Science Enabled by Specimen Data

Zhao, Y., G. A. O’Neill, N. C. Coops, and T. Wang. 2024. Predicting the site productivity of forest tree species using climate niche models. Forest Ecology and Management 562: 121936. https://doi.org/10.1016/j.foreco.2024.121936

Species occurrence-based climate niche models (CNMs) serve as valuable tools for predicting the future ranges of species’ suitable habitats, aiding the development of climate change adaptation strategies. However, these models do not address an essential aspect - productivity, which holds economic significance for timber production and ecological importance for carbon sequestration and ecosystem services. In this study, we investigated the potential to extend the CNMs to predict species productivity under various climate conditions. Lodgepole pine (Pinus contorta Dougl. ex Loud.) and Douglas-fir (Pseudotsuga menziesii Franco.) were selected as our model species due to their comprehensive range-wide occurrence data and measurement of site productivity. To achieve this, we compared and optimized the performance of four individual modeling algorithms (Random Forest (RF), Maxent, Generalized Boosted Models (GBM), and Generalized Additive Model (GAM)) in reflecting site productivity by evaluating the effect of spatial filtering, and the ratio of presence to absence (p/a ratio) observations. Additionally, we applied a binning process to capture the overarching trend of climatic effects while minimizing the impact of other factors. We observed consistency in optimal performance across both species when using the unfiltered data and a 1:1.5 p/a ratio, which could potentially be extended to other species. Among the modeling algorithms explored, we selected the ensemble model combining RF and Maxent as the final model to predict the range-wide site productivity for both species. The predicted range-wide site productivity was validated with an independent dataset for each species and yielded promising results (R2 above 0.7), affirming our model’s credibility. Our model introduced an innovative approach for predicting species productivity with high accuracy using only species occurrence data, and significantly advanced the application of CNMs. It provided crucial tools and insights for evaluating climate change's impact on productivity and holds a better potential for informed forest management and conservation decisions.

Anest, A., Y. Bouchenak-Khelladi, T. Charles-Dominique, F. Forest, Y. Caraglio, G. P. Hempson, O. Maurin, and K. W. Tomlinson. 2024. Blocking then stinging as a case of two-step evolution of defensive cage architectures in herbivore-driven ecosystems. Nature Plants. https://doi.org/10.1038/s41477-024-01649-4

Dense branching and spines are common features of plant species in ecosystems with high mammalian herbivory pressure. While dense branching and spines can inhibit herbivory independently, when combined, they form a powerful defensive cage architecture. However, how cage architecture evolved under mammalian pressure has remained unexplored. Here we show how dense branching and spines emerged during the age of mammalian radiation in the Combretaceae family and diversified in herbivore-driven ecosystems in the tropics. Phylogenetic comparative methods revealed that modern plant architectural strategies defending against large mammals evolved via a stepwise process. First, dense branching emerged under intermediate herbivory pressure, followed by the acquisition of spines that supported higher speciation rates under high herbivory pressure. Our study highlights the adaptive value of dense branching as part of a herbivore defence strategy and identifies large mammal herbivory as a major selective force shaping the whole plant architecture of woody plants. This study explores the evolution of two traits, branching density and spine presence, in the globally distributed plant family Combretaceae. These traits were found to have appeared in a two-step process in response to mammalian herbivory pressure, revealing the importance of large mammals in the evolution of plant architecture diversity.

Xiao, S., S. Li, J. Huang, X. Wang, M. Wu, R. Karim, W. Deng, and T. Su. 2024. Influence of climate factors on the global dynamic distribution of Tsuga (Pinaceae). Ecological Indicators 158: 111533. https://doi.org/10.1016/j.ecolind.2023.111533

Throughout the Quaternary period, climate change has significantly influenced plant distribution, particularly affecting species within the genus Tsuga (Endl.) Carrière. This climatic impact ultimately led to the extinction of all Tsuga species in Europe. Today, there are ten recognized species of Tsuga worldwide, one of listed as a vulnerable species and four as near-threatened species. The genus Tsuga exhibits a disjunctive distribution in East Asia (EA), eastern North America (ENA), and western North America (WNA). It is crucial to comprehend the mechanisms underlying these distributional changes and to identify key climate variables to develop effective conservation strategies for Tsuga under future climate scenarios. In this study, we applied the maximum entropy (MaxEnt) model by combining distribution data for Tsuga with abundant pollen fossil data. Our objective was to investigate the climate factors that shape the distribution of Tsuga, identify climate thresholds, and elucidate distribution dynamics in the context of significant climate changes over the past 1070 thousand years (ka). Our findings highlight the pivotal role of precipitation as the key climate factor affecting the distribution of Tsuga. Specifically, in EA, summer precipitation was the key driver, while in North America (NA), winter precipitation exerted greater importance. Moreover, we observed similarities in climatic requirements between Tsuga species in Europe and EA, and declines in summer precipitation and winter temperature were major factors contributing to the extinction of Tsuga species in Europe. Quaternary glacial and interglacial fluctuations exerted substantial impacts on Tsuga distribution dynamics. The disappearance of Tsuga species in the Korean Peninsula may have occurred during the LGM (Last Glacial Maximum). The potential suitable area for Tsuga species in EA expanded during the cold periods, while in NA, it contracted. In the future, climate change may result Tsuga distribution area contraction in both the EA and NA. Our study has identified distinct response patterns of Tsuga in various geographic regions to Quaternary climate change and offers corresponding suggestions for Tsuga conservation. In the future, it will be imperative to prioritize the conservation of natural Tsuga distributions in EA and NA, with a focus on the impacts of precipitation fluctuation on the dynamic distribution of this genus.

Novoa, A., H. Hirsch, M. L. Castillo, S. Canavan, L. González, D. M. Richardson, P. Pyšek, et al. 2023. Genetic and morphological insights into the Carpobrotus hybrid complex around the world. NeoBiota 89: 135–160. https://doi.org/10.3897/neobiota.89.109164

The genus Carpobrotus N.E.Br. comprises between 12 and 25 species, most of which are native to South Africa. Some Carpobrotus species are considered among the most damaging invasive species in coastal dune systems worldwide. In their introduced areas, these species represent a serious threat to native species and significantly impact soil conditions and geochemical processes. Despite being well studied, the taxonomy of Carpobrotus remains problematic, as the genus comprises a complex of species that hybridize easily and are difficult to distinguish from each other. To explore the population genetic structure of invasive Carpobrotus species (i.e., C. acinaciformis and C. edulis) across a significant part of their native and non-native ranges, we sampled 40 populations across Argentina, Italy, New Zealand, Portugal, South Africa, Spain, and the USA. We developed taxon-specific microsatellite markers using a Next Generation Sequencing approach to analyze the population genetic structure and incidence of hybridization in native and non-native regions. We identified three genetically distinct clusters, which are present in both the native and non-native regions. Based on a set of selected morphological characteristics, we found no clear features to identify taxa morphologically. Our results suggest that the most probable sources of global introductions of Carpobrotus species are the Western Cape region of South Africa and the coastline of California. We suggest that management actions targeting Carpobrotus invasions globally should focus on preventing additional introductions from the east coast of South Africa, and on searching for prospective biocontrol agents in the Western Cape region of South Africa.

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. https://doi.org/10.3390/plants12142721

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.

Maurin, O., A. Anest, F. Forest, I. Turner, R. L. Barrett, R. C. Cowan, L. Wang, et al. 2023. Drift in the tropics: Phylogenetics and biogeographical patterns in Combretaceae. Global Ecology and Biogeography. https://doi.org/10.1111/geb.13737

Aim The aim of this study was to further advance our understanding of the species-rich, and ecologically important angiosperm family Combretaceae to provide new insights into their evolutionary history. We assessed phylogenetic relationships in the family using target capture data and produced a dated phylogenetic tree to assess fruit dispersal modes and patterns of distribution. Location Tropical and subtropical regions. Time Period Cretaceous to present. Major Taxa Studied Family Combretaceae is a member of the rosid clade and comprises 10 genera and more than 500 species, predominantly assigned to genera Combretum and Terminalia, and occurring on all continents and in a wide range of ecosystems. Methods We use a target capture approach and the Angiosperms353 universal probes to reconstruct a robust dated phylogenetic tree for the family. This phylogenetic framework, combined with seed dispersal traits, biome data and biogeographic ranges, allows the reconstruction of the biogeographical history of the group. Results Ancestral range reconstructions suggest a Gondwanan origin (Africa/South America), with several intercontinental dispersals within the family and few transitions between biomes. Relative abundance of fruit dispersal types differed by both continent and biome. However, intercontinental colonizations were only significantly enhanced by water dispersal (drift fruit), and there was no evidence that seed dispersal modes influenced biome shifts. Main Conclusions Our analysis reveals a paradox as drift fruit greatly enhanced dispersal distances at intercontinental scale but did not affect the strong biome conservatism observed.

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. https://doi.org/10.1016/j.jnc.2023.126407

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. https://doi.org/10.1002/tax.12885

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.

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. https://doi.org/10.1016/j.ecolind.2023.110072

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. https://doi.org/10.1016/j.gloplacha.2023.104073

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.