Abstract
From a genomics perspective, bivalves (Mollusca: Bivalvia) have been poorly explored with the exception for those of high economic value. The bivalve order Unionida, or freshwater mussels, ...has been of interest in recent genomic studies due to their unique mitochondrial biology and peculiar life cycle. However, genomic studies have been hindered by the lack of a high-quality reference genome. Here, I present a genome assembly of Potamilus streckersoni using Pacific Bioscience single-molecule real-time long reads and 10X Genomics-linked read sequencing. Further, I use RNA sequencing from multiple tissue types and life stages to annotate the reference genome. The final assembly was far superior to any previously published freshwater mussel genome and was represented by 2,368 scaffolds (2,472 contigs) and 1,776,755,624 bp, with a scaffold N50 of 2,051,244 bp. A high proportion of the assembly was comprised of repetitive elements (51.03%), aligning with genomic characteristics of other bivalves. The functional annotation returned 52,407 gene models (41,065 protein, 11,342 tRNAs), which was concordant with the estimated number of genes in other freshwater mussel species. This genetic resource, along with future studies developing high-quality genome assemblies and annotations, will be integral toward unraveling the genomic bases of ecologically and evolutionarily important traits in this hyper-diverse group.
Lesbians in sport may reside in a culture of silence due to the fear of being negatively labeled. Often, ideologies regarding lesbian athletes validate social inequalities through institutional ...practices. The purpose of this study was to examine the experiences of NCAA female sexual minority student-athletes. Employing purposeful sampling, nine current and former female student-athletes participated in semi-structured interviews. Through a combination of inductive and narrative analyses during the data collection and analysis processes, the findings revealed five higher order themes: (1) climate, (2) validation and norms of behavior, (3), misunderstandings and misconceptions, (4) negotiating identities and risk, and (5) gender ideology and assumptions. Although results of the present study are not generalizable, this study can inform inclusive practices to improve the experiences of sexual minority student-athletes. Further, this study will create awareness regarding the obstacles female sexual minority student-athletes endure on college campuses and within the setting of intercollegiate sport.
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BFBNIB, NUK, PILJ, SAZU, UL, UM, UPUK
The COVID-19 pandemic has been one of the most severe disruptions to normal life, impacting how businesses operate. The academic literature in the areas of supply chain and operations management has ...been trying to explain how this has affected decision-making in businesses. However, the existing literature has predominantly overlooked organisational culture and behavioural economic theories. This paper contends that considering the decisions made in supply chain disruption management involve groups and the individuals within them, the relevance of behavioural economic concepts becomes paramount. As such, the objective of this paper is to conduct an integrative literature review, utilising the purposive sampling method to explore the dearth of academic work connecting behavioural economic theories and organisational culture to supply chain disruption management. Additionally, the paper aims to offer guidelines for future research in this domain. Enhancing our comprehension of these domains concerning supply chain disruption management would empower firms to better anticipate their parties’ decisions, refine their decision-making models, and cultivate stronger relationships with suppliers and customers.
Abstract
In 2011, the first high-quality genome assembly of a squamate reptile (lizard or snake) was published for the green anole. Dozens of genome assemblies were subsequently published over the ...next decade, yet these assemblies were largely inadequate for answering fundamental questions regarding genome evolution in squamates due to their lack of contiguity or annotation. As the “genomics age” was beginning to hit its stride in many organismal study systems, progress in squamates was largely stagnant following the publication of the green anole genome. In fact, zero high-quality (chromosome-level) squamate genomes were published between the years 2012 and 2017. However, since 2018, an exponential increase in high-quality genome assemblies has materialized with 24 additional high-quality genomes published for species across the squamate tree of life. As the field of squamate genomics is rapidly evolving, we provide a systematic review from an evolutionary genomics perspective. We collated a near-complete list of publicly available squamate genome assemblies from more than half-a-dozen international and third-party repositories and systematically evaluated them with regard to their overall quality, phylogenetic breadth, and usefulness for continuing to provide accurate and efficient insights into genome evolution across squamate reptiles. This review both highlights and catalogs the currently available genomic resources in squamates and their ability to address broader questions in vertebrates, specifically sex chromosome and microchromosome evolution, while addressing why squamates may have received less historical focus and has caused their progress in genomics to lag behind peer taxa.
Freshwater mussels are a species‐rich group with biodiversity patterns strongly shaped by a life history strategy that includes an obligate parasitic larval stage. In this study, we set out to ...reconstruct the life history evolution and systematics in a clade of freshwater mussels adapted to parasitizing a molluscivorous host fish. Anchored hybrid enrichment and ancestral character reconstruction revealed a complex pattern of life history evolution with host switching and multiple instances of convergence, including reduction in size of larvae, increased fecundity, and growth during encapsulation. Our phylogenomic analyses also recovered non‐monophyly of taxa exhibiting multiple traits used as the basis for previous taxonomic hypotheses. Taxa with axe‐head shaped glochidia were resolved as paraphyletic, but our results strongly suggest the complex morphology is an adaptation to reduce larval size, with reduction in size further accentuated in taxa previously assigned to Leptodea. To more accurately reflect the evolutionary history of this group, we make multiple systematic changes, including the description of a new genus, Atlanticoncha gen. nov., and the synonymy of the genus Leptodea under Potamilus. Our findings contribute to the growing body of literature showing that cladistic hypotheses based solely on morphological characters, including larval morphology, can be flawed in freshwater mussels.
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FZAB, GIS, IJS, IZUM, KILJ, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Abstract
Genetic elements encoded in nuclear DNA determine the sex of an individual in many animals. In certain bivalve lineages that possess doubly uniparental inheritance (DUI), mitochondrial DNA ...(mtDNA) has been hypothesized to contribute to sex determination. In these cases, females transmit a female mtDNA to all offspring, while male mtDNA (M mtDNA) is transmitted only from fathers to sons. Because M mtDNA is inherited in the same way as Y chromosomes, it has been hypothesized that mtDNA may be responsible for sex determination. However, the role of mitochondrial and nuclear genes in sex determination has yet to be validated in DUI bivalves. In this study, we used DNA, RNA, and mitochondrial short noncoding RNA (sncRNA) sequencing to explore the role of mitochondrial and nuclear elements in the sexual development pathway of the freshwater mussel Potamilus streckersoni (Bivalvia: Unionida). We found that the M mtDNA sheds a sncRNA partially within a male-specific mitochondrial gene that targets a pathway hypothesized to be involved in female development and mitophagy. RNA-seq confirmed the gene target was significantly upregulated in females, supporting a direct role of mitochondrial sncRNAs in gene silencing. These findings support the hypothesis that M mtDNA inhibits female development. Genome-wide patterns of genetic differentiation and heterozygosity did not support a nuclear sex-determining region, although we cannot reject that nuclear factors are involved with sex determination. Our results provide further evidence that mitochondrial loci contribute to diverse, nonrespiratory functions and additional insights into an unorthodox sex-determining system.
Freshwater mussels are considered the most imperiled group of organisms in North America and systematics research has played an integral role in the development and implementation of their ...conservation. Despite the importance of systematics in conservation planning, the evolutionary relationships between many mussel taxa remain poorly explored, clearly illustrated by
Strophitus undulatus
. This species is wide-ranging, occurring in streams across the United States and Canada with a disjunct population in the Colorado River drainage in central Texas. The widespread distribution of
S. undulatus
, as well as high intraspecific morphological variation, has led previous authors to doubt the taxon is representative of a single species. In this study, we set out to investigate species boundaries in
S. undulatus
by integrating environmental, molecular, and morphological datasets. Molecular and morphological data supported
S. undulatus
from the Colorado River as distinct, which was supplemented by a species distribution modeling approach, suggesting potential adaptation to Edwards Plateau streams has contributed to speciation. Given our findings, we formally describe a new species of freshwater mussel,
Strophitus howellsi
, endemic to streams along the Edwards Plateau in the Colorado River drainage. A conservation assessment of
S. howellsi
suggests the species is extremely rare within a highly restricted distribution and may warrant future recovery actions. Our findings build on a growing body of literature highlighting aquatic endemism along the Edwards Plateau and have significant conservation implications for freshwater mussels in Texas.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Abstract
Genomic resources across squamate reptiles (lizards and snakes) have lagged behind other vertebrate systems and high-quality reference genomes remain scarce. Of the 23 chromosome-scale ...reference genomes across the order, only 12 of the ~60 squamate families are represented. Within geckos (infraorder Gekkota), a species-rich clade of lizards, chromosome-level genomes are exceptionally sparse representing only two of the seven extant families. Using the latest advances in genome sequencing and assembly methods, we generated one of the highest-quality squamate genomes to date for the leopard gecko, Eublepharis macularius (Eublepharidae). We compared this assembly to the previous, short-read only, E. macularius reference genome published in 2016 and examined potential factors within the assembly influencing contiguity of genome assemblies using PacBio HiFi data. Briefly, the read N50 of the PacBio HiFi reads generated for this study was equal to the contig N50 of the previous E. macularius reference genome at 20.4 kilobases. The HiFi reads were assembled into a total of 132 contigs, which was further scaffolded using HiC data into 75 total sequences representing all 19 chromosomes. We identified 9 of the 19 chromosomal scaffolds were assembled as a near-single contig, whereas the other 10 chromosomes were each scaffolded together from multiple contigs. We qualitatively identified that the percent repeat content within a chromosome broadly affects its assembly contiguity prior to scaffolding. This genome assembly signifies a new age for squamate genomics where high-quality reference genomes rivaling some of the best vertebrate genome assemblies can be generated for a fraction of previous cost estimates. This new E. macularius reference assembly is available on NCBI at JAOPLA010000000.
Objectively delimiting species boundaries remains an important challenge in systematics and becomes urgent when unresolved taxonomy complicates conservation and recovery efforts. We examined species ...boundaries in the imperiled freshwater mussel genus Cyclonaias (Bivalvia: Unionidae) using morphometrics, molecular phylogenetics, and multispecies coalescent models to help guide pending conservation assessments and legislative decisions. Congruence across multiple lines of evidence indicated that current taxonomy overestimates diversity in the C. pustulosa species complex. The only genetically and morphologically diagnosable species in the C. pustulosa species complex were C. pustulosa and C. succissa and we consider C. aurea, C. houstonensis, C. mortoni, and C. refulgens to be synonyms of C. pustulosa. In contrast, all three species in the C. nodulata complex (C. necki, C. nodulata, and C. petrina) were genetically, geographically, and morphologically diagnosable. Our findings have important conservation and management implications, as three nominal species (C. aurea, C. houstonensis, and C. petrina) are being considered for protection under the Endangered Species Act.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
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•We resolved relationships in Anodontoides using an integrative dataset.•Our investigation resolved Strophitus and Anodontoides as paraphyletic.•We resurrect Strophitus radiatus to ...accurately represent ‘A. radiatus’.•We resurrect Pseudodontoides to represent ‘S. connasaugaensis’ and ‘S. subvexus’.•An integrative dataset suggests S. raditatus may include as many as four species.
Accurate taxonomic placement is vital to conservation efforts considering many intrinsic biological characteristics of understudied species are inferred from closely related taxa. The rayed creekshell, Anodontoides radiatus (Conrad, 1834), exists in the Gulf of Mexico drainages from western Florida to Louisiana and has been petitioned for listing under the Endangered Species Act. We set out to resolve the evolutionary history of A. radiatus, primarily generic placement and species boundaries, using phylogenetic, morphometric, and geographic information. Our molecular matrix contained 3 loci: cytochrome c oxidase subunit I, NADH dehydrogenase subunit I, and the nuclear-encoded ribosomal internal transcribed spacer I. We employed maximum likelihood and Bayesian inference to estimate a phylogeny and test the monophyly of Anodontoides and Strophitus. We implemented two coalescent-based species delimitation models to test seven species models and evaluate species boundaries within A. radiatus. Concomitant to molecular data, we also employed linear morphometrics and geographic information to further evaluate species boundaries. Molecular and morphological evidence supports the inclusion of A. radiatus in the genus Strophitus, and we resurrect the binomial Strophitus radiatus to reflect their shared common ancestry. We also found strong support for polyphyly in Strophitus and advocate the resurrection of the genus Pseudodontoideus to represent ‘Strophitus’ connasaugaensis and ‘Strophitus’ subvexus. Strophitus radiatus exists in six well-supported clades that were distinguished as evolutionary independent lineages using Bayesian inference, maximum likelihood, and coalescent-based species delimitation models. Our integrative approach found evidence for as many as 4 evolutionary divergent clades within S. radiatus. Therefore, we formally describe two new species from the S. radiatus species complex (Strophitus williamsi and Strophitus pascagoulaensis) and recognize the potential for a third putative species (Strophitus sp. cf. pascagoulaensis). Our findings aid stakeholders in establishing conservation and management strategies for the members of Anodontoides, Strophitus, and Pseudodontoideus.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
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