Consistent phenological shifts in the making of a biodiversity hotspot: the Cape flora

Background The best documented survival responses of organisms to past climate change on short (glacial-interglacial) timescales are distributional shifts. Despite ample evidence on such timescales for local adaptations of populations at specific sites, the long-term impacts of such changes on evolutionary significant units in response to past climatic change have been little documented. Here we use phylogenies to reconstruct changes in distribution and flowering ecology of the Cape flora - South Africa's biodiversity hotspot - through a period of past (Neogene and Quaternary) changes in the seasonality of rainfall over a timescale of several million years. Results Forty-three distributional and phenological shifts consistent with past climatic change occur across the flora, and a comparable number of clades underwent adaptive changes in their flowering phenology (9 clades; half of the clades investigated) as underwent distributional shifts (12 clades; two thirds of the clades investigated). Of extant Cape angiosperm species, 14-41% have been contributed by lineages that show distributional shifts consistent with past climate change, yet a similar proportion (14-55%) arose from lineages that shifted flowering phenology. Conclusions Adaptive changes in ecology at the scale we uncover in the Cape and consistent with past climatic change have not been documented for other floras. Shifts in climate tolerance appear to have been more important in this flora than is currently appreciated, and lineages that underwent such shifts went on to contribute a high proportion of the flora's extant species diversity. That shifts in phenology, on an evolutionary timescale and on such a scale, have not yet been detected for other floras is likely a result of the method used; shifts in flowering phenology cannot be detected in the fossil record

Macro-evolutionary and macro-ecological studies on the Cape flora, with focus on the Pentaschistis clade (Poaceae)

Diese Arbeit behandelt die Makroevolution und die Makroökologie einer artenreichen Gruppe von Grasen der Kapflora (der Pentaschistis „Clade“), und anderer „Clades“, welche dieselbe Verbreitung aufweisen. Im ersten Kapitel untersuche ich die Evolution und Funktion von mehrzelligen Drüsen und von anatomischen Blatttypen in der Pentaschistis Gruppe. Um Merkmalsevolution zu untersuchen, benötigt man eine phylogenetische Hypothese. Schliesslich werden einige unklare Punkte betreffend zwischenartlichen Beziehungen aufgelöst. Prionanthium ist innerhalb Pentaschistis anzusiedeln und dieser „Clade“ kann als Schwestergruppe zu Pentameris und Pentaschistis tysonii betrachtet werden. Im zweiten Kapitel untersuche ich den Artenreichtum des Pentaschistis „Clade“ in der Kapflora, mit der Drakensberg Region als Vergleich. Die Habitatsdiversität der Landstriche (zwischen Regionen) und die Habitatsunterschiede zwischen unterschiedlichen Landstrichen (innerhalb der Regionen) werden verglichen. Diese Resultate werden also Vorhersage von Artreichtum und Artenfluktuation für die jeweiligen Regionen getestet. Trotz einer gut untersuchten Flora werden immer noch neue Arten von der Region der Kapflora (CFR) entdeckt und beschrieben. Kapitel drei ist eine Beschreibung von dreier neuer Arten der CFR. Kapitel vier ist eine Metaanalyse die sich auf die Ursprünge der „Cape Clades“ konzentriert, welche ca. 50% der am Kap vorkommenden Pflanzenarten ausmachen. Die „Cape Clades“ haben räumlich und zeitlich sehr unterschiedliche Ursprünge. Kapitel fünf untersucht die Wanderrouten von vier Linien, welche hauptsächlich am Kap beheimatet sind, durch die Regionen des gemässigten Afrikas. Ein generelles Migrationsmuster um die Region des gemässigten Afrikas wird identifiziert. Zusätzlich wird das Ausmass lokaler Diversifikation in verschiedenen Regionen verglichen. Abstract This thesis is a macro-evolutionary and macro-ecological study of a species rich group of grasses from the Cape flora (the Pentaschistis clade), and other clades which share its distribution. In chapter one I investigate the evolution and function of multicellular glands and leaf anatomical types in the Pentaschistis clade, using a phylogenetic approach to understand how often, and under which circumstances glands were gained, maintained or lost. Some issues regarding inter-generic relationships are resolved. Prionanthium is nested within Pentaschistis and this clade is sister to Pentameris plus Pentaschistis tysonii. In chapter two I investigate the species richness of the Pentaschistis clade in the Cape Floristic Region (Cape), using the Drakensberg region as a comparison. The habitat heterogeneity of landscapes and turnover between landscapes are compared between the Cape and the Drakensberg, and also tested as predictors of species richness and turnover in each area. Chapter three is the description of three new species from the CFR; despite being a well collected flora, the discovery and description of new species from the CFR are continuing. Chapter four is a meta analysis focussing on the origins of the ‘Cape clades’, which represent ~50% of the species in the Cape flora. A wide range of source areas is identified as well as a wide time span over which the recruitment into the Cape took place. In chapter five I investigate the migration routes of Cape centred lineages, through the Afrotemperate Regions. Four lineages are included in this meta analysis. A general pattern of migrations around the Afrotemperate Region is identified and the ages of these migrations are estimated. The rates of diversification in each of the Afrotemperate regions are compared. 17

The migration of the palaeotropical arid flora: Zygophylloideae as an example

The rate and direction of biotic exchange between the Palaeotropical arid floras of Asia, Africa, and Australia is poorly understood because of a lack of phylogenetic hypotheses for relevant plant groups. Periodic aridification may have facilitated migrations of arid-adapted plants between southwestern Africa and the Horn of Africa as recently as the last glacial maximum, allowing further exchange with the arid floras of Asia. However, no conclusive evidence of the age and direction of such migrations have been documented. We use a molecular phylogeny of the Zygophylloideae to infer a biogeographic scenario for the arid Palaeotropics, using relaxed clock dating and likelihood and parsimony based ancestral area reconstruction methods. We infer up to five migrations across the African continent (in contrast to just one each to Australia and Asia from Africa). The three most recent were in the Pliocene/Pleistocene and from southern to northern Africa, while the oldest dates to the Oligocene to Miocene. For the recruitment of the arid Palaeotropical flora, the preponderance of migrations across the African continent points to a repeated pattern of dispersal mediated by periodically more contiguous habitat, the so called `African arid corridor,' with rarer long distance dispersal events between other disjunct areas

Soil carbon sequestration potential bounded by population growth, land availability, food production, and climate change

Improving soil management to enhance soil carbon sequestration (SCS)—a cost-efficient carbon dioxide (CO2) removal approach—can result in co-benefits or trade-offs. Here we address this issue by setting up a modeling framework for Switzerland that combines soil carbon (C) storage, food production and agricultural greenhouse gas (GHG) emissions. The link to food production is crucial because crop types and livestock numbers influence soil organic C (SOC) stocks, through soil C inputs from plants and manure. We estimated SCS rates for the years 2020–2050 for three scenarios, each with two variants for biochar: cover cropping (0.30 t CO2 equivalents [CO2-eq] ha−1 yr−1), biochar addition (0.36–1.8 t CO2-eq ha−1 yr−1) and agroforestry-biochar addition (2.2–2.3 t CO2-eq ha−1 yr−1). Different limiting factors (land and biomass availability, population growth) affected SCS rates and indicated that they cannot be sustained until 2100 under all scenarios (cover cropping: 0.10 t CO2-eq ha−1 yr−1 [2051–2100]; biochar addition: 0.35–1.8 t CO2-eq ha−1 yr−1; agroforestry-biochar addition: 1.0–1.7 t CO2-eq ha−1 yr−1). This information together with the associated GHG emissions is critical for planning net zero strategies and highlights the importance of integrated assessments that capture links between SCS and the food system

Model uncertainty in ancestral area reconstruction: a parsimonious solution?

Increasingly complex likelihood-based methods are being developed to infer biogeographic history. The results of these methods are highly dependent on the underlying model which should be appropriate for the scenario under investigation. Our example concerns the dispersal among the southern continents of the grass subfamily Danthonioideae (Poaceae). We infer ancestral areas and dispersals using likelihood-based Bayesian methods and show the results to be indecisive (reversible-jump Markov chain Monte Carlo; RJ-MCMC) or contradictory (continuous-time Markov chain with Bayesian stochastic search variable selection; BSSVS) compared to those obtained under Fitch parsimony (FP), in which the number of dispersals is minimised. The RJ-MCMC and BSSVS results differed because of the differing (and not equally appropriate) treatments of model uncertainty under these methods. Such uncertainty may be unavoidable when attempting to infer a complex likelihood model with limited data, but we show with simulated data that it is not necessarily a meaningful reflection of the credibility of a result. At higher overall rates of dispersal FP does become increasingly inaccurate. However, at and below the rate observed in Danthonioideae multiple dispersals along branches are not observed and the correct root state can be inferred reliably. Under these conditions parsimony is a more appropriate model

Loss of soil organic carbon in Swiss long-term agricultural experiments over a wide range of management practices

Soil carbon sequestration (SCS) is one of the cheapest and technically least demanding carbon dioxide (CO2) removal (CDR) or negative CO2 emission technologies. For a realistic assessment of SCS, it is critical to evaluate how much carbon (C) can be stored in soil organic matter under actual agricultural practices. This includes typical crop rotations and fertilization strategies, depends on resources that are available (e.g. farmyard manure (FYM)) and are affordable for farmers. Furthermore, it is important to assess SCS based on given climatic and soil conditions. Here, we evaluate changes in soil C storage for Switzerland using data from eleven long-term field experiments on cropland and permanent grassland that include common local practices. At all sites, changes in soil organic carbon (SOC) stocks were measured in topsoil (∼0-0.2 m) in response to a total of 80 different treatments including different types of mineral or organic fertilization (e.g. FYM, slurry, peat, compost) or soil management (tillage vs. no-till). The treatments were applied to different, diverse crop rotations or grass mixtures that are representative for Switzerland. We found that topsoils lost C at an average rate of 0.29 Mg C ha−1 yr−1, although many of the investigated treatments were expected to lead to SOC increases. Based on a linear mixed effects model we showed that SOC change rates (ΔSOC) were driven by C inputs to soil (harvest residues and organic fertilizer), soil cover and initial SOC stocks. The type of land use or soil tillage had no significant effect. Our analysis suggests that current efforts to manage soils sustainably need to be intensified and complemented with further techniques if Switzerland wants to achieve the goal of the 4 per 1000 initiative