Geology topics

Jason Coombs

Publications and source records attributed to Jason Coombs.

4 recordsLinked to original sources

USGS2025

The complete mitochondrial genomes of the freshwater mussel Ortmanniana ligamentina (Lamarck, 1819): male and female mitotypes

Freshwater mussels of the Unionida order are important to freshwater ecosystems but are highly imperiled worldwide. Improving our understanding of these species is crucial to their continued conservation. Some Unionid mussels exhibit double uniparental inheritance (DUI) in which individuals have two mitochondrial genomes. Of those species with DUI, sequences of the female mitotype are most prevalent in genetic databases. Here, we demonstrate the ability to recover both mitotypes of Ortmanniana ligamentina (Lamarck, 1819) from a non-lethal collection method coupled with high-throughput sequencing. Increased male mitotype sequence representation facilitates understanding Unionid genetic diversity and development of molecular tools for species detection.

Missouri, Pennsylvania↗

USGS2023

Identifying mechanisms underlying individual body size increases in a changing, highly seasonal environment: The growing trout of West Brook

As air temperature increases, it has been suggested that smaller individual body size may be a general response to climate warming. However, for ectotherms inhabiting cold, highly seasonal environments, warming temperatures may increase the scope for growth and result in larger body size. In a long-term study of individual brook trout Salvelinus fontinalis and brown trout Salmo trutta inhabiting a small stream network, individual lengths increased over the course of 15 years. As size-selective gains and losses to the population acted to reduce body sizes and mean body size at first tagging in the autumn (<60 mm) were not observed to change substantially over time, the increase in body size was best explained by higher individual growth rates. For brook trout, increasing water temperatures during the spring (when both trout species accomplish most of their total annual growth) was the primary driver of growth rate for juvenile fish and the environmental factor which best explained increases in individual body size over time. For brown trout, by contrast, reduction in and subsequent elimination of juvenile Atlantic salmon Salmo salar midway through the study period explained most of the increases in juvenile growth and body size. In addition to these major trends, a considerable amount of interannual variation in trout growth and body size was explained by other abiotic (stream flow) and biotic (population density) factors with the direction and magnitude of these effects differing by season, age-class and species. For example, stream flow was the dominant growth rate driver for adult fish with strong positive effects in the summer and autumn, but flow variation could not explain increases in body size as we observed no trend in flow. Overall, our work supports the general contention that for high-latitude ectotherms, increasing spring temperatures associated with a warming climate can result in increased growth and individual body size (up to a point), but context-dependent change in other factors can substantially contribute to both interannual variation and longer-term effects.

Massachusetts↗

USGS2021

Understanding genetics for successful conservation and restoration of resilient Chesapeake Bay brook trout populations

Traditionally, fisheries management has focused on the abundance, distribution, and size structure of populations. Although these factors remain key aspects of management, a large and growing body of evidence highlights the importance of genetics in conserving wild populations, especially when populations are small and isolated (Frankham et al. 2017). Local adaptations are very common among fishes and help populations cope with specific conditions in their local environment (Fraser et al. 2011). The field of conservation genetics and genomics is highly technical and has advanced rapidly in recent years, offering a wealth of information to support brook trout conservation and restoration. A major impediment to successfully incorporating these advances into conservation outcomes is that most fisheries managers have only a basic understanding of fish genetics and its relevance to their management decisions.

Maryland, Virginia↗

USGS2018

Three visualization approaches for communicating and exploring PIT tag data

As the number, size and complexity of ecological datasets has increased, narrative and interactive raw data visualizations have emerged as important tools for exploring and understanding these large datasets. As a demonstration, we developed three visualizations to communicate and explore passive integrated transponder tag data from two long-term field studies. We created three independent visualizations for the same dataset, allowing separate entry points for users with different goals and experience levels. The first visualization uses a narrative approach to introduce users to the study. The second visualization provides interactive cross-filters that allow users to explore multi-variate relationships in the dataset. The last visualization allows users to visualize the movement histories of individual fish within the stream network. This suite of visualization tools allows a progressive discovery of more detailed information and should make the data accessible to users with a wide variety of backgrounds and interests.

Maine, Massachusetts↗