Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes.

The self-fertile nematode worms Caenorhabditis elegans, C. briggsae, and C. tropicalis evolved independently from outcrossing male-female ancestors and have genomes 20-40% smaller than closely related outcrossing relatives. This pattern of smaller genomes for selfing species and larger genomes for closely related outcrossing species is also seen in plants. We use comparative genomics, including the first high quality genome assembly for an outcrossing member of the genus (C. remanei) to test several hypotheses for the evolution of genome reduction under a change in mating system. Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size. Instead, all functional genomic categories are lost in approximately equal proportions. Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes. Contrary to this, we find that the self-fertile C. briggsae and C. elegans have larger intergenic spaces and larger protein-coding genes on the X chromosome when compared to autosomes, while C. remanei actually has smaller introns on the X chromosome than either self-reproducing species. Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se

Genome content analysis across the <i>Caenorhabditis</i> Elegans supergroup (with outgroup species <i>C. angaria</i> and the distantly related <i>P. pacificus</i>).

<p>Genome content analysis does not support expansion of repeat elements in outcrossing species. The Elegans supergroup contains at least 17 species [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005323#pgen.1005323.ref093" target="_blank">93</a>], but only the species whose genomes are analyzed here used are shown. The Elegans supergroup evolved from a common ancestor with a gonochoristic (<i>e.g</i>., male-female) mating system (identified with the red and blue symbols) and <i>C. japonica</i>, <i>C. brenneri</i>, <i>C. remanei</i> and <i>C. sinica</i> have retained the ancestral mating system. <i>C. elegans</i>, <i>C. briggsae</i>, and <i>C. tropicalis</i> have an androdioecious mating system with self-fertile hermaphrodites and males segregating at low levels in the populations.</p

Whole chromosome comparisons among <i>C. elegans</i>, <i>C. briggsae</i>, and <i>C. remanei</i>.

<p>The <i>C. remanei</i> The linkage map was sufficient to assemble and order 98.93% of the scaffolds with orthologous genes aligning to <i>C. elegans</i> chromosome X, 78.38% of the scaffolds with orthologous genes aligning to <i>C. elegans</i> chromosome II and 81.40% of the scaffolds with orthologous genes aligning to <i>C. elegans</i> chromosome IV. (a) <i>C. remanei</i> linkage groups were assigned to chromosomes based on gene orthology to <i>C. elegans</i> chromosomes. Reproductive incompatibility between the <i>C. remanei</i> strains used to construct the linkage map resulted in over-dispersion of the linkage map and 13 linkage groups instead of the 6 chromosomes expected (both <i>C. elegans</i> and <i>C. briggsae</i> have 6 chromosomes, respectively). (b) The cumulative size and orthologous gene alignments for scaffolds that were not assigned to linkage groups. c-e) Orthologous gene alignments indicated blocks of syntenic DNA between <i>C. elegans</i>, <i>C. briggsae</i>, and <i>C. remanei</i>. The panels c-e show orthologous genes on chromosomes X, II, and IV, with chromosome size scaled to linkage group size in <i>C. remanei</i> (X 18.5Mb, II 12.5Mb, IV 14.5 Mb). Orthologous genes were connected between species pairs, and grouped together if the genes were within 50,000 nucleotides of each other. Single gene translocations were excluded for clarity. Green indicates orthologs identified between <i>C. elegans</i> and <i>C. remanei</i>, blue indicates orthologs identified between <i>C. remanei</i> and <i>C. briggsae</i>, and grey indicates orthologs identified between <i>C. briggsae</i> and <i>C. elegans</i>. The outer rings are chromosomes X, II, and IV in each species. Each gray line is an orthologous gene located on the same chromosome in the other species and each black line is an orthologous gene that is located on a different chromosome in one of the other species. There are few blocks of interchromosomal translocation, and few black lines. White indicates regions of the chromosome where there were no orthologous genes identified between the species. (c) There was a large region of divergence (roughly 3.6Mb) on the <i>C. remanei</i> X; (d) Chromosome II is not completely assembled in <i>C. remanei</i>, and there were several regions of <i>C. elegans</i> and <i>C. briggsae</i> chromosome II that were not represented in <i>C. remanei</i>; (e) Chromosome IV.</p

Comparison of intergenic spaces between autosomes and X chromosomes.

<p>(a) Kernel smoothed distribution of intergenic spaces across the entire genome for <i>C. elegans</i>, <i>C. briggsae</i> and <i>C. remanei</i>. (b) Intergenic spaces differ between autosomes and the X chromosome in <i>C. briggsae</i> (Kruskal-Wallis <i>χ</i>² = 556.09, <i>df</i> = 1, <i>p</i> < 2<i>x</i>10⁻¹⁶), <i>C. elegans</i> (Kruskal-Wallis <i>χ</i>² = 476.32, <i>df</i> = 1, <i>p</i> < 2<i>x</i>10⁻¹⁶) and <i>C. remanei</i> (Kruskal-Wallis <i>χ</i>² = 76.76, <i>df</i> = 1, <i>p</i> < 2<i>x</i>10⁻¹⁶). The boxplot indicates the bottom and top quartiles (black lines), middle quartiles (blue boxes), and median value (central notch) with outliers are shown as black dots. Intergenic spaces differ significantly between species on autosomes (Kruskal-Wallis <i>χ</i>² = 328.4957; <i>df</i> = 2, <i>p</i> < 2<i>x</i>10⁻¹⁶; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum <i>C. remanei</i>:<i>C. elegans</i><i>p</i> < 2<i>x</i>10⁻¹⁶, <i>C. remanei</i>:<i>C. briggsae</i><i>p</i> < 0.039; <i>C. briggsae</i>:<i>C. elegans</i><i>p</i> < 2<i>x</i>10⁻¹⁶) and the X chromosome (Kruskal-Wallis <i>χ</i>² = 112.52, <i>df</i> = 2, <i>p</i> < 2<i>x</i>10⁻¹⁶; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum <i>C. remanei</i>:<i>C. elegans</i><i>p</i> < 1.6<i>x</i>10⁻⁷, <i>C. remanei</i>:<i>C. briggsae</i><i>p</i> < 2<i>x</i>10⁻¹⁶; <i>C. briggsae</i>:<i>C. elegans</i><i>p</i> < 0.0005).</p

Differences in total gene size (introns and exons) versus protein coding size (exons) in <i>C. elegans</i>, <i>C. briggsae</i> and <i>C. remanei</i>.

<p>(a-b) Gene Size differs between autosomes and the X chromosome in <i>C. briggsae</i> (Kruskal-Wallis <i>χ</i>² = 24.63, <i>df</i> = 1, <i>p</i> < 6.96<i>x</i>10⁻⁷), <i>C. elegans</i> (Kruskal-Wallis <i>χ</i>² = 58.04, <i>df</i> = 1, <i>p</i> < 2.56<i>x</i>10⁻¹⁴) and <i>C. remanei</i> (Kruskal-Wallis <i>χ</i>² = 99.10, <i>df</i> = 1, <i>p</i> < 2<i>x</i>10⁻¹⁶) but protein size does not (<i>C. briggsae</i> Kruskal-Wallis <i>χ</i>² = 0.94, <i>df</i> = 1, <i>p</i> = 0.66; <i>C. elegans</i> Kruskal-Wallis <i>χ</i>² = 0.29, <i>df</i> = 1, <i>p</i> = 1; <i>C. remanei</i> Kruskal-Wallis <i>χ</i>² = 4.3096, <i>df</i> = 1, <i>p</i> = 0.08). Gene size differs significantly among the species on autosomes (Kruskal-Wallis <i>χ</i>² = 152.86; <i>df</i> = 2, <i>p</i> < 2<i>x</i>10⁻¹⁶; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum <i>C. remanei</i>:<i>C. elegans</i><i>p</i> < 2<i>x</i>10⁻¹⁶, <i>C. remanei</i>:<i>C. briggsae</i><i>p</i> < 2<i>x</i>10⁻¹⁶; <i>C. briggsae</i>:<i>C. elegans</i><i>p</i> < 6<i>x</i>10⁻⁵) and between <i>C. remanei</i> and the self-fertile hermaprodites on the X chromsome (Kruskal-Wallis <i>χ</i>² = 64.39; <i>df</i> = 2, <i>p</i> < 1<i>x</i>10⁻¹⁴; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum <i>C. remanei</i>:<i>C. elegans</i><i>p</i> < 2<i>x</i>10⁻¹⁰, <i>C. remanei</i>:<i>C. briggsae</i><i>p</i> < 1.8<i>x</i>10⁻¹¹; <i>C. briggsae</i>:<i>C.elegans</i><i>p</i> = 1). (c-d) Protein size differs significantly between <i>C. briggsae</i> and <i>C. elegans</i> and <i>C. briggsae</i> and <i>C. remanei</i> on both the autosomes (Kruskal-Wallis <i>χ</i>² = 91.32; <i>df</i> = 2, <i>p</i> < 2<i>x</i>10⁻¹⁶; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum <i>C. remanei</i>:<i>C. elegans</i><i>p</i> = 1, <i>C. remanei</i>:<i>C. briggsae</i><i>p</i> < 2<i>x</i>10⁻¹⁶; <i>C. briggsae</i>:<i>C.elegans</i><i>p</i> < 1.5<i>x</i>10⁻¹¹) and X chromosome (Kruskal-Wallis <i>χ</i>² = 40.36; <i>df</i> = 2, <i>p</i> < 1.7<i>x</i>10⁻⁹; Bonferroni-adjusted Pairwise Wilcoxon Rank Sum <i>C. remanei</i>:<i>C. elegans</i><i>p</i> = 0.92, <i>C. remanei</i>:<i>C. briggsae</i><i>p</i> < 4<i>x</i>10⁻⁹; <i>C. briggsae</i>:<i>C.elegans</i><i>p</i> < 2<i>x</i>10⁻⁵).</p

Man or Human? A Note on the Translation of Ἄνθρωπος in Mark 10.1-9 and Masculinity Studies

The past decades have seen an increased sensitivity among Bible translators when it comes to matters of gender, in particular in relation to inclusive and exclusive aspects of language and their rendering in translation. Building on this feminist agenda, it can also be asked, following the lead of masculinity studies in general and its use in biblical studies in particular, what role masculinity plays in texts and their translation. This will be explored in this contribution using the example of the meaning and translation of ἄνθρωπος in Mark 10.7 and 9, which, it will be proposed, is, for gender-sensitive exegetical reasons, best translated as “man” (in the exclusive sense of the word), rather than as “human” (as an inclusive expression)