Science Enabled by Specimen Data

Glison, N., D. Romero, V. Rosso, J. C. Guerrero, and P. R. Speranza. 2023. Understanding the Geographic Patterns of Closely-Related Species of Paspalum (Poaceae) Using Distribution Modelling and Seed Germination Traits. Plants 12: 1342. https://doi.org/10.3390/plants12061342

The sexual species of the Dilatata complex (Paspalum dasypleurum, P. flavescens, P. plurinerve, P. vacarianum, and P. urvillei) are closely related phylogenetically and show allopatric distributions, except P. urvillei. These species show microhabitat similarities and differences in germination traits. We integrated species distribution models (SDMs) and seed germination assays to determine whether germination divergences explain their biogeographic pattern. We trained SDMs in South America using species’ presence–absence data and environmental variables. Additionally, populations sampled from highly favourable areas in the SDMs of these species were grown together, and their seeds germinated at different temperatures and dormancy-breaking conditions. Differences among species in seed dormancy and germination niche breadth were tested, and linear regressions between seed dormancy and climatic variables were explored. SDMs correctly classified both the observed presences and absences. Spatial factors and anthropogenic activities were the main factors explaining these distributions. Both SDMs and germination analyses confirmed that the niche of P. urvillei was broader than the other species which showed restricted distributions, narrower germination niches, and high correlations between seed dormancy and precipitation regimes. Both approaches provided evidence about the generalist-specialist status of each species. Divergences in seed dormancy between the specialist species could explain these allopatric distributions.

Song, X.-J., G. Liu, Z.-Q. Qian, and Z.-H. Zhu. 2023. Niche Filling Dynamics of Ragweed (Ambrosia artemisiifolia L.) during Global Invasion. Plants 12: 1313. https://doi.org/10.3390/plants12061313

Determining whether the climatic ecological niche of an invasive alien plant is similar to that of the niche occupied by its native population (ecological niche conservatism) is essential for predicting the plant invasion process. Ragweed (Ambrosia artemisiifolia L.) usually poses serious threats to human health, agriculture, and ecosystems within its newly occupied range. We calculated the overlap, stability, unfilling, and expansion of ragweed’s climatic ecological niche using principal component analysis and performed ecological niche hypothesis testing. The current and potential distribution of A. artemisiifolia was mapped by ecological niche models to identify areas in China with the highest potential risk of A. artemisiifolia invasion. The high ecological niche stability indicates that A. artemisiifolia is ecologically conservative during the invasion. Ecological niche expansion (expansion = 0.407) occurred only in South America. In addition, the difference between the climatic and native niches of the invasive populations is mainly the result of unpopulated niches. The ecological niche model suggests that southwest China, which has not been invaded by A. artemisiifolia, faces an elevated risk of invasion. Although A. artemisiifolia occupies a climatic niche distinct from native populations, the climatic niche of the invasive population is only a subset of the native niche. The difference in climatic conditions is the main factor leading to the ecological niche expansion of A. artemisiifolia during the invasion. Additionally, human activities play a substantial role in the expansion of A. artemisiifolia. Alterations in the A. artemisiifolia niche would help explain why this species is so invasive in China.

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.

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. https://doi.org/10.1093/evolut/qpad044

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. 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.

Wilson Brown, M. K., and E. B. Josephs. 2023. Evaluating niche changes during invasion with seasonal models in Capsella bursa‐pastoris. American Journal of Botany. https://doi.org/10.1002/ajb2.16140

Premise Researchers often use ecological niche models to predict where species might establish and persist under future or novel climate conditions. However, these predictive methods assume species have stable niches across time and space. Furthermore, ignoring the time of occurrence data can obscure important information about species reproduction and ultimately fitness. Here, we assess compare ecological niche models generated from full-year averages to seasonal models Methods In this study, we generate full-year and monthly ecological niche models for Capsella bursa-pastoris in Europe and North America to see if we can detect changes in the seasonal niche of the species after long-distance dispersal. Key Results We find full-year ecological niche models have low transferability across continents and there are continental differences in the climate conditions that influence the distribution of C. bursa-pastoris. Monthly models have greater predictive accuracy than full-year models in cooler seasons, but no monthly models are able to predict North American summer occurrences very well. Conclusions The relative predictive ability of European monthly models compared to North American monthly models suggests a change in the seasonal timing between the native range to the non-native range. These results highlight the utility of ecological niche models at finer temporal scales in predicting species distributions and unmasking subtle patterns of evolution.

Granja-Fernández, R., B. Maya-Alvarado, F. A. Rodríguez-Zaragoza, and A. López-Pérez. 2023. Ophiuroidea (Echinodermata) diversity partitioning across the eastern tropical Pacific. Regional Studies in Marine Science 60: 102835. https://doi.org/10.1016/j.rsma.2023.102835

Ophiuroidea is one of the most suitable marine groups for exploring diversity partitioning in the ocean due to its wide distribution and particular lifestyles. Nevertheless, diversity and its variation have yet to be investigated, and even basic information for large areas such as the eastern tropical Pacific (ETP) is still lacking. The present contribution explores α, β, and γ-diversity patterns of Ophiuroidea from the ETP at four spatial scales (Operational Geographic Units, Ecoregions, Provinces, and Realms). Based on literature records, databases, and scientific collections, an occurrence matrix was constructed for 69 shallow water (0–200 m) Ophiuroidea of the ETP (Mexico–Peru). Diversity evaluation based on rarefaction curves indicated that the observed richness tends to reach the asymptote. At the province and the ecoregion levels, β-diversity was the most important component explaining γ-diversity. The components that mainly contributed to the differentiation between provinces and ecoregions were the intersection of nestedness and β-diversity. PERMANOVA and SIMPER results showed that species composition presented significant differences at all spatial levels. The PCO ordination indicated that the first component (PCO1) explained the variation in species composition in a longitudinal gradient between coastal and oceanic ecoregions, while PCO2 showed a latitudinal gradient. The shade plot yielded three clusters (northern, southern, and widely distributed species). In general, α-diversity was explained by differences in sampling effort and methods; in contrast, β-diversity and its components were mainly explained by patterns and processes occurring at different spatial scales (provinces and ecoregions) such as oceanographic conditions, geographic extension, dispersal, and environmental heterogeneity. This work represents the first attempt to analyze the distribution patterns of shallow-water Ophiuroidea from the ETP.

Smith, A. B., S. J. Murphy, D. Henderson, and K. D. Erickson. 2023. Including imprecisely georeferenced specimens improves accuracy of species distribution models and estimates of niche breadth. Global Ecology and Biogeography. https://doi.org/10.1111/geb.13628

Aim Museum and herbarium specimen records are frequently used to assess the conservation status of species and their responses to climate change. Typically, occurrences with imprecise geolocality information are discarded because they cannot be matched confidently to environmental conditions and are thus expected to increase uncertainty in downstream analyses. However, using only precisely georeferenced records risks undersampling of the environmental and geographical distributions of species. We present two related methods to allow the use of imprecisely georeferenced occurrences in biogeographical analysis. Innovation Our two procedures assign imprecise records to the (1) locations or (2) climates that are closest to the geographical or environmental centroid of the precise records of a species. For virtual species, including imprecise records alongside precise records improved the accuracy of ecological niche models projected to the present and the future, especially for species with c. 20 or fewer precise occurrences. Using only precise records underestimated loss of suitable habitat and overestimated the amount of suitable habitat in both the present and the future. Including imprecise records also improves estimates of niche breadth and extent of occurrence. An analysis of 44 species of North American Asclepias (Apocynaceae) yielded similar results. Main conclusions Existing studies examining the effects of spatial imprecision typically compare outcomes based on precise records against the same records with spatial error added to them. However, in real-world cases, analysts possess a mix of precise and imprecise records and must decide whether to retain or discard the latter. Discarding imprecise records can undersample the geographical and environmental distributions of species and lead to mis-estimation of responses to past and future climate change. Our method, for which we provide a software implementation in the enmSdmX package for R, is simple to use and can help leverage the large number of specimen records that are typically deemed “unusable” because of spatial imprecision in their geolocation.

Gómez Díaz, J. A., A. Lira-Noriega, and F. Villalobos. 2023. Expanding protected areas in a Neotropical hotspot. International Journal of Sustainable Development & World Ecology: 1–15. https://doi.org/10.1080/13504509.2022.2163717

The region of central Veracruz is considered a biodiversity hotspot due to its high species richness and environmental heterogeneity, but only 2% of this region is currently protected. This study aimed to assess the current protected area system’s effectiveness and to identify priority conservation areas for expanding the existing protected area system. We used the distribution models of 1186 species from three kingdoms (Animalia, Plantae, and Fungi) together with ZONATION software, a conservation planning tool, to determine areas that could help expand the current network of protected areas. We applied three different parametrizations (including only species, using the boundary quality penalty, and using corridor connectivity). We found that protecting an additional 15% of the area would increase, between 16.2% and 19.3%, the protection of the distribution area of all species. We propose that the regions with a consensus of the three parametrizations should be declared as new protected areas to expand 374 km2 to the 216 km2 already protected. Doing so would double the protected surface in central Veracruz. The priority areas identified in this study have more species richness, carbon stock values, natural vegetation cover, and less human impact index than the existing protected areas. If our identified priority areas are declared protected, we could expect a future recovery of endangered species populations for Veracruz. The proposed new protected areas are planned and designed as corridors connecting currently isolated protected areas to promote biodiversity protection.