Evolutionary divergence between homologous X–Y chromosome genes shapes sex-biased biology
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FISH mapping in Xenopus pygmaeus refines understanding of genomic rearrangements and reveals jumping NORs in African clawed frogs
Chromosomal rearrangements are fundamental evolutionary drivers leading to genomic diversification. African clawed frogs (genus Xenopus, subgenera Silurana and Xenopus) represent an allopolyploid model system with conserved chromosome numbers in species with the same ploidy within each subgenus. Two significant interchromosomal rearrangements have been identified: a translocation between chromosomes 9 and 2, found in subgenus Silurana, and a fusion between chromosomes 9 and 10, probably widespread in subgenus Xenopus. Here, we study the allotetraploid Xenopus pygmaeus (subgenus Xenopus) based on in-depth karyotype analysis using chromosome measurements and fluorescent in situ hybridization (FISH). We designed FISH probes for genes associated with translocation and fusion to test for the presence of the two main types of rearrangements. We also examined the locations of 5S and 28S ribosomal tandem repeats, with the former often associated with telomeric regions and the latter with nucleolus organizer regions (NORs). The translocation-associated gene mapping did not detect the translocation in X. pygmaeus, supporting the hypothesis that the translocation is restricted to Silurana, but instead identified a pericentromeric inversion on chromosome 2S. The fusion-associated gene mapping confirmed the fusion of chromosomes 9 and 10, supporting this fusion as an ancestral state in subgenus Xenopus. As expected, the 5S repeats were found predominantly in telomere regions on almost all chromosomes. The nucleolar 28S repeats were localized on chromosome 6S, a position previously found only in the closely related species X. parafraseri, whereas other, phylogenetically more distant species have NORs located on different chromosomes. We therefore hypothesize that a jumping mechanism could explain the relatively frequent changes in the location of NORs during Xenopus evolution.
Accelerated differentiation of neo-W nuclear-encoded mitochondrial genes between two climate-associated bird lineages signals potential co-evolution with mitogenomes
There is considerable evidence for mitochondrial-nuclear co-adaptation as a key evolutionary driver. Hypotheses regarding the roles of sex-linkage have emphasized Z-linked nuclear genes with mitochondrial function (N-mt genes), whereas it remains contentious whether the perfect co-inheritance of W genes with mitogenomes could hinder or facilitate co-adaptation. Young (neo-) sex chromosomes that possess relatively many N-mt genes compared to older chromosomes provide unprecedented hypothesis-testing opportunities. Eastern Yellow Robin (EYR) lineages in coastal and inland habitats with different climates are diverged in mitogenomes, and in a ~ 15.4 Mb nuclear region enriched with N-mt genes, in contrast with otherwise-similar nuclear genomes. This nuclear region maps to passerine chromosome 1A, previously found to be neo-sex in the inland EYR genome. To compare sex-linked Chr1A-derived genes between lineages, we assembled and annotated the coastal EYR genome. We found that: (i) the coastal lineage shares a similar neo-sex system with the inland lineage, (ii) neo-W and neo-Z N-mt genes are not more diverged between lineages than are comparable non-N-mt genes, and showed little evidence for broad positive selection, (iii) however, W-linked N-mt genes are more diverged between lineages than are their Z-linked gametologs. The latter effect was ~7 times stronger for N-mt than non-N-mt genes, suggesting that W-linked N-mt genes might have diverged between lineages under environmental selection through co-evolution with mitogenomes. Finally, we identify a candidate gene driver for divergent selection, NDUFA12. Our data represent a rare example suggesting a possible role for W-associated mitochondrial-nuclear interactions in climate-associated adaptation and lineage differentiation.
A wide range of chromosome numbers result from unreduced gamete production in Brassica juncea × B. napus (AABC) interspecific hybrids
The establishment of successful interspecies hybrids requires restoration of a stable “2n” chromosome complement which can produce viable “n” gametes. This may occur (rarely) via recombination between non-homologous chromosomes, or more commonly is associated with a doubling of parental chromosome number to produce new homologous pairing partners in the hybrid. The production of unreduced “2n” gametes (gametes with the somatic chromosome number) may therefore be evolutionarily useful by serving as a key pathway for the formation of new polyploid hybrids, as might specific mechanisms permitting recombination between non-homologous chromosomes. Here, we investigated chromosome complements and fertility in third generation interspecific hybrids (AABC) resulting from a cross between allopolyploids Brassica juncea (AABB) × B. napus (AACC) followed by self-pollination for two generations. Chromosome numbers ranged from 2n = 48–74 in the experimental population (35 plants), with 9–16 B genome chromosomes and up to 4 copies of A genome chromosomes. Unreduced gamete production leading to a putative genome structure of approximately AAAABBCC was hence predicted to explain the high chromosome numbers observed. Additionally, the estimation of nuclei number in post-meiotic sporads revealed a higher frequency of unreduced gametes (0.04–5.21%) in the third generation AABC interspecific hybrids compared to the parental Brassica juncea (0.07%) and B. napus (0.13%). Our results suggest that unreduced gamete production in the subsequent generations following interspecific hybridization events may play a critical role in restoration of more stable, fertile chromosome complements.
Macroevolution along developmental lines of least resistance in fly wings
Evolutionary change requires genetic variation, and a reigning paradigm in biology is that rates of microevolution can be predicted from estimates of available genetic variation within populations. However, the accuracy of such predictions should decay on longer evolutionary timescales, as the influence of genetic constraints diminishes. Here we show that intrinsic developmental variability and standing genetic variation in wing shape in two distantly related flies, Drosophila melanogaster and Sepsis punctum, are aligned and predict deep divergence in the dipteran phylogeny, spanning >900 taxa and 185 million years. This alignment cannot be easily explained by constraint hypotheses unless most of the quantified standing genetic variation is associated with deleterious side effects and is effectively unusable for evolution. However, phenotyping of 71 genetic lines of S. punctum revealed no covariation between wing shape and fitness, lending no support to this hypothesis. We also find little evidence for genetic constraints on the pace of wing shape evolution along the dipteran phylogeny. Instead, correlational selection related to allometric scaling, simultaneously shaping developmental variability and deep divergence in fly wings, emerges as a potential explanation for the observed alignment. This suggests that pervasive natural selection has the potential to shape developmental architectures of some morphological characters such that their intrinsic variability predicts their long-term evolution.
The genetic origins of species boundaries at subtropical and temperate ecoregions in the North American racers (Coluber constrictor)
Phylogeographically structured lineages are a common outcome of range-wide population genetic studies. In the southeastern United States, disconnection between populations found at the intersection of the southeastern coastal plains of peninsular Florida and the southeastern plains of the adjacent continent is readily apparent among many plants and animals. However, the timing and maintenance of species boundaries between these distinctly different subtropical and temperate regions remains unknown for all organisms studied there. Using genome-scale data, we examine the timing of origins, gene flow, and the movement of genes under selection in unique ecoregions within the North American racers (Coluber constrictor). Isolation-migration models along with tests of genome-wide selection, locus-environment associations, and spatial and genomic clines demonstrate that two unrecognized species are present and are in contact at the boundary of these two ecoregions. We show that selection at several loci associated with unique environments have maintained species boundaries despite constant levels of gene flow between these lineages over thousands of generations. This research provides a new avenue of research to examine speciation processes in poorly studied biodiversity hotspots.
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