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At least 19 recordsLinked to original sources
PubMed2025

Pleistocene island connectivity did not enhance dispersal or impact population size change in Galápagos geckos.

Patterns of biodiversity on remote archipelagos are largely shaped by intra-archipelago colonization followed by in situ diversification. Pleistocene sea-level fluctuations purportedly enhanced gene flow among terrestrial organisms by increasing connectivity during periods of lower sea level. Furthermore, changes in sea-level are hypothesized to impact population sizes as a result of fluctuations in island sizes. Here, we used genomic data to test the role of Pleistocene island connectivity on the diversification and demographics of leaf-toed geckos (Phyllodactylus) endemic to the Galápagos. Consistent with previous studies, we found that present diversity of Galápagos Phyllodactylus stems from three independent dispersal events. Contrary to the hypothesis of Pleistocene-driven diversification, we found no correspondence between lineage divergence and island connectivity. Furthermore, we found no evidence of introgression; demographic modelling indicated that all species increased rapidly in effective population size in the period 20-150 ka, and these inferred demographic expansions were largely asynchronous and apparently unassociated with species or island age. Collectively, these results indicate that more complex abiotic and/or biotic factors may better explain the recent demographic history of Phyllodactylus and underscore the need for additional population genomic studies of terrestrial taxa to understand the impact of past climate cycles on Galápagos island communities.

Animals↗
PubMed2025

A model for background selection in non-equilibrium populations.

In many taxa, levels of genetic diversity are observed to vary along their genome. The framework of background selection models this variation in terms of linkage to constrained sites, and recent applications have been able to explain a large portion of the variation in human genomes. However, these studies have also yielded conflicting results, stemming from two key limitations. First, existing models are inaccurate in a critical region of parameter space (), where the local reduction in diversity is sharpest. Second, they assume a constant population size over time. Here, we develop predictions for diversity under background selection based on the Hill-Robertson system of two-locus statistics, which allows for population size changes. We treat the joint effect of multiple selected loci independently, but we show that interference among them is well captured through local rescaling of mutation, recombination and selection in an iterative procedure that converges quickly. We further accommodate existing background selection theory to non-equilibrium demography, bridging the gap between weak and strong selection. Simulations show that our predictions are accurate across the entire range of selection coefficients. We characterize the temporal dynamics of linked selection under population size changes and demonstrate that patterns of diversity can be misinterpreted by other models. Specifically, biases due to the incorrect assumption of equilibrium carry over to downstream inferences of the distribution of fitness effects and deleterious mutation rate. Jointly modeling demography and linked selection therefore improves our understanding of the genomic landscape of diversity, which will help refine inferences of linked selection in humans and other species.

Journal Article↗
PubMed2026

Phlag: scalable detection of genomics regions with unexplained phylogenetic heterogeneity.

MOTIVATION: Phylogenetic analyses of entire genomes (phylogenomics) have revealed abundant heterogeneity of evolutionary histories. While much has been done to model this heterogeneity and to infer species trees despite it, the current toolkit has a limitation. Most methods assume that gene trees across the genome differ but are all sampled from the same distribution, defined by models such as the multi-species coalescent (MSC), and parametrized consistently across the genome. Empirical data strongly suggest this assumption is often violated because the species tree, its parameters, or the process generating the gene trees can all change across the genome. Errors in the data can further compound this heterogeneity. RESULTS: To address this challenge, we define the problem of detecting what segments of the genome are inconsistent with a putative species tree, even after allowing discordance according to MSC. We model gene trees not as a set, but rather as a series (a realization of a stochastic process) along genomic positions. We propose a Hidden Markov Model (HMM) approach applied to quartet statistics measured from gene trees and tie the model to MSC using simulations. The combined use of these three ideas leads to a scalable method called Phlag. On simulated and real data, we show that Phlag can detect many cases of change in underlying evolutionary processes, including reduced recombination rates, population size changes, and admixture, all using the same algorithm. AVAILABILITY AND IMPLEMENTATION: Phlag is available at github.com/bo1929/phlag. All results and scripts can be found at github.com/bo1929/shared.phlag.

Phylogeny↗
PubMed2026

Phlag: Scalable detection of genomics regions with unexplained phylogenetic heterogeneity.

MOTIVATION: Phylogenetic analyses of entire genomes (phylogenomics) have revealed abundant heterogeneity of evolutionary histories. While much has been done to model this heterogeneity and to infer species trees despite it, the current toolkit has a limitation. Most methods assume that gene trees across the genome differ but are all sampled from the same distribution , defined by models such as the multi-species coalescent (MSC), and parametrized consistently across the genome. Empirical data strongly suggest this assumption is often violated because the species tree, its parameters, or the process generating the gene trees can all change across the genome. Errors in the data can further compound this heterogeneity. RESULTS: To address this challenge, we define the problem of detecting what segments of the genome are inconsistent with a putative species tree, even after allowing discordance according to MSC. We model gene trees not as a set, but rather as a series (a realization of a stochastic process) along genomic positions. We propose a Hidden Markov Model (HMM) approach applied to quartet statistics measured from gene trees and tie the model to MSC using simulations. The combined use of these three ideas leads to a scalable method called Phlag. On simulated and real data, we show that Phlag can detect many cases of change in underlying evolutionary processes, including reduced recombination rates, population size changes, and admixture, all using the same algorithm. AVAILABILITY AND IMPLEMENTATION: Phlag is available at github.com/bo1929/phlag . All results and scripts can be found at github.com/bo1929/shared.phlag .

Journal Article↗
PubMed1992

Relationship of total viable and culturable cells in epiphytic populations of Pseudomonas syringae.

The direct viable count method, used to detect viable but nonculturable bacteria in aquatic systems, was modified to examine epiphytic populations of Pseudomonas syringae. Viable-population sizes determined from the number of cells that elongated when incubated with yeast extract and nalidixic acid were compared with those determined by the conventional plate count method. The plate count method accurately determined the number of viable cells in epiphytic P. syringae populations in a state of active growth under conditions of high relative humidity. The plate count method also accurately determined the number of viable cells in P. syringae inoculum, or a growing P. syringae population, subject to desiccation stress under conditions of low relative humidity. In epiphytic populations of P. syringae older than 80 h, however, the plate count underestimated the viable-population size by about two- to fourfold, suggesting that up to 75% of the P. syringae population was nonculturable. These nonculturable cells may have entered a starvation-survival state, induced by low nutrient availability in the phyllosphere environment. Epiphytic P. syringae populations undergoing rapid size changes due to growth and death under fluctuating environmental conditions in the field should be accurately enumerated by the plate count method. However, the possible underestimation of viable-population size under some circumstances should be considered in epidemiological studies of phytopathogenic bacteria and when genetically engineered microorganisms in terrestrial ecosystems are monitored.

Colony Count, Microbial↗
PubMed1986

Dental reduction in post-pleistocene Nubia.

Tooth size changes among Nubian archaeological populations dating from the Mesolithic through the Christian era, a period of approximately 12,000 years, are analyzed. Standard length and breadth dimensions of all permanent teeth from several cultural horizons are combined to form three large samples: Mesolithic, 10000-70000 B.C.; Agriculturalist, 3300-1100 B.C. (A-group, C-group, Pharaonic); and Intensive Agriculturalist, A.D. 0-1400 (Meroitic, X-Group, Christian). Such information not only fills a void in the knowledge of Nubian skeletal biology, but also provides a much needed African reference point for the comparison of tooth size data among anatomically modern Homo sapiens from various regions of the world. Changes in mean tooth size and associated t-tests reveal strong and significant reduction in dental size between the Mesolithic and Agriculturalist samples, followed by a continued although diminished trend of reduction for only the molar teeth between the two Agriculturalist groups. These patterns are best observed by examining tooth breadths, which are considered as the most reliable indicator of tooth size. Previously published odontometrics of the Nubian Mesolithic are briefly compared to the findings of this diachronic analysis of Nubian dental change.

Egypt, Ancient↗
PubMed2026

Inferring the demographic history of Chinese and Indian rhesus macaque (Macaca mulatta) populations from PacBio HiFi long-read sequencing data.

The rhesus macaque (Macaca mulatta) is one of the most widely used animal models in biomedical research, both as it resembles humans in key biological aspects and as it is characterized by a broad geographic range. Most of the individuals housed in U.S. research colonies have been sampled from either China or India, though notably the source population of these animals has significantly shifted over time. Given the substantial genetic and immunological differences between these populations, a deeper understanding of the underlying population structure is critically important for biomedical interpretation. Despite this, the demographic histories of these two populations remain poorly resolved. Here, we present an analysis of whole-genome, PacBio HiFi long-read sequencing data from ten unrelated individuals of each population, applying four related model- and non-model based demographic inference approaches, in order to reconstruct their ancestral history. We evaluated the fit of the subsequently estimated models against the empirical data, and incorporated underlying uncertainty in the mutation rates used for scaling. We inferred a well-fitting population history characterized by substantial structure between Chinese and Indian populations, with a split time ∼140,000 generations ago from an ancestral population of ∼65,000 individuals. We additionally inferred the subsequent history of size change within, and gene flow between, these populations, reaching the current estimated sizes of ∼220,000 individuals in the Chinese population and ∼14,000 individuals in the Indian population. The robust baseline demographic model established in this study will serve as a valuable resource for future research on this species, including for improved fine-scale recombination mapping, selection inference, and association studies.

Cercopithecidae↗
PubMed1985

The direct effects of interleukin 1, interleukin 2, interferon-alpha, interferon-gamma, B-cell growth factor, and a B-cell differentiation factor on resting and activated human B cells.

A wide variety of cytokines have been demonstrated to affect B-cell function. However, it is unclear which of these mediators actually exert direct effects on the B cells themselves. In the present study, the direct role of interleukin (IL) 1, IL-2, Interferon-gamma, or Interferon-alpha in human B-cell activation, proliferation, or differentiation was examined and compared with the effects of a B-cell growth factor (BCGF) or a B-cell differentiation factor (BCDF). Highly purified human B lymphocytes were separated according to size into two nonoverlapping populations. The fraction of small B cells was incubated with IL-1, IL-2, Interferon-gamma, Interferon-alpha, BCGF, or BCDF, and cell size changes, RNA synthesis, DNA synthesis, or supernatant immunoglobulin (Ig) production were measured. Neither IL-1, IL-2, Interferon-alpha, Interferon-gamma, nor the BCGF induced substantial cell size changes, RNA synthesis, DNA synthesis, or Ig production by the small fraction of B lymphocytes; however, the BCDF could directly activate a proportion of resting B lymphocytes to secrete Ig. The fraction of large B cells was also incubated with these cytokines. While neither IL-1, Interferon-alpha, nor Interferon-gamma enhanced DNA synthesis or Ig production by the fraction of large B lymphocytes, DNA synthesis was augmented 23-fold by BCGF and IgG production was increased 7-fold by BCDF. Additionally, IL-2 slightly enhanced both proliferation and differentiation of large B cells but substantially less so than BCGF and BCDF; DNA synthesis was increased 4-fold, while Ig production in the presence of IL-2 was increased by approximately 50%. Thus, the most important lymphokines modulating the function of these two fractions of tonsillar lymphocytes were a BCGF and a BCDF.

B-Lymphocytes↗
PubMed1976

Changes in liver cells ploidy of young rats following isoprenaline treatment.

Cell proliferation induced by isoprenaline (IPR) stimulation in very high doses was assayed in the liver of young rats, and the formation of polyploid cells was studied form the 15th to the 70th day of life. A general stimulatory effect on a complex process of cellular multiplication, leading to a population of tetraploid cells, was found to be accelerated; the earlier appearance of binucleate cells and the subsequent significant variations in their incidence confirmed the role of this cell type as an intermediate step in the process of polyploidization. Evidence was found of concomitant size changes of the hepatocytes, which might be partially independent of the effect of DNA content. The stimulation was no longer evident 20--30 days from the end of treatment, by when the cells which had come into contact with IPR should have completed the whole sequence of events leading to the formation of tetraploid mononucleate cells.

Animals↗
PubMed1988

Functional and phenotypic characterization of human B lymphocyte subsets isolated by unit gravity sedimentation.

We report the use of unit gravity sedimentation with a CelSep apparatus to generate two volumetrically similar but functionally and phenotypically distinct subsets of human peripheral blood B cells. One subset, comprised of small B lymphocytes, underwent a significant size change in response to anti-mu, proliferated synergistically to low concentrations of anti-mu plus B cell growth factor (BCGF) or phorbol myristate acetate plus BCGF, and could be induced to produce immunoglobulin in response to pokeweed-mitogen-derived T-lymphocyte-replacing factors. These cells were primarily sIg+, B1+, B2+, and were virtually free of monocytes (less than 0.01%). Unlike these resting B lymphocytes, the large cells proliferated directly to BCGF, without displaying synergy with anti-mu. These cells displayed very little B2 (less than 7%), did not increase in volume in the presence of anti-mu, and made more immunoglobulin in response to TRF than the small resting B lymphocytes. However, neither population synthesized immunoglobulin spontaneously. This technique, which is highly reproducible, not equipment intensive, and produces high cell recovery (greater than 90%), allows for a precise analysis of the steps involved in the maturation of a resting B lymphocyte to an immunoglobulin-secreting cell.

B-Lymphocytes↗
PubMed1986

Cholinergic amacrine cells in the rat retina.

Staining of rat retinal wholemounts with a monoclonal antibody against choline-acetyl-transferase (ChAT) reveals two matching populations of amacrine cells in pigmented and albino rat retinae. One population has cell bodies in the inner nuclear layer (INL). Their dendrites are confined to a narrow stratum in the outer half of the inner plexiform layer (IPL). The other, displaced, population has cell bodies in the ganglion cell layer (GCL) with dendrites stratifying in the middle of the IPL. The density changes with eccentricity, ranging from 1,700 cells/mm2 centrally to 600 cells/mm2 in the periphery. Presumptive cholinergic cells were filled with the fluorescent dye Lucifer yellow. Both subpopulations have the same "starburstlike" morphology as described for rabbit cholinergic amacrine cells (Famiglietti, '83; Tauchi and Masland, '84; Masland et al., '84b). Their dendritic tree sizes change with eccentricity and range from 160 to 300 microns in diameter. Counterstaining of Lucifer yellow-filled cells by ChAT immunohistochemistry did not yield an unequivocal double staining. Nevertheless, indirect evidence of same soma size, same number and form of primary dendrites, same level of stratification, and the good fit into the cholinergic mosaic makes it very likely that the "starburstlike" amacrine cells in the rat use acetylcholine as their transmitter. A comparison with the rabbit cholinergic system strengthens this assumption and reveals a striking similarity between both species.

Animals↗
PubMed1976

Endotoxin-induced size change in bone marrow progenitors of granulocytes and macrophages.

Injection of 5 mug endotoxin to adult C57BL mice caused a marked increase in the sedimentation velocity of granulocytic and macrophage progenitor (colony-forming) cells in the bone marrow. This change was maximal two days after injection and was not accompanied by corresponding changes in total marrow nucleated cell populations. The endotoxin-induced shift was not dependent on the presence of the thymus but did not occur in mice challenged after preinjection with endotoxin. No changes in buoyant density, cell cycle status, pattern of differentiation and responsiveness of granulocytic and macrophage progenitor cells were observed after the injection of endotoxin. The increased sedimentation velocity of progenitor cells appears to indicate an increase in cell volume but the mechanisms involved have not been identified.

Animals↗
PubMed1986

Size and contrast have only small effects on the responses to faces of neurons in the cortex of the superior temporal sulcus of the monkey.

There is a population of neurons in the cortex in the middle and anterior part of the superior temporal sulcus (STS) of the monkey with responses which are selective for faces. To investigate whether the responses of these neurons show some of the perceptual properties of face recognition such as tolerance to changes in the size and contrast of the face, the effects of alteration of the size and contrast of an effective face stimulus on the responses of these neurons were analysed quantitatively in macaque monkeys. First, it was shown that the majority of these neurons had responses which were relatively invariant with respect to the size of the stimulus. The median size change tolerated with a response of greater than half the maximal response was 12 times. Second, it was found that for a few of these neurons, the size of the face did affect the neuronal response. For most of these neurons, it was found that when the size of the image and its distance were altered, the neuronal response was related to the retinal angle subtended by the image. But for four neurons the absolute size of the image determined the magnitude of the neuronal response, independently of the distance of the image. Thus these four neurons showed size constancy. It is suggested that these neurons would be useful as part of a face recognition system, because only objects in a certain absolute size range should normally be classified as faces. Third, the responses of the neurons were relatively invariant with respect to the contrast of the face. The mean contrast at which the neurons still responded with more than half the maximal response was 0.26. Fourth, the responses of the neurons were relatively invariant with respect to the sign of the contrast of the face, that is the neurons responded to negative as well as to positive images of faces. Fifth, the neurons typically responded to a face when the information in it had been reduced from 3D to a 2D representation in gray on a monitor, with a response which was on average 0.5 that to a real face. These results show that the responses of these neurons have some of the invariant properties with respect to size and contrast alteration shown by face perception, and show that their processing is at a level which would be useful in face recognition.(ABSTRACT TRUNCATED AT 400 WORDS)

Action Potentials↗
PubMed1989

Temperature-induced fusion of small unilamellar vesicles formed from saturated long-chain lecithins and diheptanoylphosphatidylcholine.

Small unilamellar vesicles which form when gel-state long-chain phosphatidylcholines are mixed with micellar short-chain lecithins undergo an increase in size as the long-chain species melts to its liquid-crystalline form. Analysis of the vesicle population with quasi-elastic light scattering shows that the particle size increases from 90-A radius to greater than 5000-A radius. Resonance energy transfer experiments show total mixing of lipid probes with unlabeled vesicles only when the Tm of the long-chain phosphatidylcholine is exceeded. This implies that the large size change represents a fusion process. Aqueous compartments are also mixed during this transition. 31P NMR analysis of the vesicle mixtures above the phase transition shows a great degree of heterogeneity with large unilamellar particles coexisting with oligo- and multilamellar structures. Upon cooling the vesicles below the Tm, the original size distribution (e.g., small unilamellar vesicles) is obtained, as monitored by both quasi-elastic light scattering and 31P NMR spectroscopy. This temperature-induced fusion of unilamellar vesicles is concentration dependent and can be abolished at lower total phospholipid concentrations. It occurs over a wide range of long-chain to short-chain ratios and occurs with 1-palmitoyl-2-stearoylphosphatidylcholine and dimyristoylphosphatidylcholine as well. Characterization of this fusion event is used to understand the anomalous kinetics of water-soluble phospholipases toward these unusual vesicles.

Kinetics↗
PubMed1985

Size changes of protamine 1 mRNA provide a molecular marker to monitor spermatogenesis in wild-type and mutant mice.

We utilized a cDNA encoding the cysteine-rich, tyrosine-containing mouse protamine, mouse protamine 1 (MP1), to detect the presence of several classes of differentiating germ cells in testicular extracts from wild-type and male sterile mutant mice. This assay is based on the changes in the poly (A) length of MP1-mRNA during spermatogenesis. Testicular extracts of sexually mature CD-1 mice contain a heterogeneous population of protamine-1 mRNA ranging in length from 450 to 580 nucleotides. When the protamine-1 probe was hybridized to testicular RNA preparations from 16- to 20-day-old animals, no MP1-mRNA was detected. Twenty-four-day-old mice contain only the 580-nucleotide form of MP1-mRNA. This size class of protamine mRNA is also present in purified populations of round spermatids, whereas elongating spermatids and residual bodies contain mRNAs ranging from 450 to 580 nucleotides in length, which are identical in size to those present in the testes of sexually mature animals. When the protamine cDNA probe was used to examine the progression of spermiogenesis in three male sterile mouse mutants, blind sterile (bs), quaking (qk) and testicular feminization (Tfm), the results demonstrated that each mutant is pathologically distinct. Analysis of the bs mutant revealed a diminution in the amount of both size classes of MP1-mRNA, in agreement with the cytological reports of reduced numbers of haploid spermatogenic cells in these animals. The presence of both size classes of protamine mRNA in the qk mutant indicates that germ-cell differentiation has proceeded at least to the step-12 spermatid in these animals.(ABSTRACT TRUNCATED AT 250 WORDS)

Androgen-Insensitivity Syndrome↗