Biology subjects

Niu, D.-K.

Publications and source records attributed to Niu, D.-K..

15 recordsLinked to original sources

bioRxiv2026

Ancestral State Reconstruction under Localized Evolutionary Change: Error Patterns and Their Control by Tree Partitioning

Localized evolutionary changes can distort ancestral state reconstruction (ASR) because conventional continuous-trait methods generally treat branchwise changes as draws from a shared background process. A disproportionately large change confined to a single branch therefore creates localized model misspecification, but how the resulting errors vary among reconstruction paradigms and phylogenetic positions remains poorly understood. Using controlled simulations on idealized and empirical mammalian phylogenies, we characterized the error patterns produced by single-branch large changes (SBLCs) across five Brownian-motion-based ASR implementations. On intact trees, errors were highly structured and method dependent: the recursive local method propagated distortion mainly upstream, whereas global methods produced multidirectional effects involving both SBLC boundary nodes, neighboring lineages, and descendants of the affected branch. We then evaluated patching, a conditional robustness procedure that partitions the phylogeny at a candidate branch, applies the same ASR method independently to the resulting subtrees, and estimates the upstream boundary node state by branch-length-weighted interpolation. Patching reduced errors near and away from the affected branch and lowered tree-wide error across trait-increasing and trait-decreasing SBLCs, a broad range of sensitivity analyses, and configurations with two co-occurring SBLCs, while introducing little additional error when no SBLC was present. Under the reference upsizing SBLC, for instance, it cut the maximum-likelihood reconstruction error at the upstream boundary node from 56.20 to 0.03 (mean true state, 4.98), matching the stable-process benchmark. In cetacean body-length evolution, patching candidate branches identified by a Levy-process model generally shifted conventional estimates toward stable-process estimates and nearby fossil references. Under an Ornstein-Uhlenbeck process with strong post-SBLC mean reversion, however, neither patching nor stable-process reconstruction recovered downstream ancestral states once the phenotypic signature of the SBLC had largely disappeared from descendant tip values, revealing an identifiability limit of terminal-only inference. Localized evolutionary change therefore creates structured, method-dependent reconstruction errors, and tree partitioning provides a complementary diagnostic of the robustness of ancestral inferences to candidate branch-localized changes.

evolutionary biology↗

bioRxiv2026

Phylogenetically Dispersed Subsetting for Species-Level Machine Learning Evaluation: Dependence-Aware Validation and Limited Effective Information

Species are widely treated as independent sampling units in comparative analyses, yet shared evolutionary history induces structured dependence that can substantially reduce the amount of independent information available for statistical evaluation and inference. This mismatch between nominal species richness and effective information content can lead to overestimation of statistical precision in species-level analyses. Here, we develop a general framework for quantifying effective information under phylogenetic dependence. We define evaluation subsets embedded within a shared phylogenetic covariance structure and introduce two complementary measures. The first, MIESS (mean-based independence-equivalent sample size), quantifies the amount of independent information available for estimating aggregate quantities under a specified phylogenetic correlation structure, derived from generalized least-squares variance principles. The second, PIESS (prediction-metric-based independence-equivalent sample size), extends this idea to predictive evaluation by mapping uncertainty in standard performance metrics (RMSE, MAE, and R{superscript 2}) onto an independence-equivalent sample size scale via calibration against independent-sample benchmarks. We evaluate this framework using empirical mammalian phylogenies (Cricetidae) and idealized tree topologies representing contrasting phylogenetic structures. Across these systems, and under standard models of trait evolution including Brownian motion (BM), Ornstein-Uhlenbeck (OU), and Early-Burst (EB) processes, we compare subsets constructed under phylogenetically dispersed, clustered, and random sampling schemes. Across all settings, dispersed subsets reduce redundancy relative to clustered subsets but do not eliminate dependence-induced information loss. For example, under the{lambda} -transformed BM analysis, the dispersed 64-species subset yielded R{superscript 2}-based PIESS values well below the nominal size under moderate to strong phylogenetic signal (14.59 at{lambda} = 1.00, increasing to 31.96 at {lambda} = 0.50). The resulting loss arises from residual phylogenetic covariance and is robust across evolutionary regimes and sampling fractions. These results indicate that nominal species counts can substantially overestimate independent information in species-level evaluation contexts, and that accounting for phylogenetic dependence is essential for interpreting statistical precision, comparing predictive performance, and designing evaluation protocols in comparative biological analyses.

evolutionary biology↗

bioRxiv2024

Enhancing Phylogenetic Analysis: Integrating Nonparametric Methods for Addressing Abrupt Evolutionary Shifts

Traditional phylogenetically aware correlation methods perform well under gradual evolutionary processes. However, abrupt evolutionary shifts--or macroevolutionary jumps, characteristic of punctuated evolution--can produce extreme phylogenetically independent contrasts (PIC), leading to inflated false positives or increased false negatives in trait correlation analyses. We introduce O(D)GC (Outlier-and Distribution-Guided Correlation), a flexible workflow that identifies outliers in PICs using a distribution-free boxplot criterion and applies Spearman correlation whenever influential outliers are detected. If no outliers are detected, Pearson correlation is used--automatically for large datasets (n [≥] 30), or guided by normality testing in smaller samples. We systematically compared PIC-O(D)GC with five widely applied phylogenetic correlation methods--PIC-Pearson, PIC-MM, PGLS (phylogenetic generalized least squares), MR-PMM (multi-response phylogenetic mixed model), and Corphylo--on 322,000 simulated datasets spanning five evolutionary scenarios (two shift settings: single-trait shifts and dual-trait co-directional jumps; and three no-shift gradual evolution settings), including both fixed-depth and randomly located shifts, tested across 11 shift or noise gradients, three tree sizes (16, 128, 256 tips), and both balanced and random topologies. Overall, PIC-O(D)GC achieved error rates comparable to--or noticeably higher than--those of PIC-MM, while yielding substantially lower error rates than most alternative methods. Under no-shift conditions, it retained power similar to other methods. Analyses of three empirical datasets likewise showed that PIC-O(D)GC and PIC-MM corrected shift-induced distortions that misled conventional methods. Moreover, PIC-O(D)GC offers a conceptually simple framework and incurs markedly lower computational cost. By design, its correlation-only output provides less mechanistic detail than regression-based approaches like PGLS. However, when paired with PIC diagnostics, this outlier-guided strategy highlights evolutionary jumps, distinguishes coupled from decoupled shifts, and--via clade partitioning or tip pruning--recovers background correlations, offering biologically informative insights into how punctuated events interact with gradual trends in trait evolution.

evolutionary biology↗

bioRxiv2024

Phylogenetic Analysis of the Impact of CRISPR Array Characteristics on Spacer Number Evolution

CRISPR-Cas systems in prokaryotes utilize spacers, segments of DNA acquired from invading phages, to guide immune defense mechanisms. This study investigates the evolution of CRISPR repertoire size by examining its relationships with repeat length, terminal repeat polymorphism, and structural stability in 1,958 bacterial genomes, identifying 5,465 CRISPR arrays. Using CRISPRCasFinder for annotation and RNAfold for predicting RNA secondary structures, we found significant variation in array characteristics. Long-repeat arrays ([≥]38 bp) showed a significant positive correlation between terminal repeat polymorphism and CRISPR spacer number, a correlation absent in short-repeat arrays (<38 bp), suggesting longer repeats facilitate recombination and spacer loss. Additionally, a negative correlation between repeat length and spacer number across all arrays indicates that longer repeats may accelerate spacer loss. Furthermore, our results show that immune demand significantly influences the evolution of spacer number. Larger CRISPR repertoires correlate with conserved repeat sequences and stable secondary structures, vital for functional arrays under continuous selective pressure. Comparing functional and obsolete CRISPR arrays (orphan arrays in genomes lacking Cas genes) revealed that obsolete arrays have fewer spacers and lower repeat consistency, indicating a degenerative state. By elucidating the factors that shape CRISPR memory size evolution, this research offers strategies to enhance bacterial defenses, mitigate resistance, and improve applications in gene editing and therapeutics.

microbiology↗

bioRxiv2024

Exploring Dependent Variable Selection in Phylogenetic Eigenvector Regression

Phylogenetic eigenvector regression (PVR) is widely used in ecology and evolution by representing phylogenetic structure through separable eigenvectors. Despite this flexibility, its implementation faces three key challenges: (1) the selection of eigenvectors, (2) the reduced robustness of ordinary least-squares (OLS) regression under shift-like evolutionary heterogeneity, and (3) the applicability of conventional model complexity rules such as the "samples-per-variable (SPV) [≥] 10" guideline. Here, we propose an optimized PVR framework that addresses these limitations. First, we show that trait-specific selections of eigenvectors often diverge, sometimes producing inconsistent results, and that using their union offers stronger control of phylogenetic non-independence. Second, we evaluate robust regression estimators within PVR, demonstrating that PVR-MM - and in most cases PVR-L2, the standard OLS estimator - maintains high accuracy under non-stationary evolutionary shifts where other non-robust methods fail. Third, through simulation, we reassess the SPV [≥] 10 rule, showing that PVR tolerates eigenvector counts well beyond this threshold, offering greater flexibility while requiring attention to potential overfitting. Extensive simulations across diverse trees and evolutionary scenarios confirm that the optimized framework improves accuracy and robustness. By addressing key aspects of eigenvector selection, regression, and model complexity, our findings strengthen the reliability and applicability of PVR.

evolutionary biology↗

bioRxiv2024

Bacterial defenses and their trade-off with growth are not ubiquitous but depend on ecological contexts

Bacteriophages, also known as bacterial viruses, significantly influence microbial ecosystems, driving bacteria to evolve diverse antiviral defense mechanisms. This study explores the intricate relationship between bacterial defenses and growth rates across diverse ecological contexts. Our investigation reveals that bacteria lacking defenses exhibit prolonged doubling times. Integrating phylogenetic eigenvectors into the ecological feature matrix, we employed a phylogenetic random forest model to identify key ecological features influencing defense presence and abundance. Further phylogenetic regressions unveil nuanced dependencies of bacterial defenses on specific environmental factors, challenging assumptions of a universal defense system distribution and underscoring reliance on subtle ecological cues. Notably, symbiotic and endosymbiotic bacteria often exhibit reduced defense systems and negative correlations between defense system abundance and the minimal doubling time. Conversely, free-living and motile bacteria show significant positive correlations between minimal doubling time and defense system abundance. Moreover, we highlight the pivotal role of ecological variables like habitat specificity and nutrient availability in shaping bacterial growth rates and defense mechanisms. Our findings underscore the complexity of microbial interactions and stress the need to consider ecological context in understanding defense strategies. We propose that trade-offs between growth and defense are ubiquitous due to sporadically inefficient optimization of limited resources, particularly in populations with small effective sizes, where both mechanisms may weaken concurrently due to genetic drift. This challenges traditional notions of trade-offs and underscores the impact of ecological context on microbial strategies.

microbiology↗

bioRxiv2023

Which Variable Should Be Dependent in Phylogenetic Generalized Least Squares Regression Analysis

Phylogenetic generalized least squares (PGLS) regression is widely used to examine evolutionary associations while accounting for phylogenetic non-independence, but it requires designating one trait as the dependent variable and the other as the independent variable. When causal relationships between traits are unclear, choosing which trait serves as the dependent variable becomes a practical concern. While studying the evolutionary relationship between bacterial growth rate and CRISPR-Cas content, we noticed that switching the roles of dependent and independent variables in PGLS analyses could lead to inconsistent conclusions in a substantial proportion of cases. To confirm this observation, we conducted 16,000 simulations of trait evolution along binary trees with 100 terminal nodes under different evolutionary models. PGLS regressions using Pagels {lambda} model were applied to each simulation, and the results consistently showed that swapping the dependent and independent variables can lead to inconsistent outcomes. We evaluated seven potential criteria for selecting the dependent variable, including log-likelihood, AIC, R2, p-value, Pagels {lambda}, Blombergs K, and the estimated {lambda} in the Pagels {lambda} model. Among these, Pagels {lambda}, Blombergs K, and the estimated {lambda} performed equally well and outperformed the others in selecting the dependent variable, providing a reliable basis for PGLS analyses when causal direction between traits is unclear.

evolutionary biology↗

bioRxiv2023

Relationship between prokaryotic GC contents and environmental salinity

BackgroundThe correlation between GC content and halophilicity has received limited attention, despite the numerous environmental factors associated with GC content evolution. While higher GC content has been linked to halophiles in some archaeal cases, it is widely believed that selective pressure from high-intensity ultraviolet radiation in halophilic archaea drives GC content increase, as it prevents DNA photoproduct formation. However, this assumption has not been statistically analyzed in a phylogenetically independent manner prior to our study. ResultsUsing phylogenetic generalized least squares, we investigated the relationship between GC content and halophilicity in 1226 bacteria and 181 archaea. Our analysis found significant positive correlations in bacteria but not in archaea. Resampling analysis indicates that the absence of significant correlation in archaea may be due to the relatively small sample size. We also observed that the strength of the correlation is negatively influenced by the functional constraint of genomic components. Additionally, we found that halophilic bacteria and archaea do not have lower photoreactivity (a measure of DNA vulnerability to ultraviolet radiation) than the photoreactivity expected from their GC contents. ConclusionsIn contrast to previous assumptions, we did not find evidence to support the widespread photoprotection hypothesis or another hypothesis that high GC content in halophiles stabilizes nucleic acid structures. Instead, our findings align with a nonadaptive hypothesis. Halophilic prokaryotes likely evolved high GC content due to frequent GC-biased gene conversion in response to DNA double-strand breaks induced directly or indirectly by high salt concentrations.

evolutionary biology↗

bioRxiv2022

A Positive Correlation between CRISPR-Cas Spacer Abundance and Cell Cycle Duration Across the Bacteria Domain

CRISPR-Cas systems provide adaptive immunity for prokaryotic cells by recognizing and eliminating the recurrent genetic invaders whose sequences had been captured in a prior infection and stored in the CRISPR arrays as spacers. However, the biological/environmental factors determining the efficiency of this immune system have yet to be fully characterized. Recent studies in cultured bacteria showed that slowing the growth rate of bacterial cells could promote their acquisition of novel spacers. This study examined the relationship between the CRISPR-Cas content and the minimal doubling time across the bacteria and the archaea domains. Every completely sequenced genome could be used to predict a minimal doubling time. With a large dataset of 4142 bacterial samples, we found that the predicted minimal doubling times are positively correlated with spacer number and other parameters of the CRISPR-Cas systems, like array number, Cas gene cluster number, and Cas gene number. Different datasets gave different results. Weak results were obtained in analyzing bacterial empirical minimal doubling times and the archaea domain. Still, the conclusion of more spacers in slowly-grown prokaryotes was supported. In addition, we found that the minimal doubling times are negatively correlated with the occurrence of prophages, and the spacer numbers per array are negatively associated with the number of prophages. These observations support the existence of an evolutionary trade-off between bacterial growth and adaptive defense against virulent phages.

evolutionary biology↗

bioRxiv2021

Bacterial CRISPR abundance jumps up at around 45°C

Although performing adaptive immunity, CRISPR-Cas systems are present in only 40% of bacterial genomes. Here, we observed an abrupt transition of bacterial CRISPR-Cas abundance at around 45{degrees}C. Phylogenetic comparative analyses confirmed that the abundance correlates with growth temperature only at the temperature range around 45{degrees}C. Meanwhile, we noticed that the diversities of cellular predators have a precipitous decline at this temperature range. The grazing risk faced by bacteria reduces substantially at around 45{degrees}C and almost disappears above 60{degrees}C. So viral lysis would become the dominating factor of bacterial mortality, and antivirus immunity has a higher priority. In temperature ranges where the abundance of cellular predators does not change with temperature, temperatures would have negligible effects on CRISPR-Cas abundance. The hypothesis predicts that bacteria should also be rich in CRISPR-Cas systems if they live in other extreme conditions inaccessible to grazing predators.

genomics↗

bioRxiv2021

Significant Correlation between Growth Temperature and Guanine-Cytosine Content in Bacteria

BackgroundGC pairs are generally more stable than AT pairs; GC-rich genomes were proposed to be more adapted to high temperatures than AT-rich genomes. Previous studies consistently showed positive correlations between growth temperature and the GC contents of structural RNA genes. However, for the whole genome sequences and the silent sites of the codons in protein-coding genes, the relationship between GC content and growth temperature is in a long-lasting debate. ResultsWith a dataset much larger than previous studies (681 bacteria and 155 archaea with completely assembled genomes), our phylogenetic comparative analyses showed positive correlations between optimal growth temperature (Topt) and GC content both in bacterial and archaeal structural RNA genes and in bacterial whole genome sequences, chromosomal sequences, plasmid sequences, core genes, and accessory genes. However, in the 155 archaea, we did not observe a significant positive correlation of Topt with whole-genome GC content (GCw) or GC content at four-fold degenerate sites. We randomly drew 155 samples from the 681 bacteria for 1000 rounds. In most cases (> 95%), the positive correlations between Topt and genomic GC contents became statistically nonsignificant (P > 0.05). This result suggested that the small sample sizes might account for the lack of positive correlations between growth temperature and genomic GC content in the 155 archaea and the bacterial samples of previous studies. Comparing the GC content among four categories (psychrophiles/psychrotrophiles, mesophiles, thermophiles, and hyperthermophiles) also revealed a positive correlation between GCw and growth temperature in bacteria. By including the GCw of incompletely assembled genomes, we expanded the sample size of archaea to 303. Positive correlations between GCw and Topt appear especially after excluding the halophilic archaea whose GC contents might be are strongly shaped by intense UV radiation. ConclusionsThis study explains the previous contradictory observations and ends a long debate. Prokaryotes growing in high temperatures have higher GC contents. Thermal adaptation is one possible explanation for the positive association. Meanwhile, we propose that the elevated efficiency of DNA repair in response to heat mutagenesis might have the by-product of increasing GC content like that happens in intracellular symbionts and marine bacterioplankton.

evolutionary biology↗

bioRxiv2021

Intron Losses and Gains in Nematodes: Not Eccentric at All

The evolution of spliceosomal introns has been widely studied among various eukaryotic groups. Researchers nearly reached the consensuses on the pattern and the mechanisms of intron losses and gains across eukaryotes. However, according to previous studies that analyzed a few genes or genomes of nematodes, Nematoda seem to be an eccentric group. Taking advantage of the recent accumulation of sequenced genomes, we carried out an extensive analysis on the intron losses and gains using 104 nematodes genomes across all the five Clades of the phylum. Nematodes have a wide range of intron density, from less than one to more than nine per 1kbp coding sequence. The rates of intron losses and gains exhibit significant heterogeneity both across different nematode lineages and across different evolutionary stages of the same lineage. The frequency of intron losses far exceeds that of intron gains. Five pieces of evidence supporting the model of cDNA-mediated intron loss have been observed in ten Caenorhabditis species, the dominance of the precise intron losses, frequent loss of adjacent introns, and high-level expression of the intron-lost genes, preferential losses of short introns, and the preferential losses of introns close to 3'-ends of genes. Like studies in most eukaryotic groups, we cannot find the source sequences for the limited number of intron gains detected in the Caenorhabditis genomes. All the results indicate that nematodes are a typical eukaryotic group rather than an outlier in intron evolution.

genomics↗

bioRxiv2019

Dosage-sensitivity of human transcription factor genes

Changes in the copy number of protein-coding genes would lead to detrimental effects if the consequent changes in protein concentration disrupt essential cellular functions. Large-scale genomic studies have identified thousands of dosage-sensitive genes in human genome. We are interested in the dosage-sensitivity of transcription factor (TF) genes whose products are essential for the growth, division and differentiation of cells by regulating the expression of the genetic information encoded in the genome. We first surveyed the enrichment of human TF genes in four recently curated datasets of dosage-sensitive genes, including the haploinsufficient genes identified by a large-scale genomic study, the haploinsufficient genes predicted by a machine learning approach, the genes with conserved copy number across mammals, and the ohnologs. Then we selected the dosage-sensitive genes that are present in all the four dataset and regarded them as the most reliable dosage-sensitive genes, and the genes that are absent from any one of the four datasets as the most reliable dosage-insensitive genes, and surveyed the enrichments of TFs genes in these two datasets. A large number of TF genes were found to be dosage-insensitive, which is beyond the expectation based on the role of TFs. In spite of this, the likeness of TF genes to be dosage-sensitive were supported by five datasets, with the conserved-copy-number genes as the exception. The nuclear receptors are the only one family of TFs whose dosage-sensitivity was consistently supported by all the six datasets. In addition, we found that TF families with very few members are also more likely to be dosage-sensitive while the largest TF family, C2H2-ZF, are most likely dosage-insensitive. The most extensively studied TFs, p53, are not special in dosage-sensitivity. They are significantly enriched in only three datasets. We also confirmed that dosage-sensitive genes generally have long coding sequences, high expression levels and experienced stronger selective pressure. Our results indicate some TFs function in a dose-dependent manner while some other not. Gene dosage changes in some TF families like nuclear receptor would result in disease phenotypes while the effects of such changes in some TFs like C2H2-ZF would be mild.

genetics↗

bioRxiv2018

Desiccation Does Not Drastically Increase the Accessibility of Foreign DNA to the Nuclear Genomes: Evidence from the Frequency of Endosymbiotic DNA Transfer

Horizontal gene transfer (HGT) is a widely accepted force in the evolution of prokaryotic genomes. However, in eukaryotes, it is still in hot debate. Some bdelloid rotifers that are resistant to extreme desiccation and radiation were reported to have a very high level of HGTs. However, a similar report in another resistant invertebrate, tardigrades, has been mired in controversy. The DNA double-strand breaks (DSBs) induced by prolonged desiccation have been postulated to open the gateway of nuclear genome for foreign DNA integration and thus facilitate the HGT process. If so, the rate of endosymbiotic DNA transfer should also be enhanced. We first surveyed the abundance of nuclear mitochondrial DNAs (NUMTs) and nuclear plastid DNAs (NUPTs) in three groups of eukaryotes that are extremely resistant to desiccation, bdelloid rotifers, A. vaga and A. ricciae, tardigrades, H. dujardini and R. varieornatus, and the resurrection plants, D. hygrometricum and S. tamariscina. Excessive NUMTs or NUPTs have not been detected. Furthermore, we compared nine groups of desiccation-tolerant organisms with their desiccation-sensitive relatives but did not find significant difference in the NUMT/NUPT contents. Desiccation could induce DSBs, but it unlikely dramatically increase the frequency of foreign sequence integration in most eukaryotes. Only in the nuclear genomes enriched in repetitive sequences, the DSBs are predominantly repaired by non-homologous end joining (NHEJ) and desiccation-induced DSBs is possible to enhance the integration of foreign sequences into nuclear genome for some degree.

evolutionary biology↗

bioRxiv2017

Aerobiosis Decreases the Genomic GC content in Prokaryotes by Guanine Oxidation

Background: Among the four bases, guanine is the most susceptible to damage from oxidative stress. Replication of DNA containing damaged guanines result in G to T mutations. Therefore, the mutations resulting from oxidative DNA damage are generally expected to predominantly consist of G to T (and C to A when the damaged guanine is not in the reference strand) and result in decreased GC content. However, the opposite pattern was reported 16 years ago in a study of prokaryotic genomes. Although that result has been widely cited and confirmed by nine later studies with similar methods, the omission of the effect of shared ancestry requires a re-examination of the reliability of the results.\n\nResults: We retrieved 70 aerobe-anaerobe pairs of prokaryotes, and members of each pair were adjacent on the phylogenetic tree. Pairwise comparisons of either whole-genome GC content or the GC content at 4-fold degenerate sites of orthologous genes among these 70 pairs did not show significant differences between aerobes and anaerobes. The signature of guanine oxidation on GC content evolution has not been detected even after extensive controlling of other influencing factors. Furthermore, the anaerobes were not different from the aerobes in the rate of either G to T, C to A, or other directions of substitutions. The presence of the enzymes responsible for guanine oxidation in anaerobic prokaryotes provided additional evidence that guanine oxidation might be prevalent in anaerobic prokaryotes. In either aerobes or anaerobes, the rates of G:C to T:A mutations were not significantly higher than the reverse mutations.\n\nConclusions: The previous counterintuitive results on the relationship between oxygen requirement and GC content should be attributed to the methodological artefact resulting from phylogenetically non-independence among the analysed samples. Our results showed that aerobiosis does not increase or decrease GC content in evolution. Furthermore, our study challenged the widespread belief that abundant G:C to T:A transversions are the signature of oxidative stress in prokaryotic evolution.

evolutionary biology↗