Restoring South African subtropical succulent thicket using Portulacaria afra: root growth of cuttings differs depending on the harvest site during a drought.

The restoration of succulent thicket (the semi-arid components of the Albany Subtropical Thicket biome endemic to South Africa) has largely focused on the reintroduction of Portulacaria afra L. Jacq-a leaf- and stem-succulent shrub-through the planting of unrooted cuttings directly into field sites. However, there has been inconsistent establishment and survival rates, with low rates potentially due to a range of factors (e.g., post-planting drought, frost or herbivory), including the poor condition of source material used. Here we test the effect of parent-plant and harvesting site on the root development of P. afra cuttings in a common garden experiment. Ten sites were selected along a ∼110 km transect, with cuttings harvested from five parent-plants per site. Leaf moisture content was determined for each parent-plant at the time of harvesting as a proxy for plant condition. Root development-percentage of rooted cuttings and mean root dry weight-was recorded for a subset of cuttings from each parent-plant after 35, 42, 48, 56, and 103 days after planting in a common garden setting. We found evidence for cutting root development (rooting percentage and root dry mass) to be strongly associated with harvesting site across all sampling days (p < 0.005 for all tests). These differences are likely a consequence of underlying physiological factors; this was supported by the significant but weak correlation (r 2 = 0.10-0.26) between the leaf moisture content of the parent-plant (at the time of harvesting) and dry root mass of the cuttings (at each of the sampling days). Our findings demonstrate that varying plant condition across sites can significantly influence root development during dry phases (i.e., intra- and inter-annual droughts) and that this may be a critical component that needs to be understood as part of any restoration programme. Further work is required to identify the environmental conditions that promote or impede root development in P. afra cuttings.

Restoring South African subtropical succulent thicket using Portulacaria afra: exploring the rooting window hypothesis.

Drought prone, arid and semi-arid ecosystems are challenging to restore once degraded due to low levels of natural recruitment and survival of reintroduced plants. This is evident in the restoration of degraded succulent thicket habitats in the Albany Subtropical Thicket Biome located in South Africa. The current restoration practice for this ecosystem focuses predominantly on reintroducing Portulacaria afra L. Jacq., which is naturally dominant in terms of cover and biomass, but largely absent in regions degraded by domestic livestock. This has been achieved by planting unrooted cuttings with limited consideration of soil water availability in a drought-prone ecosystem. This study tests the effects of the timing of water availability after planting on the root development of P. afra cuttings. Cuttings were harvested from seven individual plants and grown in a glasshouse setting. Eighty four cuttings were taken from each individual, twelve for each of the seven watering treatments per individual plant. The treatments represented a time-staggered initial watering after planting, including: on the day of planting, 4 days, 7 days, 14 days, 21 days, and 28 days after planting. After 32 days, all treatments were watered on a bi-weekly basis for two weeks; a control treatment with no watering throughout the experiment was included. The proportion of rooted cuttings per treatment and dry root mass were determined at the end of the experimental period (day 42). The early onset of watering was associated with a higher percentage of rooting (X2(5) = 11.352, p = 0.045) and had a weak, but non-significant, impact on the final dry root mass (F5,36 = 2.109, p = 0.0631). Importantly, no clear rooting window within 28 days was detected as the majority of cuttings exhibited root development (greater than 50% of cuttings rooted for each individual parent-plant); this suggests that watering at the time of planting P. afra cuttings in-field for restoration may not be necessary. An unexpected, but important, result was that parent-plant identity had a strong interaction with the accumulation of root mass (F36,460 = 5.026, p < 0.001; LR7 = 122.99, p < 0.001). The control treatment, which had no water throughout the experiment, had no root development. These findings suggest that water availability is required for the onset of rooting in P. afra cutting. However, the duration of the experiment was insufficient to detect the point at which P. afra cuttings could no longer initiate rooting once exposed to soil moisture, and thus no rooting window could be defined. Despite harvesting material from the same source population, parent-plant identity strongly impacted root development. Further work is required to characterise the rooting window, and to explore the effect of parent-plant condition on in-field and experimental restoration results; we urge that experiments using P. afra closely track the parent-source at the individual level as this may be a factor that may have a major impact on results.

Automated mapping of Portulacaria afra canopies for restoration monitoring with convolutional neural networks and heterogeneous unmanned aerial vehicle imagery.

Ecosystem restoration and reforestation often operate at large scales, whereas monitoring practices are usually limited to spatially restricted field measurements that are (i) time- and labour-intensive, and (ii) unable to accurately quantify restoration success over hundreds to thousands of hectares. Recent advances in remote sensing technologies paired with deep learning algorithms provide an unprecedented opportunity for monitoring changes in vegetation cover at spatial and temporal scales. Such data can feed directly into adaptive management practices and provide insights into restoration and regeneration dynamics. Here, we demonstrate that convolutional neural network (CNN) segmentation algorithms can accurately classify the canopy cover of Portulacaria afra Jacq. in imagery acquired using different models of unoccupied aerial vehicles (UAVs) and under variable light intensities. Portulacaria afra is the target species for the restoration of Albany Subtropical Thicket vegetation, endemic to South Africa, where canopy cover is challenging to measure due to the dense, tangled structure of this vegetation. The automated classification strategy presented here is widely transferable to restoration monitoring as its application does not require any knowledge of the CNN model or specialist training, and can be applied to imagery generated by a range of UAV models. This will reduce the sampling effort required to track restoration trajectories in space and time, contributing to more effective management of restoration sites, and promoting collaboration between scientists, practitioners and landowners.

Fuel trait effects on flammability of native and invasive alien shrubs in coastal fynbos and thicket (Cape Floristic Region).

In June 2017, extreme fires along the southern Cape coast of South Africa burnt native fynbos and thicket vegetation and caused extensive damage to plantations and residential properties. Invasive alien plants (IAPs) occur commonly in the area and were thought to have changed the behaviour of these fires through their modification of fuel properties relative to that of native vegetation. This study experimentally compared various measures of flammability across groups of native and alien invasive shrub species in relation to their fuel traits. Live plant shoots of 30 species (10 species each of native fynbos, native thicket, and IAPs) were sampled to measure live fuel moisture, dry biomass, fuel bed porosity and the proportions of fine-, coarse- and dead fuels. These shoots were burnt experimentally, and flammability measured in terms of maximum temperature (combustibility), completeness of burn (consumability), and time-to-ignition (ignitability). Multiple regression models were used to assess the relationships between flammability responses and fuel traits, while the Kruskal-Wallis H test was used to establish if differences existed in flammability measures and fuel traits among the vegetation groups. Dry biomass significantly enhanced, while live fuel moisture significantly reduced, maximum temperature, whereas the proportion of fine fuels significantly increased completeness of burn. Unlike other similar studies, the proportion of dead fuels and fuel bed porosity were not retained by any of the models to account for variation in flammability. Species of fynbos and IAPs generally exhibited greater flammability in the form of higher completeness of burn and more rapid ignition than species of thicket. Little distinction in flammability and fuel traits could be made between species of fynbos and IAPs, except that fynbos species had a greater proportion of fine fuels. Thicket species had higher proportions of coarse fuels and greater dry biomass (~fuel loading) than species of fynbos and IAPs. Live fuel moisture did not differ among the vegetation groups, contrary to the literature often ascribing variation in flammability to fuel moisture differences. The fuel traits investigated only explained 21-53% of the variation in flammability and large variation was evident among species within vegetation groups suggesting that species-specific and in situ community-level investigations are warranted, particularly in regard fuel moisture and chemical contents.

The response of geophytes to continuous human foraging on the Cape south coast, South Africa and its implications for early hunter-gatherer mobility patterns.

Current ecological understanding of plants with underground storage organs (USOs) suggests they have, in general, low rates of recruitment and thus as a resource it should be rapidly exhausted, which likely had implications for hunter-gatherer mobility patterns. We focus on the resilience (defined here as the ability of species to persist after being harvested) of USOs to human foraging. Human foragers harvested all visible USO material from 19 plots spread across six Cape south coast (South Africa) vegetation types for three consecutive years (2015-2017) during the period of peak USO apparency (September-October). We expected the plots to be depleted after the first year of harvesting since the entire storage organ of the USO is removed during foraging, i.e. immediate and substantial declines from the first to the second harvest. However, over 50% of the total weight harvested in 2015 was harvested in 2016 and 2017; only after two consecutive years of harvesting, was there evidence of significantly lower yield (p = 0.034) than the first (2015) harvest. Novel emergence of new species and new individuals in year two and three buffered the decline of harvested USOs. We use our findings to make predictions on hunter-gatherer mobility patterns in this region compared to the Hadza in East Africa and the Alyawara in North Australia.

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.

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.

Do Centres of Endemism provide a spatial context for predicting and preserving plant phylogeographic patterns in the Cape Floristic Region, South Africa?

AIM: The evolutionary forces that gave rise to the exceptional plant species richness of the Cape Floristic Region (CFR) have also likely played a role at the intraspecific level (i.e. plant populations)-and thereby generating shared phylogeographic patterns among taxa. Here we test whether plant populations in the CFR exhibit phylogeographic breaks across the boundaries between Centres of Endemism (CoEs). The boundaries between CoEs (derived from the distribution ranges of endemic taxa and currently mapped at a coarse, Quarter Degree Square scale) represent a spatial proxy for the evolutionary diversifying drivers acting on plant taxa in the CFR. LOCATION: The CFR, located along the southern Cape of South Africa. METHODS: Published phylogeographic literature were compiled and spatial patterns of genetic divergence re-analysed to assess the frequency at which CFR plant taxa exhibit phylogeographic breaks either (1) across or (2) within CoE boundaries. Population pairs from each study were compared across and within CoEs and scored as either exhibiting a phylogeographic break or not. RESULTS: Phylogeographic breaks in Cape plants were found to occur across the boundaries of CoEs more often than not. Significantly more population pairs exhibited phylogeographic breaks across CoE boundaries (506 of the 540, χ2 = 886, p < 0.001) and fewer breaks within CoEs (94 of 619, χ2 = 300, p < 0.001) than would be expected if there was equal probability of a genetic break occurring across CoE boundaries. MAIN CONCLUSIONS: The evolutionary forces that have produced and maintained the exceptional plant diversity in the CFR appear to have operated at the population level, producing similar patterns of phylogeographic structuring of plant lineages regardless of life history or taxonomy. This tendency for Cape plants to exhibit shared patterns of spatially structured genetic diversity that match the distribution of endemic taxa may assist CFR phylogeographers to streamline sampling efforts and test novel hypotheses pertaining to the distribution of genetic diversity among CFR plant taxa. Additionally, the resolution at which CoEs are mapped should be refined, which may provide a valuable tool for future conservation planning and the development of precautionary guidelines for the translocation of genetic material during species reintroductions and commercial cultivation of Cape endemic crops. Thus, to answer the question 'Do Centres of Endemism provide a spatial context for predicting and preserving plant phylogeographic patterns in the Cape Floristic Region, South Africa?'-yes, CoEs do appear to be an important tool for Cape phylogeographers. However, the data is limited and more plant phylogeography work is needed in the CFR.

Applied phylogeography of Cyclopia intermedia (Fabaceae) highlights the need for 'duty of care' when cultivating honeybush.

BACKGROUND: The current cultivation and plant breeding of Honeybush tea (produced from members of Cyclopia Vent.) do not consider the genetic diversity nor structuring of wild populations. Thus, wild populations may be at risk of genetic contamination if cultivated plants are grown in the same landscape. Here, we investigate the spatial distribution of genetic diversity within Cyclopia intermedia E. Mey.-this species is widespread and endemic in the Cape Floristic Region (CFR) and used in the production of Honeybush tea. METHODS: We applied High Resolution Melt analysis (HRM), with confirmation Sanger sequencing, to screen two non-coding chloroplast DNA regions (two fragments from the atpI-aptH intergenic spacer and one from the ndhA intron) in wild C. intermedia populations. A total of 156 individuals from 17 populations were analyzed for phylogeographic structuring. Statistical tests included analyses of molecular variance and isolation-by-distance, while relationships among haplotypes were ascertained using a statistical parsimony network. RESULTS: Populations were found to exhibit high levels of genetic structuring, with 62.8% of genetic variation partitioned within mountain ranges. An additional 9% of genetic variation was located amongst populations within mountains, suggesting limited seed exchange among neighboring populations. Despite this phylogeographic structuring, no isolation-by-distance was detected (p > 0.05) as nucleotide variation among haplotypes did not increase linearly with geographic distance; this is not surprising given that the configuration of mountain ranges dictates available habitats and, we assume, seed dispersal kernels. CONCLUSIONS: Our findings support concerns that the unmonitored redistribution of Cyclopia genetic material may pose a threat to the genetic diversity of wild populations, and ultimately the genetic resources within the species. We argue that 'duty of care' principles be used when cultivating Honeybush and that seed should not be translocated outside of the mountain range of origin. Secondarily, given the genetic uniqueness of wild populations, cultivated populations should occur at distance from wild populations that is sufficient to prevent unintended gene flow; however, further research is needed to assess gene flow within mountain ranges.

Application of High Resolution Melt analysis (HRM) for screening haplotype variation in a non-model plant genus: Cyclopia (Honeybush).

AIM: This study has three broad aims: to (a) develop genus-specific primers for High Resolution Melt analysis (HRM) of members of Cyclopia Vent., (b) test the haplotype discrimination of HRM compared to Sanger sequencing, and (c) provide an example of using HRM to detect novel haplotype variation in wild C. subternata Vogel. populations. LOCATION: The Cape Floristic Region (CFR), located along the southern Cape of South Africa. METHODS: Polymorphic loci were detected through a screening process of sequencing 12 non-coding chloroplast DNA segments across 14 Cyclopia species. Twelve genus-specific primer combinations were designed around variable cpDNA loci, four of which failed to amplify under PCR; the eight remaining were applied to test the specificity, sensitivity and accuracy of HRM. The three top performing HRM Primer combinations were then applied to detect novel haplotypes in wild C. subternata populations, and phylogeographic patterns of C. subternata were explored. RESULTS: We present a framework for applying HRM to non-model systems. HRM accuracy varied across the PCR products screened using the genus-specific primers developed, ranging between 56 and 100%. The nucleotide variation failing to produce distinct melt curves is discussed. The top three performing regions, having 100% specificity (i.e. different haplotypes were never grouped into the same cluster, no false negatives), were able to detect novel haplotypes in wild C. subternata populations with high accuracy (96%). Sensitivity below 100% (i.e. a single haplotype being clustered into multiple unique groups during HRM curve analysis, false positives) was resolved through sequence confirmation of each cluster resulting in a final accuracy of 100%. Phylogeographic analyses revealed that wild C. subternata populations tend to exhibit phylogeographic structuring across mountain ranges (accounting for 73.8% of genetic variation base on an AMOVA), and genetic differentiation between populations increases with distance (p < 0.05 for IBD analyses). CONCLUSIONS: After screening for regions with high HRM clustering specificity-akin to the screening process associated with most PCR based markers-the technology was found to be a high throughput tool for detecting genetic variation in non-model plants.

Site selection for subtropical thicket restoration: mapping cold-air pooling in the South African sub-escarpment lowlands.

Restoration of subtropical thicket in South Africa using the plant Portulacaria afra (an ecosystem engineer) has been hampered, in part, by selecting sites that are frost prone-this species is intolerant of frost. Identifying parts of the landscape that are exposed to frost is often challenging. Our aim is to calibrate an existing cold-air pooling (CAP) model to predict where frost is likely to occur in the valleys along the sub-escarpment lowlands (of South Africa) where thicket is dominant. We calibrated this model using two valleys that have been monitored during frost events. To test the calibrated CAP model, model predictions of frost-occurrence for six additional valleys were assessed using a qualitative visual comparison of existing treelines in six valleys-we observe a strong visual match between the predicted frost and frost-free zones with the subtropical thicket (frost-intolerant) and Nama-Karoo shrubland (frost-tolerant) treelines. In addition, we tested the model output using previously established transplant experiments; ∼300 plots planted with P. afra (known as the Thicket-Wide Plots) were established across the landscape-without consideration of frost-to assess the potential factors influencing the survival and growth of P. afra. Here we use a filtered subset of these plots (n = 70), and find that net primary production of P. afra was significantly lower in plots that the model predicted to be within the frost zone. We suggest using this calibrated CAP model as part of the site selection process when restoring subtropical thicket in sites that lie within valleys-avoiding frost zones will greatly increase the likelihood of restoration success.

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 dataset 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 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.

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.

Foraging potential of underground storage organ plants in the southern Cape, South Africa.

Underground storage organs (USOs) serve as a staple source of carbohydrates for many hunter-gatherer societies and they feature prominently in discussions of diets of early modern humans. While the way of life of hunter-gatherers in South Africa's Cape no longer exists, there is extensive ethnographic, historical, and archaeological evidence of hunter-gatherers' use of USOs. This is to be expected, given that the Cape supports the largest concentration of plant species with USOs globally. The southern Cape is the location of several Middle Stone Age sites that are highly significant to research on the origins of behaviourally modern humans, and this provided the context for our research. Here, we evaluate the foraging potential of USOs by identifying how abundant edible biomass is in the southern Cape, how easily it is gathered, and how nutritious it is. One hundred 5 × 5 m plots were assessed in terms of USO species and abundance. Nearly all of the sites sampled (83%) contained edible USOs and some had high concentrations of edible biomass. Extrapolating from these sites suggests that the edible USO biomass falls within the range of biomass observed in areas supporting extant hunter-gatherer communities. The nutritional content for six USO species was assessed; these contained between 40 and 228 calories/100 g. Furthermore, foraging events were staged to provide an indication of the potential return rates for the same six USOs. The target species grow near the soil surface, mostly in sandy soils, and were gathered with minimal effort. Some 50% of the foraging events conducted yielded enough calories to meet the daily requirements of a hunter-gatherer within two hours. In conclusion, we demonstrate that USOs are a readily available source of carbohydrates in the southern Cape landscape and, therefore, there is a strong possibility that USOs played a critical role in providing food for early humans.

Seasonal availability of edible underground and aboveground carbohydrate resources to human foragers on the Cape south coast, South Africa.

The coastal environments of South Africa's Cape Floristic Region (CFR) provide some of the earliest and most abundant evidence for the emergence of cognitively modern humans. In particular, the south coast of the CFR provided a uniquely diverse resource base for hunter-gatherers, which included marine shellfish, game, and carbohydrate-bearing plants, especially those with Underground Storage Organs (USOs). It has been hypothesized that these resources underpinned the continuity of human occupation in the region since the Middle Pleistocene. Very little research has been conducted on the foraging potential of carbohydrate resources in the CFR. This study focuses on the seasonal availability of plants with edible carbohydrates at six-weekly intervals over a two-year period in four vegetation types on South Africa's Cape south coast. Different plant species were considered available to foragers if the edible carbohydrate was directly (i.e. above-ground edible portions) or indirectly (above-ground indications to below-ground edible portions) visible to an expert botanist familiar with this landscape. A total of 52 edible plant species were recorded across all vegetation types. Of these, 33 species were geophytes with edible USOs and 21 species had aboveground edible carbohydrates. Limestone Fynbos had the richest flora, followed by Strandveld, Renosterveld and lastly, Sand Fynbos. The availability of plant species differed across vegetation types and between survey years. The number of available USO species was highest for a six-month period from winter to early summer (Jul-Dec) across all vegetation types. Months of lowest species' availability were in mid-summer to early autumn (Jan-Apr); the early winter (May-Jun) values were variable, being highest in Limestone Fynbos. However, even during the late summer carbohydrate "crunch," 25 carbohydrate bearing species were visible across the four vegetation types. To establish a robust resource landscape will require additional spatial mapping of plant species abundances. Nonetheless, our results demonstrate that plant-based carbohydrate resources available to Stone Age foragers of the Cape south coast, especially USOs belonging to the Iridaceae family, are likely to have comprised a reliable and nutritious source of calories over most of the year.

A new research strategy for integrating studies of paleoclimate, paleoenvironment, and paleoanthropology.

Paleoanthropologists (scientists studying human origins) universally recognize the evolutionary significance of ancient climates and environments for understanding human origins. Even those scientists working in recent phases of human evolution, when modern humans evolved, agree that hunter-gatherer adaptations are tied to the way that climate and environment shape the food and technological resource base. The result is a long tradition of paleoanthropologists engaging with climate and environmental scientists in an effort to understand if and how hominin bio-behavioral evolution responded to climate and environmental change. Despite this unusual consonance, the anticipated rewards of this synergy are unrealized and, in our opinion, will not reach potential until there are some fundamental changes in the way the research model is constructed. Discovering the relation between climate and environmental change to human origins must be grounded in a theoretical framework and a causal understanding of the connection between climate, environment, resource patterning, behavior, and morphology, then move beyond the strict correlative research that continues to dominate the field.

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 sample of clones or fragment sequences from next generation sequencing (NGS). 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 data sets. 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 NGS), especially at the intrageneric or intraspecific level.