Biology subjects

Shapiro, A. M.

Publications and source records attributed to Shapiro, A. M..

6 recordsLinked to original sources

bioRxiv2025

Allochronic isolation between sympatric populations of an alpine butterfly

The role of isolation by distance in contributing to population structure across space is well understood, and the same principles should operate over time. Allochrony, the isolation of populations due to separation in time, can be a source of genetic differentiation, but remains infrequently documented between yearly asynchronous populations. In this study, we investigate divergence between two putative sympatric populations of the alpine butterfly Oeneis chryxus ivallda at Castle Peak, CA, USA. We find clear genetic differentiation between butterflies collected in odd and even years, with limited instances of admixture. The observed GST of 0.05 between the two populations is approximately equivalent to 26 km based on pairwise GST values observed between O. chryxus populations across space. These results demonstrate a potential source of population differentiation in systems that promote prolonged development, often found in high-elevation and high-latitude environments.

evolutionary biology↗

bioRxiv2024

Language model-guided anticipation and discovery of unknown metabolites

Despite decades of study, large parts of the mammalian metabolome remain unexplored. Mass spectrometry-based metabolomics routinely detects thousands of small molecule-associated peaks within human tissues and biofluids, but typically only a small fraction of these can be identified, and structure elucidation of novel metabolites remains a low-throughput endeavor. Biochemical large language models have transformed the interpretation of DNA, RNA, and protein sequences, but have not yet had a comparable impact on understanding small molecule metabolism. Here, we present an approach that leverages chemical language models to discover previously uncharacterized metabolites. We introduce DeepMet, a chemical language model that learns the latent biosynthetic logic embedded within the structures of known metabolites and exploits this understanding to anticipate the existence of as-of-yet undiscovered metabolites. Prospective chemical synthesis of metabolites predicted to exist by DeepMet directs their targeted discovery. Integrating DeepMet with tandem mass spectrometry (MS/MS) data enables automated metabolite discovery within complex tissues. We harness DeepMet to discover several dozen structurally diverse mammalian metabolites. Our work demonstrates the potential for language models to accelerate the mapping of the metabolome.

bioinformatics↗

bioRxiv2022

Assessing risk for butterflies in the context of climate change, demographic uncertainty, and heterogenous data sources

AbstractOngoing declines in insect populations have led to substantial concern and calls for conservation action. However, even for relatively well-studied groups, like butterflies, information relevant to species-specific status and risk is scattered across field guides, the scientific literature, and agency reports. Consequently, attention and resources have been spent on a miniscule fraction of insect diversity, including a few well-studied butterflies. Here we bring together heterogenous sources of information for 396 butterfly species to provide the first regional assessment of butterflies for the 11 western US states. For 184 species, we use monitoring data to characterize historical and projected trends in population abundance. For another 212 species (for which monitoring data are not available, but other types of information can be collected), we use exposure to climate change, development, geographic range, number of host plants, and other factors to rank species for conservation concern. A phylogenetic signal is apparent, with concentrations of declining and at-risk species in the families Lycaenidae and Hesperiidae. A geographic bias exists in that many species that lack monitoring data occur in more southern states where we expect that impacts of warming and drying trends will be most severe. Legal protection is rare among the taxa with the highest risk values: of the top 100 species, one is listed as threatened under the US Endangered Species Act and one is a candidate for listing. Among the many taxa not currently protected, we highlight a short list of species in decline, including Vanessa annabella, Thorybes mexicanus, Euchloe ausonides, and Pholisora catullus. Notably, many of these species have broad geographic ranges, which perhaps highlights a new era of insect conservation in which small or fragmented ranges will not be the only red flags that attract conservation attention.

ecology↗

bioRxiv2020

Insects and recent climate change

Insects have diversified through 400 million years of Earths changeable climate, yet recent and ongoing shifts in patterns of temperature and precipitation pose novel challenges as they combine with decades of other anthropogenic stressors including the conversion and degradation of land. Here we consider how insects are responding to recent climate change, while summarizing the literature on long-term monitoring of insect populations in the context of climatic fluctuations. Results to date suggest that climate change impacts on insects have the potential to be considerable, even when compared to changes in land use. The importance of climate is illustrated with a case study from the butterflies of Northern California, where we find that population declines have been severe in high-elevation areas removed from the most immediate effects of habitat loss. These results shed light on the complexity of montane-adapted insects responding to changing abiotic conditions and raise questions about the utility of temperate mountains as refugia during the Anthropocene. We consider methodological issues that would improve syntheses of results across long-term insect datasets and highlight directions for future empirical work. Significance statementAnthropogenic climate change poses multiple threats to society and biodiversity, and challenges our understanding of the resilience of the natural world. We discuss recent ideas and evidence on this issue and conclude that the impacts of climate change on insects in particular have the potential to be more severe than might have been expected a decade ago. Finally, we suggest practical measures that include the protection of diverse portfolios of species, not just those inhabiting what are currently the most pristine areas.

ecology↗

bioRxiv2019

A winner in the Anthropocene: changing host plant distribution explains geographic range expansion in the gulf fritillary butterfly

O_LIThe changing climate is altering the geographic distributions of species around the world with consequences for population dynamics, resulting in winners and losers in the Anthropocene.\nC_LIO_LIAgraulis vanillae, the gulf fritillary butterfly, has expanded its range in the past one hundred years in the western United States. We combine time series analysis with species distribution modeling to investigate factors limiting the distribution of A. vanillae and to predict future shifts under warming scenarios.\nC_LIO_LIIn the western US, where we have time series and geographic data, urban development has a positive influence (the host plant is an ornamental in gardens), being associated with year of colonization. Colonization was also associated to a lesser extent with winter maximum temperatures, while a negative impact of minimum temperatures and precipitation was apparent on population growth rates.\nC_LIO_LIAcross the country, the butterfly is primarily limited by host availability and positively affected by human presence. Perhaps counter-intuitively for a largely tropical ectotherm, current effects of a warming climate (in the years post-colonization) are either negative (on population growth rate) or indirect, likely mediated through availability of areas that can support the host.\nC_LIO_LIUnder future climate scenarios, conditions are predicted to become more suitable for Passiflora in many urban areas, which would likely result in further expansion of A. vanillae during the dispersive season. These results illustrate the value of combining time series with spatial modeling to understand and predict shifting geographic ranges in the Anthropocene.\nC_LI

ecology↗

bioRxiv2018

Impacts of a millennium drought on butterfly faunal dynamics

Climate change is challenging plants and animals not only with increasing temperatures, but also with shortened intervals between extreme weather events. Relatively little is known about diverse assemblages of organisms responding to extreme weather, and even less is known about landscape and life history properties that might mitigate effects of extreme weather. We find that northern California butterflies were impacted by a millennium-scale drought differentially at low and high elevations. At low elevations, phenological shifts facilitated persistence and even recovery during drought, while at higher elevations a shortened flight season was associated with decreases in species richness. Phenological and faunal dynamics are predicted by temperature and precipitation, thus advancing the possibility of understanding and forecasting biological responses to extreme weather.

ecology↗