209 research outputs found
Data for: Repeated genetic divergence plays a minor role in repeated phenotypic divergence of lake-stream stickleback
No full textRecent studies have shown that the repeated evolution of similar phenotypes in response to similar ecological conditions (here 'parallel evolution') often occurs through mutations in the same genes. However, many previous studies have focused on known candidate genes in a limited number of systems. Thus, the question of how often parallel phenotypic evolution is due to parallel genetic changes remains open. Here, we used quantitative trait locus (QTL) mapping in F2 intercrosses between lake and stream threespine stickleback (Gasterosteus aculeatus) from four independent watersheds on Vancouver Island, Canada to determine whether the same QTL underlie divergence in the same phenotypes across, between, and within watersheds. We find few parallel QTL, even in independent crosses from the same watershed or for phenotypes that have diverged in parallel. These findings suggest that different mutations can lead to similar phenotypes. The low genetic repeatability observed in these lake-stream systems contrasts with the higher genetic repeatability observed in other stickleback systems. We speculate that differences in evolutionary history, gene flow, and/or the strength and direction of selection might explain these differences in genetic parallelism and emphasize that more work is needed to move beyond documenting genetic parallelism to identifying the underlying causes.All datasets are provided as .csv, .txt, or .tab files. Analyses were conducted in R (script files are indicated as .r), bash (script files are indicated as .sh), and PERL (script files are indicated as .pl).Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB-1144773Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB-1144556All methods are described in the accompanying manuscript: Hilary A. Poore, Yoel E. Stuart, Diana J. Rennison, Marius Roesti, Andrew P. Hendry, Daniel I. Bolnick, Catherine L. Peichel (2022) Repeated genetic divergence plays a minor role in repeated phenotypic divergence of lake-stream stickleback. Evolution, in press.
All datasets and scripts are described in the README file
Intersecting families of permutations
No full textResearch of the second author was supported in part by the Israel Science Foundation, grant no. 0397684, and NSERC grant 341527.
Research of the third author was supported in part by the Giora Yoel Yashinsky Memorial Grant
Data from: Inferring the evolution of reproductive isolation in a lineage of fossil threespine stickleback, Gasterosteus doryssus
No full text<p>Darwin attributed the absence of species transitions in the fossil record to his hypothesis that speciation occurs within isolated habitat patches too geographically restricted to be captured by fossil sequences. Mayr's peripatric speciation model added that such speciation would be rapid, further explaining missing evidence of diversification. Indeed, Eldredge and Gould's original punctuated equilibrium model combined Darwin's conjecture, Mayr's model, and 124 years of unsuccessfully sampling the fossil record for transitions. Observing such divergence, however, could illustrate the tempo and mode of evolution during early speciation. Here, we investigate peripatric divergence in a Miocene stickleback fish, <em>Gasterosteus doryssus</em>. This lineage appeared and, over ~8,000 generations, evolved significant reduction of twelve of sixteen traits related to armor, swimming, and diet, relative to its ancestral population. This was greater morphological divergence than we observed between reproductively isolated, benthic-limnetic ecotypes of extant <em>Gasterosteus aculeatus</em>. Therefore, we infer that reproductive isolation was evolving. However, local extinction of low-armoured <em>G. doryssus</em> lineages shows how young isolate populations often disappear, supporting Darwin's explanation for missing evidence and revealing a mechanism behind morphological stasis. Exctinction may also account for limited sustained divergence within the stickleback species complex and help reconcile speciation rate variation observed across time scales.</p><p>Microsoft Excel is helpful to open the data files.</p>
<p>R and R Studio are necessary to run the analysis scripts.</p><p>Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: https://ror.org/021nxhr62<br>Award Number: EAR-2145830</p><p>(a) Fossil specimen data</p>
<p>To quantify morphological divergence in the fossils, we compiled published data from the D (Bell et al. 1985), L (Bell et al. 2006), and K series (Stuart et al. 2020, Voje et al. 2022). See Figure 1A for stratigraphic correlations among series. Series D consisted of 26 samples spaced at ~5,000-year intervals over an estimated 108,275 years (Figure 1A). Six traits were measured from D: standard length, pelvic score, and the number of pre-dorsal pterygiophores, dorsal spines, anal-fin rays, and dorsal-fin rays (Bell et al. 1985). Series L comprised a section starting ~4,500 years before the replacement event until ~16,500 years after and was sampled continuously. Three armour traits were measured for series L: pelvic score, number of dorsal spines, and number of touching pre-dorsal pterygiophores. This series confirmed replacement of lineage I by lineage II within ~125 years (Bell et al. 2006) and that subsequent evolution of lineage II was probably caused by directional natural selection (Hunt et al. 2008). Our analysis focuses on series K (Stuart et al. 2020; Voje et al. 2022) because 16 traits were measured for K (Table S1), allowing estimates of multivariate divergence of traits that should reflect swimming, feeding, and defense. These traits are also divergent between benthic and limnetic ecotypes in the species-pair lakes as well as among allopatric generalist populations of <em>G. aculeatus</em> (Walker 1997; Spoljaric and Reimchen 2007; Willacker et al. 2010). Series K consisted of 18 samples taken at ~1000-year intervals, and mean sample times span ~16,363 years. Series K starts at the replacement, when lineage I and lineage II specimens occurred in a single sample. We removed lineage I fish from this sample for morphological analysis. Traits measured and their sample sizes are provided in Table S1 and Table S2, respectively. Finally, we note that a parapatric, highly armored form with a benthic diet (Bell 2009) was collected from Quarry E (of Brown 1986), approximately 1.7km from the depositional environment studied here. This site was dated to roughly the same time as the K series (Brown 1986) and appears to have been a nearshore sample, based on abundant terrestrial plant fossils and thick clastic layers embedded within the diatomite (Bell 2009). This contrasts the open water habitat that characterized the depositional environment of series D, L, and K (Bell 2009). </p>
<p>(b) Extant specimen data</p>
<p>For comparison to fossil divergence, we measured benthic and limnetic ecotypes from five species-pair lakes (Table 2) for the same 16 traits that were scored in the K-series fossils (Table S1). Specimens were loaned by D. Schluter's lab (University of British Columbia). They collected from Enos Lake in 1988 and from Emily, Little Quarry, Paxton, and Priest Lakes in 2018. The Enos specimens were fixed in formalin and stored in 40% isopropanol. The other specimens were initially preserved in 95% ethanol in the field before being transferred to water then formalin in the lab and stored in 40% isopropanol. In 2019, we stained these specimens for bone using Alizarin Red. Standard length as well as pelvic-spine lengths were measured with calipers. We used a dissection microscope to count dorsal spines, pelvic spines, dorsal-fin rays, and anal-fin rays. Right and left-side pelvic girdle and ectocoracoid lengths were measured from ventral photographs (Canon EOS Rebel T7, Tamron 16-300 mm MACRO lens, Kaiser RS1 copy stand). Lateral X-rays were used to measure dorsal spine length, number of pterygiophores anterior to the pterygiophore holding the third spine, length of the pterygiophore just anterior to the third spine, cleithrum length, and pre-maxilla ascending branch length. We also counted vertebrae from X-rays: abdominal vertebrae were counted anterior to the first vertebra with a haemal spine contacting an anal fin pterygiophore. Caudal vertebrae were posterior, including the first vertebra with the haemal spine contacting the anal fin pterygiophore (Aguirre et al. 2014). X-rays were taken with an AXR Hot Shot X-ray Machine (Associated X-ray Corporation) at the Field Museum of Natural History. Specimens were exposed at 35kV and 4mA for 7 to 10 seconds. We developed the film and scanned individual fish images using the B&W Negatives setting on an Epson Perfection 4990 Photo flatbed at 2400 dpi. Measurements from photographs and X-rays were taken with FIJI (Schindelin et al. 2012) and its plugin ObjectJ (<a href="https://sils.fnwi.uva.nl/bcb/objectj/">https://sils.fnwi.uva.nl/bcb/objectj/</a>). Table S3 reports sample sizes by population, ecotype, and trait.</p>
Data from: Inferring the evolution of reproductive isolation in a lineage of fossil threespine stickleback, Gasterosteus doryssus
No full text<p>Darwin attributed the absence of species transitions in the fossil record to his hypothesis that speciation occurs within isolated habitat patches too geographically restricted to be captured by fossil sequences. Mayr's peripatric speciation model added that such speciation would be rapid, further explaining missing evidence of diversification. Indeed, Eldredge and Gould's original punctuated equilibrium model combined Darwin's conjecture, Mayr's model, and 124 years of unsuccessfully sampling the fossil record for transitions. Observing such divergence, however, could illustrate the tempo and mode of evolution during early speciation. Here, we investigate peripatric divergence in a Miocene stickleback fish, <em>Gasterosteus doryssus</em>. This lineage appeared and, over ~8,000 generations, evolved significant reduction of twelve of sixteen traits related to armor, swimming, and diet, relative to its ancestral population. This was greater morphological divergence than we observed between reproductively isolated, benthic-limnetic ecotypes of extant <em>Gasterosteus aculeatus</em>. Therefore, we infer that reproductive isolation was evolving. However, local extinction of low-armoured <em>G. doryssus</em> lineages shows how young isolate populations often disappear, supporting Darwin's explanation for missing evidence and revealing a mechanism behind morphological stasis. Exctinction may also account for limited sustained divergence within the stickleback species complex and help reconcile speciation rate variation observed across time scales.</p><p>Microsoft Excel is helpful to open the data files.</p>
<p>R and R Studio are necessary to run the analysis scripts.</p><p>Funding provided by: National Science Foundation<br>Crossref Funder Registry ID: https://ror.org/021nxhr62<br>Award Number: EAR-2145830</p><p>(a) Fossil specimen data</p>
<p>To quantify morphological divergence in the fossils, we compiled published data from the D (Bell et al. 1985), L (Bell et al. 2006), and K series (Stuart et al. 2020, Voje et al. 2022). See Figure 1A for stratigraphic correlations among series. Series D consisted of 26 samples spaced at ~5,000-year intervals over an estimated 108,275 years (Figure 1A). Six traits were measured from D: standard length, pelvic score, and the number of pre-dorsal pterygiophores, dorsal spines, anal-fin rays, and dorsal-fin rays (Bell et al. 1985). Series L comprised a section starting ~4,500 years before the replacement event until ~16,500 years after and was sampled continuously. Three armour traits were measured for series L: pelvic score, number of dorsal spines, and number of touching pre-dorsal pterygiophores. This series confirmed replacement of lineage I by lineage II within ~125 years (Bell et al. 2006) and that subsequent evolution of lineage II was probably caused by directional natural selection (Hunt et al. 2008). Our analysis focuses on series K (Stuart et al. 2020; Voje et al. 2022) because 16 traits were measured for K (Table S1), allowing estimates of multivariate divergence of traits that should reflect swimming, feeding, and defense. These traits are also divergent between benthic and limnetic ecotypes in the species-pair lakes as well as among allopatric generalist populations of <em>G. aculeatus</em> (Walker 1997; Spoljaric and Reimchen 2007; Willacker et al. 2010). Series K consisted of 18 samples taken at ~1000-year intervals, and mean sample times span ~16,363 years. Series K starts at the replacement, when lineage I and lineage II specimens occurred in a single sample. We removed lineage I fish from this sample for morphological analysis. Traits measured and their sample sizes are provided in Table S1 and Table S2, respectively. Finally, we note that a parapatric, highly armored form with a benthic diet (Bell 2009) was collected from Quarry E (of Brown 1986), approximately 1.7km from the depositional environment studied here. This site was dated to roughly the same time as the K series (Brown 1986) and appears to have been a nearshore sample, based on abundant terrestrial plant fossils and thick clastic layers embedded within the diatomite (Bell 2009). This contrasts the open water habitat that characterized the depositional environment of series D, L, and K (Bell 2009). </p>
<p>(b) Extant specimen data</p>
<p>For comparison to fossil divergence, we measured benthic and limnetic ecotypes from five species-pair lakes (Table 2) for the same 16 traits that were scored in the K-series fossils (Table S1). Specimens were loaned by D. Schluter's lab (University of British Columbia). They collected from Enos Lake in 1988 and from Emily, Little Quarry, Paxton, and Priest Lakes in 2018. The Enos specimens were fixed in formalin and stored in 40% isopropanol. The other specimens were initially preserved in 95% ethanol in the field before being transferred to water then formalin in the lab and stored in 40% isopropanol. In 2019, we stained these specimens for bone using Alizarin Red. Standard length as well as pelvic-spine lengths were measured with calipers. We used a dissection microscope to count dorsal spines, pelvic spines, dorsal-fin rays, and anal-fin rays. Right and left-side pelvic girdle and ectocoracoid lengths were measured from ventral photographs (Canon EOS Rebel T7, Tamron 16-300 mm MACRO lens, Kaiser RS1 copy stand). Lateral X-rays were used to measure dorsal spine length, number of pterygiophores anterior to the pterygiophore holding the third spine, length of the pterygiophore just anterior to the third spine, cleithrum length, and pre-maxilla ascending branch length. We also counted vertebrae from X-rays: abdominal vertebrae were counted anterior to the first vertebra with a haemal spine contacting an anal fin pterygiophore. Caudal vertebrae were posterior, including the first vertebra with the haemal spine contacting the anal fin pterygiophore (Aguirre et al. 2014). X-rays were taken with an AXR Hot Shot X-ray Machine (Associated X-ray Corporation) at the Field Museum of Natural History. Specimens were exposed at 35kV and 4mA for 7 to 10 seconds. We developed the film and scanned individual fish images using the B&W Negatives setting on an Epson Perfection 4990 Photo flatbed at 2400 dpi. Measurements from photographs and X-rays were taken with FIJI (Schindelin et al. 2012) and its plugin ObjectJ (<a href="https://sils.fnwi.uva.nl/bcb/objectj/">https://sils.fnwi.uva.nl/bcb/objectj/</a>). Table S3 reports sample sizes by population, ecotype, and trait.</p>
BioSTEAM: The open-source bioprocess simulation and techno-economic analysis modules in Python
Get PDFPreliminary techno-economic analysis (TEA) of a chemical process provides critical information on the economic feasibility, technological bottlenecks, and venture risks due to process uncertainties. Current TEA methods generally rely on proprietary software to evaluate two to three design configurations with single point sensitivity analysis. Such classical methods neglect the effect of process uncertainties and fail to evaluate the complete landscape of design decisions. The limited scope of current literature obscures comparisons between process evaluations and makes it difficult to predict how possible technological developments can impact the sustainability of a process. The main difficulties in adding rigorous uncertainty analysis is high computational time and low rate of successful convergence. Additionally, relying on proprietary software presents both an economic and intellectual barrier for evaluating emerging and conceptual processes. The Bioprocess Simulation and Techno-Economic Analysis Modules, BioSTEAM, is an open-source steady state process simulation package in python for preliminary TEA that will enable rigorous uncertainty analysis through its fast and flexible platform. BioSTEAM presents an intuitive toolset of objects that handle thermodynamic properties, material flows, unit operations, recycle systems, and process specifications. The applicability of BioSTEAM is demonstrated here in the context of a design for the co-production of biodiesel and ethanol from lipid cane. The evaluation of the lipid cane biorefinery in BioSTEAM closely matches a previous evaluation of the design using SuperPro Designer (a proprietary process simulation software). BioSTEAM is well documented and readily available at the Python Package Index, a repository for published Python packages. Although BioSTEAM has not yet incorporated many of the unit operation models presented in proprietary process simulators, its extendable and transparent architecture offers users the power to build new unit operation models and share their designs without any barriers. BioSTEAM may help foster a new open-source community that can accelerate advancements in the field of process design and simulation.Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2021-05-01The student, Yoel Cortes-Pena, accepted the attached license on 2019-04-26 at 00:22.The student, Yoel Cortes-Pena, submitted this Thesis for approval on 2019-04-26 at 00:57.This Thesis was approved for publication on 2019-04-26 at 11:17.DSpace SAF Submission Ingestion Package generated from Vireo submission #13940 on 2019-08-22 at 16:24:01Made available in DSpace on 2019-08-23T20:48:28Z (GMT). No. of bitstreams: 2
CORTES-PENA-THESIS-2019.pdf: 1154067 bytes, checksum: 399e5f4e1739b1d3973738a48e6c500c (MD5)
LICENSE.txt: 4213 bytes, checksum: 69420ec4d0e1822a1e39d562dee90ec0 (MD5)
Previous issue date: 2019-04-26Embargo set by: Seth Robbins for item 112395
Lift date: 2021-08-23T20:48:32Z
Reason: Author requested closed access (OA after 2yrs) in Vireo ETD systemLimited Restriction Lifted for Item 112395 on 2021-08-24T09:15:16Z
Many-to-one form-to-function mapping weakens parallel morphological evolution
No full textEvolutionary ecologists aim to explain and predict evolutionary change under different selective regimes. Theory suggests that such evolutionary prediction should be more difficult for biomechanical systems in which different trait combinations generate the same functional output: "many-to-one mapping." Many-to-one mapping of phenotype to function enables multiple morphological solutions to meet the same adaptive challenges. Therefore, many-to-one mapping should undermine parallel morphological evolution, and hence evolutionary predictability, even when selection pressures are shared among populations. Studying 16 replicate pairs of lake- and stream-adapted threespine stickleback (Gasterosteus aculeatus), we quantified three parts of the teleost feeding apparatus and used biomechanical models to calculate their expected functional outputs. The three feeding structures differed in their form-to-function relationship from one-to-one (lower jaw lever ratio) to increasingly many-to-one (buccal suction index, opercular 4-bar linkage). We tested for (1) weaker linear correlations between phenotype and calculated function, and (2) less parallel evolution across lake-stream pairs, in the many-to-one systems relative to the one-to-one system. We confirm both predictions, thus supporting the theoretical expectation that increasing many-to-one mapping undermines parallel evolution. Therefore, sole consideration of morphological variation within and among populations might not serve as a proxy for functional variation when multiple adaptive trait combinations exist
Recommended from our members
Character displacement and community assembly in Anolis lizards
Get PDFAt broad scales, community ecologists study how biogeographic factors like environmental dissimilarity and geographic distance influence community assembly and composition. At small scales, community ecologists study how one or several species interact to determine habitat partitioning and coexistence. In this dissertation, I present studies at both scales. Chapter One investigates community assembly across the Caribbean, Central, and South American radiations of Anolis lizards and Eleutherodactylid frogs to test whether oceanic islands are unique in their assembly processes. Such uniqueness is suggested by high levels of endemism on islands; however, comparable levels of endemism can be found in mainland communities. I modeled the rate of species turnover between mainland communities, with respect to geographic distance and environmental dissimilarity, and then used the mainland model to predict turnover among islands. Turnover among island communities was significantly higher than predicted from the mainland model, confirming the long-held but untested assumption that island assemblages accumulate biodiversity differently than their mainland counterparts. Chapter Two reviews the evidence for ecological character displacement (ECD), an evolutionary process whereby two resource competitors diverge from one another in phenotype and resource use, facilitating coexistence in a community. I find that, despite current scientific opinion, the evidence for ECD is equivocal; most cases of ECD pattern fail to rule out processes alternative to resource competition that could create the same pattern. I conclude that better evidence may come from real time tests of ECD. Chapters Three and Four describe just such a test in small island populations of Anolis carolinensis. In Chapter Three, I find that small island populations of A. carolinensis that have come into sympatry with a novel competitor, the invasive A. sagrei, shift their habitat use to become more arboreal, compared to allopatric populations. Consistent with prediction, individuals from sympatric populations have larger toepads with additional adhesive scales - a common adaptation to arboreality in Anolis. In Chapter Four, I describe a common garden experiment that finds that the observed toepad divergence is an evolved response, suggesting rates of divergence for toepad area and scale number on par with well known examples of contemporary evolution
Made in America : American goods - American jobs : A cluster based business development project
No full textMade in America, American Goods, American Jobs was designed to provide business development support to a cluster of locally owned small garment manufacturers in Washington State. This sector had been negatively affected by global competition and trade deficits with foreign markets, resulting in business closures and job losses. A community economic development project with the goal of retaining local garment manufacturers, the Made In America project supplied assistance to companies to increase competitiveness; and to create 50 employment opportunities for low-income residents. Through customized technical assistance and resource development, the project was successful in assisting twelve (12) companies to increase their sales and market access; and created 69 jobs for low-income individuals. (Author abstract)Lemmons, T. (2006). Made in America: American goods - American jobs: A cluster based business development project. Retrieved from http://academicarchive.snhu.eduMaster of Science (M.S.)School of Community Economic Developmen
- …
