Project description:We used custom Nimblegen microarrays representing whole-larval transcriptomes for two species (Papilio zelicaon [this submission] and Erynnis propertius [submitted seperately]) to assess gene expression differences affecting tolerance to climatic regimes. Many individuals were sourced from populations from the northern periphery and center of the species' (shared) range; these were each divided into groups treated under peripheral and central climate regimes, resulting in 4 experimental groups for each species (Peripheral Source, Peripheral treatment; Peripheral Source, Central Treatment; Central Source, Peripheral Treatment; Central Source, Central Treatment). Using technical microarray replicates allowed us to use ANOVA to identify genes whose expression may underlie local adaptation to climate (i.e., those showing an interaction term between source and population). Abstract: Population differences may determine geographic range shifts and adaptive evolution under climate change. Local adaptation in peripheral populations could preclude or slow range expansions, and populations with different genetic make-up could have distinct trajectories that produce complex spatial patterns of population change. To investigate the genetic extent of local responses to climate change, we exposed poleward-periphery and central populations of two Lepidoptera to reciprocal, common-garden climatic conditions and compared whole-transcriptome expression. We found significant expression differences between populations in both species. In addition, several hundred genes including genes involved in energy metabolism and oxidative stress responded in a localized fashion in the species that exhibits greater population structure and local adaptation. Expression levels of these genes are most divergent in the same environment in which we previously detected phenotypic divergence in metabolism. By contrast, we found no localized genes in the species with higher gene flow, reflecting the lack of previously observed local adaptation. These results suggest that population differences do not generalize easily, even for related species living in the same climate, but some taxa deserve population-level consideration when predicting the effects of climate change.

Project description:We used custom Nimblegen microarrays representing whole-larval transcriptomes for two species (Erynnis propertius [this submission] and Papilio zelicaon [submitted seperately]) to assess gene expression differences affecting tolerance to climatic regimes. Many individuals were sourced from populations from the northern periphery and center of the species' (shared) range; these were each divided into groups treated under peripheral and central climate regimes, resulting in 4 experimental groups for each species (Peripheral Source, Peripheral treatment; Peripheral Source, Central Treatment; Central Source, Peripheral Treatment; Central Source, Central Treatment). Using technical microarray replicates allowed us to use ANOVA to identify genes whose expression may underlie local adaptation to climate (i.e., those showing an interaction term between source and population). Abstract: Population differences may determine geographic range shifts and adaptive evolution under climate change. Local adaptation in peripheral populations could preclude or slow range expansions, and populations with different genetic make-up could have distinct trajectories that produce complex spatial patterns of population change. To investigate the genetic extent of local responses to climate change, we exposed poleward-periphery and central populations of two Lepidoptera to reciprocal, common-garden climatic conditions and compared whole-transcriptome expression. We found significant expression differences between populations in both species. In addition, several hundred genes including genes involved in energy metabolism and oxidative stress responded in a localized fashion in the species that exhibits greater population structure and local adaptation. Expression levels of these genes are most divergent in the same environment in which we previously detected phenotypic divergence in metabolism. By contrast, we found no localized genes in the species with higher gene flow, reflecting the lack of previously observed local adaptation. These results suggest that population differences do not generalize easily, even for related species living in the same climate, but some taxa deserve population-level consideration when predicting the effects of climate change.

Project description:We used custom Nimblegen microarrays representing whole-larval transcriptomes for two species (Papilio zelicaon [this submission] and Erynnis propertius [submitted seperately]) to assess gene expression differences affecting tolerance to climatic regimes. Many individuals were sourced from populations from the northern periphery and center of the species' (shared) range; these were each divided into groups treated under peripheral and central climate regimes, resulting in 4 experimental groups for each species (Peripheral Source, Peripheral treatment; Peripheral Source, Central Treatment; Central Source, Peripheral Treatment; Central Source, Central Treatment). Using technical microarray replicates allowed us to use ANOVA to identify genes whose expression may underlie local adaptation to climate (i.e., those showing an interaction term between source and population). Abstract: Population differences may determine geographic range shifts and adaptive evolution under climate change. Local adaptation in peripheral populations could preclude or slow range expansions, and populations with different genetic make-up could have distinct trajectories that produce complex spatial patterns of population change. To investigate the genetic extent of local responses to climate change, we exposed poleward-periphery and central populations of two Lepidoptera to reciprocal, common-garden climatic conditions and compared whole-transcriptome expression. We found significant expression differences between populations in both species. In addition, several hundred genes including genes involved in energy metabolism and oxidative stress responded in a localized fashion in the species that exhibits greater population structure and local adaptation. Expression levels of these genes are most divergent in the same environment in which we previously detected phenotypic divergence in metabolism. By contrast, we found no localized genes in the species with higher gene flow, reflecting the lack of previously observed local adaptation. These results suggest that population differences do not generalize easily, even for related species living in the same climate, but some taxa deserve population-level consideration when predicting the effects of climate change. Previously we sequenced and assembled whole larval transcriptome ESTs sourced from pooled central-population individuals subjected to environmental stressors (see O'Neil et al., 2008). From these assemblies custom Nimblegen microarrays were designed (Nimblegen, Inc.), representing 34,609 putative gene sequences for E. propertius (submitted separately) and 25,735 putative gene sequences for P. zelicaon (this submission). Probe designs sought 5 representative 60mer probes for E.propertius and 4 representative probes for P. zelicaon. Messenger RNA was was sampled from multiple individuals of each experimental group and pooled before being converted to cDNA and hybridized to technical replicate microarrays. Three technical replicates for each experimental group were used, for a total of 12 microarrays (per species). Microarray data were log2 transformed and quintile-normalized (Bolstad et al. 2003) on a per-species basis.

Project description:We used custom Nimblegen microarrays representing whole-larval transcriptomes for two species (Erynnis propertius [this submission] and Papilio zelicaon [submitted seperately]) to assess gene expression differences affecting tolerance to climatic regimes. Many individuals were sourced from populations from the northern periphery and center of the species' (shared) range; these were each divided into groups treated under peripheral and central climate regimes, resulting in 4 experimental groups for each species (Peripheral Source, Peripheral treatment; Peripheral Source, Central Treatment; Central Source, Peripheral Treatment; Central Source, Central Treatment). Using technical microarray replicates allowed us to use ANOVA to identify genes whose expression may underlie local adaptation to climate (i.e., those showing an interaction term between source and population). Abstract: Population differences may determine geographic range shifts and adaptive evolution under climate change. Local adaptation in peripheral populations could preclude or slow range expansions, and populations with different genetic make-up could have distinct trajectories that produce complex spatial patterns of population change. To investigate the genetic extent of local responses to climate change, we exposed poleward-periphery and central populations of two Lepidoptera to reciprocal, common-garden climatic conditions and compared whole-transcriptome expression. We found significant expression differences between populations in both species. In addition, several hundred genes including genes involved in energy metabolism and oxidative stress responded in a localized fashion in the species that exhibits greater population structure and local adaptation. Expression levels of these genes are most divergent in the same environment in which we previously detected phenotypic divergence in metabolism. By contrast, we found no localized genes in the species with higher gene flow, reflecting the lack of previously observed local adaptation. These results suggest that population differences do not generalize easily, even for related species living in the same climate, but some taxa deserve population-level consideration when predicting the effects of climate change. Previously we sequenced and assembled whole larval transcriptome ESTs sourced from pooled central-population individuals subjected to environmental stressors (see O'Neil et al., 2008). From these assemblies custom Nimblegen microarrays were designed (Nimblegen, Inc.), representing 34,609 putative gene sequences for E. propertius (this submission) and 25,735 putative gene sequences for P. zelicaon (submitted seperately). Probe designs sought 5 representative 60mer probes for E.propertius and 4 representative probes for P. zelicaon. Messenger RNA was was sampled from multiple individuals of each experimental group and pooled before being converted to cDNA and hybridized to technical replicate microarrays. Three technical replicates for each experimental group were used, for a total of 12 microarrays (per species). Microarray data were log2 transformed and quintile-normalized (Bolstad et al. 2003) on a per-species basis.

Project description:Only 59% of Alaska Native people have been adequately screened for colorectal cancer (CRC) despite having the highest reported incidence of CRC in the world. A new at-home multi-target stool DNA screening test (MT-sDNA; Cologuard) with high sensitivity for pre-cancerous polyps and CRC is now available. MT-sDNA has not been tested for feasibility or acceptability within the Alaska tribal health care delivery system, and it is unknown whether use of this new test will increase Alaska Native CRC screening rates. The long-term study goal is to improve screening and reduce CRC-attributable mortality. The objective of this application is to test the effectiveness of MT-sDNA for increasing CRC screening in Alaska Native communities using a mixed methods, community-based participatory research (CBPR) approach. The study will be conducted in collaboration with regional Tribal health organizations responsible for providing health care to geographically remote Alaska Native communities. Although the proposed implementation strategy is evidence-informed and promising, it is novel in that MT-sDNA has not been evaluated in the tribal health setting or among rural/remote populations. Using the Social Ecological Model, the research will be multi-level, examining influence on patients, providers, and tribal health organizations (THOs). This research study will pursue two specific aims: (1) Identify patient-, provider-, and system-level factors associated with CRC screening preferences, uptake, and follow-up; and (2) test the effectiveness of graded intensity MT-sDNA intervention in the Alaska Native community setting. For the first aim, focus groups with Alaska Native people who are not adherent to CRC screening guidelines and interviews with healthcare providers will be used to identify factors for future intervention. For the second aim, a three-arm cluster randomized controlled trial (high intensity with patient navigation, medium intensity with mailed reminders, usual care) will provide evidence on the MT-sDNA usefulness (MT-sDNA sample quality and neoplastic yield) as well as the first data on MT-sDNA follow up adherence rates in the Alaska Native population, which will inform plans to scale-up the intervention model. This research has the potential to sustainably improve public health by increasing CRC screening rates among a rural/remote tribal population as well as provide a model for other integrated health systems that provide care to high-risk or underserved populations in the U.S. and worldwide.

Project description:Domesticated animal populations often show profound reductions in predator avoidance and fear-related behavior compared to wild populations. These reductions are remarkably consistent and have been observed in a diverse array of taxa including fish, birds, and mammals. Experiments conducted in common environments indicate that these behavioral differences have a genetic basis. In this study, we quantified differences in fear-related behavior between wild and domesticated zebrafish strains and used microarray analysis to identify genes that may be associated with this variation. Compared to wild zebrafish, domesticated zebrafish spent more time near the water surface and were more likely to occupy the front of the aquarium nearest a human observer. Microarray analysis of the brain transcriptome identified high levels of population variation in gene expression, with 1,749 genes significantly differentially expressed among populations. Genes that varied among populations belonged to functional categories that included DNA repair, DNA photolyase activity, response to light stimulus, neuron development and axon guidance, cell death, iron-binding, chromatin reorganization, and homeobox genes. Comparatively fewer genes (112) differed between domesticated and wild strains with notable genes including gpr177 (wntless), selenoprotein P1a, synaptophysin and synaptoporin, and acyl-CoA binding domain containing proteins (acbd3 and acbd4). Microarray analysis identified a large number of genes that differed among zebrafish populations and may underlie behavioral domestication. Comparisons with similar microarray studies of domestication in rainbow trout and canids identified sixteen evolutionarily or functionally related genes that may represent components of shared molecular mechanisms underlying convergent behavioral evolution during vertebrate domestication. However, this conclusion must be tempered by limitations associated with comparisons among microarray studies and the low level of population-level replication inherent to these studies. RNA was extracted from the brains of fish from four behaviorally distinct strains of zebrafish and hybridized on Affymetrix microarrays. Brains from 2-5 individual fish of the same sex were pooled and homogenized together, for a total of two biological replicate pools per sex per strain (16 microarrays total).

Project description:Domesticated animal populations often show profound reductions in predator avoidance and fear-related behavior compared to wild populations. These reductions are remarkably consistent and have been observed in a diverse array of taxa including fish, birds, and mammals. Experiments conducted in common environments indicate that these behavioral differences have a genetic basis. In this study, we quantified differences in fear-related behavior between wild and domesticated zebrafish strains and used microarray analysis to identify genes that may be associated with this variation. Compared to wild zebrafish, domesticated zebrafish spent more time near the water surface and were more likely to occupy the front of the aquarium nearest a human observer. Microarray analysis of the brain transcriptome identified high levels of population variation in gene expression, with 1,749 genes significantly differentially expressed among populations. Genes that varied among populations belonged to functional categories that included DNA repair, DNA photolyase activity, response to light stimulus, neuron development and axon guidance, cell death, iron-binding, chromatin reorganization, and homeobox genes. Comparatively fewer genes (112) differed between domesticated and wild strains with notable genes including gpr177 (wntless), selenoprotein P1a, synaptophysin and synaptoporin, and acyl-CoA binding domain containing proteins (acbd3 and acbd4). Microarray analysis identified a large number of genes that differed among zebrafish populations and may underlie behavioral domestication. Comparisons with similar microarray studies of domestication in rainbow trout and canids identified sixteen evolutionarily or functionally related genes that may represent components of shared molecular mechanisms underlying convergent behavioral evolution during vertebrate domestication. However, this conclusion must be tempered by limitations associated with comparisons among microarray studies and the low level of population-level replication inherent to these studies.

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Hawaiian picture wing Drosophila sproati exhibit adaptive population divergence along a narrow climatic gradient on Hawaii Island

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