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At least 343 records · Page 19Linked to original sources
PubMed2006

Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage.

At the center of the debate on the emergence of modern humans and their spread throughout the globe is the question of whether archaic Homo lineages contributed to the modern human gene pool, and more importantly, whether such contributions impacted the evolutionary adaptation of our species. A major obstacle to answering this question is that low levels of admixture with archaic lineages are not expected to leave extensive traces in the modern human gene pool because of genetic drift. Loci that have undergone strong positive selection, however, offer a unique opportunity to identify low-level admixture with archaic lineages, provided that the introgressed archaic allele has risen to high frequency under positive selection. The gene microcephalin (MCPH1) regulates brain size during development and has experienced positive selection in the lineage leading to Homo sapiens. Within modern humans, a group of closely related haplotypes at this locus, known as haplogroup D, rose from a single copy approximately 37,000 years ago and swept to exceptionally high frequency (approximately 70% worldwide today) because of positive selection. Here, we examine the origin of haplogroup D. By using the interhaplogroup divergence test, we show that haplogroup D likely originated from a lineage separated from modern humans approximately 1.1 million years ago and introgressed into humans by approximately 37,000 years ago. This finding supports the possibility of admixture between modern humans and archaic Homo populations (Neanderthals being one possibility). Furthermore, it buttresses the important notion that, through such adminture, our species has benefited evolutionarily by gaining new advantageous alleles. The interhaplogroup divergence test developed here may be broadly applicable to the detection of introgression at other loci in the human genome or in genomes of other species.

Adaptation, Biological↗
PubMed2024

Mitochondrial DNA control-region and coding-region data highlight geographically structured diversity and post-domestication population dynamics in worldwide donkeys.

Donkeys (Equus asinus) have been used extensively in agriculture and transportations since their domestication, ca. 5000-7000 years ago, but the increased mechanization of the last century has largely spoiled their role as burden animals, particularly in developed countries. Consequently, donkey breeds and population sizes have been declining for decades, and the diversity contributed by autochthonous gene pools has been eroded. Here, we examined coding-region data extracted from 164 complete mitogenomes and 1392 donkey mitochondrial DNA (mtDNA) control-region sequences to (i) assess worldwide diversity, (ii) evaluate geographical patterns of variation, and (iii) provide a new nomenclature of mtDNA haplogroups. The topology of the Maximum Parsimony tree confirmed the two previously identified major clades, i.e. Clades 1 and 2, but also highlighted the occurrence of a deep-diverging lineage within Clade 2 that left a marginal trace in modern donkeys. Thanks to the identification of stable and highly diagnostic coding-region mutational motifs, the two lineages were renamed as haplogroup A and haplogroup B, respectively, to harmonize clade nomenclature with the standard currently adopted for other livestock species. Control-region diversity and population expansion metrics varied considerably between geographical areas but confirmed North-eastern Africa as the likely domestication center. The patterns of geographical distribution of variation analyzed through phylogenetic networks and AMOVA confirmed the co-occurrence of both haplogroups in all sampled populations, while differences at the regional level point to the joint effects of demography, past human migrations and trade following the spread of donkeys out of the domestication center. Despite the strong decline that donkey populations have undergone for decades in many areas of the world, the sizeable mtDNA variability we scored, and the possible identification of a new early radiating lineage further stress the need for an extensive and large-scale characterization of donkey nuclear genome diversity to identify hotspots of variation and aid the conservation of local breeds worldwide.

Animals↗
PubMed2002

Germ cell lineage from a single blastomere at 8-cell stage in shiro-uo (ice goby).

Shiro-uo (ice goby; teleost fish), Leucopsarion petersii, shows a unique cleavage pattern characterized by two tires of blastomeres at 8-cell stage, like that of echinoderm and amphibian embryo. Such a pattern is suitable to isolation and cell lineage experiments. In this study, cell lineage of germ-line was traced by histological observation and cell labelling experiment at the 8-cell stage. Primordial germ cells (PGCs) were first detected histologically at the 10-somite stage, and migrated to gonadal anlage at 10 days post-fertilization, through usual way described in other teleost species. When a single blastomere was labelled with tracer dye at 8-cell stage, both upper and lower tires generated labelled PGCs at gonadal anlage although upper tires occasionally. This result suggests that all blastomeres at the 8-cell stage have potential to produce PGCs in shiro-uo.

Animals↗
PubMed1999

Cell lineage of the midline cells in the amphipod crustacean Orchestia cavimana (Crustacea, Malacostraca) during formation and separation of the germ band.

Cell lineages of identified midline cells were traced in the amphipod Orchestia cavimana (Crustacea, Malacostraca) by in vivo labelling. Midline cells are a common phenomenon in the germ band of crustaceans and insects. Studies in midline cells of Drosophila showed an origin from separate, paired anlagen and a differentiation into three types of cells. The in vivo labelling of midline cells of Orchestia demonstrates that they originate from the same material as the neural and epidermal ectoderm, divide in a stereotyped cell division pattern and give rise to at least two different types of cells. During the following evolutionarily derived mode of germ band elongation in Orchestia, a morphogenetic process is intercalated that separates germ band halves. On the level of single cells, it can be shown that midline cells are the only ectodermal cells that bridge the large distance between the separated parts. The cells are stretched extensively but do not proliferate. Comparing the midline cells of Orchestia with non-malacostracan crustaceans and insects, the results favour the hypothesis that midline cells are a distinct population of cells homologous in crustaceans and insects.

Animals↗
PubMed1994

Late Precambrian bilaterians: grades and clades.

A broad variety of body plans and subplans appear during a period of perhaps 8 million years (my) within the Early Cambrian, an unequaled explosion of morphological novelty, the ancestral lineages represented chiefly or entirely by trace fossils. Evidence from the fossil record can be combined with that from molecular phylogenetic trees to suggest that the last common ancestor of (i) protostomes and deuterostomes was a roundish worm with a blood vascular system and (ii) of arthropods and annelids was similar, with a hydrostatic hemocoel; these forms are probably among trace makers of the late Precambrian. Cell-phenotype numbers in living phyla, and a model of cell-phenotype number increase, suggest an origin of metazoans near 600 my ago, followed by a passive rise in body-plan complexity. Living phyla appearing during the Cambrian explosion have a Hox/HOM gene cluster, implying its presence in the common ancestral trace makers. The explosion required a repatterning of gene expression that mediated the development of novel body plans but evidently did not require an important, abrupt increase in genomic or morphologic complexity.

Animals↗
PubMed2026

ARGformer: learning on ancestral recombination graphs with transformers.

MOTIVATION: Recent advances in inference of the ancestral recombination graph (ARG), which describes how segments of chromosomes trace back through recombination and shared lineages, have made it possible to reconstruct genome-wide genealogies for large cohorts, but it remains difficult to summarize and use this information for population genetic analyses. RESULTS: We present ARGformer, an encoder-only transformer that learns context-dependent embeddings with a self-supervised masked objective finetuned with contrastive learning for downstream retrieval tasks. We train ARGformer on genealogies from coalescent simulations and on genealogies inferred from ancient and present-day Homo sapiens genomes. Using only these learned embeddings, without access to genotype matrices, ARGformer captures patterns of global population structure and supports ancestry inference through clustering and nearest-neighbor retrieval. On genealogies that include archaic hominins, ARGformer can highlight Denisovan-derived segments in Oceanian genomes and reveals Oceanian-like ancestry in South American Indigenous populations. AVAILABILITY AND IMPLEMENTATION: ARGformer is available at https://github.com/AI-sandbox/ARGformer.

Humans↗
PubMed2002

Evolutionary dynamics of satellite DNA family PIM357 in species of the genus Pimelia (Tenebrionidae, Coleoptera).

A large number of repeats of a satellite DNA (stDNA) family have been cloned and sequenced from species and populations of the genus Pimelia (Tenebrionidae, Coleoptera). The beetles were collected in the Canary Islands, Morocco, the Iberian Peninsula, and the Balearic Islands in order to analyze the evolutionary forces and processes acting on abundant stDNAs conserved at the genus level. This repetitive family is composed of an abundant A-T-rich stDNA, with basic units of 357 bp. All the sequences obtained showed similarity to the 22 repeat units of the PIM357 stDNA family described previously for six Iberian Pimelia species (Pons et al. 1997 ). An analysis based on similarity shows the presence of three different groups of sequences clearly in accordance with their geographical origin. One is composed of satellite sequences from Iberian and Balearic species, a second group from the Moroccan taxa, whereas the third one is from the Pimelia species endemic to the Canary Islands. The latter group shows higher nucleotide diversities for their stDNA sequences and a lack of relationship between transition stages to fixation and sequence divergence. Phylogeographic data of Canarian Pimelia show that the PIM357 stDNA family has persisted for more than 8 Myr and could probably be traced to the origin of the lineage. The data suggest that distinct demographic and phylogenetic patterns related to the colonization of the volcanic Canarian island chain account for particular evolutionary dynamics of the repeat DNA family in this group.

Animals↗
PubMed2000

Isolation of chicken vasa homolog gene and tracing the origin of primordial germ cells.

To obtain a reliable molecular probe to trace the origin of germ cell lineages in birds, we isolated a chicken homolog (Cvh) to vasa gene (vas), which plays an essential role in germline formation in Drosophila. We demonstrate the germline-specific expression of CVH protein throughout all stages of development. Immunohistochemical analyses using specific antibody raised against CVH protein indicated that CVH protein was localized in cytoplasm of germ cells ranging from presumptive primordial germ cells (PGCs) in uterine-stage embryos to spermatids and oocytes in adult gonads. During the early cleavages, CVH protein was restrictively localized in the basal portion of the cleavage furrow. About 30 CVH-expressing cells were scattered in the central zone of the area pellucida at stage X, later 45-60 cells were found in the hypoblast layer and subsequently 200-250 positive cells were found anteriorly in the germinal crescent due to morphogenetic movement. Furthermore, in the oocytes, CVH protein was predominantly localized in granulofibrillar structures surrounding the mitochondrial cloud and spectrin protein-enriched structure, indicating that the CVH-containing cytoplasmic structure is the precursory germ plasm in the chicken. These results strongly suggest that the chicken germline is determined by maternally inherited factors in the germ plasm.

Amino Acid Sequence↗
PubMed1992

Molecular markers for identified neuroblasts and ganglion mother cells in the Drosophila central nervous system.

The first step in generating cellular diversity in the Drosophila central nervous system is the formation of a segmentally reiterated array of neural precursor cells, called neuroblasts. Subsequently, each neuroblast goes through an invariant cell lineage to generate neurons and/or glia. Using molecular lineage markers, I show that (1) each neuroblast forms at a stereotyped time and position; (2) the neuroblast pattern is indistinguishable between thoracic and abdominal segments; (3) the development of individual neuroblasts can be followed throughout early neurogenesis; (4) gene expression in a neuroblast can be reproducibly modulated during its cell lineage; (5) identified ganglion mother cells form at stereotyped times and positions; and (6) the cell lineage of four well-characterized neurons can be traced back to two identified neuroblasts. These results set the stage for investigating neuroblast specification and the mechanisms controlling neuroblast cell lineages.

Animals↗
PubMed1994

Clonal analysis of the origin of primordial germ cells in the mouse.

Qualitative and quantitative clonal analysis has been used to answer three basic questions about the establishment of the germ cell lineage in the mouse. Where do primordial germ cells originate? What is the size of the founding population at the time of lineage restriction? When and where does lineage restriction occur? Single epiblast cells of 6.0 dpc and 6.5 dpc mouse embryos were injected with a short-term lineage label (lysinated rhodamine dextran, LRDX) and their descendants traced after 40 h embryo culture at neural plate and early somite stages, respectively. An objective matching technique was used to detect the lineage marker in primordial germ cells identified by their characteristic alkaline phosphatase staining. Precursors of the primordial germ cells were found in the proximal epiblast close to the extraembryonic ectoderm in both pregastrulation and early-streak stage embryos. They form part of the presumptive extraembryonic mesoderm and are not lineage restricted while in the epiblast. Quantitative analysis gives a best fit to a model of a founding population of 45 at the time of lineage restriction. The data indicate that the generation time lengthens at the time of allocation. Calculation of clonal histories gives a best fit of 16 h generation time after allocation compared with < 7 h before allocation, with lineage restriction occurring at the early midstreak stage, presumably in the region posterior to the streak in which primordial germ cells are first identifiable. Therefore primordial germ cells are probably allocated early during gastrulation in a group of > 40 cells already segregated in the extraembryonic mesoderm.

Animals↗
PubMed2002

Pancreatic cell lineage analyses in mice.

Considerable knowledge of the ontogeny of the endocrine pancreas has been gained in recent years, mainly through the use of two complementary genetic approaches in transgenic mice: gene inactivation or overexpression (to assess gene function) and genetic labeling of precursor cells (to determine cell lineages). In recent years, in vivo Cre/loxP-based direct cell tracing experiments show that (i) all pancreatic cells differentiate from pdx1-expressing precursors, (ii) p48 is involved in the exocrine and endocrine pancreatic lineages, (iii) islet endocrine cells derive from ngn3-expressing progenitor cells, and (iv) insulin cells do not derive from glucagon- expressing progenitors. Lineage analyses allow the identification of progenitor cells from which mature cell types differentiate. Once identified, such progenitors can be labeled and isolated, and their differentiation and gene expression profiles studied in vitro. Understanding pancreatic cell lineages is highly relevant for future cell replacement therapies in diabetic patients, helping to define the identity of putative (endodermal) pancreatic stem cells.

Animals↗
PubMedDate not supplied

Histogenesis of Reed-Sternberg and dendritic interdigitating cells in nodular sclerosing Hodgkin's disease. Immunohistochemical evidence for monocytoid precursors.

Reed-Sternberg (R-S) and dendritic interdigitating (DI) cells share many features in nodular sclerosing Hodgkin's disease (NSHD). Such features include commonalities of location (paracortex), histochemistry (paranuclear acid phosphatase and nonspecific esterase activity), and immunohistochemical reactivity (positivity for Mr 70,000 antigen). Because of these similarities, it is hypothesized that there may be a common precursor for R-S and DI cells. To investigate this possibility, paraffin-embedded material from five (5) archival cases of NSHD were reacted in immunohistochemical procedures with antibodies to detect the following antigens: CD15, CD30, S-100 protein, CD68 and IL-9, respectively. Double immunostaining for lysozyme or CD45RB (leukocyte common antigen) or S-100 protein and one of the aforementioned was carried out on representative slides from selected cases. Both relatively large dendriform cells and a population of small mononuclear cells with monocytic karyomorphism showed immunoreactivity for S-100 protein. Similarly, IL-9 antigen which is characteristically found in R-S cells in NSHD was strongly expressed in a population of CD45RB- monocytoid cells. Coexpression of lysozyme antigen in some of the CD30+ R-S cells and Hodgkin's cells is also consistent with a monocytic/histiocytic lineage. Finally, CD30 antigen occasionally could be traced from monocytoid cells, where it was found in a pancytoplasmic distribution to histiocytic cells with a pancytoplasmic and sometimes also paranuclear (Golgizone) pattern of immunoreactivity, to R-S cells with paranuclear and plasmalemmal immunopositivity. In sum, the results of these studies support the contention that there are monocytoid precursors for R-S, Hodgkin's, and DI cells in NSHD and suggest a role for IL-9 in the development of R-S cells from tissue monocytes and monocytoid histiocytes.

Antigens, CD↗
PubMed2000

Melanophore lineage and clonal organization of the epidermis in Xenopus embryos as revealed by expression of a biogenic marker, GFP.

Melanophore lineage during embryogenesis of Xenopus laevis was traced using the overexpression of a biogenic marker, green fluorescent protein (GFP). Two different approaches were applied after injection of GFP mRNA (hence a marker construct) into each blastomere at the 16-cell stage. In in vivo experiments, the embryos injected with a marker construct were grown until stage 45, in which melanophores were distributed over the whole body and were good enough for checking GFP expression at their migratory destination. In in vitro experiments, neural tubes of the embryos injected with a marker construct were isolated and cultured at stage 21 to examine by virtue of GFP expression how neural crest cells differentiate into melanophores. The results obtained from both in vivo and in vitro experiments indicated the following: 1) selected animal blastomeres vastly contribute to the development of melanophores, whereas other animal blastomeres do so slightly at a limited pace; and 2) vegetal blastomeres never contribute to melanophores in normal development, whereas certain vegetal blastomeres have a potential to give rise to melanophores in vitro. The analyses using GFP also disclosed that the dorsal and ventral epidermis derive from the restricted animal blastomeres in the normal development. Since the dorso-ventrality of the epidermis has been inseparably coupled with integumental pigmentation, the clonal organization of the epidermis observed in the present study is discussed in the light of pigment pattern formation attributed by melanophores.

Animals↗
PubMed1999

Analysis of puumala hantavirus genome in patients with nephropathia epidemica and rodent carriers from the sites of infection.

Reverse transcription-polymerase chain reaction (RT-PCR) followed by sequence and phylogenetic analyses were used to study specimens from nine Finnish nephropathia epidemica (NE) patients admitted to hospital during the epidemic in winter 1996-1997. Blood samples from six patients were found to be positive for the partial M- and/or S-segment sequences of Puumala hantavirus (PUUV). Analyses of these sequences (nt 2168-2610 for the M segment, and nt 819-1082 for the S segment) revealed six distinct PUUV strains showing highest similarity to previously described PUUV strains from Finland: 90-95% for the S segment, and 90-99% for the M segment. Accordingly, on the phylogenetic trees calculated for both viral segments, all six human strains were placed within the Finnish genetic lineage of PUUV. Attempts were made to trace five RT-PCR-positive patients to local bank voles (Clethrionomys glareolus) infected with wild-type PUUV, and for two patients a comparative analysis of human- and rodent-originated viral sequences was undertaken. Whereas in the first case the differences between the sequences were substantial (5. 7% for the S segment, and 10.8%, for the M segment), in the other case the M segment sequence recovered from the clinical specimen was 100% identical to three sequences recovered from rodent lungs, and the S sequences differed by one silent substitution only. This is the first finding of virtually identical PUUV sequences in an NE patient and a natural rodent host from the site of infection.

Adolescent↗
PubMed1991

Premutation for the Martin-Bell syndrome analyzed in a large pedigree segregating also for G6PD-deficiency. I: A working hypothesis on the nature of the FRAX-mutations.

A large Sardinian family including 13 Martin-Bell syndrome (MBS) patients, several instances of normal transmitting males or females, and the G6PD-Mediterranean mutant segregating in some of its branches, has been thoroughly investigated with the hope of gaining further insight on the nature of the FRAX-mutation. All the MBS patients and the 15 obligate heterozygous women present in the pedigree could be traced back through their X-chromosome lineage to the same ancestress, who must have been heterozygous for a silent premutation at the FRAX-locus. This premutation appears to have turned into a true FRAX-mutation at least 9 times during the gametogenesis of the ancestress' X-related descendants of whom four are males. This finding alone suggests that the transition from the FRAX premutation to the true mutation can be the result of intra- as well as interchromosomal events. This conclusion is supported by the additional observation that the genetic phase between the FRAX and the G6PD loci remained unaltered when the transition occurred in a repulsion double heterozygote for the premutation and the G6PD-Mediterranean mutant. The data described are compatible with the hypothesis that MBS patients and normal transmitting males are, respectively, hemizygous for deletion or duplication products generated by aberrant recombination events at a highly recombinogenic site of the region Xq27-Xqter. The overall message stemming from this report is that no firm conclusion can be drawn on the genetic linkage between the FRAX-locus and other markers of this region until the nature of the FRAX-mutations and the mechanism of their occurrence are fully understood.

Adult↗
PubMed1993

First appearance, distribution, and origin of macrophages in the early development of the avian central nervous system.

A phagocytic cell system of hemopoietic origin exists in the early avian embryo (Cuadros, Coltey, Nieto, and Martin: Development 115:157-168, '92). In this study we investigated the presence of cells belonging to this system in the central nervous system (CNS) of chick and quail embryos by using both histochemical staining for acid phosphatase and immunolabelling with antibodies recognizing cells of quail hemangioblastic lineage. The origin of these cells was traced in interspecific chick-quail yolk sac chimeras. Hemopoietic cells were detected within the CNS from developmental stage HH15 on, and steadily increased in number at subsequent stages. Analysis of yolk sac chimeras revealed that most of these cells were of yolk sac origin, although some hemopoietic cells of intramebryonic origin were also found in the CNS. Immunocytochemical, histochemical, and ultrastructural characterization allowed us to identify hemopoietic cells in the CNS as macrophages. These cells were consistently found in the brain vesicles and spinal cord, appearing (1) between undifferentiated neuroepithelial cells at dorsal levels of the CNS; (2) in areas of cell death; (3) in the marginal layer in close relationship with developing axons; (4) in large extracellular spaces in the subventricular layer; (5) on vascular buds growing through the marginal and subventricular layers; and (6) in the ventricular lumen. Macrophages in different locations varied in morphology and ultrastructure, suggesting that in addition to their involvement in phagocytosis, they play a role in other processes in the developing CNS, such as axonal growth and vascular development. The first macrophages migrate to the CNS independently of its vascularization, apparently traversing the pial basal lamina to reach the nervous parenchyma. Other macrophages may enter the CNS together with vascular buds at subsequent stages during CNS vascularization.

Acid Phosphatase↗
PubMedDate not supplied

Diversity and evolution of mitochondrial RNA editing systems.

'RNA editing' describes the programmed alteration of the nucleotide sequence of an RNA species, relative to the sequence of the encoding DNA. The phenomenon encompasses two generic patterns of nucleotide change, 'insertion/deletion' and 'substitution', defined on the basis of whether the sequence of the edited RNA is colinear with the DNA sequence that encodes it. RNA editing is mediated by a variety of pathways that are mechanistically and evolutionarily unrelated. Messenger, ribosomal, transfer and viral RNAs all undergo editing in different systems, but well-documented cases of this phenomenon have so far been described only in eukaryotes, and most often in mitochondria. Editing of mRNA changes the identity of encoded amino acids and may create translation initiation and termination codons. The existence of RNA editing violates one of the long-accepted tenets of genetic information flow, namely, that the amino acid sequence of a protein can be directly predicted from the corresponding gene sequence. Particular RNA editing systems display a narrow phylogenetic distribution, which argues that such systems are derived within specific eukaryotic lineages, rather than representing traits that ultimately trace to a common ancestor of eukaryotes, or even further back in evolution. The derived nature of RNA editing raises intriguing questions about how and why RNA editing systems arise, and how they become fixed as additional, essential steps in genetic information transfer.

Amino Acid Sequence↗
PubMed2001

Adaptive evolution in LINE-1 retrotransposons.

We traced the sequence evolution of the active lineage of LINE-1 (L1) retrotransposons over the last approximately 25 Myr of human evolution. Five major families (L1PA5, L1PA4, L1PA3B, L1PA2, and L1PA1) of elements have succeeded each other as a single lineage. We found that part of the first open-reading frame (ORFI) had a higher rate of nonsynonymous (amino acid replacement) substitution than synonymous substitution during the evolution of the ancestral L1PA5 through the L1PA3B families. This segment encodes the coiled coil region of the protein-protein interaction domain of the ORFI protein (ORFIp). Statistical analysis of these changes indicates that positive selection had been acting on this region. In contrast, the coiled coil segment hardly changed during the evolution of the L1PA3B to the present L1PA1 family. Therefore, selective pressure on the coiled coil segment has changed over time. We suggest that the fast rate of amino acid replacement in the coiled coil segment reflects the adaptation of L1 either to a changing genomic environment or to host repression factors. In contrast, the second open-reading frame and the nucleic acid-binding domain of the first open-reading frame are extremely well conserved, attesting to the strong purifying selection acting on these regions.

Amino Acid Sequence↗