The aim of this study was to correlate plumage variation with the amount of genomic hybrid content in hybrids between Azure Tits Cyanistes cyanus(Pallas,1770)and European Blue Tit Cyanistes caeruleus(Linnaeus,1758),by...The aim of this study was to correlate plumage variation with the amount of genomic hybrid content in hybrids between Azure Tits Cyanistes cyanus(Pallas,1770)and European Blue Tit Cyanistes caeruleus(Linnaeus,1758),by re-sequencing the genomes of museum specimens of non-hybrids and presumed hybrids with varying plumages.The project was funded by crowdsourcing and initiated when two presumed Azure Tits,observed by hundreds of Swedish birdwatchers,were rejected as hybrids based on minor plumage deviations assumed to indicate hybrid contents from the European Blue Tit.The results confirm that hybrids with intermediate plumages,so called Pleske’s Tits,are first generation hybrids(F1 hybrids).Individuals,whose plumages are similar to Azure Tits,but assessed as hybrids based on minor plumage deviations,are all backcrosses but vary in their degree of hybrid content.However,some individuals morphologically recognized as pure Azure Tits expressed similar degrees of hybrid content.The results indicate that:(1)hybrid content may be widespread in Azure Tits in the western part of its habitat distribution;(2)plumage deviation in backcrosses is not linearly correlated with the genetic degree of hybrid origin;and(3)all Azure Tits observed in Europe outside its natural distribution may have some degree of hybrid origin.We therefore suggest that it is very difficult to phenotypically single out hybrids beyond first generation backcrosses.We argue that decreased sequencing costs and improved analytical tools open the doors for museomic crowd-sourced projects that may not address outstanding biological questions but have a major interest for lay citizens such as birdwatchers.展开更多
The family Erinaceidae encompasses 27 extant species in two subfamilies:Erinaceinae,which includes spiny hedgehogs,and Galericinae,which comprises silky-furred gymnures and moonrats.Although they are commonly recogniz...The family Erinaceidae encompasses 27 extant species in two subfamilies:Erinaceinae,which includes spiny hedgehogs,and Galericinae,which comprises silky-furred gymnures and moonrats.Although they are commonly recognized by the general public,their phylogenetic history remains incompletely understood,and several species have never been included in any molecular analyses.Additionally,previous research suggested that the species diversity of Erinaceidae might be underestimated.In this study,we sequenced the mitochondrial genomes of 29 individuals representing 18 erinaceid species using 18 freshly collected tissue and 11 historical museum specimens.We also integrated previously published data for a concatenated analysis.We aimed to elucidate the evolutionary-relationships within Erinaceidae,estimate divergence times,and uncover potential underestimated species diversity.Our data finely resolved intergeneric and interspecific relationships and presented the first molecular evidence-for the phylogenetic position of Mesechinus wangi,Paraechinus micropus,and P.nudiventris.Our results revealed-a sister relationship between Neotetracus and Neohylomys gymnures,as well as a sister relationship between-Hemiechinus and Mesechinus,supporting previous hypotheses.Additionally,our findings provided a novel-phylogenetic position for Paraechinus aethiopicus,placing it in a basal position within the genus.Furthermore,-our study uncovered cryptic species diversity within Hylomys suillus as well as in Neotetracus sinensis,Atelerix-albiventris,P.aethiopicus,and Hemiechinus auratus,most of which have been previously overlooked.展开更多
Family Cortinariaceae currently includes only one genus,Cortinarius,which is the largest Agaricales genus,with thousands of species worldwide.The species are important ectomycorrhizal fungi and form associations with ...Family Cortinariaceae currently includes only one genus,Cortinarius,which is the largest Agaricales genus,with thousands of species worldwide.The species are important ectomycorrhizal fungi and form associations with many vascular plant gen-era from tropicals to arctic regions.Genus Cortinarius contains a lot of morphological variation,and its complexity has led many taxonomists to specialize in particular on infrageneric groups.The previous attempts to divide Cortinarius have been shown to be unnatural and the phylogenetic studies done to date have not been able to resolve the higher-level classification of the group above section level.Genomic approaches have revolutionized our view on fungal relationships and provide a way to tackle difficult groups.We used both targeted capture sequencing and shallow whole genome sequencing to produce data and to perform phylogenomic analyses of 75 single-copy genes from 19 species.In addition,a wider 5-locus analysis of 245 species,from the Northern and Southern Hemispheres,was also done.Based on our results,a classification of the family Cortinariaceae into ten genera-Cortinarius,Phlegmacium,Thaxterogaster,Calonarius,Aureonarius,Cystinarius,Volvanarius,Hygronarius,Mystinarius,and Austrocortinarius-is proposed.Seven genera,10 subgenera,and four sec-tions are described as new to science and five subgenera are introduced as new combinations in a new rank.In addition,41 section names and 514 species names are combined in new genera and four lecto-and epitypes designated.The position of Stephanopus in suborder Agaricineae remains to be studied.Targeted capture sequencing is used for the first time in fungal taxonomy in Basidiomycetes.It provides a cost-efficient way to produce-omics data in species-rich groups.The-omics data was produced from fungarium specimens up to 21 years old,demonstrating the value of museum specimens in the study of the fungal tree of life.This study is the first family revision in Agaricales based on genomics data and hopefully many others will soon follow.展开更多
基金This project was crowd sourced and mainly financed by interested birdwatchers.MI also acknowledge financial support from the Swedish research council(2019-03900)Riksmusei vanner.
文摘The aim of this study was to correlate plumage variation with the amount of genomic hybrid content in hybrids between Azure Tits Cyanistes cyanus(Pallas,1770)and European Blue Tit Cyanistes caeruleus(Linnaeus,1758),by re-sequencing the genomes of museum specimens of non-hybrids and presumed hybrids with varying plumages.The project was funded by crowdsourcing and initiated when two presumed Azure Tits,observed by hundreds of Swedish birdwatchers,were rejected as hybrids based on minor plumage deviations assumed to indicate hybrid contents from the European Blue Tit.The results confirm that hybrids with intermediate plumages,so called Pleske’s Tits,are first generation hybrids(F1 hybrids).Individuals,whose plumages are similar to Azure Tits,but assessed as hybrids based on minor plumage deviations,are all backcrosses but vary in their degree of hybrid content.However,some individuals morphologically recognized as pure Azure Tits expressed similar degrees of hybrid content.The results indicate that:(1)hybrid content may be widespread in Azure Tits in the western part of its habitat distribution;(2)plumage deviation in backcrosses is not linearly correlated with the genetic degree of hybrid origin;and(3)all Azure Tits observed in Europe outside its natural distribution may have some degree of hybrid origin.We therefore suggest that it is very difficult to phenotypically single out hybrids beyond first generation backcrosses.We argue that decreased sequencing costs and improved analytical tools open the doors for museomic crowd-sourced projects that may not address outstanding biological questions but have a major interest for lay citizens such as birdwatchers.
文摘The family Erinaceidae encompasses 27 extant species in two subfamilies:Erinaceinae,which includes spiny hedgehogs,and Galericinae,which comprises silky-furred gymnures and moonrats.Although they are commonly recognized by the general public,their phylogenetic history remains incompletely understood,and several species have never been included in any molecular analyses.Additionally,previous research suggested that the species diversity of Erinaceidae might be underestimated.In this study,we sequenced the mitochondrial genomes of 29 individuals representing 18 erinaceid species using 18 freshly collected tissue and 11 historical museum specimens.We also integrated previously published data for a concatenated analysis.We aimed to elucidate the evolutionary-relationships within Erinaceidae,estimate divergence times,and uncover potential underestimated species diversity.Our data finely resolved intergeneric and interspecific relationships and presented the first molecular evidence-for the phylogenetic position of Mesechinus wangi,Paraechinus micropus,and P.nudiventris.Our results revealed-a sister relationship between Neotetracus and Neohylomys gymnures,as well as a sister relationship between-Hemiechinus and Mesechinus,supporting previous hypotheses.Additionally,our findings provided a novel-phylogenetic position for Paraechinus aethiopicus,placing it in a basal position within the genus.Furthermore,-our study uncovered cryptic species diversity within Hylomys suillus as well as in Neotetracus sinensis,Atelerix-albiventris,P.aethiopicus,and Hemiechinus auratus,most of which have been previously overlooked.
文摘Family Cortinariaceae currently includes only one genus,Cortinarius,which is the largest Agaricales genus,with thousands of species worldwide.The species are important ectomycorrhizal fungi and form associations with many vascular plant gen-era from tropicals to arctic regions.Genus Cortinarius contains a lot of morphological variation,and its complexity has led many taxonomists to specialize in particular on infrageneric groups.The previous attempts to divide Cortinarius have been shown to be unnatural and the phylogenetic studies done to date have not been able to resolve the higher-level classification of the group above section level.Genomic approaches have revolutionized our view on fungal relationships and provide a way to tackle difficult groups.We used both targeted capture sequencing and shallow whole genome sequencing to produce data and to perform phylogenomic analyses of 75 single-copy genes from 19 species.In addition,a wider 5-locus analysis of 245 species,from the Northern and Southern Hemispheres,was also done.Based on our results,a classification of the family Cortinariaceae into ten genera-Cortinarius,Phlegmacium,Thaxterogaster,Calonarius,Aureonarius,Cystinarius,Volvanarius,Hygronarius,Mystinarius,and Austrocortinarius-is proposed.Seven genera,10 subgenera,and four sec-tions are described as new to science and five subgenera are introduced as new combinations in a new rank.In addition,41 section names and 514 species names are combined in new genera and four lecto-and epitypes designated.The position of Stephanopus in suborder Agaricineae remains to be studied.Targeted capture sequencing is used for the first time in fungal taxonomy in Basidiomycetes.It provides a cost-efficient way to produce-omics data in species-rich groups.The-omics data was produced from fungarium specimens up to 21 years old,demonstrating the value of museum specimens in the study of the fungal tree of life.This study is the first family revision in Agaricales based on genomics data and hopefully many others will soon follow.
