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opencc-zeroJul 2020View details →

Data from: Pollination and fruit set in two rewardless slipper orchids and their hybrids (Cypripedium, Orchidaceae): large yellow flowers outperform small white flowers in the northern tall grass prairie

• Species with rewardless flowers often have low fruit to flower ratios, although wide temporal and spatial variation in fruiting success can occur. We compared floral phenotypes, insect visitors, and fruiting success in four populations of the small white (Cypripedium candidum) and yellow lady's slipper orchids (C. parviflorum) and their hybrids near the northern extent of North America's tall grass prairie. • Flower and fruit numbers were observed for two seasons on marked individuals (n = 1811). Floral traits were measured on 82-140 individuals per taxon, and analyzed in relation to fruiting success. All insects found inside flowers were collected, inspected for pollen smears, and measured for comparison to floral features. • Among orchid taxa, C. candidum had the smallest flowers, lowest number and variety of insect visitors, and lowest fruit to flower ratios. These measures were intermediate in hybrids and highest in C. parviflorum, despite low flower numbers in the latter. Within orchid taxa, fruit number was positively related to flower number, but fruit to flower ratios decreased slightly, as would be expected if pollinators left unrewarding patches. Potential pollinators included the dipteran Odontomyia pubescens and hymenopterans Andrena spp., Apis mellifera, and Lasioglossum zonulum. • Cypripedium parviflorum had a reproductive advantage over C. candidum across multiple populations and years. Hybrids showed segregation for floral traits, and hybrid fruiting success increased with a deeper intensity of yellow pigment and larger escape routes for floral visitors. These same attributes likely contributed to the relatively high fruit set in C. parviflorum in the study region.

opencc-zeroJun 2020View details →

Data from: Sperm quality, aggressiveness and generation turnover can facilitate unidirectional Y chromosome introgression across the European house mouse hybrid zone

The widespread and locally massive introgression of Y chromosomes of the eastern house mouse (Mus musculus musculus) into the range of the western subspecies (M. m. domesticus) in Central Europe calls for an explanation of its underlying mechanisms. Given the paternal inheritance pattern, obvious candidates for traits mediating the introgression are characters associated with sperm quantity and quality. We can also expect traits such as size, aggression, or the length of generation cycles to facilitate the spread. We have created two consomic strains carrying the non-recombining region of the Y chromosome of the opposite subspecies, allowing us to study introgression in both directions, something impossible in nature due to the unidirectionality of introgression. We analysed several traits potentially related to male fitness. Transmission of the domesticus Y onto the musculus background had negative effects on all studied traits. Likewise , domesticus males possessing the musculus Y had, on average, smaller body and testes and lower sperm count than the parental strain. However, the same consomic males tended to produce less dissociated sperm heads, to win more dyadic encounters, and to have shorter generation cycles than pure domesticus males. These data suggest the domesticus Y is disadvantageous on the musculus background while introgression in the opposite direction can confer a recognizable, though not always significant, selective advantage. Our results are thus congruent with the unidirectional musculus→domesticus Y chromosome introgression in Central Europe. In addition to some previous studies, they show this to be a multifaceted phenomenon demanding a multidisciplinary approach.

opencc-zeroJun 2020View details →

Novel hybrid finds a peri-urban niche: Allen's Hummingbirds in southern California

Species range expansions and contractions can have ecological and genetic consequences, and thus are important areas of study for conservation. Hybridization and introgression are not uncommon in closely related populations that experience secondary contact during a range expansion. Allen's Hummingbird (Selasphorus sasin) in California comprises two subspecies: the migratory S. s. sasin, which winters in central Mexico and breeds in central and northern California, and the resident S. s. sedentarius, which lives and breeds year-round on several of the Channel Islands off the California coast. Within recent decades, Allen's Hummingbirds have been found living and breeding year-round in the southern California peri-urban mainland near Los Angeles. Ornithologists assumed that the L.A. birds were an expansion of the island subspecies, S. s. sedentarius due to similar but very subtle morphological characteristics. However, the genetic relationships among the three putative populations of Allen's hummingbird—migratory, southern California mainland, and island—are unknown. We investigated these relationships by analyzing variation of single nucleotide polymorphisms from the three geographic regions where S. sasin are present. Our population genomic analyses indicate that S. sasin hummingbirds inhabiting mainland southern California are a hybrid population resulting from admixture between S. s. sasin and S. s. sedentarius. From one perspective, these results may be interpreted as a positive development for S. s. sasin as the growing population represent an overall increase in the S. sasin population, and the expanding population contains a significant representation of S. s. sasin alleles.

opencc-zeroJun 2020View details →

Hidden hybridization and habitat differentiation ina Mediterranean macrophyte, the euryhaline genus Ruppia

In many aquatic plant taxa, classification and identification based on morphology has always been difficult. Molecular markers revealed that the complexity in several of these aquatic taxa could be addressed to recurrent hybridization events and cryptic species diversity. The submerged macrophyte genus Ruppia is one of these aquatic genera with a complex taxonomy due to the absence of clear distinguishable traits and several hybridization events. Two species co-exist throughout Europe, R. maritima and R. spiralis (previously known as R. cirrhosa), but recent molecular studies also found several indications of hybridization, introgression and chloroplast capture between these species. However, the full extent and frequency of hybridization and introgression in this genus has not been studied so far, nor is it clear how these hybrid lineages can co-exist locally with their parental species. In this paper, we wanted to detect whether a single coastal wetland where both species co-exist can act as a Ruppia hybrid zone. As a case study, we chose the Camargue, a Mediterranean coastal wetland that harbours a wide diversity in aquatic habitats, especially in terms of salinity and hydro regime. We sampled several Ruppia populations within this wetland. To identify each sample and reconstruct the local genetic structure of the two parental species and their hybrids, we used both chloroplast and nuclear microsatellite markers. Afterwards, we tested whether different species had different habitat preferences. Our results confirmed that R. maritima and R. spiralis are two strongly divergent species with different reproductive ecologies and different habitat preferences. This prevents frequent hybridization and consequently we could not detect any trace of a recent hybridization event. However, we found several populations of later-generation hybrids, including a population of R. maritima x hybrid backcrosses. These hybrid populations occupy a different habitat and are genetically distinct from their parental species, although they tend to be morphological similar to parental R. maritima. Although hybridization and introgression in Ruppia is less frequent than we expected, the taxonomy of Ruppia is complicated due to ancient hybridizations and several back-crossings.

opencc-by-4.0Jul 2020View details →

PTP dataset of "Narrowband magnetosonic waves near the lower hybrid resonance frequency in the inner magnetosphere: Wave properties and excitation conditions"

PTP dateset of "Narrowband magnetosonic waves near the lower hybrid resonance frequency in the inner magnetosphere: Wave properties and excitation conditions", including the data of Plasmapause Test Particle (PTP) Simulation to identify the plasmapause location with a time resolution of 15 min.

opennotspecifiedMay 2020View details →

FIGURE 6 in Record of the Non-native Suckermouth armored catfish hybrid Pterygoplichthys pardalis (Castelnau,1985) x Pterygoplichtys disjunctivus (Weber, 1991) (Siluriformes: Loricariidae) in Honduras

FIGURE 6. Eggs found in female Pterygoplichthys pardalis x disjunctivus Specimen MUVS-204. A. Eggs measuring 2 mm B. Eggs Measuring 3 mm.

opennotspecifiedMay 2020View details →

FIGURE 2 in Record of the Non-native Suckermouth armored catfish hybrid Pterygoplichthys pardalis (Castelnau,1985) x Pterygoplichtys disjunctivus (Weber, 1991) (Siluriformes: Loricariidae) in Honduras

FIGURE 2. Map detailing sample localities for specimens of Pterygoplichthys pardalis x disjunctivus: A) Lake Yojoa B) Jucutuma lagoon.

opennotspecifiedMay 2020View details →

FIGURE 4 in Record of the Non-native Suckermouth armored catfish hybrid Pterygoplichthys pardalis (Castelnau,1985) x Pterygoplichtys disjunctivus (Weber, 1991) (Siluriformes: Loricariidae) in Honduras

FIGURE 4. Variations in ventral spots of the three specimens of hybrid Pterygoplichthys pardalis x disjunctivus captured in the Yojoa Lake, Honduras and Jucutuma Lagoon, 2018: A) MUVS-203 intermediate forms in ventral vermiculations, B) MUVS-204 with intermediate ventral spots C) La Naturaleza Tank specimen with intermediate ventral vermiculations and spots.

Data from: Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks

Inferring the frequency and mode of hybridization among closely related organisms is an important step for understanding the process of speciation and can help to uncover reticulated patterns of phylogeny more generally. Phylogenomic methods to test for the presence of hybridization come in many varieties and typically operate by leveraging expected patterns of genealogical discordance in the absence of hybridization. An important assumption made by these tests is that the data (genes or SNPs) are independent given the species tree. However, when the data are closely linked, it is especially important to consider their non-independence. Recently, deep learning techniques such as convolutional neural networks (CNNs) have been used to perform population genetic inferences with linked SNPs coded as binary images. Here we use CNNs for selecting among candidate hybridization scenarios using the tree topology (((P1,P2),P3),Out) and a matrix of pairwise nucleotide divergence (dXY) calculated in windows across the genome. Using coalescent simulations to train and independently test a neural network showed that our method, HyDe-CNN, was able to accurately perform model selection for hybridization scenarios across a wide-breath of parameter space. We then used HyDe-CNN to test models of admixture in Heliconius butterflies, as well as comparing it to a random forest classifier trained on introgression-based statistics. Given the flexibility of our approach, the dropping cost of long-read sequencing, and the continued improvement of CNN architectures, we anticipate that inferences of hybridization using deep learning methods like ours will help researchers to better understand patterns of admixture in their study organisms.

Data from: Evolutionary networks from RADseq loci point to hybrid origins of Medicago carstiensis and Medicago cretacea

Premise: Although hybridization has played an important role in the evolution of many plant species, phylogenetic reconstructions that include hybridizing lineages have been historically constrained by the available models and data. RADseq has been a popular sequencing technique for the reconstruction of hybridization in the Next Generation Sequencing era. However, the utility of RADseq for the reconstruction of complex evolutionary networks has not been thoroughly investigated. Conflicting phylogenetic relationships in the genus Medicago have been mainly attributed to hybridization but the specific hybrid origins of taxa have not been yet clarified. Methods: We obtained new molecular data from diploid species of Medicago section Medicago using single-digest RADseq to reconstruct evolutionary networks from gene trees, an approach that is computationally tractable with datasets that include several species and complex hybridization patterns. Results: Our analyses revealed that assembly filters to exclusively select a small set of loci with high phylogenetic information led to the most divergent network topologies. Conversely, alternative clustering thresholds or filters on the number of samples per locus had a lower impact on networks. A strong hybridization signal was detected for M. carstiensis and M. cretacea, while less clear signals were observed for M. rugosa, M. rhodopea, M. suffruticosa, M. marina, M. scutellata and M. sativa. Conclusions: Complex network reconstructions from RADseq gene trees were not robust under variations of the assembly parameters and filters. But when most divergent networks were discarded, all remaining analyses consistently supported a hybrid origin for M. carstiensis and M. cretacea.

Maladaptive migration behaviour in hybrids links to predator-mediated ecological selection

1. Different migratory species have evolved distinct migratory characteristics that improve fitness in their particular ecological niches. However, when such species hybridize, migratory traits from parental species can combine maladaptively and cause hybrids to fall between parental fitness peaks, with potential consequences for hybrid viability and species integrity. 2. Here, we take advantage of a natural cross-breeding incident to study migratory behaviour in naturally occurring hybrids as well as in their parental species and explore links between migratory traits and predation risk. 3. To achieve this, we used electronic tags and passive telemetry to record detailed individual migration patterns (timing and number of migratory trips) in two common freshwater fish species, roach (Rutilus rutilus), common bream (Abramis brama) as well as their hybrids. Next, we scanned for tags regurgitated by a key avian predator (great cormorant, Phalacrocorax carbo) at nearby roosting sites, allowing us to directly link migratory behaviour to predation risk in the wild. 4. We found that hybrid individuals showed a higher number of short, multi-trip movements between lake and stream habitats as compared to both parental species. The mean date of first lake departure differed between bream and roach by more than 10 days, while hybrids departed in two distinct peaks that overlapped with the parental species' averages. Moreover, the probability of cormorant predation increased with multi-trip movement frequency across species and was higher for hybrids. 5. Our data provide novel insights into hybrid viability, with links to predator-mediated ecological selection. Increased exposure to predators via maladaptive migratory behaviour reduces hybrid survival and can thereby reinforce species integrity.

Data from: Rapid generation of ecologically relevant behavioural novelty in experimental cichlid hybrids

The East African cichlid radiations are characterised by repeated and rapid diversification into many distinct species with different ecological specialisations and by a history of hybridization events between non-sister species. Such hybridization might provide important fuel for adaptive radiation. Interspecific hybrids can have extreme trait values or novel trait combinations and such transgressive phenotypes may allow some hybrids to explore ecological niches neither of the parental species could tap into. Here, we investigate the potential of second-generation (F2) hybrids between two generalist cichlid species from Lake Malawi to exploit a resource neither parental species is specialised on: feeding by sifting sand. Some of the F2 hybrids phenotypically resembled fish of species that are specialised on sand sifting. We combined experimental behavioural and morphometric approaches to test whether the F2 hybrids are transgressive in both morphology and behaviour related to sand sifting. We then performed a quantitative trait loci (QTL) analysis using RADseq markers to investigate the genetic architecture of morphological and behavioural traits. We show that transgression is present in several morphological traits, that novel trait combinations occur, and we observe transgressive trait values in sand sifting behaviour in some of the F2 hybrids. Moreover, we find QTLs for morphology and for sand sifting behaviour, suggesting the existence of some loci with moderate to large effects. We demonstrate that hybridization has the potential to rapidly generate novel and ecologically relevant phenotypes that may be suited to a niche neither of the parental species occupies. Interspecific hybridization may thereby contribute to the rapid generation of ecological diversity in cichlid radiations.

Data for: Angels in disguise: Sympatric hybridization in the marine angelfishes is widespread and occurs between deeply divergent lineages

Hybridization is not uncommon in marine environments where physical barriers are attenuated. Research conducted on hybridization in coral reefs has grown rapidly, but the majority of studies have focused on parapatric species along biogeographical suture zones. Comparatively little attention has been directed towards sympatric hybridization on coral reefs, despite the large amount of biogeographical overlap that occurs among coral reef species. Here we investigate if the propensity for hybridization along suture zones represents a general phenomenon among coral reef fishes, by focusing on the marine angelfishes (Pomacanthidae). Although hybridization has been reported for this family, it has not been thoroughly surveyed, with more recent hybridization studies focusing instead on closely related species from a population genetics perspective. Here we provide a comprehensive survey of hybridization among the angelfishes, characterize the upper limits of genetic divergences between hybridizing species, and investigate the occurrence of sympatric hybridization within this group. Our results indicate that the marine angelfishes are among the groups of coral reef fishes with the highest incidences of hybridization, not only between sympatric species, but also between deeply divergent, sympatric lineages.

Riverscape properties contribute to the origin and structure of a hybrid zone in a Neotropical freshwater fish

Understanding the structure of hybrid zones provides valuable insights about species boundaries and speciation, such as the evolution of barriers to gene flow and the strength of selection. In river networks, studying evolutionary processes in hybrid zones can be especially challenging, given the influence of past and current river properties along with biological species-specific traits. Here, we suggest that a natural hybrid zone between two divergent lineages of the sexually dimorphic Neotropical fish Nematocharax venustus was probably established by secondary contact as a result of a river capture event between the Contas and Pardo river basins. This putative river capture is supported by hydrogeological evidence of elbows of capture, wind gaps, and geological faults. The morphological (color pattern) and genetic (mtDNA and RADseq) variation reveal a clinal transition between parental lineages along the main river, with predominance of F2 hybrids at the centre of the hybrid zone, absence of early generation backcrosses, and different levels of hybridization in the tributaries. We highlight that different sources of information are crucial for understanding how the riverscape spatial history influences the connectivity between and within rivers systems and, consequently, the dynamics of gene flow between freshwater lineages/species.

Data from: RADseq resolves the Hawaiian Island radiation of Myrsine L. (Primulaceae) and provides evidence for hybridization

The Hawaiian radiation of Myrsine (primrose family, Primulaceae) is the only one of the ten most species Hawaiian plant lineages that has never been included in a phylogenetic analysis. Our study is based on a RADseq dataset of nearly all Hawaiian Myrsine species and a Sanger sequencing dataset based on a worldwide sampling of Myrsine and related genera. Myrsine as a whole might be paraphyletic with respect to the monotypic Macaronesian genera Heberdenia and Pleiomeris, while Hawaiian Myrsine is resolved as monophyletic. Hawaiian Myrsine consists of three main lineages of which one contains the majority of species and is mainly confined to Kauaʻi, while the other two lineages primarily consist of few widespread species. While phylogenetic reconstructions delivered fully resolved and supported tree topologies, Quartet Sampling and HyDe analyses reveal phylogenetic incongruence throughout the phylogeny and provide the first molecular evidence of extensive hybridization in the lineage.

opencc-by-4.0Aug 2020View details →

113Cd Solid-State NMR at 21.1 T Reveals the Local Structure and Passivation Mechanism of Cadmium in Hybrid and All-Inorganic Halide Perovskites

Raw NMR data in Bruker Topspin format. Input and output files of the quantum mechanical calculations.

opencc-zeroSep 2020View details →

Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species - Data supporting published version

<a name="_Hlk503794553">Invasive freshwater fish systems are known to readily hybridize with indigenous congeneric species, driving loss of unique and irreplaceable genetic resources. Here we reveal that newly discovered (2013-2016) evolutionarily significant populations of Korogwe tilapia (Oreochromis korogwe) from southern Tanzania are threatened by hybridization with the larger invasive Nile tilapia (Oreochromis niloticus). We use a combination of morphology, microsatellite allele frequencies and whole genome sequences to show that O. korogwe from southern lakes (Nambawala, Rutamba and Mitupa) are distinct from geographically-disjunct populations in northern Tanzania (Zigi River and Mlingano Dam). We also provide genetic evidence of O. korogwe x niloticus hybrids in three southern lakes and </a>demonstrate heterogeneity in the extent of admixture across the genome. Finally, using the least admixed genomic regions we estimate that the northern and southern O. korogwe populations most plausibly diverged approximately 140,000 years ago, suggesting that the geographical separation of the northern and southern groups is not a result of a recent translocation, and instead these populations represent independent evolutionarily significant units. We conclude that these newly-discovered and phenotypically unique cichlid populations are already threatened by hybridization with an invasive species, and propose that these irreplaceable genetic resources would benefit from conservation interventions.

opencc-zeroSep 2020View details →

How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels

The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study "replicated" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.

opencc-zeroSep 2020View details →

The evolution of sex is tempered by costly hybridization in Boechera (rock cress)

Despite decades of research, the evolution of sex remains an enigma in evolutionary biology. Typically, research addresses the costs of sex and asexuality to characterize the circumstances favoring one reproductive mode. Surprisingly few studies address the influence of common traits that are, in many organisms, obligately correlated with asexuality, including hybridization and polyploidy. These traits have substantial impacts on traits under selection. In particular, the fitness consequences of hybridization (that is, reduced fitness due to interspecific reproductive isolation) will influence the evolution of sex. This may comprise a cost of either sex or asexuality, due to the link between hybridity and asexuality. We examined reproductive isolation in the formation of de novo hybrid lineages between two widespread species in the ecological model system Boechera. 17% of 664 crosses produced F1 fruits, and only 10% of these were viable, suggesting that postmating prezygotic and postzygotic barriers inhibit hybrid success in this system. The postmating prezygotic barrier was asymmetrical, with 110 of 115 total F1 fruits produced when B. stricta acted as maternal parent. This asymmetry was confirmed in wild-collected lineages, using a chloroplast phylogeny of wild-collected B. stricta, B. retrofracta, and hybrids. We next compared fitness of F2 hybrids and selfed parental B. stricta lines, finding that F2 fitness was reduced by substantial hybrid sterility. Multiple reproductively isolating barriers likely influence the formation and fitness of hybrid lineages in the wild, and the costs of hybridization likely have profound impacts on the evolution of sex in the natural environment.