Genomics of Adaptation and Speciation

Wolfsberger, Walter; Battistuzzi, Fabia U.; Oleksyk, Tarás K.

doi:10.3390/genes13071187

Cited by 3 publications

(3 citation statements)

References 24 publications

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“…What role, if any, non-coding DNA and heterochromatin play in the process of speciation and adaptive radiations remains largely unknown and awaits further investigation into the finer molecular details of genome architecture and DNA metabolism. The growing body of genome-wide data from different taxa and the emergence of new bioinformatic tools have opened up the field of the genomics of speciation by allowing detailed analyses at the levels of the gene, the genome, and the transcriptome [130][131][132].…”

Section: Discussionmentioning

confidence: 99%

DNA Damage, Genome Stability, and Adaptation: A Question of Chance or Necessity?

Herrick

2024

Genes

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DNA damage causes the mutations that are the principal source of genetic variation. DNA damage detection and repair mechanisms therefore play a determining role in generating the genetic diversity on which natural selection acts. Speciation, it is commonly assumed, occurs at a rate set by the level of standing allelic diversity in a population. The process of speciation is driven by a combination of two evolutionary forces: genetic drift and ecological selection. Genetic drift takes place under the conditions of relaxed selection, and results in a balance between the rates of mutation and the rates of genetic substitution. These two processes, drift and selection, are necessarily mediated by a variety of mechanisms guaranteeing genome stability in any given species. One of the outstanding questions in evolutionary biology concerns the origin of the widely varying phylogenetic distribution of biodiversity across the Tree of Life and how the forces of drift and selection contribute to shaping that distribution. The following examines some of the molecular mechanisms underlying genome stability and the adaptive radiations that are associated with biodiversity and the widely varying species richness and evenness in the different eukaryotic lineages.

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Section: Discussionmentioning

confidence: 99%

DNA Damage, Genome Stability, and Adaptation: A Question of Chance or Necessity?

Herrick

2024

Genes

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“…Colonization of novel environments is a fundamental driver of biodiversity, often resulting in locally adapted, ecologically divergent populations, ecotypes or species (Rundle & Nosil, 2005). Uncovering the genomic changes underlying this process of adaptation is critical to understanding how the multifarious selection pressures of a novel environment can lead to ecological divergence and, ultimately, speciation (Wolfsberger et al, 2022). Over the past fifty years, it has become clear that sequence divergence at gene loci, especially within protein coding regions, is insufficient to explain major morphological, physiological, and behavioral divergence between species.…”

Section: Introductionmentioning

confidence: 99%

Evolved and plastic gene expression in adaptation to a novel niche

Steward,

Ortega Giménez,

Choudhary

et al. 2024

Preprint

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Gene expression, resulting from complex regulatory interactions, plays an important role in adaptation and speciation. While gene expression historically has been studied in the context of reproductive isolation in speciation research, a role for evolved differences in gene expression in adaptation to novel niches is increasingly appreciated. How gene expression evolves and enables divergent ecological adaptation, and how changes in gene expression relate to genomic architecture and genetic divergence are pressing questions in understanding the processes of adaptation and ecological speciation. Further, how plasticity in gene expression can both contribute to and be affected by the process of ecological adaptation is a crucial component in understanding gene expression evolution. To address these questions, we investigate the role of evolved and plastic gene expression differences in adaptation leveraging an established host plant shift in the peacock fly Tephritis conura. Using a cross-fostering design where larvae feed on either natal or alternate host plants, we uncover extensive evolved differences in gene expression between the ecotypes, strikingly in genes associated with processing of host plant chemicals. We find limited evidence for plasticity, with some indications of higher plasticity in the ancestral ecotype where the expression of three gene coexpression modules is altered when larvae are cross-fostered to the derived host plant. Interestingly, we find an enrichment of differentially expressed genes within a large, ecotype-specific inversion in the T. conura genome. This finding adds to evidence that inversions are important for enabling diversification in the face of gene flow and underscores that effects on gene expression may be key to understanding the role of inversions.

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“…The rapid development in the field of molecular genetics during the past decade, particularly the advances in genome sequencing technologies, has led to an accumulation of genomic data for many species, including primates [1,2]. These data have the potential to refine phylogenetic and population genetic analyses [3,4] and broaden our understanding of adaptation and speciation [5]. These data can also have an impact on conservation planning and the preservation of endangered species [6][7][8].…”

Section: Introductionmentioning

confidence: 99%

Recent Advances in Genetics and Genomics of Snub-Nosed Monkeys (Rhinopithecus) and Their Implications for Phylogeny, Conservation, and Adaptation

Kuang

Zinner

et al. 2023

Genes

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The snub-nosed monkey genus Rhinopithecus (Colobinae) comprises five species (Rhinopithecus roxellana, Rhinopithecus brelichi, Rhinopithecus bieti, Rhinopithecus strykeri, and Rhinopithecus avunculus). They are range-restricted species occurring only in small areas in China, Vietnam, and Myanmar. All extant species are listed as endangered or critically endangered by the International Union for Conservation of Nature (IUCN) Red List, all with decreasing populations. With the development of molecular genetics and the improvement and cost reduction in whole-genome sequencing, knowledge about evolutionary processes has improved largely in recent years. Here, we review recent major advances in snub-nosed monkey genetics and genomics and their impact on our understanding of the phylogeny, phylogeography, population genetic structure, landscape genetics, demographic history, and molecular mechanisms of adaptation to folivory and high altitudes in this primate genus. We further discuss future directions in this research field, in particular how genomic information can contribute to the conservation of snub-nosed monkeys.

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Genomics of Adaptation and Speciation

Abstract: The availability of genome data provides a unique window into speciation mechanisms with virtually infinite amounts of information, providing a pathway for a better understanding of major evolutionary questions [...]

Cited by 3 publications

References 24 publications

DNA Damage, Genome Stability, and Adaptation: A Question of Chance or Necessity?

DNA Damage, Genome Stability, and Adaptation: A Question of Chance or Necessity?

Evolved and plastic gene expression in adaptation to a novel niche

Recent Advances in Genetics and Genomics of Snub-Nosed Monkeys (Rhinopithecus) and Their Implications for Phylogeny, Conservation, and Adaptation

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