| 1. |
- Künstner, Axel, et al.
(författare)
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Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species
- 2010
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 19:Suppl.1, s. 266-276
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Tidskriftsartikel (refereegranskat)abstract
- Next-generation sequencing technology provides an attractive means to obtain largescale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across the avian genome, we performed brain transcriptome sequencing using Roche 454 technology of 10 different non-model avian species. Contigs from de novo assemblies were aligned to the two available avian reference genomes, chicken and zebra finch. In total, we identified 6499 different genes across all 10 species, with ∼1000 genes found in each full run per species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes (male-biased mutation) and a negative correlation between the neutral substitution rate (dS) and chromosome size. Analyses of the mean dN/dS ratio (ω) of genes across chromosomes supported the Hill-Robertson effect (the effect of selection at linked loci) and point at stochastic problems with x as an independent measure of selection. Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms.
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| 2. |
- Pörschmann, Ulrich, et al.
(författare)
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Male reproductive success and its behavioural correlates in a polygynous mammal, the Galapagos sea lion (Zalophus wollebaeki)
- 2010
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 19:12, s. 2574-2586
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Tidskriftsartikel (refereegranskat)abstract
- Sexual selection theory predicts competitive males and choosy females. Nevertheless, since molecular marker-based studies, paternity outside the expected mating patterns has increasingly been described. Even in highly polygynous systems, where paternity is expected to be strongly skewed towards large, dominant males, alternative mating tactics have been suggested. We examined reproductive success in the polygynous Galapagos sea lion (Zalophus wollebaeki). Semiaquatic territoriality allows females to move freely and may lower the degree of polygyny otherwise suggested by both territorial behaviour and strong sexual dimorphism. We assigned paternities with 22 microsatellites and analysed how male reproductive success was related to size, dominance status, intrasexual agonistic behaviour, proximity to females, and attendance in the colony. Male behaviour was consistent across two seasons for all parameters under consideration. Attendance was by far the most important determinant of paternal success. Skew in reproductive success towards large, dominant males was weak and dominance status played no role. This appears to be caused by an extremely long reproductive season lasting five or more months, making it difficult for any male to monopolize receptive females. Females seem to choose displaying males that were present in the colony for a long time rather than dominance per se. Sexual dimorphism in Galapagos sea lions may thus be more influenced by selection for fasting than fighting ability. Our data provide further evidence for alternative mating tactics, as several males gained relatively high reproductive success despite short attendance and hardly any involvement in agonistic interactions.
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| 3. |
- Wolf, Jochen B. W., et al.
(författare)
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Nucleotide divergence vs. gene expression differentiation : comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow
- 2010
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Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 19:Suppl. 1, s. 162-175
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Tidskriftsartikel (refereegranskat)abstract
- Recent advances in sequencing technology promise to provide new strategies for studying population differentiation and speciation phenomena in their earliest phases. We focus here on the black carrion crow (Corvus [corone] corone), which forms a zone of hybridization and overlap with the grey coated hooded crow (Corvus [corone] cornix). However, although these semispecies are taxonomically distinct, previous analyses based on several types of genetic markers did not reveal significant molecular differentiation between them. We here corroborate this result with sequence data obtained from a set of 25 nuclear intronic loci. Thus, the system represents a case of a very early phase of species divergence that requires new molecular approaches for its description. We have therefore generated RNAseq expression profiles using barcoded massively parallel pyrosequencing of brain mRNA from six individuals of the carrion crow and five individuals from a hybrid zone with the hooded crow. We obtained 856 675 reads from two runs, with average read length of 270 nt and coverage of 8.44. Reads were assembled de novo into 19 552 contigs, 70% of which could be assigned to annotated genes in chicken and zebra finch. This resulted in a total of 7637 orthologous genes and a core set of 1301 genes that could be compared across all individuals. We find a clear clustering of expression profiles for the pure carrion crow animals and disperse profiles for the animals from the hybrid zone. These results suggest that gene expression differences may indeed be a sensitive indicator of initial species divergence.
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| 4. |
- Dussex, Nicolas, et al.
(författare)
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A genome-wide investigation of adaptive signatures in protein-coding genes related to tool behaviour in New Caledonian and Hawaiian crows
- 2021
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 30:4, s. 973-986
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Tidskriftsartikel (refereegranskat)abstract
- Very few animals habitually manufacture and use tools. It has been suggested that advanced tool behaviour co-evolves with a suite of behavioural, morphological and life history traits. In fact, there are indications for such an adaptive complex in tool-using crows (genus Corvus species). Here, we sequenced the genomes of two habitually tool-using and ten non-tool-using crow species to search for genomic signatures associated with a tool-using lifestyle. Using comparative genomic and population genetic approaches, we screened for signals of selection in protein-coding genes in the tool-using New Caledonian and Hawaiian crows. While we detected signals of recent selection in New Caledonian crows near genes associated with bill morphology, our data indicate that genetic changes in these two lineages are surprisingly subtle, with little evidence at present for convergence. We explore the biological explanations for these findings, such as the relative roles of gene regulation and protein-coding changes, as well as the possibility that statistical power to detect selection in recently diverged lineages may have been insufficient. Our study contributes to a growing body of literature aiming to decipher the genetic basis of recently evolved complex behaviour.
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| 5. |
- Foote, Andrew D., et al.
(författare)
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Killer whale genomes reveal a complex history of recurrent admixture and vicariance
- 2019
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Ingår i: Molecular Ecology. - : WILEY. - 0962-1083 .- 1365-294X. ; 28:14, s. 3427-3444
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Tidskriftsartikel (refereegranskat)abstract
- Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to fourfold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.
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| 6. |
- Grosser, Stefanie, et al.
(författare)
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Fur seal microbiota are shaped by the social and physical environment, show mother-offspring similarities and are associated with host genetic quality
- 2019
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 28:9, s. 2406-2422
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Tidskriftsartikel (refereegranskat)abstract
- Despite an increasing appreciation of the importance of host-microbe interactions in ecological and evolutionary processes, the factors shaping microbial communities in wild populations remain poorly understood. We therefore exploited a natural experiment provided by two adjacent Antarctic fur seal (Arctocephalus gazella) colonies of high and low social density and combined 16S rRNA metabarcoding with microsatellite profiling of mother-offspring pairs to investigate environmental and genetic influences on skin microbial communities. Seal-associated bacterial communities differed profoundly between the two colonies, despite the host populations themselves being genetically undifferentiated. Consistent with the hypothesis that social stress depresses bacterial diversity, we found that microbial alpha diversity was significantly lower in the high-density colony. Seals from one of the colonies that contained a stream also carried a subset of freshwater-associated bacteria, indicative of an influence of the physical environment. Furthermore, mothers and their offspring shared similar microbial communities, in support of the notion that microbes may facilitate mother-offspring recognition. Finally, a significant negative association was found between bacterial diversity and heterozygosity, a measure of host genetic quality. Our study thus reveals a complex interplay between environmental and host genetic effects, while also providing empirical support for the leash model of host control, which posits that bacterial communities are driven not only by bottom-up species interactions, but also by top-down host regulation. Taken together, our findings have broad implications for understanding host-microbe interactions as well as prokaryotic diversity in general.
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| 7. |
- Hooper, Rebecca, et al.
(författare)
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Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin
- 2019
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 28:2, s. 484-502
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Tidskriftsartikel (refereegranskat)abstract
- Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers 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 characterize the skin microbiome and investigate how host social and geographical 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 geographical 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.
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| 8. |
- Poelstra, Jelmer W., et al.
(författare)
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Transcriptomics of colour patterning and coloration shifts in crows
- 2015
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 24:18, s. 4617-4628
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Tidskriftsartikel (refereegranskat)abstract
- Animal coloration is one of the most conspicuous phenotypic traits in natural populations and has important implications for adaptation and speciation. Changes in coloration can occur over surprisingly short evolutionary timescales, while recurrence of similar colour patterns across large phylogenetic distances is also common. Even though the genetic basis of pigment production is well understood, little is known about the mechanisms regulating colour patterning. In this study, we shed light on the molecular elements regulating regional pigment production in two genetically near-identical crow taxa with striking differences in a eumelanin-based phenotype: black carrion and grey-coated hooded crows. We produced a high-quality genome annotation and analysed transcriptome data from a 2 3 2 design of active melanogenic feather follicles from head (black in both taxa) and torso (black in carrion and grey in hooded crow). Extensive, parallel expression differences between body regions in both taxa, enriched for melanogenesis genes (e.g. ASIP, CORIN, and ALDH6), indicated the presence of cryptic prepatterning also in all-black carrion crows. Meanwhile, colour-specific expression (grey vs. black) was limited to a small number of melanogenesis genes in close association with the central transcription factor MITF (most notably HPGDS, NDP and RASGRF1). We conclude that colour pattern differences between the taxa likely result from an interaction between divergence in upstream elements of the melanogenesis pathway and genes that provide an underlying prepattern across the body through positional information. A model of evolutionary stable prepatterns that can be exposed and masked through simple regulatory changes may explain the phylogenetically independent recurrence of colour patterns that is observed across corvids and many other vertebrate groups.
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| 9. |
- Shafer, Aaron B. A., et al.
(författare)
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Demographic inferences using short-read genomic data in an approximate Bayesian computation framework : in silico evaluation of power, biases and proof of concept in Atlantic walrus
- 2015
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 24:2, s. 328-345
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Tidskriftsartikel (refereegranskat)abstract
- Approximate Bayesian computation (ABC) is a powerful tool for model-based inference of demographic histories from large genetic data sets. For most organisms, its implementation has been hampered by the lack of sufficient genetic data. Genotyping-by-sequencing (GBS) provides cheap genome-scale data to fill this gap, but its potential has not fully been exploited. Here, we explored power, precision and biases of a coalescent-based ABC approach where GBS data were modelled with either a population mutation parameter () or a fixed site (FS) approach, allowing single or several segregating sites per locus. With simulated data ranging from 500 to 50000 loci, a variety of demographic models could be reliably inferred across a range of timescales and migration scenarios. Posterior estimates were informative with 1000 loci for migration and split time in simple population divergence models. In more complex models, posterior distributions were wide and almost reverted to the uninformative prior even with 50000 loci. ABC parameter estimates, however, were generally more accurate than an alternative composite-likelihood method. Bottleneck scenarios proved particularly difficult, and only recent bottlenecks without recovery could be reliably detected and dated. Notably, minor-allele-frequency filters - usual practice for GBS data - negatively affected nearly all estimates. With this in mind, we used a combination of FS and approaches on empirical GBS data generated from the Atlantic walrus (Odobenus rosmarus rosmarus), collectively providing support for a population split before the last glacial maximum followed by asymmetrical migration and a high Arctic bottleneck. Overall, this study evaluates the potential and limitations of GBS data in an ABC-coalescence framework and proposes a best-practice approach.
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| 10. |
- Vijay, Nagarjun, et al.
(författare)
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Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments
- 2013
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 22:3, s. 620-634
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Tidskriftsartikel (refereegranskat)abstract
- Transcriptome Shotgun Sequencing (RNA-seq) has been readily embraced by geneticists and molecular ecologists alike. As with all high-throughput technologies, it is critical to understand which analytic strategies are best suited and which parameters may bias the interpretation of the data. Here we use a comprehensive simulation approach to explore how various features of the transcriptome (complexity, degree of polymorphism p, alternative splicing), technological processing (sequencing error e, library normalization) and bioinformatic workflow (de novo vs. mapping assembly, reference genome quality) impact transcriptome quality and inference of differential gene expression (DE). We find that transcriptome assembly and gene expression profiling (EdgeR vs. BaySeq software) works well even in the absence of a reference genome and is robust across a broad range of parameters. We advise against library normalization and in most situations advocate mapping assemblies to an annotated genome of a divergent sister clade, which generally outperformed de novo assembly (Trans-Abyss, Trinity, Soapdenovo-Trans). Transcriptome complexity (size, paralogs, alternative splicing isoforms) negatively affected the assembly and DE profiling, whereas the effects of sequencing error and polymorphism were almost negligible. Finally, we highlight the challenge of gene name assignment for de novo assemblies, the importance of mapping strategies and raise awareness of challenges associated with the quality of reference genomes. Overall, our results have significant practical and methodological implications and can provide guidance in the design and analysis of RNA-seq experiments, particularly for organisms where genomic background information is lacking.
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