| 1. |
- Bergh, Jan-Erik, et al.
(författare)
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Insect DNA Exposed to Two Insecticides
- 2007
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Ingår i: International Conference Directions in Preventive Conservation Sibiu. - Sibiu, Rumänien.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Analyses of DNA is now a standard method in exploring taxonomical relationships between taxa or when studying intraspecific genetic variation. For these purposes museum specimen are often used. During their “museum history”, biological collections often have been treated with various insecticides to avoid museum pest attacks. There is a risk that some insecticides have more or less destroyed the specimen DNA, and thus it is important to know to what extent this happens to be able to estimate if old collection are useful for DNA screening and also to avoid future mistakes. Kigawa et al. (2003) showed that methyl bromide, methyl bromide/ethylene oxide (mixed), ethylene oxide, propylene oxide and methyl iodide all caused degradation of DNA in samples of mushroom and chicken muscle. We have tested possible negative effects on insect DNA from exposure of paradichlorobenzene and diclorvos. Species used were Schistocerca gregaria (Orthoptera), Musca domestica (Diptera), Dermestes hemeroidalis (Coleoptera), Periplaneta americana (Blattodea). The specimens were cut into two parts before completely dried in silica gel in closed containers for about 2 weeks. Three serials were set up in sealed, small glass containers for each species: (1) paradichlorobenzene (0.5g ±0.02g, representing saturated concentration); (2) diclorvos (0.5g ±0.02g, representing saturated concentration); and (3) no chemicals (blank). Each serial was sampled after 1 and 4 weeks. Immediately after sampling, the insect tissues were exposed to clean air for 8 hours in order to eliminate chemicals from the tissue before subsequent treatment. Together with the blank samples, the exposed tissues were stored in deep freezers before extracted for DNA after the last tissue sampling. After extraction, a 658 bp (base pair) COI gene fragment of the DNA was amplified using the forward and reverse primers HCO2198 (TAA ACT TCA GGG TGA CCA AAA AAT CA) and HCOout (CCA GGT AAA ATT AAA ATA TAA ACT TC), respectively. Electrophoresis of the PCR products was run for about 2h and presence or absence of the amplified COI gene fragment showed as band or absence of band in UV light. The gel was photographed for documentation of the results. For S. gregaria we did not obtain any clear results, probably because the primer did not work for the COI gene of this species. For the other three species no effect could be seen from the exposure of paradichlorobenzene, while dichlorvos destroyed the COI gene fragment after 28 days. For M. domestica a band was present after one week exposure. Our conclusion is that dichlorvos has a deteriorating effect on DNA. A more extensive experimental series on M. domestica has been started at the Swedish Museum of Natural History. Reference: Kigawa, R., Nochide, H., Kimura, H. and Miura, S., Effects of various fumigants, thermal methods and carbon dioxide treatment on DNA extraction and amplification: A case study on freeze-dried mushroom and free-dried muscle specimens. Collection Forum 2003, 18 (1-2): 74-89.
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| 2. |
- Alström, Per, Professor, et al.
(författare)
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Integrative taxonomy reveals unrecognised species diversity in African Corypha larks (Aves: Alaudidae)
- 2024
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Ingår i: Zoological Journal of the Linnean Society. - : Oxford University Press. - 0024-4082 .- 1096-3642. ; 200:4, s. 1080-1108
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Tidskriftsartikel (refereegranskat)abstract
- The species complex comprising the rufous-naped lark Corypha africana, Sharpe's lark Corypha sharpii, the red-winged lark Corypha hypermetra, the Somali long-billed lark Corypha somalica and Ash's lark Corypha ashi encompasses 31 recognised taxa across sub-Saharan Africa, many of which are extremely poorly known and some not observed for decades. Only 17 taxa have been studied molecularly and none comprehensively for morphology, vocalisations or other behaviours. Here, we undertake comprehensive integrative taxonomic analyses based on plumage and morphometrics (for 97% of the taxa), mitochondrial and nuclear loci (77%), <= 1.3 million genome-wide single nucleotide polymorphisms (68%), song (many described for the first time; 52%) and additional behavioural data (45%). All polytypic species as presently circumscribed are paraphyletic, with eight primary clades separated by <= 6.3-6.8 Myr, broadly supported by plumage, morphometrics, song and other behaviours. The most recent divergences concern sympatric taxon pairs usually treated as separate species, whereas the divergence of all clades including C. africana subspecies is as old as sister species pairs in other lark genera. We propose the recognition of nine instead of five species, while C. ashi is synonymised with C. somalica rochei as C. s. ashi. The geographical distributions are incompletely known, and although the nine species are generally para-/allopatric, some might be sympatric.
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| 3. |
- Ghorbani, F., et al.
(författare)
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Densely sampled phylogenetic analyses of the Lesser Short-toed Lark (Alaudala rufescens) - Sand Lark (A. raytal) species complex (Aves, Passeriformes) reveal cryptic diversity
- 2020
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409.
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Tidskriftsartikel (refereegranskat)abstract
- The taxonomy of the Lesser/Asian Short-toed Lark Alaudala rufescens-cheleensis complex has been debated for decades, mainly because of minor morphological differentiation among the taxa within the complex, and different interpretations of the geographical pattern of morphological characters among different authors. In addition, there have been few studies based on non-morphological traits. It has recently been suggested based on a molecular study of the lark family Alaudidae that the Sand Lark A. raytal is nested within this complex. We here analysed mitochondrial cytochrome b (cyt b) from 130 individuals across the range of this complex (hereafter called Alaudala rufescens-raytal complex), representing all except two of the 18 currently recognized subspecies. We also analysed 11 nuclear markers from a subsample of these individuals, representing all of the clades found in the cyt b tree. Five primary clades were recovered, which confirmed that A. raytal is nested within this complex. Divergence time estimates among these five clades ranged from 1.76 to 3.16 million years (my; 95% highest posterior density [HPD] 1.0-4.51 my) or 1.99-2.53 my (95% HPD 0.96-4.3 my) in different analyses. Only four of the currently recognized subspecies were recovered as monophyletic in the cyt b tree. Our results call for a taxonomic revision, and we tentatively suggest that at least four species should be recognized, although we stress the need for an approach integrating molecular, morphological and other data that are not yet available.
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| 4. |
- Alström, Per, et al.
(författare)
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Comprehensive molecular phylogeny of the grassbirds and allies (Locustellidae) reveals extensive non-monophyly of traditional genera, and a proposal for a new classification
- 2018
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 127, s. 367-375
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Tidskriftsartikel (refereegranskat)abstract
- The widespread Old World avian family Locustellidae ('grassbirds and allies') comprises 62 extant species in 11 genera. In the present study, we used one mitochondrial and, for most species, four nuclear loci to infer the phylogeny of this family. We analysed 59 species, including the five previously unsampled genera plus two genera that had not before been analysed in a densely sampled dataset. This study revealed extensive disagreement with current taxonomy; the genera Bradypterus, Locustella, Megalurus, Megalurulus and Schoenicola were all found to be non-monophyletic. Non-monophyly was particularly pronounced for Megalurus, which was widely scattered across the tree. Three of the five monotypic genera (Amphilais, Buettikoferella and Malia) were nested within other genera; one monotypic genus (Chaetornis) formed a Glade with one of the two species of Schoenicola; whereas the position of the fifth monotypic genus (Elaphrornis) was unresolved. Robsonius was confirmed as sister to the other genera. We propose a phylogenetically informed revision of genus-level taxonomy, including one new generic name. Finally, we highlight several non-monophyletic species complexes and deep intra-species divergences that point to conflict in taxonomy and suggest an underestimation of current species diversity in this group.
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| 5. |
- Bakker, F. T., et al.
(författare)
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The Global Museum: natural history collections and the future of evolutionary science and public education
- 2020
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Ingår i: PeerJ. - : PeerJ. - 2167-8359. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the 'Global Museum') is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow's technologies and hence further increasing the relevance of natural history museums.
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| 6. |
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| 7. |
- Alström, Per, et al.
(författare)
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Multiple species within the Striated Prinia Prinia crinigera-Brown Prinia P. polychroa complex revealed through an integrative taxonomic approach
- 2020
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Ingår i: Ibis. - : Wiley. - 0019-1019 .- 1474-919X. ; 162:3, s. 936-967
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Tidskriftsartikel (refereegranskat)abstract
- We re-evaluated the taxonomy of the Striated Prinia Prinia crinigera-Brown Prinia P. polychroa complex using molecular, morphological and vocal analyses. The extensive seasonal, sexual, age-related, geographical and taxon-specific variation in this complex has never before been adequately studied. As no previous genetic or vocal analyses have focused on this group, misinterpretation of taxonomic signals from limited conventional morphological study alone was likely. Using mitochondrial and nuclear DNA, we found that P. crinigera sensu lato (s.l.) comprises two non-sister groups of taxa (Himalayan crinigera and Chinese striata groups) that differ substantially morphologically and vocally and that are broadly sympatric in Yunnan Province, China. Prinia polychroa cooki (Myanmar) and P. p. rocki (southern Vietnam) are each morphologically, vocally and genetically distinct. Thai, Cambodian and Laotian populations formerly ascribed to P. p. cooki are morphologically and vocally most similar to and most closely related to Javan P. p. polychroa, and require a new name, proposed here. Prinia p. bangsi of Yunnan is part of the crinigera group rather than of P. polychroa, and hence there is no evidence for sympatry between P. polychroa s.l. and P. crinigera s.l., nor of the occurrence of P. polychroa in mainland China or Taiwan. We recommend the recognition of five species in the complex, with the following suggestions for new English names: Himalayan Prinia P. crinigera sensu stricto (s.s.; with subspecies striatula, crinigera, yunnanensis and bangsi); Chinese Prinia P. striata (subspecies catharia, parumstriata and striata); Burmese Prinia P. cooki (monotypic); Annam Prinia P. rocki (monotypic) and Deignan's Prinia P. polychroa s.s. (subspecies Javan polychroa and the new Southeast Asian taxon). This study underlines the importance of using multiple datasets for the elucidation of diversity of cryptic bird species and their evolutionary history and biogeography.
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| 8. |
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| 9. |
- Chattopadhyay, Balaji, et al.
(författare)
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Novel genome reveals susceptibility of popular gamebird, the red-legged partridge (Alectoris rufa, Phasianidae), to climate change
- 2021
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Ingår i: Genomics. - : Elsevier BV. - 0888-7543 .- 1089-8646.
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Tidskriftsartikel (refereegranskat)abstract
- We produced a high-quality de novo genome assembly of the red-legged partridge A. rufa, the first reference genome of its genus, by utilising novel 10× Chromium technology. The estimated genome size was 1.19 Gb with an overall genome heterozygosity of 0.0022; no runs of homozygosity were observed. In total, 21,589 protein coding genes were identified and assigned to 16,772 orthologs. Of these, 201 emerged as unique to Alectoris and were enriched for positive regulation of epithelial cell migration, viral genome integration and maturation. Using PSMC analysis, we inferred a major demographic decline commencing ~140,000 years ago, consistent with forest expansion and reduction of open habitats during the Eemian interglacial. Present-day populations exhibit the historically lowest genetic diversity. Besides implications for management and conservation, this genome also promises key insights into the physiology of these birds with a view to improving poultry husbandry practices.
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| 10. |
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