Genome sequence for the blue-flowered Andean shrub Iochroma cyaneum reveals extensive discordance across the berry clade of Solanaceae

The tomato family, Solanaceae, is a model clade for a wide range of applied and basic research questions. Currently, reference-quality genomes are available for over 30 species from seven genera, and these include numerous crops as well as wild species (e.g., Jaltomata sinuosa and Nicotiana attenuata). Here we present the genome of the showy-flowered Andean shrub Iochroma cyaneum, a woody lineage from the tomatillo subfamily Physalideae. The assembled size of the genome (2.7Gb) is more similar in size to chilipepper (2.6Gb) than to other sequenced diploid members of the berry clade of Solanaceae (e.g., potato, tomato, and Jaltomata). Our assembly recovers 92% of the conserved orthologous set, suggesting a nearly complete genome for this species. Most of the genomic content is repetitive (69%), with gyspy elements alone accounting for 52% of the genome. Despite the large amount of repetitive content, most of the 12 Iochroma chromosomes are highly syntenic with tomato. Bayesian concordance analysis provides strong support for the berry clade, including Iochroma, but reveals extensive discordance along the backbone, with placement of pepper and Jaltomata being highly variable across gene trees. The Iochroma genome contributes to a growing wealth of genomic resources in Solanaceae and underscores the need for expanded sampling of diverse berry genomes to dissect major morphological transitions.

Acoustic and postural displays in a miniature and transparent teleost fish, Danionella dracula

Individuals can reveal their relative competitive ability or mate quality through acoustic communication, varying signals in form and frequency to mediate adaptive interactions including competitive aggression. We report robust acoustic displays during aggressive interactions for a laboratory colony of Danionella dracula, a recently discovered miniature and transparent species of teleost fish closely related to zebrafish (Danio rerio). Males produce bursts of pulsatile, click-like sounds and a distinct postural display, extension of a hypertrophied lower jaw, during resident-intruder dyad interactions. Females lack a hypertrophied lower jaw and show no evidence of sound production or jaw extension under such conditions. Novel pairs of size-matched or mismatched males were combined in resident-intruder assays where sound production and jaw extension could be linked to individuals. Resident males produce significantly more sound pulses than intruders in both dyad contexts; larger males are consistently more sonic in size-mismatched pairs. For both conditions, males show a similar pattern of increased jaw extension that frequently coincided with acoustic displays during periods of heightened sonic activity. These studies firmly establish D. dracula as a sound-producing species that modulates both acoustic and postural displays during social interactions based on either residency or body size, thus providing a foundation for investigating the role of these displays in a new model clade for neurogenomic studies of aggression, courtship and other social interactions.

Hybridization and introgression in sympatric and allopatric populations of four oak species

Background Hybridization and introgression are vital sources of novel genetic variation driving diversification during reticulated evolution. Quercus is an important model clade, having extraordinary diverse and abundant members in the Northern hemisphere, that are used to studying the introgression of species boundaries and adaptive processes. China is the second-largest distribution center of Quercus, but there are limited studies on introgressive hybridization. Results Here, we screened 17 co-dominant nuclear microsatellite markers to investigate the hybridization and introgression of four oaks (Quercus acutissima, Quercus variabilis, Quercus fabri, and Quercus serrata) in 10 populations. We identified 361 alleles in the four-oak species across 17 loci, and all loci were characterized by high genetic variability (HE = 0.844–0.944) and moderate differentiation (FST = 0.037–0.156) levels. A population differentiation analysis revealed the following: allopatric homologous (FST = 0.064) < sympatric heterogeneous (FST = 0.071) < allopatric heterogeneous (FST = 0.084). A Bayesian admixture analysis determined four types of hybrids (Q. acutissima × Q. variabilis, Q. fabri × Q. serrata, Q. acutissima × Q. fabri, and Q. acutissima × Q. variabilis × Q. fabri) and their asymmetric introgression. Our results revealed that interspecific hybridization is commonly observed within the section Quercus, with members having tendency to hybridize. Conclusions Our study determined the basic hybridization and introgression states among the studied four oak species and extended our understanding of the evolutionary role of hybridization. The results provide useful theoretical data for formulating conservation strategies.

Species delimitation in the genus Quercus (Fagaceae)

Background: Quercus is recognized as a taxonomically complex genus, but also as a model clade in many important fields in biology, such that a good recognition of its species is necessary. The chosen species concept to use in Quercus will determine the empirical criteria used to recognize them, which will impact several areas of knowledge. Questions: What are the main sources of variation that hinder the delimitation of species in Quercus? What species concepts we use explicitly to recognize species in Quercus? What is the advantage of using different empirical criteria both integrally and simultaneously in delimitation of species of oaks? Studied species: Species of Quercus Method: Bibliographic review of the main sources of variation in Quercus, and the species concepts, specifically those used in Quercus. Results: Plasticity, convergence, hybridization and introgression, and incomplete divergence were identified as the main sources of variation in oaks. Taxonomic and ecological species concepts are those mainly and traditionally used in Quercus. Syngameons are important to know and understand the biology and evolution of Quercus species. These systems indicate that there are preserved genes that provide coherence and morphologic, ecologic and genetic identity to species, even if hybridization, backcrossing and introgression occur. Conclusions: Preserved genes that provide coherence to species, suggest using taxonomic, ecologic and genetic concepts to delimit problematic species in species complexes in Quercus. The simultaneous use of data that these concepts support (multicriteria analysis), will give more confidence to get closer to the nature of the species and build an integrative taxonomy.

Long-distance dispersal shaped the diversity of tribe Dorstenieae (Moraceae)

AimThe Neotropics have the highest terrestrial biodiversity on earth. Investigating the relationships between the floras of the Neotropics and other tropical areas is critical to understanding the origin and evolution of this mega-diverse region. Tribe Dorstenieae (Moraceae) has a pantropical distribution and almost equal number of species on both sides of the Atlantic. In this study, we investigate the relationship between the African and Neotropical floras using Dorstenieae (15 genera, 156 species, Moraceae) as a model clade.Locationthe Neotropics and Africa.MethodsWe used a targeted enrichment strategy with herbarium samples and a nuclear bait set to assemble a data set of 102 genes sampled from 83 (53%) species and fifteen genera (100%) of Dorstenieae, and five outgroup species. Phylogenetic relationships were reconstructed with maximum likelihood and coalescent approaches. This phylogeny was dated with a Bayesian relaxed clock model and four fossil calibrations. The biogeographic history of the group was then reconstructed with several dispersal-extinction-cladogenesis models (incl. DEC and DEC+J).ResultsThe crown-group ages of Dorstenieae and Dorstenia were estimated in the Cretaceous (65.8-79.8 Ma) and the Paleocene (50.8-67.3 Ma), respectively. Tribe Dorstenieae as a whole appears to have originated in the joint area of continental Africa, Madagascar and Asia-Oceania area. The Neotropical species of Dorstenia diversified in the Eocene (29.8-44.7 Ma) and formed a clade nested within the African lineages in the genus. Brosimum s.l., with a crown-group age at the period of the Oligocene and Miocene (14.9-31.1 Ma), represents another Neotropical clade in Dorstenieae.Main conclusionsTribe Dorstenieae originated in the joint area of continental Africa, Madagascar and Asia-Oceania area in the Cretaceous and then dispersed into Neotropics twice. Neotropical diversification after long-distance dispersal across the Atlantic is the most plausible explanation for the extant distribution pattern of Dorstenieae.