Catchments catch all in South African coastal lowlands: topography and palaeoclimate restricted gene flow in Nymania capensis (Meliaceae)—a multilocus phylogeographic and distribution modelling approach

Background This study investigates orbitally-forced range dynamics at a regional scale by exploring the evolutionary history of Nymania capensis (Meliaceae) across the deeply incised landscapes of the subescarpment coastal lowlands of South Africa; a region that is home to three biodiversity hotspots (Succulent Karoo, Fynbos, and Maputaland-Pondoland-Albany hotspots). Methods A range of methods are used including: multilocus phylogeography (chloroplast and high- and low-copy nuclear DNA), molecular dating and species distribution modelling (SDM). Results The results support an ‘evolutionarily distinct catchment’ hypothesis where: (1) different catchments contain genetically distinct lineages, (2) limited genetic structuring was detected within basins whilst high structuring was detected between basins, and (3) within primary catchment populations display a high degree of genealogical lineage sorting. In addition, the results support a glacial refugia hypothesis as: (a) the timing of chloroplast lineage diversification is restricted to the Pleistocene in a landscape that has been relatively unchanged since the late Pliocene, and (b) the projected LGM distribution of suitable climate for N. capensis suggest fragmentation into refugia that correspond to the current phylogeographic populations. Discussion This study highlights the interaction of topography and subtle Pleistocene climate variations as drivers limiting both seed and pollen flow along these lowlands. This lends support to the region’s large-scale conservation planning efforts, which used catchments as foundational units for conservation as these are likely to be evolutionarily significant units

Flammability of indigenous and invasive alien woody plants in coastal fynbos and thicket

Globally, extreme fires have become more common in wildland-urban interface areas, and more recently, along the southern Cape coast of South Africa. The 2017 Knysna fires prompted greater understanding of the flammability of, and the fire risk posed by, different vegetation groups, which is essential to develop fire risk mitigation strategies. In this study, I experimentally assessed flammability of 30 woody plant species from the vegetation groups indigenous fynbos, thicket, and invasive alien plants (IAPs) that occur along the southern Cape coast. Live plant shoots were sampled across varying fire weather conditions and burnt experimentally to measure flammability in relation to fire weather conditions, fuel moisture, and fuel load. Flammability measures considered were: burn intensity, completeness of burn, time-to-ignition, and the likelihood of spontaneous ignition. I further assessed the flammability of partially dried plant material as a crude proxy for drought effects, to ascertain whether drying of fuels would differentially affect the flammability of the vegetation groups. I used generalized linear mixed-effects models to assess flammability measures in relation to the predictor variables: fire weather, fuel moisture, fuel load, vegetation groups, and species (as a random factor). Results showed that increasing severity of fire weather significantly increased flammability through increasing burn intensity, increasing completeness of burn, increasing the likelihood of spontaneous ignition, and also reducing time-to-ignition. Increasing fuel moisture significantly decreased burn intensity, completeness of burn, and the likelihood of spontaneous ignition. Fuel load significantly increased burn intensity and time-to-ignition. Flammability was highest in IAPs, intermediate in fynbos, and lowest in thicket. IAPs and fynbos showed significantly higher ignitability, and thus present risks under moderate and high fire weather conditions, whereas thicket presents lower risks under low and moderate fire weather conditions. The drying out of fuels considerably increased flammability equally in the three vegetation groups, and by implication, fire risk due to an increase in dead:live ratio. Flammability was furthermore assessed in relation to fuel traits, i.e. the proportion of fine fuels, coarse fuels, and dead fuels, fuel bed porosity, fuel load, and fuel moisture, using multiple regression analysis and stepwise selection of factors. This revealed that fuel moisture was the most important factor affecting flammability in terms of all the flammability measures. Results further showed that the increase in v the proportions of fine fuels increased flammability by increasing completeness of burn. Lastly, vegetation groups were compared (using Kruskal Wallis) in terms of their flammability and fuel traits. I found that fynbos and IAPs exhibited greater flammability on account of higher completeness of burn and more rapid ignition than thicket species, but no clear distinction was evident between fynbos and IAPs. Fynbos’ high flammability was attributed to high proportions of fine and porous fuels. Thicket’s low flammability was attributed to high proportions of coarse and dense fuels. Little distinction in fuel traits could be made between fynbos and IAPs, except that fynbos had a greater proportion of fine fuels. There is a potential risk posed by the IAPs in terms of increased flammability and fire severity, on an indigenous landscape that is invaded. Fire managers need to encourage the prioritization of the management of IAPs that present high flammability as an attempt to reduce fire risk along the southern Cape coast of South Africa

Pleistocene range dynamics in the eastern Greater Cape Floristic Region: A case study of the Little Karoo endemic Berkheya cuneata (Asteraceae)

AbstractThe glacial–interglacial climate cycles of the Pleistocene played a significant role in dramatically altering species distributions across the globe. However, the climate of the Greater Cape Floristic Region is thought to have been decoupled from global fluctuations and the current Mediterranean climate remained relatively buffered during this period. Here we explore the roles of climate stability and the topographic complexity of the region on the range history of an endemic Little Karoo plant, Berkheya cuneata, using ensemble species distribution modelling and multi-locus phylogeography. The species distribution models projected onto downscaled climate simulation of the Last Glacial Maximum demonstrated a considerable range contraction and fragmentation into the western and eastern Little Karoo, separated by the Rooiberg inselberg. This population fragmentation is mirrored in the phylogeographic structuring of both chloroplast and nuclear DNA. These results suggest that sufficient climatic buffering coupled with regionally complex topography ensured the localised population persistence during Pleistocene climate cycles but these features have also promoted population vicariance in this, and likely other, Little Karoo lowland species

Phylogenetic relationships in the southern African genus Drosanthemum (Ruschioideae, Aizoaceae)

Background. Drosanthemum, the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, Drosanthemum together with the highly succulent and species-rich tribe Ruschieae constitute the 'core ruschioids' in Aizoaceae. Within Drosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution. Methods. Using chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species of Drosanthemum with multiple accessions for widespread species. A well-curated, geo-referenced occurrence data set comprising the 134 genetically analysed and 863 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole. Results. Phylogenetic inference supports nine clades within Drosanthemum, seven of which group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera within Drosanthemum, with exceptions such as (pseudo-) cryptic species. In-depth analyses of sequence patterns in each gene region were used to reveal phylogenetic affinities inside the retrieved clades in more detail. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgenera Drosanthemum p.p., Vespertina, Xamera) that are genetically and morphologically diverse. In contrast, less species-rich, genetically less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua, Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest that the main lineages arose from an initial rapid radiation, with subsequent diversification in some clades.Raw data, code, analysis output, and species occurrence The zip file contains a ReadMe file and 4 folders: 1_main_data_and_results (the files used to produce the figures in the main text); 2_ML_phylogenetics (raw data, code, and analysis output of ML phylogenetic analyses); 3_MJ_networks (raw data [SNP/sequence motive recoded DNA alignment matrices], and output of median-joining network analyses)

Science is the fuel required for lifting ecosystem restoration into the orbit of hundreds of millions of hectares

Restoring the hundreds of millions of hectares of degraded ecosystems worldwide will require new approaches to raise the required funds and new systems to implement at the required scales. Two decades of large-scale restoration in the subtropical thicket biome in the Eastern Cape, South Africa, have generated valuable information for developing such approaches and systems. The successful upscaling of restoration in this biome can be attributed to four main actions. First, from the outset in 2003, peer-reviewed science was foundational to the entire restoration initiative. Second, also from the outset, there was a commitment to large-scale, long-term ecological research by the public sector (the then Department of Water Affairs and Forestry in South Africa), which resulted in what is to our knowledge the world’s largest ecosystem restoration experiment, comprising 330 quarter-hectare plots distributed over ∼75,000 km2. Third, retrospective scientific description of previous restoration work — done by farmers in the 1960s and 1970s — provided valuable information on restoration’s multiple benefits, without having to wait for the large-scale restoration experiment to yield results. Lastly, diverse and short-term scoping studies were undertaken to address questions that emerged during the large-scale implementation of restoration. These studies were vital for rapid adaptive management and planning new scientific experiments, filling a gap between long-term ecological research and retrospective science

The soil microbiomics of intact, degraded and partially-restored semi-arid succulent thicket (Albany Subtropical Thicket)

This study examines the soil bacterial diversity in the Portulacaria afra-dominated succulent thicket vegetation of the Albany Subtropical Thicket biome; this biome is endemic to South Africa. The aim of the study was to compare the soil microbiomes between intact and degraded zones in the succulent thicket and identify environmental factors which could explain the community compositions. Bacterial diversity, using 16S amplicon sequencing, and soil physicochemistry were compared across three zones: intact (undisturbed and vegetated), degraded (near complete removal of vegetation due to browsing) and restored (a previously degraded area which was replanted approximately 11 years before sampling). Amplicon Sequence Variant (ASV) richness was similar across the three zones, however, the bacterial community composition and soil physicochemistry differed across the intact and degraded zones. We identified, via correlation, the potential drivers of microbial community composition as soil density, pH and the ratio of Ca to Mg. The restored zone was intermediate between the intact and degraded zones. The differences in the microbial communities appeared to be driven by the presence of plants, with plant-associated taxa more common in the intact zone. The dominant taxa in the degraded zone were cosmopolitan organisms, that have been reported globally in a wide variety of habitats. This study provides baseline information on the changes of the soil bacterial community of a spatially restricted and threatened biome. It also provides a starting point for further studies on community composition and function concerning the restoration of degraded succulent thicket ecosystems.The research presented here was part of a BSc (Hons) thesis (MS).Supplement 1 : Evidence of long-term degradation of the Sundays Arid Thicket (Albany Subtropical Thicket biome) on the slopes of the study site. Aerial images show that this degraded state has been in effect for at least 60 years: (A) satellite image from 2020 (Map data: ©2021 Google Earth, Maxar Technologies), (B) aerial photo taken in 1961 by the South African Chief Directorate of National Geo-spatial information (Reproduced under Government’s Printer Authorisation [Authorisation No. 11851 dated 08 September 2021]). Ground-based repeat photography demonstrates the loss of the majority of remaining trees since 1986: photos taken in (C) 2016 and (D) 1986 (Photo credit: MT Hoffman). Note that, in (C) and (D), the area in this study is not in the area photographed (it is off to the right). DOI: 10.7717/peerj.12176/supp-1Supplement 2 : Trends lines of soil relative humidity and temperature. Trend lines of soil relative humidity (blue) and temperature (red) over (A–C) the full duration of measurements or (D–F) the daily average. The pale points show the individual measurements and the grey border around the trend lines depicts the 95% confidence interval. DOI: 10.7717/peerj.12176/supp-2Supplement 3 : Comparison of soil temperature between the different vegetation types. (A) Boxplots of data points from three iButtons per zone. Significant differences were determined using the Wilcox test. (B) Mean daily maximum (solid lines) and minimum (dashed lines) temperature over the three zones. (C) Daily difference between the mean temperatures shown in (B). DOI: 10.7717/peerj.12176/supp-3Supplement 4 : Comparison of soil relative humidity between the different vegetation types. Boxplots of data points from three iButtons per zone (A). Significant differences were determined using the Wilcox test. Mean daily maximum (solid lines) and minimum (dashed lines) relative humidity over the three zones (B). Daily difference between the mean relative humidities shown in B (C). DOI: 10.7717/peerj.12176/supp-4Alpha diversity of samples as the number of (A) observed ASVs or (B) Shannon index. Significance was determined using the Wilcox test. DOI: 10.7717/peerj.12176/supp-5Supplement 6 : Heatmap of samples using weighted Jaccard distance. Overall the samples show low levels of similarity to one another. DOI: 10.7717/peerj.12176/supp-6Supplement 7 : Genus-level differences between zones. Relative abundance of genus-level ASVs that account for ≥1% of the reads in the different zones. Significance was determined using the Wilcox test. DOI: 10.7717/peerj.12176/supp-7Supplement 8 : Network taxa with significantly different abundances in intact vs degraded zones. Genus-level ASVs used in the network construction are displayed with the name of the genus, if available, and show the relative abundance in both the intact and degraded zones. Each genus is coloured according to the clustering in the degraded network (Fig. 5). Significance was determined using the Wilcox test and only the genera which had significant differences between their abundance in the different zones are shown. DOI: 10.7717/peerj.12176/supp-8Supplement 9 : Succulent thicket metadata. DOI: 10.7717/peerj.12176/supp-9Supplement 10 : Summary statistics of iButton measurements in the succulent thicket. DOI: 10.7717/peerj.12176/supp-10Supplement 11 : Core bacterial community of the succulent thicket. DOI: 10.7717/peerj.12176/supp-11Supplement 12 : Core bacterial community of the intact succulent thicket. DOI: 10.7717/peerj.12176/supp-12Supplement 13 : Core bacterial community of the degraded succulent thicket. DOI: 10.7717/peerj.12176/supp-13Supplement 14 : Core bacterial community of the restored succulent thicket. DOI: 10.7717/peerj.12176/supp-14Supplement 15 : Unique core bacterial community members of different vegetation conditions in the succulent thicket. DOI: 10.7717/peerj.12176/supp-15Supplement 16 : The number of unique to near-unique ASVs detected in the intact and degraded zone according to the prevalence threshold within and out of the specific zone. Prevalence thresholds are given both as a percentage (%) and as the equivalent number of sites (n) in the intact and degraded zones. The thresholds and resultant ASV counts analysed in this study are shown in bold DOI: 10.7717/peerj.12176/supp-16The University of Pretoria, the National Research Foundation of South Africa and the Department of Environment, Forestry and Fisheries: Natural Resource Management Programme.https://peerj.comam2022BiochemistryGeneticsMicrobiology and Plant Patholog

Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial.

Importance: Evidence regarding corticosteroid use for severe coronavirus disease 2019 (COVID-19) is limited. Objective: To determine whether hydrocortisone improves outcome for patients with severe COVID-19. Design, Setting, and Participants: An ongoing adaptive platform trial testing multiple interventions within multiple therapeutic domains, for example, antiviral agents, corticosteroids, or immunoglobulin. Between March 9 and June 17, 2020, 614 adult patients with suspected or confirmed COVID-19 were enrolled and randomized within at least 1 domain following admission to an intensive care unit (ICU) for respiratory or cardiovascular organ support at 121 sites in 8 countries. Of these, 403 were randomized to open-label interventions within the corticosteroid domain. The domain was halted after results from another trial were released. Follow-up ended August 12, 2020. Interventions: The corticosteroid domain randomized participants to a fixed 7-day course of intravenous hydrocortisone (50 mg or 100 mg every 6 hours) (n = 143), a shock-dependent course (50 mg every 6 hours when shock was clinically evident) (n = 152), or no hydrocortisone (n = 108). Main Outcomes and Measures: The primary end point was organ support-free days (days alive and free of ICU-based respiratory or cardiovascular support) within 21 days, where patients who died were assigned -1 day. The primary analysis was a bayesian cumulative logistic model that included all patients enrolled with severe COVID-19, adjusting for age, sex, site, region, time, assignment to interventions within other domains, and domain and intervention eligibility. Superiority was defined as the posterior probability of an odds ratio greater than 1 (threshold for trial conclusion of superiority >99%). Results: After excluding 19 participants who withdrew consent, there were 384 patients (mean age, 60 years; 29% female) randomized to the fixed-dose (n = 137), shock-dependent (n = 146), and no (n = 101) hydrocortisone groups; 379 (99%) completed the study and were included in the analysis. The mean age for the 3 groups ranged between 59.5 and 60.4 years; most patients were male (range, 70.6%-71.5%); mean body mass index ranged between 29.7 and 30.9; and patients receiving mechanical ventilation ranged between 50.0% and 63.5%. For the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively, the median organ support-free days were 0 (IQR, -1 to 15), 0 (IQR, -1 to 13), and 0 (-1 to 11) days (composed of 30%, 26%, and 33% mortality rates and 11.5, 9.5, and 6 median organ support-free days among survivors). The median adjusted odds ratio and bayesian probability of superiority were 1.43 (95% credible interval, 0.91-2.27) and 93% for fixed-dose hydrocortisone, respectively, and were 1.22 (95% credible interval, 0.76-1.94) and 80% for shock-dependent hydrocortisone compared with no hydrocortisone. Serious adverse events were reported in 4 (3%), 5 (3%), and 1 (1%) patients in the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively. Conclusions and Relevance: Among patients with severe COVID-19, treatment with a 7-day fixed-dose course of hydrocortisone or shock-dependent dosing of hydrocortisone, compared with no hydrocortisone, resulted in 93% and 80% probabilities of superiority with regard to the odds of improvement in organ support-free days within 21 days. However, the trial was stopped early and no treatment strategy met prespecified criteria for statistical superiority, precluding definitive conclusions. Trial Registration: ClinicalTrials.gov Identifier: NCT02735707

Data from: Constructing phylogenies in the presence of Intra-Individual Site Polymorphisms (2ISPs) with a focus on the nuclear ribosomal cistron

Nuclear DNA is widely used to estimate phylogenetic and phylogeographic relationships. Nuclear gene variants may be present in an individual's genome, and these result in Intra-Individual Site Polymorphisms (2ISP; pronounced 'twisp') in direct-PCR or individual-consensus sequences based on a clone sample. 2ISPs can occur fairly often, especially within, but not restricted to, high-copy-number regions such as the widely used internal transcribed spacers of the nuclear ribosomal cistron. Dealing with 2ISPs has been problematic as phylogeny reconstruction optimality criteria generally do not take account of this variation. Here we test whether an approach that treats 2ISPs as additional (termed ‘informative’), rather than ambiguous, characters offers improved support in three common criteria used for phylogenetic inference: Minimum Evolution (via Neighbour Joining), Maximum Parsimony and Maximum Likelihood. We demonstrate significant improvements using the 2ISP-informative treatment with simulated, real-world and case study datasets. We envisage that this 2ISP-informative approach will greatly aid phylogenetic inference using any nuclear DNA regions that contain polymorphisms within individuals (including consensus sequences generated from next generation sequencing), especially at the intrageneric or intraspecific level

Fire weather effects on flammability of indigenous and invasive alien plants in coastal fynbos and thicket shrublands (Cape Floristic Region)

Background Globally, and in the Cape Floristic Region of South Africa, extreme fires have become more common in recent years. Such fires pose societal and ecological threats and have inter alia been attributed to climate change and modification of fuels due to alien plant invasions. Understanding the flammability of different types of indigenous and invasive alien vegetation is essential to develop fire risk prevention and mitigation strategies. We assessed the flammability of 30 species of indigenous and invasive alien plants commonly occurring in coastal fynbos and thicket shrublands in relation to varying fire weather conditions. Methods Fresh plant shoots were sampled and burnt experimentally across diverse fire weather conditions to measure flammability in relation to fire weather conditions, live fuel moisture, fuel load and vegetation grouping (fynbos, thicket and invasive alien plants). Flammability measures considered were: burn intensity, completeness of burn, time-to-ignition, and the likelihood of spontaneous ignition. We also investigated whether the drying of plant shoots (simulating drought conditions) differentially affected the flammability of vegetation groups. Results Fire weather conditions enhanced all measures of flammability, whereas live fuel moisture reduced burn intensity and completeness of burn. Live fuel moisture was not significantly correlated with fire weather, suggesting that the mechanism through which fire weather enhances flammability is not live fuel moisture. It furthermore implies that the importance of live fuel moisture for flammability of evergreen shrublands rests on inter-specific and inter-vegetation type differences in fuel moisture, rather than short-term intra-specific fluctuation in live fuel moisture in response to weather conditions. Fuel load significantly increased burn intensity, while reducing ignitability. Although fire weather, live fuel moisture, and fuel load had significant effects on flammability measures, vegetation and species differences accounted for most of the variation. Flammability was generally highest in invasive alien plants, intermediate in fynbos, and lowest in thicket. Fynbos ignited rapidly and burnt completely, whereas thicket was slow to ignite and burnt incompletely. Invasive alien plants were slow to ignite, but burnt with the highest intensity, potentially due to volatile organic composition. The drying of samples resulted in increases in all measures of flammability that were comparable among vegetation groups. Flammability, and by implication fire risk, should thus not increase disproportionately in one vegetation group compared to another under drought conditions—unless the production of dead fuels is disproportionate among vegetation groups. Thus, we suggest that the dead:live fuel ratio is a potentially useful indicator of flammability of evergreen shrublands and that proxies for this ratio need to be investigated for incorporation into fire danger indices

Nymania.capensis.ITS.alignments

The raw and edited alignments for the Nymania capensis alignment of DNA sequences from the internal transcribed spacers and 5.8S regions