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Serra‐Diaz, J. M., J. Borderieux, B. Maitner, C. C. F. Boonman, D. Park, W. Guo, A. Callebaut, et al. 2024. occTest: An integrated approach for quality control of species occurrence data. Global Ecology and Biogeography.

Aim Species occurrence data are valuable information that enables one to estimate geographical distributions, characterize niches and their evolution, and guide spatial conservation planning. Rapid increases in species occurrence data stem from increasing digitization and aggregation efforts, and citizen science initiatives. However, persistent quality issues in occurrence data can impact the accuracy of scientific findings, underscoring the importance of filtering erroneous occurrence records in biodiversity analyses.InnovationWe introduce an R package, occTest, that synthesizes a growing open‐source ecosystem of biodiversity cleaning workflows to prepare occurrence data for different modelling applications. It offers a structured set of algorithms to identify potential problems with species occurrence records by employing a hierarchical organization of multiple tests. The workflow has a hierarchical structure organized in testPhases (i.e. cleaning vs. testing) that encompass different testBlocks grouping different testTypes (e.g. environmental outlier detection), which may use different testMethods (e.g. Rosner test, jacknife,etc.). Four different testBlocks characterize potential problems in geographic, environmental, human influence and temporal dimensions. Filtering and plotting functions are incorporated to facilitate the interpretation of tests. We provide examples with different data sources, with default and user‐defined parameters. Compared to other available tools and workflows, occTest offers a comprehensive suite of integrated tests, and allows multiple methods associated with each test to explore consensus among data cleaning methods. It uniquely incorporates both coordinate accuracy analysis and environmental analysis of occurrence records. Furthermore, it provides a hierarchical structure to incorporate future tests yet to be developed.Main conclusionsoccTest will help users understand the quality and quantity of data available before the start of data analysis, while also enabling users to filter data using either predefined rules or custom‐built rules. As a result, occTest can better assess each record's appropriateness for its intended application.

Jiménez-López, D. A., M. J. Carmona-Higuita, G. Mendieta-Leiva, R. Martínez-Camilo, A. Espejo-Serna, T. Krömer, N. Martínez-Meléndez, and N. Ramírez-Marcial. 2023. Linking different resources to recognize vascular epiphyte richness and distribution in a mountain system in southeastern Mexico. Flora: 152261.

Mesoamerican mountains are important centers of endemism and diversity of epiphytes. The Sierra Madre of Chiapas in southeastern Mexico is a mountainous region of great ecological interest due to its high biological richness. We present the first checklist of epiphytes for this region based on a compilation of various information sources. In addition, we determined the conservation status for each species based on the Mexican Official Standard (NOM-059-SEMARNAT-2010), endemism based on geopolitical boundaries, spatial completeness with inventory completeness index, richness distribution with range maps, and the relationship between climatic variables (temperature and rainfall) with species richness using generalized additive models. Our dataset includes 9,799 records collected between 1896-2017. Our checklist includes 708 epiphytes within 160 genera and 26 families; the most species-rich family was Orchidaceae (355 species), followed by Bromeliaceae (82) and Polypodiaceae (79). There were 74 species within a category of risk and 59 species considered endemic. Completeness of epiphyte richness suggests that sampling is still largely incomplete, particularly in the lower parts of the mountain system. Species and family range maps show the highest richness at high elevations, while geographically richness increases towards the southeast. Epiphyte richness increases with increased rainfall, although a unimodal pattern was observed along the temperature gradient with a species richness peak between 16-20 C°. The Sierra Madre of Chiapas forms a refuge to more than 40% of all epiphytes reported for Mexico and its existing network of protected areas overlaps with the greatest epiphyte richness.

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.

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.

Coca‐de‐la‐Iglesia, M., N. G. Medina, J. Wen, and V. Valcárcel. 2022. Evaluation of the tropical‐temperate transitions: An example of climatic characterization in the Asian Palmate group of Araliaceae. American Journal of Botany.

(no abstract available)

Alvarez, K., C. A. Bota-Sierra, and J. M. Vásquez-Ramos. 2022. New species records in Acanthagrion, Nehalennia, and Perilestes (Odonata: Zygoptera) for Colombia. Biota Colombiana 23: e1061.

We record for the first time Acanthagrion jessei, Nehalennia minuta, and Perilestes solutus in Colombia, based on males and females taken at the campus Barcelona at the Universidad de Los Llanos, located in the foothills of the Colombian Eastern Andes in the Orinoco river basin.

Boyd, R. J., M. A. Aizen, R. M. Barahona‐Segovia, L. Flores‐Prado, F. E. Fontúrbel, T. M. Francoy, M. Lopez‐Aliste, et al. 2022. Inferring trends in pollinator distributions across the Neotropics from publicly available data remains challenging despite mobilization efforts Y. Fourcade [ed.],. Diversity and Distributions 28: 1404–1415.

Aim Aggregated species occurrence data are increasingly accessible through public databases for the analysis of temporal trends in the geographic distributions of species. However, biases in these data present challenges for statistical inference. We assessed potential biases in data available through GBIF on the occurrences of four flower-visiting taxa: bees (Anthophila), hoverflies (Syrphidae), leaf-nosed bats (Phyllostomidae) and hummingbirds (Trochilidae). We also assessed whether and to what extent data mobilization efforts improved our ability to estimate trends in species' distributions. Location The Neotropics. Methods We used five data-driven heuristics to screen the data for potential geographic, temporal and taxonomic biases. We began with a continental-scale assessment of the data for all four taxa. We then identified two recent data mobilization efforts (2021) that drastically increased the quantity of records of bees collected in Chile available through GBIF. We compared the dataset before and after the addition of these new records in terms of their biases and estimated trends in species' distributions. Results We found evidence of potential sampling biases for all taxa. The addition of newly-mobilized records of bees in Chile decreased some biases but introduced others. Despite increasing the quantity of data for bees in Chile sixfold, estimates of trends in species' distributions derived using the postmobilization dataset were broadly similar to what would have been estimated before their introduction, albeit more precise. Main conclusions Our results highlight the challenges associated with drawing robust inferences about trends in species' distributions using publicly available data. Mobilizing historic records will not always enable trend estimation because more data do not necessarily equal less bias. Analysts should carefully assess their data before conducting analyses: this might enable the estimation of more robust trends and help to identify strategies for effective data mobilization. Our study also reinforces the need for targeted monitoring of pollinators worldwide.

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.

Reichgelt, T., D. R. Greenwood, S. Steinig, J. G. Conran, D. K. Hutchinson, D. J. Lunt, L. J. Scriven, and J. Zhu. 2022. Plant Proxy Evidence for High Rainfall and Productivity in the Eocene of Australia. Paleoceanography and Paleoclimatology 37.

During the early to middle Eocene, a mid‐to‐high latitudinal position and enhanced hydrological cycle in Australia would have contributed to a wetter and “greener” Australian continent where today arid to semi‐arid climates dominate. Here, we revisit 12 southern Australian plant megafossil sites from the early to middle Eocene to generate temperature, precipitation and seasonality paleoclimate estimates, net primary productivity (NPP) and vegetation type, based on paleobotanical proxies and compare to early Eocene global climate models. Temperature reconstructions are uniformly subtropical (mean annual, summer, and winter mean temperatures 19–21 °C, 25–27 °C and 14–16 °C, respectively), indicating that southern Australia was ∼5 °C warmer than today, despite a >20° poleward shift from its modern geographic location. Precipitation was less homogeneous than temperature, with mean annual precipitation of ∼60 cm over inland sites and >100 cm over coastal sites. Precipitation may have been seasonal with the driest month receiving 2–7× less than mean monthly precipitation. Proxy‐model comparison is favorable with an 1680 ppm CO2 concentration. However, individual proxy reconstructions can disagree with models as well as with each other. In particular, seasonality reconstructions have systemic offsets. NPP estimates were higher than modern, implying a more homogenously “green” southern Australia in the early to middle Eocene, when this part of Australia was at 48–64 °S, and larger carbon fluxes to and from the Australian biosphere. The most similar modern vegetation type is modern‐day eastern Australian subtropical forest, although distance from coast and latitude may have led to vegetation heterogeneity.