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

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

Ancient geological dynamics impact neutral biodiversity accumulation and are detectable in phylogenetic reconstructions

ACKNOWLEDGMENTS This work was supported by grants from the Ministry of Research and Technology, Indonesia to Berry Juliandi (No. 2488/IT3.L1/PN/2020 and No. 3982/IT3.L1/PN/2020) and funding from NERC/NEWTON sto Adam C. Algar, Greta Bocedi, Cecile Gubry-Rangin, Lesley Lancaster, Alexander S. T. Papadopulos and Justin M. J. Travis.Peer reviewedPublisher PD

Fauxcurrence: simulating multi-species occurrences for null models in species distribution modelling and biogeography

The work was funded by Newton Fund (UK)/NERC (UK)/RISTEKDIKTI (Indonesia) grants awarded to JT, BJ, ACA, ASTP, CG-R, GB and LTL (grant no.: NE/S006923/1, NE/S006893/1, 2488/IT3.L1/PN/2020 and 3982/IT3.L1/PN/2020). GB and CG-R are funded by Royal Society Univ. Research Fellowships (UF160614 and UF150571 respectively).Peer reviewedPublisher PD

Unconfined Aquifer Flow Theory - from Dupuit to present

Analytic and semi-analytic solution are often used by researchers and practicioners to estimate aquifer parameters from unconfined aquifer pumping tests. The non-linearities associated with unconfined (i.e., water table) aquifer tests makes their analysis more complex than confined tests. Although analytical solutions for unconfined flow began in the mid-1800s with Dupuit, Thiem was possibly the first to use them to estimate aquifer parameters from pumping tests in the early 1900s. In the 1950s, Boulton developed the first transient well test solution specialized to unconfined flow. By the 1970s Neuman had developed solutions considering both primary transient storage mechanisms (confined storage and delayed yield) without non-physical fitting parameters. In the last decade, research into developing unconfined aquifer test solutions has mostly focused on explicitly coupling the aquifer with the linearized vadose zone. Despite the many advanced solution methods available, there still exists a need for realism to accurately simulate real-world aquifer tests

How to make a sex chromosome

Sex chromosomes can evolve once recombination is halted between a homologous pair of chromosomes. Owing to detailed studies using key model systems, we have a nuanced understanding and a rich review literature of what happens to sex chromosomes once recombination is arrested. However, three broad questions remain unanswered. First, why do sex chromosomes stop recombining in the first place? Second, how is recombination halted? Finally, why does the spread of recombination suppression, and therefore the rate of sex chromosome divergence, vary so substantially across clades? In this review, we consider each of these three questions in turn to address fundamental questions in the field, summarize our current understanding, and highlight important areas for future work

Inner/Outer Nuclear Membrane Fusion in Nuclear Pore Assembly: Biochemical Demonstration and Molecular Analysis

The nuclear pore complex (NPC) is characterized by a long-lived membrane-lined channel connecting the inner and outer nuclear membranes. This stabilized membrane channel, within which the nuclear pore is built, has little evolutionary precedent. In this report we demonstrate and map the inner/outer nuclear membrane fusion in NPC assembly