Complex regions in eukaryotic genomes are typically characterized by duplications of chromosomal stretches that often include one or more genes repeated in a tandem array or in relatively close proximity. Nevertheless...Complex regions in eukaryotic genomes are typically characterized by duplications of chromosomal stretches that often include one or more genes repeated in a tandem array or in relatively close proximity. Nevertheless, the repetitive nature of these regions,together with the often high sequence identity among repeats, have made complex regions particularly recalcitrant to proper molecular characterization, often being misassembled or completely absent in genome assemblies. This limitation has prevented accurate functional and evolutionary analyses of these regions. This is becoming increasingly relevant as evidence continues to support a central role for complex genomic regions in explaining human disease, developmental innovations, and ecological adaptations across phyla. With the advent of long-read sequencing technologies and suitable assemblers, the development of algorithms that can accommodate sample heterozygosity, and the adoption of a pangenomic-like view of these regions, accurate reconstructions of complex regions are now within reach. These reconstructions will finally allow for accurate functional and evolutionary studies of complex genomic regions, underlying the generation of genotype-phenotype maps of unprecedented resolution.展开更多
Hybridisation was traditionally considered rare on coral reefs. However, a rapid increase in hybrid studies over the last 20 years has revealed that hybridisation on coral reefs is common and widespread. In this revie...Hybridisation was traditionally considered rare on coral reefs. However, a rapid increase in hybrid studies over the last 20 years has revealed that hybridisation on coral reefs is common and widespread. In this review, we summarise the growing body of evidence arising from studies on stony corals and reef fishes to verify the occurrence of hybridisatiori, and we examine the influence hybridisation has had on the enormous level of biodiversity present on coral reefs. We discuss the challenges of dis- tinguishing hybridisation from alternative hypotheses （e.g. incomplete lineage sorting）. This review also explores the evolutio- nary consequences of hybridisation, which range from increasing genetic diversity and the production of novel lineages that may outperform the parent species, to reverse speciation and extinction by genetic swamping. Instances of hybridisation can be natural or occur as a result of human impacts （e.g. habitat degradation） and distinguishing between these two very different causal me- chanisms is important for management. Currently, the legislative status of hybrids is unclear and hybrids are rarely protected in conservation programs. Failing to adequately manage hybridisation and hybrid lineages may lead to potential losses of evolutio- nary novelty, declines in phylogenetic diversity or species extinctions. To conserve existing coral reef biodiversity, and the processes that generate biodiversity, conservation policies must be re-defined and instances of hybridisation must be assessed and managed on a case-by-case basis [Current Zoology 61 （1）： 132 145, 2015].展开更多
基金supported by a National Science Foundation Grant(MCB-1157876)to J.M.R
文摘Complex regions in eukaryotic genomes are typically characterized by duplications of chromosomal stretches that often include one or more genes repeated in a tandem array or in relatively close proximity. Nevertheless, the repetitive nature of these regions,together with the often high sequence identity among repeats, have made complex regions particularly recalcitrant to proper molecular characterization, often being misassembled or completely absent in genome assemblies. This limitation has prevented accurate functional and evolutionary analyses of these regions. This is becoming increasingly relevant as evidence continues to support a central role for complex genomic regions in explaining human disease, developmental innovations, and ecological adaptations across phyla. With the advent of long-read sequencing technologies and suitable assemblers, the development of algorithms that can accommodate sample heterozygosity, and the adoption of a pangenomic-like view of these regions, accurate reconstructions of complex regions are now within reach. These reconstructions will finally allow for accurate functional and evolutionary studies of complex genomic regions, underlying the generation of genotype-phenotype maps of unprecedented resolution.
文摘Hybridisation was traditionally considered rare on coral reefs. However, a rapid increase in hybrid studies over the last 20 years has revealed that hybridisation on coral reefs is common and widespread. In this review, we summarise the growing body of evidence arising from studies on stony corals and reef fishes to verify the occurrence of hybridisatiori, and we examine the influence hybridisation has had on the enormous level of biodiversity present on coral reefs. We discuss the challenges of dis- tinguishing hybridisation from alternative hypotheses （e.g. incomplete lineage sorting）. This review also explores the evolutio- nary consequences of hybridisation, which range from increasing genetic diversity and the production of novel lineages that may outperform the parent species, to reverse speciation and extinction by genetic swamping. Instances of hybridisation can be natural or occur as a result of human impacts （e.g. habitat degradation） and distinguishing between these two very different causal me- chanisms is important for management. Currently, the legislative status of hybrids is unclear and hybrids are rarely protected in conservation programs. Failing to adequately manage hybridisation and hybrid lineages may lead to potential losses of evolutio- nary novelty, declines in phylogenetic diversity or species extinctions. To conserve existing coral reef biodiversity, and the processes that generate biodiversity, conservation policies must be re-defined and instances of hybridisation must be assessed and managed on a case-by-case basis [Current Zoology 61 （1）： 132 145, 2015].
