Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Phylogenetic analysis of chromosome numbers and genetic markers

A phylogenetic tree captures the evolutionary relationships among sampled taxa – major taxonomic groups, species, infraspecific taxa, or isolates. Phylogenetic analysis is a central component of evolutionary and ecological studies, as it lends a unifying framework to draw inferences about evolutionary and ecological processes that form biodiversity. Via phylogenetic comparative methods, trait data (for example, morphological or physiological data) and geographical data may be analyzed jointly with a given phylogeny to test specific hypotheses about the evolution and ecology of focal groups of organisms. In this thesis dissertation, I present four studies demonstrating how phylogenetic analysis can yield new evolutionary and ecological insights. In the first two studies, I compare the evolutionary fates of polyploid versus diploid lineages in fish and to test whether polyploidization coincides with speciation events in land plants. Polyploid species arise from whole genome duplication and often exhibit morphological, physiological, and ecological differentiation from their diploid parents. Understanding their evolutionary patterns in the background of diploid species help us to understand why polyploidization is abundant in some organisms (plants) but not in others (fishes). In the other two studies, I explore the biodiversity of freshwater red algae in the wild and aquarium shops, using phylogenetic analyses to reveal potential introductions of these organisms via the global aquarium trade. Furthermore, I identify candidate genetic markers that may be more suitable than commonly used markers to facilitate future studies of phylogenetic community ecology of the red algae. Not only do these studies illustrate the utility of phylogenetic analyses to tackle diverse questions in evolution and ecology, but they also have forwarded the discussion on those four distinct topics.Science, Faculty ofGraduat

Data from: Phylogenetic evidence for cladogenetic polyploidization in land plants

Premise of the study: Polyploidization is a common and recurring phenomenon in plants and is often thought to be a mechanism of "instant speciation." Whether polyploidization is associated with the formation of new species ("cladogenesis") or simply occurs over time within a lineage ("anagenesis") has never, however, been assessed systematically. Methods: Here, we tested this hypothesis using phylogenetic and karyotypic information from 235 plant genera (mostly angiosperms). We first constructed a large database of combined sequence and chromosome number data sets using an automated procedure. We then applied likelihood models (ClaSSE) that estimate the degree of synchronization between polyploidization and speciation events in maximum likelihood and Bayesian frameworks. Key results: Our maximum likelihood analysis indicated that 35 genera supported a model that includes cladogenetic transitions over a model with only anagenetic transitions, whereas three genera supported a model that incorporates anagenetic transitions over one with only cladogenetic transitions. Furthermore, the Bayesian analysis supported a preponderance of cladogenetic change in four genera but did not support a preponderance of anagenetic change in any genus. Conclusions: Overall, these phylogenetic analyses provide the first broad confirmation that polyploidization is temporally associated with speciation events, suggesting that it is indeed a major speciation mechanism in plants, at least in some genera

ndhF_alignment

Multiple alignment of ndhF gene

CHS_alignment

Multiple alignment of CHS gene

CHS_alignment

Multiple alignment of CHS gene

ndhF_alignment

Multiple alignment of ndhF gene

PHYA_alignment

Multiple alignment of PHYA gene

Data from: Multi-speed genome diploidization and diversification after an ancient allopolyploidization

Hybridization and genome doubling (allopolyploidy) have led to evolutionary novelties as well as to the origin of new clades and species. Despite the importance of allopolyploidization, the dynamics of post-polyploid diploidization (PPD) at the genome level has been only sparsely studied. The Microlepidieae (MICR) is a crucifer tribe of 17 genera and c. 56 species endemic to Australia and New Zealand. Our phylogenetic and cytogenomic analyses revealed that MICR originated via an inter-tribal hybridization between ancestors of Crucihimalayeae (n = 8; maternal genome) and Smelowskieae (n = 7; paternal genome), both native to the Northern Hemisphere. The reconstructed ancestral allopolyploid genome (n = 15) originated probably in north-eastern Asia or western North America during the Late Miocene (c. 10.6 - 7 million years ago) and reached the Australian mainland via long-distance dispersal. In Australia, the allotetraploid genome diverged into at least three main subclades exhibiting different levels of PPD and diversity: 1.25-fold descending dysploidy (DD) of n = 15 → n = 12 (autopolyploidy → 24) in perennial Arabidella (3 species), 1.5-fold DD of n = 15 → n = 10 in the perennial Pachycladon (11 spp.), and 2.1 to 3.75-fold DD of n = 15 → n = 7 - 4 in the largely annual crown group genera (42 spp. in 15 genera). These results are among the first to demonstrate multi-speed genome evolution in taxa descending from a common allopolyploid ancestor. It is suggested that clade-specific PPD can operate at different rates and efficacies, and can be tentatively linked to life histories and the extent of taxonomic diversity

PHYA_alignment

Multiple alignment of PHYA gene