Introduction: integrative molecular ecology is rapidly advancing the study of adaptation and speciation

Rogers, Sean M.; Xu, Shuqing; Schlüter, Philipp M.

doi:10.1111/mec.13947

Cited by 12 publications

(11 citation statements)

References 39 publications

(67 reference statements)

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“…The cloacal microbiotas of woodlark and skylark resembled those of other (passerine) bird species with respect to Shannon diversity [ 76 ] and the dominant bacterial groups [ 76 – 80 ]. Unfortunately, we cannot compare our OTU richness estimates with other studies, because OTU binning and sequencing/rarefaction depth strongly determine OTU richness estimation.…”

Section: Discussionmentioning

confidence: 99%

Multi-level comparisons of cloacal, skin, feather and nest-associated microbiota suggest considerable influence of horizontal acquisition on the microbiota assembly of sympatric woodlarks and skylarks

2017

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BackgroundWorking toward a general framework to understand the role of microbiota in animal biology requires the characterisation of animal-associated microbial communities and identification of the evolutionary and ecological factors shaping their variation. In this study, we described the microbiota in the cloaca, brood patch skin and feathers of two species of birds and the microbial communities in their nest environment. We compared patterns of resemblance between these microbial communities at different levels of biological organisation (species, individual, body part) and investigated the phylogenetic structure to deduce potential microbial community assembly processes.ResultsUsing 16S rRNA gene amplicon data of woodlarks (Lullula arborea) and skylarks (Alauda arvensis), we demonstrated that bird- and nest-associated microbiota showed substantial OTU co-occurrences and shared dominant taxonomic groups, despite variation in OTU richness, diversity and composition. Comparing host species, we uncovered that sympatric woodlarks and skylarks harboured similar microbiota, dominated by Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria. Yet, compared with the nest microbiota that showed little variation, each species’ bird-associated microbiota displayed substantial variation. The latter could be partly (~ 20%) explained by significant inter-individual differences. The various communities of the bird’s body (cloaca, brood patch skin and feathers) appeared connected with each other and with the nest microbiota (nest lining material and surface soil). Communities were more similar when the contact between niches was frequent or intense. Finally, bird microbiota showed significant phylogenetic clustering at the tips, but not at deeper branches of the phylogeny.ConclusionsOur interspecific comparison suggested that the environment is more important than phylogeny in shaping the bird-associated microbiotas. In addition, variation among individuals and among body parts suggested that intrinsic or behavioural differences among females and spatial heterogeneity among territories contributed to the microbiome variation of larks. Modest but significant phylogenetic clustering of cloacal, skin and feather microbiotas suggested weak habitat filtering in these niches. We propose that lark microbiota may be primarily, but not exclusively, shaped by horizontal acquisition from the regional bacterial pool at the breeding site. More generally, we hypothesise that the extent of ecological niche-sharing by avian (or other vertebrate) hosts may predict the convergence of their microbiota.Electronic supplementary materialThe online version of this article (10.1186/s40168-017-0371-6) contains supplementary material, which is publicly available.

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Section: Discussionmentioning

confidence: 99%

Multi-level comparisons of cloacal, skin, feather and nest-associated microbiota suggest considerable influence of horizontal acquisition on the microbiota assembly of sympatric woodlarks and skylarks

2017

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“…The year started with a Special Issue on the “Molecular mechanisms of adaptation and speciation: integrating genomic and molecular approaches.” The issue, edited by Sean Rogers, Shuqing Xu and Philipp Schlüter, aimed at promoting an integrative approach to the study of adaptation and speciation and to provide a forward‐looking framework for studies in these areas (Rogers, Xu, & Schluter, ). Several manuscripts focused on patterns of genomic divergence in scenarios of divergence with gene flow (e.g., Christe et al., ; Dennenmoser, Vamosi, Nolte, & Rogers, ; Eyres et al., ; Marques et al., ; Meier et al., ; Rougemont et al., ), others aimed at investigating the genomic basis of adaptive traits (e.g., Gould & Stinchcombe, ; Raffini, Fruciano, Franchini, & Meyer, ), and some focused on structural variants (Dion‐Cote et al., ; Gould, Chen, & Lowry, ) or whole‐genome duplications (Shimizu‐Inatsugi et al., ) and their role in adaptation and speciation.…”

Section: Special Issuesmentioning

confidence: 99%

“…Finally, a smaller set of papers made encouraging attempts at integrating the genomic and the molecular perspectives (e.g., Des Roches, Sollmann, Calhoun, Rothstein, & Rosenblum, ; Kusakabe et al., ; Navon, Olearczyk, & Albertson, ) or reviewed and provided theoretical advances on the issue (Byers, Xu, & Schluter, ; Gompert, Egan, Barrett, Feder, & Nosil, ; Korunes & Noor, ; Schneider & Meyer, ). As the editors emphasize at the end of their introduction to the issue, “we still have a lot to learn about adaptation and speciation” (Rogers et al., ).…”

Section: Special Issuesmentioning

confidence: 99%

Editorial 2018

Rieseberg¹,

Geraldes²,

Chambers³

et al. 2018

Molecular Ecology

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Molecular Ecology continues to perform well. It was the second largest evolutionary biology journal (392 articles) in 2016 according to ISI Web of Knowledge, and had the sixth highest citation impact factor (6.1). In terms of overall impact, Molecular Ecology ranks second among ecology or evolution journals according to Google Scholar's h5-index, which rates journals by cumulative hindex over the past five years. Our push to streamline the review process over the past year has begun to pay off, and the time to decision on original manuscript submissions averaged 30 days in 2017.We continue in our efforts to enhance the experience of our authors. Wiley has introduced a new page design for Molecular Ecology, which has been optimized for the online environment. Our website has been updated and reformatted to increase usability, and our Author Guidelines have been updated in a format intended to be less "text dense" for our authors. In addition, the scope statement for the journal now appears in both English and Chinese, as we strive to be more welcoming to our Chinese authors.In October 2017, we were most pleased to welcome a dedicated Editorial Assistant, David Crespo, to the Molecular Ecology staff. Many of you may have heard from him already as he manages the molecol email box and patrols our Scholar One Manuscript Central site. Thus, we expect that the editorial office will be able to respond more quickly to author questions and concerns in 2018. | AN NOUNCEMEN TS | Molecular ecology prizeThe 2017 Molecular Ecology Prize has been awarded to Professor Nancy Moran for her pioneering studies of symbiosis and bacterial genome evolution. The Prize is awarded annually to "an outstanding scientist who has made significant contributions to molecular ecology," as selected by an independent award committee. A biography of Nancy and her contributions to the field of molecular ecology can be found on pages XX-XX of this issue. | The Harry Smith prizeAt the Molecular Ecology editorial meeting this summer, we decided to offer a new prize to that would recognize the best paper published in Molecular Ecology by graduate students or early career scholars with no more than five years of postdoctoral or fellowship experience. As with the Molecular Ecology Prize, the winner of this annual prize will be selected by an independent award committee. A call for nominations will be made in spring, 2018.The prize is named after Professor Harry Smith FRS, who founded the journal and served as both its Chief and Managing Editor during the journal's critical early years. He continued as the journal's Managing Editor until 2008, and he went out of his way to encourage early career scholars. In addition to his editorial work, Harry was one of the world's foremost researchers in photomorphogenesis, where he determined how plants respond to shading, leading to concepts such as "neighbour detection" and "shade avoidance," which are fundamental to understanding plant responses to crowding and competition. More broadly, his research provided an ear...

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“…Bacterial communities are reported to contribute to their host beetles’ reproductive success, community interactions and niche diversification ( Cardoza et al 2006 , Scott et al 2008 , Douglas 2009 , Morales-Jiménez et al 2013 ). Bacteria can contribute to the nutrition of phloeophagous and xylophagous larvae, which rely on a nutrient-poor food source, by exploiting nitrogen and carbon compounds in woody substrates and providing nutritional supplements that are absent from the substrate, such as amino acids and essential vitamins ( Dillon and Dillon 2004 , Geib et al 2008 , Morales-Jiménez et al 2009 , Berasategui et al 2017 ).…”

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confidence: 99%

Bacterial Communities Associated With the Pine Wilt Disease Vector Monochamus alternatus (Coleoptera: Cerambycidae) During Different Larval Instars

Raffa

et al. 2017

Journal of Insect Science

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We investigated the influence of larval instar on the structure of the gut bacterial community in the Japanese pine sawyer, Monochamus alternatus (Hope; Coleoptera: Cerambycidae). The diversity of the gut bacterial community in early, phloem-feeding larvae is significantly higher than in later, wood-feeding larvae. Many of these associates were assigned into a few taxonomic groups, of which Enterobacteriaceae was the most abundant order. The predominant bacterial genus varied during the five instars of larval development. Erwinia was the most abundant genus in the first and fifth instars, Enterobacter was predominant in the third and fourth instars, and the predominant genus in the second instars was in the Enterobacteriaceae (genus unclassified). Actinobacteria were reported in association with M. alternatus for the first time in this study. Cellulomonadaceae (Actinobacteria) was the second most abundant family in the first instar larvae (10.6%). These data contribute to our understanding of the relationships among gut bacteria and M. alternatus, and could aid the development of new pest control strategies.

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Introduction: integrative molecular ecology is rapidly advancing the study of adaptation and speciation

Cited by 12 publications

References 39 publications

Multi-level comparisons of cloacal, skin, feather and nest-associated microbiota suggest considerable influence of horizontal acquisition on the microbiota assembly of sympatric woodlarks and skylarks

Multi-level comparisons of cloacal, skin, feather and nest-associated microbiota suggest considerable influence of horizontal acquisition on the microbiota assembly of sympatric woodlarks and skylarks

Editorial 2018

Bacterial Communities Associated With the Pine Wilt Disease Vector Monochamus alternatus (Coleoptera: Cerambycidae) During Different Larval Instars

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