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Science Enabled by Specimen Data

Calvente, A., A. P. Alves da Silva, D. Edler, F. A. Carvalho, M. R. Fantinati, A. Zizka, and A. Antonelli. 2023. Spiny but photogenic: amateur sightings complement herbarium specimens to reveal the bioregions of cacti. American Journal of Botany.

Premise: Cacti are characteristic elements of the Neotropical flora and of major interest for biogeographic, evolutionary, and ecological studies. Here we test global biogeographic boundaries for Neotropical Cactaceae using specimen‐based occurrences coupled with data from visual observations, as a means to tackle the known collection biases in the family.MethodsSpecies richness and record density were assessed for preserved specimens and human observations and a bioregional scheme tailored to Cactaceae was produced using the interactive web application Infomap Bioregions based on data from 261,272 point records cleaned through automated and manual steps.Key ResultsWe find that areas in Mexico and southwestern USA, Eastern Brazil and along the Andean region have the greatest density of records and the highest species richness. Human observations complement information from preserved specimens substantially, especially along the Andes. We propose 24 cacti bioregions, among which the most species‐rich are: northern Mexico/southwestern USA, central Mexico, southern central Mexico, Central America, Mexican Pacific coast, central and southern Andes, northwestern Mexico/extreme southwestern USA, southwestern Bolivia, northeastern Brazil, Mexico/Baja California.ConclusionsThe bioregionalization proposed shows biogeographical boundaries specific to cacti, and can thereby aid further evolutionary, biogeographic, and ecological studies by providing a validated framework for further analyses. This classification builds upon, and is distinctive from, other expert‐derived regionalization schemes for other taxa. Our results showcase how observation data, including citizen‐science records, can complement traditional specimen‐based data for biogeographic research, particularly for taxa with specific specimen collection and preservation challenges and those that are threatened or internationally protected.This article is protected by copyright. All rights reserved.

Rosas, M. R., R. A. Segovia, and P. C. Guerrero. 2023. Climatic Niche Dynamics of the Astereae Lineage and Haplopappus Species Distribution following Amphitropical Long-Distance Dispersal. Plants 12: 2721.

The tribe Astereae (Asteraceae) displays an American Amphitropical Disjunction. To understand the eco-evolutionary dynamics associated with a long-distance dispersal event and subsequent colonization of extratropical South America, we compared the climatic and geographic distributions of South American species with their closest North American relatives, focusing on the diverse South American Astereae genus, Haplopappus. Phylogenetic analysis revealed that two South American genera are closely related to seven North American genera. The climatic niche overlap (D = 0.5) between South and North America exhibits high stability (0.89), low expansion (0.12), and very low unfilling (0.04). The distribution of the North American species predicted the climatic and geographic space occupied by the South American species. In central Chile, Haplopappus showed a non-random latitudinal gradient in species richness, with Mediterranean climate variables mainly explaining the variation. Altitudinal patterns indicated peak richness at 600 m, declining at lower and higher elevations. These findings support climatic niche conservatism in shaping Haplopappus species distribution and diversity. Two major endemism zones were identified in central Chile and the southern region, with a transitional zone between Mediterranean and Temperate macro-bioclimates. Our results indicate strong niche conservatism following long-distance dispersal and slight niche expansion due to unique climatic variables in each hemisphere.

González-Pérez, A., R. Álvarez-Esteban, Á. Penas, and S. del Río. 2023. Bioclimatic Characterisation of Specific Native Californian Pinales and Their Future Suitability under Climate Change. Plants 12: 1966.

Rising temperatures and changes in precipitation patterns under climate change scenarios are accelerating the depletion of soil moisture and increasing the risk of drought, disrupting the conditions that many plant species need to survive. This study aims to establish the bioclimatic characterisation, both qualitative and quantitative, of ten native Californian Pinales for the period 1980–2019, and to determine their habitat suitability by 2050. To achieve this, an exhaustive search of the Gbif database for records of ten conifer taxa was carried out. To conduct the bioclimatic characterisation of the studied taxa, we worked with the monthly values of average temperature and precipitation for the period 1980–2019 from 177 meteorological stations. Linear regressions was performed in order to compile the future evolution of California’s climate. Suitable areas and optimal areas were defined at the present time (1980–2019) and its future projection (2050). We applied Boolean logic and, in this investigation, the Conditional Logic Operator (CON) was used to determine the possible species presence (one) or absence (zero) for each of the 15 variables analysed. In general, most of the conifers studied here will experience a reduction in their habitat range in California by the year 2050 due to climate change, as well as the displacement of species towards optimal areas. Furthermore, the results have highlighted the applicability of bioclimatology to future conditions under climate change. This will aid conservation managers in implementing strategic measures to ameliorate the detrimental impacts of climate change, thereby ensuring the ecological integrity and sustainability of the affected conifer species.

Sáenz-Ceja, J. E., and M. E. Mendoza. 2023. Priority areas for the conservation of the genus Abies Mill. (Pinaceae) in North America. Journal for Nature Conservation: 126407.

Fir forests (Abies, Pinaceae) are dominant in temperate regions of North America; however, they have experienced high degradation rates that can threaten their long-term continuity. This study aimed to identify the priority areas for the conservation of the genus Abies in North America. First, we modeled the species distribution of the 17 native species through ecological niche modeling, considering 21 environmental variables. Then, we defined the priority areas through multi-criteria analysis, considering the species richness, geographic rareness, irreplaceability, habitat degradation, and risk extinction. We also built six scenarios, giving more priority to each criterion. Finally, we identified the proportion of the extent of the priority areas covered by protected areas. Elevation, precipitation seasonality, and winter precipitation influenced the distribution of most of the Abies species. When considering equal weights to each criterion, the priority areas summed up 6% of the total extent covered by the Abies species in North America. Most priority areas were located on the West Coast of the United States, the Eastern Sierra Madre, Southern Sierra Madre, Sierras of Chiapas and Central America, and the Trans-Mexican Volcanic Belt ecoregions. In these ecoregions, the Abies species are restricted to small areas facing high degradation levels. Only 16% of the area covered by the Abies species in North America is protected, mainly under restrictive schemes such as National Parks and Wilderness Areas. The priority areas identified could be the basis for establishing or enlarging protected areas. The preservation of the genus Abies could also maintain other ecological features and processes such as biodiversity, forest resources, and environmental services.

Huang, T., J. Chen, K. E. Hummer, L. A. Alice, W. Wang, Y. He, S. Yu, et al. 2023. Phylogeny of Rubus (Rosaceae): Integrating molecular and morphological evidence into an infrageneric revision. TAXON.

Rubus (Rosaceae), one of the most complicated angiosperm genera, contains about 863 species, and is notorious for its taxonomic difficulty. The most recent (1910–1914) global taxonomic treatment of the genus was conducted by Focke, who defined 12 subgenera. Phylogenetic results over the past 25 years suggest that Focke's subdivisions of Rubus are not monophyletic, and large‐scale taxonomic revisions are necessary. Our objective was to provide a comprehensive phylogenetic analysis of the genus based on an integrative evidence approach. Morphological characters, obtained from our own investigation of living plants and examination of herbarium specimens are combined with chloroplast genomic data. Our dataset comprised 196 accessions representing 145 Rubus species (including cultivars and hybrids) and all of Focke's subgenera, including 60 endemic Chinese species. Maximum likelihood analyses inferred phylogenetic relationships. Our analyses concur with previous molecular studies, but with modifications. Our data strongly support the reclassification of several subgenera within Rubus. Our molecular analyses agree with others that only R. subg. Anoplobatus forms a monophyletic group. Other subgenera are para‐ or polyphyletic. We suggest a revised subgeneric framework to accommodate monophyletic groups. Character evolution is reconstructed, and diagnostic morphological characters for different clades are identified and discussed. Based on morphological and molecular evidence, we propose a new classification system with 10 subgenera: R. subg. Anoplobatus, R. subg. Batothamnus, R. subg. Chamaerubus, R. subg. Cylactis, R. subg. Dalibarda, R. subg. Idaeobatus, R. subg. Lineati, R. subg. Malachobatus, R. subg. Melanobatus, and R. subg. Rubus. The revised infrageneric nomenclature inferred from our analyses is provided along with synonymy and type citations. Our new taxonomic backbone is the first systematic and complete global revision of Rubus since Focke's treatment. It offers new insights into deep phylogenetic relationships of Rubus and has important theoretical and practical significance for the development and utilization of these important agronomic crops.

Ivey, C. T., N. M. Habecker, J. P. Bergmann, J. Ewald, M. E. Frayer, and J. M. Coughlan. 2023. Weak reproductive isolation and extensive gene flow between Mimulus glaucescens and M. guttatus in northern California. Evolution.

Abstract Barriers to reproduction are often how progress in speciation is measured. Nonetheless, an unresolved question concerns the extent to which reproductive barriers diminish gene flow between incipient species. The Sierra Nevada foothill endemic Mimulus glaucescens and the widespread M. guttatus are considered distinct species based on striking differences in vegetative morphology, but barriers to reproduction have not been previously identified, nor has gene flow between species been characterized. Here, we examined 15 potential reproductive barriers within a Northern California area of broad sympatry. Most barriers, with the exception of ecogeographic isolation, were weak or absent, and total isolation for each species was incomplete. Population genomic analyses of range-wide and broadly sympatric accessions revealed extensive gene flow between these taxa, particularly in sympatry. Despite widespread introgression, Mimulus glaucescens, emerged as monophyletic and largely comprised a single ancestry that was found at intermediate frequency within M. guttatus. This result, along with observed ecological and phenotypic differentiation, suggests that natural selection may contribute to the maintenance of distinct phenotypic forms in the earliest stages of speciation. Integrating estimates of barrier strength with direct estimates of gene flow can strengthen a more nuanced interpretation of the process of speciation in natural communities.

Zhao, Y., G. A. O’Neill, and T. Wang. 2023. Predicting fundamental climate niches of forest trees based on species occurrence data. Ecological Indicators 148: 110072.

Species climate niche models (CNMs) have been widely used for assessing climate change impact, developing conservation strategies and guiding assisted migration for adaptation to future climates. However, the CNMs built based on species occurrence data only reflect the species’ realized niche, which can overestimate the potential loss of suitable habitat of existing forests and underestimate the potential of assisted migration to mitigate climate change. In this study, we explored building a fundamental climate niche model using widely available species occurrence data with two important forest tree species, lodgepole pine (Pinus contorta Dougl. ex Loud.) and Douglas-fir (Pseudotsuga menziesii Franco.), which were introduced to many countries worldwide. We first compared and optimized three individual modeling techniques and their ensemble by adjusting the ratio of presence to absence (p/a) observations using an innovative approach to predict the realized climate niche of the two species. We then extended the realized climate niches to their fundamental niches by determining a new cut-off threshold based on species occurrence data beyond the native distributions. We found that the ensemble model comprising Random Forest and Maxent had the best performance and identified a common cut-off threshold of 0.3 for predicting the fundamental climate niches of the two species, which is likely applicable to other species. We then predicted the fundamental climate niches of the two species under current and future climate conditions. Our study demonstrated a novel approach for predicting species’ fundamental climate niche with high accuracy using only species occurrence data, including both presence and absence data points. It provided a new tool for assessing climate change impact on the future loss of existing forests and implementing assisted migration for better adapting to future climates.

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.

Latron, M., J. Arnaud, E. Schmitt, and A. Duputié. 2022. Idiosyncratic shifts in life‐history traits at species’ geographic range edges. Oikos.

Anthropogenic changes drive shifts in species' geographic distributions and increase the occurrence of leading or trailing‐edge marginal populations. Theoretical predictions and empirical observations indicate substantial changes in life‐history traits in marginal populations, often involving dispersal and reproductive abilities. Using a common garden experiment, we studied the variation of life‐history traits of populations sampled on spatial gradients extending from range‐core to range‐edge habitats for three expanding (miner's lettuce Claytonia perfoliata, Danish scurvygrass Cochlearia danica and rock samphire Crithmum maritimum) and one receding plant species (dune pansy Viola tricolor subs. curtisii). We monitored life‐history traits related to dispersal, phenology, survival, reproductive output and selfing ability. Significant shifts in life‐history traits between central and marginal populations strongly differed among species. Marginal populations of the three expanding species displayed modified seed weight in natura, suggesting increased dispersal abilities in leading‐edge populations. Discarding unassessed maternal effects, this trait modification can be due to phenotypic plasticity or to genetic differentiation. In miner's lettuce, marginal expanding populations show advanced phenology and higher reproductive output, that may potentially influence their colonization ability. In rock samphire, life‐history traits showed large intra‐ and inter‐population variability that did not follow a core‐to‐edge geographic trend, except for seed size. Finally, the receding populations of the dune pansy displayed a shift towards a plant architecture maximizing survival but reducing individual reproductive success. Altogether, our results indicated a common trend for increased dispersal abilities in marginal populations of expanding species. However, shifts in species' distributions may drive idiosyncratic changes in other life‐history traits, for which we observed no general evolutionary syndrome at range edges. These findings go along a stochastic view of trait evolution during range expansion, and question how to draw predictive projections of species' distribution shifts under current global change.

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.