FIGURE 6 - uploaded by Isabel Sanmartin
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Scheme representing changes in vegetation composition in response to major shifts in Cenozoic climate based on paleobotanical evidence (see online Appendix 2 for more details on how the vegetation maps were constructed), together with the biogeographic history of genus Hypericum as inferred from the integrative approach adopted here (Fig. 4). The close-canopy tropical forest in the Southern Hemisphere is represented by light green color over a yellow background. The northern vegetation belt in dark green color represents alternatively the boreotropical forest (Fig. 6a), and its successors: the mixed-mesophytic forest (Fig. 6b,c) and the temperate forest (Fig. 6d). The boreal forest belt in the northern regions of Eurasia and North America (Fig. 6c,d) is represented by a darker shade of green; starbursts represent the expansion of grassland biomes. Red dots represent selected fossil locations. Area name abbreviations follow Figure 4.
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In disciplines such asmacroevolution that are not amenable to experimentation, scientists usually rely on current observations to test hypotheses about historical events, assuming that “the present is the key to the past.” Biogeographers, for example, used this assumption to reconstruct ancestral ranges from the distribution of extant species. Yet,...
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... However, these shallow timescales are often insufficient to discern how much evolutionary history loss is anthropogenic-induced or a result of the natural cycling of diversification rates in long-term species dynamics (Moen and Morlon, 2014;Huang et al., 2015). In contrast, evolutionary data that spans deeper timescales, e.g., tens of millions of years, is expected to provide a more accurate understanding of organisms' persistence and adaptational responses, which are built over generations of genetic changes (Willis and MacDonald, 2011;Svenning et al., 2015;Meseguer et al., 2018;Burke et al., 2018), and hence, a more accurate prediction on the impact of ongoing and future climate change on a species geographic range (Martínez-Meyer et al., 2004;Diniz-Filho and Bini, 2008;Romdal et al., 2013;Meseguer et al., 2015;Burke et al., 2018). One climate change event of major scientific and societal concern is the current aridification trend that affects areas such as the African continent, the Mediterranean Basin and Arabia-Western Asia (Berdugo et al., 2020). ...
... Biogeographic inferences, based on a time-calibrated phylogeny and associated taxa distributions, can be used to infer ancestral geographic ranges and the sequence of geographic range shifts that led to the current distributions (Ree and Smith, 2008;Ronquist and Sanmartín, 2011). Ecological niche models (ENM), based on occurrence data, can be used to estimate the environmental preferences (climatic envelope) of species, allowing for spatial exploration of similar climate conditions in the past, present, and future (Araújo and New, 2007;Meseguer et al., 2015;Mairal et al., 2017;Carboni et al., 2018;Haeuser et al., 2018). The two approaches have their advantages and shortcomings. ...
... ENMs implicitly assume that an organism's climatic niche is conserved over evolutionary time, which might be unrealistic under repeated cycles of ciimate change and over long timescales (Peterson, 2006). The use of ENMs to hindcast across time is also limited by the availability of paleoclimatic data, and most ENMs have been projected onto the recent geological past (Pleistocene, Martínez-Meyer et al., 2004;Mairal et al., 2018; but see Meseguer et al., 2015 andMairal et al., 2017). ...
Geographic range shifts are one major organism response to climate change, especially if the rate of climate change is higher than that of species adaptation. Ecological niche models (ENM) and biogeographic inferences are often used in estimating the effects of climatic oscillations on species range dynamics. ENMs can be used to track climatic suitable areas over time, but have often been limited to shallow timescales; biogeographic inference can reach greater evolutionary depth, but often lacks spatial resolution. Here, we present a simple approach that treats them as independent and complementary sources of evidence, which, when used in partnership, can be employed to reconstruct geographic range shifts over deep evolutionary timescales. For testing this, we chose two extreme African disjunctions: Camptoloma (Scrophulariaceae) and Canarina (Campanulaceae), each comprising of three species disjunctly distributed in Macaronesia and eastern/southern Africa. Using inferred ancestral ranges in tandem with preindustrial and paleoclimate ENM hindcastings, we show that the disjunct pattern was the result of fragmentation and extinction events linked to Neogene aridification cycles. Our results highlight the importance of considering temporal resolution when building ENMs for rare endemics with small population sizes and restricted climatic tolerances such as Camptoloma , for which models built on averaged monthly variables were more informative than those based on annual bioclimatic variables. Additionally, we show that biogeographic information can be used as truncation threshold criteria for building ENMs in the distant past. Our approach is suitable when there is sparse sampling on species occurrences and associated patterns of genetic variation, such as in the case of ancient endemics with widely disjunct distributions as a result of climate change.
In the nineteenth century, Alexander von Humboldt and Alfred Russel Wallace laid out the basis for the field of biogeography, the discipline that studies the relation between organisms and their geographic distribution. Almost in parallel with the birth of biogeography, the foundations of geology were laid out, providing a dimension of time to spatial changes of the landscape. In this paper, we review the historical context of the early biogeographers and explore what the lasting significance of the nineteenth-century holistic research approach is in present research. We also discuss the historical context in which biogeography and geology developed, and how the concept of deep time, plate tectonics, and mountain building provided a broader perspective to biogeography. To illustrate the benefits of integrating geological and biological methods, we focus on the genesis and chronology of the elevational gradient, core to Humboldt’s work. In particular, we use as example the evolution of two mountain systems, the Andes in South America, and the Tibet-Himalaya-Hengduan region in Asia. We conclude that in the nineteenth century, an interdisciplinary approach and progress in the different scientific fields led to a paradigm shift in the understanding of drivers of biogeography. Implementing such integrative vision today, and aided by advances in molecular phylogenetics and geology, has enabled biogeographers to form new, and more accurate, models of mountain building, climate, and species evolution. These models are particularly relevant in view of present scenarios of climate change and conservation strategies.KeywordsBiogeographyEvolutionGeologyHumboldtMountain geobiodiversity hypothesis
Historical biogeographic processes shaped the distribution of life throughout space and time. A species range might expand, contract, or subdivide throughout its evolutionary history, during which extrinsic factors such as the palaeogeographic arrangement of land masses can influence how a species range evolves. Phylogenetic studies can therefore benefit from incorporating biogeographic and palaeogeographic evidence into their analyses in order to better estimate species divergence times and species relationships. This chapter begins by outlining a conceptual framework for using biogeography to date phylogenies, with some emphasis on the inherent uncertainty of reconstructing past events. Following this, the chapter explores two methods (prior- and process-based methods) for estimating divergence times using biogeographic evidence and discusses their applications and merits.
Historical biogeography helps us keep track of organisms over time and space. However, microbial ecology and evolutionary studies are fraught with challenges due to their unknown life histories, a poor fossil record, and problematic taxonomy. Mycorrhizal fungi are key players for most terrestrial ecosystems and interact with a vast number of plants, including many woody trees that dominate temperate, tropical, and boreal ecosystems. They are also highly polyphyletic and disproportionally diverse globally and across the fungal tree of life, making them biogeographically intriguing. In this review, we focus on describing phylogenetic approaches that have been or could be applied in mycorrhizal biogeographic studies. We start by summarizing molecular-based studies and methods for species delimitation, pointing out the need for robust phylogenetic hypotheses in a phylogenomic or multi-locus framework. We describe methods for the reconstruction of ancestral states or areas and their use in biogeography, also synthesizing some of the progress with respect to generalized patterns in mycorrhizal biogeography. Next, we go through aspects related to time-calibrating fungal phylogenies and their time-of-origin, as well as downstream analyzes involving the estimation of diversification rates. Diversification rate, trait evolution, and phylo-community analyses are also put in the context of relevant evolutionary ecology hypotheses. Finally, we dedicate a section to methodological biases and caveats, which are often associated with global mycological fieldwork and sampling, and some phylogenetic methods.
Bayesian relaxed-clock dating has significantly influenced our understanding of the timeline of plant evolution. This approach requires the use of priors on the branching process, yet little is known about their impact on divergence time estimates. We investigated the effect of branching priors using the iconic cycads. We conducted phylogenetic estimations for 237 cycad species using three genes and two calibration strategies incorporating up to six fossil constraints to (i) test the impact of two different branching process priors on age estimates, (ii) assess which branching prior better fits the data, (iii) investigate branching prior impacts on diversification analyses, and (iv) provide insights into the diversification history of cycads.
Using Bayes factors, we compared divergence time estimates and the inferred dynamics of diversification when using Yule versus birth-death priors. Bayes factors were calculated with marginal likelihood estimated with stepping-stone sampling. We found striking differences in age estimates and diversification dynamics depending on prior choice. Dating with the Yule prior suggested that extant cycad genera diversified in the Paleogene and with two diversification rate shifts. In contrast, dating with the birth-death prior yielded Neogene diversifications, and four rate shifts, one for each of the four richest genera. Nonetheless, dating with the two priors provided similar age estimates for the divergence of cycads from Ginkgo (Carboniferous) and their crown age (Permian). Of these, Bayes factors clearly supported the birth-death prior.
These results suggest the choice of the branching process prior can have a drastic influence on our understanding of evolutionary radiations. Therefore, all dating analyses must involve a model selection process using Bayes factors to select between a Yule or birth-death prior, in particular on ancient clades with a potential pattern of high extinction. We also provide new insights into the history of cycad diversification because we found (i) periods of extinction along the long branches of the genera consistent with fossil data, and (ii) high diversification rates within the Miocene genus radiations.
