BackgroundAdaptive radiations are triggered by ecological opportunity – the access to novel niche domains with abundant available resources that facilitate the formation of new ecologically divergent species. Therefore, as new species saturate niche space, clades experience a diversity-dependent slowdown of diversification over time. At the other extreme of the radiation continuum, non-adaptively radiating lineages undergo diversification with minimal niche differentiation when ‘spatial opportunity’ (i.e. areas with suitable ‘ancestral’ ecological conditions) is available. Traditionally, most research has focused on adaptive radiations, while empirical studies on non-adaptive radiations remain lagging behind. A prolific clade of African fish with extremely short lifespan (Nothobranchius killifish), show the key evolutionary features of a candidate non-adaptive radiation – primarily allopatric species with minimal niche and phenotypic divergence. Here, we test the hypothesis that Nothobranchius killifish have non-adaptively diversified. We employ phylogenetic modelling to investigate the tempo and mode of macroevolutionary diversification of these organisms.ResultsNothobranchius diversification has proceeded with minor niche differentiation and minimal morphological disparity among allopatric species. Additionally, we failed to identify evidence for a role of body size or biogeography in influencing diversification rates. Diversification has been homogeneous within this genus, with the only hotspot of species-richness not resulting from rapid diversification. However, species in sympatry show higher disparity, which may have been caused by character displacement among coexisting species.ConclusionsNothobranchius killifish have proliferated following the tempo and mode of a non-adaptive radiation. Our study confirms that this exceptionally short-lived group have diversified with minimal divergent niche adaptation, while one group of coexisting species seems to have facilitated spatial overlap among these taxa via the evolution of ecological character displacement.Electronic supplementary materialThe online version of this article (10.1186/s12862-019-1344-0) contains supplementary material, which is available to authorized users.

Aim: Biodiversity on islands is affected by various geo-physical processes and sea-level fluctuations. Oceanic islands (never connected to a landmass) are initially vacant with diversity accumulating via colonisation and speciation, followed by a decline as islands shrink. Continental islands have species upon formation (when disconnected from the mainland) and may have transient land-bridge connections. Theoretical predictions for the effects of these geo-processes on rates of colonisation, speciation and extinction have been proposed, but methods of phylogenetic inference assume only oceanic island scenarios without accounting for island ontogeny, sea-level changes or past landmass connections. Here, we analyse to what extent ignoring geodynamics affects the inference performance of a phylogenetic island model, DAISIE, when confronted with simulated data that violate its assumptions. Location: Simulation of oceanic and continental islands. Methods: We extend the DAISIE simulation model to include: area-dependent rates of colonisation and diversification associated with island ontogeny and sea-level fluctuations, and continental islands with biota present upon separation from the mainland, and shifts in rates to mimic temporary land-bridges. We quantify the error made when geo-processes are not accounted for by applying DAISIE's inference method to geodynamic simulations. Results: We find that the robustness of the model to dynamic island area is high (error is small) for oceanic islands and for continental islands that have been separated for a long time, suggesting that, for these island types, it is possible to obtain reliable results when ignoring geodynamics. However, for continental islands that have been recently or frequently connected, robustness of DAISIE is low, and inference results should not be trusted. Main conclusions: This study highlights that under a large proportion of island biogeographic geo-scenarios (oceanic islands and ancient continental fragments) a simple phylogenetic model ignoring geodynamics is empirically applicable and informative. However, recent connection to the continent cannot be ignored, requiring development of a new inference model.

Aim Biodiversity on islands is influenced by geophysical processes and sea‐level fluctuations. Oceanic islands (never connected to a landmass) are initially vacant with diversity accumulating via colonisation and speciation, and then declining as islands shrink. Continental islands have species upon disconnection from the mainland and may have transient land‐bridge connections. Theoretical predictions for the effects of these geophysical processes on rates of colonisation, speciation, and extinction have been proposed. However, paleogeographic reconstructions are currently unavailable for most islands, and phylogenetic models overlook island ontogeny, sea‐level changes, or past landmass connections. We analyse to what extent ignoring geodynamics in the inference model affects model predictions when confronted with data simulated with geodynamics. Location Simulations of oceanic and continental islands. Taxa Simulated lineages. Methods We extend the island biogeography simulation model DAISIE to include: (i) area‐dependent rates of colonisation and diversification associated with island ontogeny and sea‐level fluctuations, (ii) continental islands with biota present upon separation from the mainland, and (iii) shifts in colonisation to mimic temporary land‐bridges. We quantify the error of ignoring geodynamic processes by applying DAISIE's inference method to geodynamic simulations. Results Robustness of the model to dynamic island area is generally high for oceanic islands and for continental islands that have been separated for a long time, suggesting that it is possible to obtain reliable results when ignoring geodynamics. However, for continental islands that have been recently or frequently connected, robustness of the model is low. Main conclusions Under many island biogeographic geodynamic scenarios (oceanic islands and ancient continental fragments) a simple phylogenetic model ignoring geodynamics is empirically applicable and informative. However, recent connection to the continent cannot be ignored, requiring new model development. Our results show that for oceanic islands, reliable insights can be obtained from phylogenetic data in the absence of paleogeographic reconstructions of island area.

1. Phylogenetic trees are commonly used to answer questions on biogeographical and diversification histories of different groups. 2. Recently, new approaches have been developed that use community phylogenetic trees requiring a data structure distinct from the single phylogenetic trees that are commonly used, which may be a barrier to the utilisation of these approaches. 3. DAISIE (Dynamic Assembly of Islands through Speciation, Immigration and Extinction) is an island biogeography model that can estimate rates of colonisation, speciation and extinction from phylogenetic data across insular communities, as well as simulate islands under those rates. 4. Here we describe the DAISIEprep R package, a set of pre-processing tools to aid the extraction of data from one or many phylogenetic trees to generate data in a format interpretable by DAISIE for the application of island biogeography inference models. We present examples to illustrate the various data types that can be used. 5. The package includes simple algorithms to extract data on island colonists and account for biogeographical, topological and taxonomic uncertainty. It also allows flexible incorporation of either missing species or entire insular lineages when phylogenetic data are not available. 6. DAISIEprep enables reproducible and user-friendly data extraction and formatting, and will facilitate addressing questions about island biogeography, diversification and anthropogenic impacts in insular systems.

Understanding macroevolution on islands requires knowledge of the closest relatives of island species on the mainland. The evolutionary relationships between island and mainland species can be reconstructed using phylogenies, to which models can be fitted to understand the dynamical processes of colonisation and diversification. But how much information on the mainland is needed to gain insight into macroevolution on islands? Here we first test whether species turnover on the mainland and incomplete mainland sampling leave recognisable signatures in community phylogenetic data. We find predictable phylogenetic patterns: colonisation times become older and the perceived proportion of endemic species increases as mainland turnover and incomplete knowledge increase. We then analyse the influence of these factors on the inference performance of the island biogeography model DAISIE, a whole-island community phylogenetic model that assumes that mainland species do not diversify, and that the mainland is fully sampled in the phylogeny. We find that colonisation and diversification rate are estimated with little bias in the presence of mainland extinction and incomplete sampling. By contrast, the rate of anagenesis is overestimated under high levels of mainland extinction and incomplete sampling, because these increase the perceived level of island endemism. We conclude that community-wide phylogenetic and endemism datasets of island species carry a signature of mainland extinction and sampling. The robustness of parameter estimates suggests that island diversification and colonisation can be studied even with limited knowledge of mainland dynamics.

No abstract

Hybridization and introgression are common processes among numerous plant species that present both challenges and opportunities for studies of species delimitation, phylogenetics, taxonomy and adaptation. Rhus integrifolia and R. ovata are two ecologically important shrubs native to the southwestern USA and Mexico, and are known to hybridize frequently, but the morphological, genetic and ecological implications of hybridization in these species are poorly studied on a broad geographic scale. Analyses were conducted using leaf morphology, genetic variation of plastid and nuclear loci, and species distribution models for both species and their putative hybrid introgressants across 19 localities in California and Arizona, USA. These analyses revealed evidence for morphological and genetic distinction among localities comprising putative parental species, but a high degree of morpho‐genetic intermediacy among localities with putative hybrids. Comparison of morphological and genetic population structure among localities revealed evidence for putative local adaptation or widespread phenotypic plasticity. Multiple regression models identified a weak but statistically significant negative association between leaf area and precipitation. Finally, species distribution modeling inferred northward range shifts over time, with both species predicted to occupy more coastal regions in the future, possibly increasing the frequency of hybridization among them. These findings underscore the importance of integrative assessment of multiple data sources in the study of hybridizing species and highlight the R. integrifolia‐ovata complex as a powerful model for investigating the adaptive implications of hybridization.

No abstract