The phylogenomics of diversification on an island: applying anchored hybrid enrichment to New Zealand Leptospermum scoparium (Myrtaceae)

2019 ◽  
Vol 191 (1) ◽  
pp. 1-17 ◽  
Author(s):  
Matt H Buys ◽  
Richard C Winkworth ◽  
Peter J de Lange ◽  
Peter G Wilson ◽  
Nora Mitchell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
Sequence Data ◽  
Large Data ◽  
Data Matrix ◽  
Data Set ◽  
Important Species ◽  
Anchored Hybrid Enrichment ◽  
Data Signal ◽  
Leptospermum Scoparium

Abstract Leptospermum scoparium (Myrtaceae) is a morphologically highly variable species found in mainland Australia, Tasmania and New Zealand. For example, in New Zealand up to six morphologically distinct varieties of this species have been described, although only two (var. scoparium and var. incanum) are now formally recognized. In the present study we provide a first examination of genetic diversity in this culturally and commercially important species with the aim of gaining insights into its origins and evolution. We used anchored hybrid enrichment to acquire sequence data from 485 orthologous low-copy nuclear loci for 27 New Zealand and three Australian accessions of L. scoparium and representatives of several other Leptospermum spp. The final concatenated data matrix contained 421 687 nucleotide positions of which 55 102 were potentially informative. Despite the relative large data set, our analyses suggest that a combination of low and incompatible data signal limits the resolution of relationships among New Zealand populations of L. scoparium. Nevertheless, our analyses are consistent with genetic diversity being geographically structured, with three groups of L. scoparium recovered. We discuss the evolutionary and taxonomic implications of our findings.

scholarly journals Evolution of the U.S. Biological Select AgentRathayibacter toxicus

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Edward W. Davis ◽  
Javier F. Tabima ◽  
Alexandra J. Weisberg ◽  
Lucas Dantas Lopes ◽  
Michele S. Wiseman ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Adaptive Immune System ◽  
The United States ◽  
Genomic Diversity ◽  
Data Set ◽  
Important Species ◽  
Content Type ◽  
Low Genetic Diversity ◽  
History Of ◽  
Short Palindromic Repeat

ABSTRACTRathayibacter toxicusis a species of Gram-positive, corynetoxin-producing bacteria that causes annual ryegrass toxicity, a disease often fatal to grazing animals. A phylogenomic approach was employed to model the evolution ofR. toxicusto explain the low genetic diversity observed among isolates collected during a 30-year period of sampling in three regions of Australia, gain insight into the taxonomy ofRathayibacter, and provide a framework for studying these bacteria. Analyses of a data set of more than 100 sequencedRathayibactergenomes indicated thatRathayibacterforms nine species-level groups.R. toxicusis the most genetically distant, and evidence suggested that this species experienced a dramatic event in its evolution. Its genome is significantly reduced in size but is colinear to those of sister species. Moreover,R. toxicushas low intergroup genomic diversity and almost no intragroup genomic diversity between ecologically separated isolates.R. toxicusis the only species of the genus that encodes a clustered regularly interspaced short palindromic repeat (CRISPR) locus and that is known to host a bacteriophage parasite. The spacers, which represent a chronological history of infections, were characterized for information on past events. We propose a three-stage process that emphasizes the importance of the bacteriophage and CRISPR in the genome reduction and low genetic diversity of theR. toxicusspecies.IMPORTANCERathayibacter toxicusis a toxin-producing species found in Australia and is often fatal to grazing animals. The threat of introduction of the species into the United States led to its inclusion in the Federal Select Agent Program, which makesR. toxicusa highly regulated species. This work provides novel insights into the evolution ofR. toxicus.R. toxicusis the only species in the genus to have acquired a CRISPR adaptive immune system to protect against bacteriophages. Results suggest that coexistence with the bacteriophage NCPPB3778 led to the massive shrinkage of theR. toxicusgenome, species divergence, and the maintenance of low genetic diversity in extant bacterial groups. This work contributes to an understanding of the evolution and ecology of an agriculturally important species of bacteria.

Intra- and interspecific genetic diversity of New Zealand hairworms (Nematomorpha)

Parasitology ◽  
2017 ◽  
Vol 144 (8) ◽  
pp. 1026-1040 ◽  
Author(s):  
ZACHARY J. C. TOBIAS ◽  
ARUN K. YADAV ◽  
ANDREAS SCHMIDT-RHAESA ◽  
ROBERT POULIN
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Population Level ◽  
Morphological Classification ◽  
Widespread Species ◽  
Sampling Locations ◽  
Host Parasite ◽  
Eggs And Larvae

SUMMARYHairworms (Nematomorpha) are a little-known group of parasites, and despite having been represented in the taxonomic literature for over a century, the implementation of molecular genetics in studies of hairworm ecology and evolution lags behind that of other parasitic taxa. In this study, we characterize the genetic diversity of the New Zealand nematomorph fauna and test for genetic structure within the most widespread species found. We provide new mitochondrial and nuclear ribosomal sequence data for three previously described species from New Zealand:Gordius paranensis, Parachordodes diblastusandEuchordodes nigromaculatus. We also present genetic data on a previously reported but undescribedGordiussp., as well as data from specimens of a newGordionussp., a genus new for New Zealand. Phylogenetic analyses of CO1 and nuclear rDNA regions correspond with morphological classification based on scanning electron microscopy, and demonstrate paraphyly of the genusGordionusand the potential for cryptic species withinG. paranensis. Population-level analyses ofE. nigromaculatusshowed no genetic differentiation among sampling locations across the study area, in contrast to previously observed patterns in known and likely definitive hosts. Taken together, this raises the possibility that factors such as definitive host specificity, intermediate host movement, and passive dispersal of eggs and larvae may influence host–parasite population co-structure in hairworms.

scholarly journals Diversification of New Zealand weta (Orthoptera: Ensifera: Anostostomatidae) and their relationships in Australasia

2008 ◽  
Vol 363 (1508) ◽  
pp. 3427-3437 ◽  
Author(s):  
Renae C Pratt ◽  
Mary Morgan-Richards ◽  
Steve A Trewick
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
New Zealand ◽  
New Caledonia ◽  
Sequence Data ◽  
Species Level ◽  
Molecular Dating ◽  
Bayesian Analyses ◽  
Dna Sequence Data ◽  
The Family

New Zealand taxa from the Orthopteran family Anostostomatidae have been shown to consist of three broad groups, Hemiandrus (ground weta), Anisoura/Motuweta (tusked weta) and Hemideina – Deinacrida (tree–giant weta). The family is also present in Australia and New Caledonia, the nearest large land masses to New Zealand. All genera are endemic to their respective countries except Hemiandrus that occurs in New Zealand and Australia. We used nuclear and mitochondrial DNA sequence data to study within genera and among species-level genetic diversity within New Zealand and to examine phylogenetic relationships of taxa in Australasia. We found the Anostostomatidae to be monophyletic within Ensifera, and justifiably distinguished from the Stenopelmatidae among which they were formerly placed. However, the New Zealand Anostostomatidae are not monophyletic with respect to Australian and New Caledonian species in our analyses. Two of the New Zealand groups have closer allies in Australia and one in New Caledonia. We carried out maximum-likelihood and Bayesian analyses to reveal several well supported subgroupings. Our analysis included the most extensive sampling to date of Hemiandrus species and indicate that Australian and New Zealand Hemiandrus are not monophyletic. We used molecular dating approaches to test the plausibility of alternative biogeographic hypotheses for the origin of the New Zealand anostostomatid fauna and found support for divergence of the main clades at, or shortly after, Gondwanan break-up, and dispersal across the Tasman much more recently.

scholarly journals Anchored Hybrid Enrichment-Based Phylogenomics of Leafhoppers and Treehoppers (Hemiptera: Cicadomorpha: Membracoidea)

2017 ◽  
Vol 1 (1) ◽  
pp. 57-72 ◽  
Author(s):  
Christopher H Dietrich ◽  
Julie M Allen ◽  
Alan R Lemmon ◽  
Emily Moriarty Lemmon ◽  
Daniela M Takiya ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Single Gene ◽  
Gene Tree ◽  
Divergence Time ◽  
Data Set ◽  
Nucleotide Sequence Data ◽  
Divergence Time Estimates ◽  
Morphological Criteria ◽  
Anchored Hybrid Enrichment

Abstract A data set comprising DNA sequences from 388 loci and >99,000 aligned nucleotide positions, generated using anchored hybrid enrichment, was used to estimate relationships among 138 leafhoppers and treehoppers representative of all major lineages of Membracoidea, the most diverse superfamily of hemipteran insects. Phylogenetic analysis of the concatenated nucleotide sequence data set using maximum likelihood produced a tree with most branches receiving high support. A separate coalescent gene tree analysis of the same data generally recovered the same strongly supported clades but was less well resolved overall. Several nodes pertaining to relationships among leafhopper subfamilies currently recognized based on morphological criteria were separated by short internodes and received low support. Although various higher taxa were corroborated with improved branch support, relationships among some major lineages of Membracoidea are only somewhat more resolved than previously published phylogenies based on single gene regions or morphology. In agreement with previous studies, the present results indicate that leafhoppers (Cicadellidae) are paraphyletic with respect to the three recognized families of treehoppers (Aetalionidae, Melizoderidae, and Membracidae). Divergence time estimates indicate that most of the poorly resolved divergence events among major leafhopper lineages occurred during the lower to middle Cretaceous and that most modern leafhopper subfamilies, as well as the lineage comprising the three recognized families of treehoppers, also arose during the Cretaceous.

scholarly journals Bacterial Diversity Profiling of the New Zealand Parasitic Blowfly Lucilia sericata Based on 16S rRNA Gene Amplicon Sequencing

2021 ◽  
Vol 10 (19) ◽  
Author(s):  
Nikola Palevich ◽  
Paul H. Maclean ◽  
Luis Carvalho ◽  
Ruy Jauregui
Keyword(s):  
New Zealand ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Sequence Data ◽  
Amplicon Sequencing ◽  
Lucilia Sericata ◽  
Rrna Gene ◽  
Data Set ◽  
Content Type

ABSTRACT Here, we present a 16S rRNA gene amplicon sequence data set and profiles demonstrating the bacterial diversity of larval and adult Lucilia sericata, collected from Ashhurst, New Zealand (May 2020). The two dominant genera among adult male and female L. sericata were Serratia and Morganella (phylum Proteobacteria), while the larvae were also dominated by the genera Lactobacillus, Carnobacterium, and Lactococcus (phylum Firmicutes).

scholarly journals Reversing “drift”: Innovation and diffusion in the London diphthong system

2008 ◽  
Vol 20 (3) ◽  
pp. 451-491 ◽  
Author(s):  
Paul Kerswill ◽  
Eivind Nessa Torgersen ◽  
Susan Fox
Keyword(s):  
New Zealand ◽  
Innovation Diffusion ◽  
Large Data ◽  
Diffusion Models ◽  
Ethnic Population ◽  
Data Set ◽  
Dialect Contact ◽  
Innovation And Diffusion ◽  
And Diffusion ◽  
Minority Ethnic

AbstractThis study contributes to innovation and diffusion models by examining phonetic changes in London English. It evaluates Sapir's notion of “drift,” which involves “natural,” unconscious change, in relation to these changes. Investigating parallel developments in two related varieties of English enables drift to be tested in terms of the effect of extralinguistic factors. The diphthongs ofprice,mouth,face, andgoatin both London and New Zealand English are characterized by “Diphthong Shift,” a process that continued unabated in New Zealand. A new, large data set of London speech shows Diphthong Shift reversal, providing counterevidence for drift. We discuss Diphthong Shift and its “reversal” in relation to innovation, diffusion, leveling, and supralocalization, arguing that sociolinguistic factors and dialect contact override natural Diphthong Shift. Studying dialect change in a metropolis, with its large and linguistically innovative minority ethnic population, is of the utmost importance in understanding the dynamics of change.

Angiosperm Phylogeny Based on 18S/26S rDNA Sequence Data: Constructing a Large Data Set Using Next-Generation Sequence Data

2014 ◽  
Vol 175 (6) ◽  
pp. 613-650 ◽  
Author(s):  
Vitor H. Maia ◽  
Matthew A. Gitzendanner ◽  
Pamela S. Soltis ◽  
Gane Ka-Shu Wong ◽  
Douglas E. Soltis
Keyword(s):  
Sequence Data ◽  
Large Data ◽  
Rdna Sequence ◽  
Next Generation ◽  
Data Set ◽  
Angiosperm Phylogeny ◽  
26S Rdna ◽  
Large Data Set ◽  
Rdna Sequence Data

scholarly journals 16S rRNA Gene Amplicon Profiling of the New Zealand parasitic blowfly Calliphora vicina

2021 ◽  
Author(s):  
Nikola Palevich ◽  
Paul H. Maclean ◽  
Luis Carvalho ◽  
Ruy Jauregui
Keyword(s):  
New Zealand ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Adult Male ◽  
Sequence Data ◽  
Calliphora Vicina ◽  
Rrna Gene ◽  
Data Set ◽  
Male And Female

ABSTRACTHere, we present a 16S rRNA gene amplicon sequence data set and profiles demonstrating the bacterial diversity of larval and adult Calliphora vicina, collected from Ashhurst, New Zealand (May 2020). The three dominant genera among adult male and female C. vicina were Serratia and Morganella (phylum Proteobacteria) and Carnobacterium (phylum Firmicutes), while the larvae were also dominated by the genera Lactobacillus (phylum Firmicutes).

Some statistical and CI models to predict chaotic high-frequency financial data

2020 ◽  
Vol 39 (5) ◽  
pp. 6419-6430
Author(s):  
Dusan Marcek
Keyword(s):  
Time Series Data ◽  
Moving Average ◽  
Methodological Approach ◽  
Back Propagation ◽  
Large Data ◽  
Series Data ◽  
Data Set ◽  
Training Time ◽  
Optimal Population ◽  
Forecast Time

To forecast time series data, two methodological frameworks of statistical and computational intelligence modelling are considered. The statistical methodological approach is based on the theory of invertible ARIMA (Auto-Regressive Integrated Moving Average) models with Maximum Likelihood (ML) estimating method. As a competitive tool to statistical forecasting models, we use the popular classic neural network (NN) of perceptron type. To train NN, the Back-Propagation (BP) algorithm and heuristics like genetic and micro-genetic algorithm (GA and MGA) are implemented on the large data set. A comparative analysis of selected learning methods is performed and evaluated. From performed experiments we find that the optimal population size will likely be 20 with the lowest training time from all NN trained by the evolutionary algorithms, while the prediction accuracy level is lesser, but still acceptable by managers.

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