Biology subjects

Rosenzweig, F.

Publications and source records attributed to Rosenzweig, F..

9 recordsLinked to original sources

bioRxiv2026

Beyond Onset Timing: Longer Sound Envelope Duration Enhances Neural Representation of the Musical Beat

Musical rhythm is often experienced with a periodic beat, serving as a temporal reference for coordination with the rhythm. Thus far, models of beat processing have mainly relied on representing sensory inputs as patterns of onset timing, with limited consideration of other sensory features. Here, we challenge this view by showing that the internal representation of beat is affected by other temporal features of the stimulus beyond onset timing alone. We recorded electroencephalography (EEG) while participants listened to rhythmic sequences designed to elicit a beat. Across conditions, we manipulated the duration of the tones conveying the rhythms, while keeping all other parameters identical, including overall intensity, speed, and rhythmic pattern structure. Crucially, the beat periodicity was enhanced in neural activity with increased sound duration, even though the beat periodicity was not prominent in the acoustic features, thus ruling out basic sensory confounds. These results demonstrate the preferential role of longer sound durations in fostering temporal scaffolding processes that integrate fast rhythmic inputs into behavior-relevant internal structures such as the beat. More generally, our findings are compatible with a holistic processing account whereby a range of features beyond onset timing may be integrated into a neural representation of rhythm. Graphical Abstract: Fig. 2EEG was recorded while listeners heard rhythmic sequences eliciting a beat. Sound duration (sonic duty cycle) was varied across four conditions while speed, pattern, and intensity stayed constant. Beat-related EEG responses increased with longer sounds, and were enhanced in all conditions compared to auditory nerve model envelopes, which did not show prominent energy at the beat periodicity, ruling out sensory confounds. Results support holistic rhythm processing beyond onset timing alone. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/721298v1_fig2.gif" ALT="Figure 2"> View larger version (27K): org.highwire.dtl.DTLVardef@10a0599org.highwire.dtl.DTLVardef@f5a95forg.highwire.dtl.DTLVardef@42d1ceorg.highwire.dtl.DTLVardef@dc58a7_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 2.C_FLOATNO EEG and auditory nerve model output analysis based on magnitude spectrum and autocorrelation. Each row represents a duty cycle condition. The two columns on the left represent the magnitude spectrum-based analysis. The first column represents the group-level averaged magnitude spectra at a pool of fronto-central electrodes, across conditions. Beat-related frequencies are shown in red, and beat-unrelated frequencies are shown in blue. Scalp topographies of the neural activity measured at the average magnitudes of beat-related (in red circle) and unrelated (in blue circle) frequencies are represented as insets. The second column represents the normalized magnitude spectra obtained from the auditory nerve model output for each duty cycle sequence. The two columns on the right represent the autocorrelation-based analysis (for visualization purposes, only a subset of lags from 0 to 2.4 s corresponding to the pattern duration is shown). The first column represents the group-level averaged autocorrelation function measured from the same pool of fronto-central electrodes, across conditions. Beat-related lags are shown in red, and beat-unrelated lags are shown in blue. The second column represents the autocorrelation function of the auditory nerve model output for each duty cycle sequence. C_FIG

neuroscience↗

bioRxiv2025

Cryptic multicellularity in wild yeast brings selective advantages under stress

Multicellularity has evolved dozens of times in many branches across the Tree of Life, in each case producing a new kind of individual that has the potential for division of labor among its constituent cells. In many of these instances, nascent multicellularity has remained facultative, manifesting only under conditions where it provides a decisive fitness advantage to the genome in which it has arisen. Here we investigate the mechanistic basis for, and the selective advantages of, cryptic multicellularity in wild strains of the yeast Saccharomyces cerevisiae. Meiotic purification of this trait, followed by genome sequencing, indicates that the genome of diploid champagne yeast DB146 is homozygous at the AMN1 locus (Antagonist of Mitotic exit Network) for an allele that dysregulates post-mitotic cell separation. Expression of this trait in haploid derivatives of DB146 results in clonal multicellular clusters in which daughters remain attached to mother cell walls. Systematic analysis of viability in haploid and diploid DB146 derivatives subjected to benign conditions as well as to starvation, desiccation, and low temperature at different cell titers demonstrates that haploid multicellular variants exhibit higher survivorship under conditions that wild yeast likely experience when they overwinter. Examining a collection of other wild strains, we find that [~]20% exhibit ploidy-dependent expression of clonal multicellularity. Altogether, our data suggest that in yeast that sporulate when starved, cryptic multicellularity may come under balancing selection because haploid multicellular progeny enjoy a transient survival advantage that fades once favorable growth conditions resume.

microbiology↗

bioRxiv2024

Genetic predisposition towards multicellularity in Chlamydomonas reinhardtii

The evolution from unicellular to multicellular organisms facilitates further phenotypic innovations, notably cellular differentiation. Multiple research groups have shown that in the laboratory simple, obligate multicellularity can evolve from a unicellular ancestor under appropriate selection. However, little is known about the extent to which deterministic factors like ancestral genotype and environmental context influence the likelihood of this evolutionary transition. To test whether certain genotypes are predisposed to evolve multicellularity in different environments, we carried out a set of 24 evolution experiments each founded by a population consisting of 10 different strains of the unicellular green alga Chlamydomonas reinhardtii, all in equal proportions. Twelve of the initially identical replicate populations were subjected to predation by the protist Parmecium tetraurelia while the other 12 were subjected to settling selection by slow centrifugation. Population subsamples were transferred to fresh media on a weekly basis for a total of 40 transfers ([~]600 generations). Heritable multicellular structures arose in four of 12 predation-selected populations (6 multicellular isolates in total), but never in the settling selection populations. By comparing whole genome sequences of the founder and evolved strains, we discovered that every multicellular isolate arose from one of two founders. Cell cluster size varied not only among evolved strains derived from different ancestors but among strains derived from the same ancestor. These findings show that both deterministic and stochastic factors influence whether initially unicellular populations can evolve simple multicellular structures.

evolutionary biology↗

bioRxiv2023

Fossil-calibrated inference of divergence times among the Volvocine algae enables reconstruction of the steps that led to differentiated multicellularity

Throughout its nearly four-billion-year history, life has undergone evolutionary transitions in which simpler subunits have become integrated to form a more complex whole. Many of these transitions opened the door to innovations that resulted in increased biodiversity and/or organismal efficiency. The evolution of multicellularity from unicellular forms represents one such transition, one that paved the way for cellular differentiation, including differentiation of male and female gametes. A useful model for studying the evolution of multicellularity and cellular differentiation is the volvocine algae, a clade of freshwater green algae whose members range from unicellular to colonial, from undifferentiated to completely differentiated, and whose gamete types can be isogamous, anisogamous, or oogamous. To better understand how multicellularity, differentiation, and gametes evolved in this group, we used comparative genomics and fossil data to establish a geologically calibrated roadmap of when these innovations occurred. Our results, presented as ancestral-state reconstructions, show that multicellularity arose independently twice in this clade. Our chronograms indicate multicellularity evolved during the Carboniferous-Triassic periods in Goniaceae + Volvocaceae, and possibly as early as the Cretaceous in Tetrabaenaceae. Using divergence time estimates we inferred when, and in what order, specific developmental changes occurred that led to differentiated multicellularity and oogamy. We find that in the volvocine algae the temporal sequence of developmental changes leading to differentiated multicellularity is much as proposed by David Kirk, and that multicellularity is correlated with the acquisition of anisogamy and oogamy. Lastly, morphological, molecular, and divergence time data suggest the possibility of cryptic species in Tetrabaenaceae.

evolutionary biology↗

bioRxiv2021

Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the volvocine algae

The volvocine algae, which include the single-celled species Chlamydomonas reinhardtii and the colonial species Volvox carteri, serve as a model in which to study the evolution of multicellularity and cellular differentiation. Studies reconstructing the evolutionary history of this group have often relied on datasets of one to a few genes for phylogenetic inference and ancestral character state reconstruction. These studies suggest that multicellularity evolved only once in the volvocine algae, that each of its three colonial families is monophyletic, and that there have been at least three independent origins of cellular differentiation in the group. We performed RNA-Seq on 55 strains representing 47 volvocine algal species and obtained similar data from curated databases on 13 additional strains. We compiled a dataset consisting of transcripts for 40 single-copy, protein-coding, nuclear genes, then subjected the predicted amino acid sequences of these genes to maximum likelihood, Bayesian inference, and coalescent-based analyses. These analyses show that multicellularity independently evolved at least twice in the volvocine algae and that the colonial family Goniaceae is not monophyletic. Our data further indicate that cellular differentiation independently arose at least four and possibly as many as six times within the group. Altogether, these results show how multicellularity and cellular differentiation are evolutionarily labile in the volvocine algae, affirming their importance for the study of major transitions in the history of life.

evolutionary biology↗

bioRxiv2019

Discrete Community Assemblages Within Hypersaline Paleolake Sediments of Pilot Valley, Utah

Hypersaline paleolake sediments are understudied ecosystems whose microbial ecology is largely unknown. Here we present mineralogical, geochemical, and small-subunit 16S rRNA gene sequence data on one such environment, the Pilot Valley Basin (PVB), a sub-basin of ancient Lake Bonneville located in northwest Utah. PVB exhibits a variety of aqueous minerals including phyllosilicates, carbonates, and sulfates, as well as microbially-induced sedimentary structures. As perchlorate occurs naturally (up to 6.5 ppb) in Pilot Valley sediments, and because recent evidence suggests that it is subject to biotic reduction, PVB has been proposed as a Mars analog site for astrobiological studies. 16S rRNA gene sequencing was used to investigate microbial diversity and community structure along horizontal and vertical transects within the upper basin sediments and beta diversity analyses indicate that the microbial communities in Pilot Valley are structured into three discrete groups. Operational taxonomic units (OTUs) belonging to the main archaeal phylum, Euryarchaeota, make up ~23% of the sequences, while OTUs belonging to three bacterial phyla, Proteobacteria, Bacteroides and Gemmatimonadetes, constitute ~60-70% of the sequences recovered at all sites. Diversity analyses indicate that the specific composition of each community correlates with sediment grain size, and with biogeochemical parameters such as nitrate and sulfate concentrations. Interestingly, OTUs belonging to the phylum Gemmatimonadetes are co-located with extreme halophilic archaeal and bacterial taxa, which suggests a potential new attribute, halophilicity, of this newly-recognized phylum. Altogether, results of this first comprehensive geomicrobial study of Pilot Valley reveal that basin sediments harbor a complex and diverse ecosystem.

microbiology↗

bioRxiv2019

Evolutionary dynamics of de novo mutations and mutant lineages arising in a simple, constant environment

A large, asexual population founded by a single clone evolves into a population teeming with many, whether or not its environment is structured, and whether or not resource levels are constant or fluctuating. The maintenance of genetic complexity in such populations has been attributed to balancing selection, or to either clonal interference or clonal reinforcement, arising from antagonistic or synergistic interactions, respectively. To distinguish among these possibilities, to identify targets of selection and establish when and how often they are hit, as well as to gain insight into how de novo mutations interact, we carried out 300-500 generation glucose-limited chemostat experiments founded by an E. coli mutator. To discover all de novo mutations reaching [≥]1% frequency, we performed whole-genome, whole-population sequencing at [~]1000X-coverage every 50 generations. To establish linkage relationships among these mutations and depict the dynamics of evolving lineages we sequenced the genomes of 96 clones from each population when allelic diversity was greatest. Operon-specific mutations that enhance glucose uptake arose to high frequency first, followed by global regulatory mutations. Late-arising mutations were related to energy conservation as well as to mitigating pleiotropic effects wrought by earlier regulatory changes. We discovered extensive polymorphism at relatively few loci, with identical mutations arising independently in different lineages, both between and within replicate populations. Out of more than 3,000 SNPs detected in nearly 1,800 genes or intergenic regions, only 17 reached a frequency [≥] 98%, indicating that the evolutionary dynamics of adaptive lineages was dominated by clonal interference. Finally, our data show that even when mutational input is increased by an ancestral defect in DNA repair, the spectrum of beneficial mutations that reach high frequency in a simple, constant resource-limited environment is narrow, resulting in extreme parallelism where many adaptive mutations arise but few ever go to fixation. Author SummaryMicrobial evolution experiments open a window on the tempo and dynamics of evolutionary change in asexual populations. High-throughput sequencing can be used to catalog de novo mutations, determine in which lineages they arise, and assess allelic interactions by tracking the fate of those lineages. This adaptive genetics approach makes it possible to discover whether clonal interactions are antagonistic or synergistic, and complements genetic screens of induced deleterious/loss-of-function mutants. We carried out glucose-limited chemostat experiments founded by an E. coli mutator and performed whole-genome, whole-population sequencing on 300-500 generation evolutions, cataloging 3,346 de novo mutations that reached [≥]1% frequency. Mutations enhancing glucose uptake rose to high frequency first, followed by global regulatory changes that modulate growth rate and limiting resource assimilation, then by mutations that favor energy conservation or mitigate pleiotropic effects of earlier regulatory changes. We discovered that a few loci were highly polymorphic, with identical mutations arising independently in different lineages, both between and within replicate populations. Thus, when mutational input is increased by an ancestral defect in DNA repair, the spectrum of beneficial mutations that arises under constant resource-limitation is narrow, resulting in extreme parallelism where many adaptive mutations arise but few ever become fixed.

evolutionary biology↗

bioRxiv2018

De novo origin of multicellularity in response to predation

The transition from unicellular to multicellular life was one of a few major events in the history of life that created new opportunities for more complex biological systems to evolve. Predation is hypothesized as one selective pressure that may have driven the evolution of multicellularity. Here we show that de novo origins of simple multicellularity can evolve in response to predation. We subjected outcrossed populations of the unicellular green alga Chlamydomonas reinhardtii to selection by the filter-feeding predator Paramecium tetraurelia. Two of five experimental populations evolved multicellular structures not observed in unselected control populations within ~750 asexual generations. Considerable variation exists in the evolved multicellular life cycles, with both cell number and propagule size varying among isolates. Survival assays show that evolved multicellular traits provide effective protection against predation. These results support the hypothesis that selection imposed by predators may have played a role in some origins of multicellularity.

evolutionary biology↗

bioRxiv2017

Motility in multicellular Chlamydomonas reinhardtii

The advent of multicellularity was a watershed event in the history of life, yet the transition from unicellularity to multicellularity is not well understood. Multicellularity opens up opportunities for innovations in intercellular communication, cooperation, and specialization, which can provide selective advantages under certain ecological conditions. The unicellular alga Chlamydomonas reinhardtii has never had a multicellular ancestor yet it is closely related to the volvocine algae, a clade containing taxa that range from simple unicells to large, specialized multicellular colonies. Simple multicellular structures have been observed to evolve in C. reinhardtii in response to predation or to settling rate-based selection. Structures formed in response to predation consist of individual cells grouped within a shared transparent extracellular matrix. Evolved isolates form such structures obligately under culture conditions in which their wild type ancestors do not, indicating that newly-evolved multicellularity is heritable. C. reinhardtii is capable of photosynthesis, and possesses an eyespot and two flagella with which it moves towards or away from light in order to optimize input of radiant energy. Motility contributes to C. reinhardtii fitness because it allows cells or colonies to achieve this optimum. Utilizing phototaxis to assay motility, we determined that newly evolved multicellular strains do not exhibit significant directional movement, even though the flagellae of their constituent unicells are present and active. In C. reinhardtii the first steps towards multicellularity in response to predation appear to result in a trade-off between motility and differential survivorship, a trade-off that must overcome by further genetic change to ensure the long-term success of the new multicellular organism.

evolutionary biology↗