Search

Hybridization can provide evolutionary benefits (e.g., population resilience to climate change) through the introduction of adaptive alleles and increase of genetic diversity. Nevertheless, management strategies may be designed based only on the parental species within a hybrid zone, without considering the hybrids. This can lead to ineffective spatial management of species, which can directly harm population diversity and negatively impact food webs. Three species of rockfish (Brown Rockfish ( Sebastes caurinus ), Copper Rockfish ( S. auriculatus ), and Quillback Rockfish ( S. maliger )) are known to hybridize within Puget Sound, Washington, but genetic data from these species are used to infer population structure in the entire genus, including in species that do not hybridize. The goal of this project was to estimate the hybridization rates within the region and determine the effect of hybridization on geographic patterns of genetic structure. We sequenced 290 Brown, Copper, and Quillback rockfish using restriction-site associated DNA sequencing (RADseq) from four regions within and outside Puget Sound, Washington. We show that (i) hybridization within Puget Sound was asymmetrical, not recent, widespread among individuals, and relatively low level within the genome, (ii) hybridization affected population structure in Copper and Brown rockfish, but not in Quillback Rockfish and (iii) after taking hybridization into account we found limited directional dispersal in Brown and Copper rockfish, and evidence for two isolated populations in Quillback Rockfish. Our results suggest that rockfish population structure is species-specific, dependent on the extent of hybridization, and cannot be inferred from one species to another despite similar life history., Competing Interests: The authors declare no conflict of interest., (© 2024 The Author(s). Evolutionary Applications published by John Wiley & Sons Ltd. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

Maintaining upright posture in quiet standing is an important skill that is often disrupted by stroke. Despite extensive study of human standing, current understanding is incomplete regarding the muscle coordination strategies that produce the ground-on-foot force (F) that regulates translational and rotational accelerations of the body. Even less is understood about how stroke disrupts that coordination. Humans produce sagittal plane variations in the location (center of pressure, xCP) and orientation (Fx/Fz) of F that, along with the force of gravity, produce sagittal plane body motions. As F changes during quiet standing there is a strong correlation between the xCP and Fx/Fz time-varying signals within narrow frequency bands. The slope of the correlation varies systematically with frequency in non-disabled populations, is sensitive to changes in both environmental and neuromuscular control factors, and emerges from the interaction of body mechanics and neural control. This study characterized the xCP versus Fx/Fz relationship as frequency-dependent Intersection Point (IP) heights for the paretic and non-paretic legs of individuals with history of a stroke (n = 12) as well as in both legs of non-disabled controls (n = 22) to reveal distinguishing motor coordination patterns. No inter-leg difference of IP height was present in the control group. The paretic leg IP height was lower than the non-paretic, and differences from control legs were in opposite directions. These results quantify disrupted coordination that may characterize the paretic leg balance deficit and non-paretic leg compensatory behavior, providing a means of monitoring balance impairment and a target for therapeutic interventions., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: The authors report that Gruben, Ochs (prev. Boehm), and Nichols hold a US Patent related to this methodology. The authors report no other conflict of interest., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Wearable sensors offer a unique opportunity to study movement in ecological contexts - that is, outside the laboratory where movement happens in ordinary life. This article discusses the purpose, means, and impact of using wearable sensors to assess movement context, kinematics, and kinetics during locomotion, and how this information can be used to better understand and influence movement. We outline the types of information wearable sensors can gather and highlight recent developments in sensor technology, data analysis, and applications. We close with a vision for important future research and key questions the field will need to address to bring the potential benefits of wearable sensing to fruition., Competing Interests: Declaration of interests The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Rainbow trout ( Oncorhynchus mykiss ) are a partially migratory species wherein some individuals undergo long-distance anadromous migrations, and others stay as residents in their native freshwater streams. The decision to migrate is known to be highly heritable, and yet, the underlying genes and alleles associated with migration are not fully characterized. Here we used a pooled approach of whole-genome sequence data from migratory and resident trout of two native populations-Sashin Creek, Alaska and Little Sheep Creek, Oregon-to obtain a genome-wide perspective of the genetic architecture of resident and migratory life history. We calculated estimates of genetic differentiation, genetic diversity, and selection between the two phenotypes to locate regions of interest and then compared these associations between populations. We identified numerous genes and alleles associated with life history development in the Sashin Creek population with a notable area on chromosome 8 that may play a critical role in the development of the migratory phenotype. However, very few alleles appeared to be associated with life history development in the Little Sheep Creek system, suggesting population-specific genetic effects are likely important in the development of anadromy. Our results indicate that a migratory life history is not controlled by a singular gene or region but supports the idea that there are many independent ways for a migratory phenotype to emerge in a population. Therefore, conserving and promoting genetic diversity in migratory individuals is paramount to conserving these populations. Ultimately, our data add to a growing body of literature that suggests that population-specific genetic effects, likely mediated through environmental variation, contribute to life history development in rainbow trout., Competing Interests: The authors declare that they do not have any conflicts of interest., (© 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Biomonitoring surveys make use of metabarcoding tools to describe the community composition. These studies match their sequencing results against public genomic databases to identify the species. However, mitochondrial genomic reference data are yet incomplete, only a few genes may be available, or the suitability of existing sequence data is suboptimal for species level resolution. Here, we present a dedicated and cost-effective workflow with no DNA amplification for generating complete fish mitogenomes for the purpose of strengthening fish mitochondrial databases. Two different strategies using long fragment sequencing with Oxford Nanopore technology coupled with mitochondrial DNA enrichment were used. One where the enrichment is achieved by preferential isolation of mitochondria followed by DNA extraction and nuclear DNA depletion ("mitoenrichment"). A second enrichment approach takes advantage of the CRISPR Cas9 targeted scission on previously dephosphorylated DNA ("targeted mitosequencing"). The sequencing results varied between tissue, species, and integrity of the DNA. The mitoenrichment method yielded 0.17%-12.33% of sequences on target and a mean coverage ranging from 74.9 to 805-fold. The targeted mitosequencing experiment from native genomic DNA yielded 1.83%-55% of sequences on target and a 38 to 2123-fold mean coverage. These produced complete mitogenomes of species with homopolymeric regions, tandem repeats, and gene rearrangements. We demonstrate that deep sequencing of long fragments of native fish DNA can be achieved with low computational resources in a cost-effective manner, opening the discovery of mitogenomes of nonmodel or understudied fish taxa to a broad range of laboratories worldwide., (© 2023 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

The C≡C stretching frequencies of terminal alkynes appear in the "clear" window of vibrational spectra, so they are attractive and increasingly popular as site-specific probes in complicated biological systems like proteins, cells, and tissues. In this work, we collected infrared (IR) absorption and Raman scattering spectra of model compounds, artificial amino acids, and model proteins that contain terminal alkyne groups, and we used our results to draw conclusions about the signal strength and sensitivity to the local environment of both aliphatic and aromatic terminal alkyne C≡C stretching bands. While the IR bands of alkynyl model compounds displayed surprisingly broad solvatochromism, their absorptions were weak enough that alkynes can be ruled out as effective IR probes. The same solvatochromism was observed in model compounds' Raman spectra, and comparisons to published empirical solvent scales (including a linear regression against four meta-aggregated solvent parameters) suggested that the alkyne C≡C stretching frequency mainly reports on local electronic interactions (i.e., short-range electron donor-acceptor interactions) with solvent molecules and neighboring functional groups. The strong solvatochromism observed here for alkyne stretching bands introduces an important consideration for Raman imaging studies based on these signals. Raman signals for alkynes (especially those that are π-conjugated) can be exceptionally strong and should permit alkynyl Raman signals to function as probes at very low concentrations, as compared to other widely used vibrational probe groups like azides and nitriles. We incorporated homopropargyl glycine into a transmembrane helical peptide via peptide synthesis, and we installed p -ethynylphenylalanine into the interior of the Escherichia coli fatty acid acyl carrier protein using a genetic code expansion technique. The Raman spectra from each of these test systems indicate that alkynyl C≡C bands can act as effective and unique probes of their local biomolecular environments. We provide guidance for the best possible future uses of alkynes as solvatochromic Raman probes, and while empirical explanations of the alkyne solvatochromism are offered, open questions about its physical basis are enunciated.

This paper presents the effectsof the Variable Stiffness Foot (VSF) on lower-limb joint mechanics in level-ground walking. Persons with transtibial amputations use lower-limb prostheses to restore level-ground walking, and foot stiffness and geometry have been shown to be the main factors for evaluating foot prostheses. Previous studies have validated the semi-active and stiffness modulation capabilities of the VSF. The core aim of this study is to investigate the mechanical effects of adjusting stiffness on knee and ankle mechanics for prosthetic users wearing the VSF. For this study, seven human participants walked with three different stiffnesses (compliant, medium, stiff) of the VSF across two force plates in a motion capture lab. Linear mixed models were utilized to estimate the significance and coefficients of determinations for the regression of stiffness on several biomechanical metrics. A stiffer VSF led to decreased ankle dorsiflexion angle (p < 0.0001, r 2  = 0.90), increased ankle plantarflexor moment (p = 0.016, r 2  = 0.40), increased knee extension (p = 0.021, r 2  = 0.37), increased knee flexor moment (p = 0.0007, r 2  = 0.63), and decreased magnitudes of prosthetic energy storage (p < 0.0001, r 2  = 0.90), energy return (p = 0.0003, r 2  = 0.67), and power (p < 0.0001, r 2  = 0.74). These results imply lower ankle, knee, and hip moments, and more ankle angle range of motion using a less stiff VSF, which may be advantageous to persons walking with lower-limb prostheses. Responsive modulation of the VSF stiffness, according to these findings, could help overcome gait deviations associated with different slopes, terrain characteristics, or footwear., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Introduction: Loading of a residual limb within a prosthetic socket can cause tissue damage such as ulceration. Computational simulations may be useful tools for estimating tissue loading within the socket, and thus provide insights into how prosthesis designs affect residual limb-socket interface dynamics. The purpose of this study was to model and simulate residual limb-socket interface dynamics and evaluate the effects of varied prosthesis stiffness on interface dynamics during gait. Methods: A spatial contact model of a residual limb-socket interface was developed and integrated into a gait model with a below-knee amputation. Gait trials were simulated for four subjects walking with low, medium, and high prosthesis stiffness settings. The effects of prosthesis stiffness on interface kinematics, normal pressure, and shear stresses were evaluated. Results: Model-predicted values were similar to those reported previously in sensor-based experiments; increased stiffness resulted in greater average normal pressure and shear stress ( p < 0.05). Conclusions: These methods may be useful to aid experimental studies by providing insights into the effects of varied prosthesis design parameters or gait conditions on residual limb-socket interface dynamics. The current results suggest that these effects may be subject-specific., Competing Interests: Declaration of conflicting interests: The author(s) declared the following potential conflicts of interest with respect to the research, authorship, and/or publication of this article: Michael McGeehan, Kieran Nichols, and Michael Hahn declare no conflicts of interest for this work. Peter Adamczyk was a partner in Intelligent Prosthetic Systems, LLC, which created the Variable Stiffness Prosthesis used in this project., (© The Author(s) 2022.)

All species inevitably leave genetic traces in their environments, and the resulting environmental DNA (eDNA) reflects the species present in a given habitat. It remains unclear whether eDNA signals can provide quantitative metrics of abundance on which human livelihoods or conservation successes depend. Here, we report the results of a large eDNA ocean survey (spanning 86 000 km 2 to depths of 500 m) to understand the abundance and distribution of Pacific hake ( Merluccius productus ), the target of the largest finfish fishery along the west coast of the USA. We sampled eDNA in parallel with a traditional acoustic-trawl survey to assess the value of eDNA surveys at a scale relevant to fisheries management. Despite local differences, the two methods yield comparable information about the broad-scale spatial distribution and abundance. Furthermore, we find depth and spatial patterns of eDNA closely correspond to acoustic-trawl estimates for hake. We demonstrate the power and efficacy of eDNA sampling for estimating abundance and distribution and move the analysis eDNA data beyond sample-to-sample comparisons to management relevant scales. We posit that eDNA methods are capable of providing general quantitative applications that will prove especially valuable in data- or resource-limited contexts.

Introduction: Simulations based on computational musculoskeletal models are powerful tools for evaluating the effects of potential biomechanical interventions, such as implementing a novel prosthesis. However, the utility of simulations to evaluate the effects of varied prosthesis design parameters on gait mechanics has not been fully realized due to the lack of a readily-available limb loss-specific gait model and methods for efficiently modeling the energy storage and return dynamics of passive foot prostheses. The purpose of this study was to develop and validate a forward simulation-capable gait model with lower-limb loss and a semi-active variable-stiffness foot (VSF) prosthesis., Methods: A seven-segment 28-DoF gait model was developed and forward kinematics simulations, in which experimentally observed joint kinematics were applied and the resulting contact forces under the prosthesis evolved accordingly, were computed for four subjects with unilateral below-knee amputation walking with a VSF., Results: Model-predicted resultant ground reaction force (GRFR) matched well under trial-specific optimized parameter conditions (mean R2: 0.97, RMSE: 7.7% body weight (BW)) and unoptimized (subject-specific, but not trial-specific) parameter conditions (mean R2: 0.93, RMSE: 12% BW). Simulated anterior-posterior center of pressure demonstrated a mean R2 = 0.64 and RMSE = 14% foot length. Simulated kinematics remained consistent with input data (0.23 deg RMSE, R2 > 0.99) for all conditions., Conclusions: These methods may be useful for simulating gait among individuals with lower-limb loss and predicting GRFR arising from gait with novel VSF prostheses. Such data are useful to optimize prosthesis design parameters on a user-specific basis., (Copyright © 2021 by ASME.)

Associations between behaviors and the development of different life history tactics have been documented in several species of salmon, trout, and charr. While it is well known that such behaviors are heritable the genes and molecular pathways connected to these behaviors remain unknown. We used an RNA-seq approach to identify genes and molecular pathways differentially regulated in brain tissue between "shy" and "bold" brook trout (Salvelinus fontinalis). A small number of genes were differentially expressed between the behavioral types at several months after hatching and two years of age. Pathway analysis revealed that EIF2 signaling differed consistently between shy and bold individuals suggesting large-scale differences in protein synthesis between behavioral types in the brain. Additionally, the RNA-seq data were used to find polymorphisms within the brook trout genome and a GWAS approach was used to test for statistical associations between genetic variants and behavior type. One allele located in a transcription factor (TSHZ3) contained a protein-coding non-synonymous SNP suggesting that functional variation within TSHZ3 is connected to the development of different behaviors. These results suggest that the molecular basis of behavioral development is complex and due to the differential expression of many genes involved in a wide-range of different molecular pathways., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Concepts of evolutionary biology suggest that morphological change may occur by rare punctual but rather large changes, or by more steady and gradual transformations. It can therefore be asked whether genetic changes underlying morphological, physiological, and/or behavioral innovations during evolution occur in a punctual manner, whereby a single mutational event has prominent phenotypic consequences, or if many consecutive alterations in the DNA over longer time periods lead to phenotypic divergence. In the marine teleost, sablefish ( Anoplopoma fimbria ), complementary genomic and genetic studies led to the identification of a sex locus on the Y Chromosome. Further characterization of this locus resulted in identification of the transforming growth factor, beta receptor 1a ( tgfbr1a ) gene, gonadal somatic cell derived factor ( gsdf ), as the main candidate for fulfilling the master sex determining (MSD) function. The presence of different X and Y Chromosome copies of this gene indicated that the male heterogametic (XY) system of sex determination in sablefish arose by allelic diversification. The gsdfY gene has a spatio-temporal expression profile characteristic of a male MSD gene. We provide experimental evidence demonstrating a pivotal role of a transposable element (TE) for the divergent function of gsdfY By insertion within the gsdfY promoter region, this TE generated allelic diversification by bringing cis -regulatory modules that led to transcriptional rewiring and thus creation of a new MSD gene. This points out, for the first time in the scenario of MSD gene evolution by allelic diversification, a single, punctual molecular event in the appearance of a new trigger for male development., (© 2021 Herpin et al.; Published by Cold Spring Harbor Laboratory Press.)

Passive energy storage and return (ESR) feet are current performance standard in lower limb prostheses. A recently developed semi-active variable-stiffness foot (VSF) prosthesis balances the simplicity of a passive ESR device with the adaptability of a powered design. The purpose of this study was to model and simulate the ESR properties of the VSF prosthesis. The ESR properties of the VSF were modeled as a lumped parameter overhung beam. The overhung length is variable, allowing the model to exhibit variable ESR stiffness. Foot-ground contact was modeled using sphere-to-plane contact models. Contact parameters were optimized to represent the geometry and dynamics of the VSF and its foam base. Static compression tests and gait were simulated. Simulation outcomes were compared to corresponding experimental data. Stiffness of the model matched that of the physical VSF (R2: 0.98, root-mean-squared error (RMSE): 1.37 N/mm). Model-predicted resultant ground reaction force (GRFR) matched well under optimized parameter conditions (R2: 0.98, RMSE: 5.3% body weight,) and unoptimized parameter conditions (R2: 0.90, mean RMSE: 13% body weight). Anterior-posterior center of pressure matched well with R2 > 0.94 and RMSE < 9.5% foot length in all conditions. The ESR properties of the VSF were accurately simulated under benchtop testing and dynamic gait conditions. These methods may be useful for predicting GRFR arising from gait with novel prostheses. Such data are useful to optimize prosthesis design parameters on a user-specific basis., (Copyright © 2021 by ASME.)

The understanding of the evolution of variable sex determination mechanisms across taxa requires comparative studies among closely related species. Following the fate of a known master sex-determining gene, we traced the evolution of sex determination in an entire teleost order (Esociformes). We discovered that the northern pike ( Esox lucius ) master sex-determining gene originated from a 65 to 90 million-year-old gene duplication event and that it remained sex linked on undifferentiated sex chromosomes for at least 56 million years in multiple species. We identified several independent species- or population-specific sex determination transitions, including a recent loss of a Y chromosome. These findings highlight the diversity of evolutionary fates of master sex-determining genes and the importance of population demographic history in sex determination studies. We hypothesize that occasional sex reversals and genetic bottlenecks provide a non-adaptive explanation for sex determination transitions., Competing Interests: QP, RF, EJ, HD, AH, BK, ER, FG, WL, LB, MT, SC, ES, GD, Fv, SC, JL, HV, KO, RG, CE, JL, CR, HH, RT, PD, KN, LJ, HP, CK, EI, VT, MS, JP, YG No competing interests declared, (© 2021, Pan et al.)

Dam construction and longitudinal river habitat fragmentation disrupt important life histories and movement of aquatic species. This is especially true for Oncorhynchus mykiss that exhibits both migratory (steelhead) and non-migratory (resident rainbow) forms. While the negative effects of dams on salmonids have been extensively documented, few studies have had the opportunity to compare population genetic diversity and structure prior to and following dam removal. Here we examine the impacts of the removal of two dams on the Elwha River on the population genetics of O. mykiss. Genetic data were produced from >1200 samples collected prior to dam removal from both life history forms, and post-dam removal from steelhead. We identified three genetic clusters prior to dam removal primarily explained by isolation due to dams and natural barriers. Following dam removal, genetic structure decreased and admixture increased. Despite large O. mykiss population declines after dam construction, we did not detect shifts in population genetic diversity or allele frequencies of loci putatively involved in migratory phenotypic variation. Steelhead descendants from formerly below and above dammed populations recolonized the river rapidly after dam removal, suggesting that dam construction did not significantly reduce genetic diversity underlying O. mykiss life history strategies. These results have significant evolutionary implications for the conservation of migratory adaptive potential in O. mykiss populations above current anthropogenic barriers.

Variation in age at maturity is an important contributor to life history and demographic variation within and among species. The optimal age at maturity can vary by sex, and the ability of each sex to evolve towards its fitness optimum depends on the genetic architecture of maturation. Using GWAS of RAD sequencing data, we show that age at maturity in Chinook salmon exhibits sex-specific genetic architecture, with age at maturity in males influenced by large (up to 20 Mb) male-specific haplotypes. These regions showed no such effect in females. We also provide evidence for translocation of the sex-determining gene between two different chromosomes. This has important implications for sexually antagonistic selection, particularly that sex linkage of adaptive genes may differ within and among populations based on chromosomal location of the sex-determining gene. Our findings will facilitate research into the genetic causes of shifting demography in Chinook salmon as well as a better understanding of sex determination in this species and Pacific salmon in general., (© 2020 John Wiley & Sons Ltd.)

Venous thromboembolism (VTE), composed of pulmonary embolism and deep venous thrombosis, is a significant cause of maternal mortality in the developed world. Normal physiological changes of pregnancy increase coagulability, which is compounded by patient-inherited and acquired risk factors. Depending on these risks and peripartum stage, the benefits of thromboprophylaxis can outweigh potential side effects. Diagnosis requires cautious clinical acumen because many symptoms of normal pregnancy mimic those of VTE and algorithmic tools used in the nonpregnant population are not equally applicable. Choice of imaging technique must account for potential risk to the fetus and altered test accuracy (sensitivity and specificity) in the setting of pregnancy. When VTE is diagnosed, anticoagulation is the backbone of treatment, with more advanced therapies being options for those with right ventricular dysfunction or unstable hemodynamics. Overall, pregnancy-associated VTE is complex, and management decisions should be individualized and informed by patient preferences., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

Delimiting intraspecific genetic variation in harvested species is crucial to the assessment of population status for natural resource management and conservation purposes. Here, we evaluated genetic population structure in lingcod ( Ophiodon elongatus ), a commercially and recreationally important fishery species along the west coast of North America. We used 16,749 restriction site-associated DNA sequencing (RADseq) markers, in 611 individuals collected from across the bulk of the species range from Southeast Alaska to Baja California, Mexico. In contrast to previous population genetic work on this species, we found strong evidence for two distinct genetic clusters. These groups separated latitudinally with a break near Point Reyes off Northern California, and there was a high frequency of admixed individuals in close proximity to the break. F-statistics corroborate this genetic break between northern and southern sampling sites, although most loci are characterized by low F ST values, suggesting high gene flow throughout most of the genome. Outlier analyses identified 182 loci putatively under divergent selection, most of which mapped to a single genomic region. When individuals were grouped by cluster assignment (northern, southern, and admixed), 71 loci were fixed between the northern and southern cluster, all of which were identified in the outlier scans. All individuals identified as admixed exhibited near 50:50 assignment to northern and southern clusters and were heterozygous for most fixed loci. Alignments of RADseq loci to a draft lingcod genome assembly and three other teleost genomes with chromosome-level assemblies suggest that outlier and fixed loci are concentrated on a single chromosome. Similar genomic patterns have been attributed to chromosomal inversions in diverse taxonomic groups. Regardless of the evolutionary mechanism, these results represent novel observations of genetic structure in lingcod and designate clear evolutionary units that could be used to inform fisheries management., Competing Interests: None declared., (© 2020 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

In studying the causative mechanisms behind migration and life history, the salmonids-salmon, trout, and charr-are an exemplary taxonomic group, as life history development is known to have a strong genetic component. A double inversion located on chromosome 5 in rainbow trout (Oncorhynchus mykiss) is associated with life history development in multiple populations, but the importance of this inversion has not been thoroughly tested in conjunction with other polymorphisms in the genome. To that end, we used a high-density SNP chip to genotype 192 F1 migratory and resident rainbow trout and focused our analyses to determine whether this inversion is important in life history development in a well-studied population of rainbow trout from Southeast Alaska. We identified 4,994 and 436 SNPs-predominantly outside of the inversion region-associated with life history development in the migrant and resident familial lines, respectively. Although F1 samples showed genomic patterns consistent with the double inversion on chromosome 5 (reduced observed and expected heterozygosity and an increase in linkage disequilibrium), we found no statistical association between the inversion and life history development. Progeny produced by crossing resident trout and progeny produced by crossing migrant trout both consisted of a mix of migrant and resident individuals, irrespective of the individuals' inversion haplotype on chromosome 5. This suggests that although the inversion is present at a low frequency, it is not strongly associated with migration as it is in populations of Oncorhynchus mykiss from lower latitudes., Competing Interests: The authors have declared that no competing interests exist.

The Dungeness crab is an economically and ecologically important species distributed along the North American Pacific coast. To predict how Dungeness crab may physiologically respond to future global ocean change on a molecular level, we performed untargeted metabolomic approaches on individual Dungeness crab juveniles reared in treatments that mimicked current and projected future pH and dissolved oxygen conditions. We found 94 metabolites and 127 lipids responded in a condition-specific manner, with a greater number of known compounds more strongly responding to low oxygen than low pH exposure. Pathway analysis of these compounds revealed that juveniles may respond to low oxygen through evolutionarily conserved processes including downregulating glutathione biosynthesis and upregulating glycogen storage, and may respond to low pH by increasing ATP production. Most interestingly, we found that the response of juveniles to combined low pH and low oxygen exposure was most similar to the low oxygen exposure response, indicating low oxygen may drive the physiology of juvenile crabs more than pH. Our study elucidates metabolic dynamics that expand our overall understanding of how the species might respond to future ocean conditions and provides a comprehensive dataset that could be used in future ocean acidification response studies.

Whole-genome duplications (WGDs) have occurred repeatedly and broadly throughout the evolutionary history of eukaryotes. However, the effects of WGD on genome function and evolution remain unclear. The salmonid WGD that occurred approximately 88 million years ago presents an excellent opportunity for studying the effects of WGD as ∼10-15% of each salmonid genome still exhibits tetrasomic inheritance. Herein, we utilized the rainbow trout ( Oncorhynchus mykiss ) genome assembly and brain transcriptome data to examine the fate of gene pairs (ohnologs) following the salmonid whole-genome duplication. We find higher sequence identity between ohnologs located within known tetrasomic regions than between ohnologs found in disomic regions, and that tetrasomically inherited ohnologs showed greater similarity in patterns of gene expression and per ohnolog were lower expressed, than disomically inherited ohnologs. Enrichment testing for Gene Ontology terms identified 49 over-represented terms in tetrasomically inherited ohnologs compared to disomic ohnologs. However, why these ohnologs are retained as tetrasomic is difficult to answer. It could be that we have identified salmonid specific "dangerous duplicates", that is, genes that cannot take on new roles following WGD. Alternatively, there may be adaptive advantages for retaining genes as functional duplicates in tetrasomic regions, as presumably, movement of these genes into disomic regions would affect both their sequence identity and their gene expression patterns., (Copyright © 2019 Campbell et al.)

Genetic selection is often implicated as the underlying cause of heritable phenotypic differences between hatchery and wild populations of steelhead trout ( Oncorhynchus mykiss ) that also differ in lifetime fitness. Developmental plasticity, which can also affect fitness, may be mediated by epigenetic mechanisms such as DNA methylation. Our previous study identified significant differences in DNA methylation between adult hatchery- and natural-origin steelhead from the same population that could not be distinguished by DNA sequence variation. In the current study, we tested whether hatchery-rearing conditions can influence patterns of DNA methylation in steelhead with known genetic backgrounds, and assessed the stability of these changes over time. Eyed-embryos from 22 families of Methow River steelhead were split across traditional hatchery tanks or a simulated stream-rearing environment for 8 months, followed by a second year in a common hatchery tank environment. Family assignments were made using a genetic parentage analysis to account for relatedness among individuals. DNA methylation patterns were examined in the liver, a relatively homogeneous organ that regulates metabolic processes and somatic growth, of juveniles at two time points: after eight months of rearing in either a tank or stream environment and after a subsequent year of rearing in a common tank environment. Further, we analyzed DNA methylation in the sperm of mature 2-year-old males from the earlier described treatments to assess the potential of environmentally-induced changes to be passed to offspring. Hepatic DNA methylation changes in response to hatchery versus stream-rearing in yearling fish were substantial, but few persisted after a second year in the tank environment. However, the early rearing environment appeared to affect how fish responded to developmental and environmental signals during the second year since novel DNA methylation differences were identified in the livers of hatchery versus stream-reared fish after a year of common tank rearing. Furthermore, we found profound differences in DNA methylation due to age, irrespective of rearing treatment. This could be due to smoltification associated changes in liver physiology after the second year of rearing. Although few rearing-treatment effects were observed in the sperm methylome, strong family effects were observed. These data suggest limited potential for intergenerational changes, but highlight the importance of understanding the effects of kinship among studied individuals in order to properly analyze and interpret DNA methylation data in natural populations. Our work is the first to study family effects and temporal dynamics of DNA methylation patterns in response to hatchery-rearing.

Quiet standing is a mechanically unstable postural objective that humans typically perform with ease. Control of upright posture requires stabilization of both translational and rotational degrees-of-freedom that is accomplished by neuro-muscular coordination. This coordination produces a force at the ground-foot interface (F) that is quantified by magnitude, direction (θ F ), and point of application (center-of-pressure, CP). Previous research has shown that the nervous system controls muscle activation such that CP motion occurs at both slow and fast time scales. However, it is unknown how θ F varies with respect to CP and how that relationship varies across time scales. We present a novel method for assessing the frequency-dependent relative variation in θ F and CP. The center-of-pressure (CP) and direction of the ground-on-foot force (F) in the sagittal-plane during quiet standing were decomposed into 0.2 Hz-width frequency bands within 0.4-8.0 Hz. The relation between the direction and CP was approximately linear with a slope positively related to frequency. These frequency-dependent features of F have critical implications for understanding balance strategy because the translational and rotational acceleration effects of F were coupled, but with opposite phasing at high versus low frequencies. Such results suggest a system tuned for one stability mode at low frequencies and another mode at higher frequencies. This frequency-wise approach to examining the translational and rotational effects of humans' preferred F may be useful for establishing balance rehabilitation metrics, directing study of the underlying neural mechanisms responsible for the observed coordination, and for setting a biometric standard to inform biomimetic prosthetics and robotics., (Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.)

While the goal of most conservation hatchery programs is to produce fish that are genetically and phenotypically indistinguishable from the wild stocks they aim to restore, there is considerable evidence that salmon and steelhead reared in hatcheries differ from wild fish in phenotypic traits related to fitness. Some evidence suggests that these phenotypic differences have a genetic basis ( e.g. , domestication selection) but another likely mechanism that remains largely unexplored is that differences between hatchery and wild populations arise as a result of environmentally-induced heritable epigenetic change. As a first step toward understanding the potential contribution of these two possible mechanisms, we describe genetic and epigenetic variation in hatchery and natural-origin adult steelhead, Oncorhynchus mykiss , from the Methow River, WA. Our main objectives were to determine if hatchery and natural-origin fish could be distinguished genetically and whether differences in epigenetic programming (DNA methylation) in somatic and germ cells could be detected between the two groups. Genetic analysis of 72 fish using 936 SNPs generated by Restriction Site Associated DNA Sequencing (RAD-Seq) did not reveal differentiation between hatchery and natural-origin fish at a population level. We performed Reduced Representation Bisulfite Sequencing (RRBS) on a subset of 10 hatchery and 10 natural-origin fish and report the first genome-wide characterization of somatic (red blood cells (RBCs)) and germ line (sperm) derived DNA methylomes in a salmonid, from which we identified considerable tissue-specific methylation. We identified 85 differentially methylated regions (DMRs) in RBCs and 108 DMRs in sperm of steelhead reared for their first year in a hatchery environment compared to those reared in the wild. This work provides support that epigenetic mechanisms may serve as a link between hatchery rearing and adult phenotype in steelhead; furthermore, DMRs identified in germ cells (sperm) highlight the potential for these changes to be passed on to future generations., (Copyright © 2018 Gavery et al.)

Objective: Satellite pediatric emergency departments (PEDs) have emerged as a strategy to increase patient capacity. We sought to determine the impact on patient visits, physician fee collections, and value of emergency department (ED) time at the primary PED after opening a nearby satellite PED. We also illustrate the spatial distribution of patient demographics and overlapping catchment areas for the primary and satellite PEDs using geographical information system., Methods: A structured, financial retrospective review was conducted. Aggregate patient demographic data and billing data were collected regarding physician fee charges, collections, and patient visits for both PEDs. All ED visits from January 2009 to December 2013 were analyzed. Geographical information system mapping using ArcGIS mapped ED patient visits., Results: Patient visits at the primary PED were 53,050 in 2009 before the satellite PED opened. The primary PED visits increased after opening the satellite PED to 55,932 in 2013. The satellite PED visits increased to 21,590 in 2013. Collections per visit at the primary PED decreased from $105.13 per visit in 2011 to $86.91 per visit in 2013. Total collections at the satellite PED decreased per visit from $155.41 per visit in 2011 to $128.53 per visit in 2013., Conclusions: After opening a nearby satellite PED, patient visits at the primary PED did not substantially decrease, suggesting that there was a previously unrecognized demand for PED services. The collections per ED visit were greater at the satellite ED, likely due to a higher collection rate.

Sex-bias in gene expression is a mechanism that can generate phenotypic variance between the sexes, however, relatively little is known about how patterns of sex-bias vary during development, and how variable sex-bias is between different populations. To that end, we measured sex-bias in gene expression in the brain transcriptome of rainbow trout (Oncorhynchus mykiss) during the first two years of development. Our sampling included from the fry stage through to when O. mykiss either migrate to the ocean or remain resident and undergo sexual maturation. Samples came from two F1 lines: One from migratory steelhead trout and one from resident rainbow trout. All samples were reared in a common garden environment and RNA sequencing (RNA-seq) was used to estimate patterns of gene expression. A total of 1,716 (4.6% of total) genes showed evidence of sex-bias in gene expression in at least one time point. The majority (96.7%) of sex-biased genes were differentially expressed during the second year of development, indicating that patterns of sex-bias in expression are tied to key developmental events, such as migration and sexual maturation. Mapping of differentially expressed genes to the O. mykiss genome revealed that the X chromosome is enriched for female upregulated genes, and this may indicate a lack of dosage compensation in rainbow trout. There were many more sex-biased genes in the migratory line than the resident line suggesting differences in patterns of gene expression in the brain between populations subjected to different forces of selection. Overall, our results suggest that there is considerable variation in the extent and identity of genes exhibiting sex-bias during the first two years of life. These differentially expressed genes may be connected to developmental differences between the sexes, and/or between adopting a resident or migratory life history.

Next generation sequencing techniques have revolutionized the collection of genome and transcriptome data from nonmodel organisms. This manuscript details the application of restriction site-associated DNA sequencing (RADseq) to generate a marker-dense genetic map for Brook Trout ( Salvelinus fontinalis ). The consensus map was constructed from three full-sib families totaling 176 F 1 individuals. The map consisted of 42 linkage groups with a total female map size of 2502.5 cM, and a total male map size of 1863.8 cM. Synteny was confirmed with Atlantic Salmon for 38 linkage groups, with Rainbow Trout for 37 linkage groups, Arctic Char for 36 linkage groups, and with a previously published Brook Trout linkage map for 39 linkage groups. Comparative mapping confirmed the presence of 8 metacentric and 34 acrocentric chromosomes in Brook Trout. Six metacentric chromosomes seem to be conserved with Arctic Char suggesting there have been at least two species-specific fusion and fission events within the genus Salvelinus In addition, the sex marker ( sdY ; sexually dimorphic on the Y chromosome) was mapped to Brook Trout BC35, which is homologous with Atlantic Salmon Ssa09qa, Rainbow Trout Omy25, and Arctic Char AC04q. Ultimately, this linkage map will be a useful resource for studies on the genome organization of Salvelinus , and facilitates comparisons of the Salvelinus genome with Salmo and Oncorhynchus ., (Copyright © 2017 Hale et al.)

Many migratory traits are heritable, but there is a paucity of evidence identifying the molecular mechanisms underlying differentiation in alternative migratory tactics, or in linking variation in gene expression to migratory behaviors. To that end, we examined differential gene expression in the brain transcriptome between young steelhead trout that had undergone the smoltification process, and resident rainbow trout (Oncorhynchus mykiss) from Sashin Creek, Alaska. Samples were sequenced from two time points: immediately before (at 20months of age) and during (2years of age) the presumed peak of smoltification. Smolt and resident individuals came from two genetic crosses, one where both parents were migratory, and another where both parents were residents. A total of 533 (1.9%) genes were differentially expressed between crosses, or between smolt and resident samples. These genes include some candidate migratory genes (such as POMC), as well as genes with no previous known involvement in the migratory process. Progeny from resident parents showed more upregulated genes than progeny from migrant parents at both time points. Pathway analysis showed enrichment in 227 biological pathways between cross type, and 171 biological pathways were enriched between residents and smolts. Enriched pathways had connections to many biofunctions, and most were only enriched in one contrast. However, pathways connected to phototransduction were enriched between both cross type and migratory tactics in 11 out of 12 contrasts, suggesting there are fundamental differences in how smolts and residents process light in the brain. The genes and pathways described herein constitute an a priori candidate list for future studies of migration in other populations of O. mykiss, and other migratory species., (Published by Elsevier Inc.)

Conservation of life history variation is an important consideration for many species with trade-offs in migratory characteristics. Many salmonid species exhibit both resident and migratory strategies that capitalize on benefits in freshwater and marine environments. In this study, we investigated genomic signatures for migratory life history in collections of resident and anadromous Oncorhynchus nerka (Kokanee and Sockeye Salmon, respectively) from two lake systems, using ~2,600 SNPs from restriction-site-associated DNA sequencing (RAD-seq). Differing demographic histories were evident in the two systems where one pair was significantly differentiated (Redfish Lake, F ST  = 0.091 [95% confidence interval: 0.087 to 0.095]) but the other pair was not (Alturas Lake, F ST  = -0.007 [-0.008 to -0.006]). Outlier and association analyses identified several candidate markers in each population pair, but there was limited evidence for parallel signatures of genomic variation associated with migration. Despite lack of evidence for consistent markers associated with migratory life history in this species, candidate markers were mapped to functional genes and provide evidence for adaptive genetic variation within each lake system. Life history variation has been maintained in these nearly extirpated populations of O. nerka, and conservation efforts to preserve this diversity are important for long-term resiliency of this species.

Cell-based therapeutics, such as marrow or peripheral blood stem cell transplantation, are a standard of care for certain malignancies. More recently, a wider variety of cell-based therapeutics including the use of mesenchymal stromal/stem cells, T-cells, and others show great promise in a wider range of diseases. With increased efforts to expand cell-based treatments to several clinical settings, many institutions around the world have developed programs to explore cellular therapy's potential for safe and effective applications. In legitimate investigations, usually conducted through academic centers or biotechnology industry-sponsored efforts, these studies are regulated and peer-reviewed to ensure safety and clear determination of potential efficacy. However, in some cases, the use of cell-based approaches is conducted with insufficient preclinical data, scientific rationale, and/or study plan for the diseases claimed to be treated, with patients being charged for these services without clear evidence of clinical benefit. In this context, patients may not be properly informed regarding the exact treatment they are receiving within a consenting process that may not be completely valid or ethical. Here, the authors emphasize the importance of distinguishing "proven cell-based therapies" from "unproven" and unauthorized cell-based therapies. This publication also addresses the necessity for improved communication between the different stakeholders in the field, patient associations, and advocacy groups in particular, to favor medical innovation and provide legitimate benefits to patients. Considering the progressive growth of cell-based treatments, their increasing therapeutic value and the expectation that society has about these therapies, it is critically important to protect patients and ensure that the risk/benefit ratio is favorable. This paper is a review article. Literature referred to in this paper has been listed in the references section. The datasets supporting the conclusions of this article are available online by searching PubMed. Some original points in this article come from the laboratory practice in our research centers and the authors' experiences., Competing Interests: There are no conflicts of interest.

Daphnia can develop tolerance to cadmium (Cd) after multi-generational exposures. Until now, Cd tolerance in this crustacean was thought to be mainly due to its sequestration via induction of metallothioneins (MTs). Our research supports other studies showing microRNAs (miRNAs) also play a role in this enhanced tolerance. We induced Cd tolerance in Daphnia pulex after exposing them for 25 generations and examined the maintenance of enhanced Cd tolerance under a Cd-free environment for an additional three generations. Acute Cd tolerance as well as long-term effects on population dynamics were measured in selected generations via 48h LC50 tests and 21 d reproductive tests, respectively. Cd tolerance was associated with differential expression of 10 miRNAs (miR-2, miR-33, miR-92, miR-96, miR-153, miR-252, miR-279, miR-283, miR-305 and miR-615). Pathway analysis revealed these miRNAs might increase Cd tolerance by suppressing cellular growth and proliferation by GTPase and cuticle protein pathways, which switch cellular energy allocation to detoxification processes. Moreover, we found increased Cd tolerance is related with induction of MT3 and MT4 and a subsequent downregulation of MT1 and MT3 expression when animals are moved to a Cd-free environment. This is the first study linking aquatic invertebrate miRNAs with induced tolerance to environmental stressors., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Migration is essential for the reproduction and survival of many animals, yet little is understood about its underlying molecular mechanisms. We used the salmonid Oncorhynchus mykiss to gain mechanistic insight into smoltification, which is a morphological, physiological and behavioural transition undertaken by juveniles in preparation for seaward migration. O. mykiss is experimentally tractable and displays intra- and interpopulation variation in migration propensity. Migratory individuals can produce nonmigratory progeny and vice versa, indicating a high degree of phenotypic plasticity. One potential way that phenotypic plasticity might be linked to variation in migration-related life history tactics is through epigenetic regulation of gene expression. To explore this, we quantitatively measured genome-scale DNA methylation in fin tissue using reduced representation bisulphite sequencing of F2 siblings produced from a cross between steelhead (migratory) and rainbow trout (nonmigratory) lines. We identified 57 differentially methylated regions (DMRs) between smolt and resident O. mykiss juveniles. DMRs were high in magnitude, with up to 62% differential methylation between life history types, and over half of the gene-associated DMRs were in transcriptional regulatory regions. Many of the DMRs encode proteins with activity relevant to migration-related transitions (e.g. circadian rhythm pathway, nervous system development, protein kinase activity). This study provides the first evidence of a relationship between epigenetic variation and life history divergence associated with migration-related traits in any species., (© 2015 John Wiley & Sons Ltd.)

Daphnia pulex is a widely used toxicological model and is known for its sensitivity to cadmium (Cd). Recent research suggests that microRNAs (miRNAs) play a critical role in animal responses to heavy metals. To investigate the functions of D. pulex miRNAs under Cd exposure, we analyzed the miRNA profiles of D. pulex after 48 h using miRNA microarrays and validated our findings by q-PCR. miRNA dpu-let-7 was identified as a stably expressed gene and used as a reference. We identified 22 and 21 differentially expressed miRNAs under low (20 μg/L CdCl2) and high-exposure (40 μg/L CdCl2) concentrations compared to controls, respectively. Cellular functions of predicted miRNA target Cd-responsive genes included oxidative stress, ion transport, mitochondrial damage, and DNA repair. An insulin-related network was also identified in relation to several Cd-responsive miRNAs. The expression of three predicted target genes for miR-71 and miR-210 were evaluated, and expression of two of them (SCN2A and SLC31A1) was negatively correlated with the expression of their regulator miRNAs. We show miR-210 is hypoxia-responsive in D. pulex and propose Cd and hypoxia induce miR-210 via a same HIF1α modulated pathway. Collectively, this research advances our understanding on the role of miRNAs in response to heavy-metal exposure.

The Opisthokonta are a eukaryotic supergroup divided in two main lineages: animals and related protistan taxa, and fungi and their allies [1, 2]. There is a great diversity of lifestyles and morphologies among unicellular opisthokonts, from free-living phagotrophic flagellated bacterivores and filopodiated amoebas to cell-walled osmotrophic parasites and saprotrophs. However, these characteristics do not group into monophyletic assemblages, suggesting rampant convergent evolution within Opisthokonta. To test this hypothesis, we assembled a new phylogenomic dataset via sequencing 12 new strains of protists. Phylogenetic relationships among opisthokonts revealed independent origins of filopodiated amoebas in two lineages, one related to fungi and the other to animals. Moreover, we observed that specialized osmotrophic lifestyles evolved independently in fungi and protistan relatives of animals, indicating convergent evolution. We therefore analyzed the evolution of two key fungal characters in Opisthokonta, the flagellum and chitin synthases. Comparative analyses of the flagellar toolkit showed a previously unnoticed flagellar apparatus in two close relatives of animals, the filasterean Ministeria vibrans and Corallochytrium limacisporum. This implies that at least four different opisthokont lineages secondarily underwent flagellar simplification. Analysis of the evolutionary history of chitin synthases revealed significant expansions in both animals and fungi, and also in the Ichthyosporea and C. limacisporum, a group of cell-walled animal relatives. This indicates that the last opisthokont common ancestor had a complex toolkit of chitin synthases that was differentially retained in extant lineages. Thus, our data provide evidence for convergent evolution of specialized lifestyles in close relatives of animals and fungi from a generalist ancestor., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Little information has been gathered regarding the ontogenetic changes that contribute to differentiation between resident and migrant individuals, particularly before the onset of gross morphological and physiological changes in migratory individuals. The aim of this study was to evaluate gene expression during early development in Oncorhynchus mykiss populations with different life histories, in a tissue known to integrate environmental cues to regulate complex developmental processes and behaviours. We sampled offspring produced from migrant and resident parents, collecting whole embryos prior to the beginning of first feeding, and brain tissue at three additional time points over the first year of development. RNA sequencing for 32 individuals generated a reference transcriptome of 30 177 genes that passed count thresholds. Differential gene expression between migrant and resident offspring was observed for 1982 genes. The greatest number of differentially expressed genes occurred at 8 months of age, in the spring a full year before the obvious physiological transformation from stream-dwelling parr to sea water-adaptable smolts begins for migrant individuals. Sex and age exhibited considerable effects on differential gene expression between migrants and resident offspring. Differential gene expression was observed in genes previously associated with migration, but also in genes previously unassociated with early life history divergence. Pathway analysis revealed coordinated differential expression in genes related to phototransduction, which could modulate photoperiod responsiveness and variation in circadian rhythms. The role for early differentiation in light sensitivity and biological rhythms is particularly intriguing in understanding early brain processes involved in differentiation of migratory and resident life history types., (© 2015 John Wiley & Sons Ltd.)

Rainbow trout (Oncorhynchus mykiss) exhibit remarkable life history diversity throughout their native range, and among the most evident is variation in migratory propensity. Although some populations and ecotypes will remain resident in freshwater habitats throughout their life history, others have the ability to undertake tremendous marine migrations. Those that migrate undergo a suite of behavioral, morphological, and physiological adaptations in a process called smoltification. We describe a quantitative genetic analysis of 22 growth, size, and morphological traits in addition to overall life history classification (resident or migrant) over the temporal process of smoltification in a large multi-generation experimental pedigree (n = 16,139) of migratory and resident rainbow trout derived from a wild population, which naturally segregates for migratory propensity. We identify significant additive genetic variance and covariance among the suite of traits that make up a component of the migratory syndrome in this species. Additionally, we identify high heritability estimates for the life history classifications and observe a strong negative genetic correlation between the migratory and resident life history trajectories. Given the large heritability estimates of all of the traits that segregate between migratory and resident rainbow trout, we conclude that these traits can respond to selection. However, given the high degree of genetic correlation between these traits, they do not evolve in isolation, but rather as a suite of coordinated characters in a predictable manner., (Copyright © 2015 Hecht et al.)

Fitness related traits often show spatial variation across populations of widely distributed species. Comparisons of genetic variation among populations in putatively neutral DNA markers and in phenotypic traits susceptible to selection (QST FST analysis) can be used to determine to what degree differentiation among populations can be attributed to selection or genetic drift. Traditionally, QST FST analyses require a large number of populations to achieve sufficient statistical power; however, new methods have been developed that allow QST FST comparisons to be conducted on as few as two populations if their pedigrees are informative. This study compared genetic and morphological divergence in three strains of brook trout Salvelinus fontinalis that were historically or currently used for stocking in the Lake Superior Basin. Herein we examined if morphological divergence among populations showed temporal variation, and if divergence could be attributed to selection or was indistinguishable from genetic drift. Multivariate QST FST analysis showed evidence for divergent selection between populations. Univariate analyses suggests that the pattern observed in the multivariate analyses was largely driven by divergent selection for length and weight, and moreover by divergence between the Assinica strain and each of the Iron River and Siskiwit strains rather than divergent selection between each population pair. While it could not be determined if divergence was due to natural selection or inadvertent artificial selection in hatcheries, selected differences were consistent with patterns of domestication commonly found in salmonids.

Rainbow and steelhead trout (Oncorhynchus mykiss), among other salmonid fishes, exhibit tremendous life history diversity, foremost of which is variation in migratory propensity. While some individuals possess the ability to undertake an anadromous marine migration, others remain resident in freshwater throughout their life cycle. Those that will migrate undergo tremendous physiological, morphological, and behavioral transformations in a process called smoltification which transitions freshwater-adapted parr to marine-adapted smolts. While the behavior, ecology, and physiology of smoltification are well described, our understanding of the proximate genetic mechanisms that trigger the process are not well known. Quantitative genetic analyses have identified several genomic regions associated with smoltification and migration-related traits within this species. Here we investigate the divergence in gene expression of 18 functional and positional candidate genes for the smoltification process in the brain, gill, and liver tissues of migratory smolts, resident parr, and precocious mature male trout at the developmental stage of out-migration. Our analysis reveals several genes differentially expressed between life history classes and validates the candidate nature of several genes in the parr-smolt transformation including Clock1α, FSHβ, GR, GH2, GHR1, GHR2, NDK7, p53, SC6a7, Taldo1, THRα, THRβ, and Vdac2.

Development rate has important implications for individual fitness and physiology. In salmonid fishes, development rate correlates with many traits later in life, including life-history diversity, growth, and age and size at sexual maturation. In rainbow trout (Oncorhynchus mykiss), a quantitative trait locus for embryonic development rate has been detected on chromosome 5 across populations. However, few candidate genes have been identified within this region. In this study, we use gene mapping, gene expression, and quantitative genetic methods to further identify the genetic basis of embryonic developmental rate in O. mykiss Among the genes located in the region of the major development rate quantitative trait locus (GHR1, Clock1a, Myd118-1, and their paralogs), all were expressed early in embryonic development (fertilization through hatch), but none were differentially expressed between individuals with the fast- or slow-developing alleles for a major embryonic development rate quantitative trait locus. In a follow-up study of migratory and resident rainbow trout from natural populations in Alaska, we found significant additive variation in development rate and, moreover, found associations between development rate and allelic variation in all 3 candidate genes within the quantitative trait locus for embryonic development. The mapping of these genes to this region and associations in multiple populations provide positional candidates for further study of their roles in growth, development, and life-history diversity in this model salmonid., (Published by Oxford University Press on behalf of the American Genetic Association 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.)

Daphnia pulex, the crustacean with the first sequenced genome, is an important organism that has been widely used in ecological and toxicological research. MicroRNAs (miRNAs) are 21-25 nucleotide small non-coding RNAs that are involved in a myriad of physiological processes. In this research, we predicted 75 D. pulex miRNAs by sequence homology and secondary structure identification from the full genome sequence. Fourteen predicted miRNAs were selected for quantitative real time polymerase chain reaction (RT-PCR) validation. Out of these, eight (mir-8, mir-9, mir-12, mir-92, mir-100, mir-133, mir-153 and mir-283) were successfully amplified and validated. Next, expression levels were quantified at three different life stages (days 4, 8 and 12 of age) using U6 spliceosomal RNA as a reference gene. The expression of mir-8, mir-9, mir-12, mir-92 and mir-100 significantly differed across time suggesting these microRNAs might play a critical role during D. pulex development. This is the first study to identify and validate miRNAs in D. pulex, which is an important first step in further studies that evaluate their roles in development and response to environmental and ecological stimuli.

Next-generation sequencing and the application of population genomic and association approaches have made it possible to detect selection and unravel the genetic basis to variable phenotypic traits. The use of these two approaches in parallel is especially attractive in nonmodel organisms that lack a sequenced and annotated genome, but only works well when population structure is not confounded with the phenotype of interest. Herein, we use population genomics in a nonmodel fish species, rainbow trout (Oncorhynchus mykiss), to better understand adaptive divergence between migratory and nonmigratory ecotypes and to further our understanding about the genetic basis of migration. Restriction site-associated DNA (RAD) tag sequencing was used to identify single-nucleotide polymorphisms (SNPs) in migrant and resident O. mykiss from two systems, one in Alaska and the other in Oregon. A total of 7920 and 6755 SNPs met filtering criteria in the Alaska and Oregon data sets, respectively. Population genetic tests determined that 1423 SNPs were candidates for selection when loci were compared between resident and migrant samples. Previous linkage mapping studies that used RAD DNA tag SNPs were available to determine the position of 1990 markers. Several significant SNPs are located in genome regions that contain quantitative trait loci for migratory-related traits, reinforcing the importance of these regions in the genetic basis of migration/residency. Annotation of genome regions linked to significant SNPs revealed genes involved in processes known to be important in migration (such as osmoregulatory function). This study adds to our growing knowledge on adaptive divergence between migratory and nonmigratory ecotypes of this species; across studies, this complex trait appears to be controlled by many loci of small effect, with some in common, but many loci not shared between populations studied.

Using 20 years of demographic and genetic data from four populations of banner-tailed kangaroo rats (Dipodomys spectabilis), we asked whether dispersing individuals gain benefits during adulthood that might compensate for the substantial survival costs they experience as juveniles. Compared to philopatric animals, within- and between-population dispersers gained no measureable advantages in adult survival, fecundity, or probability of recruiting offspring to adulthood. Restricting analyses to members of two central populations living more than 15 times the median dispersal distance from the study site edge, and using peripheral populations only to detect dispersal or offspring recruitment "offsite," did not change this result. Population density during year of birth had small negative effects on adult survival and fecundity, but there were no interactions with dispersal phenotype. We found no evidence that dispersers gained access to superior habitat or that their offspring suffered less inbreeding depression. Our results are consistent with fitness advantages being indirect; by leaving, dispersers release their kin from competition. Our results are also consistent with the possibility that dispersal is the "best of a bad lot." If dispersal is a conditional strategy, then the benefits may be obscured in observational data that compare dispersing individuals to philopatric individuals rather than to individuals whose dispersal phenotype is experimentally manipulated.

We report the genetic map location of 14 genes involved in the inflammatory response to salmonid bacterial and viral pathogens, which brings the total number of immune genes mapped in rainbow trout (RT, Oncorhynchus mykiss) to 61. These genes were mapped as candidate genes that may be involved in resistance to bacterial kidney disease, as well as candidates for known QTL for resistance to infectious hematopoietic necrosis virus, infectious pancreatic necrosis virus and Ceratomyxa shasta. These QTL map to one or more of the linkage groups containing immune genes. The combined analysis of these linkage results and those of previously mapped immune genes in RT shows that many immune genes are found in syntenic blocks of genes that have been retained in teleosts despite species divergence and genome duplication events., (© 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.)