Apolygus lucorum (Miridae) is an omnivorous pest that occurs world‐wide and is notorious for its serious damage to various crops and substantial economic losses. Although some studies have examined the biological characteristics of this mirid bugs, no reference genome is available in Miridae, limiting in‐depth studies of this pest. Here, we present a chromosome‐scale reference genome of A. lucorum

To characterize microbiomes and other ecological assemblages, ecologists routinely sequence and compare loci that differ among focal taxa. Counts of these sequences convey information regarding the occurrence and relative abundances of taxa, but provide no direct measure of their absolute abundances, due to the technical limitations of the sequencing process. The relative abundances in compositional

Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling genomes at unprecedented quality and contiguity. However, the difficulty to assemble repeat‐rich and GC‐rich regions (genomic “dark matter”) limits insights into the evolution of genome structure and regulatory

Plasmid transfers among bacterial populations can directly influence the ecological adaptation of these populations and their interactions with host species and environment. In this study, we developed a selective multiply‐primed rolling circle amplification (smRCA) approach to enrich and characterize circular plasmid DNA from sponge microbial symbionts via high‐throughput sequencing (HTS). DNA (plasmid

Simultaneous molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics and species delimitation studies. In these investigations, multiple sequence alignments consist of both intra‐ and interspecies samples (mixed samples). As a result, the phylogenetic trees contain interspecies, interpopulation and within‐population

Sarcophaga peregrina is considered to be of great ecological, medical and forensic significance, and has unusual biological characteristics such as an ovoviviparous reproductive pattern and adaptation to feed on carrion. The availability of a high‐quality genome will help to further reveal the mechanisms underlying these charcateristics. Here we present a de novo‐assembled genome at chromosome scale

Collectively called zooxanthellae, photosynthetic dinoflagellates in the family Symbiodiniaceae are typical endosymbionts that unequivocally mediate coral responses to environmental changes. Symbiodiniaceae are genetically diverse, encompassing at least nine phylogenetically distinct genera (clades A–I). The ribosomal internal transcribed spacer 2 (ITS2) region is commonly utilized for determining

As most ecosystems around the world are threatened by anthropogenic degradation and climate change, there is an increasing urgency to implement restoration strategies aiming at ensuring ecosystem self‐sustainability and resilience. An initial step towards that goal relies on selecting the most suitable seed sources for a successful revegetation, which can be extremely challenging in highly degraded

Black gram (Vigna mungo) is an important short duration grain legume crop. Black gram seeds provide an inexpensive source of dietary protein. Here, we applied the 10X Genomics linked‐read technology to obtain a de novo whole genome assembly of V. mungo cultivated variety Chai Nat 80 (CN80). The preliminary assembly contained 12,228 contigs and had an N50 length of 5.2 Mb. Subsequent scaffolding using

Shifting from the analysis of single nucleotide polymorphisms to the reconstruction of selected haplotypes greatly facilitates the interpretation of evolve and resequence (E&R) experiments. Merging highly correlated hitchhiker SNPs into haplotype blocks reduces thousands of candidates to few selected regions. Current methods of haplotype reconstruction from Pool‐seq data need a variety of data‐specific

Estimating the effective population size and effective number of breeders per year (Nb) can facilitate early detection of population declines. We used computer simulations to quantify bias and precision of the one‐sample LDNe estimator of Nb in age‐structured populations using a range of published species life history types, sample sizes, and DNA markers. Nb estimates were biased by ~5–10% when using

Luffa spp. (sponge gourd or ridge gourd) is an economically important vegetable crop widely cultivated in China, India and Southeast Asia. Here, we employed PacBio long‐read single‐molecule real‐time (SMRT) sequencing to perform de novo genome assemblies of two commonly cultivated Luffa species, L. acutangula and L. cylindrica. We obtained preliminary draft genomes of 734.6 Mb and 689.8 Mb with scaffold

The article entitled “A genomic approach to inferring kinship reveals limited intergenerational dispersal in the yellow fever mosquito” which published in Molecular Ecology Resources (volume 19, Issue 5, pages 1254–1264). The authors of the above article, first published online in Wiley Online Library (wileyonlinelibrary.com) in Molecular Ecology Resources, would like to note that in the original paper

Telomere length dynamics are an established biomarker of health and ageing in animals. The study of telomeres in numerous species has been facilitated by methods to measure telomere length by real‐time quantitative PCR (qPCR). In this method, telomere length is determined by quantifying the amount of telomeric DNA repeats in a sample and normalizing this to the total amount of genomic DNA. This normalization

The Cephalopoda are a group of highly diverse marine species in the phylum Mollusca, which are distributed worldwide. They have evolved some vertebrate‐like biological traits and exhibit complicated behavioural repertoires. Thus, they are interesting species for studying the mechanisms of evolutionary convergence, innovational functional structures and evolutionary adaptation to a highly active, predatory

A long‐standing question in biology is how organisms change through time and space in response to their environment. This knowledge is of particular relevance to predicting how organisms might respond to future environmental changes caused by human‐induced global change. Usually researchers make inferences about past events based on an understanding of current static genetic patterns, but these are

A popular approach to learning about admixture from population genetic data is by computing the allele‐sharing summary statistics known as f‐statistics. Compared to some methods in population genetics, f‐statistics are relatively simple, but interpreting them can still be complicated at times. In addition, f‐statistics can be used to build admixture graphs (multi‐population trees allowing for admixture

The ‘One Health’ framework emphasizes the ecological relationships between soil, plant, animal and human health. Microbiomes play important roles in these relationships, as they modify the health and performance of the different compartments and influence the transfer of energy, matter and chemicals between them. Standardized methods to characterize microbiomes along food chains are, however, currently

The Odonata are considered among the most endangered freshwater faunal taxa. Their DNA‐based monitoring relies on validated reference data sets that are often lacking or do not cover important biogeographical centres of diversification. This study presents the results of a DNA barcoding campaign on Odonata, based on the standard 658‐bp 5′ end region of the mitochondrial COI gene, involving the collection

Yak is an important livestock animal for the people indigenous to the harsh, oxygen‐limited Qinghai‐Tibetan Plateau and Hindu Kush ranges of the Himalayas. The yak genome was sequenced in 2012, but its assembly was fragmented because of the inherent limitations of the Illumina sequencing technology used to analyse it. An accurate and complete reference genome is essential for the study of genetic variations

As coral populations decline worldwide in the face of ongoing environmental change, documenting their distribution, diversity and conservation status is now more imperative than ever. Accurate delimitation and identification of species is a critical first step. This task, however, is not trivial as morphological variation and slowly evolving molecular markers confound species identification. New approaches

The brown planthopper Nilaparvata lugens , white‐backed planthopper Sogatella furcifera , and small brown planthopper Laodelphax striatellus are three major insect pests of rice. They are genetically close, however they differ in several ecological traits such as host range, migration capacity, and in their sex chromosomes. Though the draft genome of these three planthoppers have been previously released

Taro (Colocasia esculenta (L.), Schott), from the Araceae family, is one of the oldest crops with important edible, medicinal, nutritional and economic value. Taro is a highly polymorphic species including diverse genotypes adapted to a broad range of environments, but the taro genome has rarely been investigated. Here, a high‐quality chromosomal‐level genome of C. esculenta was assembled using data

The interbreeding of individuals coming from genetically differentiated but incompletely isolated populations can lead to the formation of admixed populations, having important implications in ecology and evolution. In this simulation study, we evaluate how individual admixture proportions estimated by the software structure are quantitatively affected by different factors. Using various scenarios

Genomic analysis of hundreds of individuals is increasingly becoming standard in evolutionary and ecological research. Individual‐based sequencing generates large amounts of valuable data from experimental and field studies, while using preserved samples is an invaluable resource for studying biodiversity in remote areas or across time. Yet, small‐bodied individuals or specimens from collections are

Horseshoe crabs, represented by only four extant species, have existed for around 500 million years. However, their existence is now under threat because of anthropogenic activities. The availability of genomic resources for these species will be valuable in planning appropriate conservation measures. Whole‐genome sequences are currently available for three species. In this study, we have generated

Metabarcoding of environmental DNA (eDNA) and DNA extracted from bulk specimen samples is a powerful tool in studies of biodiversity, diet and ecological interactions as its inherent labelling of amplicons allows sequencing of taxonomically informative genetic markers from many samples in parallel. However, the occurrence of so‐called ‘tag‐jumps’ can cause incorrect assignment of sequences to samples

Mealybugs (Hemiptera: Pseudococcidae) are economically important agricultural pests with several compelling biological phenomena including paternal genome elimination (PGE). However, limited high‐quality genome assemblies of mealybugs hinder a full understanding of this striking and unusual biological phenomenon. Here, we generated a chromosome‐level genome assembly of cotton mealybug, Phenacoccus

Targeted amplicon sequencing methods, such as genotyping‐in‐thousands by sequencing (GT‐seq), facilitate rapid, accurate, and cost‐effective analysis of hundreds of genetic loci in thousands of individuals. Development of GT‐seq panels is nontrivial, but studies describing trade‐offs associated with different steps of GT‐seq panel development are rare. Here, we construct a dual‐purpose GT‐seq panel

Quantitative proteomics via mass spectrometry can provide valuable insight into molecular and phenotypic characteristics of a living system. Recent mass spectrometry developments include data‐independent acquisition (SWATH/DIA‐MS), an accurate, sensitive and reproducible method for analysing the whole proteome. The main requirement for this method is the creation of a comprehensive spectral library

Dietary metabarcoding—the process of taxonomic identification of food species from DNA in consumer guts or faeces—has been rapidly adopted by ecologists to gain insights into biocontrol, invasive species and the structure of food webs. However, an outstanding issue with metabarcoding is the semi‐quantitative nature of the data it provides: because metabarcoding is likely to produce false negatives

Sex‐determining modes remain unknown in numerous species, notably in fishes, in which a variety of modalities have been reported. Additionally, noninvasive individual sexing is problematic for species without external sex attributes or for early life stages, requiring cytogenetic or molecular analyses when sex chromosomes or sex‐linked markers have been characterized. Genomics now provide a means to

Pines are some of the most ecologically and economically important tree species in the world, and many have enormous natural distributions or have been extensively planted. However, a lack of rapid genotyping capability is hampering progress in understanding the molecular basis of genetic variation in these species. Here, we deliver an efficient tool for genotyping thousands of single nucleotide polymorphism

For the past decades, simulation‐based likelihood‐free inference methods have enabled researchers to address numerous population genetics problems. As the richness and amount of simulated and real genetic data keep increasing, the field has a strong opportunity to tackle tasks that current methods hardly solve. However, high data dimensionality forces most methods to summarize large genomic data sets

Symbiotic relationships between vestimentiferan tubeworms and chemosynthetic Gammaproteobacteria build the foundations of many hydrothermal vent and hydrocarbon seep ecosystems in the deep sea. The association between the vent tubeworm Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone has become a model system for symbiosis research in deep‐sea vestimentiferans, while markedly

As molecular ecologists, we have by necessity become adept at working across computational platforms. A diverse community of scientists has developed a broad array of analytical resources spanning command line to graphical user interface across Linux, Mac, and Windows environments and a dizzying array of program‐specific input formats. In light of this, we often explore our data like free divers –

Thrips are tiny insects from the order Thysanoptera (Hexapoda: Condylognatha), including many sap‐sucking pests that are causing increasing damage to crops worldwide. In contrast to their closest relatives of Hemiptera (Hexapoda: Condylognatha), including numerous sap‐sucking species, there are few genomic resources available for thrips. In this study, we assembled the first thrips genome at the chromosomal

As species extinction rates increase, genomics provides a powerful tool to support intensive management of threatened species. We use the Tasmanian devil (Sarcophilus harrisii ) to demonstrate how conservation genomics can be implemented in threatened species management. We conducted whole genome sequencing (WGS) of 25 individuals from the captive breeding programme and reduced‐representation sequencing

The leopard coral grouper, Plectropomus leopardus , belonging to the family Epinephelinae, is a carnivorous coral reef fish widely distributed in tropical and subtropical waters of the Indo‐Pacific. Due to its appealing body appearance and delicious taste, P. leopardus has become a popular commercial fish for aquaculture in many countries. However, the lack of genomic and molecular resources for P

Only a fraction of species found so far has been described, particularly cryptic species uncovered by molecular data. The latter might require the use of molecular data for its diagnosis, but it is important to make use of the diagnostic content of the molecular data itself. The molecular character‐based model provides discrete molecular diagnostic characters within DNA sequences that can be used in

Understanding how landscape features affect gene flow has implications for numerous fields including molecular and evolutionary ecology. Despite this, modelling landscape resistance surfaces has remained a significant challenge. The R package resistancega was developed to provide a framework for optimizing landscape resistance surfaces. In this study, we assessed ResistanceGA's ability to recover the

In recent years, genome‐scan methods have been extensively used to detect local signatures of selection and introgression. Most of these methods are either designed for one or the other case, which may impair the study of combined cases. Here, we introduce a series of versatile genome‐scan methods applicable for both cases, the detection of selection and introgression. The proposed approaches are based

Onychostoma macrolepis is an emerging commercial cyprinid fish species. It is a model system for studies of sexual dimorphism and genome evolution. Here, we report the chromosome‐level assembly of the O.macrolepis genome obtained from the integration of nanopore long‐read sequencing with physical maps produced using Bionano and Hi‐C technology. A total of 87.9 Gb of nanopore sequence provided approximately

The rapid wide‐scale spread of fall armyworm (Spodoptera frugiperda ) has caused serious crop losses globally. However, differences in the genetic background of subpopulations and the mechanisms of rapid adaptation behind the invasion are still not well understood. Here we report the assembly of a 390.38‐Mb chromosome‐level genome of fall armyworm derived from south‐central Africa using Pacific Bioscience

Captive populations play a vital role in conservation, supporting both in situ and ex situ conservation projects. A healthy, self‐sustaining captive population serves as valuable insurance against extinctions and a source of individuals for reintroduction into the wild. Genetic and genomic data can advance conservation and management across a range of scenarios. Although expanding, genomic data do

With recent advances in sequencing technology, genomic data are changing how important conservation management decisions are made. Applications such as Close‐Kin Mark‐Recapture demand large amounts of data to estimate population size and structure, and their full potential can only be realised through ongoing improvements in genotyping strategies. Here we introduce DArTcap, a cost‐efficient method

Whole‐genome sequencing is still often a difficult, costly and time‐consuming task. The emergence of various genome reduced‐representation sequencing (RRS) protocols such as restriction site‐associated DNA sequencing (RADseq) has facilitated the access to genome‐wide information, without the need for whole‐genome sequencing. Reaching the full potential of RRS protocols though requires adjustments and

Parasitoid wasps represent a large proportion of hymenopteran species. They have complex evolutionary histories and are important biocontrol agents. To advance parasitoid research, a combination of Illumina short‐read, PacBio long‐read and Hi‐C scaffolding technologies was used to develop a high‐quality chromosome‐level genome assembly for Pteromalus puparum , which is an important pupal endoparasitoid

Sewall Wright developed F ST for describing population differentiation and it has since been extended to many novel applications, including the detection of homomorphic sex chromosomes. However, there has been confusion regarding the expected estimate of F ST for a fixed difference between the X‐ and Y‐chromosome when comparing males and females. Here, we attempt to resolve this confusion by contrasting

Noninvasive genotyping methods have become key elements of wildlife research over the last two decades, but their widespread adoption is limited by high costs, low success rates and high error rates. The information lost when genotyping success is low may lead to decreased precision in animal population densities, which could misguide conservation and management actions. Single nucleotide polymorphisms

Recent advances in environmental DNA (eDNA) analysis using high‐throughput sequencing (HTS) enable evaluation of intraspecific genetic diversity in a population. As the intraspecific genetic diversity provides invaluable information for wildlife conservation and management, there is an increasing demand to apply eDNA analysis to population genetics and the phylogeography by quantitative evaluation

DNA metabarcoding was utilized for a large‐scale, multiyear assessment of biodiversity in Malaise trap collections from the Bavarian Forest National Park (Germany, Bavaria). Principal component analysis of read count‐based biodiversities revealed clustering in concordance with whether collection sites were located inside or outside of the National Park. Jaccard distance matrices of the presences of

DNA metabarcoding offers new perspectives, especially with regard to the high‐throughput identification and diagnostics of pathogens. Microsporidia are an example of widely distributed, opportunistic and pathogenic microorganisms in which molecular identification is important for both environmental research and clinical diagnostics. We have developed a method for parallel detection of both microsporidian

The feasibility to sequence entire genomes of virtually any organism provides unprecedented insights into the evolutionary history of populations and species. Nevertheless, many population genomic inferences – including the quantification and dating of admixture, introgression and demographic events, and inference of selective sweeps – are still limited by the lack of high‐quality haplotype information

Tunicates occupy the evolutionary position at the boundary of invertebrates and vertebrates. It exhibits adaptation to broad environmental conditions and is distributed globally. Despite hundreds of years of embryogenesis studies, the genetic basis of the invasive habits of ascidians remains largely unknown. The leathery sea squirt, Styela clava , is an important invasive species. We used the chromosomal‐level

Environmental DNA studies targeting multiple taxa using metabarcoding provide remarkable insights into levels of species diversity in any habitat. The main drawbacks are the presence of primer bias and difficulty in identifying rare species. We tested a DNA sequence‐capture method in parallel with the metabarcoding approach to reveal possible advantages of one method over the other. Both approaches

Despite the importance of climate‐adjusted provenancing to mitigate the effects of environmental change, climatic considerations alone are insufficient when restoring highly degraded sites. Here we propose a comprehensive landscape genomic approach to assist the restoration of moderately disturbed and highly degraded sites. To illustrate it we employ genomic data sets comprising thousands of single

Gene annotation is a critical bottleneck in genomic research, especially for the comprehensive study of very large gene families in the genomes of nonmodel organisms. Despite the recent progress in automatic methods, state‐of‐the‐art tools used for this task often produce inaccurate annotations, such as fused, chimeric, partial or even completely absent gene models for many family copies, errors that

Antheraea pernyi is a semi‐domesticated lepidopteran insect species valuable to the silk industry, human health, and ecological tourism. Owing to its economic influence and developmental properties, it serves as an ideal model for investigating divergence of the Bombycoidea super family. However, studies on the karyotype evolution and functional genomics of A. pernyi are limited by scarce genomic resource