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Molecular sexing of birds using quantitative PCR (qPCR) of sex‐linked genes and logistic regression models Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-03-04 Eleni L. Petrou, Laura C. Scott, Cherie M. McKeeman, Andrew M. Ramey
The ability to sex individuals is an important component of many behavioural and ecological investigations and provides information for demographic models used in conservation and species management. However, many birds are difficult to sex using morphological characters or traditional molecular sexing methods. In this study, we developed probabilistic models for sexing birds using quantitative PCR
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Estimates of heterozygosity from single nucleotide polymorphism markers are context‐dependent and often wrong Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-03-04 Jarrod Sopniewski, Renee A. Catullo
Genetic diversity is frequently described using heterozygosity, particularly in a conservation context. Often, it is estimated using single nucleotide polymorphisms (SNPs); however, it has been shown that heterozygosity values calculated from SNPs can be biased by both study design and filtering parameters. Though solutions have been proposed to address these issues, our own work has found them to
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Development and validation of a DNA‐based multi‐species biomonitoring toolkit using a high‐throughput qPCR platform: A case study of Irish shellfish species Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-03-02 Dennis van der Pouw Kraan, Conor T. Graham, Fiona Kavanagh, Luca Mirimin
Biomonitoring of marine life has been enhanced in recent years by the integration of innovative DNA‐based approaches, which offer advantages over more laborious techniques (e.g. microscopy). However, trade‐offs between throughput, sensitivity and quantitative measurements must be made when choosing between the prevailing molecular methodologies (i.e. metabarcoding or qPCR/dPCR). Thus, the aim of the
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Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short‐read nanopore sequencing as a potential biomonitoring tool Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-02-29 Kaviarasu Munian, Farah Farhana Ramli, Nursyuhada Othman, Nur Aina Amira Mahyudin, Nur Hartini Sariyati, Nurfatiha Akmal Fawwazah Abdullah‐Fauzi, Hidayah Haris, Mohd Lokman Ilham‐Norhakim, Muhammad Abu Bakar Abdul‐Latiff
The approach of combining cost‐effective nanopore sequencing and emerging environmental DNA (eDNA) metabarcoding could prove to be a promising tool for biodiversity documentation, especially in Malaysia. Given the substantial funding constraints in recent years, especially in relation to the country's biodiversity, many researchers have been limited to conduct restricted research without extended monitoring
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RIDGE, a tool tailored to detect gene flow barriers across species pairs Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-02-29 Ewen Burban, Maud I. Tenaillon, Sylvain Glémin
Characterizing the processes underlying reproductive isolation between diverging lineages is central to understanding speciation. Here, we present RIDGE—Reproductive Isolation Detection using Genomic polymorphisms—a tool tailored for quantifying gene flow barrier proportion and identifying the relevant genomic regions. RIDGE relies on an Approximate Bayesian Computation with a model‐averaging approach
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A case study on the application of spore sampling for the monitoring of macrofungi Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-02-27 Markus Schlegel, Artemis D. Treindl, Jenny Panziera, Veronika Zengerer, Deborah Zani, Jonas Brännhage, Andrin Gross
Fungi play a vital role in ecosystem functioning, yet significant knowledge gaps persist in understanding their diversity and distribution leading to uncertainties about their threat status and extinction risk. This is partly owed to the difficulty of monitoring fungi using traditional fruiting body surveys. The present study evaluates airborne environmental DNA (eDNA) sampling as a monitoring tool
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Delimiting the rare, endangered and actively speciating Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-02-26 Kristen M. Martinet, Luke J. Harmon
Species delimitation is a contentious topic. The genomics revolution initially brought hope that identifying and classifying species would be easier through better methods and more data, but genomics has also brought complexity and controversy to delimitation. One solution can be to collect a larger sample of individuals at a finer geographic scale. But what if taxa are rare and collecting more samples
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mapmixture: An R package and web app for spatial visualisation of admixture and population structure Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-02-23 Tom L. Jenkins
The mapmixture R package and interactive web app are tools to aid visualisation of admixture and population structure in geographic space. The purpose of mapmixture is to enable and encourage molecular ecologists, and in particular population geneticists and phylogeneticists, to plot their admixture, ancestry or assignment results on a map when location information is available. mapmixture accepts
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Methylation‐based markers for the estimation of age in African cheetah, Acinonyx jubatus Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-02-23 Louis‐Stéphane Le Clercq, Antoinette Kotzé, J. Paul Grobler, Desiré L. Dalton
Age is a key demographic in conservation where age classes show differences in important population metrics such as morbidity and mortality. Several traits, including reproductive potential, also show senescence with ageing. Thus, the ability to estimate age of individuals in a population is critical in understanding the current structure as well as their future fitness. Many methods exist to determine
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Optimizing waterborne eDNA capture from waterholes in savanna systems under remote field conditions Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-02-23 Tamara Schenekar, Janine Baxter, Metlholo Andries Phukuntsi, Irmgard Sedlmayr, Byron Weckworth, Monica Mwale
Environmental DNA (eDNA) is used for biodiversity assessments in a variety of ecosystems across the globe, whereby different eDNA concentration, preservation and extraction methods can outperform others depending on the sampling conditions and environment. Tropical and subtropical ecosystems in Africa are among the less studied systems concerning eDNA‐based monitoring. Waterholes in arid parts of southern
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Finding the perfect pairs: A matchmaking of plant markers and primers for multi-marker eDNA metabarcoding Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-02-16 Armando Espinosa Prieto, Laurent Hardion, Nicolas Debortoli, Jean-Nicolas Beisel
As the scope of plant eDNA metabarcoding diversifies, so do the primers, markers and methods. A wealth of primers exists today, but their comparative evaluation is lacking behind. Similarly, multi-marker approaches are recommended but debates persist regarding barcode complementarity and optimal combinations. After a literature compilation of used primers, we compared in silico 102 primer pairs based
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A simple and effective method to enrich endogenous DNA from mammalian faeces Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-02-19 Liang Yu Cui, Bo Yang Liu, Hai Meng Li, Yi Xin Zhu, Yong Heng Zhou, Chang Su, Yin Ping Tian, Hai Tao Xu, Dan Liu, Xiao Ping Li, Yue Ma, Guang Shun Jiang, Huan Liu, Shu Hui Yang, Tian Ming Lan, Yan Chun Xu
Utilization of faeces has long been a popular approach for genetic and ecological studies of wildlife. However, the success of molecular marker genotyping and genome resequencing is often unpredictable due to insufficient enrichment of endogenous DNA in the total faecal DNA that is dominated by bacterial DNA. Here, we report a simple and cheap method named PEERS to predominantly lyse animal cells over
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Enhancing amphibian biomonitoring through eDNA metabarcoding Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-02-12 Yawen Mu, Jingwen Zhang, Jianghua Yang, Jun Wu, Yong Zhang, Hongxia Yu, Xiaowei Zhang
Surveying biodiversity has taken a quantum leap with environmental DNA (eDNA) metabarcoding, an immensely powerful approach lauded for its efficiency, sensitivity, and non-invasiveness. This approach emerges as a game-changer for the elusive realm of endangered and rare species—think nocturnal, environmentally elusive amphibians. Here, we have established a framework for constructing a reliable metabarcoding
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Template-specific optimization of NGS genotyping pipelines reveals allele-specific variation in MHC gene expression Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-02-08 Artemis Efstratiou, Arnaud Gaigher, Sven Künzel, Ana Teles, Tobias L. Lenz
Using high-throughput sequencing for precise genotyping of multi-locus gene families, such as the major histocompatibility complex (MHC), remains challenging, due to the complexity of the data and difficulties in distinguishing genuine from erroneous variants. Several dedicated genotyping pipelines for data from high-throughput sequencing, such as next-generation sequencing (NGS), have been developed
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Predicting downstream transport distance of fish eDNA in lotic environments Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-02-06 Didier Pont
Environmental DNA (eDNA) is an effective tool for describing fish biodiversity in lotic environments, but the downstream transport of eDNA released by organisms makes it difficult to interpret species detection at the local scale. In addition to biophysical degradation and exchanges at the water–sediment interface, hydrological conditions control the transport distance. A new eDNA transport model described
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Seq2Sat and SatAnalyzer toolkit: Towards comprehensive microsatellite genotyping from sequencing data Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-01-30 Peng Liu, Paul Wilson, Bridget Redquest, Sonesinh Keobouasone, Micheline Manseau
Accurate and efficient microsatellite loci genotyping is an essential process in population genetics that is also used in various demographic analyses. Protocols for next-generation sequencing of microsatellite loci enable high-throughput and cross-compatible allele scoring, common issues that are not addressed by conventional capillary-based approaches. To improve this process, we have developed an
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The unknown unknown: A framework for assessing environmental DNA assay specificity against unsampled taxa Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-01-23 Taylor M. Wilcox, John A. Kronenberger, Michael K. Young, Daniel H. Mason, Thomas W. Franklin, Michael K. Schwartz
Taxon-specific quantitative PCR (qPCR) assays are commonly used for environmental DNA sampling-based inference of animal presence. These assays require thorough validation to ensure that amplification truly indicates detection of the target taxon, but a thorough validation is difficult when there are potentially many non-target taxa, some of which may have incomplete taxonomies. Here, we use a previously
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Population genetic simulation: Benchmarking frameworks for non-standard models of natural selection Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-01-21 Olivia L. Johnson, Raymond Tobler, Joshua M. Schmidt, Christian D. Huber
Population genetic simulation has emerged as a common tool for investigating increasingly complex evolutionary and demographic models. Software capable of handling high-level model complexity has recently been developed, and the advancement of tree sequence recording now allows simulations to merge the efficiency and genealogical insight of coalescent simulations with the flexibility of forward simulations
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Express barcoding with NextGenPCR and MinION for species-level sorting of ecological samples Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-01-19 Cristina Vasilita, Vivian Feng, Aslak Kappel Hansen, Emily Hartop, Amrita Srivathsan, Robin Struijk, Rudolf Meier
The use of DNA barcoding is well established for specimen identification and large-scale biodiversity discovery, but remains underutilized for time-sensitive applications such as rapid species discovery in field stations, identifying pests, citizen science projects, and authenticating food. The main reason is that existing express barcoding workflows are either too expensive or can only be used in
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A cost-effective blood DNA methylation-based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus) and Panthera species, using targeted bisulphite sequencing and machine learning models Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-01-18 Huiyuan Qi, Qi Luan Lim, Kodzue Kinoshita, Nobuyoshi Nakajima, Miho Inoue-Murayama
Individual age can be used to design more efficient and suitable management plans in both in situ and ex situ conservation programmes for targeted wildlife species. DNA methylation is a promising marker of epigenetic ageing that can accurately estimate age from small amounts of biological material, which can be collected in a minimally invasive manner. In this study, we sequenced five targeted genetic
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GeneMiner: A tool for extracting phylogenetic markers from next-generation sequencing data Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-01-10 Pulin Xie, Yongling Guo, Yue Teng, Wenbin Zhou, Yan Yu
The advancement of next-generation sequencing (NGS) technologies has been revolutionary for the field of evolutionary biology. This technology has led to an abundance of available genomes and transcriptomes for researchers to mine. Specifically, researchers can mine for various types of molecular markers that are vital for phylogenetic, evolutionary and ecological studies. Numerous tools have been
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Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-01-08 Y. Lammers, P. Taberlet, E. Coissac, L. D. Elliott, M. F. Merkel, I. Pitelkova, , , I. G. Alsos
Sedimentary ancient DNA (sedaDNA) has rarely been used to obtain population-level data due to either a lack of taxonomic resolution for the molecular method used, limitations in the reference material or inefficient methods. Here, we present the potential of multiplexing different PCR primers to retrieve population-level genetic data from sedaDNA samples. Vaccinium uliginosum (Ericaceae) is a widespread
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A pan-genomic approach reveals novel Sulfurimonas clade in the ferruginous meromictic Lake Pavin Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-01-08 Corinne Biderre-Petit, Damien Courtine, Claire Hennequin, Pierre E. Galand, Stefan Bertilsson, Didier Debroas, Arthur Monjot, Cécile Lepère, Anna-Maria Divne, Corentin Hochart
The permanently anoxic waters in meromictic lakes create suitable niches for the growth of bacteria using sulphur metabolisms like sulphur oxidation. In Lake Pavin, the anoxic water mass hosts an active cryptic sulphur cycle that interacts narrowly with iron cycling, however the metabolisms of the microorganisms involved are poorly known. Here we combined metagenomics, single-cell genomics, and pan-genomics
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Lessons from assembling UCEs: A comparison of common methods and the case of Clavinomia (Halictidae) Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-01-06 Silas Bossert, Alain Pauly, Bryan N. Danforth, Michael C. Orr, Elizabeth A. Murray
Sequence data assembly is a foundational step in high-throughput sequencing, with untold consequences for downstream analyses. Despite this, few studies have interrogated the many methods for assembling phylogenomic UCE data for their comparative efficacy, or for how outputs may be impacted. We study this by comparing the most commonly used assembly methods for UCEs in the under-studied bee lineage
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Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data Mol. Ecol. Resour. (IF 7.7) Pub Date : 2024-01-03 Madleina Caduff, Raphael Eckel, Christoph Leuenberger, Daniel Wegmann
The identification of sex-linked scaffolds and the genetic sex of individuals, i.e. their sex karyotype, is a fundamental step in population genomic studies. If sex-linked scaffolds are known, single individuals may be sexed based on read counts of next-generation sequencing data. If both sex-linked scaffolds as well as sex karyotypes are unknown, as is often the case for non-model organisms, they
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A CRISPR-based strategy for targeted sequencing in biodiversity science Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-12-28 Bethan Littleford-Colquhoun, Tyler R. Kartzinel
Many applications in molecular ecology require the ability to match specific DNA sequences from single- or mixed-species samples with a diagnostic reference library. Widely used methods for DNA barcoding and metabarcoding employ PCR and amplicon sequencing to identify taxa based on target sequences, but the target-specific enrichment capabilities of CRISPR-Cas systems may offer advantages in some applications
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A memorial to Professor Louis Bernatchez (1960–2023) Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-12-28
Louis Bernatchez in his office in 2018 at Laval University, Québec, Canada. Photo taken by Marc Robitaille. With much sorrow, we pay tribute to Professor Louis Bernatchez who died on the 28 September 2023 at the age of 63. His passing represents an immense loss to the molecular ecology community. It is difficult to overstate the profound impact that Louis had on the wider field of genomics applied
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Metazoa-level USCOs as markers in species delimitation and classification Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-12-26 Lars Dietz, Christoph Mayer, Eckart Stolle, Jonas Eberle, Bernhard Misof, Lars Podsiadlowski, Oliver Niehuis, Dirk Ahrens
Metazoa-level universal single-copy orthologs (mzl-USCOs) are universally applicable markers for DNA taxonomy in animals that can replace or supplement single-gene barcodes. Previously, mzl-USCOs from target enrichment data were shown to reliably distinguish species. Here, we tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome and therefore able to cope
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Chromosome-level genome assembly of the aster leafhopper (Macrosteles quadrilineatus) reveals the role of environment and microbial symbiosis in shaping pest insect genome evolution Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-12-26 Yumary M. Vasquez, Zheng Li, Allen Z. Xue, Gordon M. Bennett
Leafhoppers comprise over 20,000 plant-sap feeding species, many of which are important agricultural pests. Most species rely on two ancestral bacterial symbionts, Sulcia and Nasuia, for essential nutrition lacking in their phloem and xylem plant sap diets. To understand how pest leafhopper genomes evolve and are shaped by microbial symbioses, we completed a chromosomal-level assembly of the aster
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slimr: An R package for tailor-made integrations of data in population genomic simulations over space and time Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-12-20 Russell Dinnage, Stephen D. Sarre, Richard P. Duncan, Christopher R. Dickman, Scott V. Edwards, Aaron C. Greenville, Glenda M. Wardle, Bernd Gruber
Software for realistically simulating complex population genomic processes is revolutionizing our understanding of evolutionary processes, and providing novel opportunities for integrating empirical data with simulations. However, the integration between standalone simulation software and R is currently not well developed. Here, we present slimr, an R package designed to create a seamless link between
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High-quality haplotype-resolved genome assembly for ring-cup oak (Quercus glauca) provides insight into oaks demographic dynamics Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-12-18 Chang-Sha Luo, Tian-Tian Li, Xiao-Long Jiang, Ying Song, Ting-Ting Fan, Xiang-Bao Shen, Rong Yi, Xiao-Ping Ao, Gang-Biao Xu, Min Deng
Quercus section Cyclobalanopsis represents a dominant woody lineage in East Asian evergreen broadleaved forests. Regardless of its ecological and economic importance, little is known about the genomes of species in this unique oak lineage. Quercus glauca is one of the most widespread tree species in the section Cyclobalanopsis. In this study, a high-quality haplotype-resolved reference genome was assembled
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Individual genotypes from environmental DNA: Fingerprinting snow tracks of three large carnivore species Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-12-15 Marta De Barba, Molly Baur, Frédéric Boyer, Luca Fumagalli, Marjeta Konec, Christian Miquel, Elena Pazhenkova, Nadège Remollino, Tomaž Skrbinšek, Céline Stoffel, Pierre Taberlet
Continued advancements in environmental DNA (eDNA) research have made it possible to access intraspecific variation from eDNA samples, opening new opportunities to expand non-invasive genetic studies of wildlife populations. However, the use of eDNA samples for individual genotyping, as typically performed in non-invasive genetics, still remains elusive. We present successful individual genotyping
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Editorial 2024 Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-12-14 Shawn Narum, Joanna Kelley, Ben Sibbett
CONFLICT OF INTEREST STATEMENT The authors have no competing interests.
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The genomes of Hercules beetles reveal putative adaptive loci and distinct demographic histories in pristine North American forests Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-12-08 My-Hanh Le, Brett Morgan, Mei-Yeh Lu, Victor Moctezuma, Oscar Burgos, Jen-Pan Huang
Beetles, despite their remarkable biodiversity and a long history of research, remain lacking in reference genomes annotated with structural variations in loci of adaptive significance. We sequenced and assembled high-quality chromosome-level genomes of four Hercules beetles which exhibit divergence in male horn size and shape and body colouration. The four Hercules beetle genomes were assembled to
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A minimally invasive, field-applicable CRISPR/Cas biosensor to aid in the detection of Pseudogymnoascus destructans, the causative fungal agent of white-nose syndrome in bats Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-12-08 Adam A. Pérez, Abigail Tobin, John V. Stechly, Jason A. Ferrante, Margaret E. Hunter
The accessibility to CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein) genetic tools has given rise to applications beyond site-directed genome editing for the detection of DNA and RNA. These tools include precise diagnostic detection of human disease pathogens, such as SARS-CoV-2 and Zika virus. Despite the technology being rapid and cost-effective, the
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Bayesian hybrid index and genomic cline estimation with the R package gghybrid Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-12-08 Richard Ian Bailey
Admixture, the interbreeding of individuals from differentiated source populations, is now known to be a widespread phenomenon. Genomic studies of natural hybridisation can help to answer many questions on the impacts of admixture on adaptive evolution, reproductive isolation, and speciation. When a large variety of admixture proportions between two source populations exist, both geographic and genomic
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Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller-size coral reef zooplankton by metatranscriptomics Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-12-08 Felipe M. G. Mattos, Niklas Dreyer, Chia-Ling Fong, Yung-Hui Victoria Wen, Dharmesh Jain, Mattia De Vivo, Yu-Sin Huang, John Karichu Mwihaki, Tzi-Yuan Wang, Ming-Jay Ho, Isheng Jason Tsai, John Wang, Benny K. K. Chan, Ryuji J. Machida
PCR-based high-throughput sequencing has permitted comprehensive resolution analyses of zooplankton diversity dynamics. However, significant methodological issues still surround analyses of complex bulk community samples, not least as in prevailing PCR-based approaches. Marine drifting animals—zooplankton—play essential ecological roles in the pelagic ecosystem, transferring energy and elements to
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In situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-12-08 Javier Tamames, Diego Jiménez-Lalana, Álvaro Redondo, Sandra Martínez-García, Asunción de los Rios
We present here a complete system for metagenomic analysis that allows performing the sequencing and analysis of a medium-size metagenome in less than one day. This unprecedented development was possible due to the conjunction of state-of-the-art experimental and computational advances: a portable laboratory suitable for DNA extraction and sequencing with nanopore technology; the powerful metagenomic
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Benchmarking the Mantel test and derived methods for testing association between distance matrices Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-12-02 Claudio S. Quilodrán, Mathias Currat, Juan I. Montoya-Burgos
Testing the association between objects is central in ecology, evolution, and quantitative sciences in general. Two types of variables can describe the relationships between objects: point variables (measured on individual objects), and distance variables (measured between pairs of objects). The Mantel test and derived methods have been extensively used for distance variables. Yet, these methods have
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Non-invasive age estimation based on faecal DNA using methylation-sensitive high-resolution melting for Indo-Pacific bottlenose dolphins Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-12-02 Genfu Yagi, Huiyuan Qi, Kana Arai, Yuki F. Kita, Kazunobu Kogi, Tadamichi Morisaka, Motoi Yoshioka, Miho Inoue-Murayama
Age is necessary information for the study of life history of wild animals. A general method to estimate the age of odontocetes is counting dental growth layer groups (GLGs). However, this method is highly invasive as it requires the capture and handling of individuals to collect their teeth. Recently, the development of DNA-based age estimation methods has been actively studied as an alternative to
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Morphological and taxonomic diversity of mesozooplankton is an important driver of carbon export fluxes in the ocean Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-11-30 Margaux Perhirin, Hannah Gossner, Jessica Godfrey, Rodney Johnson, Leocadio Blanco-Bercial, Sakina-Dorothée Ayata
Mesozooplankton is a very diverse group of small animals ranging in size from 0.2 to 20 mm not able to swim against ocean currents. It is a key component of pelagic ecosystems through its roles in the trophic networks and the biological carbon pump. Traditionally studied through microscopes, recent methods have been however developed to rapidly acquire large amounts of data (morphological, molecular)
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A novel target-enriched multilocus assay for sponges (Porifera): Red Sea Haplosclerida (Demospongiae) as a test case Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-11-27 Joëlle van der Sprong, Nicole Joy de Voogd, Grace Patricia McCormack, Kenneth Sandoval, Simone Schätzle, Oliver Voigt, Dirk Erpenbeck, Gert Wörheide, Sergio Vargas
With declining biodiversity worldwide, a better understanding of species diversity and their relationships is imperative for conservation and management efforts. Marine sponges are species-rich ecological key players on coral reefs, but their species diversity is still poorly understood. This is particularly true for the demosponge order Haplosclerida, whose systematic relationships are contentious
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Comparative genomics of a vertically transmitted thiotrophic bacterial ectosymbiont and its close free-living relative Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-11-27 Salvador Espada-Hinojosa, Clarissa Karthäuser, Abhishek Srivastava, Lukas Schuster, Teresa Winter, André Luiz de Oliveira, Frederik Schulz, Matthias Horn, Stefan Sievert, Monika Bright
Thiotrophic symbioses between sulphur-oxidizing bacteria and various unicellular and metazoan eukaryotes are widespread in reducing marine environments. The giant colonial ciliate Zoothamnium niveum, however, is the only host of thioautotrophic symbionts that has been cultivated along with its symbiont, the vertically transmitted ectosymbiont Candidatus Thiobius zoothamnicola (short Thiobius). Because
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Plant-derived environmental DNA complements diversity estimates from traditional arthropod monitoring methods but outperforms them detecting plant–arthropod interactions Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-11-27 Sven Weber, Manuel Stothut, Lisa Mahla, Alanah Kripp, Lena Hirschler, Nina Lenz, Anneke Junker, Sven Künzel, Henrik Krehenwinkel
Our limited knowledge about the ecological drivers of global arthropod decline highlights the urgent need for more effective biodiversity monitoring approaches. Monitoring of arthropods is commonly performed using passive trapping devices, which reliably recover diverse communities, but provide little ecological information on the sampled taxa. Especially the manifold interactions of arthropods with
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A framework for identifying fertility gene targets for mammalian pest control Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-11-27 Anna C. Clark, Rey Edison, Kevin Esvelt, Sebastian Kamau, Ludovic Dutoit, Jackson Champer, Samuel E. Champer, Philipp W. Messer, Alana Alexander, Neil J. Gemmell
Fertility-targeted gene drives have been proposed as an ethical genetic approach for managing wild populations of vertebrate pests for public health and conservation benefit. This manuscript introduces a framework to identify and evaluate target gene suitability based on biological gene function, gene expression and results from mouse knockout models. This framework identified 16 genes essential for
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How do threatened plant species with low genetic diversity respond to environmental stress? Insights from comparative conservation epigenomics and phenotypic plasticity Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-11-21 Brigette R. Williams, Allison J. Miller, Christine E. Edwards
Many threatened plants have low genetic diversity, which may reduce their capacity for genetically based adaptation, increasing their extinction risk. Non-genetic variation (e.g. epigenomic modifications such as DNA methylation) and plasticity may facilitate the persistence of threatened plants, yet are rarely incorporated into conservation assessments. We present a case study investigating variation
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Pan-genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-11-23 Yancan Li, Jun Yao, Huiling Sang, Quangui Wang, Long Su, Xiaomeng Zhao, Zhenyu Xia, Feiran Wang, Kai Wang, Delong Lou, Guizhi Wang, Robert M. Waterhouse, Huihua Wang, Shudong Luo, Cheng Sun
The Asian honeybee, Apis cerana, is an ecologically and economically important pollinator. Mapping its genetic variation is key to understanding population-level health, histories and potential capacities to respond to environmental changes. However, most efforts to date were focused on single nucleotide polymorphisms (SNPs) based on a single reference genome, thereby ignoring larger scale genomic
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Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long-term microscopy-based monitoring of the phytoplankton community Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-11-23 Amy C. Thorpe, Eleanor B. Mackay, Tim Goodall, James A. Bendle, Stephen J. Thackeray, Stephen C. Maberly, Daniel S. Read
Palaeolimnological records provide valuable information about how phytoplankton respond to long-term drivers of environmental change. Traditional palaeolimnological tools such as microfossils and pigments are restricted to taxa that leave sub-fossil remains, and a method that can be applied to the wider community is required. Sedimentary DNA (sedDNA), extracted from lake sediment cores, shows promise
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MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-11-23 Ulisses Rocha, Jonas Coelho Kasmanas, René Kallies, Joao Pedro Saraiva, Rodolfo Brizola Toscan, Polonca Štefanič, Marcos Fleming Bicalho, Felipe Borim Correa, Merve Nida Baştürk, Efthymios Fousekis, Luiz Miguel Viana Barbosa, Julia Plewka, Alexander J. Probst, Petr Baldrian, Peter F. Stadler
Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool tailored
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Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae) Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-11-16 Vera Opatova, Kellie Bourguignon, Jason E. Bond
The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit
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Leveraging whole-genome sequencing to estimate telomere length in plants Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-11-15 Michelle Zavala-Paez, Jason Holliday, Jill A. Hamilton
Changes in telomere length are increasingly used to indicate species' response to environmental stress across diverse taxa. Despite this broad use, few studies have explored telomere length in plants. Thus, evaluation of new approaches for measuring telomeres in plants is needed. Rapid advances in sequencing approaches and bioinformatic tools now allow estimation of telomere content from whole-genome
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Genomics and conservation: Guidance from training to analyses and applications Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-11-15 Lauren M. Schiebelhut, Annie S. Guillaume, Arianna Kuhn, Rena M. Schweizer, Ellie E. Armstrong, Mark A. Beaumont, Margaret Byrne, Ted Cosart, Brian K. Hand, Leif Howard, Steven M. Mussmann, Shawn R. Narum, Rita Rasteiro, Angel G. Rivera-Colón, Norah Saarman, Arun Sethuraman, Helen R. Taylor, Gregg W. C. Thomas, Maren Wellenreuther, Gordon Luikart
Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights
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simRestore: A decision-making tool for adaptive management of the native genetic status of wild populations Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-11-15 Flor Hernández, Thijs Janzen, Philip Lavretsky
Anthropogenic hybridization, or higher and non-natural rates of gene flow directly and indirectly induced by human activities, is considered a significant threat to biodiversity. The primary concern for conservation is the potential for genomic extinction and loss of adaptiveness for native species due to the extensive introgression of non-native genes. To alleviate or reverse trends for such scenarios
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Genomic evolution of island birds from the view of the Swinhoe's pheasant (Lophura swinhoii) Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-11-13 Xiao Xu, Chen Wang, Chunzhong Xu, Jiaqing Yuan, Guiqiang Wang, Yajiang Wu, Chen Huang, Haohao Jing, Peng Yang, Lulu Xu, Shiming Peng, Fen Shan, Xiaochao Xia, Fuyuan Jin, Fanghui Hou, Jinhong Wang, Da Mi, Yandong Ren, Yang Liu, David M. Irwin, Xuejuan Li, Wu Chen, Gang Li
Island endemic birds account for the majority of extinct vertebrates in the past few centuries. To date, the evolutionary characteristics of island endemic bird's is poorly known. In this research, we de novo assembled a high-quality chromosome-level reference genome for the Swinhoe's pheasant, which is a typical endemic island bird. Results of collinearity tests suggest rapid ancient chromosome rearrangement
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Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep-sea hydrothermal vents Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-11-13 Won-Kyung Lee, Benny K. K. Chan, Jae-Yoon Kim, Se-Jong Ju, Se-Joo Kim
Thoracican barnacles are a diverse group of marine organisms for which the availability of genome assemblies is currently limited. In this study, we sequenced the genomes of two neolepadoid species (Ashinkailepas kermadecensis, Imbricaverruca yamaguchii) from hydrothermal vents, in addition to two intertidal species. Genome sizes ranged from 481 to 1054 Mb, with repetitive sequence contents of 21.2%
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Estimation of the contemporary effective population size from SNP data while accounting for mating structure Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-11-08 Enrique Santiago, Armando Caballero, Carlos Köpke, Irene Novo
A new method is developed to estimate the contemporary effective population size (Ne) from linkage disequilibrium (LD) between SNPs without information on their location, which is the usual scenario in non-model species. The general theory of linkage disequilibrium is extended to include the contribution of full-sibs to the measure of LD, leading naturally to the estimation of Ne in monogamous and
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PoolParty2: An integrated pipeline for analysing pooled or indexed low-coverage whole-genome sequencing data to discover the genetic basis of diversity Mol. Ecol. Resour. (IF 7.7) Pub Date : 2023-11-03 Stuart Willis, Steven Micheletti, Kimberly R. Andrews, Shawn Narum
Whole-genome sequencing data allow survey of variation from across the genome, reducing the constraint of balancing genome sub-sampling with estimating recombination rates and linkage between sampled markers and target loci. As sequencing costs decrease, low-coverage whole-genome sequencing of pooled or indexed-individual samples is commonly utilized to identify loci associated with phenotypes or environmental