Bias assessments to expand research harnessing biological collections

Meineke, Emily K.; Daru, Barnabas H.

doi:10.1016/j.tree.2021.08.003

Cited by 43 publications

(34 citation statements)

References 69 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A more pernicious problem is that herbarium‐based meta‐analyses are subject to spatial bias in collecting, digitization and georeferencing efforts (Beck et al, 2012; Boakes et al, 2010; Meineke & Daru, 2021; Spalink, Kriebel, et al, 2018; Spalink, Pender, et al, 2018; Yang et al, 2013), not to mention potential regional or taxonomic errors in species identification. Bias is manifest in our data, where sampling effort varies substantially across the globe (Figure 2d).…”

Section: Discussionmentioning

confidence: 99%

“…Thus, specimens housed in biological collections represent a wealth of crucial data that spans across centuries. However, in many cases, these data are subject to a hoard of potential bias (Meineke & Daru, 2021). These include geographic, temporal and taxonomic bias in collecting efforts, as well as bias in sequencing and digitization efforts.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

A global analysis of mosses reveals low phylogenetic endemism and highlights the importance of long‐distance dispersal

Sanbonmatsu

Spalink

2022

Journal of Biogeography

View full text Add to dashboard Cite

Aim: Digitization of herbarium specimens and DNA sequencing efforts in the past decade have enabled integrative analyses of patterns of diversity and endemism in a phylogenetic context. Here, we compare the best available floristic databases to a comprehensive specimen database to examine spatial patterns of moss phylogenetic assembly. We test the hypotheses that (1) mosses exhibit phylogenetic regionalization, (2) islands contain significantly high phylogenetic diversity and (3) that moss phylogenetic endemism is low on a global scale. Location: Global.Taxon: Mosses. Methods:We developed a phylogeny of 3654 moss species using 25 markers and compiled a global specimen database from online repositories. We calculated floristic and phylogenetic measures of diversity and endemism and performed randomizations to test for significant deviations from expectations. We use rarefaction and extrapolation to alleviate substantial differences in sampling effort across the globe. We used both phylogenetic and floristic methods to test for spatial regionalization. We compare our specimen-based results to those obtained using a floristic dataset.Results: Phylogenetic diversity is more robust to missing data than species richness. Mean phylogenetic distance was significantly higher than expected in areas with high species richness, indicating that reported richness in these areas is likely a product of repeated colonization. Phylogenetic endemism is low globally. Phylogenetic regionalizations cluster into a Holarctic/Holantarctic temperate region, a pantropical region, and a region composed of Australia, New Zealand and South Africa.Main Conclusions: Future efforts for collecting, sequencing and databasing moss species should focus on the tropics, particularly Africa and Southeast Asia. We provide further evidence to support several important theories developed in moss biogeography, including the role of long-distance dispersal in shaping floristic patterns, the dominance of anagenesis in driving patterns of island diversity, and the role of climatic instability in driving patterns of assembly in the Holarctic.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A global analysis of mosses reveals low phylogenetic endemism and highlights the importance of long‐distance dispersal

Sanbonmatsu

Spalink

2022

Journal of Biogeography

View full text Add to dashboard Cite

show abstract

“…This was assessed on a single plant or, if the specimen/herbarium sheet contained more than one plant, as a mean. As a measure of flowering timing, we used the earliest date of peak flowering, since this is less susceptible to biases in natural history collections than first flowering (Meineke & Daru, 2021 ). For each species, peak flowering intensity was assessed as the flowering intensity at or above the 75% quantile of all flowering intensity records for that species.…”

Section: Methodsmentioning

confidence: 99%

A regionally coherent ecological fingerprint of climate change, evidenced from natural history collections

Speed

Evankow

Petersen

et al. 2022

Ecology and Evolution

View full text Add to dashboard Cite

Climate change has dramatic impacts on ecological systems, affecting a range of ecological factors including phenology, species abundance, diversity, and distribution. The breadth of climate change impacts on ecological systems leads to the occurrence of fingerprints of climate change. However, climate fingerprints are usually identified across broad geographical scales and are potentially influenced by publication biases. In this study, we used natural history collections spanning over 250 years, to quantify a range of ecological responses to climate change, including phenology, abundance, diversity, and distributions, across a range of taxa, including vertebrates, invertebrates, plants, and fungi, within a single region, Central Norway. We tested the hypotheses that ecological responses to climate change are apparent and coherent at a regional scale, that longer time series show stronger trends over time and in relation to temperature, and that ecological responses change in trajectory at the same time as shifts in temperature. We identified a clear regional coherence in climate signal, with decreasing abundances of limnic zooplankton (on average by 7691 individuals m −3 °C −1 ) and boreal forest breeding birds (on average by 1.94 territories km −2 °C −1 ), and earlier plant flowering phenology (on average 2 days °C −1 ) for every degree of temperature increase. In contrast, regional‐scale species distributions and species diversity were largely stable. Surprisingly, the effect size of ecological response did not increase with study duration, and shifts in responses did not occur at the same time as shifts in temperature. This may be as the long‐term studies include both periods of warming and temperature stability, and that ecological responses lag behind warming. Our findings demonstrate a regional climate fingerprint across a long timescale. We contend that natural history collections provide a unique window on a broad spectrum of ecological responses at timescales beyond most ecological monitoring programs. Natural history collections are thus an essential source for long‐term ecological research.

show abstract

“…Other baseline limitations are less likely to be overcome with technical advances but are equally important, this includes the fact that historical specimens are simply not available for many taxa. The taxonomic and geographic biases in natural history collections mean that most species are not well represented (Meineke & Daru, 2021 ). If specimens exist, critical meta‐data such as date of collection and geographic location are often missing.…”

Section: Challenges and Considerations For Temporal Population Genomi...mentioning

confidence: 99%

Using temporal genomics to understand contemporary climate change responses in wildlife

Jensen

Leigh

2022

Ecology and Evolution

View full text Add to dashboard Cite

Monitoring the evolutionary responses of species to ongoing global climate change is critical for informing conservation. Population genomic studies that use samples from multiple time points (“temporal genomics”) are uniquely able to make direct observations of change over time. Consequently, only temporal studies can show genetic erosion or spatiotemporal changes in population structure. Temporal genomic studies directly examining climate change effects are currently rare but will likely increase in the coming years due to their high conservation value. Here, we highlight four key genetic indicators that can be monitored using temporal genomics to understand how species are responding to climate change. All indicators crucially rely on having a suitable baseline that accurately represents the past condition of the population, and we discuss aspects of study design that must be considered to achieve this.

show abstract

Bias assessments to expand research harnessing biological collections

Cited by 43 publications

References 69 publications

A global analysis of mosses reveals low phylogenetic endemism and highlights the importance of long‐distance dispersal

A global analysis of mosses reveals low phylogenetic endemism and highlights the importance of long‐distance dispersal

A regionally coherent ecological fingerprint of climate change, evidenced from natural history collections

Using temporal genomics to understand contemporary climate change responses in wildlife

Contact Info

Product

Resources

About