Biology subjects

Pirie, M. D.

Publications and source records attributed to Pirie, M. D..

5 recordsLinked to original sources

bioRxiv2026

Gene tree discordance, rapid diversification and convergence impact phylogenetic inference in Zygophylloideae

The Zygophyllaceae subfamily Zygophylloideae includes seven genera and around 180 species distributed worldwide particularly in arid areas where they show adaptations to drought including C4 and CAM photosynthesis. Phylogenetic relationships of Zygophylloideae have been analysed in several studies using Sanger sequenced markers, but none have been able to resolve all deeper relationships between genera in the subfamily. Here, we use ion semi-conductor sequencing of chloroplast and nuclear ribosomal regions to analyse these relationships and assess why they have proved so challenging to resolve. We sequenced 39 chloroplast genes and nuclear ribosomal 18S, 5.8S, and 26S genes and internal transcribed spacers (ITS) for key species of Zygophyllum sensu stricto, Roepera, Tetraena, Fagonia, Zygophyllum stapffii and monotypic Augea capensis; and Tribulus of the subfamily Tribuloideae as outgroup. We aligned these with data from published chloroplast genomes followed by phylogenetic analyses using Maximum Likelihood and Bayesian approaches, summarising phylogenetic results separately for non-coding introns and intergenic spacers, and for genes that are, or are not, involved in photosynthesis. We combined the chloroplast data with sequences of three highly variable noncoding chloroplast regions used in previous studies of greater numbers of taxa, and similarly the nuclear ribosomal data with more densely sampled ITS sequences and assessed whether adding such data resulted in improved support for consistent topologies. We used a chloroplast sequence matrix to infer a dated phylogeny. Adding data did not always improve phylogenetic resolution which was apparently impacted by non-informative variation in chloroplast photosynthesis related genes as well as by conflicting chloroplast and nuclear signals. Chloroplast genes not related to photosynthesis provide robust support for a topology that is consistent with independent data and may therefore represent a useful species tree hypothesis. The cause of the gene tree conflicts remains unclear: potential explanations include functional constraints in photosynthesis related genes and introgressive hybridization and/or incomplete lineage sorting during an ancient rapid divergence. Further testing will require a broader sampling of lineages with different photosynthetic modes and multiple informative, independent, and selectively neutral gene trees.

evolutionary biology↗

bioRxiv2023

The dynamics of species divergence in South Africa's megadiverse Cape region.

Deciphering the ecological and geographic factors that influence the dynamics of population divergence can aid in understanding why some groups of organisms diversify more prolifically than others. One such diverse group is the heathers (Erica, Ericaceae), whose exceptional species richness in the Cape Floristic Region is enigmatic. Here, we study Erica abietina, a small but highly variable species complex with four described subspecies differing in geographic range, habitat, and floral characters associated with pollination. To understand the factors and forces that shaped its evolution, we evaluate the status of the subspecies and test for hybridisation, introgression, pollinator-driven divergence, and geographic population structure using genotyping-by-sequencing on samples across the entire distribution. We find that the four subspecies form variably distinct genetic groups, however, the most widespread subspecies exhibits cryptic diversity comprising two independent lineages that are geographically isolated and occur on different soil types. Phylogenetic results suggest that shifts between bird- and insect-pollination syndromes have occurred twice independently, with accompanying genetic divergence. However, for one pair of genetically distinct populations (FST{approx} 0.06) with different pollinators we uncover several individuals of hybrid origin at a site where they occur sympatrically. Together, these results suggest that floral differentiation driven by divergent selection acts in concert with geographic isolation to maintain reproductive isolation. Finally, we show that a reticulate history involving "ghost" introgression best explains the groups evolution. Our results reveal a highly dynamic system whose diversity has been shaped by a variety of interacting forces, and we suggest that such systems are likely to have contributed substantially to the diversity of Erica and the Cape flora in general.

evolutionary biology↗

bioRxiv2019

Diversification in evolutionary arenas -- assessment and synthesis

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 diversification literature and synthesize these into a simple, general framework for studying rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions and across spatial and temporal scales. Our framework describes the diversification rate (d) as a function of the abiotic environment (a), the biotic environment (b) and clade-specific phenotypes or traits (c); thus d[~]a,b,c. We refer to the four components (a-d) and their interactions collectively as the Evolutionary Arena. We outline analytical approaches to this framework and present a case study on conifers, for which we parameterise the general model. We also discuss three conceptual examples: the Lupinus radiation in the Andes in the context of emerging ecological opportunity and fluctuating connectivity due to climatic oscillations; oceanic island radiations in the context of island formation and erosion; and biotically driven radiations of the Mediterranean orchid genus Ophrys. The results of the conifer case study are consistent with the long-standing scenario that low competition and high rates of niche evolution promote diversification. The conceptual examples illustrate how using the synthetic Evolutionary Arena framework helps to identify and structure future directions for research on evolutionary radiations. In this way, the Evolutionary Arena framework promotes a more general understanding of variation in evolutionary rates by making quantitative results comparable between case studies, thereby allowing new syntheses of evolutionary and ecological processes to emerge.

evolutionary biology↗

bioRxiv2018

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

AO_SCPCAPBSTRACTC_SCPCAPThe 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 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. We infer that the overall dispersal history of Erica across the Afrotemperate is the result of infrequent colonisation limited by geographic proximity and niche similarity. However, the Drakensberg Mountains represent a colonisation sink, rather than acting as a \"stepping stone\" between more distant and ecologically dissimilar Cape and Tropical African regions. Strikingly, the most dramatic examples of species radiations in Erica were the result of single unique dispersals over longer distances between ecologically dissimilar areas, contradicting the rule of phylogenetic biome conservatism. These results highlight the importance of rare biome shifts, in which a unique dispersal event fuels evolutionary radiation.\n\nThis article has been peer-reviewed and recommended by: Peer Community in Evolutionary Biology (DOI: 10.24072/pci.evolbiol.100065)

evolutionary biology↗

bioRxiv2017

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

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 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 phylogenies based on c. 80% of recognised species of each clade using plastid and nuclear encoded sequence markers, revealing similar patterns of geographically restricted clades. Using molecular dating we showed that diversifications in the different areas occurred in parallel, with timing consistent with Andean vicariance and Central American geodispersal. In apparent contradiction of high dispersal abilities of rainforest trees, Cremastosperma clades within Amazonia are also geographically restricted, with a southern/montane clade that appears to have diversified along the foothills of the Andes sister to one of more northern/lowland species that diversified in a region once inundated by lake Pebas. Ecological niche modelling approaches show phylogenetically conserved niche differentiation, particularly within Cremastosperma. Niche similarity and recent common ancestry of Amazon and Guianan Mosannona species contrasts with dissimilar niches and more distant ancestry of Amazon, Venezuelan and Guianan species of Cremastosperma suggesting that this element of the similar patterns of disjunct distributions in the two genera is instead a biogeographic parallelism, with differing origins. The results provide further independent evidence for the importance of the Andean orogeny, the drainage of Lake Pebas, and the formation of links between South and Central America in the evolutionary history of Neotropical lowland rainforest trees.

evolutionary biology↗