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Predicting sample success for large‐scale ancient DNA studies on marine mammals Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-19 Xénia Keighley; Maiken Hemme Bro‐Jørgensen; Hans Ahlgren; Paul Szpak; Marta Maria Ciucani; Fátima Sánchez Barreiro; Lesley Howse; Anne Birgitte Gotfredsen; Aikaterini Glykou; Peter Jordan; Kerstin Lidén; Morten Tange Olsen
In recent years, nonhuman ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful
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Complex genetic admixture histories reconstructed with Approximate Bayesian Computation Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-16 Cesar A. Fortes‐Lima; Romain Laurent; Valentin Thouzeau; Bruno Toupance; Paul Verdu
Admixture is a fundamental evolutionary process that has influenced genetic patterns in numerous species. Maximum‐likelihood approaches based on allele frequencies and linkage‐disequilibrium have been extensively used to infer admixture processes from genome‐wide data sets, mostly in human populations. Nevertheless, complex admixture histories, beyond one or two pulses of admixture, remain methodologically
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Assessing genome assembly quality prior to downstream analysis: N50 versus BUSCO Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-24 April A. Jauhal; Richard D. Newcomb
With the ever‐increasing number of publicly available eukaryotic genome assemblies and user‐friendly bioinformatics tools, there are increasing opportunities for researchers to use genomic resources in their research. While there are multiple dimensions to genome quality, it is often reduced to a single score that may not be correlated with other metrics, or appropriate for all applications of an assembly
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A chromosome‐level genome of the mud crab (Scylla paramamosain estampador) provides insights into the evolution of chemical and light perception in this crustacean Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-19 Ming Zhao; Wei Wang; Fengying Zhang; Chunyan Ma; Zhiqiang Liu; Meidi‐Huang Yang; Wei Chen; Qingsong Li; Mingshu Cui; Keji Jiang; Chunlei Feng; Jiong Tang Li; Lingbo Ma
Mud crabs, found throughout the Indo‐Pacific region, are coastal species that are important fisheries resources in many tropical and subtropical Asian countries. Here, we present a chromosome‐level genome assembly of a mud crab (Scylla paramamosain). The genome is 1.55 Gb (contig N50 191 kb) in length and encodes 17,821 proteins. The heterozygosity of the assembled genome was estimated to be 0.47%
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Chromosome‐level genome of Poropuntius huangchuchieni provides a diploid progenitor‐like reference genome for the allotetraploid Cyprinus carpio Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-23 Lin Chen; Bijun Li; Baohua Chen; Chengyu Li; Zhixiong Zhou; Tao Zhou; Weidi Yang; Peng Xu
The diploid Poropuntius huangchuchieni in the cyprinid family, which is widely distributed in the Mekong and Red River basins, is one of the most closely related diploid progenitor‐like species of allotetraploid common carp, which was generated by merging of two diploid genomes during evolution. Therefore, the P. huangchuchieni genome is essential for polyploid evolution studies in Cyprinidae. Here
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Corrigendum Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-24
In the article entitled “New approaches to species delimitation and population structure of anthozoans: Two case studies of octocorals using ultraconserved elements and exons” which was published in Molecular Ecology Resources (volume 21, Issue 1, pages 78–92), the authors noticed an error in the GenBank accession numbers which are listed in the ‘Data Availability Statement’ section. The correct GenBank
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Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-27 Carmelo Andújar; Thomas J. Creedy; Paula Arribas; Heriberto López; Antonia Salces‐Castellano; Antonio José Pérez‐Delgado; Alfried P. Vogler; Brent C. Emerson
Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co‐amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence variants (ASVs). However, these procedures do not fully
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Genomic analysis of Medicago ruthenica provides insights into its tolerance to abiotic stress and demographic history Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-21 Mou Yin; Shangzhe Zhang; Xin Du; Rubén G. Mateo; Wei Guo; Ao Li; Zhenyue Wang; Shuang Wu; Jinyuan Chen; Jianquan Liu; Guangpeng Ren
Medicago ruthenica has been recently cultivated as a new forage crop and has been recognized as a source of genes to improve abiotic stress tolerance in cultivated alfalfa because of its remarkable tolerance to drought, salinity‐alkalinity, and cold and snowy winters. Here, we reveal a chromosome‐scale genome sequence of M. ruthenica based on Illumina, PacBio, and Hi‐C data. The assembled genome consists
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Two different approaches of microbial community structure characterization in riverine epilithic biofilms under multiple stressors conditions: Developing molecular indicators Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-02 Lorenzo Pin; Alexander Eiler; Stefano Fazi; Nikolai Friberg
Microbial communities are major players in the biogeochemical processes and ecosystem functioning of river networks. Despite their importance in the ecosystem, biomonitoring tools relying on prokaryotes are still lacking. Only a few studies have employed both metabarcoding and quantitative techniques such as catalysed reported deposition fluorescence in situ hybridization (CARD‐FISH) to analyse prokaryotic
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Genome insights give cause for optimism in the ongoing battle to save the vaquita Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-04 Annabel Whibley
Whilst the global threat to biodiversity is accelerating, recent advances in sequencing and assembly technologies, along with decreasing costs, are ushering in a golden age for biodiversity genomics. In a From the Cover article in this issue of Molecular Ecology Resources, Morin et al. report an exceptionally high‐quality draft genome assembly of the vaquita (Phocoena sinus), a porpoise first described
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Chromosome‐scale assembly of the genome of Salix dunnii reveals a male‐heterogametic sex determination system on chromosome 7 Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-20 Li He; Kai‐Hua Jia; Ren‐Gang Zhang; Yuan Wang; Tian‐Le Shi; Zhi‐Chao Li; Si‐Wen Zeng; Xin‐Jie Cai; Natascha Dorothea Wagner; Elvira Hörandl; Aline Muyle; Ke Yang; Deborah Charlesworth; Jian‐Feng Mao
Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads, and Hi‐C reads to assemble the first chromosome‐scale genome of a female willow tree (Salix dunnii), and to predict genes using transcriptome sequences and available databases. The final genome sequence of 328
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SambaR: An R package for fast, easy and reproducible population‐genetic analyses of biallelic SNP data sets Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-27 Menno J. de Jong; Joost F. de Jong; A. Rus Hoelzel; Axel Janke
SNP data sets can be used to infer a wealth of information about natural populations, including information about their structure, genetic diversity, and the presence of loci under selection. However, SNP data analysis can be a time‐consuming and challenging process, not in the least because at present many different software packages are needed to execute and depict the wide variety of mainstream
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The influence of intraspecific sequence variation during DNA metabarcoding: A case study of eleven fungal species Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-18 Eva Lena F. Estensmo; Sundy Maurice; Luis Morgado; Pedro M. Martin‐Sanchez; Inger Skrede; Håvard Kauserud
DNA metabarcoding has become a powerful approach for analysing complex communities from environmental samples, but there are still methodological challenges limiting its full potential. While conserved DNA markers, like 16S and 18S, often are not able to discriminate among closely related species, other more variable markers – like the fungal ITS region, may include considerable intraspecific variation
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Modern, archaeological, and paleontological DNA analysis of a human‐harvested marine gastropod (Strombus pugilis) from Caribbean Panama Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-17 Alexis P. Sullivan; Stephanie Marciniak; Aaron O’Dea; Thomas A. Wake; George H. Perry
Although protocols exist for the recovery of ancient DNA from land snail and marine bivalve shells, marine conch shells have yet to be studied from a paleogenomic perspective. We first present reference assemblies for both a 623.7 Mbp nuclear genome and a 15.4 kbp mitochondrial genome for Strombus pugilis, the West Indian fighting conch. We next detail a method to extract and sequence DNA from conch
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TaxonTableTools ‐ A comprehensive, platform‐independent graphical user interface software to explore and visualise DNA metabarcoding data Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-16 Till‐Hendrik Macher; Arne J. Beermann; Florian Leese
DNA metabarcoding is increasingly used as a tool to assess biodiversity in research and environmental management. Powerful analysis software exists to process raw data. However, the translation of sequence read data into biological information and downstream analyses may be difficult for end users with limited expertise in bioinformatics. Thus, there is a growing need for easy‐to‐use, graphical user
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RADSex: a computational workflow to study sex determination using Restriction Site‐Associated DNA Sequencing data Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-16 Romain Feron; Qiaowei Pan; Ming Wen; Boudjema Imarazene; Elodie Jouanno; Jennifer Anderson; Amaury Herpin; Laurent Journot; Hugues Parrinello; Christophe Klopp; Verena A. Kottler; Alvaro S. Roco; Kang Du; Susanne Kneitz; Mateus Adolfi; Catherine A. Wilson; Braedan McCluskey; Angel Amores; Thomas Desvignes; Frederick W. Goetz; Ato Takanashi; Mari Kawaguchi; H. William Detrich; Marcos Oliveira; Rafael
The study of sex determination and sex chromosome organisation in non‐model species has long been technically challenging, but new sequencing methodologies now enable precise and high‐throughput identification of sex‐specific genomic sequences. In particular, Restriction Site‐Associated DNA Sequencing (RAD‐Seq) is being extensively applied to explore sex determination systems in many plant and animal
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Novel genotyping approaches to easily detect genomic admixture between the major Afrotropical malaria vector species, Anopheles coluzzii and An. gambiae Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-15 Beniamino Caputo; Verena Pichler; Giordano Bottà; Carlo De Marco; Christina Hubbart; Eleonora Perugini; Joao Pinto; Kirk A. Rockett; Alistair Miles; Alessandra della Torre
The two most efficient and most recently radiated Afrotropical vectors of human malaria ‐ Anopheles coluzzii and An. gambiae – are identified by single‐locus diagnostic PCR assays based on species‐specific markers in a 4 Mb region on chromosome‐X centromere. Inherently, these diagnostic assays cannot detect interspecific autosomal admixture shown to be extensive at the westernmost and easternmost extremes
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Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-12-15 Luise Schulte; Nadine Bernhardt; Kathleen Stoof‐Leichsenring; Heike H. Zimmermann; Luidmila A. Pestryakova; Laura S. Epp; Ulrike Herzschuh
Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional
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Chromosome‐level assembly of the brown planthopper genome with a characterized Y chromosome Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-18 Yu‐Xuan Ye; Hou‐Hong Zhang; Dan‐Ting Li; Ji‐Chong Zhuo; Yan Shen; Qing‐Ling Hu; Chuan‐Xi Zhang
Hundreds of insect genome sequences have been reported; however, most sequencing projects have not determined the sex chromosomes, and no Y chromosomes from a heterometabolous insect have been identified and characterized to date. The brown planthopper (Nilaparvata lugens Stål) is the most economically damaging pest to rice and is also an ideal research subject for paddy ecology and functional genomics
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A multitiered sequence capture strategy spanning broad evolutionary scales: Application for phylogenetic and phylogeographic studies of orchids Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-16 Rod Peakall; Darren C. J. Wong; Ryan D. Phillips; Monica Ruibal; Rodney Eyles; Claudia Rodriguez‐Delgado; Celeste C. Linde
With over 25,000 species, the drivers of diversity in the Orchidaceae remain to be fully understood. Here, we outline a multitiered sequence capture strategy aimed at capturing hundreds of loci to enable phylogenetic resolution from subtribe to subspecific levels in orchids of the tribe Diurideae. For the probe design, we mined subsets of 18 transcriptomes, to give five target sequence sets aimed at
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New model species for arctic‐alpine plant molecular ecology Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-27 Tanja Pyhäjärvi; Tiina M. Mattila
Arctic and alpine, high latitude and high elevation environments are one of the most stressful environments for species to inhabit. This harshness manifests itself in lower species richness in comparison to more southern vegetation zones (Francis & Currie, 2003). Furthermore, the climatic oscillations—past and predicted—have the most dramatic effect on these ecosystems. For example, in regions of continental
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A chromosome‐level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth‐associated genes Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-15 Tanaporn Uengwetwanit; Wirulda Pootakham; Intawat Nookaew; Chutima Sonthirod; Pacharaporn Angthong; Kanchana Sittikankaew; Wanilada Rungrassamee; Sopacha Arayamethakorn; Thidathip Wongsurawat; Piroon Jenjaroenpun; Duangjai Sangsrakru; Rungnapa Leelatanawit; Jutatip Khudet; Jasper J. Koehorst; Peter J. Schaap; Vitor Martins dos Santos; Frédéric Tangy; Nitsara Karoonuthaisiri
To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained from available genome sequence of marine organisms has accelerated marine aquaculture in many cases. The black tiger shrimp (Penaeus monodon) is one of the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production of half a
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eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA (eDNA) sequences exploiting Nextflow and Singularity Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-13 Mahsa Mousavi‐Derazmahalleh; Audrey Stott; Rose Lines; Georgia Peverley; Georgia Nester; Tiffany Simpson; Michal Zawierta; Marco De La Pierre; Michael Bunce; Claus T. Christophersen
Metabarcoding of Environmental DNA (eDNA) when coupled with high throughput sequencing is revolutionising the way biodiversity can be monitored across a wide range of applications. However, the large number of tools deployed in downstream bioinformatic analyses often places a challenge in configuration and maintenance of a workflow, and consequently limits the research reproducibility. Furthermore
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Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta‐analyses Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-12 Toshiaki Jo; Toshifumi Minamoto
Understanding the processes of environmental DNA (eDNA) persistence and degradation is essential to determine the spatiotemporal scale of eDNA signals and accurately estimate species distribution. The effects of environmental factors on eDNA persistence have previously been examined; however, the influence of the physiochemical and molecular states of eDNA on its persistence is not completely understood
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A chromosome‐level assembly of the harlequin ladybird Harmonia axyridis as a genomic resource to study beetle and invasion biology Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-02 Mengyao Chen; Yang Mei; Xu Chen; Xi Chen; Da Xiao; Kang He; Qiang Li; Mengmeng Wu; Su Wang; Fan Zhang; Fei Li
The harlequin ladybird, Harmonia axyridis (Pallas), is a well‐known model organism for genetic studies and is also a well‐studied natural enemy used for pest control. It became an invasive species after being introduced to North America and Europe as a pest control agent. Though two genome assemblies for this insect have been previously reported, a high‐quality genome assembly at the chromosome level
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User‐friendly bioinformatics pipeline gDAT (graphical downstream analysis tool) for analysing rDNA sequences Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-01 Martti Vasar; John Davison; Lena Neuenkamp; Siim‐Kaarel Sepp; J. Peter W. Young; Mari Moora; Maarja Öpik
High‐throughput sequencing (HTS) of multiple organisms in parallel (metabarcoding) has become a routine and cost‐effective method for the analysis of microbial communities in environmental samples. However, careful data treatment is required to identify potential errors in HTS data, and the large volume of data generated by HTS requires in‐house experience with command line tools for downstream analysis
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Chromosome‐level reference genome of the soursop (Annona muricata): a new resource for Magnoliid research and tropical pomology Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-11 Joeri S. Strijk; Damien D. Hinsinger; Mareike M. Roeder; Lars W. Chatrou; Thomas L.P. Couvreur; Roy H.J. Erkens; Hervé Sauquet; Michael D. Pirie; Daniel C. Thomas; Kunfang Cao
The flowering plant family Annonaceae includes important commercially grown tropical crops, but development of promising species is hindered by a lack of genomic resources to build breeding programs. Annonaceae are part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades remain unclear. To provide resources to breeders and evolutionary researchers
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Factors affecting the efficiency of molecular species delimitation in a species‐rich insect family Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-10 Giulia Magoga; Diego Fontaneto; Matteo Montagna
In the contest of global biodiversity loss, molecular species delimitation approaches can be very useful for accelerating species discovery through DNA taxonomy and inventory through DNA metabarcoding. In this study, the effect of some intrinsic factors on the efficiency of various single‐marker species delimitation methods (fixed and variable nucleotide distance thresholds, ABGD, ASAP, GMYC, mPTP)
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Regarding the F‐word: the effects of data Filtering on inferred genotype‐environment associations Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-10 Collin W Ahrens; Rebecca Jordan; Jason Bragg; Peter A Harrison; Tara Hopley; Helen Bothwell; Kevin Murray; Dorothy A Steane; John W Whale; Margaret Byrne; Rose Andrew; Paul D. Rymer
Genotype‐environment association (GEA) methods have become part of the standard landscape genomics toolkit, yet, we know little about how to best filter genotype‐by‐sequencing data to provide robust inferences for environmental adaptation. In many cases, default filtering thresholds for minor allele frequency and missing data are applied regardless of sample size, having unknown impacts on the results
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The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles (Terrapene spp.) Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-10 Bradley T. Martin; Tyler K. Chafin; Marlis R. Douglas; John S. Placyk; Roger D. Birkhead; Christopher A. Phillips; Michael E. Douglas
Model‐based approaches that attempt to delimit species are hampered by computational limitations as well as the unfortunate tendency by users to disregard algorithmic assumptions. Alternatives are clearly needed, and machine‐learning (M‐L) is attractive in this regard as it functions without the need to explicitly define a species concept. Unfortunately, its performance will vary according to which
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The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-12 Caroline Vernette; Nicolas Henry; Julien Lecubin; Colomban de Vargas; Pascal Hingamp; Magali Lescot
The Ocean Barcode Atlas (OBA) is a user friendly web service designed for biologists who wish to explore the biodiversity and biogeography of marine organisms locked in otherwise difficult to mine planetary scale DNA metabarcode data sets. Using just a web browser, a comprehensive picture of the diversity of a taxon or a barcode sequence is visualized graphically on world maps and interactive charts
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Not just a pathogen: the importance of recognizing genetic variability to mitigate a wildlife pandemic. Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-09 Claudio Azat
Emerging infectious diseases (EIDs) are increasingly recognized as a threat to both biodiversity and human health (Scheele et al., 2019; Wells et al., 2020). But pathogens cannot been seen as unique entities; their intra‐specific genetic variability represented in variants, strains, antigenic types or genetic lineages may cause different impacts at the population level (Nelson & Holmes, 2007; Greenspan
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Pairwise Linkage Disequilibrium Estimation for Polyploids Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-08 David Gerard
Many tasks in statistical genetics involve pairwise estimation of linkage disequilibrium (LD). The study of LD in diploids is mature. However, in polyploids, the field lacks a comprehend sive characterization of LD. Polyploids also exhibit greater levels of genotype uncertainty than diploids, and yet no methods currently exist to estimate LD in polyploids in the presence of such genotype uncertainty
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Model‐based genotype and ancestry estimation for potential hybrids with mixed‐ploidy Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-22 Vivaswat Shastry; Paula E. Adams; Dorothea Lindtke; Elizabeth G. Mandeville; Thomas L. Parchman; Zachariah Gompert; C. Alex Buerkle
Non‐random mating among individuals can lead to spatial clustering of genetically similar individuals and population stratification. This deviation from panmixia is commonly observed in natural populations. Consequently, individuals can have parentage in single populations or involving hybridization between differentiated populations. Accounting for this mixture and structure is important when mapping
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A chromosome‐level genome assembly for the tertiary relict plant Tetracentron sinense oliv. (trochodendraceae) Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-23 Minjie Li; Yongzhi Yang; Renping Xu; Wenjie Mu; Ying Li; Xingxing Mao; Zeyu Zheng; Hao Bi; Guoqian Hao; Xiaojie Li; Xiaoting Xu; Zhenxiang Xi; Nawal Shrestha; Jianquan Liu
Tetracentron sinense and Trochodendron aralioides are two Tertiary relict species of large trees in the family Trochodendraceae with narrow distributions on the mainland and islands of eastern Asia. They belong to the order Trochodendrales, which is one of the four early‐diverged eudicot lineages. These two relict species provide a good system in which to examine genomic changes that occurred as they
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A reference‐free approach to analyse RADseq data using standard next generation sequencing toolkits Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-12 Rasmus Heller; Casia Nursyifa; Genís Garcia‐Erill; Jordi Salmona; Lounes Chikhi; Jonas Meisner; Thorfinn Sand Korneliussen; Anders Albrechtsen
Genotyping‐by‐sequencing methods such as RADseq are popular for generating genomic and population‐scale data sets from a diverse range of organisms. These often lack a usable reference genome, restricting users to RADseq specific software for processing. However, these come with limitations compared to generic next generation sequencing (NGS) toolkits. Here, we describe and test a simple pipeline for
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A large genome with chromosome‐scale assembly sheds light on the evolutionary success of a true toad (Bufo gargarizans) Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-11 Bin Lu; Jianping Jiang; Hua Wu; Xiaohong Chen; Xiaowei Song; Wenbo Liao; Jinzhong Fu
We present a high‐quality genome assembly for the Asiatic toad (Bufo gargarizans) and explore the evolution of several large gene families in amphibians. With a large genome assembly size of 4.55 Gb, the chromosome‐scale assembly includes 747 scaffolds with an N50 of 539.8 Mb and 1.79% gaps. Long terminal repeats (LTRs) constitute a high proportion of the genome and their expansion is a key contributor
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Chromosome‐level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi‐C sequencing technologies Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-07 Dongna Ma; Zejun Guo; Qiansu Ding; Zhizhu Zhao; Zhijun Shen; Mingyue Wei; Changhao Gao; Ludan Zhang; Huan Li; Shan Zhang; Jing Li; Xueyi Zhu; Hai‐Lei Zheng
Aegiceras corniculatum is a major mangrove plant species adapted to waterlogging and saline conditions, grows in the coastal intertidal zone of tropical and subtropical regions. Here, we present a chromosome‐level genome assembly of A. corniculatum by incorporating PacBio long‐read sequencing and Hi‐C technology. The results showed that the PacBio draft genome size is 906.63 Mb. Hi‐C scaffolding anchored
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pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-16 Katharine L. Korunes; Kieran Samuk
Population genetic analyses often use summary statistics to describe patterns of genetic variation and provide insight into evolutionary processes. Among the most fundamental of these summary statistics are π and dXY, which are used to describe genetic diversity within and between populations, respectively. Here, we address a widespread issue in π and dXY calculation: systematic bias generated by missing
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Benchmarking the performance of Pool‐seq SNP callers using simulated and real sequencing data Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-03 Sara Guirao‐Rico; Josefa González
Population genomics is a fast‐developing discipline with promising applications in a growing number of life sciences fields. Advances in sequencing technologies and bioinformatics tools allow population genomics to exploit genome‐wide information to identify the molecular variants underlying traits of interest and the evolutionary forces that modulate these variants through space and time. However
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Panoramic: A package for constructing eukaryotic pan‐genomes Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-03 Lior Glick; Itay Mayrose
The study of intraspecific genomic variation in eukaryotic species has been the focus of numerous genome resequencing projects in recent years. One emerging approach for the analysis of intraspecific diversity uses the concept of a pan‐genome, which theoretically represents the full set of genomic sequences and coding genes from all individuals of a given species. This approach has many advantages
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A high‐quality genome assembly of the eggplant provides insights into the molecular basis of disease resistance and chlorogenic acid synthesis Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-14 Dandan Li; Jun Qian; Weiliu Li; Ning Yu; Guiyun Gan; Yaqin Jiang; Wenjia Li; Xuyu Liang; Riyuan Chen; Yongcheng Mo; Jinmin Lian; Yongchao Niu; Yikui Wang
The eggplant (Solanum melongena L.) is one of the most important Solanaceae crops, ranking third for total production and economic value in its genus. Herein, we report a high‐quality, chromosome‐scale eggplant reference genome sequence of 1155.8 Mb, with an N50 of 93.9 Mb, which was assembled by combining PacBio long reads and Hi‐C sequencing data. Repetitive sequences occupied 70.1% of the assembly
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DILS: Demographic inferences with linked selection by using ABC Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-15 Christelle Fraïsse; Iva Popovic; Clément Mazoyer; Bruno Spataro; Stéphane Delmotte; Jonathan Romiguier; Étienne Loire; Alexis Simon; Nicolas Galtier; Laurent Duret; Nicolas Bierne; Xavier Vekemans; Camille Roux
We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single‐population or two‐population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model
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Elucidating shark diets with DNA metabarcoding from cloacal swabs Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-02-02 Maurits P. M. van Zinnicq Bergmann; Bautisse D. Postaire; Kirk Gastrich; Michael R. Heithaus; Lisa A. Hoopes; Kady Lyons; Yannis P. Papastamatiou; Eric V. C. Schneider; Bradley A. Strickland; Brendan S. Talwar; Demian D. Chapman; Judith Bakker
Animal dietary information provides the foundation for understanding trophic relationships, which is essential for ecosystem management. Yet, in marine systems, high‐resolution diet reconstruction tools are currently under‐developed. This is particularly pertinent for large marine vertebrates, for which direct foraging behaviour is difficult or impossible to observe and, due to their conservation status
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Genotype by sequencing: An alternative new method to amplicon metabarcoding and shotgun metagenomics for the assessment of eukaryote biodiversity Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-10 Josep Piñol
The use of high‐throughput DNA sequencing (HTS) has revolutionized the assessment of biodiversity in plant and animal communities. There are two main approaches to estimate the identity and the relative species abundance (RSA) in complex mixtures using HTS: amplicon metabarcoding and shotgun metagenomics. While amplicon metabarcoding targets one or a few genomic regions, shotgun metagenomics randomly
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Analysing landscape effects on dispersal networks and gene flow with genetic graphs Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-18 Paul Savary; Jean‐Christophe Foltête; Hervé Moal; Gilles Vuidel; Stéphane Garnier
Graph‐theoretic approaches have relevant applications in landscape genetic analyses. When species form populations in discrete habitat patches, genetic graphs can be used (a) to identify direct dispersal paths followed by propagules or (b) to quantify landscape effects on multi‐generational gene flow. However, the influence of their construction parameters remains to be explored. Using a simulation
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Chromosome‐level assembly of Southern catfish (Silurus meridionalis) provides insights into visual adaptation to the nocturnal and benthic lifestyles Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-27 Shuqing Zheng; Feng Shao; Wenjing Tao; Zhilong Liu; Juan Long; Xiaoshuang Wang; Shuai Zhang; Qingyuan Zhao; Karen L. Carleton; Thomas D. Kocher; Li Jin; Zhijian Wang; Zuogang Peng; Deshou Wang; Yaoguang Zhang
The Southern catfish (Silurus meridionalis) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries. In this study, we constructed a chromosome‐level draft genome of S. meridionalis using 69.7 Gb Nanopore long reads and 49.5 Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4
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Long read sequencing of Toona sinensis (A. Juss) Roem: A chromosome‐level reference genome for the family Meliaceae Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-09 Yun‐Tao Ji; Zhihui Xiu; Chun‐Hai Chen; Youru Wang; Jing‐Xia Yang; Juan‐Juan Sui; San‐Jie Jiang; Ping Wang; Shao‐Yun Yue; Qian‐Qian Zhang; Ji‐liang Jin; Guo‐Shu Wang; Qian‐Qian Wei; Bing Wei; Juan Wang; Hai‐Lin Zhang; Qiu‐Yan Zhang; Jun Liu; Chang‐Jin Liu; Jian‐Bo Jian; Chang‐Qing Qu
Chinese mahogany (Toona sinensis) is a woody plant that is widely cultivated in China and Malaysia. Toona sinensis is important economically, including as a nutritious food source, as material for traditional Chinese medicine and as a high‐quality hardwood. However, the absence of a reference genome has hindered in‐depth molecular and evolutionary studies of this plant. In this study, we report a high‐quality
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Pedigree reconstruction and distant pairwise relatedness estimation from genome sequence data: A demonstration in a population of rhesus macaques (Macaca mulatta) Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-01 Lauren E. Petty; Kathrine Phillippi‐Falkenstein; H. Michael Kubisch; Muthuswamy Raveendran; R. Alan Harris; Eric J. Vallender; Chad D. Huff; Rudolf P. Bohm; Jeffrey Rogers; Jennifer E. Below
A primary challenge in the analysis of free‐ranging animal populations is the accurate estimation of relatedness among individuals. Many aspects of population analysis rely on knowledge of relatedness patterns, including socioecology, demography, heritability and gene mapping analyses, wildlife conservation and the management of breeding colonies. Methods for determining relatedness using genome‐wide
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The discernible and hidden effects of clonality on the genotypic and genetic states of populations: Improving our estimation of clonal rates Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-01 Solenn Stoeckel; Barbara Porro; Sophie Arnaud‐Haond
Partial clonality is widespread across the tree of life, but most population genetic models are designed for exclusively clonal or sexual organisms. This gap hampers our understanding of the influence of clonality on evolutionary trajectories and the interpretation of population genetic data. We performed forward simulations of diploid populations at increasing rates of clonality (c), analysed their
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The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-12-16 Annabel Whibley; Joanna L. Kelley; Shawn R. Narum
The quality of genome assemblies has improved rapidly in recent years due to continual advances in sequencing technology, assembly approaches, and quality control. In the field of molecular ecology, this has led to the development of exceptional quality genome assemblies that will be important long‐term resources for broader studies into ecological, conservation, evolutionary, and population genomics
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Corrigendum Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-17
In the article entitled “A DNA mini‐barcode for marine macrophytes” which was published in Molecular Ecology Resources (volume 20, Issue 4, pages 920–935), the authors noticed an error in the GenBank accession numbers which are listed in the ‘Data Availability Statement’ section. The correct GenBank accession numbers should read as: The GenBank accession numbers for the Illumina and Sanger sequences
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Chromosome‐level genome assembly of the aphid parasitoid Aphidius gifuensis using Oxford Nanopore sequencing and Hi‐C technology Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-12-13 Bingyan Li; Zhenyong Du; Li Tian; Limeng Zhang; Zhihua Huang; Shujun Wei; Fan Song; Wanzhi Cai; Yanbi Yu; Hailin Yang; Hu Li
Aphidius gifuensis is a parasitoid wasp that has been commercially bred and released in large scale as a biocontrol agent for the management of aphid pests. As a highly efficient endoparasitoid, it is also an important model for exploring mechanisms of parasitism. Currently, artificially bred populations of this wasp are facing rapid decline with undetermined cause, and mechanisms underlying its parasitoid
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Effective double‐digest RAD sequencing and genotyping despite large genome size Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-12-22 Roberta Gargiulo; Tiiu Kull; Michael F. Fay
Obtaining informative data is the ambition of any genomic project, but in nonmodel species with very large genomes, pursuing such a goal requires surmounting a series of analytical challenges. Double‐digest RAD sequencing is routinely used in nonmodel organisms and offers some control over the volume of data obtained. However, the volume of data recovered is not always an indication of the reliability
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RepeatProfiler: A pipeline for visualization and comparative analysis of repetitive DNA profiles Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-12-04 Sherif Negm; Anya Greenberg; Amanda M. Larracuente; John S. Sproul
Study of repetitive DNA elements in model organisms highlights the role of repetitive elements (REs) in many processes that drive genome evolution and phenotypic change. Because REs are much more dynamic than single‐copy DNA, repetitive sequences can reveal signals of evolutionary history over short time scales that may not be evident in sequences from slower‐evolving genomic regions. Many tools for
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SCycDB: A curated functional gene database for metagenomic profiling of sulphur cycling pathways Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-12-07 Xiaoli Yu; Jiayin Zhou; Wen Song; Mengzhao Xu; Qiang He; Yisheng Peng; Yun Tian; Cheng Wang; Longfei Shu; Shanquan Wang; Qingyun Yan; Jihua Liu; Qichao Tu; Zhili He
Microorganisms play important roles in the biogeochemical cycling of sulphur (S), an essential element in the Earth's biosphere. Shotgun metagenome sequencing has opened a new avenue to advance our understanding of S cycling microbial communities. However, accurate metagenomic profiling of S cycling microbial communities remains technically challenging, mainly due to low coverage and inaccurate definition
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Chromosome‐level reference genome assembly provides insights into aroma biosynthesis in passion fruit (Passiflora edulis) Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-12-16 Dongna Ma; Shanshan Dong; Shengcheng Zhang; Xiuqing Wei; Qingjun Xie; Qiansu Ding; Rui Xia; Xingtan Zhang
Passion fruit, native to tropical America, is an agriculturally, economically and ornamentally important fruit plant that is well known for its acid pulp, rich aroma and distinctive flavour. Here, we present a chromosome‐level genome assembly of passion fruit by incorporating PacBio long HiFi reads and Hi‐C technology. The assembled reference genome is 1.28 Gb size with a scaffold N50 of 126.4 Mb and
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Identification of determinants of pollen donor fecundity using the hierarchical neighborhood model Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-12-08 Igor J. Chybicki; Andrzej Oleksa; Monika Dering
Individual differences in male reproductive success drive genetic drift and natural selection, altering genetic variation and phenotypic trait distributions in future generations. Therefore, identifying the determinants of reproductive success is important for understanding the ecology and evolution of plants. Here, based on the spatially explicit mating model (the neighborhood model), we develop a
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Whole genome sequencing of silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) provide novel insights into their evolution and speciation Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-11-15 Jianbo Jian; Liandong Yang; Xiaoni Gan; Bin Wu; Li Gao; Honghui Zeng; Xuzhen Wang; Zhiqiang Liang; Ying Wang; Lihua Fang; Jie Li; Sanjie Jiang; Kang Du; Beide Fu; Mingzhou Bai; Ming Chen; Xiaodong Fang; Huanzhang Liu; Shunping He
The edible silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis), which are two of the “Four Domesticated Fish” of China, are cultivated intensively worldwide. Here, we constructed 837‐ and 845‐Mb draft genome assemblies for the silver carp and the bighead carp, respectively, including 24,571 and 24,229 annotated protein‐coding genes. Genetic maps, anchoring 71.7% and 83.8% of all
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