in the southern states as in the northern states are differentiated at the species level in some instances, possibly in most. Southern species push northward along the Atlantic Coast for varying distances, one species having reached Nova Scotia and Newfoundland probably during the warm interval in mid-Postglacial time. Thus, when species are studied closely to define their morphological limits, cosmopolitanism disappears, and patterns of distribution emerge that are very similar to those of other animals and plants. The ‘species’ that have been claimed to be cosmopolitan are being shown to be groups or complexes of morphologically similar species instead, each member species of which has a much more restricted distribution than the group or complex as a whole. To explain how the different continents can have such similar lists of ‘species’ without intercontinental dispersal of resting eggs occurring almost continuously, we are suggesting plate tectonics and the drifting of continents, either apart or together.     

Phylogeny and biogeography in the evolution of migration: shorebirds of the Charadrius complex

Aim We explore whether molecular phylogeny and biogeography can complement evolutionary ecology in developing a method to address a long-standing issue in the evolution of migration: have migrations between breeding and non-breeding grounds, which may be on different continents, evolved through origins in the breeding grounds with successive shifts of the non-breeding distribution or vice versa? Methods To accommodate the biology of migration, we treated breeding and non-breeding distributions as characters to be mapped onto a phylogeny derived from mitochondrial DNA sequence data and so examined the ancestral home issue as a study in the direction of character evolution. Results Our main findings from applying this approach to a subset of the Charadrius complex of shorebirds (Aves: Charadriinae) are that a case can be made for shifts of breeding distributions having occurred in the ancestries of C. alexandrinus and C. veredus as those species evolved their present migration patterns. Our results also argue for a southern hemisphere origin (specifically South America) for the Charadrius complex as a whole. A South American origin implies other shifts in breeding distributions having occurred in the evolution of the species C. semipalmatus and C. vociferus. On applying the methods we developed for dealing with phylogenetic uncertainty, these results are reinforced and the merit of testing them further is suggested. Conclusions By way of a new approach to the evolution of migration, our study adds to a consensus emerging from the evolutionary ecology of migrant birds, arguing that shifts of breeding distributions are commonly, though not necessarily exclusively, involved in the evolution of migration.     

Phylogeny of the Neotropical moth tribe Josiini (Notodontidae: Dioptinae): a hidden case of Miillerian mimicry

The Neotropical moth tribe Josiini (Notodontidae: Dioptinae) contains over 100 described species in 11 genera. All are diurnal, with brightly-coloured, presumably aposematic wing patterns. Larval hostplants are exclusively in the genus Passiflora (Passifloraceae) except for two new records, reported here, from Tumera (Turneraceae). A comparative morphological study of 26 representative josiine species yielded 86 characters from adults, larvae and pupae, all of which are figured and discussed. Phylogenetic analysis of these data produced a single most-parsimonious cladogram. According to the phylogenetic results: (1) monophyly of the Josiini is strongly supported; (2) the currently accepted generic classification is in disarray; (3) morphological character variation is extensive, and adult traits reflect phylogeny more effectively than do those of immature stages; (4) wing pattern types have undergone convergent evolution. A rare phenotype, longitudinal wing stripes, appears in two widely divergent clades, suggesting the evolution of Miillerian mimicry within the Josiini.     

Toward a Better Understanding of the Phylogeny of the Asplanchnidae (Rotifera)

We investigated the phylogenetic relationships of Family Asplanchnidae using both morphological and molecular data. The morphological database, comprising 23 characters from 19 taxa (15 Asplanchnidae and 4 outgroups), was compiled from a survey of the literature and our own observations; the molecular data (ITS and V4 region nuclear regions and mitochondrial cox1) was sequenced from specimens that we collected. Our analysis of the morphological data set (maximum parsimony) yielded 12 most-parsimonious trees with a tree length of 27 steps. From this analysis we conclude (1) Asplanchnidae is a monophyletic group as are the three genera comprising it, (2) there is no compelling support for the argument that Asplanchna should be separated into two discrete genera, and (3) there is some support for the proposal that Asplanchnidae and Synchaetidae are sister groups. Our analysis of the molecular data set supports the first two of these conclusions while the sister group of the family varied depending on the gene region analyzed and families and genera included. Current understanding of the phylogeny of Asplanchnidae is hampered by the need for additional informative morphological characters and a lack of molecular data for the genus Harringia and several other members of the Asplanchnidae.     

Genetic variation in threshold reaction norms for alternative reproductive tactics in male Atlantic salmon, Salmo salar

Alternative reproductive tactics may be a product of adaptive phenotypic plasticity, such that discontinuous variation in life history depends on both the genotype and the environment. Phenotypes that fall below a genetically determined threshold adopt one tactic, while those exceeding the threshold adopt the alternative tactic. We report evidence of genetic variability in maturation thresholds for male Atlantic salmon (Salmo salar) that mature either as large (more than 1 kg) anadromous males or as small (10-150 g) parr. Using a common-garden experimental protocol, we find that the growth rate at which the sneaker parr phenotype is expressed differs among pure- and mixed-population crosses. Maturation thresholds of hybrids were intermediate to those of pure crosses, consistent with the hypothesis that the life-history switch points are heritable. Our work provides evidence, for a vertebrate, that thresholds for alternative reproductive tactics differ genetically among populations and can be modelled as discontinuous reaction norms for age and size at maturity.     

Morpho-anatomy of the lobopod Magadictyon cf. haikouensis from the Early Cambrian Chengjiang Lagerstätte, South China

Magadictyon haikouensis (Luo and Hu, 1999) from the Early Cambrian Chengjiang Lagerstätte, an incomplete specimen of a large lobopod with strong appendages, has been regarded as related to the lobopods Microdictyon and Onychodictyon. Newly discovered complete specimens of Magadictyon cf. haikouensis (found by the Early Life Institute field team) show that the taxon, in addition to its strong appendages with appendicules, also had a head bearing similar caecum‐like structures to those of the arthropod Naraoia and Chelicerate, ‘Peytoia’‐like mouthparts and frontal appendages. Because of their similarity, the caecum‐like structures of Magadictyon cf. haikouensis are considered to be homologous with those of stem‐group arthropods. The ‘Peytoia’‐like mouthparts and the frontal appendages are similar to those of the AOPK (Anomalocaris–Opabinia–Pambdelurion–Kerygmachela) group. In addition, the appendages with appendicules show that Magadictyon cf. haikouensis is closely related to Onychodictyon. Therefore, Magadictyon cf. haikouensis is regarded here as a rare transitional form between lobopods and arthropods. Besides, together with other lobopods, the morphology of Magadictyon cf. haikouensis demonstrates that the Cambrian lobopods appear to have been diverse and not particularly closely related to one another, and do not seem to represent a monophyletic clade.     

Phylogeny and radiation of pollination systems in DISA (Orchidaceae)

We studied the patterns of adaptive radiation in Disa, a large orchid genus in southern Africa. A cladogram for 27 species was constructed using 44 morphological characters. Pollination systems were then mapped onto the phylogeny in order to analyze pathways of floral evolution. Shifts from one pollination system to another have been a major feature of the evolutionary diversification of Disa. Unlike many plant genera that are pollinated mainly by a single group of insects, radiation in Disa has encompassed nearly all major groups of pollinating insects; in all, 19 different specialized pollination systems have been found in the 27 species included in this analysis. Another striking pattern is the repeated evolution of broadly similar pollination systems in unrelated clades. For example, butterfly-pollinated flowers have evolved twice; showy deceptive flowers pollinated by carpenter bees, twice; long-spurred flowers pollinated by long-tongued flies, four times; night-scented flowers pollinated by moths, three times; and self-pollination, three times. This suggests that a few dominant pollinator species in a region may be sufficient to generate diversification in plants through repeated floral shifts that never retrace the same pathways.     

Factors affecting the duration of nest defense and reproductive lifespan of female sockeye salmon, Oncorhynchus nerka

Reproductive success of female animals is often affected by a combination of fecundity and parental care. In female salmonid fishes, acquisition of nest (redd) sites and prevention of their use by other females are critical to reproductive success. These factors are particularly important for stocks that spawn at high densities. Body size is positively correlated with fecundity and egg size, and has been hypothesized to control the outcome of intrasexual competition and longevity. We tested this hypothesis by evaluating the influences of body size, intrasexual aggression and arrival date on duration and success of redd guarding by female sockeye salmon, Oncorhynchus nerka, in a small Alaskan creek. Contrary to the hypothesis, larger females guarded their redds no longer than smaller females, and did not live as long in the stream. Aggression was not related to body size or overall longevity but was positively correlated with residence period on the redd. Females that entered the creek earlier lived longer, spent longer on their redds, and spent more time guarding their redds after spawning than females that entered the creek later. However, despite their longevity, early-arriving fish were more likely to have their redds reused by another female because they died before all the females had selected redd sites. The small average body size in this stock is consistent with weak selection for large size, and with our evidence that size provided little if any advantage in nest guarding.     

Phylogeny, biogeography and evolution of clutch size in South American lizards of the genus Kentropyx (Squamata: Teiidae)

The lizard genus Kentropyx (Squamata: Teiidae) comprises nine species, which have been placed in three species groups (calcarata group, associated to forests ecosystems; paulensis and striata groups, associated to open ecosystems). We reconstructed phylogenetic relationships of Kentropyx based on morphology (pholidosis and coloration) and mitochondrial DNA data (12S and 16S), using maximum parsimony and Bayesian methods, and evaluated biogeographic scenarios based on ancestral areas analyses and molecular dating by Bayesian methods. Additionally, we tested the life‐history hypothesis that species of Kentropyx inhabiting open ecosystems (under seasonal environments) produce larger clutches with smaller eggs and that species inhabiting forest ecosystems (under aseasonal conditions) produce clutches with fewer and larger eggs, using Stearns’ phylogenetic‐subtraction method and canonical phylogenetic ordination to take in to account the effects of phylogeny. Our results showed that Kentropyx comprises three monophyletic groups, with K. striata occupying a basal position in opposition to previous suggestions of relationships. Additionally, Bayesian analysis of divergence time showed that Kentropyx may have originated at the Tertiary (Eocene/Oligocene) and the ‘Pleistocene Refuge Hypothesis’ may not explain the species diversification. Based on ancestral reconstruction and molecular dating, we argued that a savanna ancestor is more likely and that historical events during the Tertiary of South America promoted the differentiation of the genus, coupled with recent Quaternary events that were important as dispersion routes and for the diversification at populational levels. Clutch size and egg volume were not significantly different between major clades and ecosystems of occurrence, even accounting for the phylogenetic effects. Finally, we argue that phylogenetic constraints and phylogenetic inertia might be playing essential roles in life history evolution of Kentropyx.     

The evolution of pedicellariae in echinoids: an arms race against pests and parasites

Coppard, S.E., Kroh, A. and Smith, A.B. (2010). The evolution of pedicellariae in echinoids: an arms race against pests and parasites. —Acta Zoologica (Stockholm) 00 :1–24. Sea urchins (Echinoidea) have evolved a diverse array of jawed appendages termed pedicellariae to deter pests and predators. Pedicellarial structure and function are reviewed and their distribution mapped in 75 extant genera. Using a phylogeny of echinoids at family level constructed from 353 skeletal characters scored across 162 extant and fossil taxa, the evolution of pedicellarial form and function is reconstructed. For much of the Palaeozoic echinoids possessed a very restricted pedicellarial armament. By the early Mesozoic a diverse array of pedicellarial types had become established, implying that the threat from predators and pests markedly increased at this time. Since the Triassic, echinoids have continued to improve their defensive capability by evolving more effective venom delivery in globiferous pedicellariae, developing spatulate‐tips and curved blades for a more efficient grab in tridentate pedicellariae, and stouter, more robust valves with a stronger bite in ophicephalous pedicellariae to disable and remove ectoparasites. However, pedicellarial types are shown to be particularly prone to subsequent secondary loss, especially among infaunal echinoids, and thus have higher homoplasy levels than other phylogenetically useful skeletal structures.     

Phylogeny of the Platyhelminthes and the evolution of parasitism

Robust phylogenies provide the basis for interpreting biological variation in the light of evolution. Homologous features provide phylogenetically informative characters whereas homoplasious characters provide phylogenetic noise. Both provide evolutionary signal. We have constructed molecular and morphologically based phylogenies of the phylum Platyhelminthes using a recently revised morphological character matrix and complete 18S and two partial 28S rRNA gene sequences in order to evaluate the emergence and subsequent divergence of parasitic forms. In total we examine 65 morphological characters, 97 18S rDNA, 41 Dl domain 28S rDNA, and 49 D3-D6 domain 28S rDNA sequences. For the molecular data there were 748, 132 and 249 phylogenetically informative sites for the 18S, Dl and D3-D6 28S rDNA data sets respectively. Morphological and molecular phylogenetic solutions are incongruent but not incompatible, and using the principles of conditional combination (18S rDNA + morphology passing Templeton's test) they demonstrate: a single and relatively early origin for the parasitic Neodermata (including the cestodes, trematodes and monogeneans); sister-group status between the cestodes and monogeneans, and between these taxa and the trematodes (digeneans and aspidogastreans). The sister-group to the Neodermata is likely to be a large clade of neoophoran turbellarians, based on combined evidence, or a clade consisting of the Fecampiid + Urastomid turbellarians, based on morphological evidence alone. The combined evidence solution for the phylogeny of fiatworms based on 18S rDNA and morphology is used to interpret morphological and life-history data and to support a model for the evolution and radiation of neodermatan parasites in the group.     

Phylogeny, biogeography, and species boundaries within the Alexandrium minutum group

The geographic range and bloom frequency of the toxic dinoflagellate Alexandrium minutum and other members of the A. minutum group have been increasing over the past few decades. Some of these species are responsible for paralytic shellfish poisoning (PSP) outbreaks throughout the world. The origins of new toxic populations found in previously unaffected areas are typically not known due to a lack of reliable plankton records with sound species identifications and to the lack of a global genetic database. This paper provides the first comprehensive study of minutum-group morphology and phylogeny on a global scale, including 45 isolates from northern Europe, the Mediterranean, Asia, Australia and New Zealand.Neither the morphospecies Alexandrium lusitanicum nor A. angustitabulatum was recoverable morphologically, due to large variation within and among all minutum-group clonal strains in characters previously used to distinguish these species: the length:width of the anterior sulcal plate, shape of the 1′ plate, connection between the 1′ plate and the apical pore complex, and the presence of a ventral pore. DNA sequence data from the D1 to D2 region of the LSU rDNA also fail to recognize these species. Therefore, we recommend that all isolates previously designated as A. lusitanicum or A. angustitabulatum be redesignated as A. minutum. A. tamutum, A. insuetum, and A. andersonii are clearly different from A. minutum on the basis of both genetic and morphological data.A. minutum strains from Europe and Australia are closely related to one another, which may indicate an introduction from Europe to Australia given the long history of PSP in Europe and its recent occurrence in Australia. A minutum from New Zealand and Taiwan form a separate phylogenetic group. Most strains of A. minutum fit into one of these two groups, although there are a few outlying strains that merit further study and may represent new species. The results of this paper have greatly improved our ability to track the spread of A. minutum species and to understand the evolutionary relationships within the A. minutum group by correcting inaccurate taxonomy and providing a global genetic database.     

Relative fitness of two hermaphroditic mating types in the androdioecious clam shrimp,Eulimnadia texana

Androdioecy (populations of males and hermaphrodites) is a rare reproductive form, being described from only a handful of plants and animals. One of these is the shrimp Eulimnadia texana, which has populations comprised of three mating types: two hermaphroditic types (monogenics and amphigenics) and males. In a recent study, the amphigenic hermaphrodites were found to be in greater abundance than that predicted from a model of this mating system. Herein, we compare the relative fitness of offspring from amphigenic and monogenic siblings, attempting to understand the greater relative abundance of the former. Populations started with offspring from selfed monogenic hermaphrodites had a net reproductive rate (R) 87% that of offspring from their amphigenic siblings. Additionally, within populations of amphigenic offspring (which included males, monogenics and amphigenics), amphigenics survived longer than monogenics. These differences help to explain the increased relative abundance of amphigenics in natural populations, but amphigenics continue to be more abundant than expected.