Natural history collections are critical resources for contemporary and future studies of urban evolution

Lack of country-wide systematic herpetology collections in Portugal jeopardizes future research and conservation

Natural History Collections (NHCs) represent the world's largest repositories of long-term biodiversity datasets. Specimen collection and voucher deposition has been the backbone of NHCs since their inception, but recent decades have seen a drastic decline in rates of growth via active collecting. Amphibians and reptiles are amongst the most threatened zoological groups on the planet and are historically underrepresented in most worldwide NHCs. As part of an ongoing project to review the Portuguese zoological collections in the country's NHCs, herpetological data from its three major museums and smaller collections was gathered and used to examine the coverage and representation of the different taxa extant in Portugal. These collections are not taxonomically, geographically, or temporally complete. Approximately 90% of the Portuguese herpetological taxa are represented in the country's NHCs, and around half of the taxa are represented by less than 50 specimens. Geographically, the collections cover less than 30% of the country's territory and almost all of the occurring taxa have less than 10% of their known distribution represented in the collections. A discussion on the implications for science of such incomplete collections and a review of the current status of Portuguese NHCs is presented.

PhyloMatcher: a tool for resolving conflicts in taxonomic nomenclature

Summary

Large-scale comparative studies rely on the application of both phylogenetic trees and phenotypic data, both of which come from a variety of sources, but due to the changing nature of phylogenetic classification over time, many taxon names in comparative datasets do not match the nomenclature in phylogenetic trees. Manual curation of taxonomic synonyms in large comparative datasets can be daunting. To address this issue, we introduce PhyloMatcher, a tool which allows for programmatic querying of the National Center for Biotechnology Information Taxonomy and Global Biodiversity Information Facility databases to find associated synonyms with given target species names.

Availability and implementation

PhyloMatcher is easily installed as a Python package with pip, or as a standalone GUI application. PhyloMatcher source code and documentation are freely available at https://github.com/Lswhiteh/PhyloMatcher, the GUI application can be downloaded from the Releases page.

PhyloMatcher: a tool for resolving conflicts in taxonomic nomenclature

Summary

Large-scale comparative studies rely on the application of both phylogenetic trees and phenotypic data, both of which come from a variety of sources, but due to the changing nature of phylogenetic classification over time, many taxon names in comparative datasets do not match the nomenclature in phylogenetic trees. Manual curation of taxonomic synonyms in large comparative datasets can be daunting. To address this issue, we introduce PhyloMatcher, a tool which allows for programmatic querying of two commonly used taxonomic databases to find associated synonyms with given target species names.

Availability and implementation

PhyloMatcher is easily installed as a Python package with pip, or as a standalone GUI application. PhyloMatcher source code and documentation are freely available at https://github.com/Lswhiteh/PhyloMatcher, the GUI application can be downloaded from the Releases page.

Contact

Lswhiteh@unc.edu.

Supplemental Information

We provide documentation for PhyloMatcher, including walkthrough instructions for the GUI application on the Releases page of https://github.com/Lswhiteh/PhyloMatcher.

Going, Going, Gone The Diminishing Capacity of Museum Specimen Collections to Address Global Change Research: A Case Study on Urban Reptiles

It has been increasingly popular to use natural history specimens to examine environmental changes. As the current functionality of museum specimens has extended beyond their traditional taxonomic role, there has been a renewed focus on the completeness of biological collections to provide data for current and future research. We used the collections of the Western Australian Museum to answer questions about the change in occurrence of five common reptile species due to the rapid urbanization of Perth. We recorded a significant decline in collection effort from the year 2000 onwards (F = 7.65, p < 0.01) compared to the period 1990–1999. Spatial analysis revealed that only 0.5% of our study region was well sampled, 8.5% were moderately sampled and the majority of the regions (91%) were poorly sampled. By analysing the trend of specimen acquisition from 1950 to 2010, we discovered a significant inconsistency in specimen sampling effort for 13 common reptile species across time and space. A large proportion of past specimens lacked information including the place and time of collection. An increase in investment to museums and an increase in geographically and temporally systematic collecting is advocated to ensure that collections can answer questions about environmental change.

Moving past the challenges and misconceptions in urban adaptation research

Although the field of urban evolutionary ecology has recently expanded, much progress has been made in identifying adaptations that arise as a result of selective pressures within these unique environments. However, as studies within urban environments have rapidly increased, researchers have recognized that there are challenges and opportunities in characterizing urban adaptation. Some of these challenges are a consequence of increased direct and indirect human influence, which compounds long-recognized issues with research on adaptive evolution more generally. In this perspective, we discuss several common research challenges to urban adaptation related to (1) methodological approaches, (2) trait-environment relationships and the natural history of organisms, (3) agents and targets of selection, and (4) habitat heterogeneity. Ignoring these challenges may lead to misconceptions and further impede our ability to draw conclusions regarding evolutionary and ecological processes in urban environments. Our goal is to first shed light on the conceptual challenges of conducting urban adaptation research to help avoid the propagation of these misconceptions. We further summarize potential strategies to move forward productively to construct a more comprehensive picture of urban adaptation, and discuss how urban environments also offer unique opportunities and applications for adaptation research.

Museum Genomics

Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.

Old Brains in Alcohol: The Usability of Legacy Collection Material to Study the Spider Neuroarchitecture

Natural history collections include rare and significant taxa that might otherwise be unavailable for comparative studies. However, curators must balance the needs of current and long-term research. Methods of data extraction that minimize the impact on specimens are therefore favored. Micro-CT has the potential to expose new character systems based on internal anatomy to taxonomic and phylogenetic analysis without dissection or thin sectioning for histology. However, commonly applied micro-CT protocols involve critical point drying, which permanently changes the specimen. Here, we apply a minimally destructive method of specimen preparation for micro-CT investigation of spider neuroanatomy suitable for application to legacy specimens in natural history collections. We used two groups of female spiders of the common species Araneus diadematus—freshly captured (n = 11) vs. legacy material between 70 and 90 years old (n = 10)—to qualitatively and quantitatively assess the viability of micro-CT scanning and the impact of aging on their neuroarchitecture. We statistically compared the volumes of the supraesophageal ganglion (syncerebrum) and used 2D geometric morphometrics to analyze variations in the gross shape of the brain. We found no significant differences in the brain shape or the brain volume relative to the cephalothorax size. Nonetheless, a significant difference was observed in the spider size. We considered such differences to be explained by environmental factors rather than preservation artifacts. Comparison between legacy and freshly collected specimens indicates that museum specimens do not degrade over time in a way that might bias the study results, as long as the basic preservation conditions are consistently maintained, and where lapses in preservation have occurred, these can be identified. This, together with the relatively low-impact nature of the micro-CT protocol applied here, could facilitate the use of old, rare, and valuable material from collections in studies of internal morphology.

Evolution in Cities

Although research performed in cities will not uncover new evolutionary mechanisms, it could provide unprecedented opportunities to examine the interplay of evolutionary forces in new ways and new avenues to address classic questions. However, while the variation within and among cities affords many opportunities to advance evolutionary biology research, careful alignment between how cities are used and the research questions being asked is necessary to maximize the insights that can be gained. In this review, we develop a framework to help guide alignment between urban evolution research approaches and questions. Using this framework, we highlight what has been accomplished to date in the field of urban evolution and identify several up-and-coming research directions for further expansion. We conclude that urban environments can be used as evolutionary test beds to tackle both new and long-standing questions in evolutionary biology.

Bias assessments to expand research harnessing biological collections

Biological collections are arguably the most important resources for investigations into the impacts of human activities on biodiversity. However, the apparent opportunities presented by museum-derived datasets have not resulted in consistent or widespread use of specimens in ecology outside phenological research and species distribution modeling. We attribute this gap between opportunity and application to biases introduced by collectors, curators, and preservation practices and an imperfect understanding of these biases and how to mitigate them. To facilitate broader use of specimen-based data, we characterize collection biases across key axes and explore interactions among them. We then present a framework for determining the bias assessments needed when extracting data from biological collections. We show that bias assessments required by particular ecological studies will depend on the response variables being measured and the predictor axes of interest. We argue that quantification of biases in specimen-derived datasets is needed to facilitate the widespread application of these data.

Genomic library preparation and hybridization capture of formalin-fixed tissues and allozyme supernatant for population genomics and considerations for combining capture- and RADseq-based single nucleotide polymorphism data sets

Until recently many historical museum specimens were largely inaccessible to genomic inquiry, but high-throughput sequencing (HTS) approaches have allowed researchers to successfully sequence genomic DNA from dried and fluid-preserved museum specimens. In addition to preserved specimens, many museums contain large series of allozyme supernatant samples, but the amenability of these samples to HTS has not yet been assessed. Here, we compared the performance of a target-capture approach using alternative sources of genomic DNA from 10 specimens of spring salamanders (Plethodontidae: Gyrinophilus porphyriticus) collected between 1985 and 1990: allozyme supernatants, allozyme homogenate pellets and formalin-fixed tissues. We designed capture probes based on double-digest restriction-site associated sequencing (RADseq) derived loci from frozen blood samples available for seven of the specimens and assessed the success and consistency of capture and RADseq approaches. This study design enabled direct comparisons of data quality and potential biases among the different data sets for phylogenomic and population genomic analyses. We found that in phylogenetic analyses, all enrichment types for a given specimen clustered together. In principal component space all capture-based samples clustered together, but RADseq samples did not cluster with corresponding capture-based samples. Single nucleotide polymorphism calls were on average 18.3% different between enrichment types for a given individual, but these discrepancies were primarily due to differences in heterozygous/homozygous single nucleotide polymorphism calls. We demonstrate that both allozyme supernatant and formalin-fixed samples can be successfully used for population genomic analyses and we discuss ways to identify and reduce biases associated with combining capture and RADseq data.

Multiple Introductions of the Pestiferous Land Snail Theba pisana (Müller, 1774) (Gastropoda: Helicidae) in Southern California

Simple Summary

In Southern California, USA, the introduced white Italian land snail, Theba pisana, is prolific and locally pestiferous. To better understand its diversity and infer its parent population(s), we collected it from Los Angeles and San Diego counties and generated and analyzed gene sequence data (CO1, 16S, ITS2) that we compared between localities and to T. pisana CO1 barcodes from around the world. We also compared the morphology of the jaw, radula, and reproductive systems in T. pisana from Los Angeles and San Diego Counties. We found that T. pisana living at several sites in Los Angeles County in 2019–2020 had a single origin and were most similar in CO1 DNA sequence, based on available data, to specimens from Malta. Theba pisana collected from one site in San Diego County differed from Los Angeles T. pisana and were most similar in CO1 barcode sequence to specimens from Morocco. Jaw and mucous gland morphology also differed between Los Angeles and San Diego populations, but it is unclear if these traits are unique to lineages of T. pisana or if they change during a snail’s lifetime. We discuss how Los Angeles and San Diego T. pisana lineages may have arrived in Southern California and anticipate that the genetic data and morphological observations generated by this study will inform future studies of T. pisana where it is native and introduced.

Abstract

The terrestrial land snail Theba pisana is circum-Mediterranean in native range and widely introduced and pestiferous in regions around the world. In California, USA, T. pisana has been recorded intermittently since 1914, but its source population(s) are unknown, and no morphological or molecular analyses within or between California populations have been published. Therefore, we compared molecular data (CO1, 16S, ITS2) and internal morphology (jaw, radula, reproductive system) in T. pisana collected from Los Angeles and San Diego counties in 2019–2020. DNA barcode (CO1 mtDNA) analysis revealed that T. pisana from Los Angeles County was most similar to T. pisana from the Mediterranean island of Malta, and northern San Diego County-collected specimens were most similar to T. pisana from Morocco. Morphology of the jaw and mucous glands also differed between Los Angeles and San Diego populations, but it is unclear if traits are lineage-specific or artifacts of ontogeny. Several pathways of introduction into Southern California are possible for this species, but evidence for intentional vs. accidental introduction of present populations is lacking. Subsequent investigation(s) could use the data generated herein to assess the provenance of T. pisana elsewhere in California and/or worldwide and inform analyses of reproductive biology and systematics in this widespread species.

Plastic ingestion by freshwater turtles: a review and call to action

Plastic pollution, and especially plastic ingestion by animals, is a serious global issue. This problem is well documented in marine systems, but it is relatively understudied in freshwater systems. For turtles, it is unknown how plastic ingestion compares between marine and non-marine species. We review the relevant turtle dietary literature, and find that plastic ingestion is reported for all 7 marine turtle species, but only 5 of 352 non-marine turtle species. In the last 10 years, despite marine turtles representing just 2% of all turtle species, almost 50% of relevant turtle dietary studies involved only marine turtles. These results suggest that the potential threat of plastic ingestion is poorly studied in non-marine turtles. We also examine plastic ingestion frequency in a freshwater turtle population, finding that 7.7% of 65 turtles had ingested plastic. However, plastic-resembling organic material would have inflated our frequency results up to 40% higher were it not for verification using Raman spectroscopy. Additionally, we showcase how non-native turtles can be used as a proxy for understanding the potential for plastic ingestion by co-occurring native turtles of conservation concern. We conclude with recommendations for how scientists studying non-marine turtles can improve the implementation, quality, and discoverability of plastic ingestion research.

Valuing the Role of Time in Urban Ecology

Cities and towns are complex ecosystems with features that can vary dramatically in space and time. Our knowledge of the spatial structure of urban land and ecological systems is expanding. These systems have been investigated across spatial scales, urban to rural gradients, networks of urban macrosystems, and global megalopolises. However, the temporal dimensions of urban ecosystems – such as those related to ecological cycles and historical legacies – are far less understood and investigated. Here, we outline the main dimensions of time that can shape how events in urban ecosystems unfold, which we categorize as: (i) time flows and duration, (ii) synchrony, lags, and delays, (iii) trends and transitions, (iv) cycles and hysteresis, (v) legacies and priming, (vi) temporal hotspots and hot moments, and (vii) stochastic vs. deterministic processes affecting our ability to forecast the future of cities and the species that live in them. First, we demonstrate the roles of these understudied dimensions by discussing exemplary studies. We then propose key future research directions for investigating how processes over time may regulate the structure and functioning of urban land and biodiversity, as well as its effects on and implications for urban ecology. Our analysis and conceptual framework highlights that several temporal dimensions of urban ecosystems – like those related to temporal hotspots/moments and stochastic vs. deterministic processes – are understudied. This offers important research opportunities to further urban ecology and a comprehensive research agenda valuing the “Urban Chronos” – the change of urban ecosystems through time.

Urban evolution comes into its own: Emerging themes and future directions of a burgeoning field

Urbanization has recently emerged as an exciting new direction for evolutionary research founded on our growing understanding of rapid evolution paired with the expansion of novel urban habitats. Urbanization can influence adaptive and nonadaptive evolution in urban-dwelling species, but generalized patterns and the predictability of urban evolutionary responses within populations remain unclear. This editorial introduces the special feature "Evolution in Urban Environments" and addresses four major emerging themes, which include: (a) adaptive evolution and phenotypic plasticity via physiological responses to urban climate, (b) adaptive evolution via phenotype-environment relationships in urban habitats, (c) population connectivity and genetic drift in urban landscapes, and (d) human-wildlife interactions in urban spaces. Here, we present the 16 articles (12 empirical, 3 review, 1 capstone) within this issue and how they represent each of these four emerging themes in urban evolutionary biology. Finally, we discuss how these articles address previous questions and have now raised new ones, highlighting important new directions for the field.