Species selection and the spatial distribution of diversity

This thesis is about Life and how it is unevenly distributed across time, space and hierarchical levels. When comparing the fossil record with the current diversity of life, the extent of the change in composition of flora and fauna over time is enormous, where some groups reigned in the past but have only few delegates surviving to the present. Spatial variation in the number of organisms is also astonishing, with the exuberance of jungles contrasting with plain arid ecosystems, one of many gradients of diversity. With a more detailed examination, one can also find examples of groups of animals or plants which have tremendously flourished producing endless forms while other groups have no more than a handful of members. In this thesis, I developed methods based on simulations and likelihood calculations. They include predictive theoretical models, and methods that are applied to case studies varying in taxonomic scope (songbirds; fish) and geographic scale (worldwide elevational distribution; lake depth gradient). I show how the spatial distribution of species is dynamic over time and has important consequences for patterns of species origination and extinction. I show that species do not have the same rates of diversification, and this can be the result of 1) regional equilibrium or out-of-equilibrium dynamics or 2) spatial distribution across gradients

Soaring Migratory Birds Avoid Wind Farm in the Isthmus of Tehuantepec, Southern Mexico

Funding: This research was made possible with funding from the World Bank to the Comisión Federal de Electricidad (CFE) for monitoring the environmental impacts of the wind farm. The funders of this study were the CFE. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Evolutionary dynamics of the elevational diversity gradient in passerine birds

These authors contributed equally: Paul van Els, Leonel Herrera-Alsina. Acknowledgements The research of P.v.E. was facilitated by the Adaptive Life Program of the Groningen Institute for Evolutionary Life Sciences, Faculty of Science and Engineering at the University of Groningen. L.H.-A. thanks the Consejo Nacional de Ciencia y Tecnología of Mexico for funding (CVU 385304 L). R.S.E. thanks the Netherlands Organization for Scientific Research (NWO) for financial support through a VICI grant. A.L.P. is funded by a Royal Society University Research Fellowship. We thank the Center for Information Technology of the University of Groningen for their support and for providing access to the Peregrine high-performance computing cluster.Peer reviewedPostprin

Detecting the dependence of diversification on multiple traits from phylogenetic trees and trait data

Species diversification may be determined by many different variables, including the traits of the diversifying lineages. The State-dependent Speciation and Extinction (SSE) framework contains methods to detect the dependence of diversification on these traits. For the analysis of traits with multiple states, MuSSE (Multiple-States dependent Speciation and Extinction) was developed. However, MuSSE and other state-dependent speciation and extinction models have been shown to yield false positives, because they cannot separate differential diversification rates from dependence of diversification on the observed traits. The recently introduced method HiSSE (Hidden- State dependent Speciation and Extinction) resolves this problem by allowing a hidden state to affect diversification rates. Unfortunately, HiSSE does not allow traits with more than two states, and, perhaps more interestingly, the simultaneous action of multiple traits on diversification. Here, we introduce an R package (SecSSE: Several examined and concealed States-dependent Speciation and Extinction) that combines the features of HiSSE and MuSSE to simultaneously infer state-dependent diversification across two or more examined (observed) traits or states while accounting for the role of a possible concealed (hidden) trait. Moreover, SecSSE also has improved functionality compared to its two ′parents′. First, it allows for an observed trait being in two or more states simultaneously, which is useful for example when a taxon is a generalist or when the exact state is not precisely known. Second, it provides the correct likelihood when conditioned on non-extinction, which has been incorrectly implemented in HiSSE and other SSE models. To illustrate our method we apply SecSSE to 7 previous studies that used MuSSE, and find that in 5 out of 7 cases, the conclusions drawn based on MuSSE were premature. We test with simulations whether SecSSE sacrifices statistical power to avoid the high type I error problem of MuSSE, but we find that this is not the case: for the majority of simulations where the observed traits affect diversification, SecSSE detects this

The influence of ecological and geographic limits on the evolution of species distributions and diversity

This manuscript was enriched by constant discussions with members of Theoretical and Evolutionary Community Ecology. L.H.‐A. is supported by a grant from Consejo Nacional de Ciencia y Tecnologia (CVU 385304). R.S.E. thanks the Netherlands Organisation for Scientific Research (NWO) for funding through a VICI grant. We are grateful to the Editor and two anonymous reviewers for the suggestions made which greatly improved the manuscript.Peer reviewedPublisher PD

Apparent effect of range size and fruit colour on palm diversification may be spurious

ACKNOWLEDGEMENTS This work was supported by the Biodiversity and Ecosystem Services in a Changing Climate Strategic Research Area at the University of Gothenburg. C.C.S. was supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Brazil and the São Paulo Research Foundation (FAPESP; 2020-09164-0). S.F. was supported by the Swedish Research Council (2017-03862); C.D.B. and M.F.T.J. were supported by the Swedish Research Council (2017-04980). The computation was enabled by resources provided by the National Academic Infrastructure for Supercomputing in Sweden (NAISS) and the Swedish National Infrastructure for Computing (SNIC) at PDC and HPC2N, respectively, partially funded by the Swedish Research Council through grant agreements no. 2022-06725 and no. 2018-05973. There were no permits required for this work. Research Funding Biodiversity and Ecosystem Services in a Changing Climate Strategic Research Area Coordenação de Aperfeiçoamento de Pessoal de Nível Superior VetenskapsrådetPeer reviewedPublisher PD

Apparent effect of range size and fruit colour on palm diversification may be spurious

Aim Fruit selection by animal dispersers with different mobility directly impacts plant geographical range size, which, in turn, may impact plant diversification. Here, we examine the interaction between fruit colour, range size and diversification rate in palms by testing two hypotheses: (1) species with fruit colours attractive to birds have larger range sizes due to high dispersal ability and (2) disperser mobility affects whether small or large range size has higher diversification, and intermediate range size is expected to lead to the highest diversification rate regardless of disperser.Location Global.Time Period Contemporary (or present).Major Taxa Studied Palms (Arecaceae).Methods Palm species were grouped based on likely animal disperser group for given fruit colours. Range sizes were estimated by constructing alpha convex hull polygons from distribution data. We examined disperser group, range size or an interaction of both as possible drivers of change in diversification rate over time in a likelihood dynamic model (Several Examined State-dependent Speciation and Extinction [SecSSE]). Models were fitted, rate estimates were retrieved and likelihoods were compared to those of appropriate null models.Results Species with fruit colours associated with mammal dispersal had larger ranges than those with colours associated with bird dispersal. The best fitting SecSSE models indicated that the examined traits were not the primary driver of the heterogeneity in diversification rates in the model. Extinction rate complexity had a marked impact on model performance and on diversification rates.Main Conclusions Two traits related to dispersal mobility, range size and fruit colour, were not identified as the main drivers of diversification in palms. Increased model extinction rate complexity led to better performing models, which indicates that net diversification should be estimated rather than speciation alone. However, increased complexity may lead to incorrect SecSSE model conclusions without careful consideration. Finally, we find palms with more mobile dispersers do not have larger range sizes, meaning other factors are more important determinants of range size

To adapt or go extinct? The fate of megafaunal palm fruits under past global change

Past global change may have forced animal-dispersed plants with megafaunal fruits to adapt or go extinct, but these processes have remained unexplored at broad spatio-temporal scales. Here, we combine phylogenetic, distributional and fruit size data for more than 2500 palm (Arecaceae) species in a time-slice diversification analysis to quantify how extinction and adaptation have changed over deep time. Our results indicate that extinction rates of palms with megafaunal fruits have increased in the New World since the onset of the Quaternary (2.6 million years ago). In contrast, Old World palms show a Quaternary increase in transition rates towards evolving small fruits from megafaunal fruits. We suggest that Quaternary climate oscillations and concurrent habitat fragmentation and defaunation of megafaunal frugivores in the New World have reduced seed dispersal distances and geographical ranges of palms with megafaunal fruits, resulting in their extinction. The increasing adaptation to smaller fruits in the Old World could reflect selection for seed dispersal by ocean-crossing frugivores (e.g. medium-sized birds and bats) to colonize Indo-Pacific islands against a background of Quaternary sea-level fluctuations. Our macro-evolutionary results suggest that megafaunal fruits are increasingly being lost from tropical ecosystems, either due to extinctions or by adapting to smaller fruit sizes.</p

The missing link in biogeographic reconstruction: Accounting for lineage extinction rewrites history

ACKNOWLEDGEMENTS This work was supported by a grant from the Ministry of Research and Technology, Indonesia, to Berry Juliandi (No. 2020/IT3.L1/PN/2021) and funding from NERC/NEWTON (NE/S006923/1 and NE/S006893/1) to Adam C. Algar, Greta Bocedi, Cecile Gubry-Rangin, Lesley Lancaster, Alexander S. T. Papadopulos and Justin M.J. Travis. The manuscript was improved by the constructive feedback from two anonymous reviewers. No permits were required to conduct this research.Peer reviewedPublisher PD

Impact of Phylogenetic Tree Completeness and Misspecification of Sampling Fractions on Trait Dependent Diversification Models

Funding This work was funded by Newton Fund (UK)/NERC (UK)/RISTEKDIKTI (Indonesia) grants awarded to JT, BJ, ACA, ASTP, CG-R, GB and LTL (Grant numbers: NE/S006923/1; NE/S006893/1; 2488/IT3.L1/PN/2020; and 3982/IT3.L1/PN/2020). GB is funded by a Royal Society University Research Fellowship (UF160614).Peer reviewedPublisher PD