| 1. |
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| 2. |
- Lubbe, Pascale, et al.
(författare)
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Mitogenomes resolve the phylogeography and divergence times within the endemic New Zealand Callaeidae (Aves: Passerida)
- 2022
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Ingår i: Zoological Journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4082 .- 1096-3642. ; 196:4, s. 1451-1463
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Tidskriftsartikel (refereegranskat)abstract
- The biogeographical origins of the endemic birds of New Zealand (Aotearoa) are of great interest, particularly Palaeogene lineages such as Callaeidae, a passerine family characterized by brightly coloured wattles behind the beak and, in some cases, extreme sexual dimorphism in bill size and shape. Ancestral representatives of Callaeidae are thought to have split from their closest relatives outside New Zealand in the Oligocene, but little is known about the timing of divergences within the family. We present a fully dated molecular phylogeny of Callaeidae mitogenomes and discuss the biogeographical implications. Our results suggest that formation of Pliocene marine seaways, such as the Manawatu Strait, are likely to have played a significant role in the differentiation of North Island and South Island kōkako (Callaeas spp.) and saddlebacks/tīeke (Philesturnus spp.).
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| 3. |
- Cockerill, Christopher Alan, 1994-, et al.
(författare)
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Genomic Consequences of Fragmentation in the Endangered Fennoscandian Arctic Fox (Vulpes lagopus)
- 2022
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Ingår i: Genes. - : MDPI AG. - 2073-4425. ; 13:11
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Tidskriftsartikel (refereegranskat)abstract
- Accelerating climate change is causing severe habitat fragmentation in the Arctic, threatening the persistence of many cold-adapted species. The Scandinavian arctic fox (Vulpes lagopus) is highly fragmented, with a once continuous, circumpolar distribution, it struggled to recover from a demographic bottleneck in the late 19th century. The future persistence of the entire Scandinavian population is highly dependent on the northernmost Fennoscandian subpopulations (Scandinavia and the Kola Peninsula), to provide a link to the viable Siberian population. By analyzing 43 arctic fox genomes, we quantified genomic variation and inbreeding in these populations. Signatures of genome erosion increased from Siberia to northern Sweden indicating a stepping-stone model of connectivity. In northern Fennoscandia, runs of homozygosity (ROH) were on average ~1.47-fold longer than ROH found in Siberia, stretching almost entire scaffolds. Moreover, consistent with recent inbreeding, northern Fennoscandia harbored more homozygous deleterious mutations, whereas Siberia had more in heterozygous state. This study underlines the value of documenting genome erosion following population fragmentation to identify areas requiring conservation priority. With the increasing fragmentation and isolation of Arctic habitats due to global warming, understanding the genomic and demographic consequences is vital for maintaining evolutionary potential and preventing local extinctions.
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| 4. |
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| 5. |
- Cole, Theresa, et al.
(författare)
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Ancient DNA of crested penguins: Testing for temporal genetic shifts in the world's most diverse penguin clade
- 2018
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 131, s. 72-79
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Tidskriftsartikel (refereegranskat)abstract
- Human impacts have substantially reduced avian biodiversity in many parts of the world, particularly on isolated islands of the Pacific Ocean. The New Zealand archipelago, including its five subantarctic island groups, holds breeding grounds for a third of the world's penguin species, including several representatives of the diverse crested penguin genus Eudyptes. While this species-rich genus has been little studied genetically, recent population estimates indicate that several Eudyptes taxa are experiencing demographic declines. Although crested penguins are currently limited to southern regions of the New Zealand archipelago, prehistoric fossil and archaeological deposits suggest a wider distribution during prehistoric times, with breeding ranges perhaps extending to the North Island. Here, we analyse ancient, historic and modern DNA sequences to explore two hypotheses regarding the recent history of Eudyptes in New Zealand, testing for (1) human-driven extinction of Eudyptes lineages; and (2) reduced genetic diversity in surviving lineages. From 83 prehistoric bone samples, each tentatively identified as ‘Eudyptes spp.’, we genetically identified six prehistoric penguin taxa from mainland New Zealand, including one previously undescribed genetic lineage. Moreover, our Bayesian coalescent analyses indicated that, while the range of Fiordland crested penguin (E. pachyrhynchus) may have contracted markedly over the last millennium, genetic DNA diversity within this lineage has remained relatively constant. This result contrasts with human-driven biodiversity reductions previously detected in several New Zealand coastal vertebrate taxa.
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| 6. |
- 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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| 7. |
- Dussex, Nicolas, et al.
(författare)
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Adaptation to the High-Arctic island environment despite long-term reduced genetic variation in Svalbard reindeer
- 2023
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Ingår i: iScience. - 2589-0042. ; 26:10
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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.
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| 8. |
- Dussex, Nicolas, et al.
(författare)
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Biomolecular analyses reveal the age, sex and species identity of a near-intact Pleistocene bird carcass
- 2020
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Ingår i: Communications biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Ancient remains found in permafrost represent a rare opportunity to study past ecosystems. Here, we present an exceptionally well-preserved ancient bird carcass found in the Siberian permafrost, along with a radiocarbon date and a reconstruction of its complete mitochondrial genome. The carcass was radiocarbon dated to approximately 44-49 ka BP, and was genetically identified as a female horned lark. This is a species that usually inhabits open habitat, such as the steppe environment that existed in Siberia at the time. This near-intact carcass highlights the potential of permafrost remains for evolutionary studies that combine both morphology and ancient nucleic acids. Nicolas Dussex et al. identify a 44,000-49,000 year old bird found in Siberian permafrost as a female horned lark using ancient DNA. This exceptionally well-preserved specimen illustrates the potential contribution to science of permafrost deposits, such as the study of ecology and evolution of ancient ecosystems, calibration of molecular clocks, and furthering our understanding of processes such as biological regulation and gene expression in relation to climate change.
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| 9. |
- Dussex, Nicolas, et al.
(författare)
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Complete genomes of two extinct New Zealand passerines show responses to climate fluctuations but no evidence for genomic erosion prior to extinction
- 2019
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Ingår i: Biology Letters. - : The Royal Society. - 1744-9561 .- 1744-957X. ; 15:9
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Tidskriftsartikel (refereegranskat)abstract
- Human intervention, pre-human climate change (or a combination of both), as well as genetic effects, contribute to species extinctions. While many species from oceanic islands have gone extinct due to direct human impacts, the effects of pre-human climate change and human settlement on the genomic diversity of insular species and the role that loss of genomic diversity played in their extinctions remains largely unexplored. To address this question, we sequenced whole genomes of two extinct New Zealand passerines, the huia (Heteralocha acutirostris) and South Island kokako (Callaeas cinereus). Both species showed similar demographic trajectories throughout the Pleistocene. However, the South Island kokako continued to decline after the last glaciation, while the huia experienced some recovery. Moreover, there was no indication of inbreeding resulting from recent mating among closely related individuals in either species. This latter result indicates that population fragmentation associated with forest clearing by Maori may not have been strong enough to lead to an increase in inbreeding and exposure to genomic erosion. While genomic erosion may not have directly contributed to their extinctions, further habitat fragmentation and the introduction of mammalian predators by Europeans may have been an important driver of extinction in huia and South Island kokako.
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| 10. |
- Dussex, Nicolas, et al.
(författare)
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Full Mitogenomes in the Critically Endangered Kakapo Reveal Major Post-Glacial and Anthropogenic Effects on Neutral Genetic Diversity
- 2018
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Ingår i: Genes. - : MDPI AG. - 2073-4425. ; 9:4
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Tidskriftsartikel (refereegranskat)abstract
- Understanding how species respond to population declines is a central question in conservation and evolutionary biology. Population declines are often associated with loss of genetic diversity, inbreeding and accumulation of deleterious mutations, which can lead to a reduction in fitness and subsequently contribute to extinction. Using temporal approaches can help us understand the effects of population declines on genetic diversity in real time. Sequencing pre-decline as well as post-decline mitogenomes representing all the remaining mitochondrial diversity, we estimated the loss of genetic diversity in the critically endangered kakapo (Strigops habroptilus). We detected a signal of population expansion coinciding with the end of the Pleistocene last glacial maximum (LGM). Also, we found some evidence for northern and southern lineages, supporting the hypothesis that the species may have been restricted to isolated northern and southern refugia during the LGM. We observed an important loss of neutral genetic diversity associated with European settlement in New Zealand but we could not exclude a population decline associated with Polynesian settlement in New Zealand. However, we did not find evidence for fixation of deleterious mutations. We argue that despite high pre-decline genetic diversity, a rapid and range-wide decline combined with the lek mating system, and life-history traits of kakapo contributed to a rapid loss of genetic diversity following severe population declines.
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| 11. |
- Dussex, Nicolas, et al.
(författare)
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Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics
- 2021
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 288:1957
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Forskningsöversikt (refereegranskat)abstract
- Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.
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| 12. |
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| 13. |
- Dussex, Nicolas
(författare)
-
Minimum Viable Population Analysis to inform the Favourable Reference Value for wolves in Sweden : Final report – April 2024
- 2024
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The aim of this report, commissioned by the Swedish Environment Protection Agency (SEPA), was to evaluate if and under which conditions a Favourable Reference Value (FRV) of 170 to 270 wolves (Canis lupus) represents a viable population in Sweden. To address this question, I performed a Population Viability Analysis using forward-in-time genome-informed simulations implemented in SLiM. I modelled a large population in Karelia and a smaller population in Scandinavia (i.e., including wolves from both Sweden and Norway) and examined the demographic and genetic viability of the population. I first modelled the effects of survival, reproductive output, population size and migration rates on the probability of extinction of the population. Secondly, using field-based empirical estimates for demographic and life-history traits, I examined the effect of varying population size and migration rates on genome-wide diversity (e.g., nucleotide diversity, inbreeding and two components of genetic load) as proxy for viability. Simulations indicate that with reduced survival rate and female reproductive output, the risk of extinction would range between 22 and 32% for a population size of 50 and between 1 and 10% for a population size of 100. However, when using higher survival rates and female reproductive output values based on field-based estimates, the risk of extinction was close to 1% for a population size of 50 and no extinction was reported for a population size ≥100.Furthermore, for a population size of 170 to 270 wolves in Sweden (i.e., 210 and 310 for the whole Scandinavian population), between 1 to 3 effective (i.e., reproducing) immigrants per decade would be needed remain within a 5% window of loss in nucleotide diversity and increase in inbreeding. However, while migration rates above a threshold of 1-3 effective immigrants per decade would increase genetic diversity and would potentially induce a genetic rescue effect, it would also represent a risk of introducing new deleterious variation, especially for lower population sizes. Moreover, the simulations showed that larger population sizes would be more immune to loss of diversity. Yet, there would also be a non-negligible risk of introduction of new deleterious variation with ≥8 migrants per decade. Consequently, the trade-off between genetic rescue and introduction of deleterious variation needs to be taken into account when determining a target population size for management.
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| 14. |
- Dussex, Nicolas, et al.
(författare)
-
Moose genomes reveal past glacial demography and the origin of modern lineages
- 2020
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 21:1
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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.
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| 15. |
- Dussex, Nicolas, et al.
(författare)
-
Population genomics of the critically endangered kākāpō
- 2021
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Ingår i: Cell Genomics. - : Elsevier BV. - 2666-979X. ; 1:1
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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.
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| 16. |
- Dussex, Nicolas, et al.
(författare)
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Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose
- 2023
-
Ingår i: Communications Biology. - 2399-3642. ; 6:1
-
Tidskriftsartikel (refereegranskat)abstract
- Ungulate species have experienced severe declines over the past centuries through overharvesting and habitat loss. Even if many game species have recovered thanks to strict hunting regulation, the genome-wide impacts of overharvesting are still unclear. Here, we examine the temporal and geographical differences in genome-wide diversity in moose (Alces alces) over its whole range in Sweden by sequencing 87 modern and historical genomes. We found limited impact of the 1900s near-extinction event but local variation in inbreeding and load in modern populations, as well as suggestion of a risk of future reduction in genetic diversity and gene flow. Furthermore, we found candidate genes for local adaptation, and rapid temporal allele frequency shifts involving coding genes since the 1980s, possibly due to selective harvesting. Our results highlight that genomic changes potentially impacting fitness can occur over short time scales and underline the need to track both deleterious and selectively advantageous genomic variation.
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| 17. |
- Dussex, Nicolas, 1982-, et al.
(författare)
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Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species
- 2018
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 8:17, s. 8736-8749
-
Tidskriftsartikel (refereegranskat)abstract
- Next‐generation reduced representation sequencing (RRS) approaches show great potential for resolving the structure of wild populations. However, the population structure of species that have shown rapid demographic recovery following severe population bottlenecks may still prove difficult to resolve due to high gene flow between subpopulations. Here, we tested the effectiveness of the RRS method Genotyping‐By‐Sequencing (GBS) for describing the population structure of the New Zealand fur seal (NZFS, Arctocephalus forsteri), a species that was heavily exploited by the 19th century commercial sealing industry and has since rapidly recolonized most of its former range from a few isolated colonies. Using 26,026 neutral single nucleotide polymorphisms (SNPs), we assessed genetic variation within and between NZFS colonies. We identified low levels of population differentiation across the species range (<1% of variation explained by regional differences) suggesting a state of near panmixia. Nonetheless, we observed subtle population substructure between West Coast and Southern East Coast colonies and a weak, but significant (p = 0.01), isolation‐by‐distance pattern among the eight colonies studied. Furthermore, our demographic reconstructions supported severe bottlenecks with potential 10‐fold and 250‐fold declines in response to Polynesian and European hunting, respectively. Finally, we were able to assign individuals treated as unknowns to their regions of origin with high confidence (96%) using our SNP data. Our results indicate that while it may be difficult to detect population structure in species that have experienced rapid recovery, next‐generation markers and methods are powerful tools for resolving fine‐scale structure and informing conservation and management efforts.
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| 18. |
- Dussex, Nicolas, et al.
(författare)
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The kākāpō (Strigops habroptilus)
- 2022
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Ingår i: Trends in Genetics. - : Elsevier. - 0168-9525 .- 1362-4555. ; 38:8
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Tidskriftsartikel (refereegranskat)
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| 19. |
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| 20. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
-
Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 21. |
- Foster, Yasmin, et al.
(författare)
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Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō
- 2021
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Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 11:11
-
Tidskriftsartikel (refereegranskat)abstract
- Events of inbreeding are inevitable in critically endangered species. Reduced population sizes and unique life-history traits can increase the severity of inbreeding, leading to declines in fitness and increased risk of extinction. Here, we investigate levels of inbreeding in a critically endangered flightless parrot, the kākāpō (Strigops habroptilus), wherein a highly inbred island population and one individual from the mainland of New Zealand founded the entire extant population. Genotyping-by-sequencing (GBS), and a genotype calling approach using a chromosome-level genome assembly, identified a filtered set of 12,241 single-nucleotide polymorphisms (SNPs) among 161 kākāpō, which together encompass the total genetic potential of the extant population. Multiple molecular-based estimates of inbreeding were compared, including genome-wide estimates of heterozygosity (FH), the diagonal elements of a genomic-relatedness matrix (FGRM), and runs of homozygosity (RoH, FRoH). In addition, we compared levels of inbreeding in chicks from a recent breeding season to examine if inbreeding is associated with offspring survival. The density of SNPs generated with GBS was sufficient to identify chromosomes that were largely homozygous with RoH distributed in similar patterns to other inbred species. Measures of inbreeding were largely correlated and differed significantly between descendants of the two founding populations. However, neither inbreeding nor ancestry was found to be associated with reduced survivorship in chicks, owing to unexpected mortality in chicks exhibiting low levels of inbreeding. Our study highlights important considerations for estimating inbreeding in critically endangered species, such as the impacts of small population sizes and admixture between diverse lineages.
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| 22. |
- Gemmell, Neil J., et al.
(författare)
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The tuatara genome reveals ancient features of amniote evolution
- 2020
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 584:7821, s. 403-409
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Tidskriftsartikel (refereegranskat)abstract
- The tuatara (Sphenodon punctatus)—the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2—is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes2,4. Here we analyse the genome of the tuatara, which—at approximately 5 Gb—is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.
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| 23. |
- Hasselgren, Malin, et al.
(författare)
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Genomic and fitness consequences of inbreeding in an endangered carnivore
- 2021
-
Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 30:12, s. 2790-2799
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Tidskriftsartikel (refereegranskat)abstract
- Reduced fitness through genetic drift and inbreeding is a major threat to small and isolated populations. Although previous studies have generally used genetically verified pedigrees to document effects of inbreeding and gene flow, these often fail to capture the whole inbreeding history of the species. By assembling a draft arctic fox (Vulpes lagopus) genome and resequencing complete genomes of 23 additional foxes born before and after a well-documented immigration event in Scandinavia, we here look into the genomic consequences of inbreeding and genetic rescue. We found a difference in genome-wide diversity, with 18% higher heterozygosity and 81% lower F-ROH in immigrant F1 compared to native individuals. However, more distant descendants of immigrants (F2, F3) did not show the same pattern. We also found that foxes with lower inbreeding had higher probability to survive their first year of life. Our results demonstrate the important link between genetic variation and fitness as well as the transient nature of genetic rescue. Moreover, our results have implications in conservation biology as they demonstrate that inbreeding depression can effectively be detected in the wild by a genomic approach.
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| 24. |
- Hasselgren, Malin, et al.
(författare)
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Genomic consequences of inbreeding and outbreeding in an endangered carnivore
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Loss of genetic variation through genetic drift and inbreeding is a major threat to small and isolated populations. Although previous studies have generally used genetically verified pedigrees to document effects of inbreeding and gene flow, these often fail to capture the whole inbreeding history. Also, empirical support for a link between genomic inbreeding and fitness is scarce. By sequencing complete genomes of 23 Scandinavian arctic foxes (Vulpes lagopus) born before and after an immigration event, we here look into the genomic consequences of inbreeding and genetic rescue. We found a significant difference, with 18% higher genome-wide heterozygosity and 81% lower genomic inbreeding in immigrant F1 compared to native individuals. However, more distant descendants of immigrants (F2, F3) did not show the same pattern. We also found that foxes surviving their first year generally had higher heterozygosity and lower inbreeding than non-survivors. Finally, pedigree-based inbreeding correlated with, but underestimated, genomic inbreeding levels. Our results demonstrate a fundamental link between genetic variation and fitness, the transient nature of genetic rescue, and that inbreeding is even more severe than captured from a genetically verified pedigree. Our results have important implications in conservation biology as inbreeding depression can be detected in populations lacking a pedigree.
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| 25. |
- Hold, Katharina, et al.
(författare)
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Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos
- 2024
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 14:1
-
Tidskriftsartikel (refereegranskat)abstract
- Climate warming at the end of the last glacial period had profound effects on the distribution of cold-adapted species. As their range shifted towards northern latitudes, they were able to colonise previously glaciated areas, including remote Arctic islands. However, there is still uncertainty about the routes and timing of colonisation. At the end of the last ice age, reindeer/caribou (Rangifer tarandus) expanded to the Holarctic region and colonised the archipelagos of Svalbard and Franz Josef Land. Earlier studies have proposed two possible colonisation routes, either from the Eurasian mainland or from Canada via Greenland. Here, we used 174 ancient, historical and modern mitogenomes to reconstruct the phylogeny of reindeer across its whole range and to infer the colonisation route of the Arctic islands. Our data shows a close affinity among Svalbard, Franz Josef Land and Novaya Zemlya reindeer. We also found tentative evidence for positive selection in the mitochondrial gene ND4, which is possibly associated with increased heat production. Our results thus support a colonisation of the Eurasian Arctic archipelagos from the Eurasian mainland and provide some insights into the evolutionary history and adaptation of the species to its High Arctic habitat.
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| 26. |
- Kutschera, Verena E., et al.
(författare)
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GenErode : a bioinformatics pipeline to investigate genome erosion in endangered and extinct species
- 2022
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Ingår i: BMC Bioinformatics. - : Springer Nature. - 1471-2105. ; 23:1
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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.
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| 27. |
- Kutschera, Verena E., et al.
(författare)
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Purifying Selection in Corvids Is Less Efficient on Islands
- 2020
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Ingår i: Molecular biology and evolution. - : OXFORD UNIV PRESS. - 0737-4038 .- 1537-1719. ; 37:2, s. 469-474
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Tidskriftsartikel (refereegranskat)abstract
- Theory predicts that deleterious mutations accumulate more readily in small populations. As a consequence, mutation load is expected to be elevated in species where life-history strategies and geographic or historical contingencies reduce the number of reproducing individuals. Yet, few studies have empirically tested this prediction using genome-wide data in a comparative framework. We collected whole-genome sequencing data for 147 individuals across seven crow species (Corvus spp.). For each species, we estimated the distribution of fitness effects of deleterious mutations and compared it with proxies of the effective population size N-e. Island species with comparatively smaller geographic range sizes had a significantly increased mutation load. These results support the view that small populations have an elevated risk of mutational meltdown, which may contribute to the higher extinction rates observed in island species.
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| 28. |
- Larsson, Petter, et al.
(författare)
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Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox
- 2019
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Ingår i: Philosophical Transactions of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8436 .- 1471-2970. ; 374:1788
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Tidskriftsartikel (refereegranskat)abstract
- Ancient DNA provides a powerful means to investigate the timing, rate and extent of population declines caused by extrinsic factors, such as past climate change and human activities. One species probably affected by both these factors is the arctic fox, which had a large distribution during the last glaciation that subsequently contracted at the start of the Holocene. More recently, the arctic fox population in Scandinavia went through a demographic bottleneck owing to human persecution. To investigate the consequences of these processes, we generated mitogenome sequences from a temporal dataset comprising Pleistocene, historical and modern arctic fox samples. We found no evidence that Pleistocene populations in mid-latitude Europe or Russia contributed to the present-day gene pool of the Scandinavian population, suggesting that postglacial climate warming led to local population extinctions. Furthermore, during the twentieth-century bottleneck in Scandinavia, at least half of the mitogenome haplotypes were lost, consistent with a 20-fold reduction in female effective population size. In conclusion, these results suggest that the arctic fox in mainland Western Europe has lost genetic diversity as a result of both past climate change and human persecution. Consequently, it might be particularly vulnerable to the future challenges posed by climate change. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'
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| 29. |
- Liu, Shanlin, et al.
(författare)
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Ancient and modem genomes unravel the evolutionary history of the rhinoceros family
- 2021
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Ingår i: Cell. - : Elsevier. - 0092-8674 .- 1097-4172. ; 184:19, s. 4874-4885.e16
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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.
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| 30. |
- Lord, Edana, et al.
(författare)
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Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros
- 2020
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Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 30:19
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Tidskriftsartikel (refereegranskat)abstract
- Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene and became extinct approximately 14 thousand years before present (ka BP). While humans and climate change have been proposed as potential causes of extinction [1-3], knowledge is limited on how the woolly rhinoceros was impacted by human arrival and climatic fluctuations [2]. Here, we use one complete nuclear genome and 14 mitogenomes to investigate the demographic history of woolly rhinoceros leading up to its extinction. Unlike other northern megafauna, the effective population size of woolly rhinoceros likely increased at 29.7 ka BP and subsequently remained stable until close to the species’ extinction. Analysis of the nuclear genome from a similar to 18.5-ka-old specimen did not indicate any increased inbreeding or reduced genetic diversity, suggesting that the population size remained steady for more than 13 ka following the arrival of humans [4]. The population contraction leading to extinction of the woolly rhinoceros may have thus been sudden and mostly driven by rapid warming in the Bolling-Allerod interstadial. Furthermore, we identify woolly rhinoceros-specific adaptations to arctic climate, similar to those of the woolly mammoth. This study highlights how species respond differently to climatic fluctuations and further illustrates the potential of palaeogenomics to study the evolutionary history of extinct species.
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| 31. |
- Martini, Denise, et al.
(författare)
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Evolution of the “world’s only alpine parrot” : Genomic adaptation or phenotypic plasticity, behaviour and ecology?
- 2021
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 30:23, s. 6370-6386
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Tidskriftsartikel (refereegranskat)abstract
- Climate warming, in particular in island environments, where opportunities for species to disperse are limited, may become a serious threat to cold adapted alpine species. In order to understand how alpine species may respond to a warming world, we need to understand the drivers that have shaped their habitat specialisation and the evolutionary adaptations that allow them to utilize alpine habitats. The endemic, endangered New Zealand kea (Nestor notabilis) is considered the only alpine parrot in the world. As a species commonly found in the alpine zone it may be highly susceptible to climate warming. But is it a true alpine specialist? Is its evolution driven by adaptation to the alpine zone, or is the kea an open habitat generalist that simply uses the alpine zone to, for example, avoid lower lying anthropogenic landscapes? We use whole genome data of the kea and its close, forest adapted sister species, the kākā (Nestor meridionalis) to reconstruct the evolutionary history of both species and identify the functional genomic differences that underlie their habitat specialisations. Our analyses do not identify major functional genomic differences between kea and kākā in pathways associated with high-altitude. Rather, we found evidence that selective pressures on adaptations commonly found in alpine species are present in both Nestor species, suggesting that selection for alpine adaptations has not driven their divergence. Strongly divergent demographic responses to past climate warming between the species nevertheless highlight potential future threats to kea survival in a warming world.
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| 32. |
- Pečnerová, Patrícia, et al.
(författare)
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Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth
- 2017
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Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 27:22, s. 3505-3510.e3
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Tidskriftsartikel (refereegranskat)abstract
- While present-day taxa are valuable proxies for understanding the biology of extinct species, it is also crucial to examine physical remains in order to obtain a more comprehensive view of their behavior, social structure, and life histories [1, 2]. For example, information on demographic parameters such as age distribution and sex ratios in fossil assemblages can be used to accurately infer socioecological patterns (e.g., [3]). Here we use genomic data to determine the sex of 98 woolly mammoth (Mammuthus primigenius) specimens in order to infer social and behavioral patterns in the last 60,000 years of the species' existence. We report a significant excess of males among the identified samples (69% versus 31%; p < 0.0002). We argue that this male bias among mammoth remains is best explained by males more often being caught in natural traps that favor preservation. Wehypothesize that this is a consequence of social structure in proboscideans, which is characterized by matriarchal hierarchy and sex segregation. Without the experience associated with living in a matriarchal family group, or a bachelor group with an experienced bull, young or solitary males may have been more prone to die in natural traps where good preservation is more likely.
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| 33. |
- Schlesselmann, Ann-Kathrin V., et al.
(författare)
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New Zealand endemic open-habitat specialist, the Black-fronted Tern (Chlidonias albostriatus), experienced population expansion during Pleistocene glaciation and recent decline
- 2023
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Ingår i: Ibis. - : Wiley. - 0019-1019 .- 1474-919X. ; 165:1, s. 288-296
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Tidskriftsartikel (refereegranskat)abstract
- Understanding how climatic and environmental changes, as well as human activities, induce changes in the distribution and population size of avian species refines our ability to predict future impacts on threatened species. Using multilocus genetic data, we show that the population of a threatened New Zealand endemic open-habitat specialist, the Black-fronted Tern Chlidonias albostriatus – in contrast to forest specialists – expanded during the last glacial period. The population has decreased subsequently despite the availability of extensive open habitat after human arrival to New Zealand. We conclude that population changes for open habitat specialists such as Black-fronted Terns in pre-human New Zealand were habitat-dependent, similar to Northern Hemisphere cold-adapted species, whereas post-human settlement populations were constrained by predators independent of habitat availability, similar to other island endemic species.
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| 34. |
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| 35. |
- von Seth, Johanna, et al.
(författare)
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Genomic trajectories of a near-extinction event in the Chatham Island black robin
- 2022
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 23
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Tidskriftsartikel (refereegranskat)abstract
- Background: Understanding the micro-evolutionary response of populations to demographic declines is a major goal in evolutionary and conservation biology. In small populations, genetic drift can lead to an accumulation of deleterious mutations, which will increase the risk of extinction. However, demographic recovery can still occur after extreme declines, suggesting that natural selection may purge deleterious mutations, even in extremely small populations. The Chatham Island black robin (Petroica traversi) is arguably the most inbred bird species in the world. It avoided imminent extinction in the early 1980s and after a remarkable recovery from a single pair, a second population was established and the two extant populations have evolved in complete isolation since then. Here, we analysed 52 modern and historical genomes to examine the genomic consequences of this extreme bottleneck and the subsequent translocation.Results: We found evidence for two-fold decline in heterozygosity and three- to four-fold increase in inbreeding in modern genomes. Moreover, there was partial support for temporal reduction in total load for detrimental variation. In contrast, compared to historical genomes, modern genomes showed a significantly higher realised load, reflecting the temporal increase in inbreeding. Furthermore, the translocation induced only small changes in the frequency of deleterious alleles, with the majority of detrimental variation being shared between the two populations.Conclusion: Our results highlight the dynamics of mutational load in a species that recovered from the brink of extinction, and show rather limited temporal changes in mutational load. We hypothesise that ancestral purging may have been facilitated by population fragmentation and isolation on several islands for thousands of generations and may have already reduced much of the highly deleterious load well before human arrival and introduction of pests to the archipelago. The majority of fixed deleterious variation was shared between the modern populations, but translocation of individuals with low mutational load could possibly mitigate further fixation of high-frequency deleterious variation.
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| 36. |
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| 37. |
- Yang, Shangchen, et al.
(författare)
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Genomic investigation of the Chinese alligator reveals wild-extinct genetic diversity and genomic consequences of their continuous decline
- 2023
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 23:1, s. 294-311
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Tidskriftsartikel (refereegranskat)abstract
- Critically endangered species are usually restricted to small and isolated populations. High inbreeding without gene flow among populations further aggravates their threatened condition and reduces the likelihood of their long-term survival. Chinese alligator (Alligator sinensis) is one of the most endangered crocodiles in the world and has experienced a continuous decline over the past c. 1 million years. In order to identify the genetic status of the remaining populations and aid conservation efforts, we assembled the first high-quality chromosome-level genome of Chinese alligator and explored the genomic characteristics of three extant breeding populations. Our analyses revealed the existence of at least three genetically distinct populations, comprising two breeding populations in China (Changxing and Xuancheng) and one breeding population in an American wildlife refuge. The American population does not belong to the last two populations of its native range (Xuancheng and Changxing), thus representing genetic diversity extinct in the wild and provides future opportunities for genetic rescue. Moreover, the effective population size of these three populations has been continuously declining over the past 20 ka. Consistent with this decline, the species shows extremely low genetic diversity, a large proportion of long runs of homozygous fragments, and mutational load across the genome. Finally, to provide genomic insights for future breeding management and conservation, we assessed the feasibility of mixing extant populations based on the likelihood of introducing new deleterious alleles and signatures of local adaptation. Overall, this study provides a valuable genomic resource and important genomic insights into the ecology, evolution, and conservation of critically endangered alligators.
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