Community ecology includes linking variation in system functions to the distribution and abundance of taxa. In inferring processes, functions, and causal taxa, it is common practice to assume a core community can be defined and that attributes of the core are representative of the entire dataset. Assuming categorical thresholds in abundance exist has the potential to be misleading, especially if rare taxa are contributing to ecological processes. Additionally, there are no standard criteria for core membership, complicating comparisons across studies. Rather, the existence of a core set of taxa can be treated as a hypothesis that may or may not be supported. We considered four methods commonly used for defining a core in studies of microbiomes and applied them to two published microbial data sets and simulations covering a range of plausible communities. We evaluated the ability of each method to correctly categorize taxa. Assignment of core taxa varied substantially among methods and datasets. Additionally, the ability of evaluated methods to capture the simulated core was contingent on the distribution of taxon abundances. While able to correctly identify core taxa in select cases, the methods disagreed more often than not. Given the lack of agreement among core assignment methods, categorization of taxa into sets corresponding to core and non-core is questionable and requires testing and validation before use in any particular context. Our results do not support applying methods of dimension reduction for core taxa classification, but instead provide additional rationale to favor analyses that use abundance data in their entirety.

The salmonid-specific fourth vertebrate whole-genome duplication (Ss4R) occurred ~80 million years ago in the ancestor of all salmonids and provides a unique opportunity to study the evolutionary history of the duplicated genome. Study of the genome of Brachymystax lenok tsinlingensis might be particularly insightful given that this is the only Brachymystax species with a published salmonid genome. Here, we present a high-quality chromosome-level genome assembly for B. l. tsinlingensis and found that the salmonids have a unique GC content and codon usage, have undergone a whole-genome duplication event and a burst of transposon-mediated repeat expansion, have a slower evolutionary rate, and possess specific expanded gene families and unique positively selected genes. Generally, the B. l. tsinlingensis genome could provide a valuable reference for the study of other salmonids as well as aid the conservation of this endangered species.

The canga of the Serra dos Carajás, in Eastern Amazon, is home to a unique open plant community, harbouring several endemic and rare species. Although a complete flora survey has been recently published, scarce to no genetic information is available for most plant species of the ironstone outcrops of the Serra dos Carajás. In this scenario, DNA barcoding appears as a fast and effective approach to assess the genetic diversity of the Serra dos Carajás flora, considering the growing need for robust biodiversity conservation planning in such an area with industrial mining activities. Thus, after testing eight different DNA barcode markers (matK, rbcL, rpoB, rpoC1, atpF-atpH, psbK-psbI, trnH-psbA and ITS2), we chose rbcL and ITS2 as the most suitable markers for a broad application in the regional flora. Here we describe DNA barcodes for 1,130 specimens of 538 species, 323 genera and 115 families of vascular plants, with a total of 344 species being barcoded for the first time. In addition, we assessed the potential of using DNA metabarcoding of bulk samples for surveying plant diversity in the canga. Upon achieving the first comprehensive DNA barcoding effort directed to a complete flora in the Brazilian Amazon, we discuss the relevance of our results to guide future conservation measures in the Serra dos Carajás.

COI-based DNA barcoding could be an efficient tool for species identification of deep-sea fishes and could lead to the discovery of cryptic species diversity. However, the availability of reference sequences of deep-sea fishes for DNA barcoding is limited, especially for fishes in the northwestern Pacific Ocean. In this study, we performed DNA barcoding of mesopelagic and demersal fish species on the continental shelf and upper slope, collected from deepwater fisheries around Japan and southern Taiwan, to accumulate the reference sequences of deep-sea fishes in the northwestern Pacific Ocean. Overall, we obtained the COI sequences of 123 species from 50 families. Genetic diversity within each species for which COI sequences were obtained from multiple specimens was examined, and we found that Chimaera phantasma (Chimaeridae), Harpadon microchir (Synodontidae), and Pyramodon ventralis (Carapidae) showed high intraspecific genetic differentiation of more than 2% Kimura two-parameter distance. Moreover, for 19 widespread deep-sea fishes, a comparison between our data and previously acquired COI sequence data suggested a high level (more than 2% Kimura two-parameter distance) of genetic differentiation between the northwestern Pacific Ocean and other oceans in each widespread species. These results suggest that many cryptic species or regional populations have not yet been discovered in deep-sea fishes. Alternatively, genetic differentiation was not found worldwide for six species. These results indicate that many taxonomic and biogeographical issues remain for deep-sea fishes, and our DNA barcoding data would provide better understanding of these issues.

DNA-barcoding and DNA-based species delimitation are major tools in DNA taxonomy. Sampling has been a central debate in this context, because the geographical composition of samples affect the accuracy and performance of DNA-barcoding. Performance of complex DNA-based species delimitation is to be tested under simpler conditions in absence of geographic sampling bias. Here, we present an empirical data set sampled from a single locality in a Southeast-Asian biodiversity hotspot (Laos: Phou Pan mountain). We investigate the performance of various species delimitation approaches on a megadiverse assemblage of herbivore chafer beetles (Coleoptera: Scarabaeidae) to infer whether species delimitation suffers in the same way from exaggerate infraspecific variation despite the lack of geographic genetic variation that led to inconsistencies between entities from DNA-based and morphology-based species inference in previous studies. For this purpose, a 658 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) was analysed for a total of 186 individuals of 56 morphospecies. Tree based and distance based species delimitation methods were used. All approaches showed a rather limited match ratio (max. 77%) with morphospecies. PTP and TCS prevailingly over-splitted morphospecies, while 3% clustering and ABGD also lumped several species into one entity. ABGD revealed the highest congruence between molecular operational taxonomic units (MOTUs) and morphospecies. Disagreements between morphospecies and MOTUs were discussed in the context of historically acquired geographic genetic differentiation, incomplete lineage sorting, and hybridization. The study once again highlights how important morphology still is in order to correctly interpret the results of molecular species delimitation.

Comparisons of microsatellite and single-nucleotide polymorphisms (SNPs) have found that SNPs outperform microsatellites in population genetic analyses, calling into the question the continued utility of microsatellites in population and landscape genetics. Yet highly polymorphic markers may be of value in species that have reduced genetic variation. This study repeated analyses previously done using microsatellites with SNPs developed from ddRAD sequencing in the black-capped vireo source-sink system. SNPs provided greater resolution of genetic diversity, population differentiation, and migrant detection but could not reconstruct parentage relationships due to insufficient heterozygosities. The biological inferences made by both sets of markers were similar: asymmetrical gene flow from source populations to the remaining sink populations. With the landscape genetic analyses, we found different results between the two molecular markers, but associations of the top environmental features (riparian, open habitat, agriculture, and human development) with dispersal estimates were shared between marker types. Despite the higher precision of SNPs, we find that microsatellites effectively uncover population processes and patterns and are superior for parentage analyses in this species with reduced genetic diversity. This study illustrates the continued applicability and relevance of microsatellites in population genetic research.

The Chinese Longsnout catfish Leiocassis longirostris (L. longirostris) is one of the most economically important freshwater catfish in China. It is a valuable model for studies on sexual dimorphism, comparative and conservation biology since its wild resources have declined sharply. However, there is lack of high-quality chromosome-level genome information for comparative genomic analysis and genome evolutionary studies. Therefore, we constructed the first high-quality chromosome-level reference genome for L. longirostris using a combined strategy of BGI-SEQ500, Nanopore, and Hi-C technologies. The assembled genome of L. longirostris contained a total length of 703.19 Mb with 389 contigs, and an N50 size of 4.29 Mb. Using the Hi-C data, we finally successfully generated 82 chromosome-level scaffolds anchored onto 26 chromosomes with a total length of 685.53 Mb (97.44% of the total genome sequences), ranging in size from 17.36 Mb to 43.97 Mb. A total of 23,708 protein-coding genes were identified in the L. longirostris genome, and up to 97.73% of L. longirostris genes were functionally annotated. In addition, the genome contained 239.11 Mb (33.99% in the total genome) repetitive sequences and 6,303 non-coding RNAs. The phylogenetic analysis indicated that the divergence time between L. longirostris and their closest relative species Pelteobagrus fulvidraco was approximately 26.6 million years. Collinearity analyses showed 26 chromosomes of L. longirostris displayed high homology with the corresponding scaffold (≥3M) of P. fulvidraco and the corresponding chromosomes of the Ictalurus punctatus. The high-quality reference genome of L. longirostris was assembled for the first time and will pave a way for genome-scale selective breeding, genome comparisons and evolution investigations.

DNA-based techniques are increasingly used to assess biodiversity both above- and belowground. Most effort has focussed on bioinformatics and sample collection, whereas less is known about the consequences of mixing collected environmental DNA (eDNA), post-extraction and pre-PCR. We applied varying degrees of pooling to stand-alone eDNA samples collected across a non-native plant invasion density gradient, and compared the fungal communities of pooled and unpooled samples. Pooling soil eDNA decreased observable fungal rarefied richness in our samples, led to phylum-specific shifts in proportional abundance, and increased the sensitivity of detection for the invasive plant’s overall impact on fungal diversity. We demonstrate that pooling fungal eDNA could change the outcome of similar eDNA studies where the aim is to: 1) identify the rare biosphere within a soil community, 2) estimate species richness and proportional abundance, or 3) assess the impact of an invasive plant on soil fungi. Sample pooling might be appropriate when determining larger-scale overarching responses of soil communities, as pooling increased the sensitivity of measurable effects of an invasive plant on soil fungal diversity.

Classical taxonomic approaches to quantifying biodiversity can be notoriously laborious and restrictive. Instead, molecular metabarcoding is emerging as a rapid, high-throughput and cost-effective tool to catalogue biodiversity. Despite the appeal of metabarcoding however, methodological and procedural biases must be understood before robust biodiversity inferences can be made. Here, we use CO1 metabarcoding to characterize marine eukaryote communities associated with the holdfasts of Ecklonia radiata, the dominant eco-engineering kelp of temperate New Zealand and Australia. To establish a standardized and reproducible community metabarcoding protocol, we examined the influence of different sample preparation, laboratory and bioinformatic steps on inferences of species richness and composition for kelp-holdfast communities. Specifically, we examined: the effect of fractioning the community into different size classes, the replicability of results across DNA extractions, PCR reactions, and sequencing. Overall, our approach identified 18 marine eukaryote Phyla in the holdfast communities. We found that size fractioning the sample before DNA extraction enabled detection of a greater diversity of taxa, especially smaller organisms. When compared with traditional morphology-based inventories of kelp-holdfast biodiversity, we found that although the taxonomic precision of our metabarcoding approach at the species and genus level was limited by the availability of reference sequences in public repositories, we recovered a greater number of operational taxonomic units, and a greater taxonomic breadth of organisms than morphological surveys. Based on our findings, we provide methodological guidelines for the use of metabarcoding as a tool for surveying and monitoring the hyperdiverse species assemblages associated with kelp-holdfasts.

Macroinvertebrate biodiversity is routinely used to assess the ecological condition of freshwater environments. Macroinvertebrates are traditionally identified morphologically to mostly family level but using DNA metabarcoding they can be rapidly and reliably identified to species. Developing standardised, robust and cost-effective protocols would enable DNA metabarcoding to be broadly used for routine freshwater biological assessments leading to both potential cost savings as well as increased taxonomic resolution. To further reduce the cost and time it takes to process samples, we examine the feasibility of DNA metabarcoding unsorted macroinvertebrates (macroinvertebrates and debris) from sweep net samples collected from stream pool or edge habitats. We processed these unsorted samples with a standardised method and tested multiple primer sets widely used for invertebrate DNA metabarcoding. We found that currently available DNA metabarcoding primers are well suited for processing unsorted samples, though some performed better than others. However, macroinvertebrate density affected the number of species detected with DNA metabarcoding, particularly the detection of rare taxa. These findings show that DNA metabarcoding of unsorted net contents could streamline macroinvertebrate sample processing for bioassessment, but the optimal amounts of unsorted material for sub-sampling needs to be considered when assessing macroinvertebrate biodiversity.

The Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve that is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is high in protein, amino acids, and microelements. In China, C. fluminea plays an important role in the diversity of freshwater ecosystems. The genome of C. fluminea has not yet been characterized, therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4,728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The expanded genes were significantly enriched in 9 terms associated with metabolite synthesis. The phylogenetic tree showed that C. fluminea diverged from the ancestors of marine bivalves ~492.00 million years ago (Mya). Additionally, we identified two MITF genes in C. fluminea and several core genes involved in vitamin B6 metabolic pathways. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research.

Silver sillago, Sillago sihama is a member of the family Sillaginidae and found in all Chinese inshore waters. It is an emerging commercial marine aquaculture species in China. In this study, high-quality chromosome-level reference genome of S. sihama was first constructed using PacBio Sequel sequencing and high-throughput chromosome conformation capture (Hi-C) technique. A total of 66.16 Gb clean reads were generated by PacBio sequencing platforms. The genome-scale was 521.63 Mb with 556 contigs, and 13.54 Mb of contig N50 length. Additionally, Hi-C scaffolding of the genome resulted in 24 chromosomes containing 96.93 % of the total assembled sequences. A total of 23,959 protein-coding genes were predicted in the genome, and 96.51 % of the genes were functionally annotated in public databases. A total of 71.86 Mb repetitive elements were detected, accounting for 13.78% of the genome. The phylogenetic relationships of silver sillago with other teleosts showed that silver sillago was separated from the common ancestor of S. sinica about 7.92 million years ago. Comparative genomic analysis of silver sillago with other teleosts showed that 45 unique and 100 expansion gene families were identified in silver sillago. Expansion gene families were involved in immune and olfactory receptors. In this study, the genomic resources provide valuable reference genomes for functional genomics research of silver sillago.

Conservation genomics research often relies on accurate sex information to make inferences about species demography, dispersal, and population structure. However, field determined sex data are not always available and can be subject to human error, while laboratory sex determination is costly and often challenging for non-model species. Conservation genomics programs increasingly use reduced-representation genome sequencing to assess neutral and functional genetic diversity, population structure, gene flow and pedigrees in threatened species. Here we demonstrate that sex can be determined from reduced-representation sequencing data produced by the increasingly popular Diversity Arrays Technology sequencing workflow (DArT-seq) using a program originally designed for application to shotgun data. This program – sexassign – compares the “dosage” of sequencing reads mapping to autosomes versus the X chromosome. In the present study, sexassign accurately determined the sex of 60 field-collected Greater Stick-Nest Rat (Leporillus conditor) samples, despite the absence of an annotated reference genome for the species. This “read-dosage” approach is not only more accurate and affordable than traditional sex determination methods, but can be applied to any diploid organism with a heterogametic sex determination system – including non-model and understudied species of conservation importance – by using FASTQs generated by DArT.

Abstract：Sophora tonkinensis (shandougen) is a woody leguminous plant widely known for its medicinal values in China. The genome of various legumes utilized as reference genetic maps for pseudomolecule assembly have been published. However, the genome of Sophora has not been mapped. In this study, we reported a chromosomal scale draft genome of S. tonkinensis assembled using PacBio single-molecule real-time sequencing reads and Hi-C technique. A high-quality draft S. tonkinensis genome of 899Mb in size was obtained, which was larger than those of some other leguminous genome, and the BUSCO analysis reviewed 95.9% completeness of the genome. We annotated 78.3% of the genome as repeat elements and transposable elements occupied 73%. A total of 36,410 protein-coding genes were identified in the S. tonkinensis genome. The comparative analysis on genome size and repetitive sequences of S. tonkinensis and four other legumes (Lupinus albus, Lupinus angustifolius, Glycyrrhiza uralensis and Medicago truncatula) revealed that the transposable elements (TEs) in S. tonkinensis were inserted after the whole genome duplication and after differentiation with other legumes. It can be speculated that the size of the S. tonkinensis genome may be related to the repetitive sequence insertion. We also analyzed matrine and flavonoids which are important compounds in S. tonkinensis. We further analyzed lignin and Nitrogen-fixing gene which plays an important role in the adaptation of S. tonkinensis to the environment. In conclusion, the high-quality genome of S. tonkinensis obtained in this study laid the foundation for genetic and molecular biology studies of legumes.

The Genome-Wide Association Studies (GWAS) are essential to determine the genetic bases of either ecological or economic phenotypic variation across individuals within populations of model and non-model organisms. For this research question, current practice is the replication of the GWAS testing different parameters and models to validate the reproducibility of results. However, straightforward methodologies that manage both replication and tetraploid data are still missing. To solve this problem, we designed the MultiGWAS, a tool that does GWAS for diploid and tetraploid organisms by executing in parallel four software, two for polyploid data (GWASpoly and SHEsis) and two for diploids data (PLINK and TASSEL). MultiGWAS has several advantages. It runs either in the command line or in an interface. It manages different genotype formats, including VCF. It executes both the full and naïve models using several quality filters. Besides, it calculates a score to choose the best gene action model across GWASPoly and TASSEL. Finally, it generates several reports that facilitate the identification of false associations from both the significant and the best-ranked association SNP among the four software. We tested MultiGWAS with tetraploid potato data. The execution demonstrated that the Venn diagram and the other companion reports (i.e., Manhattan and QQ plots, heatmaps for associated SNP profiles, and chord diagrams to trace associated SNP by chromosomes) were useful to identify associated SNP shared among different models and parameters. Therefore, we confirmed that MultiGWAS is a suitable wrapping tool that successfully handles GWAS replication in both diploid and tetraploid organisms.

Chinese flowering cabbage (Brassica rapa var. parachinensis) is a popular and widely cultivated leaf vegetable crop in Asia. Here, we performed a high quality de novo assembly of the 384 Mb genome of 10 chromosomes of a typical cultivar of Chinese flowering cabbage with an integrated approach using PacBio, Illumina, and Hi-C technology. We modeled 47,598 protein-coding genes in this analysis and annotated 52% (205.9/384) of its genome as repetitive sequences including 17% in DNA elements and 22% in long terminal retrotransposons (LTRs). Phylogenetic analysis reveals the genome of the Chinese flowering cabbage has a closer evolutionary relationship with the AA diploid progenitor of the allotetraploid species, Brassica juncea. Comparative genomic analysis of Brassica species with different subgenome types (A, B and C) reveals that the pericentromeric regions on chromosome 5 and 6 of the AA genome have been significantly expanded compared to the orthologous genomic regions in the BB and CC genomes, largely drive by LTR-retrotransposon amplification. This lineage-specific expansion may play a role in the species divergence in the Brassica genus. Furthermore, we found that a large amount of structural variations (SVs) identified within B. rapa lines that could impact coding genes, suggesting the functional significance of SVs on Brassica genome evolution. Overall, our high-quality genome assembly of the Chinese flowering cabbage provides a valuable genetic resource for deciphering the genome evolution of Brassica species and it can potentially serve as the reference genome guiding the molecular breeding practice of B. rapa crops.

Abstract: Natural hybridization is a common key evolutionary process and a long-standing topic in the plant taxon. Hybrid zones, where two closely related species interact, can provide an avenue to insight the process, illuminating the maintenance of the taxon diversity. Incomplete isolation barriers between Ligularia species generally form hybrid zones. In this study, we used the double digest restriction-site associated DNA sequencing technology (ddRAD-seq) to examine genetic structure and estimate introgression in four newly discovered hybrid zones between L. tongolensis and L. cymbulifera. Our results showed high differentiation between parental species, whereas pairwise FST between parents and their hybrids was low, further corroborating sympatric site form hybrid zones. Moreover, most F1 hybrid individuals were observed within the four hybrid zones implying the presence of substantial barriers to interbreeding. An analysis of genomic clines indicated that a large fraction of loci deviated from a model of neutral introgression in the four hybrid zones, of which most loci exhibited selection favouring L. cymbulifera genotypes. Our analysis demonstrated bidirectional but asymmetric introgression appearing in the four hybrid zones. The different habitats among four hybrid zones may affect isolation barriers between both species. Natural hybridization with post-zygotic isolation barriers may significantly contribute to the diversification of Ligularia in the HMR.

Arachnids are the most abundant land predators. Despite the importance of their functional roles as predators and the of necessity to understand their diet for conservation and nutrient fluxes, the trophic ecology of many arachnid species is not fully understood. In the case of the wandering spider, Phoneutria boliviensis F. O. Pickard-Cambridge, 1897, only selected field and laboratory observational studies about their diet exist. By using a DNA metabarcoding approach, we compared the prey found in the gut content of males and females from three distant Colombian populations of P. boliviensis. By DNA metabarcoding of the cytochrome c oxidase subunit I (COI), we detected and identified 234 prey records belonging to 96 operational taxonomic units (OTUs), as prey for this wandering predator. Our results broaden the known diet of P. boliviensis with at least 75 prey taxa not previously registered in fieldwork or laboratory experimental trials. These results suggest that P. boliviensis feeds predominantly on invertebrates (Diptera, Lepidoptera, Coleoptera and Orthoptera) and opportunistically on small squamates. Intersex and interpopulation differences are observed. Assuming that prey preference does not vary between populations, these differences are likely associated with a higher local prey availability. Finally, we suggest that DNA metabarcoding can be used for evaluating subtle differences in the diet of distinct populations of P. boliviensis, particularly when predation records in the field cannot be established or quantified using direct observation