Science Enabled by Specimen Data

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.

Nuñez Landa, M. de L., J. C. Montero Castro, T. C. Monterrubio-Rico, S. I. Lara-Cabrera, and D. A. Prieto-Torres. 2023. Predicting co-distribution patterns of parrots and woody plants under global changes: The case of the Lilac-crowned Amazon and Neotropical dry forests. Journal for Nature Conservation 71: 126323. https://doi.org/10.1016/j.jnc.2022.126323

Global climate and land-use changes are the most significant causes of the current habitat loss and biodiversity crisis. Although there is information measuring these global changes, we lack a full understanding of how they impact community assemblies and species interactions across ecosystems. Herein, we assessed the potential distribution of eight key woody plant species associated with the habitat of the endangered Lilac-crowned Amazon (Amazon finschi) under global changes scenarios (2050′s and 2070′s), to answer the following questions: (1) how do predicted climate and land-use changes impact these species’ individual distributions and co-distribution patterns?; and (2) how effective is the existing Protected Area network for safeguarding the parrot species, the plant species, and their biological interactions? Our projections were consistent identifying the species that are most vulnerable to climate change. The distribution ranges of most of the species tended to decrease under future climates. These effects were strongly exacerbated when incorporating land-use changes into models. Even within existing protected areas, >50 % of the species’ remaining distribution and sites with the highest plant richness were predicted to be lost in the future under these combined scenarios. Currently, both individual species ranges and sites of highest richness of plants, shelter a high proportion (ca. 40 %) of the Lilac-crowned Amazon distribution. However, this spatial congruence could be reduced in the future, potentially disrupting the ecological associations among these taxa. We provide novel evidence for decision-makers to enhance conservation efforts to attain the long-term protection of this endangered Mexican endemic parrot and its habitat.

Ecke, F., B. A. Han, B. Hörnfeldt, H. Khalil, M. Magnusson, N. J. Singh, and R. S. Ostfeld. 2022. Population fluctuations and synanthropy explain transmission risk in rodent-borne zoonoses. Nature Communications 13. https://doi.org/10.1038/s41467-022-35273-7

Population fluctuations are widespread across the animal kingdom, especially in the order Rodentia, which includes many globally important reservoir species for zoonotic pathogens. The implications of these fluctuations for zoonotic spillover remain poorly understood. Here, we report a global empirical analysis of data describing the linkages between habitat use, population fluctuations and zoonotic reservoir status in rodents. Our quantitative synthesis is based on data collated from papers and databases. We show that the magnitude of population fluctuations combined with species’ synanthropy and degree of human exploitation together distinguish most rodent reservoirs at a global scale, a result that was consistent across all pathogen types and pathogen transmission modes. Our spatial analyses identified hotspots of high transmission risk, including regions where reservoir species dominate the rodent community. Beyond rodents, these generalities inform our understanding of how natural and anthropogenic factors interact to increase the risk of zoonotic spillover in a rapidly changing world. Many rodent species are known as hosts of zoonotic pathogens, but the ecological conditions that trigger spillover are not well-understood. Here, the authors show that population fluctuations and association with human-dominated habitats explain the zoonotic reservoir status of rodents globally.

Inman, R. D., T. C. Esque, and K. E. Nussear. 2022. Dispersal limitations increase vulnerability under climate change for reptiles and amphibians in the southwestern United States. The Journal of Wildlife Management. https://doi.org/10.1002/jwmg.22317

Species conservation plans frequently rely on information that spans political and administrative boundaries, especially when predictions are needed of future habitat under climate change; however, most species conservation plans and their requisite predictions of future habitat are often limited in geographical scope. Moreover, dispersal constraints for species of concern are not often incorporated into distribution models, which can result in overly optimistic predictions of future habitat. We used a standard modeling approach across a suite of 23 taxa of amphibians and reptiles in the North American deserts (560,024 km2 across 13 ecoregions) to assess impacts of climate change on habitat and combined landscape population dispersal simulations with species distribution modeling to reduce the risk of predicting future habitat in areas that are not available to species given their dispersal abilities. We used 3 general circulation models and 2 representative concentration pathways (RCPs) to represent multiple scenarios of future habitat potential and assess which study species may be most vulnerable to changes forecasted under each climate scenario. Amphibians were the most vulnerable taxa, but the most vulnerable species tended to be those with the lowest dispersal ability rather than those with the most specialized niches. Under the most optimistic climate scenario considered (RCP 2.6; a stringent scenario requiring declining emissions from 2020 to near zero emissions by 2100), 76% of the study area may experience a loss of >20% of the species examined, while up to 87% of the species currently present may be lost in some areas under the most pessimistic climate scenario (RCP 8.5; a scenario wherein greenhouse gases continue to increase through 2100 based on trajectories from the mid‐century). Most areas with high losses were concentrated in the Arizona and New Mexico Plateau ecoregion, the Edwards Plateau in Texas, and the Southwestern Tablelands in New Mexico and Texas, USA. Under the most pessimistic climate scenario, all species are predicted to lose some existing habitat, with an average of 34% loss of extant habitat across all species. Even under the most optimistic scenario, we detected an average loss of 24% of extant habitat across all species, suggesting that changing climates may influence the ranges of reptiles and amphibians in the Southwest.

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. https://doi.org/10.3390/plants11172224

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.

Arana, C., V. Pulido, A. Arana, A. Carlos, and L. Salinas. 2022. Distribución geográfica y abundancia poblacional de Plegadis ridgwayi, el ibis de la Puna (Threskiornithidae) con énfasis en las poblaciones del Perú. Revista Peruana de Biología 29: e22533. https://doi.org/10.15381/rpb.v29i3.22533

El ibis de la puna Plegadis ridgwayi, es una especie de Threskiornithidae que habita humedales andinos y realiza migraciones altitudinales hacia la costa. Datos propios, de GBIF, información bibliográfica y del Censo Neotropical de Aves Acuáticas (1992 a 2015) muestran que el ibis de la puna Plegadis ridgwayi se distribuye en Ecuador, Perú, Bolivia, Argentina y Chile, con las mayores densidades poblacionales en Perú y Bolivia en siete y tres localidades respectivamente, que acumulan más del 1% de la población biogeográfica. Se encuentran de 0 a 5000 m de altitud, con las mayores densidades entre 3000 a 4500 m y 0 a 500 m. La mayor incidencia de registros ocurre al sur y centro del Perú, así como costa del centro y norte del Perú. La ampliación de la distribución hacia el norte y costa peruana puede deberse a la disponibilidad ambiental y al deterioro de su hábitat andino. En cuatro humedales costeros del centro del Perú se registraron hasta 818 ibis en 2006, la gran mayoría en Pantanos de Villa y Paraíso. El número de migrantes costeros parece relacionado a la intensidad de sequías en la sierra del Perú central. La abundancia de ibis en el lago altoandino de Junín muestra una disminución histórica, con énfasis después de la sequía de 2004-2005. La expansión distribucional requiere investigar la posible hibridación con las otras especies del género antes alopátridas.

GÓMEZ-MARTÍNEZ, R. F., J. M. LÓPEZ-VILA, W. A. MATAMOROS, A. A. GONZÁLEZ-DÍAZ, and A. E. GÓMEZ-GONZÁLEZ. 2022. Diversity of Cichlid Fishes (Cichliformes: Cichlidae) in Chiapas, Mexico: A practical identification key with updated distribution maps. Zootaxa 5175: 231–252. https://doi.org/10.11646/zootaxa.5175.2.3

To accurately identify the species that make up the assemblage of the family Cichlidae in the Mexican state of Chiapas, we first updated the total species account (36 species) for the state and then created an identification key. For the distribution maps, the geographic records were projected using a geographic information system considering the layers of the two largest basins in the state (Grijalva and Usumacinta) and the Chiapas coast basin. The dichotomous key includes meristic, morphometric and coloration patterns that facilitate species identification present in the state. Rheoheros coeruleus (Stawikowski and Werner 1987) and Vieja breidohri Werner and Stawikowski 1987 are included in a key for the first time. The distributions of Paraneetroplus gibbiceps Steindachner 1864a, Rheoheros coeruleus, and Vieja zonata Meek 1905 in the state are mapped for the first time, and the range of 16 species was expanded. By updating and creating tools of great taxonomic use, we contribute to the study of this complex family with high morphological diversity.

Sánchez-González, L. A., H. Cayetano, D. A. Prieto-Torres, O. R. Rojas-Soto, and A. G. Navarro-Sigüenza. 2022. The role of ecological and geographical drivers of lineage diversification in the Squirrel cuckoo Piaya cayana in Mexico: a mitochondrial DNA perspective. Journal of Ornithology. https://doi.org/10.1007/s10336-022-02008-w

The Squirrel Cuckoo ( Piaya cayana ) is a widely distributed neotropical species with 14 recognized subspecies. Two parapatric subspecies are distributed in Mexico. P. c. mexicana is endemic to the seasonally dry tropical forests of western Mexico, and P. c. thermophila is found in humid forests from eastern Mexico to western Colombia. The 2 taxa have a small area of overlap on the Isthmus of Tehuantepec, but there is pronounced phenotypic differentiation, and very few reported intermediate individuals between these forms, leading to debate about the taxonomic status of the Mesoamerican taxa. Based on two mitochondrial genes, we used phylogenetic, phylogeographic, morphological, and ecological modelling analyses to describe the evolutionary relationships and paleo-distributional patterns of P. cayana in Mexico. Divergence time estimates suggest that the split between P. c. mexicana and P. c. thermophila occurred during the Pleistocene, about 1.24 Mya. Morphometrics of Mexican subspecies indicate that tail length and the white tail tips are significantly longer in P. c. mexicana , while P. c. thermophila has a longer and wider bill. Ecological niche analyses indicated that niche similarity between both lineages was lower than expected by chance, while low values on cross-prediction tests suggested that the two lineages have inhabited different environmental spaces since at least the Late Pleistocene. The ecological niche difference may also be associated with a steep humidity gradient, suggesting a significant contemporary environmental barrier. Overall, our results indicate that P. c. mexicana and P. c. thermophila have divergent evolutionary histories; therefore, the current taxonomic status of the Piaya populations in Mexico reflects neither their evolutionary relationships nor their apparent divergence. Our results suggest a major split in the polytypic P. cayana coinciding with the Andes, suggesting that the western endemic P. c. mexicana and P. c. thermophila are best treated as separate species-level taxa . Die Rolle ökologischer und geografischer Faktoren bei der Abstammung und Diversifikation des Eichhornkuckucks Piaya cayana in Mexiko: von der mitochondrialen DNA her betrachtet Der Eichhornkuckuck ( Piaya cayana ) ist eine weit verbreitete neotropische Art mit 14 anerkannten Unterarten. In Mexiko gibt es zwei parapatrische Unterarten. P. c. mexicana ist in den je nach Jahreszeit trockenen tropischen Wäldern Westmexikos beheimatet, während P. c. thermophila in den feuchten Wäldern von Ostmexiko bis Westkolumbien vorkommt. Die beiden Taxa überschneiden sich in einem kleinen Gebiet an der Landenge von Tehuantepec, aber es gibt einen ausgeprägten phänotypischen Unterschied und nur sehr wenige bekannte Mischtypen zwischen den beiden und damit Anlass zu Diskussionen über den taxonomischen Status dieser mittelamerikanischen Taxa. Auf der Grundlage zweier mitochondrialer Gene haben wir phylogenetische, phylogeografische, morphologische und ökologische Modell-Analysen durchgeführt, um die abstammungsbiologischen Verbindungen und Verbreitungsmuster von P. cayana im Paläozän in Mexiko zu bestimmen. Schätzungen der Entstehungszeit der Unterschiede deuten darauf hin, dass die Trennung zwischen P. c. mexicana und P. c. thermophila während des Pleistozäns stattfand, vor etwa 1,24 Millionen Jahren. Die morphometrischen Daten der mexikanischen Unterarten zeigen, dass die Schwanzlänge und die weißen Schwanzspitzen bei P. c. mexicana deutlich länger sind, während P. c. thermophila einen längeren und breiteren Schnabel hat. Analysen der ökologischen Nischen zeigten, dass die Übereinstimmungen zwischen den beiden Linien geringer waren als durch Zufall zu erwarten wäre, während niedrige Werte bei Kreuz-Vorhersagetests darauf hindeuteten, dass die beiden Linien mindestens seit dem späten Pleistozän in unterschiedlichen Lebensräumen gelebt haben müssen. Der ökologische Nischenunterschied kann auch mit dem starken Feuchtigkeitsgradienten zusammenhängen, was auf eine bedeutende gegenwärtige Umweltbarriere hinweist. Insgesamt deuten unsere Ergebnisse darauf hin, dass P. c. mexicana und P. c. thermophila eine unterschiedliche Entwicklungsgeschichte haben; daher gibt der derzeitige taxonomische Status der Piaya-Populationen in Mexiko weder ihre evolutionäre Verwandtschaft, noch ihre offensichtlichen Unterschiede wieder. Unsere Ergebnisse deuten darauf hin, dass sich der polytypische P. cayana in den Anden aufgespalten hat, was bedeuten könnte, dass die im Westen endemischen P. c. mexicana und P. c. thermophila am besten als separate Taxa auf Artniveau behandelt werden sollten.

Führding‐Potschkat, P., H. Kreft, and S. M. Ickert‐Bond. 2022. Influence of different data cleaning solutions of point‐occurrence records on downstream macroecological diversity models. Ecology and Evolution 12. https://doi.org/10.1002/ece3.9168

Digital point‐occurrence records from the Global Biodiversity Information Facility (GBIF) and other data providers enable a wide range of research in macroecology and biogeography. However, data errors may hamper immediate use. Manual data cleaning is time‐consuming and often unfeasible, given that the databases may contain thousands or millions of records. Automated data cleaning pipelines are therefore of high importance. Taking North American Ephedra as a model, we examined how different data cleaning pipelines (using, e.g., the GBIF web application, and four different R packages) affect downstream species distribution models (SDMs). We also assessed how data differed from expert data. From 13,889 North American Ephedra observations in GBIF, the pipelines removed 31.7% to 62.7% false positives, invalid coordinates, and duplicates, leading to datasets between 9484 (GBIF application) and 5196 records (manual‐guided filtering). The expert data consisted of 704 records, comparable to data from field studies. Although differences in the absolute numbers of records were relatively large, species richness models based on stacked SDMs (S‐SDM) from pipeline and expert data were strongly correlated (mean Pearson's r across the pipelines: .9986, vs. the expert data: .9173). Our results suggest that all R package‐based pipelines reliably identified invalid coordinates. In contrast, the GBIF‐filtered data still contained both spatial and taxonomic errors. Major drawbacks emerge from the fact that no pipeline fully discovered misidentified specimens without the assistance of taxonomic expert knowledge. We conclude that application‐filtered GBIF data will still need additional review to achieve higher spatial data quality. Achieving high‐quality taxonomic data will require extra effort, probably by thoroughly analyzing the data for misidentified taxa, supported by experts.

Malpica, A., L. Mendoza-Cuenca, and C. González. 2022. Color and morphological differentiation in the Sinaloa Wren (Thryophilus sinaloa) in the tropical dry forests of Mexico: The role of environment and geographic isolation M. Shawkey [ed.],. PLOS ONE 17: e0269860. https://doi.org/10.1371/journal.pone.0269860

The role and the degree to which environment and geographic isolation contribute to phenotypic diversity has been widely debated. Here, we studied phenotypic variation (morphology and plumage reflectance) in the Sinaloa Wren, an endemic bird distributed throughout the tropical dry forest (TDF) on the Mexican pacific slope where a pronounced variability in environmental conditions has been reported. In particular, we aimed: 1) to characterize phenotypic variation between subspecies; 2) to analyze the relationship between phenotypic and environmental variation in the context of classic ecogeographic rules, such as Bergmann’s, Allen’s, Gloger’s, and Bogert’s, and to quantify the relative roles of environment and geographic isolation and their interaction in shaping phenotypic variation; and 3) to test for niche conservatism between subspecies. Our data revealed significant differences among subspecies morphology and plumage reflectance. The environment explained a higher proportion of the morphological variation, while geography explained a smaller proportion. However, variation in plumage reflectance was mainly explained by the joint effect of geography and environment. Our data did not support for Bergmann´s and Allen´s rule. However, longer tails and wings were positively associated with higher elevations, larger tarsus and culmens were positively related to higher latitudes and to greater tree cover, respectively. Our data partially supported Gloger´s rule, where darker plumages were associated with more humid environments. The effects of temperature on plumage coloration were more consistent with Bogert´s rule. In addition, we found darker plumages related to higher levels of UV-B radiation. Finally, niche divergence was detected between T. s. cinereus and T. s. sinaloa vs. T. s. russeus. In a continuously distributed ecosystem such as the TDF on the pacific slope of Mexico, the environmental conditions and geographic isolation have played an important role in promoting phenotypic differentiation in the Sinaloa Wren.