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Science, technology, engineering, mathematics, and medicine (STEMM) fields change rapidly and are increasingly interdisciplinary. Commonly, STEMM practitioners use short-format training (SFT) such as workshops and short courses for upskilling and reskilling, but unaddressed challenges limit SFT’s effectiveness and inclusiveness. Prior work, including the NSF 2026 Reinventing Scientific Talent proposal, called for addressing SFT challenges, and a diverse international group of experts in education, accessibility, and life sciences came together to do so. This paper describes the phenomenography and content analyses that produced a set of 14 actionable recommendations to systematically strengthen SFT. Recommendations were derived from findings in the educational sciences and the experiences of several of the largest life science SFT programs. Recommendations cover the breadth of SFT contexts and stakeholder groups and include actions for instructors (e.g., make equity and inclusion an ethical obligation), programs (e.g., centralize infrastructure for assessment and evaluation), as well as organizations and funders (e.g., professionalize training SFT instructors; deploy SFT to counter inequity). Recommendations are aligned into a purpose-built framework— “The Bicycle Principles”—that prioritizes evidenced-based teaching, inclusiveness, and equity, as well as the ability to scale, share, and sustain SFT. We also describe how the Bicycle Principles and recommendations are consistent with educational change theories and can overcome systemic barriers to delivering consistently effective, inclusive, and career-spanning SFT.SIGNIFICANCE STATEMENTSTEMM practitioners need sustained and customized professional development to keep up with innovations. Short-format training (SFT) such as workshops and short-courses are relied upon widely but have unaddressed limitations. This project generated principles and recommendations to make SFT consistently effective, inclusive, and career-spanning. Optimizing SFT could broaden participation in STEMM by preparing practitioners more equitably with transformative skills. Better SFT would also serve members of the STEMM workforce who have several decades of productivity ahead, but who may not benefit from education reforms that predominantly focus on undergraduate STEMM. The Bicycle Principles and accompanying recommendations apply to any SFT instruction and may be especially useful in rapidly evolving and multidisciplinary fields such as artificial intelligence, genomics, and precision medicine.

The Neches River Rose Mallow (Hibiscus dasycalyx) is a rare wildflower endemic to Texas that is federally protected in the U.S.A. While previous work suggests that H. dasycalyx may be hybridizing with its widespread congeners, the Halberd-leaved Rose Mallow (H. laevis) and the Woolly Rose Mallow (H. moscheutos), this has not been studied in detail. We evaluated the relative threats to H. dasycalyx posed by hybridization with H. laevis and H. moscheutos by 1) examining their relatedness to one another via modern phylogenomic methods, 2) examining the species’ ecological (dis)similarities to one another using ecological niche modeling, and 3) looking for genomic evidence of hybridization among the three species. Our results suggest that H. dasycalyx is very closely related and ecologically similar to H. laevis, and suggest that H. laevis is interbreeding with H. dasycalyx in the wild. Conversely, H. moscheutos appears to be more distantly related to H. dasycalyx and more ecologically dissimilar, and the two are most likely not hybridizing. For these reasons, we believe that H. laevis poses a greater threat to H. dasycalyx than H. moscheutos. We offer some hypotheses as to why H. dasycalyx and H. laevis are coming into secondary contact where hybridization can occur.

Late diagnosis, unreliable prognostic assessment, and poorly-guided therapeutic planning result in dismal survival of ovarian cancer (OC) patients. Therefore, identifying novel functional biomarker(s) is highly desired for improved clinical management. MYB is an oncogenic transcription factor with emerging functional significance in OC. Here we examined its clinicopathologic significance by immunohistochemistry and TCGA/GTex data analyses. Aberrant MYB expression was detected in 94% of OC cases (n = 373), but not in the normal ovarian tissues (n = 23). MYB was overexpressed in all major epithelial OC histological subtypes exhibiting the highest incidence (~ 97%) and overall expression in serous and mucinous carcinomas. MYB expression correlated positively with tumor grades and stages. Moreover, MYB exhibited race-specific prognostic association. Moderate-to-high MYB levels were significantly associated with both poor overall- (p = 0.02) and progression-free (p = 0.02) survival in African American (AA), but not in the Caucasian American (CA) patients. Consistent with immunohistochemistry data, we observed significantly higher MYB transcripts in OC cases (n = 426) than normal ovary (n = 88). MYB transcripts were significantly higher in all epithelial OC subtypes, compared to normal, and its greater levels predicted poor survival in AA OC, but not CA OC, patients. Thus, MYB appears to be a useful clinical biomarker for prognostication, especially in AA patients.

Lung cancer killed 1.8 million people globally in 2020. In the United States, there will be over 235,760 cases of lung cancer with an estimated death of 131,880 individuals in 2021. Despite significant improvement in multimodal therapeutic approaches, overall 5-year survival rate is only 21.7%. Lung cancer appears to be mitochondria enriched cancer, however, alteration pattern of hallmark molecular pathways associated with diverse mitochondrial functions remain largely unknown in lung tumorigenesis. Utilizing high-throughput genomic profiling, we identified altered copy number of a panel of 40 mitochondria targeted molecules in primary lung cancer patients and their histologically normal appearing follow up mucosal biopsies. These altered molecules are critical components of the mitochondrial protein carrier, OXPHOS, stress response, amino acid metabolism and apoptosis pathways. This finding suggests for clonal genetic relationship between multifocal lesions and potential role of these alterations in the evolution of second primary tumors, which is an existing problem among lung cancer patients. The Human Cancer Genome Atlas database was utilized to further assess the mRNA expression pattern of these 40 molecules and determine their clinico-pathological correlations. Immunohistochemistry and digital pathology system based evaluations were performed to validate expression pattern of key altered molecules. We identified overexpression of various critical mitochondria pathway molecules including AARS2, AGMAT, SDHA, NDUFB7, LONP1, DGUOK, MRM1 and GCAT in both lung adenocarcinomas (LUAD) and squamous cell carcinomas (LUSC), predicting poor prognosis. Significant loss of expression of ACSF2, ACSS1, MTCH1, SLC25A4, ACAD8 and NAGS was evident in both adenocarcinoma and squamous cell carcinoma subtypes. Molecular characterization of both LUAD and LUSC tumor subtypes identified significant association of various key molecules including ACAD8, AGMAT, DGUOK and NDUFAB1 with proximal-inflammatory, proximal-proliferative and terminal respiratory unit pathways in LUAD; and an association of DGUOK, MDH2, MRM1 and MRPL10 with basal, classical, primitive and secretory pathways in LUSC. Significant loss of SLC25A4 protein expression was evident in lung cancer tissues, which predicted poor survival of the lung cancer patients. Capturing the compendium of hallmark mitochondrial alterations in lung tumorigenesis may open up novel avenues for therapeutic and biomarker interventions to improve the overall survival of the lung cancer patients. Citation Format: Kate L. Hertweck, Brian Persing, Pranitha Prodduturvar, Seema Singh, Ajay Singh, Santanu Dasgupta. Frequent alteration of mitochondria functional pathways in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3776.

Training and documentation for on-premises infrastructure represent the foundation of most institutional support for computational researchers. For most academic research institutions, however, these approaches fall short of meeting the needs of diverse researchers with different levels of experience with data-intensive research. We describe a framework for characterizing levels of computational expertise and relate this model to informational support provided for biomedical researchers at a non-profit/academic research center. Our model differentiates between novice, competent practitioner, and expert users of reproducible computational methods, and is related to the composition and needs of an entire research community. We specify methods best suited for researchers with different levels of expertise, including formally structured short courses, code examples/templates, and online wiki-style documentation. We provide recommendations to encourage the development and deployment of these resources, and suggest methods for assessing their effectiveness. Supporting multiple types of informational resources for researchers with different computational needs can be labor-intensive, but ideally increases computational ability for the entire institution.

Triple negative breast cancer (TNBC) has poor survival, exhibits rapid metastases, lacks targeted therapies and reliable prognostic markers. Here, we examined metastasis promoting role of cancer testis antigen SPANXB1 in TNBC and its utility as a therapeutic target and prognostic biomarker. Expression pattern of SPANXB1 was determined using matched primary cancer, lymph node metastatic tissues and circulating small extracellular vesicles (sEVs). cDNA microarray analysis of TNBC cells stably integrated with a metastasis suppressor SH3GL2 identified SPANXB1 as a potential target gene. TNBC cells overexpressing SH3GL2 exhibited decreased levels of both SPANXB1 mRNA and protein. Silencing of SPANXB1 reduced migration, invasion and reactive oxygen species production of TNBC cells. SPANXB1 depletion augmented SH3GL2 expression and decreased RAC-1, FAK, A-Actinin and Vinculin expression. Phenotypic and molecular changes were reversed upon SPANXB1 re-expression. SPANXB1 overexpressing breast cancer cells with an enhanced SPANXB1:SH3GL2 ratio achieved pulmonary metastasis within 5 weeks, whereas controls cells failed to do so. Altered expression of SPANXB1 was detected in the sEVs of SPANXB1 transduced cells. Exclusive expression of SPANXB1 was traceable in circulating sEVs, which was associated with TNBC progression. SPANXB1 represents a novel and ideal therapeutic target for blocking TNBC metastases due to its unique expression pattern and may function as an EV based prognostic marker to improve TNBC survival. Uniquely restricted expression of SPANXB1 in TNBCs, makes it an ideal candidate for targeted therapeutics and prognostication.

Triple negative breast cancer (TNBC) has poor survival, exhibits rapid metastases, lacks targeted therapies and reliable prognostic markers. Here, we examined metastasis promoting role of cancer testis antigen SPANXB1 in TNBC and its utility as a therapeutic target and prognostic biomarker. Expression pattern of SPANXB1 was determined using matched primary cancer, lymph node metastatic tissues and circulating small extracellular vesicles (sEVs). cDNA microarray analysis of TNBC cells stably integrated with a metastasis suppressor SH3GL2 identified SPANXB1 as a potential target gene. TNBC cells overexpressing SH3GL2 exhibited decreased levels of both SPANXB1 mRNA and protein. Silencing of SPANXB1 reduced migration, invasion and reactive oxygen species production of TNBC cells. SPANXB1 depletion augmented SH3GL2 expression and decreased RAC-1, FAK, A-Actinin and Vinculin expression. Phenotypic and molecular changes were reversed upon SPANXB1 re-expression. SPANXB1 overexpressing breast cancer cells with an enhanced SPANXB1:SH3GL2 ratio achieved pulmonary metastasis within 5 weeks, whereas controls cells failed to do so. Altered expression of SPANXB1 was detected in the sEVs of SPANXB1 transduced cells. Exclusive expression of SPANXB1 was traceable in circulating sEVs, which was associated with TNBC progression. SPANXB1 represents a novel and ideal therapeutic target for blocking TNBC metastases due to its unique expression pattern and may function as an EV based prognostic marker to improve TNBC survival. Uniquely restricted expression of SPANXB1 in TNBCs, makes it an ideal candidate for targeted therapeutics and prognostication.

Estimates suggest that at least half of all extant insect genera harbor obligate bacterial mutualists. Whereas an endosymbiotic relationship imparts many benefits upon host and symbiont alike, the intracellular lifestyle has profound effects on the bacterial genome. The obligate endosymbiont genome is a product of opposing forces: genes important to host survival are maintained through physiological constraint, contrasted by the fixation of deleterious mutations and genome erosion through random genetic drift. The obligate cockroach endosymbiont, Blattabacterium – providing nutritional augmentation to its host in the form of amino acid synthesis – displays radical genome alterations when compared to its most recent free-living relative Flavobacterium. To date, eight Blattabacterium genomes have been published, affording an unparalleled opportunity to examine the direction and magnitude of selective forces acting upon this group of symbionts. Here, we find that the Blattabacterium genome is experiencing a 10-fold increase in selection rate compared to Flavobacteria. Additionally, the proportion of selection events is largely negative in direction, with only a handful of loci exhibiting signatures of positive selection. These findings suggest that the Blattabacterium genome will continue to erode, potentially resulting in an endosymbiont with an even further reduced genome, as seen in other insect groups such as Hemiptera.

Nontuberculous mycobacterial lung disease (NTM), including Mycobacterium avium complex (MAC), is a growing health problem in North America and worldwide. Little is known about the molecular alterations occurring in the tissue microenvironment during NTM pathogenesis. Utilizing next generation sequencing, we sequenced sputum and matched lymphocyte DNA in 15 MAC patients for a panel of 19 genes known to harbor cancer susceptibility associated mutations. Thirteen of 15 NTM subjects had a diagnosis of breast cancer (BCa) before or after NTM infection. Thirty three percent (4/12) of these NTM-BCa cases exhibited at least 3 somatic mutations in sputa compared to matched lymphocytes. Twenty four somatic mutations were detected with at least one mutation in ATM, ERBB2, BARD1, BRCA1, BRCA2, AR, TP53, PALB2, CASP8, BRIP1, NBN and TGFB1 genes. All four NTM-BCa patients harboring somatic mutations also exhibited 15 germ line BRCA1 and BRCA2 mutations. The two NTM subjects without BCa exhibited twenty somatic mutations spanning BRCA1, BRCA1, BARD1, BRIP1, CHEK2, ERBB2, TP53, ATM, PALB2, TGFB1 and 3 germ line mutations in BRCA1 and BRCA2 genes. A single copy loss of STK11 and AR gene was noted in NTM-BCa subjects. Periodic screening of sputa may aid to develop risk assessment biomarkers for neoplastic diseases in NTM patients.

Mitochondria (mt) encoded respiratory complex-I (RCI) mutations and their pathogenicity remain largely unknown in prostate cancer (PCa). Little is known about the role of mtDNA loss on mt integrity in PCa. We determined mtDNA mutation in human and mice PCa and assessed the impact of mtDNA depletion on mt integrity. We also examined whether the circulating exosomes from PCa patients are transported to mt and carry mtDNA or mt proteins. We have employed next generation sequencing of the whole mt genome in human and Hi-myc PCa. The impact of mtDNA depletion on mt integrity, presence of mtDNA, and protein in sera exosomes was determined. A co-culture of human PCa cells and the circulating exosomes followed by confocal imaging determined co-localization of exosomes and mt. We observed frequent RCI mutations in human and Hi-myc PCa which disrupted corresponding complex protein expression. Depletion of mtDNA in PCa cells influenced mt integrity, increased expression of MFN1, MFN2, PINK1, and decreased expression of MT-TFA. Increased mt fusion and expression of PINK1 and DNM1L were also evident in the Hi-myc tumors. RCI-mtDNA, MFN2, and IMMT proteins were detected in the circulating exosomes of men with benign prostate hyperplasia (BPH) and progressive PCa. Circulating exosomes and mt co-localized in PCa cells. Our study identified new pathogenic RCI mutations in PCa and defined the impact of mtDNA loss on mt integrity. Presence of mtDNA and mt proteins in the circulating exosomes implicated their usefulness for biomarker development.

Resolution of evolutionary relationships among some monocot orders remains problematic despite the application of various taxon and molecular locus sampling strategies. In this study we sequenced and analysed a fragment of the low-copy, nuclear phytochrome C (PHYC) gene and combined these data with a previous multigene data set (four plastid, one mitochondrial, two nuclear ribosomal loci) to determine if adding this marker improved resolution and support of relationships among major lineages of monocots. Our results indicate the addition of PHYC to the multigene dataset increases support along the backbone of the monocot tree, although relationships among orders of commelinids remain elusive. We also estimated divergence times in monocots by applying newly evaluated fossil calibrations to our resolved phylogenetic tree. Inclusion of early-diverging angiosperm lineages confirmed the origin of extant monocots c. 131 Mya and strengthened the hypothesis of recent divergence times for some lineages, although current divergence time estimation methods may inadequately model rate heterogeneity in monocots. We note significant shifts in diversification in at least two monocot orders, Poales and Asparagales. We describe patterns of diversification in the context of radiation of other relevant plant and animal lineages. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178, 375–393.

Human papilloma virus-16 (HPV-16) associated oropharyngeal cancer (HPVOPC) is increasing alarmingly in the United States. We performed whole genome sequencing of a 44 year old, male HPVOPC subject diagnosed with moderately differentiated tonsillar carcinoma. We identified new somatic mutation in MUC16 (A.k.a. CA-125), MUC12, MUC4, MUC6, MUC2, SIRPA, HLA-DRB1, HLA-A and HLA-B molecules. Increased protein expression of MUC16, SIRPA and decreased expression of HLA-DRB1 was further demonstrated in this HPVOPC subject and an additional set of 15 HPVOPC cases. Copy number gain (3 copies) was also observed for MUC2, MUC4, MUC6 and SIRPA. Enhanced expression of MUC16, SIRPA and HPV-16-E7 protein was detectable in the circulating exosomes of numerous HPVOPC subjects. Treatment of non-tumorigenic mammary epithelial cells with exosomes derived from aggressive HPVOPC cells harboring MUC16, SIRPA and HPV-16-E7 proteins augmented invasion and induced epithelial to mesenchymal transition (EMT) accompanied by an increased expression ratio of the EMT markers Vimentin/E-cadherin. Exosome based screening of key HPVOPC associated molecules could be beneficial for early cancer diagnosis, monitoring and surveillance.

What are the genomic foundations of adaptation in sexual populations? We address this question using fitness–character and whole-genome sequence data from 30 Drosophila laboratory populations. These 30 populations are part of a nearly 40-year laboratory radiation featuring 3 selection regimes, each shared by 10 populations for up to 837 generations, with moderately large effective population sizes. Each of 3 sets of the 10 populations that shared a selection regime consists of 5 populations that have long been maintained under that selection regime, paired with 5 populations that had only recently been subjected to that selection regime. We find a high degree of evolutionary parallelism in fitness phenotypes when most-recent selection regimes are shared, as in previous studies from our laboratory. We also find genomic parallelism with respect to the frequencies of single-nucleotide polymorphisms, transposable elements, insertions, and structural variants, which was expected. Entirely unexpected was a high degree of parallelism for linkage disequilibrium. The evolutionary genetic changes among these sexual populations are rapid and genomically extensive. This pattern may be due to segregating functional genetic variation that is abundantly maintained genome-wide by selection, variation that responds immediately to changes of selection regime.

The collaborative development methods pioneered by the open source software community offer a way to create lessons that are open, accessible, and sustainable. This paper presents ten simple rules for doing this drawn from our experience with several successful projects., Comment: 11 pages, 3 figures

The Tradescantia alliance (subtribes Tradescantiinae and Thyrsantheminae of tribe Tradescantieae, family Commelinaceae) comprises a group of closely related New World genera exhibiting considerable variation in morphological, life history, and genomic traits. Despite ecological and cytogenetic significance of the Tradescantia alliance, phylogenetic relationships among genera and species remain uncertain. In particular, variation in inflorescence morphology has confounded classification and taxonomy. We inferred phylogenetic relationships using two plastid loci (rpL16, trnL-trnF) for 85 taxa in Commelinaceae, with sampling focused in the Tradescantia alliance. Constraint tests supported only subtribe Tradescantiinae, Tripogandra and Tinantia as monophyletic, with Tripogandra nested within Callisia. We estimated ancestral states for both breeding system and inflorescence condensation and tested for a correlation. Inflorescence morphology, an important character for generic identification, is more l...

We investigate the taxonomic status of the Texas garter snake, Thamnophis sirtalis annectens, a species of greatest conservation need in Texas. We broadly test the hypothesis that an integrative approach to species conservation has greater utility than using only a single data type (e.g., molecular, morphological, behavioral, or ecological) by demonstrating how ecological niche modeling and molecular genetics can be used synergistically to resolve taxonomic classifications. Using a phylogenetic analysis based on molecular data, we found that some putative T. s. annectens specimens actually represent a co-occurring subspecies (the red-sided garter snake, Thamnophis sirtalis parietalis), which is not of conservation concern. However, both T. s. annectens and T. s. parietalis are genetically distinctive from another co-occurring subspecies, Thamnophis sirtalis sirtalis, and the ecological distinctness of T. s. annectens from T. s. parietalis suggests that T. s. annectens is, in fact, a distinct evolutionary subunit. Only when both genetic and ecological information were included was the distinctiveness of T. s. annectens apparent, thus highlighting the need for integrative approaches in conservation management regardless of the taxa in question.

The research field of comparative genomics is moving from a focus on genes to a more holistic view including the repetitive complement. This study aimed to characterize relative proportions of the repetitive fraction of large, complex genomes in a nonmodel system. The monocotyledonous plant order Asparagales (onion, asparagus, agave) comprises some of the largest angiosperm genomes and represents variation in both genome size and structure (karyotype). Anonymous, low coverage, single-end Illumina data from 11 exemplar Asparagales taxa were assembled using a de novo method. Resulting contigs were annotated using a reference library of available monocot repetitive sequences. Mapping reads to contigs provided rough estimates of relative proportions of each type of transposon in the nuclear genome. The results were parsed into general repeat types and synthesized with genome size estimates and a phylogenetic context to describe the pattern of transposable element evolution among these lineages. The major finding is that although some lineages in Asparagales exhibit conservation in repeat proportions, there is generally wide variation in types and frequency of repeats. This approach is an appropriate first step in characterizing repeats in evolutionary lineages with a paucity of genomic resources.

Mitochondria (mt) encoded respiratory complex-I (RCI) mutations and their pathogenicity remain largely unknown in prostate cancer (PCa). Little is known about the role of mtDNA loss on mt integrity in PCa. We determined mtDNA mutation in human and mice PCa and assessed the impact of mtDNA depletion on mt integrity. We also examined whether the circulating exosomes from PCa patients are transported to mt and carry mtDNA or mt proteins. We have employed next generation sequencing of the whole mt genome in human and Hi-myc PCa. The impact of mtDNA depletion on mt integrity, presence of mtDNA, and protein in sera exosomes was determined. A co-culture of human PCa cells and the circulating exosomes followed by confocal imaging determined co-localization of exosomes and mt. We observed frequent RCI mutations in human and Hi-myc PCa which disrupted corresponding complex protein expression. Depletion of mtDNA in PCa cells influenced mt integrity, increased expression of MFN1, MFN2, PINK1, and decreased expression of MT-TFA. Increased mt fusion and expression of PINK1 and DNM1L were also evident in the Hi-myc tumors. RCI-mtDNA, MFN2, and IMMT proteins were detected in the circulating exosomes of men with benign prostate hyperplasia (BPH) and progressive PCa. Circulating exosomes and mt co-localized in PCa cells. Our study identified new pathogenic RCI mutations in PCa and defined the impact of mtDNA loss on mt integrity. Presence of mtDNA and mt proteins in the circulating exosomes implicated their usefulness for biomarker development.

Phylogenetic relationships in Mentha were inferred from DNA sequences of the chloroplast (cp) rpl16 intron and trnL-trnF region. The objectives were to test monophyly of Mentha and each of its sections and assess relationships among Mentha species. Based on cpDNA data, Mentha is strongly supported as monophyletic. The suggestions that M. cervina and M. cunninghamii should be placed in other genera gain no support from this analysis. Mentha cervina is sister to M. gattefossei, and the New Zealand endemic, M. cunninghamii, is allied with species from Australia (M. australis, M. diemenica, M. satureioides). No recognized section with more than one species sampled forms a monophyletic group. Section Pulegium may be monophyletic, but the third member of this section, M. grandiflora, was not sampled. Chloroplast DNA sequences of the putative allopolyploids M. canadensis and M. spicata suggest that M. arvensis and M. longifolia, respectively, may be their maternal parents.

Book details Mean genes: From sex to money to food: Taming our primal instincts, by Terry Burnham and Jay Phelan. New York: Basic, 2012. Pp. xvii + 297. S/b $16.99. Is evolutionary theory useful in the context of our everyday lives? The newly released second edition of Mean Genes by Terry Burnham and Jay Phelan is written as a Darwinian self-help book for what we all use everyday: our own minds and bodies. The authors begin with the general premise that evolutionary thought can inform all areas of scientific inquiry. In the four sections of the book that follow, they use this assumption to explain the annoying yet constant struggles that persist in our lives. The book draws rationale from evolutionary psychology and behavior to justify our attitudes toward debt, fat, drugs, risk, greed, gender, beauty, infidelity, family, and friends/foes. Each topic is framed as a problem we confront in day-to-day life, documented with evidence from published anthropological, behavioral, and psychological scientific literature as well as examples from popular culture and personal anecdotes. Though the title may be reminiscent of Richard Dawkins’ The Selfish Gene (1976), Burnham and Phelan rely less on a strict interpretation of evolutionary theory and more on telling an entertaining narrative to describe and provide resolution for complex, multifaceted problems with which we are all intimately familiar. The first edition of Mean Genes was released over a decade ago. The second edition is supplemented by commentary at the beginning of each section as well as general reflections in a preface and at the conclusion. These additions discuss the contemporary social and cultural context of the book. For example, the preface to “Thin Wallets and Fat Bodies” includes updated 2010 statistics for incidence of obesity in the United States to document the continued relevance of their arguments since the first edition (p. 15). The companion website at www.meangenes.org offers a “Notes and cited research section” with footnotes for the sometimes vague or oblique

 Premise of the study: Genome survey sequences (GSS) from massively parallel sequencing have potential to provide large, cost-effective data sets for phylogenetic inference, replace single gene or spacer regions as DNA barcodes, and provide a plethora of data for other comparative molecular evolution studies. Here we report on the application of this method to estimating the molecular phylogeny of core Asparagales, investigating plastid gene losses, assembling complete plastid genomes, and determining the type and quality of assembled genomic data attainable from Illumina 80 – 120-bp reads.  Methods: We sequenced total genomic DNA from samples in two lineages of monocotyledonous plants, Poaceae and Asparagales, on the Illumina platform in a multiplex arrangement. We compared reference-based assemblies to de novo contigs, evaluated consistency of assemblies resulting from use of various references sequences, and assessed our methods to obtain sequence assemblies in nonmodel taxa.  Key results: Our method returned reliable, robust organellar and nrDNA sequences in a variety of plant lineages. High quality assemblies are not dependent on genome size, amount of plastid present in the total genomic DNA template, or relatedness of available reference sequences for assembly. Phylogenetic results revealed familial and subfamilial relationships within Asparagales with high bootstrap support, although placement of the monotypic genus Aphyllanthes was placed with moderate confi dence.  Conclusions: The well-supported molecular phylogeny provides evidence for delineation of subfamilies within core Asparagales. With advances in technology and bioinformatics tools, the use of massively parallel sequencing will continue to become easier and more affordable for phylogenomic and molecular evolutionary biology investigations.

Fungal diversity and composition are still relatively unknown in many ecosystems; however, host identity and environmental conditions are hypothesized to influence fungal community assembly. To test these hypotheses, we characterized the richness, diversity, and composition of rhizosphere fungi colonizing three alpine plant species, Taraxacum ceratophorum, Taraxacum officinale, and Polemonium viscosum. Roots were collected from open meadow and willow understory habitats at treeline on Pennsylvania Mountain, Colorado, USA. Fungal small subunit ribosomal DNA was sequenced using fungal-specific primers, sample-specific DNA tags, and 454 pyrosequencing. We classified operational taxonomic units (OTUs) as arbuscular mycorrhizal (AMF) or non-arbuscular mycorrhizal (non-AMF) fungi and then tested whether habitat or host identity influenced these fungal communities. Approximately 14% of the sequences represented AMF taxa (44 OTUs) with the majority belonging to Glomus groups A and B. Non-AMF sequences represented 186 OTUs belonging to Ascomycota (58%), Basidiomycota (26%), Zygomycota (14%), and Chytridiomycota (2%) phyla. Total AMF and non-AMF richness were similar between habitats but varied among host species. AMF richness and diversity per root sample also varied among host species and were highest in T. ceratophorum compared with T. officinale and P. viscosum. In contrast, non-AMF richness and diversity per root sample were similar among host species except in the willow understory where diversity was reduced in T. officinale. Fungal community composition was influenced by host identity but not habitat. Specifically, T. officinale hosted a different AMF community than T. ceratophorum and P. viscosum while P. viscosum hosted a different non-AMF community than T. ceratophorum and T. officinale. Our results suggest that host identity has a stronger effect on rhizosphere fungi than habitat. Furthermore, although host identity influenced both AMF and non-AMF, this effect was stronger for the mutualistic AMF community.

Tree Thinking: An Introduction to Phylogenetic Biology, by David Baum and Stacey Smith. Greenwood Village, CO: Roberts and Company Publishers, 2013. Pp. xx +476. ISBN:9781936221165. H/b $75.00.