Capensis Research Articles

The role of odds ratios in joint species distribution modeling

Joint species distribution modeling is attracting increasing attention these days, acknowledging the fact that individual level modeling fails to take into account expected dependence/interaction between species. These joint models capture species dependence through an associated correlation matrix arising from a set of latent multivariate normal variables. However, these associations offer limited insight into realized dependence behavior between species at sites. We focus on presence/absence data using joint species modeling, which, in addition, incorporates spatial dependence between sites. For pairs of species selected from a collection, we emphasize the induced odds ratios (along with the joint occurrence probabilities); they provide a better appreciation of the practical dependence between species that is implicit in these joint species distribution modeling specifications. For any pair of species, the spatial structure enables a spatial odds ratio surface to illuminate how dependence varies over the region of interest. We illustrate with a dataset from the Cape Floristic Region of South Africa consisting of more than 600 species at more than 600 sites. We present the spatial distribution of odds ratios for pairs of species that are positively correlated and pairs that are negatively correlated under the joint species distribution model.

Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups.

Previous studies show that the indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting ~400 years ago and their descendants are today mixed with Europeans and Asians. To gain insight on the occupants of the Vaalkrans Shelter located at the southernmost tip of Africa, we investigated the genetic make-up of an individual who lived there about 200 years ago. We further contextualize the genetic ancestry of this individual among prehistoric and current groups. From a hair sample excavated at the shelter, which was indirectly dated to about 200 years old, we sequenced the genome (1.01 times coverage) of a Later Stone Age individual. We analyzed the Vaalkrans genome together with genetic data from 10 ancient (pre-colonial) individuals from southern Africa spanning the last 2000 years. We show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter-gatherers and ~20% to a mixed East African-Eurasian source. This genetic make-up is similar to modern-day Khoekhoe individuals from the Northern Cape Province (South Africa) and Namibia, but in the southern Cape, the Vaalkrans man's descendants have likely been assimilated into mixed-ancestry "Coloured" groups. The Vaalkrans man's genome reveals that Khoekhoe pastoralist groups/individuals lived in the southern Cape as late as 200 years ago, without mixing with non-African colonists or Bantu-speaking farmers. Our findings are also consistent with the model of a Holocene pastoralist migration, originating in Eastern Africa, shaping the genomic landscape of historic and current southern African populations.

One in four die from acute infectious illness in an emergency department in Eastern Cape Province, South Africa.

Despite the breadth of data supporting evidence-based practice for sepsis care in high-resource settings, there are relatively few data to guide the management of sepsis in low-resource settings, particularly in areas where HIV and tuberculosis (TB) are prevalent. Furthermore, few studies had broadened sepsis parameters to include all patients with acute infectious illness or followed patients up after hospital discharge. Understanding the epidemiology and outcomes of acute infections in a local context is the critical first step to developing locally informed targeted management strategies. To quantify and describe the incidence of and risk factors for mortality in a cohort of patients with undifferentiated acute infectious illnesses who presented to an emergency department (ED) in the Eastern Cape region of South Africa (SA). In this prospective cohort study, patients with suspected acute infectious illness were enrolled at a district casualty ward in Mthatha, SA, between 1 July and 1 September 2017. Demographic data, interventions, diagnostic studies and disposition were prospectively collected during the initial encounter and during the hospital stay. Follow-up was conducted both in hospital and via phone interviews 30days after the index visit. A total of 301 patients presented to the ED with acute infectious illness during the study period, of whom 54.8% had complete 30-day follow-up. Of the study population, only 5.7% had a complete set of vital signs (heart rate, respiratory rate, blood pressure and temperature) documented. Of the cohort, 51.8% had HIV and 32.9% active or treated TB; 25.2% of patients died within 30 days. Accounting for medical history, diagnosis and ED interventions, risk of mortality was independently associated with age (odds ratio (OR) 1.03; 95% confidence interval (CI) 1.00 - 1.06), HIV-positive status (OR 4.10; 95% CI 1.44 - 11.67) and Quick Sequential (Sepsis-Related) Organ Failure Assessment (qSOFA) score (OR 1.90; 95% CI 1.14 - 3.19) in an adjusted model. No ED interventions were protective for mortality, with intravenous fluid administration associated with increased 30-day mortality in this cohort (OR 3.65; 95% CI 1.38 - 9.62). Among adults with suspected acute infectious illness in Mthatha, SA, 30-day mortality was concerningly high. Mortality was highest in patients with concomitant HIV infection. In particular, vital sign assessment to identify possible sepsis in this cohort is crucial, as it affects mortality to a meaningful extent, yet is often unavailable. Future research is needed on the management of sepsis in low-resource settings, particularly in HIV-positive individuals.

Cash flow management by contractors

The paper focuses on various cash flow management techniques selected and incorporated by contractors into their daily processes and the effects of poor cash flow management on their business. A quantitative research approach was used using a web-based questionnaire. The questionnaire was distributed to all contractors registered with the Master Builders Association within the Eastern Cape Province. Results revealed that majority of contractors successfully implement cash flow management techniques and are therefore able to meet their monthly obligations. Respondents further agreed that late payments are detrimental in terms of their cash flow causing project delays. Increased capital expenses and higher levels of competition in the construction industry market, force the construction companies to consent to an increased number of risks, effectively ensuring their vulnerability to negative impacts on their cash flow and inevitably exposure to unforeseen events that are innate in any construction project. The study was limited to the Eastern Cape region, therefore reducing the targeted population and number of responses. The study investigated the competency level of financial management by building contractors with reference to the implications caused by poor financial management on the contractual parties involved within a project. The aim of the study was to deduce the extent to which contractors in the Eastern Cape implemented effective cash flow management techniques to sustain their businesses. The study highlighted the link between factors negatively impacting cash flow and its subsequent cause of failing contractors within the construction industry. The paper responds to the conference theme given that the effective cash flow management by contractors within their own firms and pertaining to construction projects, promotes the sustainability of the Built Environment.

OCBIL theory examined: reassessing evolution, ecology and conservation in the world’s ancient, climatically buffered and infertile landscapes

AbstractOCBIL theory was introduced as a contribution towards understanding the evolution, ecology and conservation of the biological and cultural diversity of old, climatically buffered, infertile landscapes (OCBILs), especially in the Southern Hemisphere. The theory addresses some of the most intransigent environmental and cultural trends of our time – the ongoing decline of biodiversity and cultural diversity of First Nations. Here we reflect on OCBILs, the origins of the theory, and its principal hypotheses in biological, anthropological and conservation applications. The discovery that threatened plant species are concentrated in the Southwest Australian Floristic Region (SWAFR) on infertile, phosphorous-impoverished uplands within 500 km of the coast formed the foundational framework for OCBIL theory and led to the development of testable hypotheses that a growing literature is addressing. Currently, OCBILs are recognized in 15 Global Biodiversity Hotspots and eight other regions. The SWAFR, Greater Cape Floristic Region of South Africa and South America’s campos rupestres (montane grasslands) are those regions that have most comprehensively been investigated in the context of OCBIL theory. We summarize 12 evolutionary, ecological and cultural hypotheses and ten conservation-management hypotheses being investigated as recent contributions to the OCBIL literature.

A review of Capezoum Adlbauer, 2003 (Coleoptera: Cerambycidae) with the description of two new species from the Succulent Karoo ecosystem in South-Africa.

Capezoum Adlbauer, 2003 is known only from male specimens. Herein, we describe two new species: Capezoum richardi sp. nov. and C. brunneopunctatus sp. nov., from the Northern Cape region in South-Africa. The discovery of these new species, one of them represented by both sexes, allowed us to describe the hitherto unknown female. Moreover, the genus is transferred to the tribe Xystrocerini and a key to the species of the genus is provided. Lastly, the position of Mythozoum Thomson, 1878 in Cerambycidae is discussed.

Active seed sowing can overcome constraints to passive restoration of a critically endangered vegetation type

Invasive alien plants negatively impact ecosystems, but recovery of native vegetation may fail following standard methods of alien species removal alone. Alternative management actions may thus be required. Cape Flats Sand Fynbos is a critically endangered vegetation type in the Cape Floristic Region of South Africa which is threatened by Acacia saligna invasion, but standard clearing methods have failed to restore native vegetation structure. A restoration study was performed comparing passive treatments i.e. clearing without burning (stack-block) versus clearing and burning (burn-block), as well as active intervention by sowing seeds of native species, either initially after burning or a year later, in which seeds were either not pre-treated or pre-treated with smoke and heat exposure before sowing. After two years all treatments resulted in different recovery trajectories, although none resembled the reference condition. Clearing without burning facilitated recovery in less degraded areas with higher initial native shrub cover, but otherwise resulted in limited vegetation recovery. Limited recovery facilitated secondary invasion by herbaceous weeds. Active seed sowing resulted in the highest recovery of native shrub cover and diversity. These findings suggest that passive restoration is constrained by seed limitation, due to the lack of recovery of vegetation components under passive clearing treatment. Active sowing was able to partially overcome this constraint through improved recovery of total shrub cover. However, non-sprouting shrub cover was higher while resprouting shrubs and species of Restionaceae were lower compared to the reference condition. Pre-treatment of seeds before sowing improved establishment of some species. Active treatment involving sowing pre-treated seeds after clearing and burning therefore resulted in best fynbos recovery compared to either of the passive treatments tested. A decision tree has been developed based on these findings in order to guide best protocol for managers.

Evolutionary stability, landscape heterogeneity, and human land-usage shape population genetic connectivity in the Cape Floristic Region biodiversity hotspot.

As human‐induced change eliminates natural habitats, it impacts genetic diversity and population connectivity for local biodiversity. The South African Cape Floristic Region (CFR) is the most diverse extratropical area for plant biodiversity, and much of its habitat is protected as a UNESCO World Heritage site. There has long been great interest in explaining the underlying factors driving this unique diversity, especially as much of the CFR is endangered by urbanization and other anthropogenic activity. Here, we use a population and landscape genetic analysis of SNP data from the CFR endemic plant Leucadendron salignum or “common sunshine conebush” as a model to address the evolutionary and environmental factors shaping the vast CFR diversity. We found that high population structure, along with relatively deeper and older genealogies, is characteristic of the southwestern CFR, whereas low population structure and more recent lineage coalescence depict the eastern CFR. Population network analyses show genetic connectivity is facilitated in areas of lower elevation and higher seasonal precipitation. These population genetic signatures corroborate CFR species‐level patterns consistent with high Pleistocene biome stability and landscape heterogeneity in the southwest, but with coincident instability in the east. Finally, we also find evidence of human land‐usage as a significant gene flow barrier, especially in severely threatened lowlands where genetic connectivity has been historically the highest. These results help identify areas where conservation plans can prioritize protecting high genetic diversity threatened by contemporary human activities within this unique cultural UNESCO site.

Evolution of Tandem Repeats Is Mirroring Post-polyploid Cladogenesis in Heliophila (Brassicaceae).

The unigeneric tribe Heliophileae encompassing more than 100 Heliophila species is morphologically the most diverse Brassicaceae lineage. The tribe is endemic to southern Africa, confined chiefly to the southwestern South Africa, home of two biodiversity hotspots (Cape Floristic Region and Succulent Karoo). The monospecific Chamira (C. circaeoides), the only crucifer species with persistent cotyledons, is traditionally retrieved as the closest relative of Heliophileae. Our transcriptome analysis revealed a whole-genome duplication (WGD) ∼26.15–29.20 million years ago, presumably preceding the Chamira/Heliophila split. The WGD was then followed by genome-wide diploidization, species radiations, and cladogenesis in Heliophila. The expanded phylogeny based on nuclear ribosomal DNA internal transcribed spacer (ITS) uncovered four major infrageneric clades (A–D) in Heliophila and corroborated the sister relationship between Chamira and Heliophila. Herein, we analyzed how the diploidization process impacted the evolution of repetitive sequences through low-coverage whole-genome sequencing of 15 Heliophila species, representing the four clades, and Chamira. Despite the firmly established infrageneric cladogenesis and different ecological life histories (four perennials vs. 11 annual species), repeatome analysis showed overall comparable evolution of genome sizes (288–484 Mb) and repeat content (25.04–38.90%) across Heliophila species and clades. Among Heliophila species, long terminal repeat (LTR) retrotransposons were the predominant components of the analyzed genomes (11.51–22.42%), whereas tandem repeats had lower abundances (1.03–12.10%). In Chamira, the tandem repeat content (17.92%, 16 diverse tandem repeats) equals the abundance of LTR retrotransposons (16.69%). Among the 108 tandem repeats identified in Heliophila, only 16 repeats were found to be shared among two or more species; no tandem repeats were shared by Chamira and Heliophila genomes. Six “relic” tandem repeats were shared between any two different Heliophila clades by a common descent. Four and six clade-specific repeats shared among clade A and C species, respectively, support the monophyly of these two clades. Three repeats shared by all clade A species corroborate the recent diversification of this clade revealed by plastome-based molecular dating. Phylogenetic analysis based on repeat sequence similarities separated the Heliophila species to three clades [A, C, and (B+D)], mirroring the post-polyploid cladogenesis in Heliophila inferred from rDNA ITS and plastome sequences.

Breeding Systems and Pollen-Ovule Ratios inEricaSpecies (Ericaceae) of the Cape Floristic Region

Premise of research. Breeding systems dictate the potential for self-fertilization in plants and may therefore have a strong influence on evolutionary and ecological processes. Previous investigations of breeding systems in Ericaceae indicate variation in self-sterility, but studies from the megadiverse genus Erica are almost entirely lacking. Here we quantify the degree of self-sterility and autofertility in Cape Erica species, quantify pollen-ovule ratios (P/Os), and test whether these are related to each other and vary across species with bird- versus insect-pollination syndromes.Methodology. We used controlled hand-pollinations, analyses of pollen tube development, and P/Os to investigate the breeding systems of 15 taxa (comprising 13 species) of Erica in the Cape Floristic Region of South Africa, spanning most main clades across the phylogeny.Pivotal results. In all but one species, seed set from autonomous selfing was almost absent and significantly lower than that from cross-pollination, and only one species had an autofertility index that was higher than 0.2. In 12 taxa, seed set following self-pollination was significantly reduced compared with that following cross-pollination, and the index of self-incompatibility (ISI) was higher than 0.8 for 10 taxa. Following self-pollination, pollen tubes reached the ovary in all species, and for two species with very low seed set in selfed flowers, fluorescence images revealed that self-pollen tubes entered into the ovules. P/Os ranged from 68 to 320 and are therefore low for obligate outcrossing species. These ratios did not correlate with the ISI and did not vary according to whether species conformed to insect- or bird-pollination syndromes.Conclusions. This study indicates that self-sterility is frequent in Cape Erica species and either involves a late-acting mechanism of self-incompatibility or is due to early inbreeding depression. P/Os in these species are consistently low and do not reflect variation in breeding systems and pollination syndromes.

A monograph of the genus Polhillia (Genisteae: Fabaceae)

Polhillia is a small, but poorly known genus of legumes endemic to the Greater Cape Floristic Region (GCFR) of South Africa. The genus was described three decades ago to accommodate species erroneously placed in Argyrolobium and other Cape legume genera. Polhillia is the third most threatened plant genus in South Africa, hence priority for taxonomic study and current knowledge on distribution patterns are essential for conservation interventions. Eight species were known at the start of this study, all of which are threatened with extinction. Species boundaries were, however, unclear and many Renosterveld fragments, in particular in the Overberg, required further exploration in pursuit of the various Polhillia species. The phylogenetic relationships among species and monophyly of the genus, especially regarding the position of the morphological aberrant P. involucrata, had not been tested. This study was built upon a foundation of widespread field sampling and analysis of herbarium specimens. Having considered morphological, anatomical, palynological and molecular data, we present an updated taxonomy of the genus Polhillia. Morphological characters between species were often obscure and unique characters were uncommon, as such species are recognized based on unique combinations of characters. Pollen and leaf anatomical studies did not provide substantial taxonomically informative characters, although some interspecific differences were noted. Molecular phylogenetic reconstructions confirm Polhillia to be monophyletic and sister to Argyrolobium, and that Argyrolobium may not be monophyletic. The morphologically distinct species, P. involucrata, is strongly supported as sister to the rest of the genus. Internal phylogenetic resolution in Polhillia is weak in many clades, due to the low variability among DNA markers studied, and several polytomies are still present. Based on the morphological and molecular evidence, we place P. involucrata in the new monotypic subgenus Roseopolhillia. Four new species are described (P. fortunata B.du Preez, P. groenewaldii B.du Preez, P. stirtoniana B.du Preez, P. xairuensis B.du Preez), and a previously recognized species (P. canescens C.H.Stirt.) is placed in synonymy under P. connata (Harv.) C.H.Stirt. Red data list assessments are provided for all species to highlight their conservation importance. Maps and compound colour plates are provided for each species.

Decision-making for nature\u2019s contributions to people in the Cape Floristic Region: the role of values, rules and knowledge

Nature conservation on privately owned land depends on land managers’ decision-making. Interactions between values, rules and knowledge (vrk) underpin decision-making, thus, it is important to understand these interactions to support conservation intentions. We investigated how different sets of vrk determine the decision-making context regarding the management and conservation of renosterveld, a critically endangered ecosystem in the Cape Floristic Region, and how this relates to land managers’ perceptions of nature’s contributions to people (NCP). From interviews with thirty land managers, we identified nine value types, four rule types, three knowledge types and 13 different NCP. We found that different vrk combinations can be grouped into three decision-making contexts: Bottom-up conservation, Top-down conservation and Utility. Each context is associated with the perception of different beneficial and detrimental NCP. Regulating NCP are perceived across all contexts, whereas more non-material NCP are associated with a Bottom-up conservation context and relational values, such as family ties. The prevalence of relational values in Bottom-up and Top-down conservation contexts illustrates the complexity and non-substitutability of the dynamic relationships between renosterveld and people. This indicates the importance of plural valuation in nature conservation to foster diverse NCP provided by renosterveld.

Antimicrobial and antibiofilm activity of certain South African plants against the oral pathogen - Streptococcus mutans

Dental caries is a serious oral infection caused by microorganism in the oral cavity. Streptococcus mutans can colonize the teeth surfaces and forming biofilm leading to dental caries. The investigation of the antibacterial activity of the plants’ secondary metabolites may lead to the development of alternative therapeutics to treat multi-resistant bacterial infections. South Africa has unique floral biodiversity especially in the Cape region and many of these plants have been used locally for medicinal use. In this study, the antibacterial activities of several South African plant extracts have been tested against S. mutans in vitro. Psoralea pinnata and Otholobium fruticans showed the highest antimicrobial activity with MIC value of 31.25 μg/mL against S. mutans. The same extracts also effectively inhibited the biofilm formation by S. mutans.

Employee Usage of Mobile Devices Within South African Municipalities, Implications on Policy and Employee Training

This paper focuses on the importance of policies, procedures and employee training and awareness as aid to manage risks associated with the usage of mobile devices in local government entities in the Namakwa District of the Northern Cape region. A quantitative research method was applied in the study by obtaining responses from a sample of participants in the Namakwa District of the Northern Cape region, using closed-ended questions in the questionnaire, which provided the participants with a predetermined list of coded responses. The results were analyzed and indicated that the majority of the respondents do utilize mobile devices in their organizations. In general, these entities make more use of laptops than any other types of mobile devices. The results indicate that these organizations also still apply the traditional approach of providing their employees with specifically approved types of mobile devices (corporate-owned device) and therefore, do not support the Bring-Your-Own-Device or Choose-Your-Own-Device strategy. There is a clear indication that more efforts are required to ensure improvement, specifically relating to the development of a privacy and security policy and/or procedures as well as providing user training and awareness within municipal organizations.

HIV testing and self-testing coverage among men and women in South Africa: an exploration of related factors.

Uptake of HIV testing is critical to halting the spread of HIV. Our study aimed to examine the coverage of HIV testing and self-testing and the individual-level, household-level and community-level factors associated with HIV testing and self-testing awareness. We analysed data of 12 312 men and women from 2016 SADHS and used multilevel mixed-effects models to examine the factors associated with uptake of HIV testing and self-testing awareness. About 80% of participants had ever tested for HIV, and 64% had tested in the past year. Only 49% of adolescents aged 15-19years had ever tested for HIV compared with over 80% of adults. Self-testing awareness was low (22%), and only 2.9% of respondents had ever self-tested for HIV. The odds of having ever tested for HIV were significantly higher among respondents who were aged 25-29 (AOR: 4.02; 95% CI: 3.27-4.95), had a higher level of education (AOR: 3.18; 95% CI: 2.19-4.61), were married (AOR: 1.63; 95% CI: 1.36-1.94), had high media exposure (AOR: 1.23; 95% CI: 1.06-1.44) and had ever had sex (AOR: 5.57; 95% CI: 4.67-6.64), but lower among men (AOR: 0.39; 95% CI: 0.35-0.44). In conclusion, HIV testing coverage is high in South Africa relative to most countries in sub-Saharan Africa, but falls short of the UNAIDS first 95. We found no evidence of socioeconomic and geographic inequalities in access to HIV testing. However, adolescents had a lower level of HIV testing uptake, suggesting a need for interventions to expand testing in this age group.

Remotely sensed characterization of Acacia longifolia invasive plants in the Cape Floristic region of the Western Cape, South Africa

Acacia longifolia, like any other invasive species, poses a threat to the natural ecosystems in South Africa and beyond. In South Africa, the species is reported to cause significant loss to vegetation biodiversity and is associated with high water use. It remains a challenge to understand the extent of their invasion in complex landscapes, where the use of ground-based surveys is difficult. Considering the heterogeneity and complexity of hydrological and ecological processes at catchment scale, the implementation of remote sensing to detect the distribution of these species becomes critical for continuous monitoring of their extent and associated impacts. We, therefore, aim at species-specific characterization of the spatial distribution of Acacia longifolia invasive wood species at catchment scale within the Cape Floristic region located in the Western Cape Province, using Sentinel 2 remotely sensed data. Overall, the distribution of A. Longifolia was found to be patchy and heterogeneous, across the catchment. However, the main hot spots were detected within the fynbos vegetation, low-lying areas, as well as along the southern coastal belt. Although the catchment is predominantly under cultivation, A. longifolia was found to occupy almost 10% of its area. Classification using combined variables, using both vegetation indices and bands produced the highest overall accuracy of 88.66%, than when bands (66.19%) and indices (76.05%) were used as independent dataset. For example, the producer’s classification accuracy of A. longifolia increased by almost 15%, whereas the user’s increased by almost 10% from spectral bands accuracies. The classification of A. longifolia was primarily attributed to near-infrared, short wave-infrared (centered at 2190 nm), red edge (705 and 740 nm), as well as, chlorophyll vegetation index, the leaf water content index, and normalized difference vegetation index, derived using the near-infrared and red-edge band (at 740 nm) variables. The findings of this study underscore the relevance of satellite-based remote sensing in monitoring invasions in natural ecosystems and can be used as baseline information for invasive-species clearing endeavors in the area.

Reconstruction of cold front frequency over Cape Town, South Africa, using daily mean sea level pressure values: 1834–1899

AbstractSurface pressure observations are invaluable for meteorological investigations as they enable reconstructions of and insights to historical large‐scale tropospheric circulation. This article endeavours to use a daily reduced mean sea level pressure (MSLP) series to reconstruct the monthly frequency of cold fronts, associated with mid‐latitude cyclones, overpassing Cape Town (southwestern Cape region of South Africa) during the 19th century. Using modern (2011–2017) daily MSLP data and synoptic charts, the relationship between MSLP values and the probability of a cold front overpassing, is established and applied to historical (1834–1899) MSLP data. Although no significant trend in cold front frequency is measured, greater interannual variability is noted during the first half of the study period (1837–1867). Results indicate a link between lower (higher) cold front frequencies and El Niño (La Niña) events, although not statistically significant. Additionally, correlations between cold front frequency and the Southern Annular Mode (SAM) appear to be weak. Although not statistically robust, we also note an apparent 1–2 year lagged association between years with above (below) average numbers of sunspots and above (below) average numbers of cold fronts.

Floral Color Variation in Drosera cistiflora Is Associated With Switches in Beetle Pollinator Assemblages.

Floral color shifts are thought to be one of the most common evolutionary transitions in plants, and pollinators are often proposed as important selective agents driving these transitions. However, shifts in flower color can also be related to neutral genetic processes or pleiotropy linked with selection via other biotic agents or abiotic factors. Here we ask whether abiotic factors or pollinators provide the best explanation for divergence in flower color among populations of the sundew Drosera cistiflora s.l. (Droseraceae). This species complex in the Greater Cape Floristic Region contains at least five distinctive floral color forms. Abiotic factors do not appear to play a significant role in color determination, as the forms are not specific to a single soil or vegetation type, sometimes co-occur in the same habitat, and maintain their color traits in common-garden and soil switching experiments. Instead, we found strong associations between flower color and the composition of pollinator assemblages which are dominated by hopliine scarab beetles. Pollinator assemblages show geographical structuring, both within and among color forms. This makes it difficult to dissect the roles of geography versus floral traits in explaining pollinator assemblages, but strong pollinator partitioning among color forms at sites where they are sympatric indicates that pollinators may select strongly on color. These results suggest that beetle pollinators are a significant factor in the evolution of D. cistiflora s.l. flower color.

Climate explains population divergence in drought-induced plasticity of functional traits and gene expression in a South African Protea.

Long-term environmental variation often drives local adaptation and leads to trait differentiation across populations. Additionally, when traits change in an environment-dependent way through phenotypic plasticity, the genetic variation underlying plasticity will also be under selection. These processes could create a landscape of differentiation across populations in traits and their plasticity. Here, we performed a dry-down experiment under controlled conditions to measure responses in seedlings of a shrub species from the Cape Floristic Region, the common sugarbush (Protea repens). We measured morphological and physiological traits, and sequenced whole transcriptomes of leaf tissues from eight populations that represent both the climatic and the geographical distribution of this species. We found that there is substantial variation in how populations respond to drought, but we also observed common patterns such as reduced leaf size and leaf thickness, and up-regulation of stress-related and down-regulation of growth-related gene groups. Both high environmental heterogeneity and milder source site climates were associated with higher plasticity in various traits and co-expression gene networks. Associations between traits, trait plasticity, gene networks and the source site climate suggest that temperature may play a greater role in shaping these patterns when compared to precipitation, in line with recent changes in the region due to climate change. We also found that traits respond to climatic variation in an environment-dependent manner: some associations between traits and climate were apparent only under certain growing conditions. Together, our results uncover common responses of P. repens populations to drought, and climatic drivers of population differentiation in functional traits, gene expression and their plasticity.

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

BackgroundClimatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world’s tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa.ResultsWe investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63–5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensification of the cold Benguela current, which caused western aridification and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fluctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by different climatic parameters, and that the niches differed substantially among the clades of the northern group but were similar among clades of the southern group.ConclusionClimatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B–Ptr, Ptt-A and Pv-A.