Biology subjects

Marx, H. E.

Publications and source records attributed to Marx, H. E..

7 recordsLinked to original sources

bioRxiv2026

A multi-tissue transcriptome strategy for genomic resource development in Pinus edulis

Premise:: Conifers comprise one-sixth of global forests and landscape genomic studies are urgently needed to understand their biology, yet relatively few conifer species have reference genomes. Targeted exon-capture is a practical alternative to whole-genome sequencing, but selecting loci without a reference genome remains a barrier. We developed a multi-tissue reference transcriptome for pi non pine (Pinus edulis) to ask how multi-tissue sampling improves probe design, and what is lost under a conventional single-tissue approach. Methods: We assembled a reference transcriptome from four diploid tissues (needle, phloem, root, vegetative bud) and one haploid tissue (megagametophyte), using the latter as a pseudo-guide. We designed a target-capture probe-set by prioritizing highly expressed P. edulis transcripts and transcripts matching a conifer exon database. Results: We recovered 76% of conserved plant genes with few duplicated transcripts. Filtering yielded 15,664 transcripts totaling 31.4 Mb, ~0.1% of the genome. Tissue-specific expression was substantial: 27.4% of transcripts occurred exclusively in non-needle tissues. Functional annotation confirmed complementary contributions, including seed-desiccation and germination genes from megagametophytes, and defense- and stress-associated genes from roots and phloem. Discussion: We built a transcriptome and efficient probe set using a roadmap suitable for other non-model plants with large genomes; keys to success were prioritizing complementary tissues and using expression-based filtering.

genomics↗

bioRxiv2020

Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae)

Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci, especially in groups experiencing whole-genome duplication (WGD) events. Common approaches for processing paralogs in target enrichment datasets include random selection, manual pruning, and mainly, the removal of entire genes that show any evidence of paralogy. These approaches are prone to errors in orthology inference or removing large numbers of genes. By removing entire genes, valuable information that could be used to detect and place WGD events is discarded. Here we use an automated approach for orthology inference in a target enrichment dataset of 68 species of Alchemilla s.l. (Rosaceae), a widely distributed clade of plants primarily from temperate climate regions. Previous molecular phylogenetic studies and chromosome numbers both suggested ancient WGDs in the group. However, both the phylogenetic location and putative parental lineages of these WGD events remain unknown. By taking paralogs into consideration, we identified four nodes in the backbone of Alchemilla s.l. with an elevated proportion of gene duplication. Furthermore, using a gene-tree reconciliation approach we established the autopolyploid origin of the entire Alchemilla s.l. and the nested allopolyploid origin of four major clades within the group. Here we showed the utility of automated tree-based orthology inference methods, previously designed for genomic or transcriptomic datasets, to study complex scenarios of polyploidy and reticulate evolution from target enrichment datasets.

evolutionary biology↗

bioRxiv2020

TagSeq for gene expression in non-model plants: a pilot study at the Santa Rita Experimental Range NEON core site

Premise of the studyTagSeq is a cost-effective approach for gene expression studies requiring a large number of samples. To date, TagSeq studies in plants have been limited to those with a high quality reference genome. We tested the suitability of reference transcriptomes for TagSeq in non-model plants, as part of a study of natural gene expression variation at the Santa Rita Experimental Range NEON core site. MethodsTissue for TagSeq was sampled from multiple individuals of four species [Bouteloua aristidoides and Eragrostis lehmanniana (Poaceae); Tidestromia lanuginosa (Amaranthaceae), and Parkinsonia florida (Fabaceae)] at two locations on three dates (56 samples total). One sample per species was used to create a reference transcriptome via standard RNA-seq. TagSeq performance was assessed by recovery of reference loci, specificity of tag alignments, and variation among samples. ResultsA high fraction of tags aligned to each reference and mapped uniquely. Expression patterns were quantifiable for tens of thousands of loci, which revealed consistent spatial differentiation in expression for all species. DiscussionTagSeq using de novo reference transcriptomes was an effective approach to quantifying gene expression in this study. Tags were highly locus specific and generated biologically informative profiles for four non-model plant species.

plant biology↗

bioRxiv2020

Progress Towards Plant Community Transcriptomics: Pilot RNA-Seq Data from 24 Species of Vascular Plants at Harvard Forest

O_LIPremise of the study: Large scale projects such as NEON are collecting ecological data on entire biomes to track and understand plant responses to climate change. NEON provides an opportunity for researchers to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a pilot study to investigate the challenges of collecting RNA-seq data from phylogenetically diverse NEON plant communities, including species with diploid and polyploid genomes. C_LIO_LIMethods: We used Illumina NextSeq to generate >20 Gb of RNA-seq for each of 24 vascular plant species representing 12 genera and 9 families at the Harvard Forest NEON site. Each species was sampled twice, in July and August 2016. We used Transrate, BUSCO, and GO analyses to assess transcriptome quality and content. C_LIO_LIResults: We obtained nearly 650 Gb of RNA-seq data that assembled into more than 755,000 translated protein sequences across the 24 species. We observed only modest differences in assembly quality scores across a range of k-mer values. On average, transcriptomes contained hits to >70% of loci in the BUSCO database. We found no significant difference in the number of assembled and annotated genes between diploid and polyploid transcriptomes. C_LIO_LIDiscussion: Our resource provides new RNA-seq datasets for 24 species of vascular plants in Harvard Forest. Challenges associated with this type of study included recovery of high quality RNA from diverse species and access to NEON sites for genomic sampling. Overcoming these challenges offers clear opportunities for large scale studies at the intersection of ecology and genomics. C_LI

genomics↗

bioRxiv2018

Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness

PREMISE OF THE STUDYAt the intersection of ecology and evolutionary biology, community phylogenetics can provide insights into overarching biodiversity patterns, particularly in remote and understudied ecosystems. To understand community assembly of the high-alpine flora of the Sawtooth National Forest, USA, we analyzed phylogenetic structure within and between nine summit communities.\n\nMETHODSWe used high-throughput sequencing to supplement existing data and infer a nearly completely sampled community phylogeny of the alpine vascular flora. We calculated mean nearest taxon distance (MNTD) and mean pairwise distance (MPD) to quantify phylogenetic divergence within summits, and assed how maximum elevation explains phylogenetic structure. To evaluate similarities between summits we quantified phylogenetic turnover, taking into consideration micro-habitats (talus vs. meadows).\n\nKEY RESULTSWe found different patterns of community phylogenetic structure within the six most species-rich orders, but across all vascular plants phylogenetic structure was largely no different from random. There was a significant negative correlation between elevation and tree-wide phylogenetic diversity (MPD) within summits: significant overdispersion degraded as elevation increased. Between summits we found high phylogenetic turnover, which was driven by greater niche heterogeneity on summits with alpine meadows.\n\nCONCLUSIONSThis study provides further evidence that stochastic processes shape the assembly of vascular plant communities in the high-alpine at regional scales. However, order-specific patterns suggest adaptations may be important for assembly of specific sectors of the plant tree of life. Further studies quantifying functional diversity will be important to disentangle the interplay of eco-evolutionary processes that likely shape broad community phylogenetic patterns in extreme environments.

evolutionary biology↗

bioRxiv2018

Polyploid plants have faster rates of multivariate climatic niche evolution than their diploid relatives

Whole genome duplication is an important evolutionary process in plants. In contrast to other speciation mechanisms, polyploid species begin with substantial postzygotic reproductive isolation from progenitors while being sympatric with one or both. These nascent polyploid species often go extinct due to ecological and evolutionary genetic obstacles. Interestingly, polyploid species appear to quickly occupy different geographic distributions and ecological niches than their diploid progenitors. Using biogeographic data from polyploid and diploid species representing 49 genera of vascular plants, we tested whether climatic niches of polyploid species evolve faster than their diploid relatives. We found polyploid species often have less climatic overlap than expected with diploid progenitors. Consistent with this pattern, we estimated that the climatic niches of polyploid plants consistently evolved faster than the niches of diploid relatives. Our results indicate ecological niche differentiation is important for polyploid establishment, and suggest ecological differentiation is important for speciation processes more widely.\n\nStatement of AuthorshipAB and MS conceived of project, AB and NA generated the dataset, AB and HM performed analyses, AB and MS cowrote manuscript.\n\nData Accessibility StatementUpon acceptance all necessary R scripts, data, and files supporting the results will be archived on FigShare with the data DOI included at the end of the article.

evolutionary biology↗

bioRxiv2018

For comparing phylogenetic diversity among communities, go ahead and use synthesis phylogenies

Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis-based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose-built phylogenies and their corresponding synthesis-based trees (two from Phylomatic and one from the Open Tree of Life [OTL]). We simulated 1,000 communities and 12,000 continuous traits along each purpose-built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagels {lambda} and Blombergs K). Synthesis-based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose-built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearmans{rho} > 0.8 in most cases). Mean pairwise distance (both alpha and beta) is the index that is most robust to the differences in tree construction that we tested. Measures of phylogenetic diversity based on the OTL showed the highest correlation with measures based on the purpose-built phylogenies. Trait phylogenetic signal estimated with synthesis-based phylogenies, especially from the OTL, were also highly correlated with estimates of Blombergs K or close to Pagels {lambda} from purpose-built phylogenies when traits were simulated under Brownian Motion. For commonly employed community phylogenetic analyses, our results justify taking advantage of recently developed and continuously improving synthesis trees, especially the Open Tree of Life.

ecology↗