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At least 19 recordsLinked to original sources
PubMed1977

Estimation of time of divergence from phylogenetic studies.

Recent studies with comparative data on base sequences of homologous DNA's or amino acid sequences of homologous proteins indicate that simultaneous estimation of phylogenetic structure and time of divergence is often cumbersome and time consuming. On the other hand, when the topology of an evolutionary tree is known, it is shown in this paper that the least squares theory may be applied to obtain simple estimates of the relative time lengths for each segment of the tree under the assumption of uniform random substitutions in each segment. The method is illustrated with amino acid sequence data on various globin molecules and cytochrome c. The evolutionary significance of some of the estimates is also discussed.

Amino Acid Sequence↗
PubMed2025

Comparative Phylogenetics Reveal Clade-specific Drivers of Recombination Rate Evolution Across Vertebrates.

Meiotic recombination is an integral cellular process, required for the production of viable gametes. Recombination rate is a fundamental genomic parameter, modulating genomic responses to selection. Our increasingly detailed understanding of its molecular underpinnings raises the prospect that we can gain insight into trait divergence by examining the molecular evolution of recombination genes from a pathway perspective, as in mammals, where protein-coding changes in later stages of the recombination pathway are connected to divergence in intra-clade recombination rate. Here, we leverage increased availability of avian and teleost genomes to reconstruct the evolution of the recombination pathway across two additional vertebrate clades: birds, which have higher and more variable rates of recombination and similar divergence times to mammals, and teleost fish, which have much deeper divergence times. Rates of molecular evolution of recombination genes are highly correlated between vertebrate clades and significantly elevated compared to control panels, suggesting that they experience similar selective pressures. Avian recombination genes are significantly more likely to exhibit signatures of positive selection than other clades, unrestricted to later stages of the pathway. Signatures of positive selection in genes linked to recombination rate variation in mammalian populations and those with signatures of positive selection across the avian phylogeny are highly correlated. In contrast, teleost fish recombination genes have significantly less evidence of positive selection despite high intra-clade recombination rate variability. Gaining clade-specific understanding of patterns of variation in recombination genes can elucidate drivers of recombination rate and thus, factors influencing genetic diversity, selection efficacy, and species divergence.

Animals↗
PubMed2026

Genomic Footprints of Historical Introgression Between Ancient Lineages of Wild Oryza AA-Genome Species With Widely Separated Contemporary Distributions.

Phylogenetic incongruence is increasingly recognized as pervasive, yet the extent to which reticulate evolution occurs between groups separated by substantial geographical distances and deep phylogenetic divergence remains poorly characterized. In the Oryza AA-genome group-a model for plant speciation and domestication-the traditional bifurcation model posits that Australian Oryza meridionalis and African Oryza longistaminata occupy basal branches, distinct from the more recently diversified monophyletic clade comprising Asian and other African lineages, including major cultivars. However, recent evidence from endogenous viral sequences has hinted at unexpected genetic relatedness between African O. longistaminata and Asian Oryza sativa, which are geographically and phylogenetically distant. Here, we conducted a genome-wide survey across 11 Oryza species to systematically identify genomic regions exhibiting phylogenetic incongruence. Widespread phylogenetic discordance was observed, notably involving genomic segments in which O. longistaminata showed phylogenetic proximity to Asian species, contradicting their established deep divergence. To distinguish between introgression and incomplete lineage sorting, we performed four-taxon ABBA-BABA tests, which provided statistical support for introgression. Furthermore, divergence time estimates for these incongruent regions were younger than the species divergence times, suggesting historical introgression between the ancestors of lineages that are currently separated by vast geographical distances. Systematic assessments indicated that potential analytical artifacts, such as compositional bias and substitution saturation, were unlikely to explain the observations. These convergent lines of evidence suggest that ancient introgression had occurred between currently geographically separated and evolutionarily divergent Oryza lineages, leaving detectable footprints across their modern genomes.

Oryza↗
PubMed2026

Parting ways: Pan-Homo divergence revisited.

The timing of divergence between hominins and the bonobo-chimpanzee clade has been at the core of palaeoanthropological debate for over a century. The earliest molecular studies indicated divergence times ranging from 5 Ma to as recently as 1.3 Ma. This study critically reviews the trends of time estimates published between 1967 and 2023, and analyses how these are supported or rejected by the current molecular and fossil records. We compiled 202 divergence estimates and defined three distinct thresholds based on fossil evidence at 4.4 Ma (Australopithecus anamensis and Ardipithecus ramidus), 6.2 Ma (Orrorin tugenensis and Ardipithecus kadabba), and 7.2 Ma (Sahelanthropus tchadensis). We then used these thresholds to filter out molecular estimates that are too young to fit the fossil record. Overall, the data suggests a divergence event within the late Miocene, with each threshold pushing it further back, 8.63-6.38, 10.33-7.81, and 10.95-8.81 Ma, respectively. We use a quadratic regression to demonstrate that estimates have been slowly shifting from ~ 6 Ma to ~ 8.5 Ma over the past 56 years. A Bayesian meta-analysis of genomic estimates filtered by our most consensual threshold (i.e., assuming Australopithecus belongs to Hominini) indicates that the split must have occurred early in the late Miocene, most likely before 7 Ma (~ 99.5% posterior probability) with a pooled effect of 8.69-7.28 Ma. We conclude that, despite an initial bias towards younger estimates, the molecular timing for the last common ancestor (LCA) of Pan-Homo has been progressively approaching the intervals suggested by the current fossil record.

Animals↗
PubMed2026

Insights into phylogenetic relationships of Veronica species (Plantaginaceae) based on comparative chloroplast genomics.

INTRODUCTION: Veronica L. is one of the most species-rich genera in Plantaginaceae and several species have medicinal, horticultural, or ecological value. METHODS: In this study, the complete chloroplast genomes of three Veronica species were assembled and annotated using Illumina sequencing data. RESULTS: The plastomes exhibited a typical quadripartite structures, with total lengths of 150,202 bp for Veronica biloba L., 151,159 bp for Veronica ciliata Fisch. and 151,098 bp for Veronica vandellioides Maxim. Each genome contained 130-132 unique genes, including 86-87 protein-coding genes, 36-37 tRNA genes, and 8 rRNA genes. Comparative analyses of 24 Veronica plastomes indicated that the IR/SC junctions were largely conserved, although slight boundary shifts occurred around rps19, ndhF, and ycf1. Forward, palindromic, complement, and reverse repeats were detected, and A/T mononucleotide repeats were the dominant SSR type. Nucleotide diversity analysis identified rpl32-trnL, trnK-rps16, rpl32, ycf1, ndhF, accD, matK, and rpoB as highly variable regions. Phylogenetic analyses recovered Veronica as a well-supported monophyletic lineage and clarified the plastid positions of the three newly sequenced species. Divergence time estimation suggested that the estimation suggested of Veronica was around 14.9 Ma, with V. biloba, V. ciliata and V. vandellioides diverging approximately 3.9 Ma, 0.6 Ma, and 6.9 Ma, respectively. DISCUSSION: Because the analyses were based on plastid genomes, the inferred topology should be interpreted as chloroplast phylogenetic evidence rather than a complete species-history reconstruction. These results provide plastome resources and molecular evidence for taxonomy, species identification, and future evolutionary studies of Veronica.

Plantaginaceae↗
PubMed2024

Comparative analysis of chloroplast genomes in ten holly (Ilex) species: insights into phylogenetics and genome evolution.

In order to clarify the chloroplast genomes and structural features of ten Ilex species and provide insights into the phylogeny and genome evolution of the genus Ilex, we conducted a comparative analysis of chloroplast genomes using bioinformatics methods. The chloroplast genomes of ten Ilex species were obtained, and their structural features and variations were compared. The results indicated that all chloroplast genomes in the genus Ilex exhibit a double-stranded circular structure, with sizes ranging from 157,356 to 158,018 bp, showing minimal differences in size. The chloroplast genomes of the ten Ilex species have a relatively conservative gene count, with a total of 134 to 135 genes, including 88 or 89 protein-coding genes, and a conserved number of 8 rRNA genes. Each chloroplast genome contains 3 to 123 SSR (Simple Sequence Repeat) sites, predominantly composed of mononucleotide and trinucleotide repeats, with no detection of pentanucleotide or hexanucleotide repeats. The variation in dispersed repeat sequences among Ilex species is minimal, with a total repeat sequence number ranging from 1 to 14, concentrated in the length range of 30 to 42 base pairs. The expansion and contraction of chloroplast genome boundaries among Ilex species are relatively stable, with only minor variations observed in individual species. Variations in non-coding regions are more pronounced than those in coding regions, with the variability in the Large Single Copy region (LSC) being the highest, while the variability in the Inverted Repeat region A (IRa) is the lowest. The divergence time among Ilex species was estimated using the MCMC-tree module, revealing the evolutionary relationships among these species, their common ancestors, and their differentiation throughout the evolutionary process. The research findings provide a valuable reference for the systematic study and molecular marker development of Ilex plants.

Genome, Chloroplast↗
PubMed2026

Characterization and comparative analysis of the complete chloroplast genomes of twelve Allium species from Kazakhstan.

The genus Allium L. represents one of the largest and taxonomically complex groups of monocots, with Central Asia recognized as a major center of its diversity. Despite the high species richness of Allium in Kazakhstan, genomic data for many native taxa remain limited. In this study, we sequenced, assembled, and analyzed the complete chloroplast genomes of 12 Allium species from Kazakhstan. All chloroplast genomes exhibited a conserved quadripartite structure, with genome sizes ranging from 152,029 to 153,521 bp and a uniform gene content of 137 genes, including 88 protein-coding genes, 38 tRNAs, 8 rRNAs, and 3 pseudogenes. Comparative analyses revealed high structural conservation, with most sequence divergence concentrated in intergenic regions. Several highly variable regions, including ycf1, matK, rpoC2, and ycf2, were identified as potential molecular markers. Phylogenetic analyses based on chloroplast genome sequences using Maximum Likelihood and Bayesian approaches recovered three major chloroplast genome-based lineages within Allium, largely consistent with previous phylogenomic studies. Divergence-time analyses suggested that major chloroplast lineage diversification events within the genus occurred during the early Eocene (ca. 47.97 Mya). Overall, this study expands the currently available chloroplast genomic resources for Allium from Kazakhstan, provides insights into chloroplast genome evolution and chloroplast genome-based relationships, and establishes a valuable foundation for future phylogenetic, taxonomic, and evolutionary studies of this diverse genus.

Genome, Chloroplast↗
PubMed2026

Uce-based phylogeny and classification of Megachilini.

The generic-level classification of the bee tribe Megachilini (Megachilidae) has remained controversial due to poor phylogenetic resolution at the base of the group, particularly among the brood parasitic genera and the numerous dauber ("Chalicodoma s. l.") lineages. We present a phylogenomic analysis of Megachilini based on ultraconserved elements (UCEs), sampling 52 ingroup taxa with emphasis on the dauber lineages. We also present a combined UCE + six-gene analysis to improve taxon coverage, resulting in a dataset with 127 ingroup taxa. Maximum likelihood, coalescent, and Bayesian analyses of multiple UCE matrices recover largely congruent topologies with substantially improved support relative to previous studies. Our results strongly support the monophyly of Megachilini, the early divergence of Noteriades and Gronoceras, and a single origin of brood parasitism. All remaining non-parasitic Megachilini form a moderately supported clade sister to the brood parasitic lineage. The leafcutter bees are monophyletic and nested within dauber lineages. Several major dauber clades are consistently recovered, including an exclusively Australian clade corresponding to the Hackeriapis group of subgenera, while several recognized subgenera are paraphyletic. The lineage known as Morphella, previously placed in synonymy with the subgenus Callomegachile, was not closely related to that subgenus and is here treated as a valid subgenus. Divergence-time analyses place the crown age of Megachilini in the late Eocene to early Oligocene, with major extant lineages diversifying during the Miocene. Limited morphological diagnosability of several clades indicates that splitting non-parasitic lineages into numerous genera would result in an impractical classification that would widen the gap between taxonomists and non-specialists and exacerbate the taxonomic impediment in bees. We therefore advocate retaining a single genus Megachile for non-parasitic Megachilini (excluding Noteriades and Gronoceras), as the classification best supported by phylogenomic evidence and most robust to future taxon sampling.

Animals↗
PubMed1978

Genetic distance between the American Indians and the three major races of man.

The genetic distances between the American Indians and the three major races of man, Caucasoids, Negroids and Mongoloids, were determined by using gene frequency data on 14 blood group and 12 protein loci. The results support the general view that the ancestry of the American Indian is predominantly Mongoloid. Using 30,000 years as the separation time between the American Indian and Mongoloid, the divergence time between the three major races of man was estimated to be 33,000-92,000 years.

Anthropology↗
PubMed2025

Climatic data sources and limitations of ecological niche models impact the estimations of historical ranges and niche overlaps in distantly related Korean salamanders.

BACKGROUND: Ecological niche models (ENMs) and analyses of niche overlap/divergence have become popular methods in ecology and evolutionary biology. These analyses rely on environmental data available from several databases. However, the influence of data sources on these analyses is rarely tested. Here, we test the impact of climatic data choice on the prediction of current and Plio-Pleistocene suitable habitats for two distantly related, but broadly sympatric, salamanders endemic to the Korean Peninsula. We ran MaxEnt separately on WorldClim and CHELSA climate data. We then hindcasted ENMs to five time periods of the Plio-Pleistocene, bracketing the estimated intraspecific divergence times for these species. We then quantified the differences in predictions between WorldClim- and CHELSA-based models. Also, given the sympatry and similar habitat requirements of the two species, we tested for niche overlaps using niche identity and background tests and tested the sensitivity of the results to climatic data choice. RESULTS: The ENMs successfully predicted contemporary suitable habitats for the two species. However, the predictions were highly sensitive to climatic data choice as well as variable combinations. The hindcasted ENMs produced contrasting predictions depending on the choice of climatic dataset and failed to predict suitable habitats for some Pleistocene time periods regardless of the climatic data choice. The niche analyses were also sensitive to climatic data choice, with results suggesting either niche overlaps or divergence depending on the climatic dataset used for the analyses. CONCLUSIONS: Our study highlights the influence of climatic data choice on the outcomes of ENMs and niche analyses. Our results also underscore the limitations of macroclimate-based ENMs, especially when the species is likely buffered from macroclimatic changes by microhabitat. We argue for the need for additional ecological, ecophysiological, and population genomic studies to better understand the range formation of these enigmatic species.

Animals↗
PubMed2025

Genomic analysis of differentiation and demography of the formerly conspecific agile (Dipodomys agilis) and Dulzura (D. simulans) kangaroo rats.

Karyotype variation within Pacific kangaroo rat Dipodomys agilis motivated its division in 1997 into the agile kangaroo rat (AKR, D. agilis, 2N = 62) in the north of its range in California, and Dulzura kangaroo rat (DKR, D. simulans, 2N = 60) to the south, with a suspected sympatric zone south of the San Gabriel and San Bernardino Mountains. This division was supported by our whole genome sequencing that sampled a ~120 km transect from north of the mountains to SW Riverside County. The taxa showed marked genetic differentiation, with no evidence of hybridization or sympatry. AKR was found at the southern edge of the mountains, precluding the mountain barrier driving isolation, suggesting ecological separation linked to habitat differences between the mountains and the arid area to the south. Adding four additional Dipodomys species, we estimated genetic divergence times in the genus back to ∼3.5 mya. AKR and DKR diverged from D. stephensi ∼1.7 mya, and from each other ∼0.5 mya, when their joint effective population size (Ne) was ~100,000. After separation, DKR's Ne declined to ~20,000, while AKR's was little changed. More recently their Ne converged at ~50,000. Runs of homozygosity were longer in AKR, indicating a smaller neighborhood size, which may have promoted the karyotype change; however, nucleotide diversity was higher in AKR, but both had levels typical for rodents, indicating neither experienced recent bottlenecks. These patterns provide a baseline for any future conservation efforts. More generally, this study shows how a detailed genomic study can resolve taxonomic and demographic questions among morphologically indistinguishable taxa.

Animals↗
PubMed2026

Mapping Sub-National Respiratory Virus Circulation in Cambodia Using Metatranscriptomic Sequencing: A Multi-Center Hospital-Based Surveillance Study.

BACKGROUND: Genomic surveillance can guide early detection of and response to emerging epidemics. Metatranscriptomic sequencing was used to investigate sub-national respiratory virus circulation in Cambodia from 2020 to 2023. METHODS: Nasopharyngeal swabs were collected from individuals aged 2 months to 65 years with influenza-like illness in four Cambodian hospitals. Metatranscriptomic data were generated by short-read RNA sequencing. Bernoulli space-time scan statistics were used to identify temporal virus clusters. Bayesian inference of phylogenetic trees was used to compute divergence times for temporally clustered, highly represented viruses (influenza A/H3N2 and B, Betacoronavirus 1, respiratory syncytial virus [RSV] A and B), and publicly available global influenza virus genomes. RESULTS: Of 1093 individuals, 499 (45.7%) had detectable respiratory viruses belonging to 68 distinct species. Moderate (N > 20) discrete time-clusters were noted of RSV-A (37 cases), Betacoronavirus 1 (21 cases), RSV-B (22 cases), and A/H3N2 (30 cases). The posterior median of time to most recent common ancestor ranged from 0.71 years (95% HPD 0.38-1.10) for Betacoronavirus 1 and 1.31 years (95% HPD 0.60-3.20) for A/H3N2, to 2.75 years (1.82-4.26) for RSV-A and 4.79 years (2.39-7.74) for RSV-B. A/H3N2 and influenza B virus genomes mapped to clades 3C.2a1b.2a.2a and Victoria 1A.3a.2, respectively, and inter-mixed with concurrent global strains. CONCLUSIONS: Multiple respiratory viruses circulated at a sub-national level in Cambodia from 2020 to 2023 despite pandemic disruptions. Influenza virus population diversity decreased during the height of lockdown but recovered in mid-2022. Re-emerging influenza strains were distinct from historically circulating strains and clustered with contemporaneous global variants, suggesting multiple external introductions.

Humans↗
PubMed2025

Extensive Recombination Suppression and Genetic Degeneration of a Young ZW Sex Chromosome System in Halfbeak Fish.

Sex chromosome systems have evolved independently across the tree of life, at different times in the past, and the evolutionary consequences of lacking recombination in sex-linked regions have been characterized in many old-established systems. However, empirical studies of young sex chromosomes are still scarce, especially in vertebrates. Integrating whole-genome sequencing data of two species of halfbeak fish, Hyporhamphus sajori and Hyporhamphus intermedius, we identified the sex-determining system in H. sajori as female heterogamety, involving a large fully sex-linked ZW region (∼26 Mb) on chromosome 5. The closest relative, H. intermedius, has a small sex-linked region on a different chromosome and shows male heterogamety, suggesting at least one turnover in this fish genus. The H. sajori sex-linked region includes two evolutionary strata, but the estimated Z-W divergence times are small, less than 3 million years for the older stratum, which is less than between the two species. Nevertheless, this evolutionarily young W-linked region is enriched with repetitive sequences, differs from the ancestral state by five inversions, and about one-third of its protein-coding genes have already become nonfunctional. Transcriptomic analysis suggests that some form of dosage compensation may already be evolving for some sex-linked genes.

Animals↗
PubMed2026

Mitogenomic Insights Into the Population Structure and Demographic History of Tree Shrews (Tupaia belangeri) in China.

The northern tree shrew (Tupaia belangeri) exhibits significant morphological and geographical variations, but its evolutionary history and subspecies boundaries remain controversial. Here, we analyzed the complete mitochondrial genomes of 63 individuals, representing 12 populations in China to study phylogenetic relationships, genetic diversity, and population history. Phylogenetic analysis consistently restored four mitochondrial branches with strong geographic structures and significant differences. The three lineages correspond to geographically restricted subspecies (T. b. tonquinia, T. b. modesta, and T. b. gaoligongensis), while individuals assigned to several traditional subspecies cluster in a broad mainland lineage (T. b. chinensis, T. b. yunalis, and T. b. yaoshanensis). The divergence time estimate places the origin of the main lineage in the Miocene, consistent with major tectonic and geomorphological events. Demographic analysis revealed different population histories, including varying degrees of expansion in recent continental and island lineages, as well as the long-term stability of T. b. gaoligongensis. Genetic diversity varied markedly among lineages, with the highest diversity observed in the T. b. gaoligongensis and the lowest diversity observed in the T. b. modesta. These findings demonstrate that landscape complexity and demographic history are key drivers of evolutionary diversification in T. belangeri, challenging classical morphology-based subspecies classifications and underscoring the need for comprehensive sampling across both domestic and international ranges.

Tupaia belangeri↗
PubMed1979

Compositional relatedness of aldehyde reductases from several species.

The amino acid compositions of several monomeric NADPH-dependent aldehyde reductases from a variety of species have been determined and analyzed by the difference index method of Metzger et al. (1968). The difference indexes among mammals range from 4.15 - 6.10 indicating considerable homology. Comparison of chicken aldehyde reductase with mammalian aldehyde reductases gave values in the range 6.8 - 9.9 suggesting a close relationship whereas the difference indexes for the enzymes from fruit fly and Baker's yeast versus vertebrate aldehyde reductases (10.9 - 14.4) indicate more distant relationships. The extent of sequence homology among aldehyde reductases from these species was estimated from a plot of difference index versus percent sequence difference for oxido-reductases of known sequence. From this plot, and using a mammal-chicken divergence time of 300 million years and a mammalian order split of 75 million years, the rate of evolution of aldehyde reductases was calculated to lie in the range 5.8 - 15.6% sequence difference per 100 million years. Comparison with rates of evolution of oligomeric dehydrogenases indicates that aldehyde reductases comprise the most rapidly evolving family of oxido-reductases. This is probably related to the monomericity of aldehyde reductases since there is a direct correlation between the number of subunits and the rate of evolution.

Aldehyde Oxidoreductases↗
PubMed2026

Pervasive hybridization and introgression in Diervilleae (Caprifoliaceae).

Diervilleae (Caprifoliaceae) is a horticulturally important lineage with striking floral diversity and a long history of interspecific crossing, suggesting reticulate evolution. We integrated nuclear SNPs and whole plastome data to reconstruct a phylogenomic backbone for the tribe and to identify hybrids, cultivated accessions, and introgression among lineages. Nuclear and plastid phylogenies consistently recover Weigela and Diervilla as reciprocally monophyletic and resolve four major lineages within Weigela, providing a reproducible framework for revising sectional limits and species boundaries. Cultivated accessions form a well supported clade sister to W. florida and show predominantly W. florida ancestry while retaining contributions from multiple wild lineages, consistent with recurrent crossing, backcrossing, and selection. Analyses of wild populations reveal recurrent hybrids and enable plausible parental combinations to be inferred. Tests across the genome further indicate strong evidence for historical introgression across Diervilleae, with the strongest signals involving W. middendorffiana, W. maximowiczii, and Diervilla. Fossil evidence, divergence time estimation, and paleodistribution modelling together suggest range expansion during the Miocene and Pliocene followed by climate driven contraction, providing a spatiotemporal context for episodic contact, introgression, and the East Asia-North America disjunction.

Hybridization, Genetic↗
PubMed2026

Comparative mitogenomics of Ocnus glacialis reveals lineage-specific evolutionary rates and complex gene rearrangements in Dendrochirotida.

The order Dendrochirotida (Class Holothuroidea) is a species-rich echinoderm group, yet its internal evolutionary history remains poorly resolved due to limited mitogenomic resources. In this study, we characterized the first complete mitochondrial genome of Ocnus glacialis and conducted comparative analyses to elucidate its phylogenetic position and molecular evolutionary patterns. The circular mitogenome of O. glacialis is 16,776 bp in length, containing the canonical set of 37 genes. Among the analyzed dendrochirotids, O. glacialis exhibited the highest A + T content (70.88%) and a near-zero AT-skew, a compositional profile often linked to lineage-specific evolution in specialized environments. Selection pressure analyses, including branch-model tests, revealed that these compositional features are associated with relaxed purifying selection and an accelerated rate of sequence evolution. Branch-site analyses further identified specific codon sites in cytb, nad2, nad4l, nad5, and nad6 under positive or relaxed constraints. Structurally, O. glacialis displayed the most complex gene rearrangement pattern among the studied species, characterized by multiple tandem duplication-random loss (TDRL) events and extensive intergenic sequences. Furthermore, divergence time estimation suggests that these structural and compositional shifts occurred in tandem with the lineage's diversification. We propose that these mitogenomic signatures reflect a synergistic outcome of habitat transition toward Arctic cold-water and deep-sea environments, coupled with demographic factors such as reduced effective population sizes inherent to its benthic life history. By resolving taxonomic uncertainties, this study provides a robust temporal and molecular framework for understanding the evolutionary history and ecological diversification of the Ocnus lineage.

Animals↗
PubMed2026

Phylogenomic subsampling and upsampling for efficient evolutionary analyses of big data.

Long runtimes, high memory demands, and reliance on high-performance computing impede phylogenomic analyses. We review a scalable phylogenomic subsampling with upsampling (PSU) framework to address this challenge, which reduces runtime and memory requirements by orders of magnitude. In PSU, small subsamples of sites from a concatenated alignment are analyzed, which are expanded by upsampling before inference, and the resulting inferences are aggregated to obtain evolutionary estimates. PSU harnesses the fact that the computational cost of maximum likelihood analysis is strongly influenced by the number of distinct site patterns in the concatenated alignment, whereas statistical power depends primarily on the amount of evolutionary information represented by the total number of sites and substitutions. By reducing the former while restoring the latter through upsampling, PSU can approximate many full-alignment analyses at substantially lower computational cost. Analysis of simulated and empirical datasets shows that PSU can accurately estimate bootstrap support values, select the optimal substitution model, test evolutionary hypotheses, and infer branch lengths, divergence times, and associated uncertainty measures. PSU also provides distributions of inferred clade support across independent subsamples, enabling detection of conflicting phylogenetic signals that may remain hidden in conventional bootstrap analysis of concatenated alignments. Automated tuning of subsample size, the number of subsamples, and the number of upsampling replicates make PSU practical. We suggest that PSU is a general approach for scalable phylogenomic inference using a broad range of statistical methods. By enabling analyses of genome-scale alignments on commodity hardware, PSU broadens research access and reduces environmental and infrastructural costs of big-data phylogenomics.

Phylogeny↗