| 1. |
- van der Meijden, Arie, et al.
(författare)
-
Target-Specificity in Scorpions : Comparing Lethality of Scorpion Venoms across Arthropods and Vertebrates
- 2017
-
Ingår i: Toxins. - : MDPI. - 2072-6651. ; 9:10
-
Tidskriftsartikel (refereegranskat)abstract
- Scorpions use their venom in defensive situations as well as for subduing prey. Since some species of scorpion use their venom more in defensive situations than others, this may have led to selection for differences in effectiveness in defensive situations. Here, we compared the LD50 of the venom of 10 species of scorpions on five different species of target organisms; two insects and three vertebrates. We found little correlation between the target species in the efficacy of the different scorpion venoms. Only the two insects showed a positive correlation, indicating that they responded similarly to the panel of scorpion venoms. We discuss the lack of positive correlation between the vertebrate target species in the light of their evolution and development. When comparing the responses of the target systems to individual scorpion venoms pairwise, we found that closely related scorpion species tend to elicit a similar response pattern across the target species. This was further reflected in a significant phylogenetic signal across the scorpion phylogeny for the LD50 in mice and in zebrafish. We also provide the first mouse LD50 value for Grosphus grandidieri.
|
|
| 2. |
- Liu, Shanlin, et al.
(författare)
-
Ancient and modem genomes unravel the evolutionary history of the rhinoceros family
- 2021
-
Ingår i: Cell. - : Elsevier. - 0092-8674 .- 1097-4172. ; 184:19, s. 4874-4885.e16
-
Tidskriftsartikel (refereegranskat)abstract
- Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (similar to 16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.
|
|
| 3. |
- Pečnerová, Patrícia, et al.
(författare)
-
Population genomics of the muskox' resilience in the near absence of genetic variation
- 2024
-
Ingår i: Molecular Ecology. - 0962-1083 .- 1365-294X. ; 33:2
-
Tidskriftsartikel (refereegranskat)abstract
- Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.
|
|
| 4. |
- Baas, Pauline, et al.
(författare)
-
Population-level assessment of genetic diversity and habitat fragmentation in critically endangered Grauer's gorillas
- 2018
-
Ingår i: American Journal of Physical Anthropology. - : Wiley. - 0002-9483 .- 1096-8644. ; 165:3, s. 565-575
-
Tidskriftsartikel (refereegranskat)abstract
- Objectives: The critically endangered Grauer's gorilla (Gorilla beringei graueri) has experienced an estimated 77% population decline within a single generation. Although crucial for informed conservation decisions, there is no clear understanding about population structure and distribution of genetic diversity across the species' highly fragmented range. We fill this gap by studying several core and peripheral Grauer's gorilla populations throughout their distribution range.Materials and Methods: We generated genetic profiles for a sampling of an unstudied population of Grauer's gorillas from within the species' core range at 13 autosomal microsatellite loci and combined them with previously published and newly generated data from four other Grauer's gorilla populations, two mountain gorilla populations, and one western lowland gorilla population.Results: In agreement with previous studies, the genetic diversity of Grauer's gorillas is intermediate, falling between western lowland and mountain gorillas. Among Grauer's gorilla populations, we observe lower genetic diversity and high differentiation in peripheral compared with central populations, indicating a strong effect of genetic drift and limited gene flow among small, isolated forest fragments.Discussion: Although genetically less diverse, peripheral populations are frequently essential for the long-term persistence of a species and migration between peripheral and core populations may significantly enrich the overall species genetic diversity. Thus, in addition to central Grauer's gorilla populations from the core of the distribution range that clearly deserve conservation attention, we argue that conservation strategies aiming to ensure long-term species viability should include preserving peripheral populations and enhancing habitat connectivity.
|
|
| 5. |
- Barcala, Maximiliano Estravis, et al.
(författare)
-
Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species
- 2024
-
Ingår i: The Plant Journal. - 0960-7412 .- 1365-313X. ; 117:3, s. 944-955
-
Tidskriftsartikel (refereegranskat)abstract
- Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype–environment and genotype–phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.
|
|
| 6. |
- Brealey, Jaelle C., et al.
(författare)
-
Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome
- 2020
-
Ingår i: Molecular biology and evolution. - : OXFORD UNIV PRESS. - 0737-4038 .- 1537-1719. ; 37:10, s. 3003-3022
-
Tidskriftsartikel (refereegranskat)abstract
- Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.
|
|
| 7. |
- Cortazar-Chinarro, Maria, et al.
(författare)
-
Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans
- 2020
-
Ingår i: BMC Genetics. - : BMC. - 1471-2156. ; 21:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background While there is evidence of both purifying and balancing selection in immune defense genes, large-scale genetic diversity in antimicrobial peptides (AMPs), an important part of the innate immune system released from dermal glands in the skin, has remained uninvestigated. Here we describe genetic diversity at three AMP loci (Temporin, Brevinin and Palustrin) in two ranid frogs (Rana arvalis and R. temporaria) along a 2000 km latitudinal gradient. We amplified and sequenced part of the Acidic Propiece domain and the hypervariable Mature Peptide domain ( 150-200 bp) in the three genes using Illumina Miseq and expected to find decreased AMP genetic variation towards the northern distribution limit of the species similarly to studies on MHC genetic patterns. Results We found multiple loci for each AMP and relatively high gene diversity, but no clear pattern of geographic genetic structure along the latitudinal gradient. We found evidence of trans-specific polymorphism in the two species, indicating a common evolutionary origin of the alleles. Temporin and Brevinin did not form monophyletic clades suggesting that they belong to the same gene family. By implementing codon evolution models we found evidence of strong positive selection acting on the Mature Peptide. We also found evidence of diversifying selection as indicated by divergent allele frequencies among populations and high Theta k values. Conclusion Our results suggest that AMPs are an important source of adaptive diversity, minimizing the chance of microorganisms developing resistance to individual peptides.
|
|
| 8. |
|
|
| 9. |
- Dehasque, Marianne, et al.
(författare)
-
Temporal dynamics of woolly mammoth genome erosion prior to extinction
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- A large number of species have recently recovered from near-extinction events. Understanding the genetic consequences of severe population declines followed by demographic recoveries is key to predict the long-term viability of species in order to mitigate future extinction risks. Although these species have avoided the immediate extinction threat, their long-term viability remains questionable due to the genetic consequences of population declines, which are not understood on a time scale beyond a few generations. The woolly mammoth (Mammuthus primigenius) population on Wrangel Island is an excellent model system to investigate long-term genetic consequences of a population bottleneck. Mammoths became isolated on the island in the early Holocene due to rising sea levels, and persisted for over 200 generations (~6,000 years) before becoming extinct ~4,000 years ago. To study the evolutionary processes leading up to the extinction of the woolly mammoth on the island, we analysed 21 Siberian woolly mammoth genomes, including that of one of the last known mammoths. Our results show that the Wrangel Island mammoths recovered quickly from an initially severe bottleneck, and subsequently remained demographically stable during the ensuing 6 millennia. Further, we find that highly deleterious mutations were gradually purged from the population, whereas there was an accumulation of mildly deleterious mutations. The gradual purging of highly deleterious mutations suggests an ongoing inbreeding depression that lasted for hundreds of generations. This time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked present-day populations.
|
|
| 10. |
|
|
| 11. |
- Díez-del-Molino, David, 1984-, et al.
(författare)
-
Genomics of adaptive evolution in the woolly mammoth
- 2023
-
Ingår i: Current Biology. - 0960-9822 .- 1879-0445. ; 33:9, s. 1753-1764
-
Tidskriftsartikel (refereegranskat)abstract
- Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of tradi-tional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.
|
|
| 12. |
- Dussex, Nicolas, et al.
(författare)
-
Adaptation to the High-Arctic island environment despite long-term reduced genetic variation in Svalbard reindeer
- 2023
-
Ingår i: iScience. - 2589-0042. ; 26:10
-
Tidskriftsartikel (refereegranskat)abstract
- Typically much smaller in number than their mainland counterparts, island populations are ideal systems to investigate genetic threats to small populations. The Svalbard reindeer (Rangifer tarandus platyrhynchus) is an endemic subspecies that colonized the Svalbard archipelago ca. 6,000–8,000 years ago and now shows numerous physiological and morphological adaptations to its arctic habitat. Here, we report a de-novo chromosome-level assembly for Svalbard reindeer and analyze 133 reindeer genomes spanning Svalbard and most of the species’ Holarctic range, to examine the genomic consequences of long-term isolation and small population size in this insular subspecies. Empirical data, demographic reconstructions, and forward simulations show that long-term isolation and high inbreeding levels may have facilitated the reduction of highly deleterious—and to a lesser extent, moderately deleterious—variation. Our study indicates that long-term reduced genetic diversity did not preclude local adaptation to the High Arctic, suggesting that even severely bottlenecked populations can retain evolutionary potential.
|
|
| 13. |
- Dussex, Nicolas, et al.
(författare)
-
Moose genomes reveal past glacial demography and the origin of modern lineages
- 2020
-
Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 21:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America.Results: We found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines.Conclusions: Taken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies.
|
|
| 14. |
- Dussex, Nicolas, et al.
(författare)
-
Population genomics of the critically endangered kākāpō
- 2021
-
Ingår i: Cell Genomics. - : Elsevier BV. - 2666-979X. ; 1:1
-
Tidskriftsartikel (refereegranskat)abstract
- Summary The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species.
|
|
| 15. |
- Feuerborn, Tatiana R., et al.
(författare)
-
Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets
- 2020
-
Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 21:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background: After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.Results: Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.Conclusions: We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.
|
|
| 16. |
|
|
| 17. |
- Hooper, Rebecca, et al.
(författare)
-
Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin
- 2019
-
Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 28:2, s. 484-502
-
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.
|
|
| 18. |
- Kutschera, Verena E., et al.
(författare)
-
GenErode : a bioinformatics pipeline to investigate genome erosion in endangered and extinct species
- 2022
-
Ingår i: BMC Bioinformatics. - : Springer Nature. - 1471-2105. ; 23:1
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Many wild species have suffered drastic population size declines over the past centuries, which have led to 'genomic erosion' processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses. Results: Here, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub (https://github.com/NBISweden/GenErode). Conclusions: GenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data.
|
|
| 19. |
- McFarlane, S. Eryn, et al.
(författare)
-
RNA sequencing provides insight into metabolic dysfunction of hybrids between a recently diverged songbird species pair
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Hybrid dysfunction is thought to gradually build up through the accumulation of clashes between genes as they diverge between the parental species. However, analyses of genetic incompatibilities are generally biased towards long diverged species that are kept under laboratory conditions. Here, we used RNAseq to evaluate 1) whether there was differential gene expression between naturally occurring Ficedula flycatcher hybrids and parental species in energetically expensive alimentary organs, and 2) if such differential gene expression was, based on Gene Ontology (GO) terms, functionally related to Resting Metabolic Rate (RMR) and energy production. We found substantial differential gene expression in all pairwise contrasts, but fewer functional differences between the parental species than between hybrids and either parental species. Some of the differentially expressed genes underlay the OXPHOS pathway, and significantly more than expected GO terms associated with metabolic function were differentially expressed between hybrids and either parental species in the liver. Our results corroborate the idea that tightly co-evolved mitochondrial and nuclear genes underlying the Oxidative Phosphorylation (OXPHOS) pathway can become miss-matched in hybrids and cause malfunctioning phenotypes. Mitonuclear interactions affecting OXPHOS have the potential to both quickly diverge in allopatry as populations adapt to different climate regimes and to cause hybrid genetic dysfunction at secondary contact
|
|
| 20. |
- Pawar, Harvinder, et al.
(författare)
-
Ghost admixture in eastern gorillas
- 2023
-
Ingår i: Nature Ecology & Evolution. - 2397-334X. ; 7:9, s. 1503-1514
-
Tidskriftsartikel (refereegranskat)
|
|
| 21. |
- Pawar, Harvinder, et al.
(författare)
-
Ghost admixture in eastern gorillas
- 2023
-
Ingår i: Nature Ecology & Evolution. - : Springer Nature. - 2397-334X. ; 7:9, s. 1503-1514
-
Tidskriftsartikel (refereegranskat)abstract
- Archaic admixture has had a significant impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. Within the great apes archaic admixture has been identified in chimpanzees and bonobos, but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using Approximate Bayesian Computation (ABC) with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic 'ghost' lineage into the common ancestor of eastern gorillas, but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, likely more than 40 thousand years ago, and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species.
|
|
| 22. |
|
|
| 23. |
- Pochon, Zoé, et al.
(författare)
-
aMeta : an accurate and memory-efficient ancient metagenomic profiling workflow
- 2023
-
Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24
-
Tidskriftsartikel (refereegranskat)abstract
- Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.
|
|
| 24. |
- Song, Kai, 1988-, et al.
(författare)
-
Inbreeding and genetic load in a pair of sibling grouse species : Tetrastes sewersowi and T. bonasia
- 2024
-
Ingår i: Avian Research. - : Elsevier. - 2053-7166. ; 15
-
Tidskriftsartikel (refereegranskat)abstract
- Genetic load and inbreeding are recognized as important factors to be considered in conservation programs. Elevated levels of both can increase the risk of population extinction by negatively impacting fitness-related characters in many species of plants and animals, including humans (inbreeding depression). Genomic techniques are increasingly used in measuring and understanding genetic load and inbreeding and their importance in evolution and conservation. We used whole genome resequencing data from two sibling grouse species in subarctic Eurasia to quantify both. We found a large range of inbreeding measured as FROH (fraction of runs of homozygosity) in individuals from different populations of Chinese Grouse (Tetrastes sewerzowi) and Hazel Grouse (T. bonasia). FROH estimated from genome-wide runs of homozygosity (ROH) ranged from 0.02 to 0.24 among Chinese Grouse populations and from 0.01 to 0.44 in Hazel Grouse. Individuals from a population of Chinese Grouse residing in the Qilian mountains and from the European populations of Hazel Grouse (including samples from Sweden, Germany and Northeast Poland) were the most inbred (FROH ranged from 0.10 to 0.23 and 0.11 to 0.44, respectively). These levels are comparable to other highly inbred populations of birds. Hazel Grouse from northern China and Chinese Grouse residing in the Qinghai-Tibetan Plateau showed relatively lower inbreeding levels. Comparisons of the ratio between deleterious missense mutations and synonymous mutations revealed higher levels in Chinese Grouse as compared to Hazel Grouse. These results are possibly explained by higher fixation rates, mutational melt down, in the range-restricted Chinese Grouse compared to the wide-ranging Hazel Grouse. However, when we compared the relatively more severe class of loss-of-function mutations, Hazel Grouse had slightly higher levels than Chinese Grouse, a result which may indicate that purifying selection (purging) has been more efficient in Chinese Grouse on this class of mutations.
|
|
| 25. |
- Song, Kai, 1988-, et al.
(författare)
-
Purifying selection in Grouse is more efficient in large populations
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Inbreeding depression and purging are recognized as essential factors to be considered in conservation programs. Elevated levels of both can increase the risk of population extinction by negatively impacting fitness-related characters in many species of plants and animals, including humans. Genomic techniques are increasingly used in measuring and understanding inbreeding and inbreeding depression and their importance in evolution and conservation. We use whole genome resequencing data from isolated, bottlenecked, and outbred Tetrastes and Lagopus populations in subarctic Eurasia to quantify inbreeding depression and purifying selection. We found a large range of inbreeding measured as FROH in populations of Chinese Grouse (Tetrastes sewerzowi) and Hazel Grouse (T. bonasia). FROH estimated from genome-wide runs of homozygosity (ROH) ranged from 0.02 to 0.24 among Chinese Grouse populations and 0.01 to 0.44 in Hazel grouse. A population of Chinese Grouse residing in the Qilian mountains and the European populations of Hazel Grouse (including samples from Sweden, Germany and North East Poland) were both highly inbred (FROH ranged from 0.10 to 0.23 and 0.11 to 0.44, respectively). Hazel grouse from northern China and Chinese grouse residing in the Qinghai-Tibetan Plateau showed relatively lower inbreeding levels. In addition, through comparison of the ratio between deleterious missense mutations and synonymous mutations, purifying selection was found to be more efficient in Hazel grouse and ptarmigan populations which hold larger population sizes than Chinese grouse. However, when we compared the ratio between loss-of-function and synonymous mutations, Hazel Grouse had slightly higher levels than Chinese Grouse while Willow Ptarmigan and Rock Ptarmigan had lower levels of genetic load. These results indicate that purifying selection has been more efficient in the wide ranging hazel grouse which thereby can sustain higher levels of inbreeding compared to Chinese grouse. Our study provides the first genetic evidence of inbreeding depression and purging patterns in boreal forest species in Eurasia from the respective sibling species and provide relevant information for future conservation and management of the species.
|
|
