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bioRxiv2018

Characterising the microbiome from host shotgun sequencing data: bacterial and diatom community dynamics derived from killer whale skin

Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the hosts biology, health and associated microorganisms. Whereas amplicon sequencing has traditionally been used to characterise the microbiome, the increasing number of published population genomics datasets offer an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterise the skin microbiome and investigate how host social and geographic factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographic factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.

evolutionary biology↗

bioRxiv2018

CLADES: A Classification-based Machine Learning Method for Species Delimitation from Population Genetic Data

Species are considered to be the basic unit of ecological and evolutionary studies. Since multi-locus genomic data are becoming increasingly available, there has been considerable interests in the use of DNA sequence data to delimit species. In this paper, we show that machine learning can be used for species delimitation. There exists no species delimitation methods that are based on machine learning. Our method treats the species delimitation problem as a classification problem. It is a problem of identifying the category of a new observation on the basis of training data. Extensive simulation is first conducted over a broad range of evolutionary parameters for training purpose. Each pair of known populations are combined to form training samples with a label of \"same species\" or \"different species\". We use Support Vector Machine (SVM) to train a classifier using a set of summary statistics computed from training samples as features. The trained classifier can classify a test sample to two outcomes: \"same species\" or \"different species\". Given multi-locus genomic data of multiple related organisms or populations, our method (called CLADES) performs species delimitation by first classifying pairs of populations. CLADES then delimits species by maximizing the likelihood of species assignment for multiple populations. CLADES is evaluated through extensive simulation and also tested on real genetic data. We show that CLADES is both accurate and efficient for species delimitation when compared with existing methods. CLADES can be useful especially when existing methods have difficulty in delimitation, e.g. with short species divergence time and gene flow.

evolutionary biology↗

bioRxiv2018

Meta-analysis challenges a textbook example of status signalling: evidence for publication bias

The status signalling hypothesis aims to explain conspecific variation in ornamentation by suggesting that some ornaments signal dominance status. Here, we use multilevel meta-analytic models to challenge the textbook example of this hypothesis, the black bib of house sparrows (Passer domesticus). We conducted a systematic review, and obtained raw data from published and unpublished studies to test whether dominance rank is positively associated with bib size across studies. Contrary to previous studies, our meta-analysis did not support this prediction. Furthermore, we found several biases in the literature that further question the support available for the status signalling hypothesis. First, the overall effect size of unpublished studies was zero, compared to the medium effect size detected in published studies. Second, the effect sizes of published studies decreased over time, and recently published effects were, on average, no longer distinguishable from zero. We discuss several explanations including pleiotropic, population- and context-dependent effects. Our findings call for reconsidering this established textbook example in evolutionary and behavioural ecology, raise important concerns about the validity of the current scientific publishing culture, and should stimulate renewed interest in understanding within-species variation in ornamental traits.

evolutionary biology↗

bioRxiv2018

Gene expression across tissues, sex, and life stages in the sea urchin Tripneustes gratilla

The pan-tropical sea urchin Tripneustes gratilla is an ecologically and economically important shallow water algal grazer. The aquaculture of T. gratilla has spurred growing interest in the population biology of the species, and by extension the generation of more molecular resources. To this purpose, de novo transcriptomes of T. gratilla were generated for two adults, a male and a female, as well as for a cohort of approximately 1,000 plutei larvae. Gene expression profiles of three adult tissue samples were quantified and compared. These samples were of gonadal tissue, the neural ring, and pooled tube feet and pedicellariae. Levels of shared and different gene expression between sexes, as well as across functional categories of interest, including the immune system, toxins, genes involved in fertilization, and sensory genes are highlighted. Differences in expression of Sex determining Region Y-related High Mobility Group box groups and general isoform expression between the sexes is observed. Additionally an expansion of the tumor suppressor DMBT1 was observed in T. gratilla when compared to the annotated genome of the sea urchin Strongylocentrotus purpuratus. The draft transcriptome of T. gratilla is presented here in order to facilitate more genomic level analysis of de-novo sea urchin systems.

molecular biology↗

bioRxiv2018

Eco-evolutionary community turnover following environmental change

Co-occurring species often differ in intraspecific genetic diversity, which in turn can affect adaptation in response to environmental change. Specifically, the simultaneous evolutionary responses of co-occurring species to temporal environmental change may influence community dynamics. Local adaptation along environmental gradients combined with gene flow can promote genetic diversity of traits under selection within populations. Here I build off existing quantitative genetic theory to study community dynamics of locally adapted species in response to temporal environmental change. I show that species with greater gene flow have lower equilibrium population size due to maladaptive immigrant genotypes (migration load). However, following abrupt environmental change that leaves all species initially maladapted, high gene flow species adapt faster due to greater standing genetic diversity. As a result, communities may undergo a transient reversal in relative abundance, sometimes only after substantial lag periods. If constant temporal environmental change is applied, the community exhibits a shift toward stable dominance by species with intermediate gene flow. High gene flow species can sometimes increase abundance under environmental change if environmental change supresses superior competitor but lower gene flow species. The community dynamics observed here parallel the purely ecological successional dynamics following disturbances and are analogous to the transient benefit of hypermutator alleles under changing environments. My results demonstrate how interspecific variation in life history can have far-reaching impacts on eco-evolutionary community response to environmental change.

evolutionary biology↗

bioRxiv2018

Large-scale gene losses underlie the genome evolution of parasitic plant Cuscuta australis

Dodders (Cuscuta spp., Convolvulaceae) are globally distributed root- and leafless parasitic plants that parasitize a wide range of hosts. The physiology, ecology, and evolution of these obligate parasites are still poorly understood. A high-quality reference genome (size 266.74 Mb and contig N50 of 3.63 Mb) of Cuscuta australis was assembled. Our analyses reveal that Cuscuta experienced accelerated evolution, and Cuscuta and the convolvulaceous morning glory (Ipomoea) shared a common whole-genome triplication event before their divergence. Importantly, C. australis genome harbors only 19805 protein-coding genes, and 11.7% of the conserved orthologs in autotrophic plants are lost in C. australis. Many of these gene loss events likely result from the plants parasitic lifestyle and large changes in its body plan. Moreover, comparison of the gene expression patterns in Cuscuta prehaustoria/haustoria and various tissues of closely related autotrophic plants suggests that Cuscuta haustorium genes largely evolved from roots. The C. australis genome provides important resources for studying the evolution of parasitism, regressive evolution, and evo-devo in plant parasites.

genomics↗

bioRxiv2018

A novel pollen-tracking method: using quantum dots as pollen labels

To understand the evolution of flowers and mating systems in animal-pollinated plants, we have to directly address the function for which flowers evolved--the movement of pollen from anthers to stigmas. However, despite a long history of making significant advances in our understanding natural selection and evolution, the field of pollination biology has largely studied pollen movement indirectly (e.g., pollen analogues or paternity assignment to seeds) due to a lack of suitable pollen tracking methods. Here, we develop and test a novel pollen-tracking technique using quantum dots as pollen-grain labels. Quantum dots are semiconductor nanocrystals so small in size that they behave like artificial atoms. When exposed to UV light, they emit extremely bright light in a range of different colours. Their photostability, broad excitation range, and customisable binding-li-gands make quantum dots ideal bio-labels. We tested the suitability of CuInSexS2-x/ZnS (core/shell) quantum dots with oleic acid (zinc-oleate complex) ligands as pollen-grain labels. We found that quantum dots attach to pollen grains of four different species even after agitation in a polar solvent, suggesting that the oleic acid ligands on quantum dots bind to pollenkitt surrounding pollen grains. We also showed that most pollen grains within anthers of the same four species are labelled with quantum dots after applying sufficient quantum-dot solution to anthers. To test whether quantum-dot pollen-labels influenced pollen transport, we conducted pollen transfer trials on Sparaxis villosa (Iridaceae) using captively reared honeybees. We found no difference in pollen transport between labelled and unlabelled pollen grains. Our experiments therefore demonstrate the potential for quantum dots to be used as easily applied pollen labels, which allow subsequent tracking of the fates of pollen grains in the field. The ability to track pollen grain movement in situ, may finally allow us to address an historically neglected aspect of plant reproductive ecology and evolution.

evolutionary biology↗

bioRxiv2018

Machine learning reveals missing edges and putative interaction mechanisms in microbial ecosystem networks

Microbes affect each others growth in multiple, often elusive ways. The ensuing interdependencies form complex networks, believed to influence taxonomic composition, as well as community-level functional properties and dynamics. Elucidation of these networks is often pursued by measuring pairwise interaction in co-culture experiments. However, combinatorial complexity precludes the exhaustive experimental analysis of pairwise interactions even for moderately sized microbial communities. Here, we use a machine-learning random forest approach to address this challenge. In particular, we show how partial knowledge of a microbial interaction network, combined with trait-level representations of individual microbial species, can provide accurate inference of missing edges in the network and putative mechanisms underlying interactions. We applied our algorithm to two case studies: an experimentally mapped network of interactions between auxotrophic E. coli strains, and a large in silico network of metabolic interdependencies between 100 human gut-associated bacteria. For this last case, 5% of the network is enough to predict the remaining 95% with 80% accuracy, and mechanistic hypotheses produced by the algorithm accurately reflect known metabolic exchanges. Our approach, broadly applicable to any microbial or other ecological network, can drive the discovery of new interactions and new molecular mechanisms, both for therapeutic interventions involving natural communities and for the rational design of synthetic consortia.\n\nImportanceDifferent organisms in a microbial community may drastically affect each others growth phenotype, significantly affecting the community dynamics, with important implications for human and environmental health. Novel culturing methods and decreasing costs of sequencing will gradually enable high-throughput measurements of pairwise interactions in systematic co-culturing studies. However, a thorough characterization of all interactions that occur within a microbial community is greatly limited both by the combinatorial complexity of possible assortments, and by the limited biological insight that interaction measurements typically provide without laborious specific follow-ups. Here we show how a simple and flexible formal representation of microbial pairs can be used for classification of interactions with machine learning. The approach we propose predicts with high accuracy the outcome of yet to be performed experiments, and generates testable hypotheses about the mechanisms of specific interactions.

bioinformatics↗

bioRxiv2018

Metagenomic assembly of new (sub)arctic Cyanobacteria and their associated microbiome from non-axenic cultures

Cyanobacteria form one of the most diversified phylum of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are notably difficult to purify and grow axenically, and most strains in culture collections contain heterotrophic bacteria that were likely associated to Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task. Here, we deploy a metagenomic pipeline that enables the easy recovery of high-quality genomes from non-axenic cultures. We tested this pipeline on 17 cyanobacterial cultures from the BCCM/ULC public collection and generated novel genome sequences for 15 arctic or subarctic strains, of which 14 early-branching organisms that will be useful for cyanobacterial phylogenomics. In parallel, we managed to assemble 31 co-cultivated bacteria from the same cultures and showed that they mostly belong to Bacteroidetes and Proteobacteria, some of them being very closely related in spite of geographically distant sampling sites.\n\nImportanceComplete genomes of cold-adapted Cyanobacteria are underrepresented in databases, due to the difficulty to grow them axenically. In this work, we report the genome sequencing of 12 (sub)arctic and 3 temperate Cyanobacteria, along with 21 Proteobacteria and 5 Bacteroidetes recovered from their microbiome. Following the use of a state-of-the-art metagenomic pipeline, 12 of our new cyanobacterial genome assemblies are of high-quality, which indicates that even non-axenic cultures can yield complete genomes suitable for phylogenomics and comparative genomics. From a methodological point of view, we investigate the fate of SSU rRNA (16S) genes during metagenomic binning and observe that multi-copy rRNA operons are lost because of higher sequencing coverage and divergent tetranucleotide frequencies. Moreover, we devised a measure of genomic identity to compare metagenomic bins of different completeness, which allowed us to show that Cyanobacteria-associated bacteria can be highly related in spite of considerable distance between collection points.

genomics↗

bioRxiv2018

Characterisation of gut microbiota of farmed Chinook salmon using metabarcoding

With the growing importance of aquaculture worldwide, characterisation of the microbial flora of high-value aquaculture species and identification of gut flora shifts induced by changes in fish physiology or nutrition is of special interest.\n\nHere we report the first metabarcoding survey of the intestinal bacteria of Chinook salmon (Oncorhynchus tshawytscha), an economically important aquacultured species. The microbiota of 30 farmed Chinook salmon from a single cohort was surveyed using metabarcode profiling of the V3-V4 hypervariable region of the bacterial 16S rRNA gene. Seawater, feed and intestinal samples, and controls were sequenced in quadruplicate to assess both biological and technical variation in the microbial profiles.\n\nOver 1,000 operational taxonomic units (OTUs) were identified within the cohort, providing a first glimpse into the gut microbiota of farmed Chinook salmon. The taxonomic distribution of the salmon microbiota was reasonably stable, with around two thirds of individuals dominated by members of the family Vibrionaceae.\n\nThis survey was performed amid a summer heat wave, during which the fish exhibited reduced feeding. Although the sampled fish appeared healthy, they had minimal intestinal content, and the observed intestinal flora may represent the microbiota of fasting and stressed fish. Limited comparison between Mycoplasma and Vibrio sequences from the Chinook salmon gut and published microbial sequences from the intestines of a variety of fish species (including Atlantic salmon) indicated that despite the starvation and temperature variations, the replacement of Vibrio with Mycoplasma is occurring within expected ecological parameters and does not necessarily reflect colonisation by atypical microbes.\n\nDATA SUMMARYRaw sequences from Chinook salmon intestinal microbiome 16S survey generated on the Illumina platform are publically available through NCBI Sequence Read Archive (SRA) database:\n\nBioproject PRJNA421844\n\nSRA study SRP134829\n\nhttps://www.ncbi.nlm.nih.gov/bioproject/PRJNA421844\n\nIMPACT STATEMENTAlthough 16S metabarcoding surveys are becoming routine, little is still known about the microbiota of fish. This is the first survey of the intestinal microbiota of Chinook salmon, a species native to the Pacific Northwest which is farmed in New Zealand and Chile. While most intestinal microbiota studies are performed on faecal material, we directly sampled the intestine epithelium and content.\n\nDuring the time of sampling, the farmed fish population was experiencing stress from a summer heat wave and had little intestinal content. Over 1,000 operational taxonomic units (OTUs) were identified within the intestines of the cohort, providing a first glimpse into the gut microbiota of farmed Chinook salmon.\n\nWe believe this survey will be of interest not only to those interested in fish biology and aquaculture, but also as an addition to the ongoing debate in the literature on sampling and DNA extraction methods for challenging samples.

microbiology↗

bioRxiv2018

Ancient DNA reveals the chronology of walrus ivory trade from Norse Greenland

The search for walruses as a source of ivory -a popular material for making luxury art objects in medieval Europe- played a key role in the historic Scandinavian expansion throughout the Arctic region. Most notably, the colonization, peak and collapse of the medieval Norse colony of Greenland have all been attributed to the proto-globalization of ivory trade. Nevertheless, no studies have directly traced European ivory back to distinct populations of walrus in the Arctic. This limits our understanding of how ivory trade impacted the sustainability of northern societies and the ecology of the species they relied on. Here, we compare the mitogenomes of 27 archaeological walrus specimens from Europe and Greenland (most dated between 900 and 1400 CE) and 10 specimens from Svalbard (dated to the 18th and 19th centuries CE) to partial mitochondrial (MT) data of over 300 modern walruses. We discover two monophyletic mitochondrial clades, one of which is exclusively found in walrus populations of western Greenland and the Canadian Arctic. Investigating the chronology of these clades in our European archaeological remains, we identify a significant shift in resource use from predominantly eastern sources towards a near exclusive representation of walruses from western Greenland. These results provide empirical evidence for the economic importance of walrus for the Norse Greenland settlements and the integration of this remote, western Arctic resource into a medieval pan-European trade network.

genomics↗

bioRxiv2018

Chronic environmentally relevant levels of Simvastatin induces non-monotonic responses in Zebrafish (Danio rerio)

Simvastatin (SIM), a hypocholesterolaemic compound, is among the most prescribed pharmaceuticals for cardiovascular disease prevention worldwide. Several studies have shown that acute exposure to SIM is able to produce multiple adverse effects in aquatic organisms. However, uncertainties still remain regarding the chronic effects of SIM in aquatic ecosystems. Therefore, the present study aimed to investigate the effects of SIM in the model freshwater teleost zebrafish (Danio rerio) following a chronic exposure (90 days) to environmentally relevant concentrations ranging from 8 ng/L to 1000 ng/L. This study used a multi-parametric approach integrating distinct ecological-relevant endpoints, i.e. survival, growth, reproduction and embryonic development, with biochemical markers (cholesterol and triglycerides). Furthermore, Real Time PCR was used to analyse the transcription levels of key genes involved in the mevalonate pathway (hmgcra, cyp51, and dhcr7). Globally, SIM induced several non-monotonic dose-responses; embryonic development, biochemical and molecular markers, were significantly impacted in the low-intermediate concentrations, 40 ng/L and 200 ng/L, whereas no effects were recorded for the highest tested SIM levels (1000 ng/L). Taken together, these findings expand our understanding of statins effects in teleosts, demonstrating significant impacts at environmentally relevant concentrations. The findings highlight the importance of addressing the effects of chemicals under chronic low-level concentrations.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC=\"FIGDIR/small/289694v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (17K):\norg.highwire.dtl.DTLVardef@1922156org.highwire.dtl.DTLVardef@caad80org.highwire.dtl.DTLVardef@44c058org.highwire.dtl.DTLVardef@1afe60f_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LISeveral uncertainties exist regarding simvastatin mode of action in non-target organisms\nC_LIO_LIThis work integrates D. rerio multi-level responses after long-term exposure to simvastatin\nC_LIO_LISimvastatin impacted cholesterol/triglycerides levels and transcript levels of genes related to mevalonate pathway.\nC_LIO_LIParental exposure to simvastatin induced offspring embryonic malformations.\nC_LIO_LIEmbryonic abnormalities, biochemical and molecular data did follow a non-monotonic curve.\nC_LI

pharmacology and toxicology↗

bioRxiv2018

Not so sterile after all: The endomicrobiome of plerocercoids of the cestode parasite Schistocephalus solidus and changes to the microbiome of its Threespine Stickleback host

Despite the growing recognition of the role of bacteria in animal biology, the microbiome of parasites remains largely unexplored. In particular, the presence of bacteria in tapeworms has never been investigated and parasites that exit the intestine would be considered sterile. We characterized for the first time the microbiome of a tapeworm. Schistocephalus solidus plerocercoids, collected from the body cavity of its stickleback host, were found to harbor a complex microbiome. The most abundant and the most prevalent bacteria was Polynucleobacter sp.. In addition, S. solidus infection was associated significant changes in the stickleback host gut microbiome with an increase in microbial load and changes in diversity and composition. Finally, the same bacteria were often found in S. solidus and the stomach and intestine of the corresponding hosts, a result that highlights the importance of characterizing the microbiome of host tissues and parasites from the same individuals to assess the potential for horizontal transmission of microbes. This study clearly emphasizes the need for further characterization of the microbiome of a broad range of parasites and for studies to determine the ecological, evolutionary and functional role that microbes play in host-parasite interactions.

microbiology↗

bioRxiv2018

Imaging the evolution of visual specializations in fungus gnats

Many insects use vision to inform their behavior, but visual information differs between habitats and the sensory demands vary with each species ecology. The small size of insects eyes constrains their optical performance, and so it is unsurprising that they have evolved specializations for optimizing the information they obtain from their habitat. Unraveling how behavioral, environmental, and phylogenetic factors influence the evolution of such specializations is difficult, however, because existing techniques to analyze insect eyes require specimens to be preserved beforehand. To facilitate broad comparative studies on insect eyes and the evolution of complex visual behavior, we developed a novel analysis technique that uses x-ray micro-computed tomography to quantify and recreate the visual world of insects. We use our methodology to investigate the eyes of fungus gnats (Orfeliini), a tribe of diminutive Dipterans, to identify the visual specializations they evolved for surviving in different forest habitats and to explore how this changed over 30 million years of evolutionary history. The specimens we studied were preserved in different ways (in ethanol, air dried, and as an endocast in amber), demonstrating that our method provides a new opportunity to quantitatively study and compare the vision of a wide range insects held in museum collections. Our analysis indicates that different visual specializations have evolved between fungus gnat species living in different forest types and that the eyes of gnats from a similar geographic location have evolved to match the changing environmental conditions. Despite the small size of fungus gnats, evolution has evidentially been able to exploit sensory specializations to meet the differing sensory demands of species from a variety of forest habitats.\n\nSignificance statementDo insects have visual specializations that evolve with changes in their environment? To answer this question, a novel analysis technique is described that uses 3D imaging and simulations to compare the vision of ancient amber-embedded insects to those of their extant relatives. This study investigated the vision of fungus gnats to understand how tiny insects use vision to negotiate forests, some of the worlds most visually complex environments. Despite being amongst the smallest of any flying insect, the gnats miniature eyes have evolved visual specializations specifically adapted for different forest types, allowing different species to meet their visual demands of their specific habitats.

evolutionary biology↗

bioRxiv2018

Population Genomics of Rapidly Invading Lionfish in the Caribbean Reveals Signals of Range Expansion in the Absence of Spatial Population Structure

Range expansions driven by global change and species invasions are likely to have significant genomic, evolutionary, and ecological implications. During range expansions, strong genetic drift characterized by repeated founder events can result in decreased genetic diversity with increased distance from the center of the historic range, or the point of invasion. The invasion of the Indo-Pacific lionfish, Pterois volitans, into waters off the U.S. East Coast, Gulf of Mexico, and Caribbean Sea provides a natural system to study rapid range expansion in an invasive marine fish with high dispersal capabilities. We report results from 12,759 loci sequenced by restriction enzyme associated DNA sequencing for nine P. volitans populations in the invaded range, including Florida and other Caribbean sites, as well as mitochondrial control region D-loop data. Analyses revealed low to no spatially explicit metapopulation genetic structure in the study area, which is partly consistent with previous finding of little structure within ocean basins, but partly divergent from reports of between-basin structure. Genetic diversity, however, was not homogeneous across all sampled sites. Patterns of genetic diversity correlate with invasion pathway. Observed heterozygosity, averaged across all loci within a population, decreases with distance from Florida while expected heterozygosity is mostly constant throughout sampled populations, indicating population genetic disequilibrium correlated with distance from the point of invasion. Using an FST outlier analysis and a Bayesian environmental correlation analysis, we identified 256 and 616 loci, respectively, that could be experiencing selection or genetic drift. Of these, 24 loci were shared between the two methods.

evolutionary biology↗

bioRxiv2018

Analysis of genome-wide differentiation between native and introduced populations of the cupped oysters Crassostrea gigas and Crassostrea angulata

The Pacific cupped oyster is genetically subdivided into two sister taxa, Crassostrea gigas and C. angulata, which are in contact in the north-western Pacific. The nature and origin of their genetic and taxonomic differentiation remains controversial due the lack of known reproductive barriers and morphologic similarity. In particular, whether ecological and/or intrinsic isolating mechanisms participate to species divergence remains unknown. The recent co-introduction of both taxa into Europe offers a unique opportunity to test how genetic differentiation maintains under new environmental and demographic conditions. We generated a pseudo-chromosome assembly of the Pacific oyster genome using a combination of BAC-end sequencing and scaffold anchoring to a new high-density linkage map. We characterized genome-wide differentiation between C. angulata and C. gigas in both their native and introduced ranges, and showed that gene flow between species has been facilitated by their recent co-introductions in Europe. Nevertheless, patterns of genomic divergence between species remain highly similar in Asia and Europe, suggesting that the environmental transition caused by the co-introduction of the two species did not affect the genomic architecture of their partial reproductive isolation. Increased genetic differentiation was preferentially found in regions of low recombination. Using historical demographic inference, we show that the heterogeneity of differentiation across the genome is well explained by a scenario whereby recent gene flow has eroded past differentiation at different rates across the genome after a period of geographical isolation. Our results thus support the view that low-recombining regions help in maintaining intrinsic genetic differences between the two species.

evolutionary biology↗

bioRxiv2018

An ultra-dense haploid genetic map for evaluating the highly fragmented genome assembly of Norway spruce (Picea abies)

Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large ([~]20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (www.congenie.org), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.

genetics↗

bioRxiv2018

Association mapping identified novel candidate loci affecting wood formation in Norway spruce

[tpltrtarr] Norway spruce (Picea abies) is an important boreal forest tree species of significant ecological and economic importance. Hence there is a strong imperative to dissect the genetics controlling important wood quality traits in the species.\n[tpltrtarr]We performed a functional genome-wide association mapping of 17 wood traits in Norway spruce using 178101 single-nucleotide polymorphisms (SNPs) generated from exome genotyping of 517 mother trees. The wood traits were defined using functional modelling of wood properties across annual growth rings.\n[tpltrtarr]Association mapping was performed using a multilocus LASSO penalized regression method and we detected a total of 51 significant SNPs from 39 candidate genes that are involved in wood formation.\n[tpltrtarr]Our study represents the first functional multi-locus genome-wide association mapping (AM) in Norway spruce. The results advance our understanding of the genetics influencing wood traits, identify novel candidate genes for further functional studies and support current Norway spruce breeding efforts.

genetics↗