Biology subjects

Mishler, B. D.

Publications and source records attributed to Mishler, B. D..

6 recordsLinked to original sources

bioRxiv2025

The microbiome of Calasterella californica is shaped mostly by the genetics of the host thalli

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSPremise of studyC_ST_ABSThe recovery of non-target organism reads, especially when whole organisms are sampled, constitutes a great opportunity for studying microbial communities. The increase in whole genome sequencing feasibility, and the development of new pipelines and databases enable the use short reads to study bacterial communities associated with organisms. MethodsWe utilized population genomic data of the liverwort Calasterella californica obtained through the California Conservation Genomics Project to characterize the composition of its associated bacterial communities and explore its variation across the geographic space. Key resultsThe bacterial communities associated with C. californica were dominated by the methanotroph Methylobacterium and other Hyphomicrobiales, a group that includes well known plant symbionts. While diversity metrics of bacteria composition was similar across localities, we found significant differences in the relative abundance of a few taxa across California regions, likely driven by differences in precipitation and temperature seasonality. ConclusionsOur results support previous observations that liverwort bacterial communities are not randomly assembled, suggesting a potential role of the plant in determining community composition, an emerging pattern that deserves more attention. Our novel off-target metagenomics approach can be applied to any population level re-sequencing where whole organisms are sequenced, opening the door to exciting avenues of microbiome research using re-purposed data from landscape genomics.

microbiology↗

bioRxiv2024

Spatial Phylogenetics with Continuous Data: an Application to California Bryophytes

Spatial phylogenetics is premised on the idea that species are not discrete categorical entities but instead lie on a hierarchical evolutionary continuum that contains rich biological information valuable for quantifying spatial biodiversity patterns. Yet while spatial phylogenetic approaches use quantitative information to represent phylogenetic patterns, most have continued to rely on methods that discard valuable information about spatial patterns by converting continuous variables into binary categories. This includes representing geographic ranges using binary presence-absence data, classifying statistical significance into categories, and quantifying biogeographic gradients into discrete regions. In this paper we show how a full suite of spatial phylogenetic analyses, including analyses of alpha and beta diversity, neo- and paleo-endemism, biogeographic hypothesis testing, and spatial conservation prioritization, can be implemented with "smooth" methods that never remove information content by categorizing continuous data. Our analysis focuses on the bryophytes of California, an understudied group in a global plant biodiversity hotspot. Using a time-calibrated phylogeny and species distribution models for 548 species of mosses and liverworts, we profile the evolutionary diversity, compositional turnover, and conservation value of bryophyte communities across the state. Our results highlight important patterns in the diversity of this key plant group, while our methods can serve as a model for future studies seeking to maximize the information content of spatial phylogenetic analyses.

evolutionary biology↗

bioRxiv2022

canaper: Categorical analysis of neo- and paleo-endemism in R

O_LIBiodiversity has typically been quantified using species richness, but this ignores evolutionary history. Due to the increasing availability of robust phylogenies, methods have been developed that incorporate phylogenetic relationships into quantification of biodiversity. CANAPE (categorical analysis of neo- and paleo-endemism) is one such method that can provide insight into the evolutionary processes generating biodiversity. The only currently available software implementing CANAPE is Biodiverse, which is written in Perl and can be used either through a graphical user interface (GUI) or user-developed scripts. However, many researchers, particularly in the fields of ecology and evolutionary biology, use the R programming language to conduct their analyses. C_LIO_LIHere, we present canaper, a new R package that provides functions to conduct CANAPE in R. canaper implements methods for efficient computation, including parallelization and encoding of community data as sparse matrices. The interface is designed for maximum simplicity and reproducibility; CANAPE can be conducted with two functions, and parallel computing can be enabled with one line of code. C_LIO_LIOur case study shows that canaper produces equivalent results to Biodiverse and can complete computations on moderately sized datasets quickly (< 10 min to reproduce a canonical study). C_LIO_LIcanaper allows researchers to conduct all analyses from data import and cleaning through CANAPE within R, thereby averting the need to manually import and export data and analysis results between programs. We anticipate canaper will become a part of the toolkit for analyzing biodiversity in R. C_LI

evolutionary biology↗

bioRxiv2022

Ultraviolet radiation and dehydration stress induce overlapping transcriptional and metabolic responses in Syntrichia mosses

O_LIProtection from excess solar radiation and access to sufficient water are important problems for terrestrial plants to solve. Desiccation tolerance (DT), defined as the ability to equilibrate to dry air and resume normal metabolic activity after rehydration, allows organisms to survive dry periods by limiting metabolic activity to periods of moisture availability. We compared separate and combined effects of chronic ultraviolet radiation (UVR) treatments (UV-A and UV-A/B) and a dehydration treatment (as a surrogate for desiccation) in the mosses Syntrichia ruralis and S. caninervis to uncover the nature of correlation between DT and UVR tolerance (UVRT). C_LIO_LIUsing a fully factorial experiment with combined transcriptomics and metabolomics, we tested for cross-talk (overlap in signaling pathways in response to different stressors but separate mechanisms of protection) in the genetic underpinnings of DT and UVRT and cross-tolerance (overlap in the mechanism of protection) these two stressors. C_LIO_LIShared transcriptomic response to the two stressors with no significant interaction between them suggested cross-talk between UVRT and DT for S. caninervis. Phenolic metabolites and transcripts were involved in the response to UVR and dehydration in both species. C_LIO_LISome candidate UVRT genes and metabolites were induced by UVR in S. ruralis, but not S. caninervis, supporting the hypothesis that S. ruralis has a more plastic, acclimatable UVR response than S. caninervis, and that these differences are predictable by their unique interaction with these stressors as poikilohydric organisms. C_LI

plant biology↗

bioRxiv2021

Exploring dimensions of biodiversity in Japanese ferns

PremiseBiodiversity is often only measured with species richness. However, this ignores evolutionary history and is not sufficient for making conservation decisions. Here, we characterize multiple facets and drivers of biodiversity to understand how these relate to bioregions and conservation status in the ferns of Japan. MethodsWe compiled a community dataset of 1,239 20 km x 20 km grid-cells including 672 taxa based on > 300,000 specimen records. We combined this with a phylogeny and functional traits to analyze taxonomic, phylogenetic, and functional diversity, and modeled biodiversity metrics in response to environmental factors and reproductive mode. Hierarchical clustering was used to delimit bioregions. Conservation status and threats were assessed by comparing the overlap of significantly diverse grid-cells with conservation zones and range maps of native Japanese deer. ResultsTaxonomic richness was highest at mid-latitudes. Phylogenetic and functional diversity and phylogenetic endemism were highest in small southern islands. Relative phylogenetic and functional diversity were high at high and low latitudes, and low at mid-latitudes. Grid-cells were grouped into three (phylogenetic) or four (taxonomic) major bioregions. Temperature and apomixis were identified as drivers of biodiversity patterns. Conservation status was generally high for grid-cells with significantly high biodiversity, but the threat due to herbivory by deer was greater for taxonomic richness than other metrics. ConclusionsOur integrative approach reveals previously undetected patterns and drivers of biodiversity in the ferns of Japan. Future conservation efforts should recognize that threats can vary by biodiversity metric and consider multiple multiple metrics when establishing conservation priorities.

evolutionary biology↗

bioRxiv2020

Spatial phylogenetics of butterflies in relation to environmental drivers and angiosperm diversity across North America

Broad-scale quantitative assessments of biodiversity and the factors shaping it remain particularly poorly explored in insects. Here, we undertook a spatial phylogenetic analysis of North American butterflies via assembly of a time-calibrated phylogeny of the region coupled with a unique, complete range assessment for ~75% of the known species. We utilized a suite of phylodiversity metrics and associated environmental data to test whether climate stability and temperature gradients have shaped North American butterfly phylogenetic diversity and endemism. We also undertook the first direct, quantitative comparisons of spatial phylogenetic patterns between butterflies and flowering plants in North America. We expected concordance between butterflies and angiosperms based on both shared historical environmental drivers and presumed strong butterfly-host plant specializations. We instead found that biodiversity patterns in butterflies are strikingly different from flowering plants in some regions of the continent. In particular, the warm desert regions of the southwestern United States and Mexico showed surprisingly high butterfly phylogenetic diversity and endemism, in contrast to much lower values for angiosperms. Butterflies did not show patterns of phylogenetic clustering as found in flowering plants, suggesting differences in habitat conservation between the two groups. Finally, we found weak relationships and spatially structured biases in relative branching timing between angiosperms and butterflies. These results suggest that shared biogeographic histories and trophic associations do not necessarily assure similar diversity outcomes. The work has applied value in conservation planning, documenting warm deserts as an important North American butterfly biodiversity hotspot.

ecology↗