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

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

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

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

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

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

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 390.38Mb chromosome‐level genome of fall armyworm derived from south‐central Africa using Pacific Bioscience

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 –

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

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

Understanding how landscape features affect gene flow has implications for numerous fields including molecular and evolutionary ecology. Despite this, modeling 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

The Cephalopods 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 behavioral repertoires. Thus, they are interesting species for studying the mechanisms of evolutionary convergence, innovational functional structures, and evolutionary adaptation to a highly active, predatory

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 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

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

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

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

As species extinction rates increase, genomics provides a powerful tool to support intensive management of threatened species. We use the Tasmanian devil 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 program and reduced‐representation sequencing (RRS) of 98 founders

The leopard coral grouper, Plectropomus leopardus , belonging to genus Plectropomus, family Epinephelinae, is a carnivorous coral reef fish widely distributing in the tropical and subtropical water of Indo‐Pacific Oceans. 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

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

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

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

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

Erosion of biodiversity generated by anthropogenic activities has been studied for decades and in many areas at the species level, using taxa monitoring. In contrast, genetic erosion within species has rarely been tracked, and is often studied by inferring past population dynamics from contemporaneous estimators. An alternative to such inferences is the direct examination of past genes, by analysing

Marine sedimentary ancient DNA (sedaDNA) provides a powerful means to reconstruct marine palaeo-communities across the food web. However, currently there are few optimized sedaDNA extraction protocols available to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) across a broad diversity of eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing

One of the most fundamental aspects of ecological research and monitoring is accurate species identification, but cryptic speciation and observer error can confound phenotype‐based identification. The CRISPR‐Cas toolkit has facilitated remarkable advances in many scientific disciplines, but the fields of ecology and conservation biology have yet to fully embrace this powerful technology. The recently

The leaf resemblance of Kallima (Nymphalidae) butterflies is an important ecological adaptive mechanism that increases their survival. However, the genetic mechanism underlying ecological adaptation remains unclear owing to a dearth of genomic information. Here, we determined the karyotype (n  = 31) of the dead‐leaf butterfly Kallima inachus , and generated a high‐quality, chromosome‐level assembly

Salmonids are of particular interest to evolutionary biologists due to their incredible diversity of life-history strategies and the speed at which many salmonid species have diversified. In Switzerland alone, over 30 species of Alpine whitefish from the subfamily Coregoninae have evolved since the last glacial maximum, with species exhibiting a diverse range of morphological and behavioural phenotypes

Species' responses at the genetic level are key to understanding the long-term consequences of anthropogenic global change. Herbaria document such responses, and, with contemporary sampling, provide high-resolution time-series of plant evolutionary change. Characterizing genetic diversity is straightforward for model species with small genomes and a reference sequence. For nonmodel species-with small

High-throughput sequencing technologies are a proposed solution for accessing the molecular data in historical specimens. However, degraded DNA combined with the computational demands of short-read assemblies has posed significant laboratory and bioinformatics challenges for de novo genome assembly. Linked-read or "synthetic long-read" sequencing technologies, such as 10× Genomics, may provide a cost-effective

The greenfin horse-faced filefish, Thamnaconus septentrionalis, is a valuable commercial fish species that is widely distributed in the Indo-West Pacific Ocean. This fish has characteristic blue-green fins, rough skin and a spine-like first dorsal fin. T. septentrionalis represents a conservation issue because its population has declined sharply, and it is an important marine aquaculture fish species

Despite the importance of the geographical arrangement of populations for the inference of species boundaries, only few approaches that integrate spatial information into species delimitation have been developed so far. Persistent differentiation of sympatrical groups of individuals is the best criterion for species status. Species delimitation becomes more prone to error if allopatric metapopulations

Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes; however, the transfer

The fall armyworm (Spodoptera frugiperda ) is a lepidopteran insect pest that causes huge economic losses. This notorious insect pest has rapidly spread over the world in the past few years. However, the mechanisms of rapid dispersal are not well understood. Here, we report a chromosome‐level assembled genome of the fall armyworm, named the ZJ‐version, using PacBio and Hi‐C technology. The sequenced

High-throughput sequencing of transcriptomes and targeted genomic regions are advancing our knowledge of The Tree of Life. Building phylogenies with regions of the genome requires 1-to-1 ortholog resources of genes and non-coding loci. One organismal group that has received little attention in this area is the Hemiptera, the fifth largest insect order represented by approximately 103,590 named species

Random sampling is an important statistical assumption, but virtually impossible when sampling a wild species as we cannot know where all the individuals exist. While inter-population or intra-taxa sampling methods have been developed, there are currently few intra-taxon sampling methods to objectively decide where to sample wild taxa. We suggest a new sampling method which computes appropriate sampling

Promoted by the barcoding approach, mitochondrial DNA is more than ever used as a molecular marker to identify species boundaries. Yet, it has been repeatedly argued that it may be poorly suited for this purpose, especially in insects where mitochondria are often associated with invasive intracellular bacteria that may promote their introgression. Here we inform this debate by assessing how divergent

Thanks to the development of high-throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routine inference of phylogenetic relationships from thousands of genomic markers. Recently, it has been shown that mitochondrial DNA (mtDNA) is frequently sequenced alongside the targeted loci in such capture experiments. Despite its broad evolutionary

To fully understand how plastic is affecting the ocean, we need to understand how marine life interacts directly with it. Besides their ecological relevance, microbes can affect the distribution, degradation and transfer of plastics to the rest of the marine food web. From amplicon sequencing and scanning electron microscopy, we know that a diverse array of microorganisms rapidly associate with plastic

The emergence of third‐generation sequencing (3GS; long‐reads) is bringing closer the goal of chromosome‐size fragments in de novo genome assemblies. This allows the exploration of new and broader questions on genome evolution for a number of nonmodel organisms. However, long‐read technologies result in higher sequencing error rates and therefore impose an elevated cost of sufficient coverage to achieve

It has become clear that hybridization between species is much more common than previously recognized. As a result, we now know that the genomes of many modern species, including our own, are a patchwork of regions derived from past hybridization events. Increasingly researchers are interested in disentangling which regions of the genome originated from each parental species using local ancestry inference

The greenhouse whitefly, Trialeurodes vaporariorum Westwood, is an agricultural pest of global importance. Here we report a 787-Mb high-quality draft genome sequence of T. vaporariorum assembled from PacBio long reads and Hi-C chromatin interaction maps, which has scaffold and contig N50 lengths of 70 Mb and 500 kb, respectively, and contains 18,275 protein-coding genes. About 98.8% of the assembled

Crassostrea hongkongensis is a popular and important native oyster species that is cultured mainly along the coast of the South China Sea. However, the absence of a reference genome has restricted genetic studies and the development of molecular breeding schemes for this species. Here, we combined PacBio and 10 × Genomics technologies to create a C. hongkongensis genome assembly, which has a size of

GenoDive v. 3.0, is a user-friendly program for the analysis of population genetic data. This version presents a major update from the previous version and now offers a wide spectrum of different types of analyses. GenoDive has an intuitive Graphical User Interface that allows direct manipulation of the data though transformation, imputation of missing data, and excluding and including individuals

Environmental DNA (eDNA) metabarcoding surveys enable rapid, non-invasive identification of taxa from trace samples with wide-ranging applications from characterising local biodiversity to identifying food-web interactions. However, the technique is prone to error from two major sources: i) contamination through foreign DNA entering the workflow, and ii) misidentification of DNA within the workflow

Dendrolimus spp. are important destructive pests of conifer forests, and Dendrolimus punctatus Walker (Lepidoptera; Lasiocampidae) is the most widely distributed Dendrolimus species. During periodic outbreaks, this species is said to make "fire without smoke" because large areas of pine forest can be quickly and heavily damaged. Yet, little is known about the molecular mechanisms that underlie the

Model based methods for genetic clustering of individuals such as those implemented in structure or ADMIXTURE allow to infer individual ancestries and study population structure. The underlying model makes several assumptions about the demographic history that shaped the analysed genetic data. One assumption is that all individuals are a result of K homogeneous ancestral populations that are all well

Advances in DNA extraction and next-generation sequencing have made a vast number of historical herbarium specimens available for genomic investigation. These specimens contain not only genomic information from the individual plants themselves, but also from associated microorganisms such as bacteria and fungi. These microorganisms may have colonized the living plant (e.g., pathogens or host-associated

High-throughput sequencing (HTS) is central to the study of population genomics and has an increasingly important role in constructing phylogenies. Choices in research design for sequencing projects can include a wide range of factors, such as sequencing platform, depth of coverage and bioinformatic tools. Simulating HTS data better informs these decisions, as users can validate software by comparing

Identification of sex determination system and sex-determining genes have important implications in conservation, ecology and evolution. However, much remains to be discovered about the evolution of different sexual determination systems in teleost fishes, of which the mechanisms of sex determination are remarkably variable. In the present study, the whole genomes of 20 males and 20 females of a Salangid

Oestrogenic wastewater treatment works (WwTW) effluents discharged into UK rivers have been shown to affect sexual development, including inducing intersex, in wild roach (Rutilus rutilus ). This can result in a reduced breeding capability with potential population level impacts. In the absence of a sex probe for roach it has not been possible to confirm whether intersex fish in the wild arise from

Environmental DNA (eDNA) analysis has recently been used as a new tool for estimating intraspecific diversity. However, whether known haplotypes contained in a sample can be detected correctly using eDNA-based methods has been examined only by an aquarium experiment. Here, we tested whether the haplotypes of Ayu fish (Plecoglossus altivelis altivelis) detected in a capture survey could also be detected

Ancherythroculter nigrocauda is a cyprinid fish endemic of the upper reaches of the Yangtze River in China, where it is an important aquaculture and commercial species. It is also a threatened species as a result of overfishing, dam construction and water pollution. In this study, a chromosome‐level genome assembly of A. nigrocauda is reported and built using PacBio sequencing and the Hi‐C technology

De novo transcriptome assembly is a powerful tool, and has been widely used over the last decade for making evolutionary inferences. However, it relies on two implicit assumptions: that the assembled transcriptome is an unbiased representation of the underlying expressed transcriptome, and that expression estimates from the assembly are good, if noisy approximations of the relative abundance of expressed