Divergence Of Mammals Research Articles

Mitochondrial Genes and Mammalian Phylogenies: Increasing the Reliability of Branch Length Estimation

Since branch lengths provide important information about the timing and the extent of evolutionary divergence among taxa, accurate resolution of evolutionary history depends as much on branch length estimates as on recovery of the correct topology. However, the empirical relationship between the choice of genes to sequence and the quality of branch length estimation remains ill defined. To address this issue, we evaluated the accuracy of branch lengths estimated from subsets of the mitochondrial genome for a mammalian phylogeny with known subordinal relationships. Using maximum-likelihood methods, we estimated branch lengths from an 11-kb sequence of all 13 protein-coding genes and compared them with estimates from single genes (0.2-1.8 kb) and from 7 different combinations of genes (2-3.5 kb). For each sequence, we separated the component of the log-likelihood deviation due to branch length differences associated with alternative topologies from that due to those that are independent of the topology. Even among the sequences that recovered the same tree topology, some produced significantly better branch length estimates than others did. The combination of correct topology and significantly better branch length estimation suggests that these gene combinations may prove useful in estimating phylogenetic relationships for mammalian divergences below the ordinal level. Thus, the proper choice of genes to sequence is a critical factor for reliable estimation of evolutionary history from molecular data.

Identification and Functional Characterization of Two Highly Divergent Aryl Hydrocarbon Receptors (AHR1 and AHR2) in the TeleostFundulus heteroclitus: EVIDENCE FOR A NOVEL SUBFAMILY OF LIGAND-BINDING BASIC HELIX LOOP HELIX-PER-ARNT-SIM (bHLH-PAS) FACTORS

The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor through which 2,3,7, 8-tetrachlorodibenzo-p-dioxin (TCDD) and related compounds cause altered gene expression and toxicity. The AHR belongs to an emerging multigene family of transcription factors possessing basic helix loop helix (bHLH) and Per-ARNT-Sim (PAS) domains. Most bHLH-PAS proteins occur as duplicates or "paralog groups" in mammals, but only a single mammalian AHR has been identified. Here we report the cDNA cloning of two distinct AHRs, designated FhAHR1 and FhAHR2, from a single vertebrate species, the teleost Fundulus heteroclitus (Atlantic killifish). Both Fundulus AHR proteins possess bHLH and PAS domains that are closely related to those of the mammalian AHR. FhAHR1 and FhAHR2 are highly divergent (40% overall amino acid identity; 61% identity in the N-terminal half), suggesting that they arose from a gene duplication predating the divergence of mammals and fish. Photoaffinity labeling with 2-azido-3-[(125)I]iodo-7, 8-dibromodibenzo-p-dioxin and velocity sedimentation analysis using 2,3,7,8-[1,6-(3)H]TCDD showed that both FhAHR1 and FhAHR2 exhibit specific, high-affinity binding of dioxins. Both AHRs also showed specific, TCDD- and ARNT-dependent interactions with a mammalian xenobiotic response element. The two Fundulus AHR genes displayed different tissue-specific patterns of expression; FhAHR1 transcripts were primarily expressed in brain, heart, ovary, and testis, while FhAHR2 transcripts were equally abundant in many tissues. Phylogenetic analysis demonstrated that Fundulus AHR1 is an ortholog of mammalian AHRs, while AHR2 forms in Fundulus and other fish are paralogous to Fundulus AHR1 and the mammalian AHRs and thus represent a novel vertebrate subfamily of ligand-binding AHRs.

High sequence similarity within ras exons 1 and 2 in different mammalian species and phylogenetic divergence of the ras gene family.

We have determined the canine and feline N-, K-, and H-ras gene sequences from position +23 to +270 covering exons I and II which contain the mutational hot spot codons 12, 13, and 61. The results were used to assess the degree of similarity between ras gene DNA regions containing the critical domains affected in neoplastic disorders in different mammalian species. The comparative analyses performed included human, canine, feline, murine, rattine, and, whenever possible, bovine, leporine (rabbit), porcelline (guinea pig), and mesocricetine (hamster) ras gene sequences within the region of interest. Comparison of feline and canine nucleotide sequences with the corresponding regions in human DNA revealed a sequence similarity greater than 85% to the human sequence. Contemporaneous analysis of previously published ras DNA sequences from other mammalian species showed a similar degree of homology to human DNA. Most nucleotide differences observed represented synonymous changes without effect on the amino acid sequence of the respective proteins. For assessment of the phylogenetic evolution of ras gene family, a maximum parsimony dendrogram based on multiple sequence alignment of the common region of exons I and II in the N-, K-, and H-ras genes was constructed. Interestingly, a higher substitution rate among the H-ras genes became apparent, indicating accelerated sequence evolution within this particular clade. The most parsimonious tree clearly shows that the duplications giving rise to the three ras genes must have occurred before the mammalian radiation.

CCK-A- and CCK-B-like Receptors in the Gallbladder and Stomach of the Alligator (Alligator mississippiensis)

Autoradiographic analysis of radioligand binding was used to localize and characterize cholecystokinin (CCK) receptors expressed in the stomach and gallbladder of the American alligator (Alligator mississippiensis). Alligator gallbladder smooth muscle expresses a CCK-A receptor subtype, and stomach oxyntic mucosa expresses a distinct receptor subtype, termed CCK-B/X because of its similarities to both CCK-B and CCK-X receptors. Both the gallbladder and the stomach binding sites have very low affinities for a panel of nonpeptide receptor agonists and antagonists that are selective for mammalian CCK-A and CCK-B receptors. These results suggest that CCK receptor subtypes diverged from the ancestral CCK-X receptor in an early amniote, prior to the divergence of mammals and reptiles in vertebrate phylogeny, and that CCK-A receptors may have evolved before CCK-B receptors. Our findings support the hypothesis that the evolution of gastrin preceded the evolution of two separate CCK receptor subtypes.

Primate species: The irreversible units in the evolution of our mammalian divergence

Primate species: The irreversible units in the evolution of our mammalian divergence

The Mouse Insulin-like Growth Factor II/Cation-Independent Mannose 6-Phosphate (IGF-II/MPR) Receptor Gene: Molecular Cloning and Genomic Organization

The mammalian insulin-like growth factor II/cation-independent mannose 6-phosphate receptor (IGF-II/MPR) is a multifunctional protein that binds both IGF-II and ligands containing a mannose 6-phosphate recognition marker through distinct high-affinity sites. This receptor plays an integral part in lysosomal enzyme transport, has a potential role in growth factor maturation and clearance, and may mediate IGF-II-activated signal transduction through a G-protein-coupled mechanism. Recent studies have shown that production of IGF-II/MPR mRNA and protein begins in the mouse embryo soon after fertilization and have demonstrated that the receptor gene is on mouse chromosome 17 and is maternally imprinted. In this paper, we report the cloning and characterization of the mouse IGF-II/MPR gene. The gene is 93 kb long, is composed of 48 exons, and codes for a predicted protein of 2482 amino acids. The extracellular part of the receptor is encoded by exons 1-46, with each of 15 related repeating motifs being determined by parts of 3-5 exons. A single fibronectin type II-like element is found in exon 39. The transmembrane portion of the receptor also is encoded by exon 46, and the cytoplasmic region by exons 46-48. The positions of exon-intron splice junctions are conserved between several of the repeats in the IGF-II/MPR and the homologous extracellular region of the gene for the other known lysosomal sorting receptor, the cation-dependent mannose 6-phosphate receptor. The gene duplications that gave rise to the modern IGF-II/MPR probably occurred before the divergence of mammals, since there is more extensive protein sequence conservation between receptors from different species than between any pair of repeating motifs within a single receptor.

Localization of the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR) in the rat to chromosome 4 and implications for the evolution of mammalian chromosomes

We have isolated a partial cDNA encoding the cystic fibrosis transmembrane conductance regulator (CFTR) in the rat. This cDNA hybridizes to a 6.1-kb RNA transcript from the human T84 epithelial cell line and a similarly sized transcript from the rat parotid gland. The nucleotide sequence of this cDNA shows 80.5% identity to the human CFTR cDNA sequence, and the deduced amino acid sequence of rat CFTR shows 75.5% identity to the amino acid sequence of human CFTR. We have used this cDNA to map the location of the gene encoding CFTR to rat chromosome 4. This result places CFTR within a syntenic group on rat chromosome 4 and on human chromosome 7 that includes the genes encoding interleukin 6 (IL6), erythropoietin (EPO), P-glycoprotein 1 (PGY1), and T cell receptor beta chain (TCRB). This group is divided between chromosomes 5 and 6 in the mouse. Mapping of CFTR to rat chromosome 4 shows that this syntenic group has been divided in the mouse lineage during the past 15 million years and further localizes that breakpoint to a sequence homologous to the human chromosome 7q21.1 and 7q32 region. Similarly, a group of five genes, CFTR, TCRB, HOX1, parathyroid hormone-like hormone (PTHLH), and Kirsten rat sarcoma 2 viral (v-Ki-ras2) oncogene homolog (KRAS2), is syntenic on rat chromosome 4 and mouse chromosome 6, but is divided between human chromosomes 7 and 12. These data suggest that the ancestral mammalian chromosome appeared as the present day rat chromosome 4, with all six genes grouped together, and that chromosomal breakages have occurred in the mouse and human lineages since the mammalian divergence.

Gene conversions within the skeletal myosin multigene family

Comparisons of the nucleotide sequences of the light meromyosin (LMM) region of developmentally regulated fast chicken myosin heavy chain (MHC) isoforms indicates that chicken MHC isoforms are more similar to each other than to MHC isoforms in other species. The sequence data provide evidence that gene conversion events have occurred recently among the isoforms. An embryonic (C emb1) isoform and neonatal isoform have the most extensive regions of sequence identity. Similar gene conversion events are present in the rat α- and β-cardiac MHCs, but were not obvious in the LMM of developmentally regulated fast human MHC isoforms. The data suggest that gene conversion events can play a significant role in the evolution of the MHC multigene families and that concerted evolution of the chicken multigene family occurred after the divergence of mammals and avians.

Linkage assignment of a DNA sequence ( ERCC2L1) homologous to a human DNA repair gene in Xiphophorus fishes: Implications for the evolutionary derivation of human chromosome 19

Fish gene mapping studies have identified several syntenic groups showing conservation over more than 400 million years of vertebrate evolution. In particular, Xiphophorus linkage group IV has been identified as a homolog of human chromosomes 15 and 19. During mammalian evolution, loci coding for glucosephosphate isomerase, peptidase D, muscle creatine kinase, and several DNA repair genes ( ERCC1, ERCC2, and XRCC1) appear as a conserved syntenic group on human chromosome 19. When X. clemenciae and X. milleri PstI endonuclease-digested genomic DNA was used in Southern analysis with a human ERCC2 DNA repair gene probe, a strongly cross-hybridizing restriction fragment length polymorphism was observed. Backcrosses to X. clemenciae from X. milleri × X. clemenciae F 1 hybrids allowed tests for linkage of the ERCC2-like polymorphism to markers covering a large proportion of the genome. Statistically significant evidence for linkage was found only for ERCC2L1 and CKM (muscle creatine kinase), with a total of 41 parents and 2 recombinants (4.7% recombination, χ 2 = 35.37, P < 0.001); no evidence for linkage to GPI and PEPD in linkage group IV was detected. The human chromosome 19 synteny of ERCC2 and CKM thus appears to be conserved in Xiphophorus, while other genes located nearby on human chromosome 19 are in a separate linkage group in this fish. If Xiphophorus gene arrangements prove to be primitive, human chromosome 19 may have arisen from chromosome fusion or translocation events at some point since divergence of mammals and fishes from a common ancestor.

Chicken and Xenopus Mannose 6-Phosphate Receptors Fail to Bind Insulin-like Growth Factor II

The recent demonstration that a single mammalian receptor protein binds both mannose 6-phosphate (Man-6-P) and insulin-like growth factor II (IGF-II) with high affinity has suggested a multifunctional physiological role for this receptor, possibly including signal transduction. In order to better understand the functions of this receptor, we have investigated the properties of Man-6-P receptors from non-mammalian species. Receptors were affinity-purified from Triton X-100 extracts of total membranes from Xenopus and chicken liver as well as rat placenta using pentamannosyl 6-phosphate-Sepharose. The Man-6-P receptor was adsorbed to the pentamannosyl 6-phosphate-Sepharose and specifically eluted by Man-6-P in all three species, as evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by silver staining. When the purified receptors from these three species were cross-linked to 125I-IGF-II with disuccinimidyl suberate, only receptors isolated from rat membranes were affinity-labeled. To further evaluate the properties of these Man-6-P receptors, binding of 125I-rat-IGF-II and 125I-chicken Tyr-Gly-Thr-Ala-IGF-II to purified receptors from Xenopus, chicken, and rat was evaluated by polyethylene glycol precipitation. Only the rat Man-6-P receptor exhibited detectable binding of 125I-IGF-II. These data suggest that the emergence of a high affinity IGF-II binding site on the Man-6-P receptor occurred in evolution after the divergence of mammals from other vertebrates. Thus, the biological actions of IGF-II in chickens and frogs appear to be initiated by the type I IGF receptor.

Human Ventricular/Slow Twitch Myosin Alkali Light Chain Gene Characterization, Sequence, and Chromosomal Location

The gene coding for the human ventricular/slow twitch myosin alkali light chain isoform was isolated and sequenced. It was found to contain a total of seven exons, the last of which is completely 3'-untranslated sequence. Comparison of this gene sequence with that of the various fast twitch skeletal isoform gene sequences revealed that the exon-intron arrangement is conserved within the myosin alkali light chain gene family. In fact the introns are in exactly the same positions within analogous codons. Comparison of the derived amino acid sequence from the human ventricular/slow twitch isoform gene with that of other isoform protein sequences indicated that the protein encoded by this gene is more homologous to the chicken cardiac isoform protein sequence than to any of the other protein sequences. These results indicate that the gene duplication which gave rise to the ventricular/slow twitch and fast twitch isoform genes must have occurred prior to the divergence of mammals and avians. We have also localized the human ventricular/slow twitch isoform gene to the short arm of human chromosome 3. Interestingly the corresponding mouse gene has been mapped to the distal region of mouse chromosome 9 which contains a conserved syntenic group of genes that map to the short arm of human chromosome 3.

An attempt to estimate the effective size of the ancestral species common to two extant species from which homologous genes are sequenced.

SummaryWhen DNA sequence data on various kinds of homologous genes sampled from two related species are available, there is a way to infer the effective size of their ancestral species, which is a simple consequence of gene genealogical considerations. This method, when applied to the common ancestral species of human and rat, human and mouse, human and bovine, or rodents and bovine estimates their effective sizes all to be of the order of 107, supporting the view that these species indeed shared, around 75 million years ago, a common ancestral species from which they are descended. The effective size thus estimated would imply that the ancestral species was abundant enough to have ample opportunity for adaptive radiation. The extent of silent polymorphism in that species might have been very large, possibly comparable to the number of silent substitutions accumulated in a gene after the mammalian divergence. Some causes that may alter these results and require a more elaborated statistical analysis are discussed.

The coding region of the human c- mos pseudogene contains Alu repeat insertions

We have determined the nucleotide sequence of an 841-bp fragment derived from a segment of the human genome previously cloned by Chumakov et al. [Gene 17 (1982) 19–26] and Zabarovsky et al. [Gene 23 (1983) 379–384] and containing regions homologous to the viral mos gene probe. This sequence displays homology with part of the coding region of the human and murine c- mos genes, contains several termination codons, and is interrupted by two Alu-family elements flanked by short direct repeats. Probably, the progenitor of the human c- mos gene was duplicated approximately at the time of mammalian divergence, was converted to a pseudogene, and acquired insertions of two Alu elements.

Recent divergence from a common ancestor of human IFN-alpha genes.

The two major classes of human type I interferons, leukocyte or α-interferon (IFN-α) and fibroblastor β-interferon (IFN-β) are antigenically distinct and encoded by separate structural genes1. Recently, genomic hybridization experiments have demonstrated the presence of ∼10 or more distinct human IFN-α (Hu IFN-α) genes which code for a family of homologous yet distinct proteins2,3, and 8 of these have been identified and sequenced3. In contrast, no evidence has been found for multiple Hu IFN-β genes3, although heterogeneity of Hu IFN-β mRNA has been observed4,5. The coding sequences of Hu IFN-α and IFN-β genes show weak but appreciable homology, indicating that they were derived from a common ancestor at a remote time6, whereas Hu IFN-α1 (a member of class D) and Hu IFN-α2 (a member of class A) diverged quite recently (∼22 Myr ago)7. We report here that all eight known IFN-α genes diverged from a common ancestor quite recently, at most ∼26 Myr ago. As mammalian divergence is known to have occurred ∼75 Myr ago8, this suggests that the IFN-α multigene family in primates is distinct in organization from that of other mammals. We provide evidence for a much lower rate of evolution for IFN-α G than for other α-interferons, and a rapid evolution of IFN-α E pseudogene similar to that of other pseudogenes9–11. A possible evolutionary origin of size heterogeneity in the 3′-noncoding region of IFN-α mRNAs is also discussed.

Mammalian Variation: Variability of Mammals . A. V. Yablokov. Translated from the Russian. L. Van Valen, Ed. Published for the Smithsonian Institution and the National Science Foundation by Amerind, New Delhi, 1974 (available as TT-58007 from the National Technical Information Service, Springfield, Va.). xvi, 350 pp., illus. $10.

Mammalian Variation: <i>Variability of Mammals</i> . A. V. Yablokov. Translated from the Russian. L. Van Valen, Ed. Published for the Smithsonian Institution and the National Science Foundation by Amerind, New Delhi, 1974 (available as TT-58007 from the National Technical Information Service, Springfield, Va.). xvi, 350 pp., illus. $10.