Molecular hyperdiversity defines populations of the nematode
            <i>Caenorhabditis brenneri</i>

Dey, Alivia; Chan, Cecilia Ka Wing; Thomas, Cristel G.; Cutter, Asher D.

doi:10.1073/pnas.1303057110

Cited by 98 publications

(104 citation statements)

References 51 publications

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“…Assuming that morphological distinction was the criterion used to establish these species, the prospect of each morphospecies being composed of multiple cryptic species would suggest a dramatic increase in the number of species in a taxon already presumed to be ''hyperdiverse'' (Ehrlich and Wilson, 1991;Puillandre et al, 2012;Dey et al, 2013). The recognition of this added diversity has a direct bearing on estimates of global nematode biodiversity and concepts of nematode biogeography.…”

Section: Discussionmentioning

confidence: 99%

Species Delimitation and Description of Mesocriconema nebraskense n. sp. (Nematoda: Criconematidae), a Morphologically Cryptic, Parthenogenetic Species from North American Grasslands

Olson

Harris

Higgins

et al. 2017

Journal of Nematology

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Nematode surveys of North American grasslands conducted from 2010 to 2015 frequently recovered a species of criconematid nematode morphologically resembling Mesocriconema curvatum. These specimens were recovered from remnant native prairies in the central tallgrass ecoregion of North America, and not from surrounding agroecosystems. Historical records indicate that M. curvatum is a cosmopolitan species feeding on a wide range of agronomic and native plants. DNA barcoding indicates North American grasslands contain at least 10 phylogenetically distinct lineages of Mesocriconema that resemble, but are not, M. curvatum. Analysis of the two most common lineages reveals two distinctly different population structures. The variation in population structure suggests unique evolutionary histories associated with their diversification. These two major lineages share a sympatric distribution and their slight morphological differences contrast with a high level of genetic separation. Based on their genetic divergence, fixed diagnostic nucleotides, population structure, species delimitation metrics, and a sympatric distribution, we believe that one of these distinct lineages warrants formal nomenclatural recognition. Herein, we provide formal recognition for Mesocriconema nebraskense n. sp. and discuss its relationship to other Mesocriconema lineages discovered in native North American grasslands.

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Section: Discussionmentioning

confidence: 99%

Species Delimitation and Description of Mesocriconema nebraskense n. sp. (Nematoda: Criconematidae), a Morphologically Cryptic, Parthenogenetic Species from North American Grasslands

Olson

Harris

Higgins

et al. 2017

Journal of Nematology

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“…Some species of Drosophila appear near the cusp of hyperdiversity (Leffler et al 2012), so tests for diversity-reducing effects of selection on synonymous sites should be considered carefully to determine θ neu , as we will describe later. Third, polymorphism averages an astonishing 14% at synonymous sites (θ neu = 0.16) in the nematode Caenorhabditis brenneri (Barriere et al 2009; Jovelin 2009; Dey et al 2013). At least two other species in this genus ( C. remanei, C. sp.…”

Section: Hyperdiverse Eukaryotes In Naturementioning

confidence: 99%

Molecular hyperdiversity and evolution in very large populations

2013

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The genomic density of sequence polymorphisms critically affects the sensitivity of inferences about ongoing sequence evolution, function, and demographic history. Most animal and plant genomes have relatively low densities of polymorphisms, but some species are hyperdiverse with neutral nucleotide heterozygosity exceeding 5%. Eukaryotes with extremely large populations, mimicking bacterial and viral populations, present novel opportunities for studying molecular evolution in sexually-reproducing taxa with complex development. In particular, hyperdiverse species can help answer controversial questions about the evolution of genome complexity, the limits of natural selection, modes of adaptation, and subtleties of the mutation process. However, such systems have some inherent complications and here we identify topics in need of theoretical developments. Close relatives of the model organisms Caenorhabditis elegans and Drosophila melanogaster provide known examples of hyperdiverse eukaryotes, encouraging functional dissection of resulting molecular evolutionary patterns. We recommend how best to exploit hyperdiverse populations for analysis, for example, in quantifying the impact of non-crossover recombination in genomes and for determining the identity and micro-evolutionary selective pressures on non-coding regulatory elements.

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“…Indeed, we computed nucleotide polymorphism with DnaSP v5 (Librado and Rozas 2009) using 3 kb of sequence upstream and downstream from each miRNA copy (using flanking sequences of the first and last clustered miRNA, see below) and aligned with T-Coffee (Notredame et al 2000). We found pairwise estimates and average nucleotide diversity (N = 71, mean π = 12.1%) similar to polymorphism reported in this species (Jovelin 2009;Dey et al 2013). Similarly, the two C. remanei mir-790 located on different contigs have highly similar flanking sequences and gene neighbors with identical protein sequences.…”

Section: Materials and Methods Mirna Data Setsmentioning

confidence: 65%

Comparative genomic analysis of upstream miRNA regulatory motifs in Caenorhabditis

Jovelin¹,

Krizus²,

Taghizada³

et al. 2016

RNA

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MicroRNAs (miRNAs) comprise a class of short noncoding RNA molecules that play diverse developmental and physiological roles by controlling mRNA abundance and protein output of the vast majority of transcripts. Despite the importance of miRNAs in regulating gene function, we still lack a complete understanding of how miRNAs themselves are transcriptionally regulated. To fill this gap, we predicted regulatory sequences by searching for abundant short motifs located upstream of miRNAs in eight species of Caenorhabditis nematodes. We identified three conserved motifs across the Caenorhabditis phylogeny that show clear signatures of purifying selection from comparative genomics, patterns of nucleotide changes in motifs of orthologous miRNAs, and correlation between motif incidence and miRNA expression. We then validated our predictions with transgenic green fluorescent protein reporters and site-directed mutagenesis for a subset of motifs located in an enhancer region upstream of let-7. We demonstrate that a CT-dinucleotide motif is sufficient for proper expression of GFP in the seam cells of adult C. elegans, and that two other motifs play incremental roles in combination with the CT-rich motif. Thus, functional tests of sequence motifs identified through analysis of molecular evolutionary signatures provide a powerful path for efficiently characterizing the transcriptional regulation of miRNA genes.

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Molecular hyperdiversity defines populations of the nematode Caenorhabditis brenneri

Cited by 98 publications

References 51 publications

Species Delimitation and Description of Mesocriconema nebraskense n. sp. (Nematoda: Criconematidae), a Morphologically Cryptic, Parthenogenetic Species from North American Grasslands

Species Delimitation and Description of Mesocriconema nebraskense n. sp. (Nematoda: Criconematidae), a Morphologically Cryptic, Parthenogenetic Species from North American Grasslands

Molecular hyperdiversity and evolution in very large populations

Comparative genomic analysis of upstream miRNA regulatory motifs in Caenorhabditis

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