Maintaining their genetic distance: Little evidence for introgression between widely hybridizing species of Geum with contrasting mating systems

Novel Tri-Segmented Rhabdoviruses: A Data Mining Expedition Unveils the Cryptic Diversity of Cytorhabdoviruses

Cytorhabdoviruses (genus Cytorhabdovirus, family Rhabdoviridae) are plant-infecting viruses with enveloped, bacilliform virions. Established members of the genus Cytorhabdovirus have unsegmented single-stranded negative-sense RNA genomes (ca. 10-16 kb) which encode four to ten proteins. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and genomic characterization of 93 novel viruses with genetic and evolutionary cues of cytorhabdoviruses. Strikingly, five unprecedented viruses with tri-segmented genomes were also identified. This finding represents the first tri-segmented viruses in the family Rhabdoviridae, and they should be classified in a novel genus within this family for which we suggest the name "Trirhavirus". Interestingly, the nucleocapsid and polymerase were the only typical rhabdoviral proteins encoded by those tri-segmented viruses, whereas in three of them, a protein similar to the emaravirus (family Fimoviridae) silencing suppressor was found, while the other predicted proteins had no matches in any sequence databases. Genetic distance and evolutionary insights suggest that all these novel viruses may represent members of novel species. Phylogenetic analyses, of both novel and previously classified plant rhabdoviruses, provide compelling support for the division of the genus Cytorhabdovirus into three distinct genera. This proposed reclassification not only enhances our understanding of the evolutionary dynamics within this group of plant rhabdoviruses but also illuminates the remarkable genomic diversity they encompass. This study not only represents a significant expansion of the genomics of cytorhabdoviruses that will enable future research on the evolutionary peculiarity of this genus but also shows the plasticity in the rhabdovirus genome organization with the discovery of tri-segmented members with a unique evolutionary trajectory.

An Atlas of Genomic Resources for Studying Rosaceae Fruits and Ornamentals

Rosaceae, a large plant family of more than 3,000 species, consists of many economically important fruit and ornamental crops, including peach, apple, strawberry, raspberry, cherry, and rose. These horticultural crops are not only important economic drivers in many regions of the world, but also major sources of human nutrition. Additionally, due to the diversity of fruit types in Rosaceae, this plant family offers excellent opportunities for investigations into fleshy fruit diversity, evolution, and development. With the development of high-throughput sequencing technologies and computational tools, an increasing number of high-quality genomes and transcriptomes of Rosaceae species have become available and will greatly facilitate Rosaceae research and breeding. This review summarizes major genomic resources and genome research progress in Rosaceae, highlights important databases, and suggests areas for further improvement. The availability of these big data resources will greatly accelerate research progress and enhance the agricultural productivity of Rosaceae.

Asymmetries of reproductive isolation are reflected in directionalities of hybridization: integrative evidence on the complexity of species boundaries

The complex nature of species boundaries has been a central topic in evolutionary biology ever since Darwin. Despite numerous separate studies on reproductive isolation and hybridization, their relationship remains underinvestigated. Are the strengths and asymmetries of reproductive barriers reflected in the extent and directionalities of interspecific genetic exchange? We combined field, experimental, and molecular data to quantify strengths and asymmetries of sympatric reproductive barriers and hybridization between florally heteromorphic primroses. We also assessed whether generalist pollinators discriminate between different floral cues and contribute to reproductive isolation, a long-debated topic. Sympatric reproductive isolation is high but incomplete, and most phenotypic intermediates are genetic F₁ hybrids, whereas backcrosses are rare, revealing low interspecific gene flow. Species integrity rests on multiple barriers, but ethological isolation is among the strongest, demonstrating that even generalist pollinators crucially contribute to the maintenance of species boundaries. Furthermore, reproductive barriers are weaker for Primula veris and short-styled plants, results corroborated by molecular data. Thus, in florally heteromorphic systems, both species- and morph-dependent asymmetries affect permeability of species boundaries. Our study illustrates how the interactions between complex floral syndromes and pollinators shape species boundaries in unique, previously undescribed ways.

Low-coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp

Population divergence and gene flow are key processes in evolution and ecology. Model-based analysis of genome-wide data sets allows discrimination between alternative scenarios for these processes even in nonmodel taxa. We used two complementary approaches (one based on the blockwise site frequency spectrum [bSFS], the second on the pairwise sequentially Markovian coalescent [PSMC]) to infer the divergence history of a fig wasp, Pleistodontes nigriventris. Pleistodontes nigriventris and its fig tree mutualist Ficus watkinsiana are restricted to rain forest patches along the eastern coast of Australia and are separated into The Northern population is to the north of the Southern populations by two dry forest corridors (the Burdekin and St. Lawrence Gaps). We generated whole genome sequence data for two haploid males per population and used the bSFS approach to infer the timing of divergence between northern and southern populations of P. nigriventris, and to discriminate between alternative isolation with migration (IM) and instantaneous admixture (ADM) models of postdivergence gene flow. Pleistodontes nigriventris has low genetic diversity (π = 0.0008), to our knowledge one of the lowest estimates reported for a sexually reproducing arthropod. We find strongest support for an ADM model in which the two populations diverged ca. 196 kya in the late Pleistocene, with almost 25% of northern lineages introduced from the south during an admixture event ca. 57 kya. This divergence history is highly concordant with individual population demographies inferred from each pair of haploid males using PSMC. Our analysis illustrates the inferences possible with genome-level data for small population samples of tiny, nonmodel organisms and adds to a growing body of knowledge on the population structure of Australian rain forest taxa.

What could be the fate of secondary contact zones between closely related plant species?

Interspecific hybridization has been fundamental in plant evolution. Nevertheless, the fate of hybrid zones throughout the generations remains poorly addressed. We analyzed a pair of recently diverged, interfertile, and sympatric Petunia species to ask what fate the interspecific hybrid population has met over time. We analyzed the genetic diversity in two generations from two contact sites and evaluated the effect of introgression. To do this, we collected all adult plants from the contact zones, including canonicals and intermediary colored individuals, and compared them with purebred representatives of both species based on seven highly informative microsatellite loci. We compared the genetic diversity observed in the contact zones with what is seen in isolated populations of each species, considering two generations of these annual species. Our results have confirmed the genetic differentiation between the species and the hybrid origin of the majority of the intermediary colored individuals. We also observed a differentiation related to genetic variability and inbreeding levels among the populations. Over time, there were no significant differences per site related to genetic diversity or phenotype composition. We found two stable populations kept by high inbreeding and backcross rates that influence the genetic diversity of their parental species through introgression.

Gene transfer across species boundaries in bryophytes: evidence from major life cycle stages in Homalothecium lutescens and H. sericeum

BACKGROUND AND AIMS

The mosses Homalothecium lutescens and H. sericeum are genetically, morphologically and ecologically differentiated; mixed populations sometimes occur. In sympatric populations, intermediate character states among gametophytes and sporophytes have been observed, suggesting hybridization and introgression in such populations.

METHODS

We determined genotypes using bi-allelic co-dominant single nucleotide polymorphism (SNP) markers, specific to either H. lutescens or H. sericeum, to estimate the degree of genetic mixing in 449 moss samples collected from seven sympatric and five allopatric populations on the island of Öland, south Sweden. The samples represented three generations: haploid maternal gametophytes; diploid sporophytes; and haploid sporelings.

KEY RESULTS

Admixture analyses of SNP genotypes identified a majority as pure H. lutescens or H. sericeum, but 76 samples were identified as mildly admixed (17 %) and 17 samples (3.8 %) as strongly admixed. Admixed samples were represented in all three generations in several populations. Hybridization and introgression were bidirectional.

CONCLUSIONS

Our results demonstrate that admixed genomes are transferred between the generations, so that the populations behave as true hybrid zones. Earlier studies of sympatric bryophyte populations with admixed individuals have not been able to show that admixed alleles are transferred beyond the first generation. The presence of true hybrid zones has strong evolutionary implications because genetic material transferred across species boundaries can be directly exposed to selection in the long-lived haploid generation of the bryophyte life cycle, and contribute to local adaptation, long-term survival and speciation.

Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae)

BACKGROUND

With an ever-growing number of published genomes, many low levels of the Tree of Life now contain several species with enough molecular data to perform shallow-scale phylogenomic studies. Moving away from using just a few universal phylogenetic markers, we can now target thousands of other loci to decipher taxa relationships. Making the best possible selection of informative sequences regarding the taxa studied has emerged as a new issue. Here, we developed a general procedure to mine genomic data, looking for orthologous single-copy loci capable of deciphering phylogenetic relationships below the generic rank. To develop our strategy, we chose the genus Rosa, a rapid-evolving lineage of the Rosaceae family in which several species genomes have recently been sequenced. We also compared our loci to conventional plastid markers, commonly used for phylogenetic inference in this genus.

RESULTS

We generated 1856 sequence tags in putative single-copy orthologous nuclear loci. Associated in silico primer pairs can potentially amplify fragments able to resolve a wide range of speciation events within the genus Rosa. Analysis of parsimony-informative site content showed the value of non-coding genomic regions to obtain variable sequences despite the fact that they may be more difficult to target in less related species. Dozens of nuclear loci outperform the conventional plastid phylogenetic markers in terms of phylogenetic informativeness, for both recent and ancient evolutionary divergences. However, conflicting phylogenetic signals were found between nuclear gene tree topologies and the species-tree topology, shedding light on the many patterns of hybridization and/or incomplete lineage sorting that occur in the genus Rosa.

CONCLUSIONS

With recently published genome sequence data, we developed a set of single-copy orthologous nuclear loci to resolve species-level phylogenomics in the genus Rosa. This genome-wide scale dataset contains hundreds of highly variable loci which phylogenetic interest was assessed in terms of phylogenetic informativeness and topological conflict. Our target identification procedure can easily be reproduced to identify new highly informative loci for other taxonomic groups and ranks.

Searching for the genetic footprint of ancient and recent hybridization

Determining the long-term consequences of hybridization remains a central quest for evolutionary biologists. A particular challenge is to establish whether and to what extent widespread hybridization results in gene flow (introgression) between parental taxa. In this issue of Molecular Ecology, Jordan et al. () search for evidence of gene flow between two closely related species of Geum (Rosaceae), which hybridize readily in contemporary populations and where hybrid swarms have been recorded for at least 200 years (Ruhsam, Hollingsworth, & Ennos, ). The authors find mixed evidence of ancient introgression when analysing allopatric populations. Intriguingly, when analysing populations of a region where the two species occur either mixed in the same population or in close proximity, and where hybrids are presently common, Jordan and colleagues find that the majority of randomly sampled individuals analysed (92/96) show no evidence of introgression (defined as individuals with admixture coefficients of <1%). The few individuals identified as hybrids are shown to likely be F1 or early-generation backcrosses, indicating that even in sympatric regions, hybridization does not penetrate beyond a few generations. Based on their findings, Geum seems to be an example of little to no introgression despite contemporary hybridization.

Maintaining their genetic distance: Little evidence for introgression between widely hybridizing species of Geum with contrasting mating systems

Within the plant kingdom, many genera contain sister lineages with contrasting outcrossing and inbreeding mating systems that are known to hybridize. The evolutionary fate of these sister lineages is likely to be influenced by the extent to which they exchange genes. We measured gene flow between outcrossing Geum rivale and selfing Geum urbanum, sister species that hybridize in contemporary populations. We generated and used a draft genome of G. urbanum to develop dd-RAD data scorable in both species. Coalescent analysis of RAD data from allopatric populations indicated that the species diverged 2-3 Mya, and that historical gene flow between them was extremely low (1 migrant every 25 generations). Comparison of genetic divergence between species in sympatry and allopatry, together with an analysis of allele frequencies in potential parental and hybrid populations, provided no evidence of contemporary introgression in sympatric populations. Cluster- and species-specific marker analyses revealed that, apart from four early-generation hybrids, individuals in sympatric populations fell into two genetically distinct groups that corresponded exactly to their morphological species classification with maximum individual admixture estimates of only 1-3%. However, we did observe joint segregation of four putatively introgressed SNPs across two scaffolds in the G. urbanum population that was associated with significant morphological variation, interpreted as tentative evidence for rare, recent interspecific gene flow. Overall, our results indicate that despite the presence of hybrids in contemporary populations, genetic exchange between G. rivale and G. urbanum has been extremely limited throughout their evolutionary history.