A New Method for Integrating Ecological Niche Modeling with Phylogenetics to Estimate Ancestral Distributions

Ancestral range estimation and projection of niche models into the past have both become common in evolutionary studies where the ancient distributions of organisms are in question. However, these methods are hampered by complementary hurdles: discrete characterization of areas in ancestral range estimation can be overly coarse, especially at shallow timescales, and niche model projection neglects evolution. Phylogenetic niche modeling accounts for both of these issues by incorporating knowledge of evolutionary relationships into a characterization of environmental tolerances. We present a new method for phylogenetic niche modeling, implemented in R. Given past and present climate data, taxon occurrence data, and a time-calibrated phylogeny, our method constructs niche models for each extant taxon, uses ancestral character estimation to reconstruct ancestral niche models, and projects these models into paleoclimate data to provide a historical estimate of the geographic range of a lineage. Models either at nodes or along branches of the phylogeny can be estimated. We demonstrate our method on a small group of dendrobatid frogs and show that it can make inferences given species with restricted ranges and little occurrence data. We also use simulations to show that our method can reliably reconstruct the niche of a known ancestor in both geographic and environmental space. Our method brings together fields as disparate as ecological niche modeling, phylogenetics, and ancestral range estimation in a user-friendly package. [Ancestral range estimation; ancestral state reconstruction; biogeography; Dendrobatidae; ecological niche modeling; paleoclimate; phylogeography; species distribution modeling.]

Into-India or out-of-India? Historical biogeography of the freshwater gastropod genus Pila (Caenogastropoda: Ampullariidae)

The biota of the Indian subcontinent was assembled through multiple associations with various landmasses during a period spanning the Late Cretaceous to the present. It consists of Gondwanan elements that subsequently dispersed ‘out-of-India’ and biota that dispersed ‘into-India’ after the subcontinent collided with Asia. However, the relative contribution of these connections to the current biotic assembly of the subcontinent has been under-explored. Our aim here was to understand the relative importance of these various routes of biotic assembly in India by studying the historical biogeography of the tropical Old World freshwater snail genus Pila. We reconstructed a near-complete phylogeny, based on nuclear and mitochondrial markers, of Ampullariidae including all the described Pila species from India and Ampullariids worldwide. Thereafter, molecular dating and ancestral range estimation analyses were carried out to ascertain the time frame and route of colonization of India by Pila. The results showed that Pila dispersed into India as well as other parts of tropical Asia from Africa after both India and Africa collided with Eurasia. Furthermore, multiple dispersals took place between Southeast Asia and India. These findings corroborate increasing evidence that much of the current Indian assemblage of biota actually dispersed ‘into-India’ after it collided with Asia.

Historical Biogeography of Holarctic Cymbiodyta Water Scavenger Beetles in the Times of Cenozoic Land Bridge Dispersal Routes

The genus Cymbiodyta Bedel, 1881 (Coleoptera: Hydrophilidae: Enochrinae) comprises 31 species distributed in both the Old and New World portions of the Holarctic realm. Although the species and taxonomy are relatively well known, the phylogenetic relationships among Cymbiodyta and the evolutionary history of the genus remain unexplored. To understand the systematics and evolution of this lineage, we sequenced five gene fragments for about half of the species in the genus, including most major morphological groups. We also estimated divergence times to test the hypothesis that Cymbiodyta beetles took advantage of the different land bridges connecting the Palearctic and Nearctic regions, that became subaerial in the Cretaceous and Paleocene. Our results recover the eastern Nearctic genus Helocombus Horn, 1890 nesting within Cymbiodyta. Therefore, we synonymize Helocombus syn. n. with Cymbiodyta, resulting in one new combination, Cymbiodyta bifidus (LeConte 1855) comb. n. Our dating analyses and ancestral range estimation support a Nearctic origin of Cymbiodyta in the late Cretaceous about 100 million year ago. The placement of the unique Palearctic species on a long branch as sister to the rest of the clade and the dating results cannot reject a role of the De Geer and/or Thulean routes in the colonization of the Palearctic region from the Nearctic; however, they do not support a role for Beringia in the more recent colonization of the Oriental region.

The Biogeography of Coelurosaurian Theropods and its Impact on their Evolutionary History

ABSTRACTThe Coelurosauria are a group of mostly feathered theropods that gave rise to birds, the only dinosaurs that survived the Cretaceous-Paleogene extinction event and are still found today. Between their first appearance in the Middle Jurassic up to the end Cretaceous, coelurosaurs were party to dramatic geographic changes on the Earth’s surface, including the breakup of the supercontinent Pangaea, and the formation of the Atlantic Ocean. These plate tectonic events are thought to have caused vicariance or dispersal of coelurosaurian faunas, influencing their evolution. Unfortunately, few coelurosaurian biogeographic hypotheses are supported by quantitative evidence. Here, we report the first, broadly-sampled quantitative analysis of coelurosaurian biogeography using the likelihood-based package BioGeoBEARS. Mesozoic geographic configurations and changes are reconstructed and employed as constraints in this analysis, including their associated uncertainties. We use a comprehensive time-calibrated coelurosaurian evolutionary tree produced from the Theropod Working Group phylogenetic data matrix. Six biogeographic models in the BioGeoBEARS package with different assumptions about the evolution of spatial distribution are tested against the geographic constraints. Our results statistically favour the DIVALIKE+J and DEC+J models, which allow vicariance and founder events, supporting continental vicariance as an important factor in coelurosaurian evolution. Ancestral range estimation indicates frequent dispersal events via the Apulian Route (connecting Europe and Africa during the Early Cretaceous) and the Bering Land Bridge (connecting North America and Asia during the Late Cretaceous). These quantitative results are consistent with commonly inferred Mesozoic dinosaurian dispersals and continental-fragmentation-induced vicariance events. In addition, we recognise the importance of Europe as a dispersal centre and gateway in the Early Cretaceous, as well as other vicariance events like those triggered by the disappearance of land-bridges.

Sensitivity of biogeographic reconstructions to the use of differential extinction rates

Effects of differential extinction rates remain being an issue in biogeographic and evolutionary studies. Here, I use empirical examples and simulated datasets to asses how the specification of different extinction rates influences ancestral range estimation in historical biogeography. The results showed that variations in scale and asymmetry of extinction rates may have notorious effects in the accuracy of biogeographic inferences, specially when the rates of extinction are high. Further work may explore the behavior of current statistical methods of biogeographic inference with different estimates of extinction based on novel developments in this field.

Sensitivity of biogeographic reconstructions to the use of differential extinction rates

Effects of differential extinction rates remain being an issue in biogeographic and evolutionary studies. Here, I use empirical examples and simulated datasets to asses how the specification of different extinction rates influences ancestral range estimation in historical biogeography. The results showed that variations in scale and asymmetry of extinction rates may have notorious effects in the accuracy of biogeographic inferences, specially when the rates of extinction are high. Further work may explore the behavior of current statistical methods of biogeographic inference with different estimates of extinction based on novel developments in this field.