Hybrid Zones and the Genetic Architecture of a Barrier to Gene Flow Between Two Sunflower Species

Abstract Genetic analyses of reproductive barriers represent one of the few methods by which theories of speciation can be tested. However, genetic study is often restricted to model organisms that have short generation times and are easily propagated in the laboratory. Replicate hybrid zones with a diversity of recombinant genotypes of varying age offer increased resolution for genetic mapping experiments and expand the pool of organisms amenable to genetic study. Using 88 markers distributed across 17 chromosomes, we analyze the introgression of chromosomal segments of Helianthus petiolaris into H. annuus in three natural hybrid zones. Introgression was significantly reduced relative to neutral expectations for 26 chromosomal segments, suggesting that each segment contains one or more factors that contribute to isolation. Pollen sterility is significantly associated with 16 of these 26 segments, providing a straightforward explanation of why this subset of blocks is disadvantageous in hybrids. In addition, comparison of rates of introgression across colinear vs. rearranged chromosomes indicates that close to 50% of the barrier to introgression is due to chromosomal rearrangements. These results demonstrate the utility of hybrid zones for identifying factors contributing to isolation and verify the prediction of increased resolution relative to controlled crosses.

Download Full-text

Migratory divides coincide with reproductive barriers across replicated avian hybrid zones above the Tibetan Plateau

Ecology Letters ◽

10.1111/ele.13420 ◽

2019 ◽

Vol 23 (2) ◽

pp. 231-241 ◽

Cited By ~ 4

Author(s):

Elizabeth S. C. Scordato ◽

Chris C. R. Smith ◽

Georgy A. Semenov ◽

Yu Liu ◽

Matthew R. Wilkins ◽

...

Keyword(s):

Tibetan Plateau ◽

The Tibetan Plateau ◽

Hybrid Zones ◽

Reproductive Barriers

Download Full-text

Genetic architecture of traits associated with reproductive barriers in Silene: Coupling, sex chromosomes and variation

Molecular Ecology ◽

10.1111/mec.14562 ◽

2018 ◽

Vol 27 (19) ◽

pp. 3889-3904 ◽

Cited By ~ 6

Author(s):

Xiaodong Liu ◽

Sophie Karrenberg

Keyword(s):

Sex Chromosomes ◽

Genetic Architecture ◽

Reproductive Barriers

Download Full-text

Genomics of isolation in hybrids

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2011.0196 ◽

2012 ◽

Vol 367 (1587) ◽

pp. 439-450 ◽

Cited By ~ 88

Author(s):

Zachariah Gompert ◽

Thomas L. Parchman ◽

C. Alex Buerkle

Keyword(s):

Reproductive Isolation ◽

Genetic Architecture ◽

Large Scale ◽

Empirical Studies ◽

Hybrid Zones ◽

Direct Measure ◽

Fitness Effects ◽

Outlier Loci ◽

Admixed Population ◽

Genome Level

Hybrid zones are common in nature and can offer critical insights into the dynamics and components of reproductive isolation. Hybrids between diverged lineages are particularly informative about the genetic architecture of reproductive isolation, because introgression in an admixed population is a direct measure of isolation. In this paper, we combine simulations and a new statistical model to determine the extent to which different genetic architectures of isolation leave different signatures on genome-level patterns of introgression. We found that reproductive isolation caused by one or several loci of large effect caused greater heterogeneity in patterns of introgression than architectures involving many loci with small fitness effects, particularly when isolating factors were closely linked. The same conditions that led to heterogeneous introgression often resulted in a reasonable correspondence between outlier loci and the genetic loci that contributed to isolation. However, demographic conditions affected both of these results, highlighting potential limitations to the study of the speciation genomics. Further progress in understanding the genomics of speciation will require large-scale empirical studies of introgression in hybrid zones and model-based analyses, as well as more comprehensive modelling of the expected levels of isolation with different demographies and genetic architectures of isolation.

Download Full-text

Male territorial vocalizations and responses are decoupled in an avian hybrid zone

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2008.0046 ◽

2008 ◽

Vol 363 (1505) ◽

pp. 2879-2889 ◽

Cited By ~ 8

Author(s):

Paula M den Hartog ◽

Hans Slabbekoorn ◽

Carel ten Cate

Keyword(s):

Hybrid Zone ◽

Acoustic Signals ◽

Hybrid Zones ◽

Natural Hybrid ◽

Individual Male ◽

Individual Strategy ◽

Intraspecific Communication ◽

Selective Sensitivity ◽

Species Specific ◽

Male Signals

A core area of speciation research concerns the coevolution of species-specific signals and the selective sensitivity to such signals. Signals and responses to them should be tuned to each other, to be effective in intraspecific communication. Hybrid zones are ideal to study the presence of such ‘behavioural coupling’ and the mechanisms governing it, and this has rarely been done. Our study examines acoustic signals of males and their response to them in the context of territorial interactions in a natural hybrid zone between two dove species, Streptopelia vinacea and Streptopelia capicola . Male signals are important in hybrid zone dynamics as they are essential for territory establishment, which is crucial for successful reproduction. We tested whether the response of individual male hybrids is linked to how similar their own signal is to the playback signal. We did not find evidence for behavioural coupling. The combined evidence from the low level of response to hybrid and heterospecific signals outside the hybrid zone and a lack of coupling within the hybrid zone suggests that perceptual learning may explain our results. Learning to respond to locally abundant signals may be the best individual strategy and is likely to contribute to the maintenance of a hybrid zone.

Download Full-text

CHROMOSOMAL REARRANGEMENTS AND THE GENETICS OF REPRODUCTIVE BARRIERS INMIMULUS(MONKEY FLOWERS)

Evolution ◽

10.1111/evo.12154 ◽

2013 ◽

Vol 67 (9) ◽

pp. 2547-2560 ◽

Cited By ~ 71

Author(s):

Lila Fishman ◽

Angela Stathos ◽

Paul M. Beardsley ◽

Charles F. Williams ◽

Jeffrey P. Hill

Keyword(s):

Chromosomal Rearrangements ◽

Reproductive Barriers

Download Full-text

Multi-ancestry genetic study in 5,876 patients identifies an association between excitotoxic genes and early outcomes after acute ischemic stroke

10.1101/2020.10.29.20222257 ◽

2020 ◽

Author(s):

Laura Ibanez ◽

Laura Heitsch ◽

Caty Carrera ◽

Fabiana H.G. Farias ◽

Rajat Dhar ◽

...

Keyword(s):

Ischemic Stroke ◽

Acute Ischemic Stroke ◽

Genetic Study ◽

Genetic Architecture ◽

Stroke Onset ◽

Neurological Deficits ◽

European Ancestry ◽

Genome Wide Association Studies ◽

Synaptic Protein ◽

Genome Wide

ABSTRACTDuring the first hours after stroke onset neurological deficits can be highly unstable: some patients rapidly improve, while others deteriorate. This early neurological instability has a major impact on long-term outcome. Here, we aimed to determine the genetic architecture of early neurological instability measured by the difference between NIH stroke scale (NIHSS) within six hours of stroke onset and NIHSS at 24h (ΔNIHSS). A total of 5,876 individuals from seven countries (Spain, Finland, Poland, United States, Costa Rica, Mexico and Korea) were studied using a multi-ancestry meta-analyses. We found that 8.7% of ΔNIHSS variance was explained by common genetic variations, and also that early neurological instability has a different genetic architecture than that of stroke risk. Seven loci (2p25.1, 2q31.2, 2q33.3, 4q34.3, 5q33.2, 6q26 and 7p21.1) were genome-wide significant and explained 2.1% of the variability suggesting that additional variants influence early change in neurological deficits. We used functional genomics and bioinformatic annotation to identify the genes driving the association from each loci. eQTL mapping and SMR indicate that ADAM23 (log Bayes Factor (LBF)=6.34) was driving the association for 2q33.3. Gene based analyses suggested that GRIA1 (LBF=5.26), which is predominantly expressed in brain, is the gene driving the association for the 5q33.2 locus. These analyses also nominated PARK2 (LBF=5.30) and ABCB5 (LBF=5.70) for the 6q26 and 7p21.1 loci. Human brain single nuclei RNA-seq indicates that the gene expression of ADAM23 and GRIA1 is enriched in neurons. ADAM23, a pre-synaptic protein, and GRIA1, a protein subunit of the AMPA receptor, are part of a synaptic protein complex that modulates neuronal excitability. These data provides the first evidence in humans that excitotoxicity may contribute to early neurological instability after acute ischemic stroke.RESEARCH INTO CONTEXTEvidence before this studyNo previous genome-wide association studies have investigated the genetic architecture of early outcomes after ischemic stroke.Added Value of this studyThis is the first study that investigated genetic influences on early outcomes after ischemic stroke using a genome-wide approach, revealing seven genome-wide significant loci. A unique aspect of this genetic study is the inclusion of all of the major ethnicities by recruiting from participants throughout the world. Most genetic studies to date have been limited to populations of European ancestry.Implications of all available evidenceThe findings provide the first evidence that genes implicating excitotoxicity contribute to human acute ischemic stroke, and demonstrates proof of principle that GWAS of acute ischemic stroke patients can reveal mechanisms involved in ischemic brain injury.

Download Full-text

ClineHelpR: an R package for genomic cline outlier detection and visualization

BMC Bioinformatics ◽

10.1186/s12859-021-04423-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Bradley T. Martin ◽

Tyler K. Chafin ◽

Marlis R. Douglas ◽

Michael E. Douglas

Keyword(s):

Management Strategies ◽

R Package ◽

Model Organisms ◽

Hybrid Zones ◽

Testing Tools ◽

File Formats ◽

Genome Wide ◽

Outlier Loci ◽

Adaptive Processes ◽

Post Hoc

Abstract Background Patterns of multi-locus differentiation (i.e., genomic clines) often extend broadly across hybrid zones and their quantification can help diagnose how species boundaries are shaped by adaptive processes, both intrinsic and extrinsic. In this sense, the transitioning of loci across admixed individuals can be contrasted as a function of the genome-wide trend, in turn allowing an expansion of clinal theory across a much wider array of biodiversity. However, computational tools that serve to interpret and consequently visualize ‘genomic clines’ are limited, and users must often write custom, relatively complex code to do so. Results Here, we introduce the ClineHelpR R-package for visualizing genomic clines and detecting outlier loci using output generated by two popular software packages, bgc and Introgress. ClineHelpR bundles both input generation (i.e., filtering datasets and creating specialized file formats) and output processing (e.g., MCMC thinning and burn-in) with functions that directly facilitate interpretation and hypothesis testing. Tools are also provided for post-hoc analyses that interface with external packages such as ENMeval and RIdeogram. Conclusions Our package increases the reproducibility and accessibility of genomic cline methods, thus allowing an expanded user base and promoting these methods as mechanisms to address diverse evolutionary questions in both model and non-model organisms. Furthermore, the ClineHelpR extended functionality can evaluate genomic clines in the context of spatial and environmental features, allowing users to explore underlying processes potentially contributing to the observed patterns and helping facilitate effective conservation management strategies.

Download Full-text

Relationship in annual spceies of Medicago. III. The complex M. littoralis Rhode-M. truncatula Gaertn

Australian Journal of Botany ◽

10.1071/bt9670035 ◽

1967 ◽

Vol 15 (1) ◽

pp. 35 ◽

Cited By ~ 9

Author(s):

JP Simon ◽

AJ Millington

Keyword(s):

Interspecific Hybrids ◽

Seed Set ◽

Chromosomal Rearrangements ◽

Chromosome Translocation ◽

Pollen Sterility ◽

Multivalent Formation ◽

Structural Differences ◽

Intraspecific Hybrids ◽

Adult Plants ◽

Cytological Behaviour

A programme of interspecific hybridization, involving species from subsections Pachyspirae, Leptospirae, and Rotatae of section Spirocarpos, resulted in only one successful combination out of the 20 attempted. Viable hybrids were obtained with ease in crosses between different accessions of M. littoralis and M. truncatula. The morphology, fertility, and cytological behaviour of interspecific hybrids involving seven strains of M. truncatula and three strains of M. littoralis was compared with intraspecific hybrids of each species. With the exception of those with N.2829, which was differentiated from the other strains by one chromosome translocation, intraspecific hybrids of M. truncatula were fully fertile. Considerable pollen sterility and reduced seed set were observed in intraspecific crosses of M. littoralis, but there was no evidence of chromosomal rearrangements. The morphology of the hybrids between M. littoralis and M. truncatula was intermediate between the parents. Chlorophyll deficiency in seedlings and adult plants, dwarfism, and other morphological irregularities were observed in F2 plants. In some FT1s failure of pairing, multivalent formation at metaphase I, and other irregularities at meiosis indicated chromosome rearrangements. Up to three independent translocations and one inversion in the hybrid combinations and pronounced sterility were observed in both FT1s and FT2s. The pollen sterility of the hybrids could be explained in several instances by structural differences, but these do not account completely for the results obtained. Inheritance studies of three possible strain markers indicated simple monohybrid segregation in most intraspecific crosses, but in the interspecific and partially fertile intraspecific crosses, ratios were disturbed and phenotypes abnormal. The agronomic implications of these studies are discussed.

Download Full-text