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

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.

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The molecular systematics of blowflies and screwworm flies (Diptera: Calliphoridae) using 28S rRNA, COX1 and EF-1α: insights into the evolution of dipteran parasitism

Parasitology ◽

10.1017/s0031182011001089 ◽

2011 ◽

Vol 138 (13) ◽

pp. 1760-1777 ◽

Cited By ~ 30

Author(s):

LAURA M. McDONAGH ◽

JAMIE R. STEVENS

Keyword(s):

Sequence Data ◽

Single Gene ◽

Nuclear Gene ◽

Evolutionary Status ◽

28S Rrna ◽

Gene Trees ◽

Data Set ◽

Protein Coding ◽

Nucleotide Sequence Data ◽

The Family

SUMMARYThe Calliphoridae include some of the most economically significant myiasis-causing flies in the world – blowflies and screwworm flies – with many being notorious for their parasitism of livestock. However, despite more than 50 years of research, key taxonomic relationships within the family remain unresolved. This study utilizes nucleotide sequence data from the protein-coding genes COX1 (mitochondrial) and EF1α (nuclear), and the 28S rRNA (nuclear) gene, from 57 blowfly taxa to improve resolution of key evolutionary relationships within the family Calliphoridae. Bayesian phylogenetic inference was carried out for each single-gene data set, demonstrating significant topological difference between the three gene trees. Nevertheless, all gene trees supported a Calliphorinae-Luciliinae subfamily sister-lineage, with respect to Chrysomyinae. In addition, this study also elucidates the taxonomic and evolutionary status of several less well-studied groups, including the genus Bengalia (either within Calliphoridae or as a separate sister-family), genus Onesia (as a sister-genera to, or sub-genera within, Calliphora), genus Dyscritomyia and Lucilia bufonivora, a specialised parasite of frogs and toads. The occurrence of cross-species hybridisation within Calliphoridae is also further explored, focusing on the two economically significant species Lucilia cuprina and Lucilia sericata. In summary, this study represents the most comprehensive molecular phylogenetic analysis of family Calliphoridae undertaken to date.

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On the phylogeny of Ophiostoma, Ceratocystis s.s., and Microascus, and relationships within Ophiostoma based on partial ribosomal DNA sequences

Canadian Journal of Botany ◽

10.1139/b93-148 ◽

1993 ◽

Vol 71 (9) ◽

pp. 1249-1265 ◽

Cited By ~ 54

Author(s):

G. Hausner ◽

J. Reid ◽

G. R. Klassen

Keyword(s):

Dna Sequences ◽

Sequence Data ◽

Large Subunit ◽

Small Subunit ◽

Data Set ◽

Rdna Sequences ◽

Morphological Criteria ◽

Small Subunit Rdna ◽

Rdna Sequence Data ◽

Large Subunit Rdna

Phylogenetic analysis of partial rDNA sequences suggests that Ophiostoma should remain the sole genus of the Ophiostomataceae, and this should be the sole family within the Ophiostomatales, whereas Ceratocystis s.s. would be best disposed within the Microascales. Although morphological criteria suggest that the genus Ophiostoma is heterogeneous, analysis of partial small subunit rDNA sequence data shows that Ophiostoma (excluding O. roraimense) represents a monophyletic taxon. Analysis of a partial large subunit rDNA data set, which included sequences from 55 species assignable to Ophiostoma, failed to support the strict subdivision of the genus based on either ascospore characters or the nature of the anamorph. Key words: Ceratocystis, Microascus, Ophiostoma, partial rDNA sequences, phylogeny.

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A Distance Method to Reconstruct Species Trees In the Presence of Gene Flow

10.1101/007955 ◽

2014 ◽

Author(s):

Lingfei Cui ◽

Laura Kubatko

Keyword(s):

Gene Flow ◽

Evolutionary Biology ◽

Sequence Data ◽

Divergence Time ◽

Species Tree ◽

Estimation Accuracy ◽

Species Trees ◽

Distance Method ◽

Data Set ◽

Divergence Time Estimates

One of the central tasks in evolutionary biology is to reconstruct the evolutionary relationships among species from sequence data, particularly from multilocus data. In the last ten years, many methods have been proposed to use the variance in the gene histories to estimate species trees by explicitly modeling deep coalescence. However, gene flow, another process that may produce gene history variance, has been less studied. In this paper, we propose a simple yet innovative method for species trees estimation in the presence of gene flow. Our method, called STEST (Species Tree Estimation from Speciation Times), constructs species tree estimates from pairwise speciation time or species divergence time estimates. By using methods that estimate speciation times in the presence of gene flow, (for example, M1 (Yang 2010) or SIM3s (Zhu and Yang 2012)), STEST is able to estimate species trees from data subject to gene flow. We develop two methods, called STEST (M1) and STEST (SIM3s), for this purpose. Additionally, we consider the method STEST (M0), which instead uses the M0 method (Yang 2002), a coalescent-based method that does not assume gene flow, to estimate speciation times. It is therefore devised to estimate species trees in the absence of gene flow. Our simulation studies show that STEST (M0) outperforms STEST(M1), STEST (SIM3s) and STEM in terms of estimation accuracy and outperfroms *BEAST in terms of running time when the degree of gene flow is small. STEST (M1) outperforms STEST (M0), STEST (SIM3s), STEM and *BEAST in term of estimation accuracy when the degree of gene flow is large. An empirical data set analyzed by these methods gives species tree estimates that are consistent with the previous results.

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Strategies for Partitioning Clock Models in Phylogenomic Dating: Application to the Angiosperm Evolutionary Timescale

10.1101/144287 ◽

2017 ◽

Author(s):

Charles S. P. Foster ◽

Simon Y. W. Ho

Keyword(s):

Sequence Data ◽

Divergence Time ◽

Molecular Dating ◽

Sequence Length ◽

Rate Heterogeneity ◽

Data Set ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

Divergence Time Estimates ◽

Time Estimates

AbstractEvolutionary timescales can be inferred from molecular sequence data using a Bayesian phylogenetic approach. In these methods, the molecular clock is often calibrated using fossil data. The uncertainty in these fossil calibrations is important because it determines the limiting posterior distribution for divergence-time estimates as the sequence length tends to infinity. Here we investigate how the accuracy and precision of Bayesian divergence-time estimates improve with the increased clock-partitioning of genome-scale data into clock-subsets. We focus on a data set comprising plastome-scale sequences of 52 angiosperm taxa. There was little difference among the Bayesian date estimates whether we chose clock-subsets based on patterns of among-lineage rate heterogeneity or relative rates across genes, or by random assignment. Increasing the degree of clock-partitioning usually led to an improvement in the precision of divergence-time estimates, but this increase was asymptotic to a limit presumably imposed by fossil calibrations. Our clock-partitioning approaches yielded highly precise age estimates for several key nodes in the angiosperm phylogeny. For example, when partitioning the data into 20 clock-subsets based on patterns of among-lineage rate heterogeneity, we inferred crown angiosperms to have arisen 198–178 Ma. This demonstrates that judicious clock-partitioning can improve the precision of molecular dating based on phylogenomic data, but the meaning of this increased precision should be considered critically.

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SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control

mSystems ◽

10.1128/msystems.00202-17 ◽

2018 ◽

Vol 3 (3) ◽

Cited By ~ 15

Author(s):

Gabriel A. Al-Ghalith ◽

Benjamin Hillmann ◽

Kaiwei Ang ◽

Robin Shields-Cutler ◽

Dan Knights

Keyword(s):

Quality Control ◽

Dna Sequences ◽

Sequence Data ◽

Background Knowledge ◽

Sequencing Technology ◽

Data Set ◽

Short Read ◽

Dna Quality ◽

Public Data ◽

User Friendly

ABSTRACT Next-generation sequencing technology is of great importance for many biological disciplines; however, due to technical and biological limitations, the short DNA sequences produced by modern sequencers require numerous quality control (QC) measures to reduce errors, remove technical contaminants, or merge paired-end reads together into longer or higher-quality contigs. Many tools for each step exist, but choosing the appropriate methods and usage parameters can be challenging because the parameterization of each step depends on the particularities of the sequencing technology used, the type of samples being analyzed, and the stochasticity of the instrumentation and sample preparation. Furthermore, end users may not know all of the relevant information about how their data were generated, such as the expected overlap for paired-end sequences or type of adaptors used to make informed choices. This increasing complexity and nuance demand a pipeline that combines existing steps together in a user-friendly way and, when possible, learns reasonable quality parameters from the data automatically. We propose a user-friendly quality control pipeline called SHI7 (canonically pronounced “shizen”), which aims to simplify quality control of short-read data for the end user by predicting presence and/or type of common sequencing adaptors, what quality scores to trim, whether the data set is shotgun or amplicon sequencing, whether reads are paired end or single end, and whether pairs are stitchable, including the expected amount of pair overlap. We hope that SHI7 will make it easier for all researchers, expert and novice alike, to follow reasonable practices for short-read data quality control. IMPORTANCE Quality control of high-throughput DNA sequencing data is an important but sometimes laborious task requiring background knowledge of the sequencing protocol used (such as adaptor type, sequencing technology, insert size/stitchability, paired-endedness, etc.). Quality control protocols typically require applying this background knowledge to selecting and executing numerous quality control steps with the appropriate parameters, which is especially difficult when working with public data or data from collaborators who use different protocols. We have created a streamlined quality control pipeline intended to substantially simplify the process of DNA quality control from raw machine output files to actionable sequence data. In contrast to other methods, our proposed pipeline is easy to install and use and attempts to learn the necessary parameters from the data automatically with a single command.

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

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boz033 ◽

2019 ◽

Vol 191 (1) ◽

pp. 1-17 ◽

Cited By ~ 3

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.

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ADOPS - Automatic Detection Of Positively Selected Sites

Journal of Integrative Bioinformatics ◽

10.1515/jib-2012-200 ◽

2012 ◽

Vol 9 (3) ◽

pp. 18-32 ◽

Cited By ~ 12

Author(s):

David Reboiro-Jato ◽

Miguel Reboiro-Jato ◽

Florentino Fdez-Riverola ◽

Cristina P. Vieira ◽

Nuno A. Fonseca ◽

...

Keyword(s):

Amino Acid ◽

Maximum Likelihood ◽

Dna Sequences ◽

Sequence Data ◽

Automatic Detection ◽

Acid Sites ◽

Nucleotide Sequence Data ◽

Software Applications ◽

Codon Substitution ◽

Positively Selected Sites

Summary Maximum-likelihood methods based on models of codon substitution have been widely used to infer positively selected amino acid sites that are responsible for adaptive changes. Nevertheless, in order to use such an approach, software applications are required to align protein and DNA sequences, infer a phylogenetic tree and run the maximum-likelihood models. Therefore, a significant effort is made in order to prepare input files for the different software applications and in the analysis of the output of every analysis. In this paper we present the ADOPS (Automatic Detection Of Positively Selected Sites) software. It was developed with the goal of providing an automatic and flexible tool for detecting positively selected sites given a set of unaligned nucleotide sequence data. An example of the usefulness of such a pipeline is given by showing, under different conditions, positively selected amino acid sites in a set of 54 Coffea putative S-RNase sequences. ADOPS software is freely available and can be downloaded from http://sing.ei.uvigo.es/ADOPS.

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The phylogeny of Staphylococcus aureus – which genes make the best intra-species markers?

Microbiology ◽

10.1099/mic.0.28620-0 ◽

2006 ◽

Vol 152 (5) ◽

pp. 1297-1305 ◽

Cited By ~ 44

Author(s):

Jessica E. Cooper ◽

Edward J. Feil

Keyword(s):

Staphylococcus Aureus ◽

Goodness Of Fit ◽

Sequence Data ◽

Strong Association ◽

Gene Tree ◽

Nucleotide Sequence Data ◽

Individual Gene ◽

Marker Loci ◽

Species Markers ◽

Candidate Loci

The ability to make informed decisions on the suitability of alternative marker loci is central for population and epidemiological investigations. This issue was addressed using Staphylococcus aureus as a model population by generating nucleotide sequence data from 33 gene fragments in a representative sample of 30 strains. Supplementing the data with pre-existing multilocus sequence typing data, an intra-species tree based on ∼17·8 kb of sequence was reconstructed and the goodness of fit of each individual gene tree was computed. No strong association was noted between gene function per se and phylogenetic reliability, but it is suggested that candidate loci should possess at least the average degree of nucleotide diversity for all genes in the genome. In the case of S. aureus this threshold is >1 % mean pairwise diversity.

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Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

10.1101/201327 ◽

2017 ◽

Cited By ~ 1

Author(s):

Mario dos Reis ◽

Gregg F. Gunnell ◽

José Barba-Montoya ◽

Alex Wilkins ◽

Ziheng Yang ◽

...

Keyword(s):

Sequence Data ◽

Divergence Time ◽

Time Estimation ◽

Test Case ◽

Base Pairs ◽

Molecular Sequence Data ◽

Divergence Time Estimation ◽

Divergence Time Estimates ◽

Time Estimates ◽

Clock Models

AbstractPrimates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the K-Pg boundary and the timing of diversification of the main crown groups remain controversial. Here we analysed a dataset of 372 taxa (367 Primates and 5 outgroups, 61 thousand base pairs) that includes nine complete primate genomes (3.4 million base pairs). We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (auto-correlated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the auto-correlated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene.

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Phylogenetic relationships of the cuscuses (Diprotodontia : Phalangeridae) of island Southeast Asia and Melanesia based on the mitochondrial ND2 gene

Australian Mammalogy ◽

10.1071/am18050 ◽

2020 ◽

Vol 42 (3) ◽

pp. 266 ◽

Cited By ~ 1

Author(s):

Shimona Kealy ◽

Stephen C. Donnellan ◽

Kieren J. Mitchell ◽

Michael Herrera ◽

Ken Aplin ◽

...

Keyword(s):

Dna Sequences ◽

Divergence Time ◽

Taxonomic Status ◽

Wide Distribution ◽

Species Level ◽

Source Population ◽

Divergence Time Estimates ◽

Time Estimates ◽

Multiple Species ◽

Nd2 Gene

The species-level systematics of the marsupial family Phalangeridae, particularly Phalanger, are poorly understood, due partly to the family’s wide distribution across Australia, New Guinea, eastern Indonesia, and surrounding islands. In order to refine the species-level systematics of Phalangeridae, and improve our understanding of their evolution, we generated 36 mitochondrial ND2 DNA sequences from multiple species and sample localities. We combined our new data with available sequences and produced the most comprehensive molecular phylogeny for Phalangeridae to date. Our analyses (1) strongly support the monophyly of the three phalangerid subfamilies (Trichosurinae, Ailuropinae, Phalangerinae); (2) reveal the need to re-examine all specimens currently identified as ‘Phalanger orientalis’; and (3) suggest the elevation of the Solomon Island P. orientalis subspecies to species level (P. breviceps Thomas, 1888). In addition, samples of P. orientalis from Timor formed a clade, consistent with an introduction by humans from a single source population. However, further research on east Indonesian P. orientalis populations will be required to test this hypothesis, resolve inconsistencies in divergence time estimates, and locate the source population and taxonomic status of the Timor P. orientalis.

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