Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks

Mohannad Elhamod, Josef C. Uyeda, Yasin Bakış, Hilmar Lapp, David Carlyn, Daniel I. Rubenstein, Mridul Khurana, Meghan A. Balk, Henry L. Bart Jr., James P. Balhoff, Wei-Lun Chao, Tanya Berger-Wolf, Wasila Dahdul, Paula M. Mabee, Caleb Charpentier, Charles V. Stewart, Anuj Karpatne. 2023. 

Abstract

Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of traits is often a subjective and labor-intensive process, making trait discovery a highly label-scarce problem. We present a novel approach for discovering evolutionary traits directly from images without relying on trait labels. Our pro- posed approach, Phylo-NN, encodes the image of an organism into a sequence of quantized feature vectors–or codes–where different segments of the sequence capture evolutionary signals at varying ancestry levels in the phylogeny. We demonstrate the effectiveness of our approach in producing biologically meaningful results in a number of downstream tasks including species image generation and species-to-species image translation, using fish species as a target example.

Low-coverage whole-genome sequencing for highly accurate population assignment: Mapping migratory connectivity in the American redstart (Setophaga ruticilla)

DeSaix M, Anderson E, Bossu C, Rayne C, Schweizer T, Bayly N, Narang D, Hagelin J, Gibbs HL, Saracco J, Sherry TW, Webster M, Smith T, Marra P, Ruegg K. Authorea Preprints. 2023. DOI: 10.22541/au.168691235.56488081/v1.

Abstract 

Understanding the geographic linkages among populations across the annual cycle is an essential component for understanding the ecology and evolution of migratory species and for facilitating their effective conservation. While genetic markers have been widely applied to describe migratory connections, the rapid development of new sequencing methods, such as low-coverage whole genome sequencing (lcWGS), provides new opportunities for improved estimates of migratory connectivity. Here, we use lcWGS to identify fine-scale population structure in a widespread songbird, the American Redstart (Setophaga ruticilla), and accurately assign individuals to genetically distinct breeding populations. Assignment of individuals from the nonbreeding range reveals population-specific patterns of varying migratory connectivity. By combining migratory connectivity results with demographic analysis of population abundance and trends, we consider full annual cycle conservation strategies for preserving numbers of individuals and genetic diversity. Notably, we highlight the importance of the Northern Temperate-Greater Antilles migratory population as containing the largest proportion of individuals in the species. Finally, we highlight valuable considerations for other population assignment studies aimed at using lcWGS. Our results have broad implications for improving our understanding of the ecology and evolution of migratory species through conservation genomics approaches.

Estimating Loss of Recreational Angling Trips from Harmful Algal Blooms in Lake Erie

Yining Wu, Brent Sohngen, Stuart Ludsin. 2023. AgEcon Search.

Abstract

Harmful algal blooms (HABs), which can cause health effects in humans, have been increasing in extent and intensity in Lake Erie. This paper assesses the relationship between HAB occurrence and intensity, and recreational angling trips in Lake Erie using spatially and temporally varying algae measures and daily boat counts in 36 major harbors collected between June and October from 2011 to 2018. We utilize Poisson pseudo-maximum likelihood for the nature of count data, as well as Control function to solve the potential endogeneity from measurement uncertainty and omitted variables. Results indicate a 1% increase of cyanobacteria concentration in the water within 2 miles around the harbors significantly decreases the count of recreational angling boats by 1.47% on weekend days and 2.52% on weekdays. In the western basin, where HAB occurrence is greatest, the numbers are 1.23% on weekend days and 2.03% on weekdays. We also estimate that 163,503 trips in total happened in the western basin of Lake Erie in 2015 during which HABs reached a peak across the ten years, while the numbers go up to 216,703 and 170,547 if we replace the HAB data with 2014 and 2016 respectively. The economic loss of HABs in 2015 on recreational angling is estimated to be at least $4.6 million if the HAB levels were as same as those in 2014, and at least $0.6 million if the HAB levels were as same as those in 2016.

Combining stable isotopes, trace elements, and distribution models to assess the geographic origins of migratory bats

Jamin G. Wieringa, Juliet Nagel, C. J. Campbell, David M. Nelson, Bryan C. Carstens, H. Lisle Gibbs. 2023. Ecosphere.

Abstract

The expansion of industrial-scale wind-energy facilities has not only increased the production of low-carbon emission energy but has also resulted in mortal- ity of wildlife, including migratory bats. Management decisions can be limited by a lack of understanding of the geographic impact of bats killed at wind-energy facilities. Several studies have leveraged stable hydrogen isotope ratios (δ2H) of bat fur to illuminate this issue but are limited in the precision of conclusion because δ2H values vary primarily across latitudinal and elevational bands. One approach to increase the precision of geographic assignment is to combine independent inferences about spatial location from additional biomarkers and other related information. To test this possibility, we assigned known-origin individuals of three bat species (Lasiurus borealis, L. cinereus, and Lasionycteris noctivagans) commonly killed at on-shore wind-energy facilities in North America to a probable origin using δ2H values, trace element concentrations, and species distribution models. We used cross-validated calibrated combined model tuning to determine the degree to which assignment probabilities improved when combining datasets. We found that combining markers typically performed better than single approaches. For Lasiurus borealis and L. cinereus, combining all three data sources outperformed any single or other combined approach. With an accuracy set at 80%, an average of 39.7% and 36.0% of each species’ total geographic range was considered a potential origin, respectively; stable hydrogen alone included 51.8% and 50.6% of the total geographic area. In contrast, for Lasionycteris noctivagans, including trace elements did not increase precision and adding distribution data to δ2H values only improved precision by 0.6%. Thus, we found that a combination of multiple biomarkers typically, but not always, outperforms single-marker approaches and optimized combinations of differ- ent markers outperform equal weighting of each marker. From a practical per- spective, δ2H values performed better than trace elements alone; in cases where cost is a limiting factor, the stable hydrogen should be the single biomarker used in conjunction with species distribution models. Overall, these results highlight the importance of validating methods for each species they are applied to and show that combining information from intrinsic biomarker approaches is a useful tool to document bat movements.