Stephanie J. Galla

Boise State University | BSU · Department of Biological Sciences

Host microbial communities (hereafter, the ‘microbiome’) are recognized as an important aspect of host health and are gaining attention as a useful biomarker to understand the ecology and demographics of wildlife populations. Several studies indicate that the microbiome may contribute to the adaptive capacity of animals to changing environments ass...

The kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analysed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to q...

Purpose of Review Ecological models can provide critical guidance to conservation programs both as problem-solving tools and by projecting future outcomes, specifically when time and resources limit directly testing alternative management approaches and scenarios. Due to the complexity of aquatic systems, environmental and climatic factors co-vary,...

The current science system is unjust — from the systems that determine its membership to its outputs and outcomes. We advocate for contextually responsive, collective action to build a more just science system that demonstrates a relational duty of care to all its participants. To achieve this, we urge the science community to harness the powerful...

Background Animal conservation often requires intensive management actions to improve reproductive output, yet any adverse effects of these may not be immediately apparent, particularly in threatened species with small populations and long lifespans. Hand-rearing is an example of a conservation management strategy which, while boosting populations,...

The EPSCoR Postdoc Integration Team was created to foster community between postdoctoral researchers from several EPSCoR institutions (Boise State University, Idaho State University, University of Idaho, University of Nevada-Reno, University of Wyoming) and also postdoctoral collaborators within EPSCoR-funded grants (e.g., Track-I GEM3 and Track-II...

Conservation genetics is a relatively new discipline, and yet has rapidly evolved in the last decade with massive advances in sequencing technologies. Here, we review the newest edition of an influential textbook in the field, “Conservation and the Genomics of Populations”, which seeks to bridge the transition from population genetics to genomics a...

The kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analyzed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to q...

Severe drought conditions and extreme weather events are increasing worldwide with climate change, threatening the persistence of native plant communities and ecosystems. Many studies have investigated the genomic basis of plant responses to drought. However, the extent of this research throughout the plant kingdom is unclear, particularly among sp...

The field of conservation biology has a long history of incorporating diverse disciplines into its ‘toolbox’ for improved outcomes. One such discipline is conservation genomics, which has experienced fast-paced growth and development over the last decade and offers exciting opportunities to help achieve the vision outlined in Aotearoa New Zealand’s...

Researchers have long debated which estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the methods used to generate markers, marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly u...

Climate change presents distinct ecological and physiological challenges to plants as extreme climate events become more common. Understanding how species have adapted to drought, especially ecologically important nonmodel organisms, will be crucial to elucidate potential biological pathways for drought adaptation and inform conservation strategies...

To conserve biological diversity in a changing world, managers must understand which species are vulnerable to the effects of climate change and whether there is sufficient capacity for these species to adapt. This is especially applicable to birds, who may experience changes in phenology (e.g., the timing of migration and/or breeding) in response...

Plant communities are composed of complex phenotypes that not only differ among taxonomic groups and habitats but also change over time within a species. Restoration projects (e.g., translocations, reseeding) can introduce new functional variation in plants, which further diversifies phenotypes and complicates our ability to identify locally adapti...

Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long-standing tools available to manage genetics - the pedigree - has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput se...

The apolipoprotein E4 (APOE4) allele represents the single greatest risk factor for late-onset Alzheimer's disease (AD) and accumulating evidence suggests that fragmentation with a toxic-gain of function may be a key molecular step associated with this risk. Recently, we demonstrated strong immunoreactivity of a 151 amino-terminal fragment of apoE4...

Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long‐standing tools available to manage genetics ‐ the pedigree ‐ has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput se...

Structural variants (SVs) are large rearrangements (> 50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, i.e. variation at genomic regions underpinning phenotype differences, that can have large effects on individual and populati...

Structural variants (SVs) are large rearrangements (> 50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, i.e. variation at genomic regions underpinning phenotype differences, that can have large effects on individual and populati...

Researchers have long debated which genomic estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the method used to generate genomic markers (e.g., reduced-representation sequencing, whole genome resequencing), marker qual...

Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long-standing tools available to manage genetics-the pedigree-has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequen...

Structural variants (SVs) are large rearrangements (> 50 bp) within the genome that impact the form and structure of chromosomes. As a result, SVs are a significant source of functional genomic diversity, i.e. variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While the...

Structural variants (SVs) are large rearrangements (> 50 bp) within the genome that impact the form and structure of chromosomes. As a result, SVs are a significant source of functional genomic diversity, i.e. variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While the...

1. To achieve the vision outlined in the national strategy for biodiversity, Te Mana o te Taiao, we will need to unite diverse disciplines, including conservation genetics/genomics. 2. As conservation genetic/genomic data generated for—and associated with—taonga (treasured) species is also taonga, we highlight the need for collaborative research p...

There is a gap in the conceptual framework linking genes to phenotypes (G2P) for non-model organisms, as most non-model organisms do not yet have genomic resources readily available. To address this, researchers often perform literature reviews to understand G2P linkages by curating a list of likely gene candidates, hinging upon other studies alrea...

Increased capability in the conservation genomics community, combined with decreased sequencing costs, is providing new opportunities for the application of whole-genome sequence data to enhance species recovery. Indeed, assessments of genome-wide diversity based on SNP data are already informing the conservation management of threatened species ar...

Increased capability in the conservation genomics community, combined with decreased sequencing costs, is providing new opportunities for the application of whole-genome sequence data to enhance species recovery. Indeed, assessments of genome-wide diversity based on SNP data are already informing the conservation management of threatened species ar...

Many species recovery programmes use pedigrees to understand the genetic ancestry of individuals to inform conservation management. However, incorrect parentage assignment may limit the accuracy of these pedigrees and subsequent management decisions. This is especially relevant for pedigrees that include wild individuals, where misassignment may no...

Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimise relatedness between individuals in an effort to avoid inbreeding, maximise diversity, and maintain e...

Reduced reproductive fitness due to maladaptive traits, like reduced fertility, hampers recovery efforts for critically endangered species. To identify putative structural variants on the Z-chromosome, we are developing a workflow to generate high resolution long-read sequence data for kākāpō (Strigops habroptilus) with known reproductive success...

Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimise relatedness between individuals in an effort to avoid inbreeding, maximise diversity, and maintain e...

Threatened species recovery programmes benefit from incorporating genomic data into conservation management strategies to enhance species recovery. However, a lack of readily available genomic resources, including conspecific reference genomes, often limits the inclusion of genomic data. Here, we investigate the utility of closely related high-qual...

Many researchers have used genotyping-by-sequencing to generate marker data since the method was published in PLoS ONE in 2011. Others have made modifications to the method resulting in different, but related, types of GBS data generated. Additional analysis pipelines have been developed, many of which are licensed under Free/Libre and Open Source...

Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing tech- nologies to inform conservation policy and the manage- ment of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective a...

Mulberry trees (Morus: Moraceae) growing in relatively undisturbed, open woodland areas of western Kentucky exhibit exceptionally large leaves (blades often >15 cm long). Fruit size is also longer than reported for other species, and leaf vein patterns are unique. Field observations, combined with the use of herbarium specimens and molecular data w...