Evolution of leaf anatomy in arid environments – A case study in southern African Tetraena and Roepera (Zygophyllaceae)

The dry biomes of southern Africa (Desert, Nama Karoo and Succulent Karoo) are home to a rich and diverse xerophytic flora. This flora includes two morphologically diverse clades of Zygophyllaceae, Tetraena and Roepera (Zygophylloideae), which inhabit some of the most arid habitats in the region. Using a plastid phylogeny of Zygophylloideae we assess whether the evolution of putatively adaptive traits (leaf shape, vasculature, mode of water storage and photosynthetic type: C3 versus C4) coincides with the successful colonisation of environments with different drought regimes within southern Africa. Our results show general niche conservatism within arid habitats in Tetraena, but niche shift…

When do different C4 leaf anatomies indicate independent C4 origins? Parallel evolution of C4 leaf types in Camphorosmeae (Chenopodiaceae).

Broad-scale phylogenetic studies give first insights in numbers, relationships, and ages of C 4 lineages. They are, however, generally limited to a model that treats the evolution of the complex C4 syndrome in different lineages as a directly comparable process. Here, we use a resolved and well-sampled phylogenetic tree of Camphorosmeae, based on three chloroplast and one nuclear marker and on leaf anatomical traits to infer a more detailed picture of C4 leaftype evolution in this lineage. Our ancestral character state reconstructions allowed two scenarios: (i) Sedobassia is a derived C3/C4 intermediate, implying two independent gains of C4 in Bassia and Camphorosma; or (ii) Sedobassia is a…

Phylogenomic Analysis Reveals Deep Divergence and Recombination in an Economically Important Grapevine Virus

The evolutionary history of the exclusively grapevine (Vitis spp.) infecting, grapevine leafroll-associated virus 3 (GLRaV-3) has not been studied extensively, partly due to limited available sequence data. In this study we trace the evolutionary history of GLRaV-3, focussing on isolate GH24, a newly discovered variant. GH24 was discovered through the use of next-generation sequencing (NGS) and the whole genome sequence determined and validated with Sanger sequencing. We assembled an alignment of all 13 available whole genomes of GLRaV-3 isolates and all other publicly available GLRaV-3 sequence data. Using multiple recombination detection methods we identified a clear signal for recombinat…

Floral Color, Anthocyanin Synthesis Gene Expression and Control in Cape Erica Species

Introduction: The Cape Floristic Region (CFR) is a biodiversity hotspot, recognized globally for its unusually high levels of endemism. The origins of this biodiversity are a long-standing topic of research. The largest “Cape clade,” Erica, radiated dramatically in the CFR, its ca. 690 species arising within 10–15 Ma. Notable between- and within-species flower color variation in Erica may have contributed to the origins of species diversity through its impact on pollinator efficiency and specificity. Methods: We investigate the expression and function of the genes of the anthocyanin biosynthesis pathway that controls floral color in 12 Erica species groups using RT-qPCR and UPLC-MS/MS. Resu…

Diversification in evolutionary arenas - assessment and synthesis

Abstract Understanding how and why rates of evolutionary diversification vary is a central issue in evolutionary biology and ecology. The concept of adaptive radiation has attracted much interest, but is metaphorical and verbal in nature, making it difficult to quantitatively compare different evolutionary lineages or geographic regions. In addition, the causes of evolutionary stasis are relatively neglected. Here we review the central concepts in the evolutionary diversification literature and bring these together by proposing a general framework for estimating rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions and across spat…

Back to Gondwanaland: can ancient vicariance explain (some) Indian Ocean disjunct plant distributions?

Oceans, or other wide expanses of inhospitable environment, interrupt present day distributions of many plant groups. Using molecular dating techniques, generally incorporating fossil evidence, we can estimate when such distributions originated. Numerous dating analyses have recently precipitated a paradigm shift in the general explanations for the phenomenon, away from older geological causes, such as continental drift, in favour of more recent, long-distance dispersal (LDD). For example, the ‘Gondwanan vicariance’ scenario has been dismissed in various studies of Indian Ocean disjunct distributions. We used the gentian tribe Exaceae to reassess this scenario using molecular dating with mi…

Accessions details from Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of South America

Accessions details for samples used and GenBank accession numbers

Testing reticulate versus coalescent origins of Erica lusitanica using a species phylogeny of the northern heathers (Ericeae, Ericaceae).

Whilst most of the immense species richness of heathers (Calluna, Daboecia and Erica: Ericeae; Ericaceae) is endemic to Africa, particularly the Cape Floristic Region, the oldest lineages are found in the Northern Hemisphere. We present phylogenetic hypotheses for the major clades of Ericeae represented by multiple accessions of all northern Erica species and placeholder taxa for the large nested African/Madagascan clade. We identified consistent, strongly supported conflict between gene trees inferred from ITS and chloroplast DNA sequences with regard to the position of Erica lusitanica. We used coalescent simulations to test whether this conflict could be explained by coalescent stochasti…

Which changes are needed to render all genera of the German lora monophyletic?

53 p., gráf.

Unique records for species distribution modelling from Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of South America

Numbers of unique records and area under the curve per species included in the species distribution modelling

Independent climate and soil variables from Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of South America

The eight independent climate layers and ten independent soil variable layers used for species distribution modelling

Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica.

Abstract Background The coincidence of long distance dispersal (LDD) and biome shift is assumed to be the result of a multifaceted interplay between geographical distance and ecological suitability of source and sink areas. Here, we test the influence of these factors on the dispersal history of the flowering plant genus Erica (Ericaceae) across the Afrotemperate. We quantify similarity of Erica climate niches per biogeographic area using direct observations of species, and test various colonisation scenarios while estimating ancestral areas for the Erica clade using parametric biogeographic model testing. Results We infer that the overall dispersal history of Erica across the Afrotemperate…

Taxas de substituições das Annonaceas: uma perspectiva do modelo códon

The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these…

A broader model for C 4 photosynthesis evolution in plants inferred from the goosefoot family (Chenopodiaceae s.s.)

C 4 photosynthesis is a fascinating example of parallel evolution of a complex trait involving multiple genetic, biochemical and anatomical changes. It is seen as an adaptation to deleteriously high levels of photorespiration. The current scenario for C 4 evolution inferred from grasses is that it originated subsequent to the Oligocene decline in CO 2 levels, is promoted in open habitats, acts as a pre-adaptation to drought resistance, and, once gained, is not subsequently lost. We test the generality of these hypotheses using a dated phylogeny of Amaranthaceae s.l. (including Chenopodiaceae), which includes the largest number of C 4 lineages in eudicots. The oldest chenopod C 4 lineage da…

The evolution of dwarf shrubs in alpine environments: a case study ofAlchemillain Africa

BACKGROUND AND AIMS Alpine and arctic environments worldwide, including high mountains, are dominated by short-stature woody plants (dwarf shrubs). This conspicuous life form asserts considerable influence on local environmental conditions above the treeline, creating its own microhabitat. This study reconstructs the evolution of dwarf shrubs in Alchemilla in the African tropical alpine environment, where they represent one of the largest clades and are among the most common and abundant plants. METHODS Different phylogenetic inference methods were used with plastid and nuclear DNA sequence markers, molecular dating (BEAST and RelTime), analyses of diversification rate shifts (MEDUSA and BA…

Do pollinator distributions underlie the evolution of pollination ecotypes in the Cape shrub Erica plukenetii?

Background and aims According to the Grant-Stebbins model of pollinator-driven divergence, plants that disperse beyond the range of their specialized pollinator may adapt to a new pollination system. Although this model provides a compelling explanation for pollination ecotype formation, few studies have directly tested its validity in nature. Here we investigate the distribution and pollination biology of several subspecies of the shrub Erica plukenetii from the Cape Floristic Region in South Africa. We analyse these data in a phylogenetic context and combine these results with information on pollinator ranges to test whether the evolution of pollination ecotypes is consistent with the Gra…

Underestimated regional species diversity in the Cape Floristic Region revealed by phylogenetic analysis of the Erica abietina/E. viscaria clade (Ericaceae)

Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of the South American continent

AbstractThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100033). Much of the immense present day biological diversity of Neotropical rainforests originated from the Miocene onwards, a period of geological and ecological upheaval in South America. We assess the impact of the Andean orogeny, drainage of lake Pebas, and closure of the Panama Isthmus on two clades of trees (Cremastosperma, c. 31 spp.; and Mosannona, c. 14 spp.; both Annonaceae) found in humid forest distributed across the transition zones between the Andes and Western (lowland) Amazonia and between Central and South America. We inferred phylogeni…

An approach to determining anthocyanin synthesis enzyme gene expression in an evolutionary context: an example from Erica plukenetii

Abstract Background and Aims Floral colour in angiosperms can be controlled by variations in the expression of the genes of the anthocyanin pathway. Floral colour shifts influence pollinator specificity. Multiple shifts in floral colour occurred in the diversification of the genus Erica (Ericaceae), from plesiomorphic pink to, for example, red or white flowers. Variation in anthocyanin gene expression and its effects on floral colour in the red-, pink- and white-flowered Erica plukenetii species complex was investigated. Methods Next generation sequencing, reverse transcriptase PCR and real-time reverse transcriptase quantitative PCR were used to quantify anthocyanin gene expression. Key Re…

Parallel diversifications of Cremastosperma and mosannona (annonaceae), tropical rainforest trees tracking neogene upheaval of South America

Much of the immense present day biological diversity of Neotropical rainforests originated from the Miocene onwards, a period of geological and ecological upheaval in South America. We assess the impact of the Andean orogeny, drainage of Lake Pebas and closure of the Panama isthmus on two clades of tropical trees ( Cremastosperma , ca 31 spp.; and Mosannona , ca 14 spp.; both Annonaceae). Phylogenetic inference revealed similar patterns of geographically restricted clades and molecular dating showed diversifications in the different areas occurred in parallel, with timing consistent with Andean vicariance and Central American geodispersal. Ecological niche modelling approaches show phyloge…

Diversification in evolutionary arenas – assessment and synthesis

Understanding how and why rates of evolutionary diversification vary is a central issue in evolutionary biology, ecology and biogeography. The concept of adaptive radiation has attracted much interest, but is metaphorical and verbal in nature, making it difficult to quantitatively compare different evolutionary lineages or geographic regions. In addition, the causes of evolutionary stasis are relatively neglected. Here we review the central concepts in the evolutionary diversification literature and bring these together by proposing a general framework for studying rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions and across s…

Sequence matrices from Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of South America

Sequence matrices analysed

Supplementary material 2 from: Pirie MD, Chatrou LW, Maas PJM (2018) A taxonomic revision of the Neotropical genus Cremastosperma (Annonaceae), including five new species. PhytoKeys 112: 1-141. https://doi.org/10.3897/phytokeys.112.24897

Full tables of Cremastosperma collections data (CSV, XLS and DBF formats) : Data type: occurences

Supplementary material 1 from: Pirie MD, Chatrou LW, Maas PJM (2018) A taxonomic revision of the Neotropical genus Cremastosperma (Annonaceae), including five new species. PhytoKeys 112: 1-141. https://doi.org/10.3897/phytokeys.112.24897

A file incorporating the georeferenced part of this data that can be opened in Google Earth :

Data from: Parallel diversifications of Cremastosperma and Mosannona (Annonaceae), tropical rainforest trees tracking Neogene upheaval of South America

Much of the immense present day biological diversity of Neotropical rainforests originated from the Miocene onwards, a period of geological and ecological upheaval in South America. We assess the impact of the Andean orogeny, drainage of lake Pebas, and closure of the Panama Isthmus on two clades of tropical trees (Cremastosperma, c. 31 spp.; and Mosannona, c. 14 spp.; both Annonaceae). Phylogenetic inference revealed similar patterns of geographically restricted clades and molecular dating showed diversifications in the different areas occurred in parallel, with timing consistent with Andean vicariance and Central American geodispersal. Ecological niche modelling approaches show phylogenet…