Science Enabled by Specimen Data

Groh, S. S., P. Upchurch, J. J. Day, and P. M. Barrett. 2023. The biogeographic history of neosuchian crocodiles and the impact of saltwater tolerance variability. Royal Society Open Science 10. https://doi.org/10.1098/rsos.230725

Extant neosuchian crocodiles are represented by only 24 taxa that are confined to the tropics and subtropics. However, at other intervals during their 200 Myr evolutionary history the clade reached considerably higher levels of species-richness, matched by more widespread distributions. Neosuchians have occupied numerous habitats and niches, ranging from dwarf riverine forms to large marine predators. Despite numerous previous studies, several unsolved questions remain with respect to their biogeographic history, including the geographical origins of major groups, e.g. Eusuchia and Neosuchia itself. We carried out the most comprehensive biogeographic analysis of Neosuchia to date, based on a multivariate K-means clustering approach followed by the application of two ancestral area estimation methods (BioGeoBEARS and Bayesian ancestral location estimation) applied to two recently published phylogenies. Our results place the origin of Neosuchia in northwestern Pangaea, with subsequent radiations into Gondwana. Eusuchia probably emerged in the European archipelago during the Late Jurassic/Early Cretaceous, followed by dispersals to the North American and Asian landmasses. We show that putative transoceanic dispersal events are statistically significantly less likely to happen in alligatoroids. This finding is consistent with the saltwater intolerant physiology of extant alligatoroids, bolstering inferences of such intolerance in their ancestral lineages.

Lee, F., N. C. Boddy, M. Bloxham, A. R. McIntosh, G. L. W. Perry, and K. S. Simon. 2023. Spatiotemporal patterns of research on Southern Hemisphere amphidromous galaxiids: A semi–quantitative review. Austral Ecology. https://doi.org/10.1111/aec.13315

Amphidromy is a distinctive life‐history strategy of some fish species that involves spawning in fresh or brackish water followed by dispersal to sea by newly hatched larvae, where they develop for a short period. Individuals then return to freshwater as juveniles, where they feed and grow, before maturing and spawning. Six amphidromous species from the Southern Hemisphere genus Galaxias (G. truttaceus, G. fasciatus, G. argenteus, G. postvectis, G. brevipinnis, G. maculatus) are recreationally, culturally, and economically important as the juveniles are harvested. Due to ongoing population declines and a lack of critical demographic information, there is growing concern about the management of the species. Here, we used semi‐quantitative review, culturomics, and bibliometric tools to analyse peer‐reviewed research conducted on the six amphidromous species of Galaxias to: (i) understand how spatiotemporal patterns of research have shifted over the last five decades, and (ii) identify critical research gaps. Forty percent of studies (n = 295) covered a spatial extent of 10 km or less and 87% of studies lasted less than 2 years – studies were largely small and short relative to the species' ranges and their longevity. Additionally, we found important research gaps; for example, studies on the effects of climate change and the associated effects of disturbance, and the marine phase are scarce in the peer‐reviewed literature. Finally, we suggest that quantitative models have been underutilized as tools for studying amphidromous galaxiids and should be embraced to answer questions not readily addressed with field and laboratory‐based techniques. If these species are to be effectively managed, their population dynamics across spatiotemporal scales must be understood and critical and long‐standing gaps in research knowledge addressed.

Carmelet‐Rescan, D., M. Morgan‐Richards, N. Pattabiraman, and S. A. Trewick. 2022. Time‐calibrated phylogeny and ecological niche models indicate Pliocene aridification drove intraspecific diversification of brushtail possums in Australia. Ecology and Evolution 12. https://doi.org/10.1002/ece3.9633

Major aridification events in Australia during the Pliocene may have had significant impact on the distribution and structure of widespread species. To explore the potential impact of Pliocene and Pleistocene climate oscillations, we estimated the timing of population fragmentation and past connectivity of the currently isolated but morphologically similar subspecies of the widespread brushtail possum (Trichosurus vulpecula). We use ecological niche modeling (ENM) with the current fragmented distribution of brushtail possums to estimate the environmental envelope of this marsupial. We projected the ENM on models of past climatic conditions in Australia to infer the potential distribution of brushtail possums over 6 million years. D‐loop haplotypes were used to describe population structure. From shotgun sequencing, we assembled whole mitochondrial DNA genomes and estimated the timing of intraspecific divergence. Our projections of ENMs suggest current possum populations were unlikely to have been in contact during the Pleistocene. Although lowered sea level during glacial periods enabled connection with habitat in Tasmania, climate fluctuation during this time would not have facilitated gene flow over much of Australia. The most recent common ancestor of sampled intraspecific diversity dates to the early Pliocene when continental aridification caused significant changes to Australian ecology and Trichosurus vulpecula distribution was likely fragmented. Phylogenetic analysis revealed that the subspecies T. v. hypoleucus (koomal; southwest), T. v. arnhemensis (langkurr; north), and T. v. vulpecula (bilda; southeast) correspond to distinct mitochondrial lineages. Despite little phenotypic differentiation, Trichosurus vulpecula populations probably experienced little gene flow with one another since the Pliocene, supporting the recognition of several subspecies and explaining their adaptations to the regional plant assemblages on which they feed.

Moreno, I., J. M. W. Gippet, L. Fumagalli, and P. J. Stephenson. 2022. Factors affecting the availability of data on East African wildlife: the monitoring needs of conservationists are not being met. Biodiversity and Conservation. https://doi.org/10.1007/s10531-022-02497-4

Understanding the status and abundance of species is essential for effective conservation decision-making. However, the availability of species data varies across space, taxonomic groups and data types. A case study was therefore conducted in a high biodiversity region—East Africa—to evaluate data biases, the factors influencing data availability, and the consequences for conservation. In each of the eleven target countries, priority animal species were identified as threatened species that are protected by national governments, international conventions or conservation NGOs. We assessed data gaps and biases in the IUCN Red List of Threatened Species, the Global Biodiversity Information Facility and the Living Planet Index. A survey of practitioners and decision makers was conducted to confirm and assess consequences of these biases on biodiversity conservation efforts. Our results showed data on species occurrence and population trends were available for a significantly higher proportion of vertebrates than invertebrates. We observed a geographical bias, with higher tourism income countries having more priority species and more species with data than lower tourism income countries. Conservationists surveyed felt that, of the 40 types of data investigated, those data that are most important to conservation projects are the most difficult to access. The main challenges to data accessibility are excessive expense, technological challenges, and a lack of resources to process and analyse data. With this information, practitioners and decision makers can prioritise how and where to fill gaps to improve data availability and use, and ensure biodiversity monitoring is improved and conservation impacts enhanced.

Williams, C. J. R., D. J. Lunt, U. Salzmann, T. Reichgelt, G. N. Inglis, D. R. Greenwood, W. Chan, et al. 2022. African Hydroclimate During the Early Eocene From the DeepMIP Simulations. Paleoceanography and Paleoclimatology 37. https://doi.org/10.1029/2022pa004419

The early Eocene (∼56‐48 million years ago) is characterised by high CO2 estimates (1200‐2500 ppmv) and elevated global temperatures (∼10 to 16°C higher than modern). However, the response of the hydrological cycle during the early Eocene is poorly constrained, especially in regions with sparse data coverage (e.g. Africa). Here we present a study of African hydroclimate during the early Eocene, as simulated by an ensemble of state‐of‐the‐art climate models in the Deep‐time Model Intercomparison Project (DeepMIP). A comparison between the DeepMIP pre‐industrial simulations and modern observations suggests that model biases are model‐ and geographically dependent, however these biases are reduced in the model ensemble mean. A comparison between the Eocene simulations and the pre‐industrial suggests that there is no obvious wetting or drying trend as the CO2 increases. The results suggest that changes to the land sea mask (relative to modern) in the models may be responsible for the simulated increases in precipitation to the north of Eocene Africa. There is an increase in precipitation over equatorial and West Africa and associated drying over northern Africa as CO2 rises. There are also important dynamical changes, with evidence that anticyclonic low‐level circulation is replaced by increased south‐westerly flow at high CO2 levels. Lastly, a model‐data comparison using newly‐compiled quantitative climate estimates from palaeobotanical proxy data suggests a marginally better fit with the reconstructions at lower levels of CO2.

Rodrigues, A. V., G. Nakamura, V. G. Staggemeier, and L. Duarte. 2022. Species misidentification affects biodiversity metrics: Dealing with this issue using the new R package naturaList. Ecological Informatics 69: 101625. https://doi.org/10.1016/j.ecoinf.2022.101625

Biodiversity databases are increasingly available and have fostered accelerated advances in many disciplines within ecology and evolution. However, the quality of the evidence generated depends critically on the quality of the input data, and species misidentifications are present in virtually any o…

Xue, T., S. R. Gadagkar, T. P. Albright, X. Yang, J. Li, C. Xia, J. Wu, and S. Yu. 2021. Prioritizing conservation of biodiversity in an alpine region: Distribution pattern and conservation status of seed plants in the Qinghai-Tibetan Plateau. Global Ecology and Conservation 32: e01885. https://doi.org/10.1016/j.gecco.2021.e01885

The Qinghai-Tibetan Plateau (QTP) harbors abundant and diverse plant life owing to its high habitat heterogeneity. However, the distribution pattern of biodiversity hotspots and their conservation status remain unclear. Based on 148,283 high-resolution occurrence coordinates of 13,450 seed plants, w…

McGowan, N. E., N. Roche, T. Aughney, J. Flanagan, P. Nolan, F. Marnell, and N. Reid. 2021. Testing consistency of modelled predictions of the impact of climate change on bats. Climate Change Ecology 2: 100011. https://doi.org/10.1016/j.ecochg.2021.100011

Species Distribution Models (SDMs) are a cornerstone of climate change conservation research but temporal extrapolations into future climate scenarios cannot be verified until later this century. One way of assessing the robustness of projections is to compare their consistency between different mod…

Hughes, A. C., M. C. Orr, K. Ma, M. J. Costello, J. Waller, P. Provoost, Q. Yang, et al. 2021. Sampling biases shape our view of the natural world. Ecography 44: 1259–1269. https://doi.org/10.1111/ecog.05926

Spatial patterns of biodiversity are inextricably linked to their collection methods, yet no synthesis of bias patterns or their consequences exists. As such, views of organismal distribution and the ecosystems they make up may be incorrect, undermining countless ecological and evolutionary studies.…

Cooper, N., A. L. Bond, J. L. Davis, R. Portela Miguez, L. Tomsett, and K. M. Helgen. 2019. Sex biases in bird and mammal natural history collections. Proceedings of the Royal Society B: Biological Sciences 286: 20192025. https://doi.org/10.1098/rspb.2019.2025

Natural history specimens are widely used across ecology, evolutionary biology and conservation. Although biological sex may influence all of these areas, it is often overlooked in large-scale studies using museum specimens. If collections are biased towards one sex, studies may not be representativ…