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1.
BMC Bioinformatics ; 24(1): 6, 2023 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-36604610

RESUMO

BACKGROUND: The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited functionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Amplicon Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas. RESULTS: The ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure. CONCLUSION: The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.


Assuntos
Biodiversidade , DNA , DNA/genética , Software , Código de Barras de DNA Taxonômico
2.
Mol Ecol ; 27(2): 449-458, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-29230900

RESUMO

Red carotenoid colours in birds are widely assumed to be sexually selected quality indicators, but this rests on a very incomplete understanding of genetic mechanisms and honesty-mediating costs. Recent progress was made by the implication of the gene CYP2J19 as an avian carotenoid ketolase, catalysing the synthesis of red C4-ketocarotenoids from yellow dietary precursors, and potentially a major mechanism behind red coloration in birds. Here, we investigate the role of CYP2J19 in the spectacular colour diversification of African weaverbirds (Ploceidae), represented by five genera and 16 species: eight red, seven yellow and one without carotenoid coloration. All species had a single copy of CYP2J19, unlike the duplication found in the zebra finch, with high expression in the retina, confirming its function in colouring red oil droplets. Expression was weak or undetected in skin and follicles of pigment-depositing feather buds, as well as in beaks and tarsi, including those of the red-billed quelea. In contrast, the hepatic (liver) expression of CYP2J19 was consistently higher (>14-fold) in seven species with C4-ketocarotenoid coloration than in species without (including one red species), an association strongly supported by a phylogenetic comparative analysis. The results suggest a critical role of the candidate ketolase, CYP2J19, in the evolution of red C4-ketocarotenoid colour variation in ploceids. As ancestral state reconstruction suggests that ketocarotenoid coloration has evolved twice in this group (once in Euplectes and once in the Quelea/Foudia clade), we argue that while CYP2J19 has retained its ancestral role in the retina, it has likely been co-opted for red coloration independently in the two lineages, via increased hepatic expression.


Assuntos
Carotenoides/genética , Passeriformes/genética , Pigmentação/genética , Aves Canoras/fisiologia , Animais , Carotenoides/fisiologia , Cor , Plumas/fisiologia , Passeriformes/fisiologia , Pigmentação/fisiologia , Retina/metabolismo , Retina/fisiologia , Aves Canoras/genética
4.
R Soc Open Sci ; 9(8): 220434, 2022 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-35937912

RESUMO

Intense red colours in birds are often owing to ketocarotenoids (KCs). In many land birds, KCs are oxidized from dietary yellow precursors, presumably by the avian carotenoid ketolase CYP2J19, the regulation and constraints of which have important implications for condition-dependence and honest signalling of carotenoid colour displays. We investigated hepatic CYP2J19 gene expression in the seasonally and sexually dichromatic southern red bishop (Euplectes orix) in relation to season, sex, progression of the prenuptial moult, testis size, body condition, redness and circulating sex steroids. A coloration function of CYP2J19 is supported by a seasonal upregulation prior to and during the carotenoid-depositing stage of the male prenuptial moult. However, CYP2J19 expression was similarly high in females (which do not moult prenuptially), and remained high in males after moult, suggesting additional or alternative roles of hepatic CYP2J19 or its products, such as detoxification or antioxidant functions. In males, the CYP2J19 upregulation preceded and was unrelated to the rise in plasma testosterone, but was correlated with androstenedione, probably of adrenal origin and compatible with luteinizing hormone-induced and (in females) oestrogen-suppressed moult. Finally, contrary to ideas that carotenoid ketolation rate mediates honest signalling of male quality, CYP2J19 expression was not related to plumage redness or male body condition.

5.
Evolution ; 64(12): 3609-19, 2010 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-20629731

RESUMO

Avian carotenoid-based signals are classic examples of sexually selected, condition-dependent threat displays or mate choice cues. In many species, male dominance or mating success is associated with redder (i.e., longer wavelength) color hues, suggesting that red colors are either more efficient or more reliable signals than yellow colors. Few studies, however, have investigated selection for redness in a macroevolutionary context. Here, we phylogenetically reconstruct the evolution of carotenoid coloration in the African widowbirds and bishops (Euplectes spp.), for which agonistic selection for redder hues, as well as pigmentary mechanisms, is well documented. Using reflectance spectrometry for objective color quantification, and accounting for phylogenetic uncertainty, we find that yellow plumage color is a retained ancestral state in Euplectes, and that red color hues have convergently evolved two or three times. Results are discussed in relation to a known diversity in pigment mechanisms, supporting independent origins of red color, and suggesting that agonistic selection and physiological constraints have interacted to generate color diversity in Euplectes.


Assuntos
Evolução Biológica , Carotenoides/fisiologia , Pigmentação , Aves Canoras/fisiologia , Animais , Carotenoides/genética , Plumas/fisiologia , Feminino , Masculino , Filogenia , Aves Canoras/classificação , Aves Canoras/genética
6.
Comp Biochem Physiol B Biochem Mol Biol ; 154(4): 373-80, 2009 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-19686862

RESUMO

Male breeding plumages of African widowbirds and bishops (Euplectes spp.) show striking variation in carotenoid-based plumage coloration, with saturated yellow or orange-red patches of different size. Yet, from observations and experiments, agonistic signaling appears to have been a generalized sexual selection pressure for redness in the genus. Recent results show that yellow and red widowbird colors derive from distinctly different pigment profiles, and suggest that species vary in their ability to metabolize ingested carotenoids. We used reflectance spectrometry and High Performance Liquid Chromatography (HPLC) to describe the species-specific colors and plumage carotenoids of the congeneric yellow-crowned bishop (E. afer) and southern red bishop (E. orix). Results show that the yellow rump color of E. afer primarily derives from direct-deposited, dietary yellow pigments, i.e. lutein and zeaxanthin. In the red breast of E. orix, these are complemented by smaller amounts of derived red C4-keto-carotenoids: mainly alpha-doradexanthin, but also beta-doradexanthin, canthaxanthin, astaxanthin and adonirubin. We also performed a diet supplementation experiment to investigate the relative importance of nutritional and metabolic constraints in determining the differential occurrence of C4-keto-carotenoids, and thus red plumage color, in the two species. Our results indicate that E. orix, but not E. afer, can manufacture red C4-keto-carotenoids (alpha-doradexanthin and canthaxanthin) from yellow dietary precursors (lutein and beta-carotene).


Assuntos
Carotenoides/metabolismo , Passeriformes/metabolismo , Pigmentação/fisiologia , Ração Animal , Animais , Cantaxantina/biossíntese , Carotenoides/análise , Cromatografia Líquida de Alta Pressão , Plumas/metabolismo , Feminino , Masculino , Oxirredução , Passeriformes/anatomia & histologia , Especificidade da Espécie , beta Caroteno/metabolismo
7.
Mol Phylogenet Evol ; 46(1): 290-302, 2008 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-17964815

RESUMO

The elaborate male displays and plumage ornaments in the African widowbirds and bishops (Euplectes spp.) have inspired classic studies on mating systems and sexual selection. In order to study the extreme divergence in ornament design and expression in this group, we present and discuss a well-supported molecular phylogeny of the genus and its placement within the Ploceinae subfamily. Parsimony and Bayesian analyses were performed on 2557bp of mitochondrial DNA (ATP6, Cyt b, ND2 and ND3) and a nuclear intron (G3PDH). All 17 Euplectes species, and 31 of 51 suggested subspecies, were included, as well as eight Ploceinae outgroups from four genera (Amblyospiza, Ploceus, Quelea and Foudia). Our results show monophyly of Euplectes, but not of the intrageneric groupings of bishops and widowbirds. Most notably, the Red-collared Widowbird E. ardens belongs to a subclade of bishops, and not to the sister subclade of 'true' widowbirds. Furthermore, the two bishops E. afer and E. aureus represent lineages that branched off before this basal split, which also refutes the proposed superspecies of E. afer and E. diadematus. Also somewhat surprisingly, and despite the striking plumage similarities among the red bishops, E. franciscanus is not closely related to either E. nigroventris or E. orix (of which it until recently was considered a subspecies). Finally, the Mountain Marsh Widowbird E. psammocromius is likely closest to the Long-tailed Widowbird E. progne, and not, as previously thought, to the Marsh Widowbird E. hartlaubi.


Assuntos
Pardais/classificação , África , Animais , DNA Mitocondrial/química , DNA Mitocondrial/genética , Genes Mitocondriais/genética , Íntrons/genética , Filogenia , Análise de Sequência de DNA , Pardais/genética
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