scholarly journals Variation and constraints in hybrid genome formation

2017 ◽  
Author(s):  
Anna Runemark ◽  
Cassandra N. Trier ◽  
Fabrice Eroukhmanoff ◽  
Jo S. Hermansen ◽  
Michael Matschiner ◽  
...  
Keyword(s):  
Dna Repair ◽  
Nuclear Genes ◽  
Species Boundaries ◽  
Z Chromosome ◽  
Parent Species ◽  
Island Populations ◽  
Hybrid Genome ◽  
Adaptive Radiations ◽  
Homoploid Hybrid ◽  
Genomic Regions

SummaryRecent genomic investigations have revealed hybridization to be an important source of variation, the working material of natural selection1,2. Hybridization can spur adaptive radiations3, transfer adaptive variation across species boundaries4, and generate species with novel niches5. Yet, the limits to viable hybrid genome formation are poorly understood. Here we investigated to what extent hybrid genomes are free to evolve or whether they are restricted to a specific combination of parental alleles by sequencing the genomes of four isolated island populations of the homoploid hybrid Italian sparrow Passer italiae6,7. Based on 61 Italian sparrow genomes from Crete, Corsica, Sicily and Malta, and 10 genomes of each of the parent species P. domesticus and P. hispaniolensis, we report that a variety of novel and fully functional hybrid genomic combinations have arisen on the different islands, with differentiation in candidate genes for beak shape and plumage colour. There are limits to successful genome fusion, however, as certain genomic regions are invariably inherited from the same parent species. These regions are overrepresented on the Z-chromosome and harbour candidate incompatibility loci, including DNA-repair and mito-nuclear genes; loci that may drive the general reduction of introgression on sex chromosomes8. Our findings demonstrate that hybridization is a potent process for generating novel variation, but variation is limited by DNA-repair and mito-nuclear genes, which play an important role in reproductive isolation and thus contribute to speciation.

scholarly journals Selection in parental species predicts hybrid evolution

2018 ◽  
Author(s):  
Anna Runemark ◽  
Richard I Bailey ◽  
Lena Bache-Mathiesen ◽  
Glenn-Peter Sætre
Keyword(s):  
Species Differences ◽  
Parental Species ◽  
Phenotypic Trait ◽  
Parent Species ◽  
Plumage Color ◽  
Trait Variation ◽  
Island Populations ◽  
Homoploid Hybrid ◽  
Phenotypic Novelty ◽  
Major Qtl

AbstractWhile hybridization is recognized as important in evolution, its contribution to adaptation and diversification remains poorly understood. Using genomically diverged island populations of the homoploid hybrid Italian sparrow, we test predictions for phenotypic trait values and evolvability based on patterns of parental species divergence in four plumage color traits. We find associations between parental divergence and trait evolution in Italian sparrows. Fixed major QTL in species differences lead to hybrids with higher trait variation, and hence evolvability, than the parent species. Back and crown plumage show no correlation between current within-parent variability and among-parent differentiation. For these traits, Italian sparrow phenotypes are biased towards axes of high parental differentiation and show greater phenotypic novelty along axes of low current parental evolvability, as predicted when major QTL are involved in species differences. Crown color has consistently evolved back towards one parent, while back color varies among islands. We also find significant among-population diversification within the Italian sparrow. Hence, hybridization of the same parent species can generate different phenotypes. In conclusion, we find support for parental phenotypic divergence patterns reflecting divergence mechanisms, and hence such patterns can be useful in predicting how hybridization alters the potential to evolve and adapt.

Hybrid Origin and Genomic Mosaicism of Dubautia scabra (Hawaiian Silversword Alliance; Asteraceae, Madiinae)

2008 ◽  
Vol 33 (3) ◽  
pp. 589-597 ◽  
Author(s):  
Elizabeth A. Friar ◽  
Linda M. Prince ◽  
Jennifer M. Cruse-Sanders ◽  
Mitchell E. McGlaughlin ◽  
Charles A. Butterworth ◽  
...  
Keyword(s):  
Single Copy ◽  
Nuclear Genes ◽  
Hybrid Origin ◽  
Internal Transcribed Spacer Region ◽  
Hybrid Species ◽  
Cytogenetic Data ◽  
Molecular Phylogenetic ◽  
Distinct Lineage ◽  
Phylogenetic Hypotheses ◽  
Genomic Regions

Incongruence among different estimates of species relationships in plants, from different molecules, cytogenetic data, biogeographic data, morphological/anatomical data or other sources, has been used frequently as an indication of introgression, hybrid species origin, or chloroplast (cp) capture. In plants, these incongruences are most often seen between data derived from the nuclear vs. the cp genomes and the nuclear markers used for comparison usually have been from the nuclear ribosomal (nr) internal transcribed spacer region (ITS). The amount of genomic material shared between introgressing species can be highly variable. In some of these cases, other nuclear genomic regions have moved between species without leaving a signature on the nrITS. An example of well-supported phylogenetic incongruence is the placement of Dubautia scabra (DC.) D. D. Keck in the Hawaiian silversword alliance (HSA); evolutionary hypotheses for D. scabra based on molecular as opposed to cytogenetic data are strongly discordant. In this paper, we test these two conflicting phylogenetic hypotheses regarding the evolutionary relationships of Dubautia scabra using evidence from six low-copy nuclear genes, as well as multiple chloroplast noncoding regions and nrITS. The nrITS region is also examined for the presence of multiple copy types. Incongruence between inferred relationships based on nuclear chromosomal arrangements and molecular phylogenetic data from chloroplast DNA and nrITS is resolved in favor of a hypothesis of ancient hybridization rather than cytogenetic homoplasy involving dysploidy. Most single-copy nuclear genes track histories of D. scabra compatible with cytogenetic data whereas chloroplast and nrITS data track a common, different history that appears to reflect hybridization with a chromosomally distinct lineage that also occurs on Maui Nui and Hawai'i (the Big Island).

scholarly journals Hybridization and genome evolution I: The role of contingency during hybrid speciation

2013 ◽  
Vol 59 (5) ◽  
pp. 667-674 ◽  
Author(s):  
Fabrice Eroukhmanoff ◽  
Richard I. Bailey ◽  
Glenn-Peter Sætre
Keyword(s):  
Chromosome Number ◽  
Genome Evolution ◽  
Hybrid Speciation ◽  
Parent Species ◽  
Large Role ◽  
Hybrid Species ◽  
Intragenomic Conflict ◽  
Hybrid Swarms ◽  
Homoploid Hybrid

Abstract Homoploid hybrid speciation (HHS) involves the recombination of two differentiated genomes into a novel, functional one without a change in chromosome number. Theoretically, there are numerous ways for two parental genomes to recombine. Hence, chance may play a large role in the formation of a hybrid species. If these genome combinations can evolve rapidly following hybridization and sympatric situations are numerous, recurrent homoploid hybrid speciation is a possibility. We argue that three different, but not mutually exclusive, types of contingencies could influence this process. First, many of these “hopeful monsters” of recombinant parent genotypes would likely have low fitness. Only specific combinations of parental genomic contributions may produce viable, intra-fertile hybrid species able to accommodate potential constraints arising from intragenomic conflict. Second, ecological conditions (competition, geography of the contact zones or the initial frequency of both parent species) might favor different outcomes ranging from sympatric coexistence to the formation of hybrid swarms and ultimately hybrid speciation. Finally, history may also play an important role in promoting or constraining recurrent HHS if multiple hybridization events occur sequentially and parental divergence or isolation differs along this continuum. We discuss under which conditions HHS may occur multiple times in parallel and to what extent recombination and selection may fuse the parent genomes in the same or different ways. We conclude by examining different approaches that might help to solve this intriguing evolutionary puzzle.

Rapid speciation via the evolution of pre-mating isolation in the Iberá Seedeater

Science ◽  
2021 ◽  
Vol 371 (6536) ◽  
pp. eabc0256 ◽  
Author(s):  
Sheela P. Turbek ◽  
Melanie Browne ◽  
Adrián S. Di Giacomo ◽  
Cecilia Kopuchian ◽  
Wesley M. Hochachka ◽  
...  
Keyword(s):  
Species Recognition ◽  
Bird Species ◽  
Species Boundaries ◽  
Sexual Signals ◽  
Rapid Radiation ◽  
Behavioral Isolation ◽  
Rapid Speciation ◽  
Ecological Barriers ◽  
Male Plumage ◽  
Genomic Regions

Behavioral isolation can catalyze speciation and permit the slow accumulation of additional reproductive barriers between co-occurring organisms. We illustrate how this process occurs by examining the genomic and behavioral bases of pre-mating isolation between two bird species (Sporophila hypoxantha and the recently discovered S. iberaensis) that belong to the southern capuchino seedeaters, a recent, rapid radiation characterized by variation in male plumage coloration and song. Although these two species co-occur without obvious ecological barriers to reproduction, we document behaviors indicating species recognition by song and plumage traits and strong assortative mating associated with genomic regions underlying male plumage patterning. Plumage differentiation likely originated through the reassembly of standing genetic variation, indicating how novel sexual signals may quickly arise and maintain species boundaries.

scholarly journals Intraspecific niche partition without speciation: individual level web polymorphism within a single island spider population

2021 ◽  
Vol 288 (1945) ◽  
pp. 20203138
Author(s):  
Darko D. Cotoras ◽  
Miyuki Suenaga ◽  
Alexander S. Mikheyev
Keyword(s):  
Cryptic Species ◽  
Sampling Site ◽  
Behavioural Plasticity ◽  
Small Islands ◽  
Ecological Specialization ◽  
Individual Level ◽  
Island Populations ◽  
Web Architecture ◽  
Translocation Experiments ◽  
Adaptive Radiations

Early in the process of adaptive radiation, allopatric disruption of gene flow followed by ecological specialization is key for speciation; but, do adaptive radiations occur on small islands without internal geographical barriers? Island populations sometimes harbour polymorphism in ecological specializations, but its significance remains unclear. On one hand, morphs may correspond to ‘cryptic’ species. Alternatively, they could result from population, developmental or behavioural plasticity. The spider Wendilgarda galapagensis (Araneae, Theridiosomatidae) is endemic to the small Isla del Coco and unique in spinning three different web types, each corresponding to a different microhabitat. We tested whether this variation is associated with ‘cryptic’ species or intraspecific behavioural plasticity. Despite analysing 36 803 loci across 142 individuals, we found no relationship between web type and population structure, which was only weakly geographically differentiated. The same pattern holds when looking within a sampling site or considering only F st outliers. In line with genetic data, translocation experiments showed that web architecture is plastic within an individual. However, not all transitions between web types are equally probable, indicating the existence of individual preferences. Our data supports the idea that diversification on small islands might occur mainly at the behavioural level producing an intraspecific niche partition without speciation.

Adaptation and adaptive radiation

2019 ◽  
pp. 199-243
Author(s):  
Geoffrey E. Hill
Keyword(s):  
Natural Selection ◽  
Mitochondrial Genome ◽  
Adaptive Evolution ◽  
Mitochondrial Function ◽  
Adaptive Radiation ◽  
Nuclear Genes ◽  
Central Component ◽  
Terrestrial Locomotion ◽  
Adaptive Radiations ◽  
Evolution By Natural Selection

A key outcome of evolution by natural selection is adaptation. Since the beginning of the age of genetics, evolutionary biologists have focused on the evolution of nuclear genes as the basis for adaptation. Changes to the mitochondrial genome were long viewed as the result of drift and unimportant to organism fitness. New theory and empirical observations, however, are implicating changes in mitochondrial function as a central component of adaptation related to temperature, oxygen pressure, and diet. Novel mitochondrial function underlying adaptive evolution is a product of interacting mitochondrial and nuclear genes to create changes to the electron transport system, and variation in mitochondrial genotypes has been found to play a key role in such adaptive evolution of eukaryotes. Evidence is emerging that changes in mitochondrial function resulting from mitonuclear coevolution underlie key evolutionary innovations associated with major adaptive radiations including the transition from terrestrial locomotion to flight. I discuss the empirical evidence that supports a key role for mitonuclear coevolution in adaptation and adaptive radiation and the implications for fundamental ideas in ecology and evolution.

scholarly journals Poly(ADP-ribose) polymerase 1 (PARP1) promotes oxidative stress–induced association of Cockayne syndrome group B protein with chromatin

2018 ◽  
Vol 293 (46) ◽  
pp. 17863-17874 ◽  
Author(s):  
Erica L. Boetefuer ◽  
Robert J. Lake ◽  
Kostiantyn Dreval ◽  
Hua-Ying Fan
Keyword(s):  
Oxidative Stress ◽  
Dna Repair ◽  
Rna Polymerase Ii ◽  
Oxidative Dna Damage ◽  
Excision Repair ◽  
Transcription Elongation ◽  
Cockayne Syndrome ◽  
Base Excision ◽  
Group B ◽  
Genomic Regions

Cockayne syndrome protein B (CSB) is an ATP-dependent chromatin remodeler that relieves oxidative stress by regulating DNA repair and transcription. CSB is proposed to participate in base-excision repair (BER), the primary pathway for repairing oxidative DNA damage, but exactly how CSB participates in this process is unknown. It is also unclear whether CSB contributes to other repair pathways during oxidative stress. Here, using a patient-derived CS1AN-sv cell line, we examined how CSB is targeted to chromatin in response to menadione-induced oxidative stress, both globally and locus-specifically. We found that menadione-induced, global CSB–chromatin association does not require CSB's ATPase activity and is, therefore, mechanistically distinct from UV-induced CSB–chromatin association. Importantly, poly(ADP-ribose) polymerase 1 (PARP1) enhanced the kinetics of global menadione-induced CSB–chromatin association. We found that the major BER enzymes, 8-oxoguanine DNA glycosylase (OGG1) and apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1), do not influence this association. Additionally, the level of γ-H2A histone family member X (γ-H2AX), a marker for dsDNA breaks, was not increased in menadione-treated cells. Therefore, our results support a model whereby PARP1 localizes to ssDNA breaks and recruits CSB to participate in DNA repair. Furthermore, this global CSB–chromatin association occurred independently of RNA polymerase II–mediated transcription elongation. However, unlike global CSB–chromatin association, both PARP1 knockdown and inhibition of transcription elongation interfered with menadione-induced CSB recruitment to specific genomic regions. This observation supports the hypothesis that CSB is also targeted to specific genomic loci to participate in transcriptional regulation in response to oxidative stress.

scholarly journals Incomplete lineage sorting and introgression in the diversification of Chinese spot-billed ducks and mallards

2018 ◽  
Vol 65 (5) ◽  
pp. 589-597 ◽  
Author(s):  
Wenjuan Wang ◽  
Yafang Wang ◽  
Fumin Lei ◽  
Yang Liu ◽  
Haitao Wang ◽  
...  
Keyword(s):  
Gene Flow ◽  
Incomplete Lineage Sorting ◽  
Z Chromosome ◽  
Lineage Sorting ◽  
Isolation With Migration ◽  
Duck Species ◽  
High Gene ◽  
Genomic Regions ◽  
Genetic Signatures ◽  
Future Work

Abstract Incomplete lineage sorting and introgression are 2 major and nonexclusive causes of species-level non-monophyly. Distinguishing between these 2 processes is notoriously difficult because they can generate similar genetic signatures. Previous studies have suggested that 2 closely related duck species, the Chinese spot-billed duck Anas zonorhyncha and the mallard A. platyrhynchos were polyphyletically intermixed. Here, we utilized a wide geographical sampling, multilocus data and a coalescent-based model to revisit this system. Our study confirms the finding that Chinese spot-billed ducks and Mallards are not monophyletic. There was no apparent interspecific differentiation across loci except those at the mitochondrial DNA (mtDNA) control region and the Z chromosome (CHD1Z). Based on an isolation-with-migration model and the geographical distribution of lineages, we suggest that both introgression and incomplete lineage sorting might contribute to the observed non-monophyly of the 2 closely related duck species. The mtDNA introgression was asymmetric, with high gene flow from Chinese spot-billed ducks to Mallards and negligible gene flow in the opposite direction. Given that the 2 duck species are phenotypically distinctive but weakly genetically differentiated, future work based on genome-scale data is necessary to uncover genomic regions that are involved in divergence, and this work may provide further insights into the evolutionary histories of the 2 species and other waterfowls.

scholarly journals Patterns of divergence across the geographic and genomic landscape of a butterfly hybrid zone associated with a climatic gradient

2017 ◽  
Author(s):  
Sean F. Ryan ◽  
Michael C. Fontaine ◽  
J. Mark Scriber ◽  
Michael E. Pfrender ◽  
Shawn T. O’Neil ◽  
...  
Keyword(s):  
Reproductive Isolation ◽  
Candidate Genes ◽  
Hybrid Zone ◽  
Z Chromosome ◽  
Hybrid Zones ◽  
Seasonal Adaptation ◽  
Developmental Threshold ◽  
Ecological Adaptations ◽  
A Genome ◽  
Genomic Regions

AbstractHybrid zones are a valuable tool for studying the process of speciation and for identifying the genomic regions undergoing divergence and the ecological (extrinsic) and non-ecological (intrinsic) factors involved. Here, we explored the genomic and geographic landscape of divergence in a hybrid zone between Papilio glaucus and Papilio canadensis. Using a genome scan of 28,417 ddRAD SNPs, we identified genomic regions under possible selection and examined their distribution in the context of previously identified candidate genes for ecological adaptations. We showed that differentiation was genome-wide, including multiple candidate genes for ecological adaptations, particularly those involved in seasonal adaptation and host plant detoxification. The Z-chromosome and four autosomes showed a disproportionate amount of differentiation, suggesting genes on these chromosomes play a potential role in reproductive isolation. Cline analyses of significantly differentiated genomic SNPs, and of species diagnostic genetic markers, showed a high degree of geographic coincidence (81%) and concordance (80%) and were associated with the geographic distribution of a climate-mediated developmental threshold (length of the growing season). A relatively large proportion (1.3%) of the outliers for divergent selection were not associated with candidate genes for ecological adaptations and may reflect the presence of previously unrecognized intrinsic barriers between these species. These results suggest that exogenous (climate-mediated) and endogenous (unknown) clines may have become coupled and act together to reinforce reproductive isolation. This approach of assessing divergence across both the genomic and geographic landscape can provide insight about the interplay between the genetic architecture of reproductive isolation and endogenous and exogenous selection.

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