Estimating the nucleotide diversity in <i>Ceratodon purpureus</i> (Ditrichaceae) from 218 conserved exon‐primed, intron‐spanning nuclear loci

McDaniel, Stuart F.; Baren, Marijke J. van; Jones, Kelly S.; Payton, Adam C.; Quatrano, Ralph S.

doi:10.3732/apps.1200387

Cited by 18 publications

(15 citation statements)

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“…We sampled only loci that were expressed in a modestly sexually dimorphic tissue (protonema), which had clearly identifiable homologs between C. purpureus and the distantly related P. patens , and which were found in both a male and a female lab strain (McDaniel et al. ). Older sex‐linked genes, in contrast, are likely to be expressed in more mature, sexually dimorphic tissues, and may be present in one sex and absent in the other.…”

Section: Discussionmentioning

confidence: 99%

“…To generate a pool of candidate genes to test for sex linkage in C. purpureus , we screened a set of 208 nuclear loci using primers described in McDaniel et al. (). These primers were developed from 1677 ESTs generated from 7‐day‐old early developmental tissue (protonema) from a single male genotype (WT4) of C. purpureus .…”

Section: Methodsmentioning

confidence: 99%

“…Here we targeted the 140 loci from C. purpureus that McDaniel et al. () reported to differ in sequence between the female lab strain GG1 (from Gross Gerunds, Austria) and the male lab strain R40 (from Petersburg Pass, New York, NY).…”

Section: Methodsmentioning

confidence: 99%

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RECENT GENE-CAPTURE ON THE UV SEX CHROMOSOMES OF THE MOSSCERATODON PURPUREUS

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Sex chromosomes evolve from ordinary autosomes through the expansion and subsequent degeneration of a region of suppressed recombination that is inherited through one sex. Here we investigate the relative timing of these processes in the UV sex chromosomes of the moss Ceratodon purpureus using molecular population genetic analyses of eight newly discovered sex-linked loci. In this system recombination is suppressed on both the female-transmitted (U) sex chromosome and the male-transmitted (V) chromosome. Genes on both chromosomes therefore should show the deleterious effects of suppressed recombination and sex-limited transmission, while purifying selection should maintain homologs of genes essential for both sexes on both sex chromosomes. Based on analyses of eight sex-linked loci, we show that the non-recombining portions of the U and V-chromosomes expanded in at least two events (~0.6 – 1.3 MYA and ~2.8 – 3.5 MYA), after the divergence of C. purpureus from its dioecious sister species, Trichodon cylindricus and Cheilothela chloropus. Both U and V-linked copies showed reduced nucleotide diversity and limited population structure, compared to autosomal loci, suggesting that the sex chromosomes experienced more recent selective sweeps that the autosomes. Collectively these results highlight the dynamic nature of gene composition and molecular evolution on non-recombining portions of the U and V sex chromosomes.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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RECENT GENE-CAPTURE ON THE UV SEX CHROMOSOMES OF THE MOSSCERATODON PURPUREUS

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“…A screening of different nuclear loci described by McDaniel & al. (2010McDaniel & al. ( , 2013 was performed, and two regions (phosphoadenosine-phosphosulphate reductase, PAP, and heme oxygenase, HO) were eventually selected for their ease of amplification and suitable levels of variation in Rhynchostegiella (see below).…”

Section: Methodsmentioning

confidence: 99%

Species delimitation in the recalcitrant moss genus Rhynchostegiella (Brachytheciaceae)

Patiño

Hedenäs

Dirkse³

et al. 2017

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Bryophytes, with their reduced morphologies and challenging taxonomy, appear as ideal candidates for the application of the fast‐developing tools of molecular species delimitation. Here, we apply species delimitation techniques to the moss genus Rhynchostegiella, which has long served as a convenient repository for small pleurocarpous species. Species delimitation analyses, including the Generalized Mixed Yule Coalescent approach and its Bayesian variant, congruently identified 13 putative species within Rhynchostegiella. To avoid inflation in the number of species with sympatric distributions that can only be recognized molecularly, we identified only one species when two or more molecular species were monophyletic, sympatric, and morphologically impossible to tell apart. After exclusion of 33 species from the genus based on earlier revisions or studies of type specimens, we recognized 11 Rhynchostegiella species. Eight of these species were already described, but were recircumscribed. In particular, the widespread R. litorea is split into three species with narrower distribution ranges: R. litorea s.str. occurs across continental Europe, western Asia and Africa (excluding Macaronesia), while R. pseudolitorea sp. nov. and R. tubulosa sp. nov. are Macaronesian and Aegean‐Cypriotic endemics, respectively. The Macaronesian endemic R. macilenta is reduced to synonymy with R. teneriffae while the Macaronesian endemic status of R. bourgeana is re‐instated. Altogether, Rhynchostegiella thus includes four Macaronesian endemic species, namely R. azorica, R. bourgeana, R. pseudolitorea, and R. trichophylla, making it the bryophyte genus with the highest number of Macaronesian endemic species. Given the difficulties in identifying some of those species from morphology, as highlighted in the identification key presented here, we describe easy‐to‐use DNA “barcodes” that can be a useful tool for specimen identification when key morphological characters lead to uncertain identification.

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“…Improvements have been made concerning taxonomy of some Arctic bryophyte species (Hesse et al 2012); however, molecular studies are still needed for most Arctic bryophyte taxa to assess species circumscriptions. DNA barcoding tools (e.g., Hassel et al 2013;Stech et al 2013;Lang et al 2014) would likely standardize identification across the Arctic and combined with other genetic tools promote the study of migration, mating system, and patterns of genetic diversity within consistent taxonomic entities (Zartman et al 2006;McDaniel et al 2013aMcDaniel et al , 2013bMagdy et al 2016). …”

Section: Introductionmentioning

confidence: 99%

Future directions and priorities for Arctic bryophyte research

et al. 2017

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The development of evidence-based international strategies for the conservation and management of Arctic ecosystems in the face of climate change is hindered by critical knowledge gaps in Arctic floristic diversity and evolution. Particularly poorly studied are the bryophytes, which dominate the vegetation across vast areas of the Arctic and consequently play an important role in global biogeochemical cycles. Currently, much of what is known about Arctic floristic evolution is based on studies of vascular plants. Bryophytes, however, possess a number of features, such as poikilohydry, totipotency, several reproductive strategies, and the ability to disperse through microscopic diaspores, that may cause their responses to Arctic environments to differ from those of the vascular plants. Here we discuss several priority areas identified in the Arctic Council's "Arctic Biodiversity Assessment" that are necessary to illuminate patterns of Arctic bryophyte evolution and diversity, including dispersal, glacial refugia, local adaptation, and ecological interactions with bryophyte-associated microbiomes. A survey of digitally available herbarium data archived in the largest online aggregate, GBIF, across the Arctic to boreal zones indicates that sampling coverage of mosses is heterogeneous and relatively sparse in the Arctic sensu stricto. A coordinated international effort across the Arctic will be necessary to address knowledge gaps in Arctic bryophyte diversity and evolution in the context of ongoing climate change.Key words: biodiversity, dispersal, local adaptation, microbiome, phylogeography.

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Estimating the nucleotide diversity in Ceratodon purpureus (Ditrichaceae) from 218 conserved exon‐primed, intron‐spanning nuclear loci

Cited by 18 publications

References 13 publications

RECENT GENE-CAPTURE ON THE UV SEX CHROMOSOMES OF THE MOSSCERATODON PURPUREUS

RECENT GENE-CAPTURE ON THE UV SEX CHROMOSOMES OF THE MOSSCERATODON PURPUREUS

Species delimitation in the recalcitrant moss genus Rhynchostegiella (Brachytheciaceae)

Future directions and priorities for Arctic bryophyte research

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