Science Enabled by Specimen Data

Silva, C. P., D. N. López, P. I. Naulin, and S. A. Estay. 2023. Can suitability indices predict plant growth in the invaded range? The case of Acacias species. Frontiers in Plant Science 14.

IntroductionForestry in many parts of the world depends on exotic species, making this industry a source of invasions in some countries. Among others, plantations of the genus Pinus, Eucalyptus, Acacia, Populus, and Pseudotsuga underpin the forestry industry and are a vital component of many countries economies. Among woody plants, the cosmopolitan genus Acacia includes some of the most commonly planted trees worldwide. In order to prevent, manage and control invasive plant species, one of the most used tools is species distribution models. The output of these models can also be used to obtain information about population characteristics, such as spatial abundance patterns or species performance. Although ecological theory suggests a direct link between fitness and suitability, this link is often absent. The reasons behind the lack of this relationship are multiple. Chile is one of the countries where Acacia species, in particular, A. dealbata and A. melanoxylon, have become invaders. MethodsHere, we used climatic and edaphic variables to predict thepotentially suitable habitats for A. dealbata and A. melanoxylon in continental Chile and evaluate if the suitability indices obtained from these models are associated with the observed performance of the trees along the country. ResultsOur models show that variable importance showed significant similarities between the variables that characterize each species’ niche. However, despite the high accuracy of our models, we did not observe an association between suitability and tree growth.DiscussionThis disconnection between suitability and performance can result from multiple causes, from structural limitations, like the lack of biotic interactions in the models, to methodological issues, like the usefulness of the performance metric used. Whatever the scenario, our results suggest that plans to control invasive species should be cautious in assuming this relationship in their design and consider other indicators such as species establishment success.

Reichgelt, T., A. Baumgartner, R. Feng, and D. A. Willard. 2023. Poleward amplification, seasonal rainfall and forest heterogeneity in the Miocene of the eastern USA. Global and Planetary Change 222: 104073.

Paleoclimate reconstructions can provide a window into the environmental conditions in Earth history when atmospheric carbon dioxide concentrations were higher than today. In the eastern USA, paleoclimate reconstructions are sparse, because terrestrial sedimentary deposits are rare. Despite this, the eastern USA has the largest population and population density in North America, and understanding the effects of current and future climate change is of vital importance. Here, we provide terrestrial paleoclimate reconstructions of the eastern USA from Miocene fossil floras. Additionally, we compare proxy paleoclimate reconstructions from the warmest period in the Miocene, the Miocene Climatic Optimum (MCO), to those of an MCO Earth System Model. Reconstructed Miocene temperatures and precipitation north of 35°N are higher than modern. In contrast, south of 35°N, temperatures and precipitation are similar to today, suggesting a poleward amplification effect in eastern North America. Reconstructed Miocene rainfall seasonality was predominantly higher than modern, regardless of latitude, indicating greater variability in intra-annual moisture transport. Reconstructed climates are almost uniformly in the temperate seasonal forest biome, but heterogeneity of specific forest types is evident. Reconstructed Miocene terrestrial temperatures from the eastern USA are lower than modeled temperatures and coeval Atlantic sea surface temperatures. However, reconstructed rainfall is consistent with modeled rainfall. Our results show that during the Miocene, climate was most different from modern in the northeastern states, and may suggest a drastic reduction in the meridional temperature gradient along the North American east coast compared to today.

Mai, J., and G. Liu. 2023. Modeling and predicting the effects of climate change on cotton-suitable habitats in the Central Asian arid zone. Industrial Crops and Products 191: 115838.

Climate change has significantly affected global agricultural production, particularly in arid zones of Central Asia. Thus, we analyzed changes in the habitat suitability of cotton in Central Asia under various shared socioeconomic pathway (SSP) scenarios during 2021–2060. The results showed that the average minimum temperature in April, precipitation seasonality, and distance to rivers were the main environmental factors influencing the suitable distribution of cotton. Suitable habitats expanded toward the north and east, reaching a maximum net increase of 10.85 × 104 km2 under the SSP5–8.5 scenario during 2041–2060, while habitats in the southwestern area showed a contracting trend. The maximum decreased and increased habitats were concentrated at approximately 68°E and 87°E, respectively. In addition, their latitudinal distributions were concentrated at approximately 40°N and 44°N. The longitudinal and latitudinal dividing lines of increased and decreased habitats were 69°E and 41°N, respectively. Habitats at the same altitude showed an increasing trend, excluding the elevation range of 125–325 m. Habitat shifts could exacerbate spatial conflicts with forest/grassland and natural reserves. The maximum spatial overlap between them was observed under the SSP5–8.5 scenario during 2041–2060. These findings could provide scientific evidence for rational cotton cultivation planning in global arid zones.

Lal, M. M., K. T. Brown, P. Chand, and T. D. Pickering. 2022. An assessment of the aquaculture potential of indigenous freshwater food fish of Fiji, Papua New Guinea, Vanuatu, Solomon Islands, Samoa and Tonga as alternatives to farming of tilapia. Reviews in Aquaculture.

An important driver behind introductions for aquaculture of alien fish species into Pacific Island Countries and Territories (PICTs) is a lack of knowledge about domestication suitability and specific culture requirements of indigenous taxa. Introductions may be appropriate in some circumstances, but in other circumstances, the associated risks may outweigh the benefits, so greater understanding of indigenous species' aquaculture potential is important. This review summarises literature for indigenous freshwater food fish species from Papua New Guinea, Fiji, Vanuatu, the Solomon Islands, Samoa and Tonga, and evaluates their aquaculture potential for food security and/or small‐scale livelihoods. A species selection criteria incorporating economic, social, biological and environmental spheres was used to score 62 candidate species. Tilapia (Oreochromis mossambicus and O. niloticus) now established in PICTs were evaluated for comparison. Results show that 13 species belonging to the families Mugilidae (Mullets), Terapontidae (Grunters), Kuhliidae (Flagtails) and Scatophagidae (Scats) have the highest culture potential according to selection criteria. These feed at a relatively low trophic level (are herbivores/detritivores), have comparatively fast growth rates and overall possess characteristics most amenable for small‐scale, inland aquaculture. The four top‐ranked candidates are all mountain mullets Cestraeus spp., followed by Nile tilapia (Oreochromis niloticus). Lower ranked candidates include three other mullets (Planiliza melinoptera, P. subviridis and Mugil cephalus) and rock flagtail Kuhlia rupestris. Importantly, many species remain data deficient in aspects of their reproductive biology or culture performance. Species profiles and ranked priority species by country are provided with logistical, technological and environmental assessments of country capacities to culture each species.

Aguirre‐Liguori, J. A., A. Morales‐Cruz, and B. S. Gaut. 2022. Evaluating the persistence and utility of five wild Vitis species in the context of climate change. Molecular Ecology.

Crop wild relatives (CWRs) have the capacity to contribute novel traits to agriculture. Given climate change, these contributions may be especially vital for the persistence of perennial crops, because perennials are often clonally propagated and consequently do not evolve rapidly. By studying the landscape genomics of samples from five Vitis CWRs (V. arizonica, V. mustangensis, V. riparia, V. berlandieri and V. girdiana) in the context of projected climate change, we addressed two goals. The first was to assess the relative potential of different CWR accessions to persist in the face of climate change. By integrating species distribution models with adaptive genetic variation, additional genetic features such as genomic load and a phenotype (resistance to Pierce’s Disease), we predicted that accessions from one species (V. mustangensis) are particularly well‐suited to persist in future climates. The second goal was to identify which CWR accessions may contribute to bioclimatic adaptation for grapevine (V. vinifera) cultivation. To do so, we evaluated whether CWR accessions have the allelic capacity to persist if moved to locations where grapevines (V. vinifera) are cultivated in the United States. We identified six candidates from V. mustangensis and hypothesized that they may prove useful for contributing alleles that can mitigate climate impacts on viticulture. By identifying candidate germplasm, this work takes a conceptual step toward assessing the genomic and bioclimatic characteristics of CWRs.

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.

Testo, W. L., A. L. de Gasper, S. Molino, J. M. G. y Galán, A. Salino, V. A. de O. Dittrich, and E. B. Sessa. 2022. Deep vicariance and frequent transoceanic dispersal shape the evolutionary history of a globally distributed fern family. American Journal of Botany.

Premise Historical biogeography of ferns is typically expected to be dominated by long-distance dispersal, due to their minuscule spores. However, few studies have inferred the historical biogeography of a large and widely distributed group of ferns to test this hypothesis. Our aims are to determine the extent to which long-distance dispersal vs. vicariance have shaped the history of the fern family Blechnaceae, to explore ecological correlates of dispersal and diversification, and to determine whether these patterns differ between the northern and southern hemispheres. Methods We used sequence data for three chloroplast loci to infer a time-calibrated phylogeny for 154 out of 265 species of Blechnaceae, including representatives of all genera in the family. This tree was used to conduct ancestral range reconstruction and stochastic character mapping, estimate diversification rates, and identify ecological correlates of diversification. Key results Blechnaceae originated in Eurasia and began diversifying in the late Cretaceous. A lineage comprising most extant diversity diversified principally in the austral Pacific region around the Paleocene-Eocene Thermal Maximum. Land connections that existed near the poles during periods of warm climates likely facilitated migration of several lineages, with subsequent climate-mediated vicariance shaping current distributions. Long-distance dispersal is frequent and asymmetrical, with New Zealand/Pacific Islands, Australia, and tropical America being major source areas. Conclusions Ancient vicariance and extensive long-distance dispersal have shaped the history of Blechnaceae in both the northern and southern hemispheres. The exceptional diversity in austral regions appears to reflect rapid speciation in these areas; mechanisms underlying this evolutionary success remain uncertain.

Clark, R. P., K.-W. Jiang, and E. Gagnon. 2022. Reinstatement of Ticanto (Leguminosae-Caesalpinioideae) – the final piece in the Caesalpinia group puzzle. PhytoKeys 205: 59–98.

A recent molecular phylogenetic analysis of the Caesalpinia group demonstrated that it comprises 26 genera, but the recognition of a putative 27th genus, Ticanto, remained in doubt. This study presents a phylogenetic analysis of ITS and five plastid loci revealing a robustly supported monophyletic group representing the Ticanto clade, sister to the morphologically distinct genus Pterolobium. Based upon this evidence, along with a morphological evaluation, the genus Ticanto is here reinstated. Descriptions are provided for all nine species of Ticanto, together with a key to the species, maps, and colour photographs. Nine new combinations are made: Ticantocaesia (Hand.-Mazz.) R. Clark & Gagnon, T.crista (L.) R. Clark & Gagnon, T.elliptifolia (S. J. Li, Z. Y. Chen & D. X. Zhang) R. Clark & Gagnon, T.magnifoliolata (Metcalf) R. Clark & Gagnon, T.rhombifolia R. Clark & Gagnon, T.sinensis (Hemsl.) R. Clark & Gagnon, T.szechuenensis (Craib) R. Clark & Gagnon, T.vernalis (Champion ex Benth.) R. Clark & Gagnon and T.yunnanensis (S. J. Li, D. X. Zhang & Z.Y. Chen) R. Clark & Gagnon. The final major question in the delimitation of segregate genera from within Caesalpiniasensu lato and the Caesalpinia group is thus resolved.

Ramirez-Villegas, J., C. K. Khoury, H. A. Achicanoy, M. V. Diaz, A. C. Mendez, C. C. Sosa, Z. Kehel, et al. 2022. State of ex situ conservation of landrace groups of 25 major crops. Nature Plants 8: 491–499.

Crop landraces have unique local agroecological and societal functions and offer important genetic resources for plant breeding. Recognition of the value of landrace diversity and concern about its erosion on farms have led to sustained efforts to establish ex situ collections worldwide. The degree to which these efforts have succeeded in conserving landraces has not been comprehensively assessed. Here we modelled the potential distributions of eco-geographically distinguishable groups of landraces of 25 cereal, pulse and starchy root/tuber/fruit crops within their geographic regions of diversity. We then analysed the extent to which these landrace groups are represented in genebank collections, using geographic and ecological coverage metrics as a proxy for genetic diversity. We find that ex situ conservation of landrace groups is currently moderately comprehensive on average, with substantial variation among crops; a mean of 63% ± 12.6% of distributions is currently represented in genebanks. Breadfruit, bananas and plantains, lentils, common beans, chickpeas, barley and bread wheat landrace groups are among the most fully represented, whereas the largest conservation gaps persist for pearl millet, yams, finger millet, groundnut, potatoes and peas. Geographic regions prioritized for further collection of landrace groups for ex situ conservation include South Asia, the Mediterranean and West Asia, Mesoamerica, sub-Saharan Africa, the Andean mountains of South America and Central to East Asia. With further progress to fill these gaps, a high degree of representation of landrace group diversity in genebanks is feasible globally, thus fulfilling international targets for their ex situ conservation. By analysing the state of representation of traditional varieties of 25 major crops in ex situ repositories, this study demonstrates conservation progress made over more than a half-century and identifies the gaps remaining to be filled.

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.

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.