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opencc-zeroDec 2019View details →

Patterns, predictors, and consequence of dominance in hybrids

Compared to those of their parents, are the traits of first-generation (F1) hybrids typically intermediate, biased toward one parent, or mismatched for alternative parental phenotypes? And how does hybrid trait expression affect fitness? To address this empirical gap, we compiled data from 198 studies in which traits were measured in a common environment for two parent taxa and their F1 hybrids. We find that individual traits in F1s are, on average, halfway between the parental midpoint and one parental value (e.g., hybrid trait values are 0.75 if parents'values are 0 &1). When considering pairs of traits together, a hybrid's bivariate phenotype tends to resemble one parent (pairwise parent-bias) about 50 % more than the other while also exhibiting a similar magnitude of mismatch due to different traits having dominance in conflicting directions. We detect no phylogenetic signal nor an effect of parental genetic distance on dominance or mismatch. Using data from an experimental field planting of recombinant hybrid sunflowers, we illustrate that pairwise parent-bias improves fitness whereas pairwise mismatch reduces fitness. In sum, our study has three major conclusions. First, hybrids between ecologically divergent natural populations are not phenotypically intermediate but rather exhibit substantial mismatch while also resembling one parent more than the other. Second, dominance and mismatch do not seem to be governed by general rules but rather by the idiosyncratic evolutionary trajectories of individual traits in individual populations or species. Finally, selection against hybrids likely results from selection against both intermediate and mismatched phenotypes.

RAD-seq reveals patterns of diversification, hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees

A common pattern observed in temperate tree clades is that species are often morphologically distinct and partially interfertile but maintain species cohesion despite ongoing hybridization where ranges overlap. Although closely related species commonly occur in sympatry in tropical ecosystems, little is known about patterns of hybridization within a clade over time, and the implications of this hybridization for the maintenance of species boundaries. In this study, we focused on a clade of sympatric trees in the genus Diospyros in the Mascarene islands and investigated whether species are genetically distinct, whether they hybridize, and how patterns of hybridization are related to the time since divergence among species. We sampled multiple populations from each of 12 Mascarene Diospyros species, generated genome-wide SNP data using 2bRADseq, and conducted population genomic and phylogenomic analyses. We found that Mascarene Diospyros species diverged millions of years ago and are largely genetically distinct from one another. Although hybridization was observed between closely related species belonging to the same subclade, more distantly related species showed little evidence of interspecific hybridization. Phylogenomic analyses also suggested that introgression occurred during the evolutionary history of the clade. This suggests that, as diversification progressed, interspecific hybridization also occurred among species, but became infrequent as lineages diverged from one another and evolved reproductive barriers. Species now co-exist in partial sympatry, and experience limited hybridization between close relatives. Additional research is needed to better understand the role introgression may have played in adaptation and diversification of Mascarene Diospyros, and its relevance for conservation.

Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population

Hybridization between divergent lineages generates new allelic combinations. One mechanism that can hinder the formation of hybrid populations is mitonuclear incompatibility, i.e. dysfunctional interactions between proteins encoded on the nuclear and mitochondrial genomes (mitogenomes) of diverged lineages. Theoretically, selective pressure due to mitonuclear incompatibility can affect genotypes in a hybrid population in which nuclear genomes and mitogenomes from divergent lineages admix. To directly and thoroughly observe this key process, we de novo sequenced the 747 Mb genome of the coastal goby, Chaenogobius annularis, and investigated its integrative genomic phylogeographics using RNA‐sequencing, RAD‐sequencing, genome re‐sequencing, whole mitogenome sequencing, amplicon‐sequencing, and small RNA‐sequencing. Chaenogobius annularis populations have been geographically separated into Pacific Ocean (PO) and Sea of Japan (SJ) lineages by past isolation events around the Japanese archipelago. Despite the divergence history and potential mitonuclear incompatibility between these lineages, the mitogenomes of the PO and SJ lineages have coexisted for generations in a hybrid population on the Sanriku Coast. Our analyses revealed accumulation of nonsynonymous substitutions in the PO‐lineage mitogenomes, including two convergent substitutions, as well as signals of mitochondrial lineage‐specific selection on mitochondria‐related nuclear genes. Finally, our data implied that a microRNA gene was involved in resolving mitonuclear incompatibility. Our integrative genomic phylogeographic approach revealed that mitonuclear incompatibility can affect genome evolution in a natural hybrid population.

Agricultural intensification drives changes in hybrid network robustness by modifying network structure

Within ecological communities, species engage in myriad interaction types, yet empirical examples of hybrid species interaction networks composed of multiple types of interactions are still scarce. A key knowledge gap is understanding how the structure and stability of such hybrid networks are affected by anthropogenic disturbance. Using 15,169 interaction observations, we constructed 16 hybrid herbivore-plant-pollinator networks along an agricultural intensification gradient to explore changes in network structure and robustness to local extinctions. We found that agricultural intensification led to declines in modularity but increases in nestedness and connectance. Notably, network connectance, a structural feature typically thought to increase robustness, caused declines in hybrid network robustness, but the directionality of changes in robustness along the gradient depended on the order of local species extinctions. Our results not only demonstrate the impacts of anthropogenic disturbance on hybrid network structure, but they also provide unexpected insights into the structure-stability relationship of hybrid networks.

The complex history of genome duplication and hybridization in North American gray treefrogs

Polyploid speciation has played an important role in evolutionary history across the tree of life, yet there remain large gaps in our understanding of how polyploid species form and persist. While systematic studies have been conducted in numerous polyploid complexes, recent advances in sequencing technology have demonstrated that conclusions from data-limited studies may be spurious and misleading. The North American gray treefrog complex, consisting of the diploid Hyla chrysoscelis and the tetraploid Hyla versicolor, has long been used as a model system in a variety of biological fields, yet all taxonomic studies to date were conducted with only a few loci from nuclear and mitochondrial genomes. Here, we utilized anchored hybrid enrichment and high-throughput sequencing to capture hundreds of loci along with whole mitochondrial genomes to investigate the evolutionary history of this complex. We used several phylogenetic and population genetic methods, including coalescent simulations and testing of polyploid speciation models with Approximate Bayesian Computation (ABC), to determine that H. versicolor was most likely formed via autopolyploidization from a now extinct lineage of H. chrysoscelis. We also uncovered evidence of significant hybridization between diploids and tetraploids where they co-occur, and show that historical hybridization between these groups led to the re-formation of distinct polyploid lineages following the initial whole genome duplication event. Our study indicates that a wide variety of methods and explicit model testing of polyploid histories can greatly facilitate efforts to uncover the evolutionary history of polyploid complexes.

opennotspecifiedDec 2020View details →

FIGURE 1. A–B in First record of hybridization in Caranx Lacepède, 1801 (Carangidae: Perciformes) in the Tropical Eastern Pacific Ocean

FIGURE 1. A–B. Specimen of C. melampygus x C. sexfasciatus, 576 mm SL (UCR 3209-001), captured at Isla Montuosa, Pacific coast of Panama (7.467472, -82.266556; 30 m depth). (A) Fresh and (B) after preservation. C–D. Preserved specimens, representatives of the parental species: (C) C. melampygus (UCR 0423-027, 153 mm SL) and (D) C. sexfasciatus (UCR 3112- 003, 122 mm SL). Scale bar=50 mm.

opennotspecifiedDec 2020View details →

FIGURE 2 in First record of hybridization in Caranx Lacepède, 1801 (Carangidae: Perciformes) in the Tropical Eastern Pacific Ocean

FIGURE 2. Consensus tree of selected members of Caranx. Topology inferred combining the information of five different models: Neighbor-Joining (NJ), Bayesian Inference (BI), Maximum-Likelihood (ML), Minimum Evolution (ME) and Maximum Parsimony (MP) for a total of 19 (626-bp) COX1 sequences. Numbers at nodes represent support values in percentage (posterior probability for BI) for each one of the five models, respectively. The tree is rooted with Nematistius pectoralis.

opencc-zeroDec 2020View details →

Data from: Hybridization patterns between two marine snails, Littorina fabalis and L. obtusata

Characterizing the patterns of hybridization between closely related species is crucial to understand the role of gene flow in speciation. In particular, systems comprising multiple contacts between sister species offer an outstanding opportunity to investigate how reproductive isolation varies with environmental conditions, demography and geographic contexts of divergence. The flat periwinkles, Littorina obtusata and L. fabalis (Gastropoda), are two intertidal sister species with marked ecological differences compatible with late stages of speciation. Although hybridization between the two was previously suggested, its extent across the Atlantic shores of Europe remained largely unknown. Here, we combined genetic (microsatellites and mtDNA) and morphological data (shell and male genital morphology) from multiple populations of flat periwinkles in north-western Iberia to assess the extent of current and past hybridization between L. obtusata and L. fabalis under two contrasting geographic settings of divergence (sympatry and allopatry). Hybridization signatures based on both mtDNA and microsatellites were stronger in sympatric sites, although evidence for recent extensive admixture was found in a single location. Misidentification of individuals into species based on shell morphology was higher in sympatric than in allopatric sites. However, despite hybridization, species distinctiveness based on this phenotypic trait together with male genital morphology remained relatively high. The observed variation in the extent of hybridization among locations provides a rare opportunity for future studies on the consequences of different levels of gene flow for reinforcement, thus informing about the mechanisms underlying the completion of speciation.

opencc-zeroDec 2020View details →

Genomic variation data for the wagtail hybrid zone

Genome-wide variation in introgression rates across hybrid zones offers a powerful opportunity for studying population differentiation. One poorly understood pattern of introgression is the geographic displacement of a trait implicated in lineage divergence from genome-wide population boundaries. While difficult to interpret, this pattern can facilitate the dissection of trait genetic architecture because traits become uncoupled from their ancestral genomic background. We studied an example of trait displacement generated by the introgression of head plumage coloration from personata to alba subspecies of the white wagtail. A previous study of the wagtail hybrid zone in Siberia revealed that the geographic transition in this sexual signal that mediates assortative mating was offset from other traits and genetic markers. We show that head plumage is associated with two small genetic regions. Despite having a simple genetic architecture, head plumage inheritance is consistent with partial dominance and epistasis, which could contribute to its asymmetric introgression.

opencc-by-4.0Dec 2020View details →

Large flux-mediated coupling in hybrid electromechanical system with a transmon qubit

The dataset contains the script and measured data to reproduce the figures shown in the publication titled "Large flux-mediated coupling in hybrid electromechanical system with a transmon qubit" written by Tanmoy Bera, Sourav Majumder, Sudhir Kumar Sahu and Vibhor Singh

opencc-zeroDec 2020View details →

Extensive hybridization reveals multiple coloration genes underlying a complex plumage phenotype

Coloration is an important target of both natural and sexual selection. Discovering the genetic basis of colour differences can help us to understand how this visually striking phenotype evolves. Hybridizing taxa with both clear colour differences and shallow genomic divergences are unusually tractable for associating coloration phenotypes with their causal genotypes. Here, we leverage the extensive admixture between two common North American woodpeckers—yellow-shafted and red-shafted flickers—to identify the genomic bases of six distinct plumage patches involving both melanin and carotenoid pigments. Comparisons between flickers across ~7.25 million genome-wide SNPs show that these two forms differ at only a small proportion of the genome (mean FST = 0.008). Within the few highly differentiated genomic regions, we identify 368 SNPs significantly associated with four of the six plumage patches. These SNPs are linked to multiple genes known to be involved in melanin and carotenoid pigmentation. For example, a gene (CYP2J19) known to cause yellow to red colour transitions in other birds is strongly associated with the yellow versus red differences in the wings and tail feathers of these flickers. Additionally, our analyses suggest novel links between known melanin genes and carotenoid coloration. Our finding of patch-specific control of plumage coloration adds to the growing body of literature suggesting colour diversity in animals could be created through selection acting on novel combinations of coloration genes.

opencc-zeroJan 2021View details →

VCF data file and code for: CYP2J19 mediates carotenoid colour introgression across a natural avian hybrid zone

It has long been of interest to identify the phenotypic traits that mediate reproductive isolation between related species, and more recently, the genes that underpin them. Much work has focused on identifying genes associated with animal colour, with the candidate gene CYP2J19 identified in laboratory studies as the ketolase converting yellow dietary carotenoids to red ketocarotenoids in birds with red pigments. But evidence that CYP2J19 explains variation between red and yellow feather coloration in wild populations of birds is lacking. Hybrid zones provide the opportunity to identify genes associated with specific traits. Here we investigate genomic regions associated with colour in red-fronted and yellow-fronted tinkerbirds across a hybrid zone in southern Africa. We sampled 85 individuals, measuring spectral reflectance of forecrown feathers and scoring colours from photographs, while testing for carotenoid presence with Raman spectroscopy. We performed a genome-wide association study to identify associations with carotenoid-based coloration, using double-digest RAD sequencing aligned to a short-read whole genome of a Pogoniulus tinkerbird. Admixture mapping using 104,933 SNPs identified a region of chromosome 8 that includes CYP2J19 as the only locus with more than two SNPs significantly associated with both crown hue and crown score, while Raman spectra provided evidence of ketocarotenoids in red feathers. Asymmetric backcrossing in the hybrid zone suggests that yellow-fronted females mate more often with red-fronted males than vice versa. Female red-fronted tinkerbirds mating assortatively with red-crowned males is consistent with the hypothesis that converted carotenoids are an honest signal of quality.

Figure 5 in Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species

Figure 5. Cline analyses of mitochondrial DNA and microsatellite data. Transects (top) through the two different contact zones of grass snake lineages (helvetica/eastern lineages – left; yellow/red lineages – right) and associated Maximum Likelihood clines for microsatellites (centre) and mtDNA (bottom). Grey: fuzzy 95% credible cline region. Red points (top) indicate cline centres. Maps were created using ARCGIS 10.2 (http://www. esri.com/arcgis) and ADOBE ILLUSTRATOR CS6 (http://www.adobe.com/products/illustrator.html).

Figure 4. PCA axes 1–2 in Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species

Figure 4. PCA axes 1–2 for microsatellite data. Samples are coloured according to mitochondrial lineages (top) or STRUCTURE clusters (bottom). Admixed individuals were identified according to HYBRIDLAB results. PCAs for the yellow and red lineages correspond to the samples from Fig. 3c. Non-native samples were excluded. The oval outlines represent 95% confidential intervals. For helvetica and the eastern lineages (left) the x axis explains 16.6% and the y axis 4.5% of variation. For the eastern lineages (right) the x axis explains 3.8% and the y axis 2.9% of variation. Analyses along axes 1–3 produced nearly identical results (see Supplementary Fig. S4).

Figure 3 in Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species

Figure 3. Genotypic structuring of grass snakes. On the left, the mitochondrial lineage of each sample is shown above the STRUCTURE diagrams, with haplotypes of Natrix natrix helvetica indicated in blue and haplotypes of the eastern lineages in colours corresponding to Fig. 1 (yellow, red, lilac, grey, green; white = missing data). In (a), orange and dark blue corresponds to non-native snakes (Italian lineages). Samples in STRUCTURE diagrams are arranged within each country from west to east (a) or from north to south (b,c). In STRUCTURE diagrams, an individual sample is represented by a vertical bar reflecting its inferred ancestry. In (a), the blue cluster corresponds to N. n. helvetica and the light green cluster to all other lineages. The isolated red/light green block (first row) represents the allochthonous population from the Neander valley, Germany. In (b), samples with genetic impact of helvetica are excluded. The pink cluster corresponds to samples from the yellow and red lineages. Brown percentages indicate genetic impact of adjacent lineages (lilac, grey, green). In (c) only samples from the yellow and red lineages and their hybrids, without genetic signatures of other lineages, were processed. Country abbreviations: Ba – Balkans (Albania, Bosnia and Herzegovina, Montenegro, Serbia, Kosovo, Former Yugoslav Republic of Macedonia, Romania, Bulgaria, and Greece), CH – Switzerland, CRO – Croatia, CZ – Czech Republic, FI – Finland, H – Hungary, N – Norway, NL – Netherlands, PL – Poland, S – Sweden. Maps were created using ARCGIS 10.2 (http://www.esri.com/arcgis) and ADOBE ILLUSTRATOR CS6 (http://www.adobe. com/products/ illustrator.html).

Figure 1 in Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species

Figure 1. Distribution of mitochondrial lineages of 1,580 grass snakes used in this study. Total sample size of each clade shown in the legend. Eight allochthonous grass snakes with haplotypes of Italian lineages caught in southern Great Britain and Hesse, Germany, not shown. Map was created using ARCGIS 10.2 (http://www.esri. com/arcgis) and ADOBE ILLUSTRATOR CS6 (http://www.adobe.com/products/illustrator.html). Inset: Natrix natrix helvetica (Linz am Rhein, Germany); photo: Wolfgang Böhme.

Figure 2 in Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species

Figure 2. Parsimony networks of mtDNA sequences. Symbol sizes reflect haplotype frequencies. Small black circles are missing node haplotypes; each line connecting two haplotypes corresponds to one mutation step, if not otherwise indicated by numbers. Haplotype colours correspond to lineages, i.e. Natrix natrix helvetica (h) in blue; eastern lineages in yellow (y) and in red (r).

opencc-by-4.0Jan 2021View details →

Nanoscale Phase Segregation in Supramolecular π‑Templating for Hybrid Perovskite Photovoltaics from NMR Crystallography

Raw and processed NMR data, molecular dynamics data, structure files, photovoltaic data, and additional characterisation data for Nanoscale Phase Segregation in Supramolecular π‑Templating for Hybrid Perovskite Photovoltaics from NMR Crystallography, DOI: 10.1021/jacs.0c11563. For more details see README file.  NMR_data.zip: Raw and processed NMR data in the file structure of the TopSpin software, which is available from Bruker.  NMR_calculations.zip: The input and output Quantum Espresso files are given for both the single point (*.scf.in and *.scf.out) and NMR calculations (*.nmr.in and *.nmr.out). cif_files_all_structures.zip: All structures in cif format.  MD_*.zip: MD trajectories of (PEA)2PbI4, (FEA)2PbI4 and configuration 1 of (PF)2PbI4. The full trajectories are given in dcd format which can be opened using the VMD software. The trajectories are also shown as movies.  PV+characterisation.zip: The data for the photovoltaic analysis, XPS spectra and XRD patterns in Excel format.

opencc-zeroOct 2019View details →

Data from: Interspecific hybridization can generate functional novelty in cichlid fish

The role of interspecific hybridization in evolution is still being debated. Interspecific hybridization has on the one hand been suggested to facilitate the evolution of ecological novelty and hence the invasion of new niches and adaptive radiation when ecological opportunity is present beyond the parental species niches. On the other hand, hybrids between two ecologically divergent species may perform less well than parental species in their respective niches because hybrids would be intermediate in performance in both niches. The evolutionary consequences of hybridization may hence be context-dependent, depending on whether additional ecological opportunities do or do not exist. Surprisingly, these complementary predictions may never have been tested in the same experiment in animals. To do so, we investigate if hybrids between ecologically distinct cichlid species perform less well than the parental types when feeding on food either parental species are adapted to, and if the same hybrids perform better compared to their parents when feeding on food none of the species are adapted to. We generated two first-generation experimental hybrid crosses between species of African cichlids. In feeding efficiency experiments we measure the performance of hybrids and parental species on food types representing both parental species niches and additional 'novel' niches, not utilized by part of the parental species but by other species in the African cichlid radiations. We found that hybrids can have higher feeding efficiencies on the 'novel' food types but typically have lower efficiencies on parental food types when compared to parental species. This suggests that hybridization can generate functional variation that can be of ecological relevance allowing the access to resources outside of either parental species niche. Hence, we provide support for the hypothesis of ecological context-dependency of the evolutionary impact of interspecific hybridization.