David A. Morrison

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

A "Silent" Polymorphism in the MDR 1 Gene Changes Substrate Specificity

Sex Differences in the Gut Microbiome Drive Hormone-Dependent Regulation of Autoimmunity

Recent Expansion of Toxoplasma Through Enhanced Oral Transmission

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

UCHIME improves sensitivity and speed of chimera detection

Resolution of ray-finned fish phylogeny and timing of diversification

One thousand plant transcriptomes and the phylogenomics of green plants

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Characterisation of the first Australian isolate of Neospora caninum from cattle

Phylogenetic Placement of Retropinnid Fishes: Data Set Incongruence Can Be Reduced by Using Asymmetric Character State Transformation Costs

Protracted Shedding of Oocysts of Neospora caninum by a Naturally Infected Foxhound

Inconsistency of Species Tree Methods under Gene Flow

Toxoplasmosis

Formal description of sequence-based voucherless Fungi: promises and pitfalls, and how to resolve them

Recent developments in the MAFFT multiple sequence alignment program

Coyotes (Canis latrans) are definitive hosts of Neospora caninum

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

Diagnosis of bovine neosporosis

CHARACTERIZATION OF THE OREGON ISOLATE OFNEOSPORA HUGHESIFROM A HORSE

Does the Leishmania major paradigm of pathogenesis and protection hold for New World cutaneous leishmaniases or the visceral disease?

Oocysts of , , and in faeces collected from dogs in Germany

IMPROVED PRODUCTION OF NEOSPORA CANINUM OOCYSTS, CYCLICAL ORAL TRANSMISSION BETWEEN DOGS AND CATTLE, AND IN VITRO ISOLATION FROM OOCYSTS

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Horizontal Gene Transfer from Diverse Bacteria to an Insect Genome Enables a Tripartite Nested Mealybug Symbiosis

Hammondia heydorni: evidence of genetic diversity among isolates from dogs

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

Characterization of the thermolysis products of Nafion membrane: A potential source of perfluorinated compounds in the environment

CALIBRATING DIVERGENCE TIMES ON SPECIES TREES VERSUS GENE TREES: IMPLICATIONS FOR SPECIATION HISTORY OF APHELOCOMA JAYS

Predicted Secondary Structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): Impact on Sequence Alignment and Phylogeny Estimation

MULTILOCUS MICROSATELLITE ANALYSIS REVEALS EXTENSIVE GENETIC DIVERSITY IN NEOSPORA CANINUM

Recent advances in understanding the epidemiology ofNeospora caninumin cattle

Using the Acropora digitifera genome to understand coral responses to environmental change

Nearly complete rRNA genes assembled from across the metazoan animals: Effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction

NEOSPORA CANINUM–LIKE OOCYSTS OBSERVED IN FECES OF FREE-RANGING RED FOXES (VULPES VULPES) AND COYOTES (CANIS LATRANS)

Multiple nuclear loci reveal patterns of incomplete lineage sorting and complex species history within western mouse lemurs (Microcebus)

Effect of a killed whole Neospora caninum tachyzoite vaccine on the crude abortion rate of Costa Rican dairy cows under field conditions

Multiple Alignment of DNA Sequences with MAFFT

Long-term passage of tachyzoites in tissue culture can attenuate virulence ofNeospora caninum in vivo

Ultra-large alignments using phylogeny-aware profiles

Shedding of Neospora caninum oocysts by dogs fed tissues from naturally infected water buffaloes (Bubalus bubalis) from Brazil

Trypanosomatid biodiversity in Costa Rica: genotyping of parasites from Heteroptera using the spliced leader RNA gene

Class of Multiple Sequence Alignment Algorithm Affects Genomic Analysis

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Studies on the Relationships between the Synonymous Codon Usage and Protein Secondary Structural Units

Application of Phylogenetic Networks in Evolutionary Studies

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments

Neospora caninum in wildlife

Tunicates and not cephalochordates are the closest living relatives of vertebrates

Reduction in transplacental transmission of Neospora caninum in outbred mice by vaccination

limma powers differential expression analyses for RNA-sequencing and microarray studies

Bonobos Fall within the Genomic Variation of Chimpanzees

Immune responses to Neospora caninum and prospects for vaccination

In vitro isolation and characterisation of the first canine Neospora caninum isolate in Australia

Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders

18S Ribosomal RNA and Tetrapod Phylogeny

Control options forNeospora caninuminfections in cattle — current state of knowledge

Dog shedding oocysts of Neospora caninum: PCR diagnosis and molecular phylogenetic approach

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

Effects of host maturity and prior exposure history on the production of Neospora caninum oocysts by dogs

Computer programs for population genetics data analysis: a survival guide

Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis

Broad phylogenomic sampling improves resolution of the animal tree of life

Canine neosporosis: clinical and pathological findings and first isolation of Neospora caninum in Germany

First Isolation ofNeospora caninumFrom the Feces of a Naturally Infected Dog

Isolation and molecular characterisation ofNeospora caninumin cattle in New Zealand

Mind the Gaps: Evidence of Bias in Estimates of Multiple Sequence Alignments

The Impact of rRNA Secondary Structure Consideration in Alignment and Tree Reconstruction: Simulated Data and a Case Study on the Phylogeny of Hexapods

ModelFinder: fast model selection for accurate phylogenetic estimates

Improved Background Correction for Spotted DNA Microarrays

Cucumber ( Cucumis sativus ) and melon ( C. melo ) have numerous wild relatives in Asia and Australia, and the sister species of melon is from Australia

adegenet: a R package for the multivariate analysis of genetic markers

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals

Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments

New Insights into Perfluorinated Sulfonic-Acid Ionomers

Detection of IgG antibody against Neospora caninum in cattle in Korea

Temporal Distribution and Parasite Load Kinetics in Blood and Tissues during Neospora caninum Infection in Mice

DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae)

Occurrence, Classification, and Biological Function of Hydrogenases:  An Overview

Multiple Sequence Alignment Accuracy and Phylogenetic Inference

Advances in leishmaniasis

Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

DNA barcodes affirm that 16 species of apparently generalist tropical parasitoid flies (Diptera, Tachinidae) are not all generalists

A Rapid Bootstrap Algorithm for the RAxML Web Servers

Epidemiology and Control of Neosporosis andNeospora caninum

Nematode Small Subunit Phylogeny Correlates with Alignment Parameters

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

Measuring the distance between multiple sequence alignments

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

Phylogenetic information and experimental design in molecular systematics

Characterizing the Phylogenetic Tree-Search Problem

The Design and Analysis of Microarray Experiments: Applications in Parasitology

Schistosoma mansoni: patterns of codon usage and bias

Networks: expanding evolutionary thinking

Effects of Sequence Alignment and Structural Domains of Ribosomal DNA on Phylogeny Reconstruction for the Protozoan Family Sarcocystidae

Evolution of RuminantSarcocystis(Sporozoa) Parasites Based on Small Subunit rDNA Sequences

The genus Hammondia is paraphyletic

Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa

Phylogenetic analysis based on full-length large subunit ribosomal RNA gene sequence comparison reveals that Neospora caninum is more closely related to Hammondia heydorni than to Toxoplasma gondii1Note: Nucleotide sequence data reported in this paper are available in the EMBL, GenBank™ and DDJB databases under the accession numbers AF159240 (Hammondia heydorni), AF101077 (Hammondia hammondi), AF076899 (Sarcocystis tenella) and AF076901 (Toxoplasma gondii ME49 strain).1

Inferring Trees

Phylogenetic relationships of the genus Frenkelia : a review of its history and new knowledge gained from comparison of large subunit ribosomal ribonucleic acid gene sequences 1Note: Nucleotide sequence data reported in this paper are available in the EMBL, GenBank™, and DDJB databases under the accession numbers U85705-6, AF012883, AF092927, and AF044250-2. 1

Networks in phylogenetic analysis: new tools for population biology

The relationship of Hammondia hammondi and Sarcocystis mucosa to other heteroxenous cyst-forming coccidia as inferred by phylogenetic analysis of the 18S SSU ribosomal DNA sequence

Comparison of the biological characteristics of two isolates of Neospora caninum

Molecular Phylogeny of Besnoitia and the Genetic Relationships Among Besnoitia of Cattle, Wildebeest and Goats

Locomotor behavior in zebrafish (Danio rerio) larvae exposed to perfluoroalkyl acids

Evolution of the genus Leishmania revealed by comparison of DNA and RNA polymerase gene sequences1Note: Nucleotide sequence data reported in this paper have been submitted to the GenBank™ data base with the accession numbers: POLA/RPOIILS (AF009134/AF009153, Leishmania adleri); (AF009135/NS, Leishmania aethiopica); (AF009136/AF009154, Leishmania amazonensis); (AF009137/NS, Leishmania arabica); (AF009138/AF009155, Leishmania braziliensis); (AF009139/NS, Leishmania chagasi); (AF009140/AF009156, Leishmania deanei); (AF009141/AF009157, Leishmania donovani); (AF009142/AF009158, Endotrypanum monterogeii); (AF009143/AF009159, Leishmania gymnodactyli); (AF009144/AF009160, Leishmania herreri); (AF009145/AF009161, Leishmania hertigi); (AF009146/AF009162, Leishmania hoogstraali); (AF009147/NS, Leishmania infantum); (AF009148/AF009163, Leishmania major); (AF009149/AF009164, Leishmania mexicana); (AF009150/AF009165, Leishmania panamensis); (AF009151/AF009166, Leishmania tarentolae); (AF009152/AF009167, Leishmania tropica).1

Increasing the Efficiency of Searches for the Maximum Likelihood Tree in a Phylogenetic Analysis of up to 150 Nucleotide Sequences

Is the Tree of Life the Best Metaphor, Model, or Heuristic for Phylogenetics?

Characterization of an alpha tubulin gene sequence from Neospora caninum and Hammondia heydorni, and their comparison to homologous genes from Apicomplexa.

Estimating Species Trees: Practical and Theoretical Aspects

A framework for phylogenetic sequence alignment

Multiple sequence alignment for phylogenetic purposes