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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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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, non‐human 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 the feasibility of such studies is the substantial financial and time investments still required during sample screening, due to uncertainty
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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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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 i) to identify direct dispersal paths followed by propagules or ii) to quantify landscape effects on multigenerational gene flow. However, the influence of their construction parameters remains to be explored. Using a simulation approach
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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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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 analyzing 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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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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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 datasets, mostly in human populations. Nevertheless, complex admixture histories, beyond one or two pulses of admixture, remain methodologically
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A multi‐tiered 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 multi‐tiered sequence capture strategy aimed at capturing 100’s 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 the
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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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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 datasets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: 1) the best demographic model
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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 1,155.8 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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A reference‐free approach to analyze RADseq data using standard Next Generation Sequencing toolkits Mol. Ecol. Resour. (IF 6.286) Pub Date : 2021-01-12 Rasmus Heller; Casia Nursyifa; Genis 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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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 datasets.
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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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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 higher proportion of the genome and their expansion is a key contributor
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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 revolutionised 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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Long read sequencing of Toona sinensis (A. Juss) Roem: a chromosome‐level reference genome for the Meliaceae family 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. T. sinensis provides important economic attributes, 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
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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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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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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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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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Sequencing platform shifts provide opportunities but pose challenges for combining genomic data sets Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-12-13 Rishi De‐Kayne; David Frei; Ryan Greenway; Sofia L. Mendes; Cas Retel; Philine G. D. Feulner
Technological advances in DNA sequencing over the last decade now permit the production and curation of large genomic data sets in an increasing number of nonmodel species. Additionally, these new data provide the opportunity for combining data sets, resulting in larger studies with a broader taxonomic range. Whilst the development of new sequencing platforms has been beneficial, resulting in a higher
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Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-11-20 Claudia Fontsere; Marina Alvarez‐Estape; Jack Lester; Mimi Arandjelovic; Martin Kuhlwilm; Paula Dieguez; Anthony Agbor; Samuel Angedakin; Emmanuel Ayuk Ayimisin; Mattia Bessone; Gregory Brazzola; Tobias Deschner; Manasseh Eno‐Nku; Anne‐Céline Granjon; Josephine Head; Parag Kadam; Ammie K. Kalan; Mohamed Kambi; Kevin Langergraber; Juan Lapuente; Giovanna Maretti; Lucy Jayne Ormsby; Alex Piel; Martha
Noninvasive samples as a source of DNA are gaining interest in genomic studies of endangered species. However, their complex nature and low endogenous DNA content hamper the recovery of good quality data. Target capture has become a productive method to enrich the endogenous fraction of noninvasive samples, such as faeces, but its sensitivity has not yet been extensively studied. Coping with faecal
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A decade of de novo transcriptome assembly: Are we there yet? Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-10-08 Martin Hölzer
A decade ago, de novo transcriptome assembly evolved as a versatile and powerful approach to make evolutionary assumptions, analyse gene expression, and annotate novel transcripts, in particular, for non‐model organisms lacking an appropriate reference genome. Various tools have been developed to generate a transcriptome assembly, and even more computational methods depend on the results of these tools
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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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Microbial networks inferred from environmental DNA data for biomonitoring ecosystem change: Strengths and pitfalls Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-11-27 Didac Barroso‐Bergadà; Charlie Pauvert; Jessica Vallance; Laurent Delière; David A. Bohan; Marc Buée; Corinne Vacher
Environmental DNA contains information on the species interaction networks that support ecosystem functions and services. Next‐generation biomonitoring proposes the use of this data to reconstruct ecological networks in real time and then compute network‐level properties to assess ecosystem change. We investigated the relevance of this proposal by assessing: (i) the replicability of DNA‐based networks
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Predicting amphibian intraspecific diversity with machine learning: Challenges and prospects for integrating traits, geography, and genetic data Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-11-29 Lisa N. Barrow; Emanuel Masiero da Fonseca; Coleen E. P. Thompson; Bryan C. Carstens
The growing availability of genetic data sets, in combination with machine learning frameworks, offers great potential to answer long‐standing questions in ecology and evolution. One such question has intrigued population geneticists, biogeographers, and conservation biologists: What factors determine intraspecific genetic diversity? This question is challenging to answer because many factors may influence
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Chromosome level assembly reveals a unique immune gene organization and signatures of evolution in the common pheasant Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-11-14 Chuan He; Lele Zhao; Lu Xiao; Ke Xu; Jinmei Ding; Hao Zhou; Yuming Zheng; Chengxiao Han; Fisayo Akinyemi; Huaixi Luo; Lingyu Yang; Lingxiao Luo; Hongyan Yuan; Xuelin Lu; He Meng
The common pheasant Phasianus colchicus, belonging to the order Galliformes and family Phasianidae, is the most widespread species. Despite a long history of captivity, the domestication of this bird is still at a preliminary stage. Recently, the demand for accelerating its transformation to poultry for meat and egg production has been increasing. In this study, we assembled high quality, chromosome
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Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-11-11 Carolina Bernhardsson; Yanjun Zan; Zhiqiang Chen; Pär K. Ingvarsson; Harry X. Wu
Norway spruce (Picea abies L. Karst) is one of the most important forest tree species with significant economic and ecological impact in Europe. For decades, genomic and genetic studies on Norway spruce have been challenging due to the large and repetitive genome (19.6 Gb with more than 70% being repetitive). To accelerate genomic studies, including population genetics, genome‐wide association studies
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The chromosome‐level genome sequence and karyotypic evolution of Megadenia pygmaea (Brassicaceae) Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-11-05 Wenjie Yang; Lei Zhang; Terezie Mandáková; Li Huang; Ting Li; Jiebei Jiang; Yongzhi Yang; Martin A. Lysak; Jianquan Liu; Quanjun Hu
Karyotypic changes in chromosome number and structure are drivers in the divergent evolution of diverse plant species and lineages. This study aimed to reveal the origins of the unique karyotype (2n = 12) and phylogenetic relationships of the genus Megadenia (Brassicaceae). A high‐quality chromosome‐scale genome was assembled for Megadenia pygmaea using Nanopore long reads and high‐throughput chromosome
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MAUI‐seq: Metabarcoding using amplicons with unique molecular identifiers to improve error correction Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-11-10 Bryden Fields; Sara Moeskjær; Ville‐Petri Friman; Stig U. Andersen; J. Peter W. Young
Sequencing and PCR errors are a major challenge when characterizing genetic diversity using high‐throughput amplicon sequencing (HTAS). We have developed a multiplexed HTAS method, MAUI‐seq, which uses unique molecular identifiers (UMIs) to improve error correction by exploiting variation among sequences associated with a single UMI. Erroneous sequences are recognized because, across the data set,
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Genome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-11-11 Mads Reinholdt Jensen; Eva Egelyng Sigsgaard; Shenglin Liu; Andrea Manica; Steffen Sanvig Bach; Michael Møller Hansen; Peter Rask Møller; Philip Francis Thomsen
Environmental DNA (eDNA) provides a promising supplement to traditional sampling methods for population genetic inferences, but current studies have almost entirely focused on short mitochondrial markers. Here, we develop one mitochondrial and one nuclear set of target capture probes for the whale shark (Rhincodon typus) and test them on seawater samples collected in Qatar to investigate the potential
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Characterization of reproductive gene diversity in the endangered Tasmanian devil Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-11-14 Parice A. Brandies; Belinda R. Wright; Carolyn J. Hogg; Catherine E. Grueber; Katherine Belov
Interindividual variation at genes known to play a role in reproduction may impact reproductive fitness. The Tasmanian devil is an endangered Australian marsupial with low genetic diversity. Recent work has shown concerning declines in productivity in both wild and captive populations over time. Understanding whether functional diversity exists at reproductive genes in the Tasmanian devil is a key
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Chromosome‐level genome of the peach fruit moth Carposina sasakii (Lepidoptera: Carposinidae) provides a resource for evolutionary studies on moths Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-10-23 Li‐Jun Cao; Wei Song; Lei Yue; Shao‐Kun Guo; Jin‐Cui Chen; Ya‐Jun Gong; Ary Anthony Hoffmann; Shu‐Jun Wei
The peach fruit moth (PFM), Carposina sasakii Matsumura, is a major phytophagous orchard pest widely distributed across Northeast Asia. Here, we report the chromosome‐level genome for the PFM, representing the first genome for the family Carposinidae, from the lepidopteran superfamily Copromorphoidea. The genome was assembled into 404.83 Mb sequences using PacBio long‐read and Illumina short‐read sequences
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Discriminating lineages of Batrachochytrium dendrobatidis using quantitative PCR Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-11-24 Pria N Ghosh; Ruhan Verster; Thomas R Sewell; Simon J O’Hanlon; Lola M Brookes; Adrien Rieux; Trenton WJ Garner; Ché Weldon; Matthew C Fisher
The ability to detect and monitor infectious disease in a phylogenetically informative manner is critical for their management. Phylogenetically informative diagnostic tests enable patterns of pathogen introduction or changes in the distribution of genotypes to be measured, enabling research into the ecology of the pathogen. Batrachochytrium dendrobatidis (Bd), a causative agent of chytridiomycosis
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A novel workflow to improve genotyping of multigene families in wildlife species: An experimental set‐up with a known model system Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-10-28 Mark A. F. Gillingham; B. Karina Montero; Kerstin Wihelm; Kara Grudzus; Simone Sommer; Pablo S. C. Santos
Genotyping complex multigene families in novel systems is particularly challenging. Target primers frequently amplify simultaneously multiple loci leading to high PCR and sequencing artefacts such as chimeras and allele amplification bias. Most genotyping pipelines have been validated in nonmodel systems whereby the real genotype is unknown and the generation of artefacts may be highly repeatable.
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Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-10-23 José Luis Blanco‐Pastor; Philippe Barre; Thomas Keep; Thomas Ledauphin; Abraham Escobar‐Gutiérrez; Anna Maria Roschanski; Evelyn Willner; Klaus J. Dehmer; Matthew Hegarty; Hilde Muylle; Elisabeth Veeckman; Klaas Vandepoele; Tom Ruttink; Isabel Roldán‐Ruiz; Stéphanie Manel; Jean‐Paul Sampoux
Germplasm from perennial ryegrass (Lolium perenne L.) natural populations is useful for breeding because of its adaptation to a wide range of climates. Climate‐adaptive genes can be detected from associations between genotype, phenotype and climate but an integrated framework for the analysis of these three sources of information is lacking. We used two approaches to identify adaptive loci in perennial
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Biased assessment of ongoing admixture using STRUCTURE in the absence of reference samples Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-10-21 Sara Ravagni; Ines Sanchez‐Donoso; Carles Vilà
Detection of hybridization and introgression is important in ecological research as in conservation and evolutionary biology. STRUCTURE is one of the most popular software to study introgression and allows estimating what proportion of the genome of each individual belongs to each ancestral population, even in cases where no reference sample from the ancestral nonadmixed populations is previously identified
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Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-10-21 Lily C. Hughes; Guillermo Ortí; Hadeel Saad; Chenhong Li; William T. White; Carole C. Baldwin; Keith A. Crandall; Dahiana Arcila; Ricardo Betancur‐R
Exon markers have a long history of use in phylogenetics of ray‐finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current
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A Comprehensive Analysis Comparing Linear and Generalized Linear Models in Detecting Adaptive SNPs Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-11-20 Lan Luo; Zheng‐zheng Tang; Sean D. Schoville; Jun Zhu
To understand how organisms adapt to their environment, a gene‐environmental association (GEA) analysis is commonly conducted. GEA methods based on mixed models, such as linear latent factor mixed models (LFMM) and LFMM2, have grown in popularity for their robust performance in terms of power and computational speed. However, it is unclear how the assumption of a Gaussian distribution for the response
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Reference genome and demographic history of the most endangered marine mammal, the vaquita Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-10-22 Phillip A. Morin; Frederick I. Archer; Catherine D. Avila; Jennifer R. Balacco; Yury V. Bukhman; William Chow; Olivier Fedrigo; Giulio Formenti; Julie A. Fronczek; Arkarachai Fungtammasan; Frances M.D. Gulland; Bettina Haase; Mads Peter Heide‐Jorgensen; Marlys L. Houck; Kerstin Howe; Ann C. Misuraca; Jacquelyn Mountcastle; Whitney Musser; Sadye Paez; Sarah Pelan; Adam Phillippy; Arang Rhie; Jacqueline
The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 years resulting from inadvertent deaths due to the increasing use of large‐mesh gillnets. To understand the evolutionary and demographic history of the vaquita, we used combined long‐read sequencing and long‐range scaffolding
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msGBS: A new high‐throughput approach to quantify the relative species abundance in root samples of multispecies plant communities Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-10-15 Cornelis A. M. Wagemaker; Liesje Mommer; Eric J. W. Visser; Alexandra Weigelt; Thomas P. van Gurp; Maarten Postuma; Annemiek E. Smit‐Tiekstra; Hans de Kroon
Plant interactions are as important belowground as aboveground. Belowground plant interactions are however inherently difficult to quantify, as roots of different species are difficult to disentangle. Although for a couple of decades molecular techniques have been successfully applied to quantify root abundance, root identification and quantification in multispecies plant communities remains particularly
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The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-10-15 Michael D. Nowak; Siri Birkeland; Terezie Mandáková; Rimjhim Roy Choudhury; Xinyi Guo; Anna Lovisa S. Gustafsson; Abel Gizaw; Audun Schrøder‐Nielsen; Marco Fracassetti; Anne K. Brysting; Loren Rieseberg; Tanja Slotte; Christian Parisod; Martin A. Lysak; Christian Brochmann
The Arctic is one of the most extreme terrestrial environments on the planet. Here, we present the first chromosome‐scale genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short‐reads, single‐molecule
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Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-10-08 Cynthia Riginos; Eric D. Crandall; Libby Liggins; Michelle R. Gaither; Rodney B. Ewing; Christopher Meyer; Kimberly R. Andrews; Peter T. Euclide; Benjamin M. Titus; Nina Overgaard Therkildsen; Antonia Salces‐Castellano; Lucy C. Stewart; Robert J. Toonen; John Deck
Genetic data represent a relatively new frontier for our understanding of global biodiversity. Ideally, such data should include both organismal DNA‐based genotypes and the ecological context where the organisms were sampled. Yet most tools and standards for data deposition focus exclusively either on genetic or ecological attributes. The Genomic Observatories Metadatabase (GEOME: geome‐db.org) provides
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Corrigendum Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-10-17
The article entitled “Combining noninvasive genetics and a new mammalian sex‐linked marker provides new tools to investigate population size, structure and individual behaviour: An application to bats” which was published in Molecular Ecology Resources (volume 18, Issue 2, pages 217–228). The authors of the above article noticed an error in the primer sequence which is detailed in the ‘Materials and
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Distinguishing among complex evolutionary models using unphased whole‐genome data through random forest approximate Bayesian computation Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-09-30 Silvia Ghirotto; Maria Teresa Vizzari; Francesca Tassi; Guido Barbujani; Andrea Benazzo
Inferring past demographic histories is crucial in population genetics, and the amount of complete genomes now available should in principle facilitate this inference. In practice, however, the available inferential methods suffer from severe limitations. Although hundreds complete genomes can be simultaneously analysed, complex demographic processes can easily exceed computational constraints, and
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TOA: A software package for automated functional annotation in non‐model plant species Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-10-18 Fernando Mora‐Márquez; Víctor Chano; José Luis Vázquez‐Poletti; Unai López de Heredia
The increase of sequencing capacity provided by high‐throughput platforms has made it possible to routinely obtain large sets of genomic and transcriptomic sequences from model and non‐model organisms. Subsequent genomic analysis and gene discovery in next‐generation sequencing experiments are, however, bottlenecked by functional annotation. One common way to perform functional annotation of sets of
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The Genomics Observatories Metadatabase (GEOME) Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-10-15 Benjamin Sibbett; Loren H. Rieseberg; Shawn Narum
Open data is fundamental to the goal of maximizing the value of research. As the culture of science transitions towards an ‘open’ model (Hampton et al, 2015), many stakeholders such as funding bodies and journals now insist on open data. Molecular Ecology and Molecular Ecology Resources have strived to be at the forefront of Open Data initiatives being amongst the first journals in ecology and evolution
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Rapture‐ready darters: Choice of reference genome and genotyping method (whole‐genome or sequence capture) influence population genomic inference in Etheostoma Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-10-15 Brendan N. Reid; Rachel L. Moran; Christopher J. Kopack; Sarah W. Fitzpatrick
Researchers studying nonmodel organisms have an increasing number of methods available for generating genomic data. However, the applicability of different methods across species, as well as the effect of reference genome choice on population genomic inference, remain difficult to predict in many cases. We evaluated the impact of data type (whole‐genome vs. reduced representation) and reference genome
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ASAP: assemble species by automatic partitioning Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-10-15 Nicolas Puillandre; Sophie Brouillet; Guillaume Achaz
Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 104 sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only
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Benchmarking DNA methylation assays in a reef‐building coral Mol. Ecol. Resour. (IF 6.286) Pub Date : 2020-10-15 Groves Dixon; Mikhail Matz
Interrogation of chromatin modifications, such as DNA methylation, has the potential to improve forecasting and conservation of marine ecosystems. The standard method for assaying DNA methylation (whole genome bisulphite sequencing), however, is currently too costly to apply at the scales required for ecological research. Here, we evaluate different methods for measuring DNA methylation for ecological