Science Enabled by Specimen Data

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.

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.

Watts, J. L., and J. E. Watkins. 2022. New Zealand Fern Distributions from the Last Glacial Maximum to 2070: A Dynamic Tale of Migration and Community Turnover. American Fern Journal 112.

The coming decades are predicated to bring widespread shifts in local, regional, and global climatic patterns. Currently there is limited understanding of how ferns will respond to these changes and few studies have attempted to model shifts in fern distribution in response to climate change. In this paper, we present a series of these models using the country of New Zealand as our study system. Ferns are notably abundant in New Zealand and play important ecological roles in early succession, canopy biology, and understory dynamics. Here we describe how fern distributions have changed since the Last Glacial Maximum to the present and predict how they will change with anthropogenic climate change – assuming no measures are taken to reduce carbon emissions. To do this, we used MaxEnt species distribution modelling with publicly available data from and to predict the past, present, and future distributions of 107 New Zealand fern species. The present study demonstrates that ferns in New Zealand have and will continue to expand their ranges and migrate southward and upslope. Despite the predicted general increased range size as a result of climate change, our models predict that the majority (52%) of many species' current suitable habitats may be climatically unsuitable in 50 years, including the ecologically important group: tree ferns. Additionally, fern communities are predicted to undergo drastic shifts in composition, which may be detrimental to overall ecosystem functioning in New Zealand.

To clarify biogeographic patterns of two mushroom species (Phallus merulinus and Geastrum courtecuissei) previously reported from Myanmar, sequence data of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA were retrieved from GenBank. The BLAST search and phylogenetic analyses of Phallus indicated that P. merulinus and P. atrovolvatus from wide areas, including Australia, Myanmar, Thailand, Brazil, and French Guiana, cannot be distinguished molecularly. The species was, therefore, considered widespread across tropical to subtropical regions. In contrast, G. courtecuissei from Myanmar was tightly clustered exclusively with G. courtecuissei from Central and South America, supporting the idea of its disjunct distribution between Southeast Asia (Myanmar) and Central-South Americas.

Chevalier, M. 2022. <i>crestr</i>: an R package to perform probabilistic climate reconstructions from palaeoecological datasets. Climate of the Past 18: 821–844.

Abstract. Statistical climate reconstruction techniques are fundamental tools to study past climate variability from fossil proxy data. In particular, the methods based on probability density functions (or PDFs) can be used in various environments and with different climate proxies because they rely on elementary calibration data (i.e. modern geolocalised presence data). However, the difficulty of accessing and curating these calibration data and the complexity of interpreting probabilistic results have often limited their use in palaeoclimatological studies. Here, I introduce a new R package (crestr) to apply the PDF-based method CREST (Climate REconstruction SofTware) on diverse palaeoecological datasets and address these problems. crestr includes a globally curated calibration dataset for six common climate proxies (i.e. plants, beetles, chironomids, rodents, foraminifera, and dinoflagellate cysts) associated with an extensive range of climate variables (20 terrestrial and 19 marine variables) that enables its use in most terrestrial and marine environments. Private data collections can also be used instead of, or in combination with, the provided calibration dataset. The package includes a suite of graphical diagnostic tools to represent the data at each step of the reconstruction process and provide insights into the effect of the different modelling assumptions and external factors that underlie a reconstruction. With this R package, the CREST method can now be used in a scriptable environment and thus be more easily integrated with existing workflows. It is hoped that crestr will be used to produce the much-needed quantified climate reconstructions from the many regions where they are currently lacking, despite the availability of suitable fossil records. To support this development, the use of the package is illustrated with a step-by-step replication of a 790 000-year-long mean annual temperature reconstruction based on a pollen record from southeastern Africa.

Qu, J., Y. Xu, Y. Cui, S. Wu, L. Wang, X. Liu, Z. Xing, et al. 2021. MODB: a comprehensive mitochondrial genome database for Mollusca. Database 2021.

Mollusca is the largest marine phylum, comprising about 23% of all named marine organisms, Mollusca systematics are still in flux, and an increase in human activities has affected Molluscan reproduction and development, strongly impacting diversity and classification. Therefore, it is necessary to e…

de Oliveira, M. H. V., B. M. Torke, and T. E. Almeida. 2021. An inventory of the ferns and lycophytes of the Lower Tapajós River Basin in the Brazilian Amazon reveals collecting biases, sampling gaps, and previously undocumented diversity. Brittonia 73: 459–480.

Ferns and lycophytes are an excellent group for conservation and species distribution studies because they are closely related to environmental changes. In this study, we analyzed collection gaps, sampling biases, richness distribution, and the species conservation effectiveness of protected areas i…

Yi, S., C.-P. Jun, K. Jo, H. Lee, M.-S. Kim, S. D. Lee, X. Cao, and J. Lim. 2020. Asynchronous multi-decadal time-scale series of biotic and abiotic responses to precipitation during the last 1300 years. Scientific Reports 10.


Chase, B. M., A. Boom, A. S. Carr, M. Chevalier, L. J. Quick, G. A. Verboom, and P. J. Reimer. 2019. Extreme hydroclimate response gradients within the western Cape Floristic region of South Africa since the Last Glacial Maximum. Quaternary Science Reviews 219: 297–307.

The Cape Floristic Region (CFR) is one of the world's major biodiversity hotspots, and much work has gone into identifying the drivers of this diversity. Considered regionally in the context of Quaternary climate change, climate stability is generally accepted as being one of the major factors promo…

Chevalier, M., B. M. Chase, L. J. Quick, L. M. Dupont, and T. C. Johnson. 2020. Temperature change in subtropical southeastern Africa during the past 790,000 yr. Geology 49: 71–75.

Across the glacial-interglacial cycles of the late Pleistocene (~700 k.y.), temperature variability at low latitudes is often considered to have been negligible compared to changes in precipitation. However, a paucity of quantified temperature records makes this difficult to reliably assess. In this…