Very Low Rates of Spontaneous Gene Deletions and Gene Duplications in Dictyostelium discoideum.

The study of spontaneous mutation rates has revealed a wide range of heritable point mutation rates across species, but there are comparatively few estimates for large-scale deletion and duplication rates. The handful of studies that have directly calculated spontaneous rates of deletion and duplication using mutation accumulation lines have estimated that genes are duplicated and deleted at orders of magnitude greater rates than the spontaneous point mutation rate. In our study, we tested whether spontaneous gene deletion and gene duplication rates are also high in Dictyostelium discoideum, a eukaryote with among the lowest point mutation rates (2.5 × 10-11 per site per generation) and an AT-rich genome (GC content of 22%). We calculated mutation rates of gene deletions and duplications using whole-genome sequencing data originating from a mutation accumulation experiment and determined the association between the copy number mutations and GC content. Overall, we estimated an average of 3.93 × 10-8 gene deletions and 1.18 × 10-8 gene duplications per gene per generation. While orders of magnitude greater than their point mutation rate, these rates are much lower compared to gene deletion and duplication rates estimated from mutation accumulation lines in other organisms (that are on the order of ~ 10-6 per gene/generation). The deletions and duplications were enriched in regions that were AT-rich even compared to the genomic background, in contrast to our expectations if low GC content was contributing to low mutation rates. The low deletion and duplication mutation rates in D. discoideum compared to other eukaryotes mirror their low point mutation rates, supporting previous work suggesting that this organism has high replication fidelity and effective molecular machinery to avoid the accumulation of mutations in their genome.

Environmental transcriptomics under heat stress: Can environmental RNA reveal changes in gene expression of aquatic organisms?

To safeguard biodiversity in a changing climate, taxonomic information about species turnover and insights into the health of organisms are required. Environmental DNA approaches are increasingly used for species identification, but cannot provide functional insights. Transcriptomic methods reveal the physiological states of macroorganisms, but are currently species-specific and require tissue sampling or animal sacrifice, making community-wide assessments challenging. Here, we test whether broad functional information (expression level of the transcribed genes) can be harnessed from environmental RNA (eRNA), which includes extra-organismal RNA from macroorganisms along with whole microorganisms. We exposed Daphnia pulex as well as phytoplankton prey and microorganism colonizers to control (20°C) and heat stress (28°C) conditions for 7 days. We sequenced eRNA from tank water (after complete removal of Daphnia) as well as RNA from Daphnia tissue, enabling comparisons of extra-organismal and organismal RNA-based gene expression profiles. Both RNA types detected similar heat stress responses of Daphnia. Using eRNA, we identified 32 Daphnia genes to be differentially expressed following heat stress. Of these, 17 were also differentially expressed and exhibited similar levels of relative expression in organismal RNA. In addition to the extra-organismal Daphnia response, eRNA detected community-wide heat stress responses consisting of distinct functional profiles and 121 differentially expressed genes across eight taxa. Our study demonstrates that environmental transcriptomics based on extra-organismal eRNA can noninvasively reveal gene expression responses of macroorganisms following environmental changes, with broad potential implications for the biomonitoring of health across the trophic chain.

Accelerated rates of large-scale mutations in the presence of copper and nickel.

Mutation rate variation has been under intense investigation for decades. Despite these efforts, little is known about the extent to which environmental stressors accelerate mutation rates and influence the genetic load of populations. Moreover, most studies on stressors have focused on unicellular organisms and point mutations rather than large-scale deletions and duplications (copy number variations [CNVs]). We estimated mutation rates in Daphnia pulex exposed to low levels of environmental stressors as well as the effect of selection on de novo mutations. We conducted a mutation accumulation (MA) experiment in which selection was minimized, coupled with an experiment in which a population was propagated under competitive conditions in a benign environment. After an average of 103 generations of MA propagation, we sequenced 60 genomes and found significantly accelerated rates of deletions and duplications in MA lines exposed to ecologically relevant concentrations of metals. Whereas control lines had gene deletion and duplication rates comparable to other multicellular eukaryotes (1.8 × 10-6 per gene per generation), the presence of nickel and copper increased these rates fourfold. The realized mutation rate under selection was reduced to 0.4× that of control MA lines, providing evidence that CNVs contribute to mutational load. Our CNV breakpoint analysis revealed that nonhomologous recombination associated with regions of DNA fragility is the primary source of CNVs, plausibly linking metal-induced DNA strand breaks with higher CNV rates. Our findings suggest that environmental stress, in particular multiple stressors, can have profound effects on large-scale mutation rates and mutational load of multicellular organisms.

Concatenation of paired-end reads improves taxonomic classification of amplicons for profiling microbial communities.

BACKGROUND: Taxonomic classification of genetic markers for microbiome analysis is affected by the numerous choices made from sample preparation to bioinformatics analysis. Paired-end read merging is routinely used to capture the entire amplicon sequence when the read ends overlap. However, the exclusion of unmerged reads from further analysis can result in underestimating the diversity in the sequenced microbial community and is influenced by bioinformatic processes such as read trimming and the choice of reference database. A potential solution to overcome this is to concatenate (join) reads that do not overlap and keep them for taxonomic classification. The use of concatenated reads can outperform taxonomic recovery from single-end reads, but it remains unclear how their performance compares to merged reads. Using various sequenced mock communities with different amplicons, read length, read depth, taxonomic composition, and sequence quality, we tested how merging and concatenating reads performed for genus recall and precision in bioinformatic pipelines combining different parameters for read trimming and taxonomic classification using different reference databases. RESULTS: The addition of concatenated reads to merged reads always increased pipeline performance. The top two performing pipelines both included read concatenation, with variable strengths depending on the mock community. The pipeline that combined merged and concatenated reads that were quality-trimmed performed best for mock communities with larger amplicons and higher average quality sequences. The pipeline that used length-trimmed concatenated reads outperformed quality trimming in mock communities with lower quality sequences but lost a significant amount of input sequences for taxonomic classification during processing. Genus level classification was more accurate using the SILVA reference database compared to Greengenes. CONCLUSIONS: Merged sequences with the addition of concatenated sequences that were unable to be merged increased performance of taxonomic classifications. This was especially beneficial in mock communities with larger amplicons. We have shown for the first time, using an in-depth comparison of pipelines containing merged vs concatenated reads combined with different trimming parameters and reference databases, the potential advantages of concatenating sequences in improving resolution in microbiome investigations.

Refining analyses of existing data sets is valuable for macrogenetics: a response to Paz-Vinas, Jensen et al., (2021).

Paz-Vinas, Jensen et al. (2021) comment on data and methodological limits of Millette, Fugère, Debyser et al. (2020)-some affect a small proportion of our data sets and analyses and others need to be tackled more generally. These points do not refute our main conclusion of no strong signal of human impacts on COI variation globally.

Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure.

BACKGROUND: Despite being one of the primary mechanisms of gene expression regulation in eukaryotes, alternative splicing is often overlooked in ecotoxicogenomic studies. The process of alternative splicing facilitates the production of multiple mRNA isoforms from a single gene thereby greatly increasing the diversity of the transcriptome and proteome. This process can be important in enabling the organism to cope with stressful conditions. Accurate identification of splice sites using RNA sequencing requires alignment to independent exonic positions within the genome, presenting bioinformatic challenges, particularly when using short read data. Although technological advances allow for the detection of splicing patterns on a genome-wide scale, very little is known about the extent of intraspecies variation in splicing patterns, particularly in response to environmental stressors. In this study, we used RNA-sequencing to study the molecular responses to acute copper exposure in three lineages of Daphnia pulex by focusing on the contribution of alternative splicing in addition to gene expression responses. RESULTS: By comparing the overall gene expression and splicing patterns among all 15 copper-exposed samples and 6 controls, we identified 588 differentially expressed (DE) genes and 16 differentially spliced (DS) genes. Most of the DS genes (13) were not found to be DE, suggesting unique transcriptional regulation in response to copper that went unnoticed with conventional DE analysis. To understand the influence of genetic background on gene expression and alternative splicing responses to Cu, each of the three lineages was analyzed separately. In contrast to the overall analysis, each lineage had a higher proportion of unique DS genes than DE genes suggesting that genetic background has a larger influence on DS than on DE. Gene Ontology analysis revealed that some pathways involved in stress response were jointly regulated by DS and DE genes while others were regulated by only transcription or only splicing. CONCLUSIONS: Our findings suggest an important role for alternative splicing in shaping transcriptome diversity in response to metal exposure in Daphnia, highlighting the importance of integrating splicing analyses with gene expression surveys to characterize molecular pathways in evolutionary and environmental studies.

No consistent effects of humans on animal genetic diversity worldwide.

Human impacts on genetic diversity are poorly understood yet critical to biodiversity conservation. We used 175 247 COI sequences collected between 1980 and 2016 to assess the global effects of land use and human density on the intraspecific genetic diversity of 17 082 species of birds, fishes, insects and mammals. Human impacts on mtDNA diversity were taxon and scale-dependent, and were generally weak or non-significant. Spatial analyses identified weak latitudinal diversity gradients as well as negative effects of human density on insect diversity, and negative effects of intensive land use on fish diversity. The observed effects were predominantly associated with species turnover. Time series analyses found nearly an equal number of positive and negative temporal trends in diversity, resulting in no net monotonic trend in diversity over this time period. Our analyses reveal critical data and theory gaps and call for increased efforts to monitor global genetic diversity.

Evolution of novel genes in three-spined stickleback populations.

Eukaryotic genomes frequently acquire new protein-coding genes which may significantly impact an organism's fitness. Novel genes can be created, for example, by duplication of large genomic regions or de novo, from previously non-coding DNA. Either way, creation of a novel transcript is an essential early step during novel gene emergence. Most studies on the gain-and-loss dynamics of novel genes so far have compared genomes between species, constraining analyses to genes that have remained fixed over long time scales. However, the importance of novel genes for rapid adaptation among populations has recently been shown. Therefore, since little is known about the evolutionary dynamics of transcripts across natural populations, we here study transcriptomes from several tissues and nine geographically distinct populations of an ecological model species, the three-spined stickleback. Our findings suggest that novel genes typically start out as transcripts with low expression and high tissue specificity. Early expression regulation appears to be mediated by gene-body methylation. Although most new and narrowly expressed genes are rapidly lost, those that survive and subsequently spread through populations tend to gain broader and higher expression levels. The properties of the encoded proteins, such as disorder and aggregation propensity, hardly change. Correspondingly, young novel genes are not preferentially under positive selection but older novel genes more often overlap with FST outlier regions. Taken together, expression of the surviving novel genes is rapidly regulated, probably via epigenetic mechanisms, while structural properties of encoded proteins are non-debilitating and might only change much later.

Spontaneous Mutation Accumulation in Daphnia pulex in Selection-Free vs. Competitive Environments.

Understanding the rates, spectra, and fitness effects of spontaneous mutations is fundamental to answering key questions in evolution, molecular biology, disease genetics, and conservation biology. To estimate mutation rates and evaluate the effect of selection on new mutations, we propagated mutation accumulation (MA) lines of Daphnia pulex for more than 82 generations and maintained a non-MA population under conditions where selection could act. Both experiments were started with the same obligate asexual progenitor clone. By sequencing 30 genomes and implementing a series of validation steps that informed the bioinformatic analyses, we identified a total of 477 single nucleotide mutations (SNMs) in the MA lines, corresponding to a mutation rate of 2.30 × 10-9 (95% CI 1.90-2.70 × 10-9) per nucleotide per generation. The high overall rate of loss of heterozygosity (LOH) of 4.82 × 10-5 per site per generation was due to a large ameiotic recombination event spanning an entire arm of a chromosome (∼6 Mb) and several hemizygous deletion events spanning ∼2 kb each. In the non-MA population, we found significantly fewer mutations than expected based on the rate derived from the MA experiment, indicating purifying selection was likely acting to remove new deleterious mutations. We observed a surprisingly high level of genetic variability in the non-MA population, which we propose to be driven by balancing selection. Our findings suggest that both positive and negative selection on new mutations is powerful and effective in a strictly clonal population.

Genomics of divergence along a continuum of parapatric population differentiation.

The patterns of genomic divergence during ecological speciation are shaped by a combination of evolutionary forces. Processes such as genetic drift, local reduction of gene flow around genes causing reproductive isolation, hitchhiking around selected variants, variation in recombination and mutation rates are all factors that can contribute to the heterogeneity of genomic divergence. On the basis of 60 fully sequenced three-spined stickleback genomes, we explore these different mechanisms explaining the heterogeneity of genomic divergence across five parapatric lake and river population pairs varying in their degree of genetic differentiation. We find that divergent regions of the genome are mostly specific for each population pair, while their size and abundance are not correlated with the extent of genome-wide population differentiation. In each pair-wise comparison, an analysis of allele frequency spectra reveals that 25-55% of the divergent regions are consistent with a local restriction of gene flow. Another large proportion of divergent regions (38-75%) appears to be mainly shaped by hitchhiking effects around positively selected variants. We provide empirical evidence that alternative mechanisms determining the evolution of genomic patterns of divergence are not mutually exclusive, but rather act in concert to shape the genome during population differentiation, a first necessary step towards ecological speciation.

Extensive copy-number variation of young genes across stickleback populations.

Duplicate genes emerge as copy-number variations (CNVs) at the population level, and remain copy-number polymorphic until they are fixed or lost. The successful establishment of such structural polymorphisms in the genome plays an important role in evolution by promoting genetic diversity, complexity and innovation. To characterize the early evolutionary stages of duplicate genes and their potential adaptive benefits, we combine comparative genomics with population genomics analyses to evaluate the distribution and impact of CNVs across natural populations of an eco-genomic model, the three-spined stickleback. With whole genome sequences of 66 individuals from populations inhabiting three distinct habitats, we find that CNVs generally occur at low frequencies and are often only found in one of the 11 populations surveyed. A subset of CNVs, however, displays copy-number differentiation between populations, showing elevated within-population frequencies consistent with local adaptation. By comparing teleost genomes to identify lineage-specific genes and duplications in sticklebacks, we highlight rampant gene content differences among individuals in which over 30% of young duplicate genes are CNVs. These CNV genes are evolving rapidly at the molecular level and are enriched with functional categories associated with environmental interactions, depicting the dynamic early copy-number polymorphic stage of genes during population differentiation.

Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks.

The observation of habitat-specific phenotypes suggests the action of natural selection. The three-spined stickleback (Gasterosteus aculeatus) has repeatedly colonized and adapted to diverse freshwater habitats across the northern hemisphere since the last glaciation, while giving rise to recurring phenotypes associated with specific habitats. Parapatric lake and river populations of sticklebacks harbour distinct parasite communities, a factor proposed to contribute to adaptive differentiation between these ecotypes. However, little is known about the transcriptional response to the distinct parasite pressure of those fish in a natural setting. Here, we sampled wild-caught sticklebacks across four geographical locations from lake and river habitats differing in their parasite load. We compared gene expression profiles between lake and river populations using 77 whole-transcriptome libraries from two immune-relevant tissues, the head kidney and the spleen. Differential expression analyses revealed 139 genes with habitat-specific expression patterns across the sampled population pairs. Among the 139 differentially expressed genes, eight are annotated with an immune function and 42 have been identified as differentially expressed in previous experimental studies in which fish have been immune challenged. Together, these findings reinforce the hypothesis that parasites contribute to adaptation of sticklebacks in lake and river habitats.

The effects of parameter choice on defining molecular operational taxonomic units and resulting ecological analyses of metabarcoding data.

The combination of DNA barcoding and high-throughput (next-generation) sequencing (metabarcoding) provides many promises but also serious challenges. Generating a reliable comparable estimate of biodiversity remains a central challenge to the application of the technology. Many approaches have been used to turn millions of sequences into distinct taxonomic units. However, the extent to which these methods impact the outcome of simple ecological analyses is not well understood. Here we performed a simple analysis of dietary overlap by skinks and shrews on Ile Aux Aigrettes, Mauritius. We used a combination of filtering thresholds and clustering algorithms on a COI metabarcoding dataset and demonstrate that all bioinformatics parameters will have interacting effects on molecular operational taxonomic unit (MOTU) recovery rates. These effects generated estimates covering two orders of magnitude. However, the effect on a simple ecological analysis was not large and, despite the wide variation in estimates of niche overlap, the same ecological conclusion was drawn in most cases. We advise that a conservative clustering programme coupled with larger sequence divergences to define a cluster, the removal of singletons, rigorous length filtering, and stringent match criteria for Molecular Identifier tags are preferable to avoid MOTU inflation and that the same parameters be used in all comparative analyses.

Sex-Biased Expression of Young Genes in Silurana (Xenopus) tropicalis.

Sex-biased gene expression can evolve from sex-specific selection and is often associated with sex-linked genes. Gene duplication is a particularly effective mechanism for the generation of sex-biased genes, in which a new copy can help resolve intralocus sexual conflicts. This study assesses sex-biased gene expression in an amphibian with homomorphic ZW sex chromosomes, the Western clawed frog Silurana (Xenopus)tropicalis. Previous work has shown that the sex chromosomes in this species are mainly undifferentiated and pseudoautosomal. Consistent with ongoing recombination between the sex chromosomes, this study detected little evidence for the general sexualization of sex-linked regions. A subset of genes closely linked to the sex determining locus displays a tendency for male-biased expression and elevated rates of evolution relative to genes in other genomic locations. This may be a symptom of an early stage of sex chromosome differentiation driven by, for example, chromosomal degeneration or natural selection on genes in this portion of the Z chromosome. Alternatively, it could reflect variation between the sexes in allelic copy number coupled with a lack of dosage compensation. Irrespective of the genomic location, lineage-specific genes and recently duplicated genes had significantly high levels of sex-biased expression, offering insights into the early transcriptional differentiation of young genes.

Epigenetic diversity of genes with copy number variations among natural populations of the three-spined stickleback.

Duplicated genes provide the opportunity for evolutionary novelty and adaptive divergence. In many cases, having more gene copies increases gene expression, which might facilitate adaptation to stressful or novel environments. Conversely, overexpression or misexpression of duplicated genes can be detrimental and subject to negative selection. In this scenario, newly duplicate genes may evade purifying selection if they are epigenetically silenced, at least temporarily, leading them to persist in populations as copy number variations (CNVs). In animals and plants, younger gene duplicates tend to have higher levels of DNA methylation and lower levels of gene expression, suggesting epigenetic regulation could promote the retention of gene duplications via expression repression or silencing. Here, we test the hypothesis that DNA methylation variation coincides with young duplicate genes that are segregating as CNVs in six populations of the three-spined stickleback that span a salinity gradient from 4 to 30 PSU. Using reduced-representation bisulfite sequencing, we found DNA methylation and CNV differentiation outliers rarely overlapped. Whereas lineage-specific genes and young duplicates were found to be highly methylated, just two gene CNVs showed a significant association between promoter methylation level and copy number, suggesting that DNA methylation might not interact with CNVs in our dataset. If most new duplications are regulated for dosage by epigenetic mechanisms, our results do not support a strong contribution from DNA methylation soon after duplication. Instead, our results are consistent with a preference to duplicate genes that are already highly methylated.

Evolution of MHC class I genes in the endangered loggerhead sea turtle (Caretta caretta) revealed by 454 amplicon sequencing.

BACKGROUND: In evolutionary and conservation biology, parasitism is often highlighted as a major selective pressure. To fight against parasites and pathogens, genetic diversity of the immune genes of the major histocompatibility complex (MHC) are particularly important. However, the extensive degree of polymorphism observed in these genes makes it difficult to conduct thorough population screenings. METHODS: We utilized a genotyping protocol that uses 454 amplicon sequencing to characterize the MHC class I in the endangered loggerhead sea turtle (Caretta caretta) and to investigate their evolution at multiple relevant levels of organization. RESULTS: MHC class I genes revealed signatures of trans-species polymorphism across several reptile species. In the studied loggerhead turtle individuals, it results in the maintenance of two ancient allelic lineages. We also found that individuals carrying an intermediate number of MHC class I alleles are larger than those with either a low or high number of alleles. CONCLUSIONS: Multiple modes of evolution seem to maintain MHC diversity in the loggerhead turtles, with relatively high polymorphism for an endangered species.

Genomic divergence between nine- and three-spined sticklebacks.

BACKGROUND: Comparative genomics approaches help to shed light on evolutionary processes that shape differentiation between lineages. The nine-spined stickleback (Pungitius pungitius) is a closely related species of the ecological 'supermodel' three-spined stickleback (Gasterosteus aculeatus). It is an emerging model system for evolutionary biology research but has garnered less attention and lacks extensive genomic resources. To expand on these resources and aid the study of sticklebacks in a phylogenetic framework, we characterized nine-spined stickleback transcriptomes from brain and liver using deep sequencing. RESULTS: We obtained nearly eight thousand assembled transcripts, of which 3,091 were assigned as putative one-to-one orthologs to genes found in the three-spined stickleback. These sequences were used for evaluating overall differentiation and substitution rates between nine- and three-spined sticklebacks, and to identify genes that are putatively evolving under positive selection. The synonymous substitution rate was estimated to be 7.1 × 10(-9) per site per year between the two species, and a total of 165 genes showed patterns of adaptive evolution in one or both species. A few nine-spined stickleback contigs lacked an obvious ortholog in three-spined sticklebacks but were found to match genes in other fish species, suggesting several gene losses within 13 million years since the divergence of the two stickleback species. We identified 47 SNPs in 25 different genes that differentiate pond and marine ecotypes. We also identified 468 microsatellites that could be further developed as genetic markers in nine-spined sticklebacks. CONCLUSION: With deep sequencing of nine-spined stickleback cDNA libraries, our study provides a significant increase in the number of gene sequences and microsatellite markers for this species, and identifies a number of genes showing patterns of adaptive evolution between nine- and three-spined sticklebacks. We also report several candidate genes that might be involved in differential adaptation between marine and freshwater nine-spined sticklebacks. This study provides a valuable resource for future studies aiming to identify candidate genes underlying ecological adaptation in this and other stickleback species.

Living on the edge: how philopatry maintains adaptive potential.

Without genetic variation, species cannot cope with changing environments, and evolution does not proceed. In endangered species, adaptive potential may be eroded by decreased population sizes and processes that further reduce gene flow such as philopatry and local adaptations. Here, we focused on the philopatric and endangered loggerhead sea turtle (Caretta caretta) nesting in Cape Verde as a model system to investigate the link between adaptive potential and philopatry. We produced a dataset of three complementary genomic regions to investigate female philopatric behaviour (mitochondrial DNA), male-mediated gene flow (microsatellites) and adaptive potential (major histocompatibility complex, MHC). Results revealed genetically distinct nesting colonies, indicating remarkably small-scale philopatric behaviour of females. Furthermore, these colonies also harboured local pools of MHC alleles, especially at the margins of the population's distribution, which are therefore important reserves of additional diversity for the population. Meanwhile, directional male-mediated gene flow from the margins of distribution sustains the adaptive potential for the entire rookery. We therefore present the first evidence for a positive association between philopatry and locally adapted genomic regions. Contrary to expectation, we propose that philopatry conserves a high adaptive potential at the margins of a distribution, while asymmetric gene flow maintains genetic connectivity with the rest of the population.

Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks.

Since the end of the Pleistocene, the three-spined stickleback (Gasterosteus aculeatus) has repeatedly colonized and adapted to various freshwater habitats probably originating from ancestral marine populations. Standing genetic variation and the underlying genomic architecture both have been speculated to contribute to recent adaptive radiations of sticklebacks. Here, we expand on the current genomic resources of this fish by providing extensive genome-wide variation data from six individuals from a marine (North Sea) stickleback population. Using next-generation sequencing and a combination of paired-end and mate-pair libraries, we detected a wide size range of genetic variation. Among the six individuals, we found more than 7% of the genome is polymorphic, consisting of 2599111 SNPs, 233464 indels and structural variation (SV) (>50 bp) such as 1054 copy-number variable regions (deletions and duplications) and 48 inversions. Many of these polymorphisms affect gene and coding sequences. Based on SNP diversity, we determined outlier regions concordant with signatures expected under adaptive evolution. As some of these outliers overlap with pronounced regions of copy-number variation, we propose the consideration of such SV when analysing SNP data from re-sequencing approaches. We further discuss the value of this resource on genome-wide variation for further investigation upon the relative contribution of standing variation on the parallel evolution of sticklebacks and the importance of the genomic architecture in adaptive radiation.