Extinction in Phylogenetics and Biogeography: From Timetrees to Patterns of Biotic Assemblage

Global climate change and its impact on biodiversity levels have made extinction a relevant topic in biological research. Yet, until recently, extinction has received less attention in macroevolutionary studies than speciation; the reason is the difficulty to infer an event that actually eliminates rather than creates new taxa. For example, in biogeography, extinction has often been seen as noise, introducing homoplasy in biogeographic relationships, rather than a pattern-generating process. The molecular revolution and the possibility to integrate time into phylogenetic reconstructions have allowed studying extinction under different perspectives. Here, we review phylogenetic (temporal) and biogeographic (spatial) approaches to the inference of extinction and the challenges this process poses for reconstructing evolutionary history. Specifically, we focus on the problem of discriminating between alternative high extinction scenarios using time trees with only extant taxa, and on the confounding effect introduced by asymmetric spatial extinction – different rates of extinction across areas – in biogeographic inference. Finally, we identify the most promising avenues of research in both fields, which include the integration of additional sources of evidence such as the fossil record or environmental information in birth–death models and biogeographic reconstructions, the development of new models that tie extinction rates to phenotypic or environmental variation, or the implementation within a Bayesian framework of parametric non-stationary biogeographic models.Financial support came from MINECO, the Spanish Ministry of Economy and Competitiveness, project CGL2012-40129-C02-01 to IS, and from a Marie-Curie FP7–COFUND (AgreenSkills fellowship–26719) to AM.Peer reviewedPeer Reviewe

Paleobiology of the genus Hypericum (Hypericaceae): A survey of the fossil record and its palaeogeographic implications

[EN]Genus Hypericum is one of the 100 largest genera in angiosperms with nearly 500 species. Despite its worldwide, nearly cosmopolitan distribution and apparently old age - there are fossil remains of relatives from the Mid Cretaceous - the fossil record of Hypericum has been largely overlooked in phylogenetic studies. Here, we survey the fossil record of Hypericum from the literature, with special emphasis on the oldest fossil remain, Hypericum antiquum, from which we reassess its diagnostic characters. We evaluate the implications of this record in reconstructing the past geographic distribution of genus Hypericum. [ES] El género Hypericum contiene 500 especies aproximadamente y es uno de los 100 géneros más grandes dentro de las angiospermas. A pesar de que tiene una distribución cosmopolita y de que es presumiblemente muy antiguo –existen restos fósiles de grupos emparentados filogenéticamente del Cretácico medio– el registro fósil de Hypericum no ha sido utilizado en estudios filogenéticos. En este trabajo hacemos una revisión de la literatura sobre el registro fósil de Hypericum con especial énfasis en los restos más antiguos de la especie Hypericum antiquum, del que reevaluamos sus caracteres diagnósticos. Finalmente, discutimos las implicaciones que este registro fósil tiene en la reconstrucción paleogeográfica del género Hypericum.This work has been funded by the Spanish Ministry of Education and Science (project CGL2009-13322-C03-01/BOS) and PhD research grant AP-2007-01698 to A.S. MeseguerPeer Reviewe

Bayesian inference of phylogeny, morphology and range evolution reveals a complex evolutionary history in St. John's wort (Hypericum)

The genus Hypericum L. (> St. John's wort>, Hypericaceae) comprises nearly 500 species of shrubs, trees and herbs distributed mainly in temperate regions of the Northern Hemisphere, but also in high-altitude tropical and subtropical areas. Until now, molecular phylogenetic hypotheses on infra-generic relationships have been based solely on the nuclear marker ITS. Here, we used a full Bayesian approach to simultaneously reconstruct phylogenetic relationships, divergence times, and patterns of morphological and range evolution in Hypericum, using nuclear (ITS) and plastid DNA sequences (psbA-trnH, trnS-trnG, trnL-trnF) of 186 species representing 33 of the 36 described morphological sections. Consistent with other studies, we found that corrections of the branch length prior helped recover more realistic branch lengths in by-gene partitioned Bayesian analyses, but the effect was also seen within single genes if the overall mutation rate differed considerably among sites or regions. Our study confirms that Hypericum is not monophyletic with the genus Triadenum embedded within, and rejects the traditional infrageneric classification, with many sections being para- or polyphyletic. The small Western Palearctic sections Elodes and Adenotrias are the sister-group of a geographic dichotomy between a mainly New World clade and a large Old World clade. Bayesian reconstruction of morphological character states and range evolution show a complex pattern of morphological plasticity and inter-continental movement within the genus. The ancestors of Hypericum were probably tropical shrubs that migrated from Africa to the Palearctic in the Early Tertiary, concurrent with the expansion of tropical climates in northern latitudes. Global climate cooling from the Mid Tertiary onwards might have promoted adaptation to temperate conditions in some lineages, such as the development of the herbaceous habit or unspecialized corollas. © 2013 Elsevier Inc.This work was funded by the Spanish Ministry of Education and Science (project CGL2009-13322-C03-01/BOS) to I.S. and a PhD research grant AP-2007-01698 to A.S.M.Peer Reviewe

Utility of low-copy nuclear markers in phylogenetic reconstruction of Hypericum L. (Hypericaceae)

Primers and sequence variation for two low-copy nuclear genes (LCG) not previously used for phylogenetic inference in the genus Hypericum, PHYC and EMB2765, are presented here in comparison with the fast-evolving nuclear intergenic spacer ITS. Substitution rates in the LCG markers were half those reported in ITS for Hypericum, which might help avoid the problems caused by substitution saturation and difficulties to establish homologies that afflict the latter marker. We included representatives of all major clades within Hypericum and found that levels of phylogenetic resolution, clade support values and internal character consistency were similar to, or even higher than, those of ITS-based phylogenies. The presence of at least two copies in EMB2765 in Hypericum imposed a methodological challenge that was circumvented by the design of an effective clade-specific primer. Both EMB2765 and, especially, PHYC appear to be good alternatives to the ITS marker, confirming the main phylogenetic relationships found in previous studies, but with improved resolution and support values for some basal relationships. © 2014 Springer-Verlag Wien.This work was funded by the Spanish Ministry of Education and Science (projects CGL2009-13322-C03-01/BOS and CGL2012-40129-C02-01) to I.S. and a PhD research grant AP- 2007-01698 to A.S.M. B.E.P. is supported by grants from the Swedish Research Council, the Royal Swedish Academy of Sciences, Lars Hiertas Minne fund, The Royal Physiographic Society in Lund, Helge Ax:son Johnsons fund and the Lundgrenska fundPeer Reviewe

Reconstructing deep-time palaeoclimate legacies in the clusioid Malpighiales unveils their role in the evolution and extinction of the boreotropical flora

Aim: During its entire history, the Earth has gone through periods of climate change similar in scale and pace to the warming trend observed today in the Anthropocene. The impact of these ancient climatic events on the evolutionary trajectories of organisms provides clues on the organismal response to climate change, including extinction, migration and persistence. Here, we examine the evolutionary response to climate cooling/warming events of the clusioid families Calophyllaceae, Podostemaceae and Hypericaceae (CPH clade) and the genus Hypericum as test cases. Location: Holarctic. Time period: Late Cretaceous–Cenozoic. Major taxa studied: Angiosperms. Methods: We use palaeoclimate simulations, species distribution models and phylogenetic comparative approaches calibrated with fossils. Results: Ancestral CPH lineages could have been distributed in the Holarctic 100 Ma, occupying tropical subhumid assemblages, a finding supported by the fossil record. Expansion to closed-canopy tropical rain forest habitats occurred after 60 Ma, in the Cenozoic, in agreement with earlier ideas of a post-Cretaceous origin of current tropical rain forest. Posterior Cooling during the Eocene triggered diversification declines in CPH tropical lineages, and was associated with a climatic shift towards temperate affinities in Hypericum. Hypericum subsequently migrated to tropical mountains, where it encountered different temperate conditions than in the Holarctic. Main conclusions: We hypothesize that most clusioid CPH lineages failed to adapt to temperate regimes during periods of Cenozoic climate change, and went extinct in the Holarctic. In contrast, boreotropical descendants including Hypericum that underwent niche evolution demonstrated selective advantages as climates became colder. Our results point toward macroevolutionary trajectories involving the altering fates of closely related clades that adapt to periods of global climate change versus those that do not. Moreover, they suggest the hypothesis that potentially many clades, particularly inhabitants of boreotropical floras, were likely extirpated from the Holarctic and persist today (if at all) in more southern tropical locations.Peer Reviewe

Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus

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Diversification dynamics in the Neotropics through time, clades and biogeographic regions

The origins and evolution of the outstanding Neotropical biodiversity are a matter of intense debate. A comprehensive understanding is hindered by the lack of deep-time comparative data across wide phylogenetic and ecological contexts. Here, we quantify the prevailing diversification trajectories and drivers of Neotropical diversification in a sample of 150 phylogenies (12,512 species) of seed plants and tetrapods, and assess their variation across Neotropical regions and taxa. Analyses indicate that Neotropical diversity has mostly expanded through time (70% of the clades), while scenarios of saturated and declining diversity account for 21% and 9% of Neotropical diversity, respectively. Five biogeographic areas are identified as distinctive units of long-term Neotropical evolution, including Pan-Amazonia, the Dry Diagonal, and Bahama-Antilles. Diversification dynamics do not differ across these areas, suggesting no geographic structure in long-term Neotropical diversification. In contrast, diversification dynamics differ across taxa: plant diversity mostly expanded through time (88%), while a substantial fraction (43%) of tetrapod diversity accumulated at a slower pace or declined towards the present. These opposite evolutionary patterns may reflect different capacities for plants and tetrapods to cope with past climate changes

Phylogeny of the Centaurea group (Centaurea, Compositae) - Geography is a better predictor than morphology

The Centaurea group is part of the Circum-Mediterranean Clade (CMC) of genus Centaurea subgenus Centaurea, a mainly Mediterranean plant group with more than 200 described species. The group is traditionally split on morphological basis into three sections: Centaurea, Phalolepis and Willkommia. This division, however, is doubtful, especially in light of molecular approaches. In this study we try to resolve this phylogenetic problem and to consolidate the circumscription and delimitation of the entire group against other closely related groups. We analyzed nuclear (internal transcribed spacer of the ribosomal genes) and chloroplast (rpl32-trnL intergenic spacer) DNA regions for most of the described species of the Centaurea group using phylogenetic and network approaches, and we checked the data for recombination. Phylogeny was used to reconstruct the evolution of the lacerate-membranaceous bract appendages using parsimony. The magnitude of incomplete lineage sorting was tested estimating the effective population sizes. Molecular dating was performed using a Bayesian approach, and the ancestral area reconstruction was conducted using the Dispersal-Extinction-Cladogenesis method. Monophyly of the Centaurea group is confirmed if a few species are removed. Our results do not support the traditional sectional division. There is a high incongruence between the two markers and between genetic data and morphology. However, there is a clear relation between geography and the structure of the molecular data. Diversification in the Centaurea group mainly took place during the Pliocene and Pleistocene. The ancestral area infered for the Circum-Mediterranean Clade of Centaurea is the Eastern Mediterranean, whereas for the Centaurea group it is most likely NW-Africa. The large incongruencies, which hamper phylogenetic reconstruction, are probably the result of introgression, even though the presence of incomplete lineage sorting as an additional factor cannot be ruled out. Convergent evolution of morphological traits may have led to incongruence between morphology-based, traditional systematics and molecular results. Our results also cast major doubts about current species delimitation. © 2014 Elsevier Inc