Developing new tools to address the impact of climate change on the evolutionary and distributional history in plant lineages

Resumen

With the Chicxulub “the dinosaur killer” meteor impact began the Cenozoic Era, an era that covers the last 65 million years of the Earth’s history. As with all the other Phanerozoic eras, the Cenozoic has been shaped by drastic environmental changes at all spatial scales, with the late Miocene Epoch attracting recent interest as a potential model system for testing future climate change scenarios. These environmental changes for this era are well documented and provide an ideal foundation from which to understand relationships between carbon cycling, climate, and species’ evolutionary and distributional history. Present day background extinction rates are higher than what would be expected from fossil record inferences, indicating that the Earth’s sixth mass extinction event (MME) may have already arrived. Here a MME is defined as significant losses of species diversity in a significantly short time period; linked to major long-term environmental change or catastrophic, geological events; and responsible for major ecosystem reordering and change. There is a belief that current background extinction rates are higher than those that caused the Big Five extinctions in geological time, and if these high rates were to continue, extinction magnitudes would be comparable in size of those of the Big Five in as little as three hundred years. With these high background extinction rates, there is a disproportionate loss of evolutionary history happening now in the Anthropocene Epoch, but as to how much of this evolutionary history loss is anthropogenic-induced extinction and how much is just natural cycling of diversification rates is unclear. There is a great need for future research, for much is still unknown in terms of understanding: whether species threatened with extinction will definitely become extinct or if they are instead experiencing a natural period of low diversification; whether the present day background extinction rates will continue their upward trajectory; and how reliable the background extinction rates in well-studied taxa can be extrapolated to other species. This understanding would allow for a more accurate classification of “threatened”, even if this global extinction could take up to 100,000 years to occur, and hence aid in the decision as to where conservation priorities should focus. The current concern on anthropogenic-induced climate change and its impact on biodiversity levels has increased the interest in reconstructing past species’ responses to climatic events, with responses defined as: adaptation (speciation may result); persistence in geographical locations; geographic range shifts (displacement, expansion and contraction); and extinctions (local, global and mass extinction events). Three popular approaches used to discover the evolutionary and distributional history signature of species’ responses under the influence of climate change are: i. the birth-death framework, to estimate speciation and background extinction rates of a time-calibrated phylogeny to interpret a species’ past responses as “adaption” or “global extinction”; ii. biogeographic inference, a time-calibrated phylogeny with species distributions used to infer ancestral ranges and past geographical movement events; and iii. the ecological niche model (ENM), where the ecological preferences of a species, based on occurrence (and presence data), are projected over palaeoclimate or future predicted climate layers to explore for similar conditions in the different time periods and/or landscapes. Respectively, these approaches look at detangling species’ responses to climate change from a phylogenetic, a biogeographical, and an ecological research point of view. However, there is a fourth approach that embodies the philosophy that ecology, phylogeny and biogeography should be combined, as these research areas are able to compliment one another’s limitations in the quest to understand the evolutionary and distributional history signature of climate change for a species. This fourth approach is to create a methodology that combines pre-existing biogeographic inference and ENM frameworks; or to use a macroecology simulation model. Within this thesis we developed new tools and methodologies to understand the evolutionary and distributional signature of plant lineages’ responses to the impact of climate change, using the two case studies: genus Camptoloma, a genus with only three species showing one of the largest known intracontinental disjunctions, between Macaronesia, Eastern Africa/Southern Arabia and Southwest Africa, in what is termed the African Rand Flora pattern, and Leslie et al. 2012’s fossil-dated conifer phylogeny contains 492 of 630 known species. Chapter 1 explored the potential of the birth-death Bayesian Birth-Death Skyline (BDSKY) model in locating and detecting MEEs, within an extant species only phylogeny, through changes in background extinction rates under a “time-slice” approach. In this approach, MEEs were defined as time intervals where the background extinction rate is greater than the speciation rate. Results showed BDSKY could detect and locate MEEs but that precision and accuracy depended on phylogenies size and MEE intensity. Comparisons of BDSKY with the single-pulse Bayesian model, CoMET, showed a similar frequency of Type II error and neither model exhibited Type I error. However, while CoMET performed better in detecting and locating MEEs for smaller phylogenies, BDSKY showed higher accuracy in estimating background extinction and speciation rates. Chapter 2 proposed a new methodology for combining pre-existing biogeographic inference and ENM frameworks. While past attempts to integrate both frameworks typically required large datasets, here, we explored a framework to combine them as independent but complementary sources of evidence for inferring evolutionary history in depauperate lineages with restricted distributions and limited associated data, with case study genus Camptoloma. Using Bayesian biogeographic inference based on nuclear and chloroplast DNA markers, combined with past and present ENM geographic projections calibrated with phylogenetic/biogeographic data, we showed that the current disjunct distribution of Camptoloma across Africa was likely the result of fragmentation and extinction/population bottlenecking events associated to historical aridification cycles, in line with the “climatic refugia” hypothesis. We also presented an approach to use evolutionary data (phylogenetic and biogeographic information) to select the truncation threshold in ENMs. Chapter 3 presented a new macroecology, computer simulation model that can be used to explore the role played by species niche conservation, the appearance of temporary dispersal barriers, and background extinction associated with climatic changes in the formation of disjunct spatial distributions in a two-dimensional gridded landscape, like that of the Rand Flora genus Camptoloma. Unlike previous models, which consider the formation of a species by a speciation rate as a unique and independent event from the rest, the proposed model allows incorporation of the lineage’s evolutionary history by phylogentic tree building as a result of the model. Speciation is assumed by a speciation rate, while the probability of extinction is dependent on abiotic factors such as climate and biotic factors, such as the number of species occupying a cell. The evaluation of the model fit is made by comparison between spatial (geographic range) and evolutionary patterns (number of species per cell and phylogenetic structure) generated by the simulation and those observed in empirical studies, such as those of the genus Rand Flora Camptoloma. Faced with the current crisis of biodiversity and global warming induced by human activity, and given the impossibility of conserving all existing biodiversity, it is necessary to develop new approaches that increase the accuracy of our predictions of the evolutionary response of species. This thesis aims to accommodate this objective.