| 1. |
- Brealey, Jaelle C., et al.
(författare)
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The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans
- 2021
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Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 31:20, s. 4650-4658.e6
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Tidskriftsartikel (refereegranskat)abstract
- Following the advent of industrial-scale antibiotic production in the 1940s,1 antimicrobial resistance (AMR) has been on the rise and now poses a major global health threat in terms of mortality, morbidity, and economic burden.2,3 Because AMR can be exchanged between humans, livestock, and wildlife, wild animals can be used as indicators of human-associated AMR contamination of the environment.4 However, AMR is a normal function of natural environments and is present in host-associated microbiomes, which makes it challenging to distinguish between anthropogenic and natural sources.4,5 One way to overcome this difficulty is to use historical samples that span the period from before the mass production of antibiotics to today. We used shotgun metagenomic sequencing of dental calculus, the calcified form of the oral microbial biofilm, to determine the abundance and repertoire of AMR genes in the oral microbiome of Swedish brown bears collected over the last 180 years. Our temporal metagenomics approach allowed us to establish a baseline of natural AMR in the pre-antibiotics era and to quantify a significant increase in total AMR load and diversity of AMR genes that is consistent with patterns of national human antibiotic use. We also demonstrated a significant decrease in total AMR load in bears in the last two decades, which coincides with Swedish strategies to mitigate AMR. Our study suggests that public health policies can be effective in limiting human-associated AMR contamination of the environment and wildlife.
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| 2. |
- Gharibi, Hassan, et al.
(författare)
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Abnormal (Hydroxy)proline Deuterium Content Redefines Hydrogen Chemical Mass
- 2022
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 144:6, s. 2484-2487
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Tidskriftsartikel (refereegranskat)abstract
- Analyzing the δ2H values in individual amino acids of proteins extracted from vertebrates, we unexpectedly found insome samples, notably bone collagen from seals, more than twice as much deuterium in proline and hydroxyproline residues than inseawater. This corresponds to at least 4 times higher δ2H than in any previously reported biogenic sample. We ruled out diet as aplausible mechanism for such anomalous enrichment. This finding puts into question the old adage that “you are what you eat”.
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| 3. |
- Meadows, Jennifer, et al.
(författare)
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Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture
- 2023
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Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24
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Tidskriftsartikel (refereegranskat)abstract
- Background: The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 x data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.Results: We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.Conclusions: We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.
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| 4. |
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| 5. |
- Granell-Ruiz, Maria, et al.
(författare)
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Genetic variation between and within two populations of bat-eared foxes (Otocyon megalotis Desmarest, 1822) in South Africa
- 2021
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Ingår i: African Zoology. - : Informa UK Limited. - 1562-7020 .- 2224-073X. ; 56:3, s. 165-172
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Tidskriftsartikel (refereegranskat)abstract
- Information on genetic variation within and among populations is relevant for a broad range of topics in biology. We use a combination of mitochondrial and nuclear microsatellite markers to evaluate genetic variation within and between two populations of bat-eared foxes (Otocyon megalotis Desmarest, 1822) in South Africa. The bat-eared fox is a small canid occurring in southern and eastern Africa. The species is currently not threatened with extinction, but a lack of information on genetic diversity has been identified as a deficit for its future conservation. We observed low to moderate genetic differentiation between the two geographically separated populations, but neither mitochondrial nor nuclear microsatellite markers suggested that there have been dispersal barriers between them. Similar genetic diversity within both populations was contrasted by interpopulational differences in relatedness variation among males and females. A high genetic relatedness within both populations, indicated by mitochondrial data, is likely caused by a common historical origin or a combination of species-specific social organization and environmental dispersal constraints. We call for further research on the genetic divergence of bat-eared fox populations as well as on the genetic consequences of interactions between environmental characteristics and social organization in this species.
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| 6. |
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| 7. |
- Hempel, Elisabeth, et al.
(författare)
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Blue Turns to Gray : Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus)
- 2022
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 39:12
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Tidskriftsartikel (refereegranskat)abstract
- The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (Hippotragus equinus) or sable (Hippotragus niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavorable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4× mean coverage from a historical specimen (∼200 years old) and one at 2.1× mean coverage from a fossil specimen dating to 9,800–9,300 cal years BP, making it currently the oldest paleogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelope, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene–Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely the decisive factor in the blue antelope's extinction.
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| 8. |
- Hempel, Elisabeth, et al.
(författare)
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Identifying the true number of specimens of the extinct blue antelope (Hippotragus leucophaeus)
- 2021
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:2100
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Tidskriftsartikel (refereegranskat)abstract
- Native to southern Africa, the blue antelope (Hippotragus leucophaeus) is the only large African mammal species known to have become extinct in historical times. However, it was poorly documented prior to its extinction ~ 1800 AD, and many of the small number of museum specimens attributed to it are taxonomically contentious. This places limitations on our understanding of its morphology, ecology, and the mechanisms responsible for its demise. We retrieved genetic information from ten of the sixteen putative blue antelope museum specimens using both shotgun sequencing and mitochondrial genome target capture in an attempt to resolve the uncertainty surrounding the identification of these specimens. We found that only four of the ten investigated specimens, and not a single skull, represent the blue antelope. This indicates that the true number of historical museum specimens of the blue antelope is even smaller than previously thought, and therefore hardly any reference material is available for morphometric, comparative and genetic studies. Our study highlights how genetics can be used to identify rare species in natural history collections where other methods may fail or when records are scarce. Additionally, we present an improved mitochondrial reference genome for the blue antelope as well as one complete and two partial mitochondrial genomes. A first analysis of these mitochondrial genomes indicates low levels of maternal genetic diversity in the ‘museum population’, possibly confirming previous results that blue antelope population size was already low at the time of the European colonization of South Africa.
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| 9. |
- Kalthoff, Daniela C., et al.
(författare)
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Biomechanical adaptations for burrowing in the incisor enamel microstructure of Geomyidae and Heteromyidae (Rodentia: Geomyoidea)
- 2021
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Ingår i: Ecology and Evolution. - : Wiley-Blackwell Publishing Inc.. - 2045-7758. ; 11, s. 9447-9459
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Tidskriftsartikel (refereegranskat)abstract
- The enamel microstructure of fossil and extant Geomyoidea (Geomyidae, Heteromyidae) lower incisors incorporates three- or two-layered schmelzmusters with uniserial, transverse Hunter-Schreger bands having parallel and perpendicular or exclusively perpendicular oriented interprismatic matrix. Phylogenetically, these schmelzmusters are regarded as moderately (enamel type 2) to highly derived (enamel type 3). Our analysis detected a zone of modified radial enamel close to the enamel–dentine junction. Modified radial enamel shows a strong phylogenetic signal within the clade Geomorpha as it is restricted to fossil and extant Geomyoidea and absent in Heliscomyidae, Florentiamyidae, and Eomyidae. This character dates back to at least the early Oligocene (early Arikareean, 29 Ma), where it occurs in entoptychine gophers. We contend that this specialized incisor enamel architecture developed as a biomechanical adaptation to regular burrowing activities including chisel-tooth digging and a fiber-rich diet and was probably present in the common ancestor of the clade. We regard the occurrence of modified radial enamel in lower incisors of scratch-digging Geomyidae and Heteromyidae as the retention of a plesiomorphic character that is selectively neutral. The shared occurrence of modified radial enamel is a strong, genetically anchored argument for the close phylogenetic relationship of Geomyidae and Heteromyidae on the dental microstructure level.
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| 10. |
- Kalthoff, Daniela C., et al.
(författare)
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Incisor enamel microstructure places New and Old World Eomyidae outside Geomorpha (Rodentia, Mammalia)
- 2022
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 51:4, s. 381-400
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Tidskriftsartikel (refereegranskat)abstract
- The lower incisor enamel microstructure of the fossil rodent family Eomyidae was believed to be three-layered and highly derived but rather uniform throughout the clade. Here, we describe a new four-layered schmelzmuster in Eomyidae consisting of a three-fold portio interna with longitudinal oriented, uniserial Hunter-Schreger bands and a one-fold portio externa, accounting for a unique enamel microstructure character combination in Rodentia. This new schmelzmuster type has developed early in eomyid evolution and is detectable already in the late Eocene (Chadronian) of North America. In European eomyids, it first occurs in the early Miocene (MN 3), implying that this four-layered schmelzmuster was not present in all members of the family but restricted to species included in Eomyini and some genera currently considered Eomyidae incertae sedis within Eomyidae. Additionally, our analysis recognizes three taxa with schmelzmuster divergent from all other eomyids. Incisor enamel microstructure does not advocate a close phylogenetic relationship of Eomyidae to either fossil or extant Heteromyidae and Geomyidae, nor to fossil Heliscomyidae and Florentiamyidae. Our results rather support the view that Eomyidae are placed outside Geomorpha.
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| 11. |
- Lagerholm, Vendela K., et al.
(författare)
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On the origin of the Norwegian lemming
- 2014
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 23:8, s. 2060-2071
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Tidskriftsartikel (refereegranskat)abstract
- The Pleistocene glacial cycles resulted in significant changes in species distributions, and it has been discussed whether this caused increased rates of population divergence and speciation. One species that is likely to have evolved during the Pleistocene is the Norwegian lemming (Lemmus lemmus). However, the origin of this species, both in terms of when and from what ancestral taxon it evolved, has been difficult to ascertain. Here, we use ancient DNA recovered from lemming remains from a series of Late Pleistocene and Holocene sites to explore the species' evolutionary history. The results revealed considerable genetic differentiation between glacial and contemporary samples. Moreover, the analyses provided strong support for a divergence time prior to the Last Glacial Maximum (LGM), therefore likely ruling out a postglacial colonization of Scandinavia. Consequently, it appears that the Norwegian lemming evolved from a small population that survived the LGM in an ice-free Scandinavian refugium.
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| 12. |
- Palkopoulou, Eleftheria, et al.
(författare)
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Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings
- 2016
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 22:5, s. 1710-1721
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Tidskriftsartikel (refereegranskat)abstract
- Recent palaeogenetic studies indicate a highly dynamic history in collared lemmings (Dicrostonyx spp.), with several demographical changes linked to climatic fluctuations that took place during the last glaciation. At the western range margin of D.torquatus, these changes were characterized by a series of local extinctions and recolonizations. However, it is unclear whether this pattern represents a local phenomenon, possibly driven by ecological edge effects, or a global phenomenon that took place across large geographical scales. To address this, we explored the palaeogenetic history of the collared lemming using a next-generation sequencing approach for pooled mitochondrial DNA amplicons. Sequences were obtained from over 300 fossil remains sampled across Eurasia and two sites in North America. We identified five mitochondrial lineages of D.torquatus that succeeded each other through time across Europe and western Russia, indicating a history of repeated population extinctions and recolonizations, most likely from eastern Russia, during the last 50000years. The observation of repeated extinctions across such a vast geographical range indicates large-scale changes in the steppe-tundra environment in western Eurasia during the last glaciation. AllHolocene samples, from across the species' entire range, belonged to only one of the five mitochondrial lineages. Thus, extant D.torquatus populations only harbour a small fraction of the total genetic diversity that existed across different stages of the Late Pleistocene. In North American samples, haplotypes belonging to both D.groenlandicus and D.richardsoni were recovered from a Late Pleistocene site in south-western Canada. This suggests that D.groenlandicus had a more southern and D.richardsoni a more northern glacial distribution than previously thought. This study provides significant insights into the population dynamics of a small mammal at a large geographical scale and reveals a rather complex demographical history, which could have had bottom-up effects in the Late Pleistocene steppe-tundra ecosystem.
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| 13. |
- Sánchez-Barreiro, Fátima, et al.
(författare)
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Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros
- 2023
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Ingår i: Molecular biology and evolution. - 0737-4038 .- 1537-1719. ; 40:9
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Tidskriftsartikel (refereegranskat)abstract
- The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north–south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.
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| 14. |
- Sánchez‐Barreiro, Fátima, et al.
(författare)
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Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros ( Ceratotherium simum )
- 2021
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 30:23, s. 6355-6369
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Tidskriftsartikel (refereegranskat)abstract
- Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.
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| 15. |
- Sandoval, Eluzai Dinai Pinto, et al.
(författare)
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Assessing the taxonomic status of the Gray Brocket Mazama simplicicornis argentina Lönnberg, 1919 (Artiodactyla: Cervidae)
- 2023
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Ingår i: Zoological Studies. - 1021-5506 .- 1810-522X. ; 62
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Tidskriftsartikel (refereegranskat)abstract
- Mazama simplicicornis argentina is the name that was given to describe a gray brocket collected by Lönberg in 1919 in the central Chaco region of Argentina. Subsequent authors, based on morphological similarities, considered this name to be a synonym for the species Subulo gouazoubira Fischer, 1814 from Paraguay. In the absence of genetic analyses to compare the Argentinian and Paraguayan gray brockets, we aimed to clarify the taxonomy of M. simplicicornis argentina through an integrative assessment using morphological, cytogenetical, and molecular data from its holotype and a current topotype. Qualitative skull features and cranio-morphometric results of M. simplicicornis argentina showed a great similarity with the S. gouazoubira neotype characters. The diploid chromosome number of M. simplicicornis argentinatopotype corresponded with the karyotypical pattern of S. gouazoubira with 2n = 70 and FN = 70, showing a great similarity in all classic and molecular cytogenetic results and revealing the homologies between karyotypes. The phylogenetic analysis of mitochondrial genes used in this study (concatenated partial ND5 and Cytb gene) allocated the M. simplicicornis argentina specimens in the monophyletic clade of S. gouazoubira with a branch value of 100%. These results show that there is no discontinuity between the Argentinian and Paraguayan gray brockets. Therefore, the individuals originally described as M. simplicicornis argentina should be recognized as S. gouazoubira.
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| 16. |
- van der Valk, Tom, et al.
(författare)
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Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas
- 2018
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Species and populations are disappearing at an alarming rate as a direct result of human activities. Loss of genetic diversity associated with population decline directly impacts species’ long-term survival. Therefore, preserving genetic diversity is of considerable conservation importance. However, to assist in conservation efforts, it is important to understand how genetic diversity is spatially distributed and how it changes due to anthropogenic pressures. In this study, we use historical museum and modern faecal samples of two critically endangered eastern gorilla taxa, Grauer’s (Gorilla beringei graueri) and mountain gorillas (Gorilla beringei beringei), to directly infer temporal changes in genetic diversity within the last century. Using over 100 complete mitochondrial genomes, we observe a significant decline in haplotype and nucleotide diversity in Grauer’s gorillas. By including historical samples from now extinct populations we show that this decline can be attributed to the loss of peripheral populations rather than a decrease in genetic diversity within the core range of the species. By directly quantifying genetic changes in the recent past, our study shows that human activities have severely impacted eastern gorilla genetic diversity within only four to five generations. This rapid loss calls for dedicated conservation actions, which should include preservation of the remaining peripheral populations.
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