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PubMed2004

Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears.

Approximately 10 miles separate the Horn of Africa from the Arabian Peninsula at Bab-el-Mandeb (the Gate of Tears). Both historic and archaeological evidence indicate tight cultural connections, over millennia, between these two regions. High-resolution phylogenetic analysis of 270 Ethiopian and 115 Yemeni mitochondrial DNAs was performed in a worldwide context, to explore gene flow across the Red and Arabian Seas. Nine distinct subclades, including three newly defined ones, were found to characterize entirely the variation of Ethiopian and Yemeni L3 lineages. Both Ethiopians and Yemenis contain an almost-equal proportion of Eurasian-specific M and N and African-specific lineages and therefore cluster together in a multidimensional scaling plot between Near Eastern and sub-Saharan African populations. Phylogeographic identification of potential founder haplotypes revealed that approximately one-half of haplogroup L0-L5 lineages in Yemenis have close or matching counterparts in southeastern Africans, compared with a minor share in Ethiopians. Newly defined clade L6, the most frequent haplogroup in Yemenis, showed no close matches among 3,000 African samples. These results highlight the complexity of Ethiopian and Yemeni genetic heritage and are consistent with the introduction of maternal lineages into the South Arabian gene pool from different source populations of East Africa. A high proportion of Ethiopian lineages, significantly more abundant in the northeast of that country, trace their western Eurasian origin in haplogroup N through assorted gene flow at different times and involving different source populations.

Base Sequence↗
PubMed2005

Prolactin receptor signaling mediates the osmotic response of embryonic zebrafish lactotrophs.

The pituitary hormone prolactin (PRL) regulates salt and water homeostasis by altering ion retention and water uptake through peripheral osmoregulatory organs. To understand the role of osmotic homeostasis in the development of PRL-secreting lactotrophs, we generated germline transgenic zebrafish coexpressing red fluorescent protein directed by Prolactin regulatory elements (PRL-RFP) and green fluorescent protein by the Pro-opiomelanocortin promoter (POMC-GFP). Transparent embryos expressing fluorescent markers specifically targeted to lactotrophs and corticotrophs, the two pituitary lineages involved in teleost osmotic adaptation, allowed in vivo dynamic tracing of pituitary ontogeny during altered environmental salinity. Physiological osmotic changes selectively regulate lactotroph but not corticotroph proliferation during early ontogeny. These changes are not suppressed by pharmacological dopamine receptor blockade but are completely abrogated by morpholino knockdown of the PRL receptor. PRL receptor signaling exerts robust effects on lactotroph development and plays a permissive role in lactotroph osmo-responsiveness, reflecting the dual peripheral and central interactions required for early pituitary development and embryonic homeostasis.

Amino Acid Sequence↗
PubMedDate not supplied

Male reproductive function and the human Y chromosome: is selection acting on the Y?

The human Y chromosome encodes genes that are essential for male sex determination, spermatogenesis and protection against Turner stigmata. In recent years mutations have been identified in Y-chromosome genes associated with these phenotypes and a series of microdeletions of the long arm of the Y have been defined that are specifically associated with male infertility. In parallel, the discovery of polymorphic markers on the Y, comprising of both slow-mutating binary markers and rapidly-mutating microsatellites, has enabled the high resolution definition of a large number of paternal lineages (haplogroups). These Y-chromosome haplogroups have been extensively used to trace population movements and understand human origins and histories, but recently a growing number of association studies have been performed aimed at assessing the relationship between the Y-chromosome background and Y-linked phenotypes such as infertility and male-specific cancers. These preliminary studies, comparing haplogroup distributions between case and control populations, are promising and suggest an association between different Y-chromosome lineages, sperm counts and prostate cancer. However, we highlight the need to extend these studies to other world populations. Increased sample numbers and a better haplogroup resolution using additional binary markers in association studies are necessary. By these approaches novel associations between Y-chromosome haplotypes and disease may be revealed and the degree to which selection is acting on the human Y chromosome may be determined.

Chromosomes, Human, Y↗
PubMed2024

Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences.

Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. These results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages.

Archaea↗
PubMed2006

Tracing the evolution and function of the Trk superfamily of receptor tyrosine kinases.

Most growth factors and their receptors have been strongly conserved during evolution. In contrast, Trks (Tropomyosin-related kinases) and related receptors in the Trk superfamily, Rors (receptor tyrosine kinase-like orphan receptors), Musks (muscle specific kinases) and Ddrs (discoidin domain receptor family), appear to be ancient, but their function has been lost in multiple lineages and the roles for the receptors have been modified over time. We will trace the evolution of the Trk superfamily and discuss possible conserved functional roles, including a unifying theme of target recognition by growing axons. We present an analogy between the evolution of G-protein-coupled receptors and receptor tyrosine kinases (RTKs), proposing that an important driving force for the divergence of receptors is the ease of divergence of their ligands.

Animals↗
PubMed1999

Unique evolution of neurohypophysial hormones in cartilaginous fishes: possible implications for urea-based osmoregulation.

Most bony vertebrate species display a great evolutionary stability of their two neurohypophysial hormones, so that two molecular lineages, isotocin-mesotocin-oxytocin and vasotocin-vasopressin, have been traced from bony fishes to mammals. Chondrichthyes, in contrast, show a striking diversity of their oxytocin-like hormones, yet show a substantial decrease in vasotocin stored in neurohypophysis when compared to nonmammalian bony vertebrates. In the rays, glumitocin ([Ser(4),Gln(8)]-oxytocin) has been identified. In the spiny dogfish, aspargtocin ([Asn4]-oxytocin) and valitocin ([Val(8)]-oxytocin) have been characterized whereas in the spotted dogfish, asvatocin ([Asn(4),Val(8)]-oxytocin) and phasvatocin ([Phe(3),Asn(4),Val(8)]-oxytocin) have been found. Finally, in the holocephalian Pacific ratfish, oxytocin, the typical peptide of placental mammals, has been discovered. The duplication of the oxytocin-like hormone gene found in dogfishes has been observed only in some Australian and American marsupials. Cartilaginous fishes have developed an original urea-based osmoregulation involving a glutamine-dependent urea synthesis and blood urea retention through renal urea transporters. Furthermore, marine species use a rectal salt gland for sodium chloride excretion. Although vasopressin, in mammals, and vasotocin, in nonmammalian tetrapods, are clearly implied in water and salt homeostasis, the hormones involved in the blood osmotic pressure regulation of elasmobranchs are still largely unknown. It is suggested that the great diversity of oxytocin-like hormones in elasmobranchs expresses a release from an evolutionary receptor-binding constraint, so that amino-acid substitutions reflect neutral evolution. In contrast, the preservation of vasotocin suggests a selective pressure, which may be related to the regulation of renal urea transporter-recruitment mechanisms, as it has been shown for vasopressin in mammals. J. Exp. Zool. 284:475-484, 1999.

Amino Acid Sequence↗
PubMed2005

Conserved versus innovative features in animal body organization.

The origin of evolutionary novelties is a central topic in evolutionary developmental biology (evo-devo) studies. In any new feature, there is a conserved component that is either structural or related to the underlying genetic control, but it is not always obvious what is really new and what is conserved. Nevertheless, disentangling this blending of old and new features is basic to understanding mechanisms of evolutionary change. The origin of arthropod appendages illustrates the complexity in tracing the origin of evolutionary novelties. At the base of the lineage, the main body axis was already segmented and antero-posteriorly patterned, and the genetic tool kit required to form lateral outgrowths was already available. The novelty was possibly the developmental decision to "read" the available axial information and to exploit it for differentiating segmentally patterned and axially segmented appendages. Some important novelties bridge the gap between what have been traditionally distinguished as systemic and local changes. For example, the origin of the body cavities evolved by several animal groups may have been initiated by simple changes in cell-to-cell adhesive properties. Any possible change in an existing ontogenetic pathway has the potential to generate novelties.

Animals↗
PubMed1998

Actin phylogeny identifies Mesostigma viride as a flagellate ancestor of the land plants.

Green algae and land plants trace their evolutionary history to a unique common ancestor. This "green lineage" is phylogenetically subdivided into two distinct assemblages, the Chlorophyta and the Streptophyta. The Chlorophyta includes the Chlorophyceae, Trebouxiophyceae, Ulvophyceae, and Prasinopohyceae, whereas the Streptophyta includes the Charophyceae plus the bryophytes, ferns, and all other multicellular land plants (Embryophyta). The Prasinophyceae is believed to contain the earliest divergences within the green lineage. Phylogenetic analyses using rDNA sequences identify the prasinophytes as a paraphyletic taxon that diverges at the base of the Chlorophyta. rDNA analyses, however, provide ambiguous results regarding the identity of the flagellate ancestor of the Streptophyta. We have sequenced the actin-encoding cDNAs from Scherffelia dubia (Prasinophyceae), Coleochaete scutata, Spirogyra sp. (Charophyceae), and the single-copy actin gene from Mesostigma viride (Prasinophyceae). Phylogenetic analyses show Mesostigma to be the earliest divergence within the Streptophyta and provide direct evidence for a scaly, biflagellate, unicellular ancestor for this lineage. This result is supported by the existence of two conserved actin-coding region introns (positions 20-3, 152-1), and one intron in the 5'-untranslated region of the actin gene shared by Mesostigma and the embryophytes.

Actins↗
PubMed2006

Comparative genomics of vertebrate Fox cluster loci.

BACKGROUND: Vertebrate genomes contain numerous duplicate genes, many of which are organised into paralagous regions indicating duplication of linked groups of genes. Comparison of genomic organisation in different lineages can often allow the evolutionary history of such regions to be traced. A classic example of this is the Hox genes, where the presence of a single continuous Hox cluster in amphioxus and four vertebrate clusters has allowed the genomic evolution of this region to be established. Fox transcription factors of the C, F, L1 and Q1 classes are also organised in clusters in both amphioxus and humans. However in contrast to the Hox genes, only two clusters of paralogous Fox genes have so far been identified in the Human genome and the organisation in other vertebrates is unknown. RESULTS: To uncover the evolutionary history of the Fox clusters, we report on the comparative genomics of these loci. We demonstrate two further paralogous regions in the Human genome, and identify orthologous regions in mammalian, chicken, frog and teleost genomes, timing the duplications to before the separation of the actinopterygian and sarcopterygian lineages. An additional Fox class, FoxS, was also found to reside in this duplicated genomic region. CONCLUSION: Comparison of loci identifies the pattern of gene duplication, loss and cluster break up through multiple lineages, and suggests FoxS1 is a likely remnant of Fox cluster duplication.

Animals↗
PubMed1985

Decidual cell-specific surface antigen(s) recognized by monoclonal antibodies: tissue and species distribution.

Decidual cells are direct descendants of endometrial stromal cells and the ultimate progeny of bone marrow-derived precursors. In view of their bone marrow genealogy and demonstrated immunoregulatory role during pregnancy, this study attempted to identify a lineage-specific differentiation marker(s) on murine decidual cells with the hope of tracing their developmental pathway and exploring their familial relationship to other lymphomyeloid cells. Two protein A-binding, IgG2b isotype monoclonal antibodies (secreted by clones 16F12 and 2G4F8) were raised by immunizing virgin CBA mice with syngeneic decidual cells. The presence and the density of the antigenic marker(s) recognized by these antibodies were examined by radioautography on various cell types in single cell suspensions of the decidua, placenta, and lymphomyeloid organs after a sandwich labeling with hybridoma supernatants followed by 125I-protein A. Both antibodies appeared to recognize antigen(s) unique for the decidual cell lineage in mice, humans, and rats. The incidence of antigen-bearing decidual cells increased with gestational age in CBA, C3H, and CD1 mice between days 8 and 14, and in humans between 6 and 10.5 wk; in rats, however, some decline was noted between days 8 and 14. The binding was always higher with 16F12 than with 2G4F8 supernatants. No significant binding of either antibody to trophoblast cells of the placenta or leukocytes within the decidua was noted in any of the above mouse strains or species. Little or no labeling of any cell type was seen on lymphomyeloid cells of the virgin or pregnant CBA mice, but a consistent labeling of a rare blast-type cell in the blood was observed with both antibodies, raising the possibility that this cell may represent the circulating precursor of the decidual cell lineage. It remains to be investigated whether these antibodies are recognizing the same or different differentiation antigen(s) on the decidual cells, and whether a conservation of this antigen(s) during speciation signifies its functional importance.

Animals↗
PubMed1984

Demographic influences on mitochondrial DNA lineage survivorship in animal populations.

Probability models of branching processes and computer simulations of these models are used to examine stochastic survivorship of female lineages under a variety of demographic scenarios. A parameter II, defined as the probability of survival of two or more independent lineages over G generations, is monitored as a function of founding size of a population, population size at carrying capacity, and the frequency distributions of surviving progeny. Stochastic lineage extinction can be very rapid under certain biologically plausible demographic conditions. For stable-sized populations initiated by n females and/or regulated about carrying capacity k = n, it is highly probable that within about 4n generations all descendants will trace their ancestries to a single founder female. For a given mean family size, increased variance decreases lineage survivorship. In expanding populations, however, lineage extinction is dramatically slowed, and the final k value is a far more important determinant of II than is the size of the population at founding. The results are discussed in the context of recent empirical observations of low mitochondrial DNA (mtDNA) sequence heterogeneity in humans and expected distributions of asexually transmitted traits among sexually reproducing species.

Animals↗
PubMed2005

Liver stem cells.

The concept of a liver stem cell or progenitor cell has not been widely accepted until the last decade. Studies investigating liver regeneration under conditions which totally or substantially preclude hepatocyte proliferation report the proliferation of a subpopulation of small, oval-shaped cells, which are first observed in the portal triad, adjacent to the terminal ducts. These cells, termed liver progenitor oval cells (LPCs) are shown to participate in liver regeneration in a variety of rodent models of chronic liver damage. They express markers common to hepatocytes and cholangiocytes suggesting they are a common precursor of both liver cell lineages. Supporting evidence for liver stem cells has also come from cell tracing studies which show transdifferentiation of bone marrow cells into hepatocytes in both human and animal models. Another important issue is the link between LPCs and hepatocellular carcinoma (HCC). The widening liver donor-recipient gap; a consequence of poor donation rates coupled with increasing incidence of liver disease highlights the importance of establishing the utility of cell transplant as an alternative to treat liver disease. In this regard, liver stem cells and progenitor cells may have a significant role to play. To successfully utilize liver stem cells or LPCs for cell therapy, we have to first develop methods for maintaining and differentiating them in culture. This technology must be based on a thorough understanding of conditions which regulate their behaviour in vitro. In particular, we need to know which growth factors and cytokines affect them and their mechanism of action. Since they are a potential source of HCC, it is also necessary to understand the mechanisms which underlie their transformation to cancer.

Animals↗
PubMed2025

Discovery of additional ancient genome duplications in yeasts.

Whole genome duplication (WGD) has had profound macroevolutionary impacts on diverse lineages1,2, preceding adaptive radiations in vertebrates3-5, teleost fish6,7, and angiosperms8,9. In contrast to the many known ancient WGDs in animals10,11 and especially plants12-14, we are aware of evidence for only four in fungi15,16. The oldest of these occurred ~100 million years ago (mya) and is shared by ~60 extant Saccharomycetales species17,18, including the baker's yeast Saccharomyces cerevisiae (Fig. 1). Notably, this is the only known ancient WGD in the yeast subphylum Saccharomycotina. The dearth of ancient WGD events in fungi remains a mystery15. Some studies have suggested that fungal lineages that experience chromosome19 and genome15 duplication quickly go extinct, leaving no trace in the genomic record, while others contend that the lack of known WGD is due to an absence of data15,16. Under the second hypothesis, additional sampling and deeper sequencing of fungal genomes should lead to the discovery of more WGD events. Coupling hundreds of recently published genomes from nearly every described Saccharomycotina species with three additional long-read assemblies, we discovered three novel WGD events. While the functions of retained duplicate genes originating from these events are broad, they bear many similarities to the well-known WGD that occurred in the Saccharomycetales17. Our results suggest that WGD may be a more common evolutionary force in fungi than previously believed.

Convergent Evolution↗
PubMed2003

Timing of early developmental events in embryos of a tropical sea urchin Echinometra mathaei.

Egg volume of a tropical sea urchin Echinometra mathaei is about one half that of other well-known species. We asked whether such a small size of eggs affected the timings of early developmental events or not. Cleavages became asynchronous from the 7th cleavage onward, and embryos hatched out before completion of the 9th cleavage. These timings were one cell cycle earlier than those in well-known sea urchins, raising the possibility that much earlier events, such as the increase in adhesiveness of blastomeres or the specification of dorso-ventral axis (DV-axis), would also occur earlier by one cell cycle. By examining the pseudopodia formation in dissociated blastomeres, it was elucidated that blastomeres in meso- and macromere lineages became adhesive after the 4th and 5th cleavages, respectively. From cell trace experiments, it was found that the first or second cleavage plane was preferentially employed as the median plane of embryo; the DV-axis was specified mainly at the 16-cell stage. Timings of these events were also one cell cycle earlier than those in Hemicentrotus pulcherrimus. The obtained results suggest that most of the early developmental events in sea urchin embryos do not depend on cleavage cycles, but on other factors, such as the nucleo-cytoplasmic ratio.

Animals↗
PubMed2006

Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota.

The evolutionary origin of "orphan" genes, genes that lack sequence similarity to any known gene, remains a mystery. One suggestion has been that most orphan genes evolve rapidly so that similarity to other genes cannot be traced after a certain evolutionary distance. This can be tested by examining the divergence rates of genes with different degrees of lineage specificity. Here the lineage specificity (LS) of a gene describes the phylogenetic distribution of that gene's orthologues in related species. Highly lineage-specific genes will be distributed in fewer species in a phylogeny. In this study, we have used the complete genomes of seven ascomycotan fungi and two animals to define several levels of LS, such as Eukaryotes-core, Ascomycota-core, Euascomycetes-specific, Hemiascomycetes-specific, Aspergillus-specific, and Saccharomyces-specific. We compare the rates of gene evolution in groups of higher LS to those in groups with lower LS. Molecular evolutionary analyses indicate an increase in nonsynonymous nucleotide substitution rates in genes with higher LS. Several analyses suggest that LS is correlated with the evolutionary rate of the gene. This correlation is stronger than those of a number of other factors that have been proposed as predictors of a gene's evolutionary rate, including the expression level of genes, gene essentiality or dispensability, and the number of protein-protein interactions. The accelerated evolutionary rates of genes with higher LS may reflect the influence of selection and adaptive divergence during the emergence of orphan genes. These analyses suggest that accelerated rates of gene evolution may be responsible for the emergence of apparently orphan genes.

Ascomycota↗
PubMed2026

Single-allele chromatin tracing reveals cytokine-dependent super-enhancer repositioning in CD4+ T cells.

Naive CD4+ T cells interpret cytokine cues to commit to T helper lineages. Here, we examined the impact of cytokines on the Ets1-Fli1 locus, which encodes paralogous transcription factors essential for T cell effector responses. Epigenomic and chromatin interaction profiling in double-positive (DP) thymocytes defined a T cell super-enhancer and a CTCF-bound boundary. Chromatin tracing at single-allele resolution revealed concurrent multi-way interactions among Ets1, Fli1, and the super-enhancer coupled to transcription. Deleting the CTCF boundary decompacted the locus without altering Ets1 expression or T cell development, whereas deleting the super-enhancer drew Ets1 and Fli1 closer; promoter proximity increased Ets1-Fli1 co-expression. In CD4+ Th1 cells, cytokines increased multi-way interactions and repositioned the super-enhancer toward the geometric center, activating both paralogs. Super-enhancer deletion rendered Th1 cells structurally and transcriptionally DP like. Thus, cytokines can drive lineage-specific gene activation by repositioning a super-enhancer, providing a mechanistic framework for how noncoding variants at the Ets1-Fli1 locus contribute to CD4+ T cell-mediated immune disorders.

Animals↗
PubMed1989

Quantitative tracing of mRNAs for T- and B-lymphocyte receptor genes in individual cells by in situ hybridization with fluorochrome-labeled gene probes. I. Expression in malignancies carrying B-lineage associated antigens.

Acute and chronic lymphatic leukemias were investigated on the single-cell level for the activity of genes coding for the IgM heavy chain and the alpha and beta chains of the T-cell antigen receptor (TCR). We used a new method for preparing highly fluorochrome-labeled gene probes for in situ hybridization, which allowed rapid and quantitative detection of mRNA at the individual cell level. Leukemic cell populations classified as belonging to the B lineage according to their surface antigenic patterns revealed increasing expression of mRNA for the IgM heavy chain (mu mRNA) in a maturation-dependent fashion, which was not correlated to rearrangement of the immunoglobulin mu chain gene--only 66% of the leukemias with rearranged mu gene also transcribed it. TCR mRNA was detected in B-antigen positive leukemic cells. High levels of both TCR and mu mRNA expression in all cells of some of these leukemias allowed the conclusion that these cells simultaneously transcribed the genes for T and B cell antigen receptors. TCR mRNA was also found in what are considered relatively mature B leukemias, lineage cross-over on the mRNA level being observed at a frequency of 23% (five of 22 cases), comparable with that of "inappropriate" receptor gene rearrangement. The quantitation of mRNA with fluorochrome-labeled gene probes in situ may allow determining the degree of gene activation in individual antigenically defined cells and may thus contribute a new tool for characterization of normal and malignant cells.

Antigens, Differentiation, B-Lymphocyte↗
PubMed2005

Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

BACKGROUND: As genomes evolve after speciation, gene content, coding sequence, gene expression, and splicing all diverge with time from ancestors with close relatives. A minimum evolution general method for continuous character analysis in a phylogenetic perspective is presented that allows for reconstruction of ancestral character states and for measuring along branch evolution. RESULTS: A software package for reconstruction of continuous character traits, like relative gene expression levels or alternative splice site usage data is presented and is available for download at http://www.rossnes.org/phyrex. This program was applied to a primate gene expression dataset to detect transcription factor binding sites that have undergone substitution, potentially having driven lineage-specific differences in gene expression. CONCLUSION: Systematic analysis of lineage-specific evolution is becoming the cornerstone of comparative genomics. New methods, like phyrex, extend the capabilities of comparative genomics by tracing the evolution of additional biomolecular processes.

Alternative Splicing↗