scholarly journals Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica

2021 ◽  
Author(s):  
Anne E. Thomas ◽  
Javier Igea ◽  
Heidi M. Meudt ◽  
Dirk C. Albach ◽  
William G. Lee ◽  
...  
Keyword(s):  
New Zealand ◽  
Target Sequence ◽  
Rapid Radiation ◽  
Sequence Capture ◽  
Phylogenetic Resolution

scholarly journals Target sequence capture in orchids: Developing a kit to sequence hundreds of single‐copy loci

2021 ◽  
Author(s):  
Lauren A. Eserman ◽  
Shawn K. Thomas ◽  
Emily E. D. Coffey ◽  
James H. Leebens‐Mack
Keyword(s):  
Single Copy ◽  
Target Sequence ◽  
Sequence Capture

scholarly journals A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

2021 ◽  
Author(s):  
William J. Baker ◽  
Paul Bailey ◽  
Vanessa Barber ◽  
Abigail Barker ◽  
Sidonie Bellot ◽  
...  
Keyword(s):  
Natural History ◽  
Flowering Plants ◽  
Tree Of Life ◽  
Flowering Plant ◽  
Target Sequence ◽  
Sequence Capture ◽  
Natural History Collections ◽  
Public Data ◽  
Data Release ◽  
Life On Earth

AbstractThe tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. This paper (i) documents our methods, (ii) describes our first data release and (iii) presents a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). Using the multi-species coalescent, we inferred a “first pass” angiosperm tree of life from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns. The tree is strongly supported and highly congruent with existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer. This major milestone towards a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardised nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections.

scholarly journals A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

2020 ◽  
Vol 10 ◽  
Author(s):  
Tobias Andermann ◽  
Maria Fernanda Torres Jiménez ◽  
Pável Matos-Maraví ◽  
Romina Batista ◽  
José L. Blanco-Pastor ◽  
...  
Keyword(s):  
Target Sequence ◽  
Sequence Capture

scholarly journals Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)

2021 ◽  
Author(s):  
Jonna Sofia Eriksson ◽  
Christine D. Bacon ◽  
Dominic J. Bennett ◽  
Bernard E. Pfeil ◽  
Bengt Oxelman ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Chromosome Numbers ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Single Copy ◽  
Target Sequence ◽  
Whole Genome ◽  
Genome Doubling ◽  
Sequence Capture ◽  
Duplication Events

Abstract Background: The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploidization. The genus Hibiscus L. (Malvaceae) has a wide diversity of chromosome numbers and a complex genomic history. Hibiscus is ideal for exploring past genomic events because although two ancient genome duplication events have been identified, more are likely to be found due to its diversity of chromosome numbers. To reappraise the history of whole-genome duplication events in Hibiscus, we tested three alternative scenarios describing different polyploidization events. Results: Using target sequence capture, we designed a new probe set for Hibiscus and generated 87 orthologous genes from four diploid species. We detected paralogues in >54% putative single-copy genes. 34 of these genes were selected for testing three different genome duplication scenarios using gene counting. All species of Hibiscus sampled shared one genome duplication with H. syriacus, and one whole genome duplication occurred along the branch leading to H. syriacus. Conclusions: Here, we corroborated the independent genome doubling previously found in the lineage leading to H. syriacus and a shared genome doubling of this lineage and the remainder of Hibiscus. Additionally, we found a previously undiscovered genome duplication shared by the /Pavonia and /Malvaviscus clades (both nested within Hibiscus) with the occurrences of two copies in what were otherwise single-copy genes. Our results highlight the complexity of genomic diversity in some plant groups, which makes orthology assessment and accurate phylogenomic inference difficult.

scholarly journals A guide to carrying out a phylogenomic target sequence capture project

2019 ◽  
Author(s):  
Tobias Andermann ◽  
Maria Fernanda Torres Jimenez ◽  
Pável Matos-Maraví ◽  
Romina Batista ◽  
José L Blanco-Pastor ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Cost Effective ◽  
Target Sequence ◽  
Sequence Capture ◽  
Large Sets ◽  
Phylogenetic Studies ◽  
Target Capture ◽  
Whole Genomes ◽  
High Throughput Dna Sequencing

High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing efforts on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing sequencing depth. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth and has proven to produce powerful, large multi-locus DNA sequence datasets of selected loci, suitable for phylogenetic analyses. However, target capture requires careful theoretical and practical considerations, which will greatly affect the success of the experiment. Here we provide an easy-to-follow flowchart for adequately designing phylogenomic target capture experiments, and we discuss necessary considerations and decisions from the first steps in the lab to the final bioinformatic processing of the sequence data. We particularly discuss issues and challenges related to the taxonomic scope, sample quality, and available genomic resources of target capture projects and how these issues affect all steps from bait design to the bioinformatic processing of the data. Altogether this review outlines a roadmap for future target capture experiments and is intended to assist researchers with making informed decisions for designing and carrying out successful phylogenetic target capture studies

scholarly journals The Origins of Coca: Museum Genomics Reveals Multiple Independent Domestications from Progenitor Erythroxylum gracilipes

2020 ◽  
Vol 70 (1) ◽  
pp. 1-13
Author(s):  
Dawson M White ◽  
Jen-Pan Huang ◽  
Orlando Adolfo Jara-Muñoz ◽  
Santiago MadriñáN ◽  
Richard H Ree ◽  
...  
Keyword(s):  
South America ◽  
Evolutionary History ◽  
Amazon Basin ◽  
Plant Domestication ◽  
Target Sequence ◽  
South American ◽  
Sequence Capture ◽  
Domestication Event ◽  
Geographic Origins ◽  
History Of

Abstract Coca is the natural source of cocaine as well as a sacred and medicinal plant farmed by South American Amerindians and mestizos. The coca crop comprises four closely related varieties classified into two species (Amazonian and Huánuco varieties within Erythroxylum coca Lam., and Colombian and Trujillo varieties within Erythroxylum novogranatense (D. Morris) Hieron.) but our understanding of the domestication and evolutionary history of these taxa is nominal. In this study, we use genomic data from natural history collections to estimate the geographic origins and genetic diversity of this economically and culturally important crop in the context of its wild relatives. Our phylogeographic analyses clearly demonstrate the four varieties of coca comprise two or three exclusive groups nested within the diverse lineages of the widespread, wild species Erythroxylum gracilipes; establishing a new and robust hypothesis of domestication wherein coca originated two or three times from this wild progenitor. The Colombian and Trujillo coca varieties are descended from a single, ancient domestication event in northwestern South America. Huánuco coca was domesticated more recently, possibly in southeastern Peru. Amazonian coca either shares a common domesticated ancestor with Huánuco coca, or it was the product of a third and most recent independent domestication event in the western Amazon basin. This chronology of coca domestication reveals different Holocene peoples in South America were able to independently transform the same natural resource to serve their needs; in this case, a workaday stimulant. [Erythroxylum; Erythroxylaceae; Holocene; Museomics; Neotropics; phylogeography; plant domestication; target-sequence capture.]

scholarly journals Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture

2019 ◽  
Vol 69 (3) ◽  
pp. 479-501 ◽  
Author(s):  
Michael R McGowen ◽  
Georgia Tsagkogeorga ◽  
Sandra Álvarez-Carretero ◽  
Mario dos Reis ◽  
Monika Struebig ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
High Throughput Sequencing ◽  
Complete Data ◽  
Divergence Times ◽  
Comparative Genomic ◽  
Target Sequence ◽  
Data Set ◽  
Sequence Capture ◽  
Combining Data ◽  
Beaked Whales

Abstract The evolution of cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, although the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for $\sim $3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from $>$38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic data set for cetaceans, spanning 6,527,596 aligned base pairs (bp) and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among oceanic dolphins, especially the problematic subfamily Delphinidae. We carried out Bayesian estimation of species divergence times using MCMCTree and compared our complete data set to a subset of clocklike genes. Analyses using the complete data set consistently showed less variance in divergence times than the reduced data set. In addition, integration of new fossils (e.g., Mystacodon selenensis) indicates that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene. [Cetaceans; phylogenomics; Delphinidae; Ziphiidae; dolphins; whales.]

Maamingidae, a new family of proctotrupoid wasp (Insecta : Hymenoptera) from New Zealand

2001 ◽  
Vol 15 (3) ◽  
pp. 341 ◽  
Author(s):  
J. W. Early ◽  
L. Masner ◽  
I. D. Naumann ◽  
A. D. Austin
Keyword(s):  
New Zealand ◽  
Wing Size ◽  
The North ◽  
New Family ◽  
Molecular Phylogenetic ◽  
Phylogenetic Resolution ◽  
Phylogenetic Hypotheses

The new family Maamingidae is proposed for Maaminga, gen. nov., comprising two species, M. rangi, sp. nov. and M. marrisi, sp. nov., from New Zealand. The delicate and slender M. rangi, sp. nov. is common in forest, particularly kauri forests of the northern part of the North Island. The more robust and stocky M. marrisi, sp. nov., which is polymorphic for wing size (brachyterous and fully winged), appears to be associated with coastal scrub and forest, particularly on offshore islands, but is also found in alpine snow tussock. Maamingidae is nominally placed within the Proctotrupoidea, and is probably related to the Diapriidae and Monomachidae. However, its relationships are unclear, at least in part due to the lack of phylogenetic resolution among the proctotrupoid families and other Proctotrupomorpha sensu Rasnitsyn. The relationships of Maamingidae are briefly discussed in the light of current morphological and molecular phylogenetic hypotheses.

Sign in / Sign up

Export Citation Format

Share Document