| 1. |
- Dalen, Love, et al.
(författare)
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Identifying Bird Remains Using Ancient DNA Barcoding
- 2017
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Ingår i: Genes. - : MDPI AG. - 2073-4425 .- 2073-4425. ; 8:6
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Tidskriftsartikel (refereegranskat)abstract
- Bird remains that are difficult to identify taxonomically using morphological methods, are common in the palaeontological record. Other types of challenging avian material include artefacts and food items from endangered taxa, as well as remains from aircraft strikes. We here present a DNA-based method that enables taxonomic identification of bird remains, even from material where the DNA is heavily degraded. The method is based on the amplification and sequencing of two short variable parts of the 16S region in the mitochondrial genome. To demonstrate the applicability of this approach, we evaluated the method on a set of Holocene and Late Pleistocene postcranial bird bones from several palaeontological and archaeological sites in Europe with good success.
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| 2. |
- 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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| 3. |
- Gilbert, M. Thomas P., et al.
(författare)
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Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes
- 2008
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 105:24, s. 8327-8332
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Tidskriftsartikel (refereegranskat)abstract
- We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, approximate to 1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the C-14 ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.
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| 4. |
- Gilbert, M. Thomas P., et al.
(författare)
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Whole-genome shotgun sequencing of mitochondria from ancient hair shafts
- 2007
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 317:5846, s. 1927-1930
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Tidskriftsartikel (refereegranskat)abstract
- Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.
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| 5. |
- Irestedt, Martin, et al.
(författare)
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Convergent evolution, habitat shifts and variable diversification rates in the ovenbird-woodcreeper family (Furnariidae).
- 2009
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 9, s. 268-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The Neotropical ovenbird-woodcreeper family (Furnariidae) is an avian group characterized by exceptionally diverse ecomorphological adaptations. For instance, members of the family are known to construct nests of a remarkable variety. This offers a unique opportunity to examine whether changes in nest design, accompanied by expansions into new habitats, facilitates diversification. We present a multi-gene phylogeny and age estimates for the ovenbird-woodcreeper family and use these results to estimate the degree of convergent evolution in both phenotype and habitat utilisation. Furthermore, we discuss whether variation in species richness among ovenbird clades could be explained by differences in clade-specific diversification rates, and whether these rates differ among lineages with different nesting habits. In addition, the systematic positions of some enigmatic ovenbird taxa and the postulated monophyly of some species-rich genera are evaluated.RESULTS: The phylogenetic results reveal new examples of convergent evolution and show that ovenbirds have independently colonized open habitats at least six times. The calculated age estimates suggest that the ovenbird-woodcreeper family started to diverge at ca 33 Mya, and that the timing of habitat shifts into open environments may be correlated with the aridification of South America during the last 15 My. The results also show that observed large differences in species richness among clades can be explained by a substantial variation in net diversification rates. The synallaxines, which generally are adapted to dry habitats and build exposed vegetative nests, had the highest diversification rate of all major furnariid clades.CONCLUSION: Several key features may have played an important role for the radiation and evolution of convergent phenotypes in the ovenbird-woodcreeper family. Our results suggest that changes in nest building strategy and adaptation to novel habitats may have played an important role in a diversification that included multiple radiations into more open and bushy environments. The synallaxines were found to have had a particularly high diversification rate, which may be explained by their ability to build exposed vegetative nests and thus to expand into a variety of novel habitats that emerged during a period of cooling and aridification in South America.
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| 6. |
- Miller, Webb, et al.
(författare)
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The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).
- 2009
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 19:2, s. 213-20
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Tidskriftsartikel (refereegranskat)abstract
- We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the thylacine's basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11%-15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first high-fidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting at a very low genetic diversity shortly before extinction. Despite the samples' heavy contamination with bacterial and human DNA and their temperate storage history, we estimate that as much as one-third of the total DNA in each sample is from the thylacine. The microbial content of the two thylacine samples was subjected to metagenomic analysis, and showed striking differences between a wild-captured individual and a born-in-captivity one. This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes.
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| 7. |
- Prost, Stefan, et al.
(författare)
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Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise
- 2019
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Ingår i: GigaScience. - : OXFORD UNIV PRESS. - 2047-217X. ; 8:5
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Tidskriftsartikel (refereegranskat)abstract
- The diverse array of phenotypes and courtship displays exhibited by birds-of-paradise have long fascinated scientists and nonscientists alike. Remarkably, almost nothing is known about the genomics of this iconic radiation. There are 41 species in 16 genera currently recognized within the birds-of-paradise family (Paradisaeidae), most of which are endemic to the island of New Guinea. In this study, we sequenced genomes of representatives from all five major clades within this family to characterize genomic changes that may have played a role in the evolution of the group's extensive phenotypic diversity. We found genes important for coloration, morphology, and feather and eye development to be under positive selection. In birds-of-paradise with complex lekking systems and strong sexual dimorphism, the core birds-of-paradise, we found Gene Ontology categories for "startle response" and "olfactory receptor activity" to be enriched among the gene families expanding significantly faster compared to the other birds in our study. Furthermore, we found novel families of retrovirus-like retrotransposons active in all three de novo genomes since the early diversification of the birds-of-paradise group, which might have played a role in the evolution of this fascinating group of birds.
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