Chris Simon

MASTING BY EIGHTEEN NEW ZEALAND PLANT SPECIES: THE ROLE OF TEMPERATURE AS A SYNCHRONIZING CUE

Masting, the intermittent production of large flower or seed crops by a population of perennial plants, can enhance the reproductive success of participating plants and drive fluctuations in seed-consumer populations and other ecosystem components over large geographic areas. The spatial and taxonomic extent over which masting is synchronized can determine its success in enhancing individual plant fitness as well as its ecosystem-level effects, and it can indicate the types of proximal cues that enable reproductive synchrony. Here, we demonstrate high intra- and intergeneric synchrony in mast seeding by 17 species of New Zealand plants from four families across >150 000 km2. The synchronous species vary ecologically (pollination and dispersal modes) and are geographically widely separated, so intergeneric synchrony seems unlikely to be adaptive per se. Synchronous fruiting by these species was associated with anomalously high temperatures the summer before seedfall, a cue linked with the La Nina phase of ...

Combined Data, Bayesian Phylogenetics, and the Origin of the New Zealand Cicada Genera

We have applied Bayesian and maximum likelihood methods of phylogenetic estimation to data from four mitochondrial genes (COI, COII, 12S, and 16S) and a single nuclear gene (EF1alpha) from several genera of New Zealand, Australian, and New Caledonian cicada taxa. We specifically focused on the heterogeneity of phylogenetic signal among the different data partitions and the biogeographic origins of the New Zealand cicada fauna. The Bayesian analyses circumvent many of the problems associated with other statistical tests for comparing data partitions. We took an information-theoretic approach to model selection based on the Akaike Information Criterion (AIC). This approach indicated that there was considerable uncertainty in identifying the best-fit model for some of the partitions. Additionally, a large amount of uncertainty was associated with many parameter estimates from the substitution model. However, a sensitivity analysis on the combined dataset indicated that the model selection uncertainty had little effect on estimates of topology because these estimates were largely insensitive to changes in the assumed model. This outcome suggests strong signal in our data. Our analyses support a New Caledonian affiliation of the New Zealand cicada genera Maoricicada, Kikihia, and Rhodopsalta and Australian affinities for the genera Amphipsalta and Notopsalta. This result was surprising, given that previous cicada biologists suspected a close relationship between Amphipsalta, Notopsalta, and Rhodopsalta based on genitalic characters. Relationships among the closely related genera Maoricicada, Kikihia, and Rhodopsalta were poorly resolved, the mitochondrial data and the EF1alpha data favoring different arrangements within this clade.

Evolution of the Mitochondrial Cytochrome Oxidase II Gene in Collembola

Abstract. The sequence of the mitochondrial COII gene has been widely used to estimate phylogenetic relationships at different taxomonic levels across insects. We investigated the molecular evolution of the COII gene and its usefulness for reconstructing phylogenetic relationships within and among four collembolan families. The collembolan COII gene showed the lowest A + T content of all insects so far examined, confirming that the well-known A + T bias in insect mitochondrial genes tends to increase from the basal to apical orders. Fifty-seven percent of all nucleotide positions were variable and most of the third codon positions appeared free to vary. Values of genetic distance between congeneric species and between families were remarkably high; in some cases the latter were higher than divergence values between other orders of insects. The remarkably high divergence levels observed here provide evidence that collembolan taxa are quite old; divergence levels among collembolan families equaled or exceeded divergences among pterygote insect orders. Once the saturated third-codon positions (which violated stationarity of base frequencies) were removed, the COII sequences contained phylogenetic information, but the extent of that information was overestimated by parsimony methods relative to likelihood methods. In the phylogenetic analysis, consistent statistical support was obtained for the monophyly of all four genera examined, but relationships among genera/families were not well supported. Within the genus Orchesella, relationships were well resolved and agreed with allozyme data. Within the genus Isotomurus, although three pairs of populations were consistently identified, these appeared to have arisen in a burst of evolution from an earlier ancestor. Isotomurus italicus always appeared as basal and I. palustris appeared to harbor a cryptic species, corroborating allozyme data.

Differentiating between Hypotheses of Lineage Sorting and Introgression in New Zealand Alpine Cicadas (Maoricicada Dugdale)

Lineage sorting and introgression can lead to incongruence among gene phylogenies, complicating the inference of species trees for large groups of taxa that have recently and rapidly radiated. In addition, it can be difficult to determine which of these processes is responsible for this incongruence. We explore these issues with the radiation of New Zealand alpine cicadas of the genus Maoricicada Dugdale. Gene trees were estimated from four putative independent loci: mitochondrial DNA (2274 nucleotides), elongation factor 1-alpha (1275 nucleotides), period (1709 nucleotides), and calmodulin (678 nucleotides). We reconstructed phylogenies using maximum likelihood and Bayesian methods from 44 individuals representing the 19 species and subspecies of Maoricicada and two outgroups. Species-level relationships were reconstructed using a novel extension of gene tree parsimony, whereby gene trees were weighted by their Bayesian posterior probabilities. The inferred gene trees show marked incongruence in the placement of some taxa, especially the enigmatic forest and scrub dwelling species, M. iolanthe. Using the species tree estimated by gene tree parsimony, we simulated coalescent gene trees in order to test the null hypothesis that the nonrandom placement of M. iolanthe among gene trees has arisen by chance. Under the assumptions of constant population size, known generation time, and panmixia, we were able to reject this null hypothesis. Furthermore, because the two alternative placements of M. iolanthe are in each case with species that share a similar song structure, we conclude that it is more likely that an ancient introgression event rather than lineage sorting has caused this incongruence.

The Polymerase Chain Reaction: DNA Extraction and Amplification

The polymerase chain reaction (PCR) is a method of cloning DNA without the use of microorganisms (Saiki et al. 1985, Mullis et al. 1986). In five short years since the development of PCR, this technology has been modified for many uses (Innes et al. 1990) and has essentially revolutionized molecular biology (Guyer and Koshland 1989). PCR allows the rapid selection, isolation and amplification of DNA regions of interest from small amounts of tissue and can be used to help prepare DNA for sequencing. Because it works well for small amounts of tissue and for small pieces of DNA, PCR allows the examination of nucleotide sequences from ancient preserved specimens which have been dried, frozen, hidden in anaerobic sediments, or soaked in alcohol or formalin (Paabo 1990). The greatly increased speed of extraction, amplification, and sequencing has made nucleotide sequence data available on the large scale necessary for population biological and systematic studies. If sequencing studies turn up consistent differences in nucleotide sequence among populations or taxa, PCR can be combined with RFLP analysis to rapidly screen for these known differences. Dot blot analysis with allele specific probes or allele specific PCR primers can be used for a similar purpose (Innes et al. 1990).

Molecular Systematics and Adaptive Radiation of Hawaii's Endemic Damselfly Genus Megalagrion (Odonata: Coenagrionidae)

Damselflies of the endemic Hawaiian genus Megalagrion have radiated into a wide variety of habitats and are an excellent model group for the study of adaptive radiation. Past phylogenetic analysis based on morphological characters has been problematic. Here, we examine relationships among 56 individuals from 20 of the 23 described species using maximum likelihood (ML) and Bayesian phylogenetic analysis of mitochondrial (1287 bp) and nuclear (1039 bp) DNA sequence data. Models of evolution were chosen using the Akaike information criterion. Problems with distant outgroups were accommodated by constraining the best ML ingroup topology but allowing the outgroups to attach to any ingroup branch in a bootstrap analysis. No strong contradictions were obtained between either data partition and the combined data set. Areas of disagreement are mainly confined to clades that are strongly supported by the mitochondrial DNA and weakly supported by the elongation factor 1alpha data because of lack of changes. However, the combined analysis resulted in a unique tree. Correlation between Bayesian posterior probabilities and bootstrap percentages decreased in concert with decreasing information in the data partitions. In cases where nodes were supported by single characters bootstrap proportions were dramatically reduced compared with posterior probabilities. Two speciation patterns were evident from the phylogenetic analysis. First, most speciation is interisland and occurred as members of established ecological guilds colonized new volcanoes after they emerged from the sea. Second, there are several instances of rapid radiation into a variety of specialized habitats, in one case entirely within the island of Kauai. Application of a local clock procedure to the mitochondrial DNA topology suggests that two of these radiations correspond to the development of habitat on the islands of Kauai and Oahu. About 4.0 million years ago, species simultaneously moved into fast streams and plant leaf axils on Kauai, and about 1.5 million years later another group moved simultaneously to seeps and terrestrial habitats on Oahu. Results from the local clock analysis also strongly suggest that Megalagrion arrived in Hawaii about 10 million years ago, well before the emergence of Kauai. Date estimates were more sensitive to the particular node that was fixed in time than to the model of local branch evolution used. We propose a general model for the development of endemic damselfly species on Hawaiian Islands and document five potential cases of hybridization (M. xanthomelas x M. pacificum, M. eudytum x M. vagabundum, M. orobates x M. oresitrophum, M. nesiotes x M. oahuense, and M. mauka x M. paludicola).

Secondary structure and conserved motifs of the frequently sequenced domains IV and V of the insect mitochondrial large subunit rRNA gene

We have analysed over 400 partial insect mitochondrial large subunit (mit LSU) sequences in order to identify conserved motifs and secondary structures for domains IV and V of this gene. Most of the secondary structure elements described by R. R. Gutell et al. (unpublished) for the LSU were identified. However, we present structures for helices 84 and 91 that are not recognized in previous universal models. The portion of the 16S gene containing domains IV and V is frequently sequenced in insect molecular systematic studies so we have many more sequences than previous studies which focused on the complete mitochondrial LSU molecule. In addition, we have the advantage of investigating several sets of closely related taxa. Aligned sequences from thirteen insect orders and nine secondary structure diagrams are presented. These conserved sequence motifs and their associated secondary structure elements can now be used to facilitate the alignment of other insect mit LSU sequences.

PHYLOGEOGRAPHY OF THE NEW ZEALAND CICADA MAORICICADA CAMPBELLI BASED ON MITOCHONDRIAL DNA SEQUENCES: ANCIENT CLADES ASSOCIATED WITH CENOZOIC ENVIRONMENTAL CHANGE

Abstract.— New Zealands isolation, its well‐studied rapidly changing landscape, and its many examples of rampant speciation make it an excellent location for studying the process of genetic differentiation. Using 1520 base pairs of mitochondrial DNA from the cytochrome oxidase subunit I, ATPase subunits 6 and 8 and tRNAAsp genes, we detected two well‐differentiated, parapatrically distributed clades within the widespread New Zealand cicada species Maoricicada campbelli that may prove to represent two species. The situation that we uncovered is unusual in that an ancient lineage with low genetic diversity is surrounded on three sides by two recently diverged lineages. Using a relaxed molecular clock model coupled with Bayesian statistics, we dated the earliest divergence within M. campbelli at 2.3 ± 0.55 million years. Our data suggest that geological and climatological events of the late Pliocene divided a oncewidespread species into northern and southern components and that near the middle of the Pleistocene the northern lineage began moving south eventually reaching the southern clade. The southern clade seems to have moved northward to only a limited extent. We discovered five potential zones of secondary contact through mountain passes that will be examined in future work. We predict that, as in North American periodical cicadas, contact between these highly differentiated lineages will exist but will not involve gene flow.

Molecular Systematics at the Species Boundary: Exploiting Conserved and Variable Regions of the Mitochondrial Genome of Animals via Direct Sequencing from Amplified DNA

Traditional morphological characters have provided a wealth of systematic information. This information has been used to establish phylogenetic relationships which we refine today using a wide variety of techniques. A common result of traditional morphological analyses has been identification of groups of related taxa. Relationships within and/or among these groups were often uncertain (e.g. orders of flowering plants, Heywood 1978; species groups of kangaroo rats, Hall 1981). Very closely related species were particularly difficult to connect phylogenetically using morphological characters (e.g. Hawaiian Drosophila Hardy 1965; cichlid fishes, Fryer and Isles 1972). The addition of detailed morphometric analyses in the 1970’s and 1980’s increased our ability to identify taxa and discriminate among them but did not prove useful for deciphering relationships among taxa (Rohlf and Bookstein 1990).

THE EFFECT OF TOPOLOGY ON ESTIMATES OF AMONG-SITE RATE VARIATION

Among-site rate variation, as quantified by the gamma-distribution shape parameter,a or α, and the ratio of transition rate to transversion rate (Ts/Tv) influence phylogenetic inference. We examine the effect of topology on estimates of these two parameters in 12S rRNA sequences from nine species of mice belonging to the generaOnychomys andPeromyscus by generating 100 random topologies and estimating these parameters using parsimony and maximum-likelihood methods for each of the random topologies. The parsimony-based estimate ofTs/Tv from the well-corroborated topology falls within the distribution of estimates based on random topologies, whereas the maximum-likelihood estimate ofTs/Tv based on the well-corroborated topology lies well outside the distribution of estimates derived from random topologies. TheTs/Tv ratio derived via maximumlikelihood estimation is three times the parsimony-based estimate, suggesting that parsimony-based estimates are severe underestimates even when the correct topology is used. Both parsimony- and likelihood-based estimates of the gamma-distribution shape parameter (α) are sensitive to topology because the best estimates based on the well-corroborated topology are well outside the distributions of estimates derived from random topologies for both methods. We show that the reason for topology dependence is the presence of long internal branches in the underlying topology.