Michael David Pirie

University of Bergen | UiB · University Museum department of Natural History

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...

This article addresses the challenges involved in estimating the ages of clades using fossils and DNA sequences. We review the principles and problems of placing fossils in trees of extant taxa and using them to constrain the ages of nodes in molecular dating analyses. Endressinia and Futabanthus provide minimum ages of 112 Mya for the stem lineage...

Background: The disproportionate species richness of the world's biodiversity hotspots could be explained by low extinction (the evolutionary "museum") and/or high speciation (the "hot-bed") models. We test these models using the largest of the species rich plant groups that characterise the botanically diverse Cape Floristic Region (CFR): the gen...

Significance Resilience is required to withstand or mitigate the effect of human-induced climate change. Today whole ecosystems are affected by climate change, but our understanding of their evolution and natural response is limited, often restricted to individual populations or species. The enigmatic flora on the tops of the African sky islands is...

We explore the potential impact of conflicting gene trees on inferences of evolutionary history above the species level. When conflict between gene trees is discovered, it is common practice either to analyze the data separately or to combine the data having excluded the conflicting taxa or data partitions for those taxa (which are then recoded as...

The Annonaceae family contains important tropical crops, but the number of species used commercially is limited, and development of other promising species for cultivation is hindered by a lack of genomic resources to support the building of breeding programmes. The family is part of the magnoliids, an ancient lineage of angiosperms for which evolu...

Heathers have been cultivated for several centuries, both the hardy heaths (Calluna, Daboecia and Erica) from the northern hemisphere and the more frost-tender species of Erica from southern Africa known as Cape heaths. In the late 19th century, a number of heather gardens were created, especially in Britain, and the popularity of heathers as long-...

Human‐caused habitat destruction and transformation is resulting in a cascade of impacts to biological diversity, of which arguably the most fundamental is species extinctions. The Global Conservation Consortia (GCC) are a means to pool efforts and expertise across national boundaries and between disciplines in the attempt to prevent such losses in...

The monumental work of Olov Hedberg provided deep insights into the spectacular and fragmented tropical alpine flora of the African sky islands. Here we review recent molecular and niche modelling studies and re-examine Hedberg’s hypotheses and conclusions. Colonisation started when mountain uplift established the harsh diurnal climate with nightly...

The flowering plant family Annonaceae includes important commercially grown tropical crops, but development of promising species is hindered by a lack of genomic resources to build breeding programs. Annonaceae are part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades remain unclear....

Understanding how and why rates of evolutionary diversification vary is a key issue in evolutionary biology, ecology, and biogeography. Evolutionary rates are the net result of interacting processes summarized under concepts such as adaptive radiation and evolutionary stasis. Here, we review the central concepts in the evolutionary diversification...

If you are baffled by the Cape’s bounty of ericas, you have plenty of company – there is even a global research network digging deep to find out why fynbos is dominated by hundreds of different erica species

Understanding how and why rates of evolutionary diversification vary is a key issue in evolutionary biology, ecology, and biogeography. Evolutionary rates are the net result of interacting processes summarized under concepts such as adaptive radiation and evolutionary stasis. Here, we review the central concepts in the evolutionary diversification...

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 Afrot...

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-sp...

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 fl...

Deep relationships and the sequence of divergence among major lineages of angiosperms (magnoliids, monocots and eudicots) remain ambiguous and differ depending on analytical approaches and datasets used. Complete genomes potentially provide opportunities to resolve these uncertainties, but two recently published magnoliid genomes instead deliver fu...

Understanding how and why rates of evolutionary diversification vary is a key issue in evolutionary biology, ecology, and biogeography, and the metaphorical concepts of adaptive radiation and evolutionary stasis describe two opposing aspects causing variation in diversification rates. Here we review the central concepts in the evolutionary diversif...

The coincidence of long distance dispersal 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 quanti...

We present a taxonomic revision of Cremastosperma , a genus of Neotropical Annonaceae occurring in lowland to premontane wet forest, mostly in areas surrounding the Andean mountain chain. We recognise 34 species, describing five as new here: from east of the Andes, C.brachypodum Pirie & Chatrou, sp. nov. and C.dolichopodum Pirie & Maas, sp. nov. ,...

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

Full tables of Cremastosperma collections data (CSV, XLS and DBF formats)

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 Mo...

This 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...

Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools,...

Exon sequence data of markers Exons sequences corresponding to the 134 markers selected for the empirical study and the complete pools of marker selected using each of the methods compared (fasta format).

Sequences alignments Sequences alignments (fasta format).

Selected 70% bootstrap support (BS) consensus gene trees inferred under maximum likelihood with RAxML, summarised with DendroPy/SumTrees and presented using Dendroscope 3.5.7 ( http://dendroscope.org/) The six nuclear markers that delivered the greatest numbers of nodes supported by ≥70% BS (A: marker 4430; B: 12303; C: 14220; D: 17845; E: 20893; F...

Summary table of markers Table documenting markers as represented in Data S1–S4.

Sequence similarity (Transcriptome aggaint empirical dataset) Plot of sequence similarity (transcriptome data; Rhododendron and Vaccinium) against sequence similarity (empirical dataset generated here; Rhododendron and Erica spp.) for individual markers.

Gene trees from empirical data Gene trees inferred under RAxML.

Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools,...

As one of the largest genera of flowering plants, the richness of species in Erica (Ericaceae) is all the more remarkable because > 80% of the > 800 species are endemic to the smallest floral kingdom, the Cape Floristic Region (CFR) of South Africa. In the CFR, pockets of narrowly endemic taxa appear in close juxtaposition with their widespread and...

Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools,...

Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools,...

Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools,...

The use of DNA sequence data in plant systematics has brought us closer than ever to formulating well-founded hypotheses about phylogenetic relationships, and phylogenetic research keeps on revealing that plant genera as traditionally circumscribed often are not monophyletic. Here, we assess the monophyly of genera documented in Rothmaler's "Exkurs...

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...

Gene trees from independent molecular markers often differ. Simple data matrix concatenation cannot represent the various biologically meaningful processes that underlie these differences, and in an age of high-throughput DNA sequencing and coalescent-based species tree inference methods, the approach seems increasingly quaint. I argue that concat...

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...

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 his