Integrating Fossils, Phylogenies, and Niche Models into Biogeography to Reveal Ancient Evolutionary History: The Case of Hypericum (Hypericaceae)

Abstract

In disciplines such as macroevolution 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, under scenarios of high extinction rates, the biodiversity we observe today might not be representative of the historical diversity and this could result in incorrect biogeographic reconstructions. Here, we introduce a new approach to incorporate into biogeographic inference the temporal, spatial, and environmental information provided by the fossil record, as a direct evidence of the extinct biodiversity fraction. First, inferences of ancestral ranges for those nodes in the phylogeny calibrated with the fossil record are constrained to include the geographic distribution of the fossil. Second, we use fossil distribution and past climate data to reconstruct the climatic preferences and potential distribution of ancestral lineages over time, and use this information to build a biogeographic model that takes into account “ecological connectivity” through time. To show the power of this approach, we reconstruct the biogeographic history of the large angiosperm genus Hypericum, which has a fossil record extending back to the Early Cenozoic. Unlike previous reconstructions based on extant species distributions, our results reveal that Hypericum stem lineages were already distributed in the Holarctic before diversification of its crown-group, and that the geographic distribution of the genus has been relatively stable throughout the climatic oscillations of the Cenozoic. Geographical movement was mediated by the existence of climatic corridors, like Beringia, whereas the equatorial tropical belt acted as a climatic barrier, preventing Hypericum lineages to reach the southern temperate regions. Our study shows that an integrative approach to historical biogeography—that combines sources of evidence as diverse as paleontology, ecology, and phylogenetics—could help us obtain more accurate reconstructions of ancient evolutionary history. It also reveals the confounding effect different rates of extinction across regions have in biogeography, sometimes leading to ancestral areas being erroneously inferred as recent colonization events.

The grass subfamily Pooideae: Cretaceous–Palaeocene origin and climate‐driven Cenozoic diversification

“…Nevertheless, our reconstruction of ancestral niches (based on bioclimatic variables) indicates that ancestors of all major Pooideae lineages experienced and could withstand frosts and mild winters in a seasonal climate (Figures and b–d). Thus, we hypothesize that Pooideae were adapted to temperate‐like climates long before the expansion of temperate biomes, contrary to many other temperate plant lineages (Favre et al, ; Kerkhoff et al, ; Meseguer et al, , ). This hypothesis is supported by two recent studies.…”

“…Many temperate‐adapted lineages evolved around and after the Eocene–Oligocene (E–O) transition, c . 34 Ma, along with the expansion of cold temperate biomes, especially in the Northern Hemisphere (Favre et al, ; Kerkhoff, Moriarty, & Weiser, ; Marcussen, Heier, Brysting, Oxelman, & Jakobsen, ; Meseguer et al, ; Meseguer, Lobo, Ree, Beerling, & Sanmartín, ; Near et al, ). The concurrence of the E–O transition and diversification into temperate climates suggests that global cooling c .…”

Ancient vicariance and climate‐driven extinction explain continental‐wide disjunctions in Africa: the case of the Rand Flora genus Canarina (Campanulaceae)

“…For past climate scenarios, we used two global Hadley Centre general circulation models that incorporate the effect of changes in atmospheric CO 2 and that have been previously used to represent major changes in global climate (Meseguer et al . ): a 280‐ppm CO 2 Late Miocene simulation (Bradshaw et al . ) and a 560‐ppm CO 2 Mid‐Pliocene simulation (Beerling et al .…”

“…By reconstructing the potential climatic niche of a species and projecting it backwards in time, we can identify areas that were in the past within the organism's range of climatic tolerances but are inhospitable today due to large‐scale climate change (Yesson & Culham ; Smith & Donoghue ; Meseguer et al . ).…”

Frequent colonization and little in situ speciation in Senecio in the tropical alpine‐like islands of eastern Africa

“…Discussion of preadaptation before colonization of the mountains of EA assumes that montane or alpine-like environments in EA were already present at the time of colonization. According to our dating analysis ( Table 2 ), diversification of the major clades containing tropical afroalpine species mostly started around the Pliocene-Pleistocene boundary but extend back to the Miocene-Pliocene boundary (crown age estimates of subclades; Table 2 ), a period that has also been inferred for the colonization of the tropical Afroalpine from SA by some other plant groups ( Stoebe L.: 3.5-2.0 Ma; Bergh and Linder, 2009 ;Hypericum L.: Mid-Miocene to Pliocene;Meseguer et al, 2014 ). However, other colonizations seem to be older (giant lobelias and dantonioid grasses; Antonelli, 2009 ;Linder et al, 2013 ).…”