Contact zones present unique opportunities to investigate ecological divergence, reproductive barriers, and gene flow between species. The two-lined salamander (Eurycea bislineata) species complex is a group of semiaquatic plethodontid salamanders with a reticulate evolutionary history that reflects the reorganization of river drainage basins. Although evidence for widespread, ancient introgression suggests an absence of reproductive isolating mechanisms in the early evolutionary history of the group, modern contact zones reveal a broader diversity of outcomes—with some putative species pairs occurring in sympatry and others exhibiting narrow hybrid zones. Here, we used RADcap data to investigate gene flow and ecological divergence in replicate contact zones between two species in the Appalachian foothills. Our results demonstrate that gene flow between these species is absent or rare, and larvae show strong, fine-scale ecological segregation among riffles, runs, and pools in streams. These results reinforce the more ambiguous conclusions of previous studies that suggested the evolutionary distinctiveness of these two species and underscore the importance of ecological factors in shaping local distributions.

Sexual reproduction may pose myriad short-term costs to females. Despite these costs, sexual reproduction is near ubiquitous. Facultative parthenogenesis is theorized to mitigate some of the costs of sex, as individuals can participate in occasional sex to limit costs while obtaining many benefits. However, most theoretical models assume sexual reproduction is fixed following mating, with no possibility of clutches of mixed reproductive ontogeny. Therefore, we asked: if coercive males are present at high frequency in a population of facultative parthenogens, will their clutches be solely sexually produced, or will there be evidence of sexually and asexually-produced offspring? How will their offspring production compare to conspecifics in low-frequency male populations? We addressed our questions by collecting females and egg clutches of the facultatively parthenogenetic Opiliones species Leiobunum manubriatum and L. globosum. In L. manubriatum, females from populations with few males were not significantly more fecund than females from populations with higher male relative frequency, despite the potential release of the former from sexual conflict. We used 3 genotyping methods along with a custom set of DNA capture probes to reveal that offspring of L. manubriatum from these high male populations were primarily produced via asexual reproduction. This is surprising because sex ratios in these southern populations approach equality, increasing the probability for females to encounter mates and produce offspring sexually. We additionally found evidence for reproductive polymorphisms within populations. Rapid and accurate SNP genotyping data will continue to allow us to address broader evolutionary questions regarding the role of facultative reproductive modes in the maintenance of sex.

Duckweeds represent a small, free-floating aquatic family (Lemnaceae) of the monocot order Alismatales with the fastest growth rate among flowering plants. They comprise five genera (Spirodela, Landoltia, Lemna, Wolffiella, and Wolffia) varying in genome size and chromosome number. Spirodela polyrhiza had the first sequenced duckweed genome. Cytogenetic maps are available for both species of the genus Spirodela (S. polyrhiza and S. intermedia). However, elucidation of chromosome homeology and evolutionary chromosome rearrangements by cross-FISH using Spirodela BAC probes to species of other duckweed genera has not been successful so far. We investigated the potential of chromosome-specific oligo-FISH probes to address these topics. We designed oligo-FISH probes specific for one S. intermedia and one S. polyrhiza chromosome (Fig. 1a). Our results show that these oligo-probes cross-hybridize with the homeologous regions of the other congeneric species, but are not suitable to uncover chromosomal homeology across duckweeds genera. This is most likely due to too low sequence similarity between the investigated genera and/or too low probe density on the target genomes. Finally, we suggest genus-specific design of oligo-probes to elucidate chromosome evolution across duckweed genera.

We study the liquid-liquid phase separation (LLPS) of a cell-free transcription-translation (TXTL) system. When the TXTL reaction, composed of a large amount of proteins, is concentrated, the uniformly mixed state becomes unstable and membrane-less droplets form spontaneously. This LLPS droplet formation can be induced when the TXTL reaction is enclosed in water-in-oil emulsion droplets in which water evaporates (dehydration) from the surface. As the emulsion droplets shrink, smaller LLPS droplets appear inside the emulsion droplets and coalesce into phase-separated domains that partition the location of proteins. We show that the LLPS in the emulsion droplets can be accelerated by interfacial drift in the outer oil phase. This further provides an experimental platform for studying the interplay between biological reactions and intracellular phase separation.

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.

Angiotensin-converting enzyme 2 (ACE2) is the main entry point in airway epithelial cells for SARS-CoV-2. ACE2 binding to the SARS-CoV-2 protein spike triggers viral fusion with the cell plasma membrane, resulting in viral RNA genome delivery into the host. Despite ACE2’s critical role in SARS-CoV-2 infection, full understanding of ACE2 expression, including in response to viral infection, remains unclear. ACE2 was thought to encode five transcripts and one protein of 805 amino acids. In the present study, we identify a novel short isoform of ACE2 expressed in the airway epithelium, the main site of SARS-CoV-2 infection. Short ACE2 is substantially upregulated in response to interferon stimulation and rhinovirus infection, but not SARS-CoV-2 infection. This short isoform lacks SARS-CoV-2 spike high-affinity binding sites and, altogether, our data are consistent with a model where short ACE2 is unlikely to directly contribute to host susceptibility to SARS-CoV-2 infection.

Morphological characterizations of genera in Cyperaceae tribe Abildgaardieae have been highly problematic and the subject of much debate. Earlier molecular phylogenetic studies based on Sanger sequencing and a limited sampling have indicated that several generic circumscriptions are not monophyletic. Here, we provide the first phylogenetic hypothesis for Abildgaardieae using targeted sequencing data obtained with the Angiosperms353 enrichment panel for 50 species. We test whether recent taxonomic decisions made based on Sanger sequencing data are validated by our targeted sequencing data. Our results support subsuming the small African genus Nemum into the large genus Bulbostylis and subsuming the monotypic genus Crosslandia into the diverse genus Fimbristylis. Also, our results support the recent publication of the new genus Zulustylis for two African species previously placed in Fimbristylis. Furthermore, we investigate the phylogenetic placement of recently described tropical Australian endemic species of Actinoschoenus, which are recognized here as the new morphologically cryptic genus Scleroschoenus. Based on our phylogenetic hypothesis and supported by morphological data, we recognize the genus Abildgaardia. The placement in Abildgaardieae of two monotypic genera Nelmesia and Trichoschoenus, only known from the type collections from the Democratic Republic of Congo and Madagascar, respectively, are also discussed. New combinations and lectotypifications are made in Abildgaardia, Actinoschoenus, Arthrostylis and Scleroschoenus.

Breeding wheat with durable resistance to the fungal pathogen Puccinia graminis f. sp. tritici (Pgt), a major threat to cereal production, is challenging due to the rapid evolution of pathogen virulence. Increased durability and broad-spectrum resistance can be achieved by introducing more than one resistance gene, but combining numerous unlinked genes by breeding is laborious. Here we generate polygenic Pgt resistance by introducing a transgene cassette of five resistance genes into bread wheat as a single locus and show that at least four of the five genes are functional. These wheat lines are resistant to aggressive and highly virulent Pgt isolates from around the world and show very high levels of resistance in the field. The simple monogenic inheritance of this multigene locus greatly simplifies its use in breeding. However, a new Pgt isolate with virulence to several genes at this locus suggests gene stacks will need strategic deployment to maintain their effectiveness.

Sugarcane (Saccharum spp.) is probably the crop with the most complex genome. Modern cultivars (2n=100-120) are derived from interspecific hybridization between the noble cane S. officinarum (2n=80) and the wild cane S. spontaneum (2n=40-128). We investigated the genome organization of important sugarcane cultivars and their parental species using chromosomespecific probes combined with genomic in situ hybridization (GISH). This allowed the genomic and genetic characterisation of Australian sugarcane cultivars and one of the major contributing parental clones, Mandalay. The S. spontaneum clone Mandalay follows the classical organization of S. spontaneum clones with x=8 with a major discrepancy related to an extra six chromosomes compared to the previously reported 2n=96 for Mandalay’s clone. Our previous results reported the rearrangements between the S. officinarum (x=10) and S. spontaneum (x=8) chromosomes, with a most likely scenario of a two-step process leading to x= 9 and then x=8, where each step involved three chromosomes that were rearranged into two. Further polyploidization led to the wide geographical dispersion of S. spontaneum clones with x= 8. In modern cultivars, the 13-20% of the S. spontaneum contribution originated from cytotypes with x=8. Modern cultivars have mainly 12 copies of each of the first four basic chromosomes and a more variable number for those basic chromosomes whose structure differs between the two parental species. These new insights and cytogenetic tools substantially improve our understanding of the extreme level of complexity of modern sugarcane cultivar genomes and could lead to guiding breeding strategies in the development of new improved varieties for the Australian industry.

Premise Resolving relationships within order Commelinales has posed quite a challenge, as reflected in its unstable infra-familial classification. Thus, we investigated (1) relationships across families and genera of Commelinales; (2) phylogenetic placement of never-before sequenced genera; (3) how well off-target plastid data integrate with other plastid-based data sets; and (4) how the novel inferences coincide with the infra-familial classification. Methods We generated two large data sets (nuclear and plastome) by means of target sequence capture using the Angiosperms353 probe set, with additional sequences mined from publicly available transcriptomes and full plastomes. A third extended-plastid data set was considered, including all species with sequences in public repositories. Species trees were inferred under a multispecies coalescent framework from individual gene trees and also using maximum likelihood analyses from concatenated and partitioned data. Results The nuclear, plastome, and extended-plastid data sets include 52, 53, and 58 genera, respectively, and up to 290 species of Commelinales, representing the most comprehensive molecular sampling for the order to date, which includes seven never-before sequenced genera. Conclusions We inferred robust phylogenies supporting the monophyly of Commelinales and its five constituent families, and we recovered the clades Pontederiaceae-Haemodoraceae and Hanguanaceae-Commelinaceae, as previously reported. The placement of Philydraceae remains contentious. Relationships within the two largest families, Commelinaceae and Haemodoraceae, are resolved. Based on the latter results, we confirm the subfamilial classification of Haemodoraceae and propose a new classification for Commelinaceae, which includes the synonymization of Tapheocarpa in Commelina.