Science Enabled by Specimen Data

Benson, C. W., M. R. Sheltra, P. J. Maughan, E. N. Jellen, M. D. Robbins, B. S. Bushman, E. L. Patterson, et al. 2023. Homoeologous evolution of the allotetraploid genome of Poa annua L. BMC Genomics 24.

Background Poa annua (annual bluegrass) is an allotetraploid turfgrass, an agronomically significant weed, and one of the most widely dispersed plant species on earth. Here, we report the chromosome-scale genome assemblies of P. annua’s diploid progenitors, P. infirma and P. supina, and use multi-omic analyses spanning all three species to better understand P. annua’s evolutionary novelty. Results We find that the diploids diverged from their common ancestor 5.5 – 6.3 million years ago and hybridized to form P. annua  ≤ 50,000 years ago. The diploid genomes are similar in chromosome structure and most notably distinguished by the divergent evolutionary histories of their transposable elements, leading to a 1.7 × difference in genome size. In allotetraploid P. annua, we find biased movement of retrotransposons from the larger (A) subgenome to the smaller (B) subgenome. We show that P. annua’s B subgenome is preferentially accumulating genes and that its genes are more highly expressed. Whole-genome resequencing of several additional P. annua accessions revealed large-scale chromosomal rearrangements characterized by extensive TE-downsizing and evidence to support the Genome Balance Hypothesis. Conclusions The divergent evolutions of the diploid progenitors played a central role in conferring onto P. annua its remarkable phenotypic plasticity. We find that plant genes (guided by selection and drift) and transposable elements (mostly guided by host immunity) each respond to polyploidy in unique ways and that P. annua uses whole-genome duplication to purge highly parasitized heterochromatic sequences. The findings and genomic resources presented here will enable the development of homoeolog-specific markers for accelerated weed science and turfgrass breeding .

Wang, Y., J. Wang, T. A. Garran, H. Liu, H. Lin, J. Luo, Q. Yuan, et al. 2023. Genetic diversity and population divergence of Leonurus japonicus and its distribution dynamic changes from the last interglacial to the present in China. BMC Plant Biology 23.

Background Leonurus japonicus , a significant medicinal plant known for its therapeutic effects on gynecological and cardiovascular diseases, has genetic diversity that forms the basis for germplasm preservation and utilization in medicine. Despite its economic value, limited research has focused on its genetic diversity and divergence. Results The avg. nucleotide diversity of 59 accessions from China were 0.00029 and hotspot regions in petN-psbM and rpl32-trnL (UAG) spacers, which can be used for genotype discrimination. These accessions divided into four clades with significant divergence. The four subclades, which split at approximately 7.36 Ma, were likely influenced by the Hengduan Mountains uplift and global temperature drop. The initial divergence gave rise to Clade D, with a crown age estimated at 4.27 Ma, followed by Clade C, with a crown age estimated at 3.39 Ma. The four clades were not showed a clear spatial distribution. Suitable climatic conditions for the species were identified, including warmest quarter precipitation 433.20 mm ~ 1,524.07 mm, driest month precipitation > 12.06 mm, and coldest month min temp > -4.34 °C. The high suitability distribution showed contraction in LIG to LGM, followed by expansion from LGM to present. The Hengduan Mountains acted as a glacial refuge for the species during climate changes. Conclusions Our findings reflected a clear phylogenetic relationships and divergence within species L. japonicus and the identified hotspot regions could facilitate the genotype discrimination. The divergence time estimation and suitable area simulation revealed evolution dynamics of this species and may propose conservation suggestions and exploitation approaches in the future.

Chaudhary, C., J. M. Alfaro-Lucas, M. V. P. Simões, A. Brandt, and H. Saeedi. 2023. Potential geographic shifts in the coral reef ecosystem under climate change. Progress in Oceanography 213: 103001.

The coral reefs are the most diverse marine ecosystem in the world. Considering its contribution as a natural resource for humanity and global biodiversity, it is critical to understand its response to climatic change. To date, no global predictions have been made about potential ecosystem changes in relation to its inhabiting species. Predicting changes in species' climatic suitability under increasing temperature and comparing them among species would be the first step in understanding the geographic and taxonomic coherence and discrepancies that may occur within the ecosystem. Using 57 species-specific global climate suitability models (of corals, molluscs, fish, crustaceans, and polychaetes) under present and future climate scenarios (RCP 4.5 and 8.5), we compared the potential coherence and differences and their cumulative impact on the ecosystem in warm, cold, shallow, and deep waters.Under the climatic scenarios, nearly 90% of 30 warm-water species were predicted to lose their suitability in the parts of the Indo-west Pacific, the Coast of Northern Australia, the South China Sea, the Caribbean Sea, and the Gulf of Mexico, resulting in the overall southward shift in their distributions. In contrast, a mixed response occurred in 27 cold-water species, with most northern temperate/boreal ones increasing their suitability in the Arctic Ocean and the Arctic species declining overall. We noticed that irrespective of their taxonomic group, the species with wider distribution ranges (thermal and geographic) had larger predicted gains in their suitability than their stenothermal counterparts, suggesting an increase of generalist species and a decline of specialist (endemic) species of the ecosystem under a warming climate.Our coherent projections of species' climatic suitability in warm and cold habitats of the tropics, temperate, boreal, and the Arctic, represent significant taxonomic groups of the ecosystem. This might indicate mass extinction risk (local– in the tropics and northern temperate regions, and overall– in the Arctic) in native habitats and a high species turnover across the ecosystem under a warming climate. This may also destabilise predator–prey dynamics in the ecosystem, especially if foraging specialists dominate coral food webs and adversely affect the associated countries. Our global projections highlight the regions of species’ potential loss and gain; stakeholders could use the information to protect biodiversity and maintain human well-being.

Marcussen, T., H. E. Ballard, J. Danihelka, A. R. Flores, M. V. Nicola, and J. M. Watson. 2022. A Revised Phylogenetic Classification for Viola (Violaceae). Plants 11: 2224.

The genus Viola (Violaceae) is among the 40–50 largest genera among angiosperms, yet its taxonomy has not been revised for nearly a century. In the most recent revision, by Wilhelm Becker in 1925, the then-known 400 species were distributed among 14 sections and numerous unranked groups. Here, we provide an updated, comprehensive classification of the genus, based on data from phylogeny, morphology, chromosome counts, and ploidy, and based on modern principles of monophyly. The revision is presented as an annotated global checklist of accepted species of Viola, an updated multigene phylogenetic network and an ITS phylogeny with denser taxon sampling, a brief summary of the taxonomic changes from Becker’s classification and their justification, a morphological binary key to the accepted subgenera, sections and subsections, and an account of each infrageneric subdivision with justifications for delimitation and rank including a description, a list of apomorphies, molecular phylogenies where possible or relevant, a distribution map, and a list of included species. We distribute the 664 species accepted by us into 2 subgenera, 31 sections, and 20 subsections. We erect one new subgenus of Viola (subg. Neoandinium, a replacement name for the illegitimate subg. Andinium), six new sections (sect. Abyssinium, sect. Himalayum, sect. Melvio, sect. Nematocaulon, sect. Spathulidium, sect. Xanthidium), and seven new subsections (subsect. Australasiaticae, subsect. Bulbosae, subsect. Clausenianae, subsect. Cleistogamae, subsect. Dispares, subsect. Formosanae, subsect. Pseudorupestres). Evolution within the genus is discussed in light of biogeography, the fossil record, morphology, and particular traits. Viola is among very few temperate and widespread genera that originated in South America. The biggest identified knowledge gaps for Viola concern the South American taxa, for which basic knowledge from phylogeny, chromosome counts, and fossil data is virtually absent. Viola has also never been subject to comprehensive anatomical study. Studies into seed anatomy and morphology are required to understand the fossil record of the genus.

Hirabayashi, K., S. J. Murch, and L. A. E. Erland. 2022. Predicted impacts of climate change on wild and commercial berry habitats will have food security, conservation and agricultural implications. Science of The Total Environment 845: 157341.

Climate change is now a reality and is altering ecosystems, with Canada experiencing 2–4 times the global average rate of warming. This will have a critical impact on berry cultivation and horticulture. Enhancing our understanding of how wild and cultivated berries will perform under changing climates will be essential to mitigating impacts on ecosystems, culture and food security. Our objective was to predict the impact of climate change on habitat suitability of four berry producing Vaccinium species: two species with primarily northern distributions (V. uliginosum, V. vitis-idaea), one species with a primarily southern distribution (V. oxycoccos), and the commercially cultivated V. macrocarpon. We used the maximum entropy (Maxent) model and the CMIP6 shared socioeconomic pathways (SSPs) 126 and 585 projected to 2041–2060 and 2061–2080. Wild species showed a uniform northward progression and expansion of suitable habitat. Our modeling predicts that suitable growing regions for commercial cranberries are also likely to shift with some farms becoming unsuitable for the current varieties and other regions becoming more suitable for cranberry farms. Both V. macrocarpon and V. oxycoccos showed a high dependence on precipitation-associated variables. Vaccinium vitis-idaea and V. uliginosum had a greater number of variables with smaller contributions which may improve their resilience to individual climactic events. Future competition between commercial cranberry farms and wild berries in protected areas could lead to conflicts between agriculture and conservation priorities. New varieties of commercial berries are required to maintain current commercial berry farms.

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.

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…

Arfianti, T., and M. J. Costello. 2021. The distribution of benthic amphipod crustaceans in Indonesian seas. PeerJ 9: e12054.

Amphipod crustaceans are an essential component of tropical marine biodiversity. However, their distribution and biogeography have not been analysed in one of the world’s largest tropical countries nested in the Coral Triangle, Indonesia. We collected and identified amphipod crustaceans from eight s…

Mairal, M., S. L. Chown, J. Shaw, D. Chala, J. H. Chau, C. Hui, J. M. Kalwij, et al. 2021. Human activity strongly influences genetic dynamics of the most widespread invasive plant in the sub‐Antarctic. Molecular Ecology 31: 1649–1665.

The link between the successful establishment of alien species and propagule pressure is well-documented. Less known is how humans influence the post-introduction dynamics of invasive alien populations. The latter requires studying parallel invasions by the same species in habitats that are differen…

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.

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…

Salinas-Ramos, V. B., L. Ancillotto, L. Cistrone, C. Nastasi, L. Bosso, S. Smeraldo, V. Sánchez Cordero, and D. Russo. 2021. Artificial illumination influences niche segregation in bats. Environmental Pollution 284: 117187.

Artificial light at night (ALAN) is a pervasive form of pollution largely affecting wildlife, from individual behaviour to community structure and dynamics. As nocturnal mammals, bats are often adversely affected by ALAN, yet some “light-opportunistic” species exploit it by hunting insects swarming …