ipyrad: Interactive assembly and analysis of RADseq datasets

Bioinformatics, Journal Year: 2019, Volume and Issue: 36(8), P. 2592 - 2594

Published: Dec. 31, 2019

Abstract Summary ipyrad is a free and open source tool for assembling analyzing restriction site-associated DNA sequence datasets using de novo and/or reference-based approaches. It designed to be massively scalable hundreds of taxa thousands samples, can efficiently parallelized on high performance computing clusters. available both as command line interface Python package with an application programming interface, the latter which used interactively write complex, reproducible scripts implement suite downstream analysis tools. Availability implementation program written in Python. Source code from GitHub repository (https://github.com/dereneaton/ipyrad/), Linux MacOS installs are distributed through conda manager. Complete documentation, including numerous tutorials, Jupyter notebooks demonstrating example assemblies applications tools online: https://ipyrad.readthedocs.io/.

Language: Английский

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How genomics can help biodiversity conservation

Trends in Genetics, Journal Year: 2023, Volume and Issue: 39(7), P. 545 - 559

Published: Feb. 16, 2023

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches applications in conservation genomics, considering practical factors, such as cost, time, prerequisite skills, current shortcomings applications. Most perform best combination with reference genomes from target species or closely related species. We review case studies to illustrate how facilitate research across tree life. conclude that time is ripe view fundamental integrate their use a practice genomics.

Language: Английский

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Complementary combination of multiplex high‐throughput DNA sequencing for molecular phylogeny

Ecological Research, Journal Year: 2021, Volume and Issue: 37(1), P. 171 - 181

Published: Oct. 7, 2021

Abstract The rapid development of DNA sequencing technology in recent years has provided new tools for phylogenetic data acquisition. By using high‐throughput technology, molecular information can be obtained more quickly and economically. Here, we describe a complementary combination two multiplex methods. One is multiplexed marker (MPM‐seq), the other inter‐simple sequence repeat (ISSR) genotyping by (MIG‐seq), whose protocol improved over that original one. Both MPM‐seq MIG‐seq begin with polymerase chain reaction (PCR), each amplifying multiple markers genome‐wide ISSR regions, respectively. After another PCR second primer set common both methods, next‐generation used to simultaneously detect sequences regions from samples method. In this case study, performed analysis Japanese fir ( Abies ) closely related species. revealed three chloroplast one nuclear internal transcribed spacer created partially informative tree 13 Whereas detected 6700 single‐nucleotide polymorphisms exhibited clear clustering species 97%–100% bootstrap support all branches tree. Hence, combination, quick, simple, economical wide range genomic studies, including phylogeny, as well investigating genetic differentiation or identification among species, hybrids, populations, even clones cultivars, barcoding technique.

Language: Английский

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The Silene latifolia genome and its giant Y chromosome

Science, Journal Year: 2025, Volume and Issue: 387(6734), P. 630 - 636

Published: Feb. 6, 2025

In many species with sex chromosomes, the Y is a tiny chromosome. However, dioecious plant Silene latifolia has giant ~550-megabase chromosome, which remained unsequenced so far. We used long- and short-read hybrid approach to obtain high-quality male genome. Comparative analysis of chromosomes their homologs in outgroups showed that highly rearranged degenerated. Recombination suppression between X extended several steps triggered massive accumulation repeats on as well nonrecombining pericentromeric region X, leading chromosomes. Using phenotype mutants, we identified candidate sex-determining genes locations consistent favoring recombination events 11 5 million years ago.

Language: Английский

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Bridgehead effect and multiple introductions shape the global invasion history of a termite

Communications Biology, Journal Year: 2021, Volume and Issue: 4(1)

Published: Feb. 12, 2021

Abstract Native to eastern Asia, the Formosan subterranean termite Coptotermes formosanus (Shiraki) is recognized as one of 100 worst invasive pests in world, with established populations Japan, Hawaii and southeastern United States. Despite its importance, native source(s) C. introductions their pathway out Asia remain elusive. Using ~22,000 SNPs, we retraced invasion history this species through approximate Bayesian computation assessed consequences on genetic patterns demography. We show a complex history, where an initial introduction resulted from two distinct events Hong Kong region. The admixed Hawaiian population subsequently served source, bridgehead, for US. A separate event southcentral China occurred Florida showing admixture first introduction. Overall, these findings further reinforce pivotal role bridgeheads shaping distributions Anthropocene illustrate that global distribution has been shaped by multiple China, which may have prevented possibly reversed loss diversity within range.

Language: Английский

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Speciation in the deep: genomics and morphology reveal a new species of beaked whaleMesoplodon eueu

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2021, Volume and Issue: 288(1961)

Published: Oct. 27, 2021

The deep sea has been described as the last major ecological frontier, much of its biodiversity is yet to be discovered and described. Beaked whales (ziphiids) are among most visible inhabitants sea, due their large size worldwide distribution, taxonomic diversity about natural history remain poorly understood. We combine genomic morphometric analyses reveal a new Southern Hemisphere ziphiid species, Ramari's beaked whale, Mesoplodon eueu , whose name linked Indigenous peoples lands from which species holotype paratypes were recovered. Mitogenome ddRAD-derived phylogenies demonstrate reciprocally monophyletic divergence between M. True's whale ( mirus ) North Atlantic, with it was previously subsumed. Morphometric skulls also distinguish two species. A time-calibrated mitogenome phylogeny analysis nuclear genomes indicate began circa 2 million years ago (Ma), geneflow ceasing 0.35–0.55 Ma. This an example how can unravelled through increasing international collaboration genome sequencing archival specimens. Our consultation involvement offers model for broadening cultural scope scientific naming process.

Language: Английский

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Commonly used Hardy–Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 22(7), P. 2599 - 2613

Published: May 20, 2022

Reduced representation sequencing (RRS) is a widely used method to assay the diversity of genetic loci across genome an organism. The dominant class RRS approaches associated with restriction sites within (restriction site DNA sequencing, or RADseq). RADseq frequently applied non-model organisms since it enables population studies without relying on well-characterized reference genomes. However, requires use many bioinformatic filters ensure quality genotyping calls. These can have direct impacts inference, and therefore require careful consideration. One filtering approach removal that do not conform expectations Hardy-Weinberg equilibrium (HWE). Despite being used, we show this rarely described in sufficient detail enable replication. Furthermore, through analyses silico empirical data sets some most HWE dramatically impact inference structure. In particular, exhibiting departures from after pooling samples significantly reduces degree inferred structure set (despite used). Based these results, provide recommendations for best practice regarding implementation sets.

Language: Английский

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Southern Hemisphere coasts are biologically connected by frequent, long-distance rafting events

Current Biology, Journal Year: 2022, Volume and Issue: 32(14), P. 3154 - 3160.e3

Published: June 8, 2022

Language: Английский

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snpfiltr: An R package for interactive and reproducible SNP filtering

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 22(6), P. 2443 - 2453

Published: April 10, 2022

Here, I describe the R package snpfiltr and demonstrate its functionality as backbone of a customizable, reproducible single nucleotide polymorphism (SNP) filtering pipeline implemented exclusively via widely adopted programming language. SNPfiltR extends existing SNP functionalities by automating visualization key parameters such sequencing depth, quality, missing data proportion, allowing users to visually optimize implement thresholds within single, cohesive work session. All functions require vcfr objects input, which can be easily generated reading set stored in standard variant call format (vcf) into an working environment using function read.vcfR() from vcfr. Performance accuracy benchmarking reveal that for moderately sized sets (up 50 M genotypes, plus associated quality information), performs with comparable efficiency current state art command-line-based programs. These results indicate most reduced-representation genomic sets, is ideal choice investigating, visualizing, SNPs part user friendly bioinformatic pipeline. The downloaded CRAN command install.packages("snpfiltr"), development version available GitHub at: (github.com/DevonDeRaad/SNPfiltR). Thorough documentation SNPfiltR, including multiple comprehensive vignettes detailing realistic use-cases, at website: devonderaad.github.io/SNPfiltR/.

Language: Английский

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An ecologist's guide for studying DNA methylation variation in wild vertebrates

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 23(7), P. 1488 - 1508

Published: April 25, 2022

Abstract The field of molecular biology is advancing fast with new powerful technologies, sequencing methods and analysis software being developed constantly. Commonly used tools originally for research on humans model species are now regularly in ecological evolutionary research. There also a growing interest the causes consequences epigenetic variation natural populations. Studying epigenetics currently challenging, especially vertebrate systems, because required technical expertise, complications analyses interpretation, limitations acquiring sufficiently high sample sizes. Importantly, neglecting experimental setup, technology may affect reliability reproducibility, extent to which unbiased conclusions can be drawn from these studies. Here, we provide practical guide researchers aiming study DNA methylation wild vertebrates. We review aspects research, concentrating using bisulfite sequencing, discuss possible pitfalls, how overcome them through rigid reproducible data analysis. This provides solid foundation proper design studies, clear roadmap best practices correct realistic view studying will help implications

Language: Английский

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