Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana.

The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single-Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily "short" timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events.

Macroinvertebrate community responses to hydrological controls and groundwater abstraction effects across intermittent and perennial headwater streams.

Intermittent rivers comprise a significant proportion of river networks globally and their spatial extent is predicted to increase with rising water abstraction pressures. Despite this, the ecological implications of hydrological modifications within intermittent rivers have received limited research attention. This paper examines macroinvertebrate assemblages across intermittent and perennial sections of headwater streams within the Hampshire Avon catchment (United Kingdom) over a five-year period. The composition of faunal assemblages was quantified in relation to four hydrological metrics: the duration of flowing conditions, the geographical proximity to the nearest perennial source along each watercourse (two observed flow parameters) and two modelled groundwater abstraction influences. The results highlight that macroinvertebrate communities inhabiting sites which dry periodically and are positioned at greater distances (>c. 2.5km) above the perennial source (the most upstream point of permanent flow within a given year) possessed the highest conservation values. These sites supported species that are rare in many areas of Europe (e.g. Ephemeroptera: Paraletophlebia werneri) or with limited geographical distribution across the United Kingdom (e.g. Trichoptera: Limnephilus bipunctatus). A range of faunal community diversity indices were found to be more sensitive to the antecedent flow duration and distance from the perennial source, rather than any effects of groundwater abstraction. Taxonomic richness responded most strongly to these observed flow parameters and varied more markedly with the distance from the perennial source compared to the antecedent flow duration. Several taxa were significantly associated with the observed flow parameters, particularly those predominantly inhabiting perennially flowing systems. However, the distance that such fauna could migrate into intermittent reaches varied between taxa. This research demonstrates the overriding importance of antecedent flow durations and the geographical proximity to perennial sources on macroinvertebrate communities within intermittent and perennial headwater streams.

Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm rapid radiation in the moss family Funariaceae.

Rapid diversifications of plants are primarily documented and studied in angiosperms, which are perceived as evolutionarily dynamic. Recent studies have, however, revealed that bryophytes have also undergone periods of rapid radiation. The speciose family Funariaceae, including the model taxon Physcomitrella patens, is one such lineage. Here, we infer relationships among major lineages within the Entosthodon-Physcomitrium complex from virtually complete organellar exomes (i.e., 123 genes) obtained through high throughput sequencing of genomic libraries enriched in these loci via targeted locus capture. Based on these extensive exonic data we (1) reconstructed a robust backbone topology of the Funariaceae, (2) confirmed the monophyly of Funaria and the polyphyly of Entosthodon, Physcomitrella, and Physcomitrium, and (3) argue for the occurrence of a rapid radiation within the Entosthodon-Physcomitrium complex that began 28 mya and gave rise more than half of the species diversity of the family. This diversification may have been triggered by a whole genome duplication and coincides with global Eocene cooling that continued through the Oligocene and Miocene. The Funariaceae join a growing list of bryophyte lineages whose history is marked by at least one burst of diversification, and our study thereby strengthens the view that bryophytes are evolutionarily dynamic lineages and that patterns and processes characterizing the evolution of angiosperms may be universal among land plants.