The Clinical Emergency Data Registry: Structure, Use, and Limitations for Research

The Clinical Emergency Data Registry (CEDR) is a qualified clinical data registry that collects data from participating emergency departments (EDs) in the United States for quality measurement, improvement, and reporting purposes. This article aims to provide an overview of the data collection and validation process, describe the existing data structure and elements, and explain the potential opportunities and limitations for ongoing and future research use. CEDR data are primarily collected for quality reporting purposes and are obtained from diverse sources, including electronic health records and billing data that are de-identified and stored in a secure, centralized database. The CEDR data structure is organized around clinical episodes, which contain multiple data elements that are standardized using common data elements and are mapped to established terminologies to enable interoperability and data sharing. The data elements include patient demographics, clinical characteristics, diagnostic and treatment procedures, and outcomes. Key limitations include the limited generalizability due to the selective nature of participating EDs and the limited validation and completeness of data elements not currently used for quality reporting purposes, including demographic data. Nonetheless, CEDR holds great potential for ongoing and future research in emergency medicine due to its large-volume, longitudinal, near real-time, clinical data. In 2021, the American College of Emergency Physicians authorized the transition from CEDR to the Emergency Medicine Data Institute, which will catalyze investments in improved data quality and completeness for research to advance emergency care.

A taxonomy of key performance errors for emergency intubation

STUDY OBJECTIVE

Currently the videographic review of emergency intubations is an unstructured, qualitative process. We created a taxonomy of errors that impede the optimal procedural performance of emergency intubation.

METHODS

This was a prospective, observational, study reviewing a convenience sample of deidentified laryngoscopy recordings of emergency department intubations that were qualitatively flagged before the study as demonstrating suboptimal technique. These videos were coded for the presence of 13 predetermined performance errors. Our primary outcome was the incidence of each of these specified errors during emergency intubation. Errors fell into 3 categories: errors of structure recognition during laryngoscope insertion, errors of vallecula manipulation, and errors of device delivery.

RESULTS

A total of 100 intubation attempts were reviewed. The most common error was inadequate lifting force with the blade tip in the vallecula which lowered the percent of glottic opening, occurring in 45% of the attempts. The least common performance error was the premature removal of the laryngoscope during bougie placement, occurring in only 9% of the videos.

CONCLUSION

We developed a taxonomy of 13 performance errors of laryngoscopy. Further study is warranted to determine how to best incorporate these into emergency airway training and the airway review process.

Race and Ethnicity and Emergency Department Discharge Against Medical Advice

Importance

Although discharges against medical advice (DAMA) are associated with greater morbidity and mortality, little is known about current racial and ethnic disparities in DAMA from the emergency department (ED) nationally.

Objective

To characterize current patterns of racial and ethnic disparities in rates of ED DAMA.

Design, Setting, and Participants

This cross-sectional study used data from the Nationwide Emergency Department Sample on all hospital ED visits made between January to December 2019 in the US.

Main Outcomes and Measures

The main outcome was odds of ED DAMA for Black and Hispanic patients compared with White patients nationally and in analysis adjusted for sociodemographic factors. Secondary analysis examined hospital-level variation in DAMA rates for Black, Hispanic, and White patients.

Results

The study sample included 33 147 251 visits to 989 hospitals, representing the estimated 143 million ED visits in 2019. The median age of patients was 40 years (IQR, 22-61 years). Overall, 1.6% of ED visits resulted in DAMA. DAMA rates were higher for Black patients (2.1%) compared with Hispanic (1.6%) and White (1.4%) patients, males (1.7%) compared with females (1.5%), those with no insurance (2.8%), those with lower income (<$27 999; 1.9%), and those aged 35 to 49 years (2.2%). DAMA visits were highest at metropolitan teaching hospitals (1.8%) and hospitals that served greater proportions of racial and ethnic minoritized patients (serving ≥57.9%; 2.1%). Odds of DAMA were greater for Black patients (odds ratio [OR], 1.45; 95% CI, 1.31-1.57) and Hispanic patients (OR, 1.16; 95% CI, 1.04-1.29) compared with White patients. After adjusting for sociodemographic characteristics (age, sex, income, and insurance status), the adjusted OR (AOR) for DAMA was lower for Black patients compared with the unadjusted OR (AOR, 1.18; 95% CI, 1.09-1.28) and there was no difference in odds for Hispanic patients (AOR, 1.03; 95% CI, 0.92-1.15) compared with White patients. After additional adjustment for hospital random intercepts, DAMA disparities reversed, with Black and Hispanic patients having lower odds of DAMA compared with White patients (Black patients: AOR, 0.94 [95% CI, 0.90-0.98]; Hispanic patients: AOR, 0.68 [95% CI, 0.63-0.72]). The intraclass correlation in this secondary analysis model was 0.118 (95% CI, 0.104-0.133).

Conclusions and Relevance

This national cross-sectional study found that Black and Hispanic patients had greater odds of ED DAMA than White patients in unadjusted analysis. Disparities were reversed after patient-level and hospital-level risk adjustment, and greater between-hospital than within-hospital variation in DAMA was observed, suggesting that Black and Hispanic patients are more likely to receive care in hospitals with higher DAMA rates. Structural racism may contribute to ED DAMA disparities via unequal allocation of health care resources in hospitals that disproportionately treat racial and ethnic minoritized groups. Monitoring variation in DAMA by race and ethnicity and hospital suggests an opportunity to improve equitable access to health care.

Spontaneous splenic hemorrhage in a patient on apixiban

Novel oral anticoagulants (NOACs) are increasingly popular. Spontaneous splenic rupture is rare and life-threatening, especially if it is not immediately recognized. Prior work has demonstrated an association with NOAC use and spontaneous splenic rupture in unusual clinical circumstances. We present the case of spontaneous splenic hemorrhage in a largely healthy 57-year old female who was recently started on apixiban for a provoked PE. She had been discharged from an outside facility, and presented just hours after discharge to our emergency department in extremis: unconscious, pale, hypotensive, and tachycardic. Her abdomen on arrival was noted to be distended with positive fluid wave, and bedside ultrasound confirmed massive peritoneal fluid. Prompt diagnostic peritoneal aspirate confirmed hemoperitoneum, and a massive transfusion protocol was initiated. The patient's blood pressure and heart rate improved, and she was stabilized for imaging. Computed tomography demonstrated large subcapsular splenic hematoma with active extravasation at the periphery of the spleen. The patient was taken emergently to interventional radiology suite where splenic artery embolization was performed and an IVC filter was placed. She subsequently developed acute respiratory distress syndrome and persistent low urine output with hypotension despite resuscitation, and was taken to the operating room for splenectomy and abdominal washout. She improved thereafter and was discharged 12 days later. Prompt diagnosis and aggressive early resuscitation contributed to this patient's outcome.

SDT: A Tree Method for Detecting Patient Subgroups with Personalized Risk Factors

Eradicating health disparity is a new focus for precision medicine research. Identifying patient subgroups is an effective approach to customized treatments for maximizing efficiency in precision medicine. Some features may be important risk factors for specific patient subgroups but not necessarily for others, resulting in a potential divergence in treatments designed for a given population. In this paper, we propose a tree-based method, called Subgroup Detection Tree (SDT), to detect patient subgroups with personalized risk factors. SDT differs from conventional CART in the splitting criterion that prioritizes the potential risk factors. Subgroups are automatically formed as leaf nodes in the tree growing procedure. We applied SDT to analyze a clinical hypertension (HTN) dataset, investigating significant risk factors for hypertensive heart disease in African-American patients, and uncovered significant correlations between vitamin D and selected subgroups of patients. Further, SDT is enhanced with ensemble learning to reduce the variance of prediction tasks.

A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla)

Ruminantia, the ruminating, hoofed mammals (cow, deer, giraffe and allies) are an unranked artiodactylan clade. Around 50-60 million years ago the BovB retrotransposon entered the ancestral ruminantian genome through horizontal gene transfer. A survey genome screen using 454-pyrosequencing of the Java mouse deer (Tragulus javanicus) and the lesser kudu (Tragelaphus imberbis) was done to investigate and to compare the landscape of transposable elements within Ruminantia. The family Tragulidae (mouse deer) is the only representative of Tragulina and phylogenetically important, because it represents the earliest divergence in Ruminantia. The data analyses show that, relative to other ruminantian species, the lesser kudu genome has seen an expansion of BovB Long INterspersed Elements (LINEs) and BovB related Short INterspersed Elements (SINEs) like BOVA2. In comparison the genome of Java mouse deer has fewer BovB elements than other ruminants, especially Bovinae, and has in addition a novel CHR-3 SINE most likely propagated by LINE-1. By contrast the other ruminants have low amounts of CHR SINEs but high numbers of actively propagating BovB-derived and BovB-propagated SINEs. The survey sequencing data suggest that the transposable element landscape in mouse deer (Tragulina) is unique among Ruminantia, suggesting a lineage specific evolutionary trajectory that does not involve BovB mediated retrotransposition. This shows that the genomic landscape of mobile genetic elements can rapidly change in any lineage.

Polythiophene Grafted on Polyethylene Film

We have successfully grafted polythiophene on polyethylene (PE) film with a three reactions step: gas phase bromination on PE, yielding PE-Br; substitution reaction of PE-Br with 2-thiophene thiolate anion, following by chemical oxidative polymerization. The polymerization was carried out in a suspension solution of anhydrous FeCl3 in CHCl3, yielding a reddish PE-PT film after dedoping with ethanol. ATR-FTIR shows that the polythiophene (PT) was grafted on PE in the 2,5-position; on the other hand, PT homopolymer shows a small amount of 2,4 coupling. XPS reveals higher intensity of the S2p, including neutral and positive sulfur. SEM image reveals the island of PT on the PE film. AFM analysis found the thickness of the island is in the range of 120–145 nm. The conductivity of these thin films is in the range of 10−6 S/cm.

Randomized clinical trial of perianal surgery performed under spinal saddle block versus total intravenous anaesthesia

Background

The aim of this randomized clinical trial was to determine whether spinal saddle block (SSB) is superior to total intravenous anaesthesia (TIVA) in perianal surgery.

Methods

Suitable patients aged 18–75 years (American Society of Anesthesiologists grade I or II) scheduled to undergo perianal surgery were randomized to SSB (1·0 ml 0·5 per cent hyperbaric bupivacaine) or TIVA with propofol and fentanyl by means of a laryngeal mask. Cumulative consumption of analgesics within 24 h after surgery was recorded, and postoperative recovery and patient satisfaction were evaluated.

Results

A total of 201 patients were randomized. Supplemental analgesia within 24 h after surgery was required by 31 of 101 patients having SSB and 58 of 100 who had TIVA (P &lt; 0·001). Median monitoring time in the recovery room was 5 (range 1–45) min for SSB versus 44 (4–148) min for TIVA (P &lt; 0·001). Patients in the SSB group were able to eat and drink more quickly, although times to mobilization and micturition were not significantly different. Patients having SSB were more likely to describe the anaesthesia as ‘better than expected’.

Conclusion

SSB is superior to TIVA in patients undergoing perianal surgery in terms of analgesic consumption within 24 h after surgery and aspects of postoperative recovery. Registration number: ISRCTN41981381 (http://www.controlled-trials.com).

Complete mitochondrial genomes of Bos taurus and Bos indicus provide new insights into intra-species variation, taxonomy and domestication

The taurine and zebuine cattle breeds comprise the majority of the world cattle population but their taxonomic status is still controversial. The two forms of cattle are currently classified as Bos taurus and Bos indicus species and are differentiated primarily by the presence or absence of a hump. However, these two species hybridize readily, producing fully fertile offspring. We have determined and analyzed complete B. taurus and B. indicus mitochondrial genome sequences to investigate the extent of sequence divergences and to study their taxonomic status by molecular dating. The sequences encompassed 16,338 and 16,339 nucleotides, respectively, and differed at 237 positions. Estimated divergence times indicated that the two cattle lineages separated 1.7-2.0 million years ago. Combined phylogenetic analyses of 18 new and 130 previously reported extant B. taurus and B. indicus control region sequences with data from 32 archaeological specimens of the extinct wild aurochs (Bos primigenius) identified four major maternal lineages. B. primigenius haplotypes were present in all but the B. indicus lineage, and one B. taurus sequence clustered with B. primigenius P haplotypes that were not previously linked with domestic cattle. The B. indicus cluster and a recently reported new B. primigenius haplotype that represents a new lineage were approximately equidistant from the B. taurus cluster. These data suggest domestications from several differentiated populations of B. primigenius and a subspecies status for taurine (B. primigenius taurus) and zebuine (B. primigenius indicus) cattle.

Expression of CD28-related costimulatory molecule and its ligand in inflammatory neuropathies

BACKGROUND

Activation of effector T lymphocytes, mediated in part by costimulatory molecules, is an important mechanism in the pathogenesis of immune-mediated diseases of the peripheral nervous system (PNS).

OBJECTIVE

To analyze the expression and distribution pattern of the inducible costimulator (ICOS), a recently identified costimulatory molecule implicated in T-cell activation, and its unique ligand (ICOS-L), in inflammatory disorders of the PNS.

METHODS

We studied RNA and protein expression in sural nerve biopsy specimens from patients with Guillain-Barré syndrome (GBS), chronic inflammatory demyelinating polyradiculoneuropathy (CIDP), and vasculitic neuropathy (VN) vs patients with hereditary neuropathies (HNs) serving as a noninflammatory control using reverse-transcriptase PCR and immunohistochemistry. In addition, in vitro analysis was performed by flow cytometry.

RESULTS

ICOS and ICOS-L mRNA was found to be significantly upregulated in samples from patients with GBS, CIDP, and VN compared to HNs. Immunohistochemistry identified T lymphocytes as the cellular source of ICOS, whereas macrophages expressed the corresponding ligand ICOS-L. Further analysis revealed that the distribution of ICOS-expressing T cells did not differ between acute and chronic inflamed PNS diseases. Correspondingly, the expression pattern of ICOS-L was similar in the inflamed tissues but differed significantly when compared to HNs.

CONCLUSIONS

Inducible costimulator, expressed by T lymphocytes, and inducible costimulator ligand, expressed by macrophages within the peripheral nerve, might not only be relevant in inducing an acute immune response but might also be critically involved in perpetuating inflammation in chronically immune-mediated disorders of the peripheral nervous system.

Whole-brain voxel-based statistical analysis of gray matter and white matter in temporal lobe epilepsy

Volumetric MRI studies based on manual labeling of selected anatomical structures have provided in vivo evidence that brain abnormalities associated with temporal lobe epilepsy (TLE) extend beyond the hippocampus. Voxel-based morphometry (VBM) is a fully automated image analysis technique allowing identification of regional differences in gray matter (GM) and white matter (WM) between groups of subjects without a prior region of interest. The purpose of this study was to determine whole-brain GM and WM changes in TLE and to investigate the relationship between these abnormalities and clinical parameters. We studied 85 patients with pharmacologically intractable TLE and unilateral hippocampal atrophy and 47 age- and sex-matched healthy control subjects. The seizure focus was right sided in 40 patients and left sided in 45. Student's t test statistical maps of differences between patients' and controls' GM and WM concentrations were obtained using a general linear model. A further regression against duration of epilepsy, age of onset, presence of febrile convulsions, and secondary generalized seizures was performed with the TLE population. Voxel-based morphometry revealed that GM pathology in TLE extends beyond the hippocampus involving other limbic areas such as the cingulum and the thalamus, as well as extralimbic areas, particularly the frontal lobe. White matter reduction was found only ipsilateral to the seizure focus, including the temporopolar, entorhinal, and perirhinal areas. This pattern of structural changes is suggestive of disconnection involving preferentially frontolimbic pathways in patients with pharmacologically intractable TLE.

Mitogenomic analyses of eutherian relationships

Reasonably correct phylogenies are fundamental to the testing of evolutionary hypotheses. Here, we present phylogenetic findings based on analyses of 67 complete mammalian mitochondrial (mt) genomes. The analyses, irrespective of whether they were performed at the amino acid (aa) level or on nucleotides (nt) of first and second codon positions, placed Erinaceomorpha (hedgehogs and their kin) as the sister group of remaining eutherians. Thus, the analyses separated Erinaceomorpha from other traditional lipotyphlans (e.g., tenrecs, moles, and shrews), making traditional Lipotyphla polyphyletic. Both the aa and nt data sets identified the two order-rich eutherian clades, the Cetferungulata (comprising Pholidota, Carnivora, Perissodactyla, Artiodactyla, and Cetacea) and the African clade (Tenrecomorpha, Macroscelidea, Tubulidentata, Hyracoidea, Proboscidea, and Sirenia). The study corroborated recent findings that have identified a sister-group relationship between Anthropoidea and Dermoptera (flying lemurs), thereby making our own order, Primates, a paraphyletic assembly. Molecular estimates using paleontologically well-established calibration points, placed the origin of most eutherian orders in Cretaceous times, 70-100 million years before present (MYBP). The same estimates place all primate divergences much earlier than traditionally believed. For example, the divergence between Homo and Pan is estimated to have taken place approximately 10 MYBP, a dating consistent with recent findings in primate paleontology.

Molecular estimates of primate divergences and new hypotheses for primate dispersal and the origin of modern humans

The concept of recent hominoid divergences has been a mainstay in molecular primatology since the 1970's. However, the ages allocated to the calibration points used to establish these divergence times and the estimates resulting from their application, notably the commonly accepted divergence between Pan (chimpanzees) and Homo 5 million years before present (MYBP), are now palaeontologically refutable. Here we estimate the ages of various primate divergences using three references with a more detailed fossil record than any of the traditional primate calibration points. Our findings suggest that the latter yield datings that are too recent by a factor of about two. For example, our estimates place the divergence between Pan and Homo 10.5-13 MYBP. The revised estimates of primate divergence times suggest a new hypothesis for primate evolution and dispersal: that the divergence between strepsirhines (lorises, lemurs) and anthropoids was contemporary with the break-up of Southern continents about 90 MYBP, with strepsirhines becoming isolated on Madagascar and later dispersing to Africa (and Asia) and anthropoids evolving in South America and subsequently colonizing Africa (and Asia), or possibly North America. In addition we present a new hypothesis, which accommodates the strikingly similar coalescence times for human mitochondrial DNA and the Y-chromosome. This hypothesis posits a common mitochondrial and Y-chromosome bottleneck about 400,000 years ago, associated with the origination of the human 2n = 46 karyotype, obstructing genetic exchange with the 2n = 48 Homo contemporaries.

The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): implications for amniote phylogeny

The complete mitochondrial genomes of two reptiles, the common iguana (Iguana iguana) and the caiman (Caiman crocodylus), were sequenced in order to investigate phylogenetic questions of tetrapod evolution. The addition of the two species allows analysis of reptilian relationships using data sets other than those including only fast-evolving species. The crocodilian mitochondrial genomes seem to have evolved generally at a higher rate than those of other vertebrates. Phylogenetic analyses of 2889 amino-acid sites from 35 mitochondrial genomes supported the bird-crocodile relationship, lending no support to the Haematotherma hypothesis (with birds and mammals representing sister groups). The analyses corroborated the view that turtles are at the base of the bird-crocodile branch. This position of the turtles makes Diapsida paraphyletic. The origin of the squamates was estimated at 294 million years (Myr) ago and that of the turtles at 278 Myr ago. Phylogenetic analysis of mammalian relationships using the additional outgroups corroborated the Marsupionta hypothesis, which joins the monotremes and the marsupials to the exclusion of the eutherians.

Molecular evidence of an African Phiomorpha-South American Caviomorpha clade and support for Hystricognathi based on the complete mitochondrial genome of the cane rat (Thryonomys swinderianus)

The complete mitochondrial genome of an African cane rat, Thryonomys swinderianus (Rodentia, Hystricognathi), was included in a phylogenetic analysis along with 4 rodents, 14 additional eutherians, and 3 noneutherian outgroups. Monophyly of the suborder Hystricognathi, represented by the cane rat and the South American guinea pig, Cavia porcellus, was strongly supported by maximum-parsimony, neighbor-joining, and maximum-likelihood methods. The molecular-based estimate of the divergence time of Old and New World Hystricognathi (approximately 85 million years before present, MYBP) is consistent with an hypothesis of vicariance divergence due to the rifting of the African and South American continents 86-100 MYBP. Monophyly of Rodentia or the superordinal clade Glires (Rodentia and Lagomorpha) were not supported.

Treatment of the gastric stump ulcer: an open study with five drugs

BACKGROUND/AIMS

Despite a great progress in the treatment of peptic ulcer disease, the management of gastric stump ulcers still remains to be established.

METHODOLOGY

Eighty-one patients with peptic ulcer developed postoperatively in the gastric remnant were treated in an open trial with 5 antiulcer drugs (cimetidine, omeprazole, sucralfate, colloidal bismuth and misoprostol) characterized by different mechanisms of action. The ulcer healing rate was evaluated endoscopically after 2, 4 and 6 weeks.

RESULTS

It was found that after 2 weeks the most rapid ulcer healing was in the omeprazole and cimetidine treated groups, 67 and 43% of healing, respectively. Also after 4 weeks the antisecretors were more effective than gastroprotective drugs; ulcer healing rate for omeprazole was 87% and cimetidine 68%, while for sucralfate, colloidal bismuth and misoprostol 50%, 52%, and 33%, respectively. After 6 weeks all drugs represented very close ulcer healing rates.

CONCLUSIONS

Both antisecretory and gastroprotective drugs may be useful in the management of stump ulcers, however, to initiate and accelerate the stump ulcer healing omeprazole appears to be the drug of choice.

The mitochondrial genome of the sperm whale and a new molecular reference for estimating eutherian divergence dates

Extant cetaceans are systematically divided into two suborders: Mysticeti (baleen whales) and Odontoceti (toothed whales). In this study, we have sequenced the complete mitochondrial (mt) genome of an odontocete, the sperm whale (Physeter macrocephalus), and included it in phylogenetic analyses together with the previously sequenced complete mtDNAs of two mysticetes (the fin and blue whales) and a number of other mammals, including five artiodactyls (the hippopotamus, cow, sheep, alpaca, and pig). The most strongly supported cetartiodactyl relationship was: outgroup,((pig, alpaca), ((cow, sheep),(hippopotamus,(sperm whale,(baleen whales))))). As in previous analyses of complete mtDNAs, the sister-group relationship between the hippopotamus and the whales received strong support, making both Artiodactyla and Suiformes (pigs, peccaries, and hippopotamuses) paraphyletic. In addition, the analyses identified a sister-group relationship between Suina (the pig) and Tylopoda (the alpaca), although this relationship was not strongly supported. The paleontological records of both mysticetes and odontocetes extend into the Oligocene, suggesting that the mysticete and odontocete lineages diverged 32-34 million years before present (MYBP). Use of this divergence date and the complete mtDNAs of the sperm whale and the two baleen whales allowed the establishment of a new molecular reference, O/M-33, for dating other eutherian divergences. There was a general consistency between O/M-33 and the two previously established eutherian references, A/C-60 and E/R-50. Cetacean (whale) origin, i.e., the divergence between the hippopotamus and the cetaceans, was dated to approximately 55 MYBP, while basal artiodactyl divergences were dated to >/=65 MYBP. Molecular estimates of Tertiary eutherian divergences were consistent with the fossil record.

The phylogenetic position of the Talpidae within eutheria based on analysis of complete mitochondrial sequences

The complete mitochondrial (mt) genome of the mole Talpa europaea was sequenced and included in phylogenetic analyses together with another lipotyphlan (insectivore) species, the hedgehog Erinaceus europaeus, and 22 other eutherian species plus three outgroup taxa (two marsupials and a monotreme). The phylogenetic analyses reconstructed a sister group relationship between the mole and fruit bat Artibeus jamaicensis (order Chiroptera). The Talpa/Artibeus clade constitutes a sister clade of the cetferungulates, a clade including Cetacea, Artiodactyla, Perissodactyla, and Carnivora. A monophyletic relationship between the hedgehog and the mole was significantly rejected by maximum parsimony and maximum likelihood. Consistent with current systematic schemes, analyses of complete cytochrome b genes including the shrew Sorex araneus (family Soricidae) revealed a close relationship between Talpidae and Soricidae. The analyses of complete mtDNAs, along with the findings of other insectivore studies, challenge the maintenance of the order Lipotyphla as a taxonomic unit and support the elevation of the Soricomorpha (with the families Talpidae and Soricidae and possibly also the Solenodontidae and Tenrecidae) to the level of an order, as previously proposed in some morphological studies.

The mitochondrial DNA molecule of the aardvark, Orycteropus afer, and the position of the Tubulidentata in the eutherian tree

An outstanding problem in mammal phylogeny is the relationship of the aardvark (Orycteropus afer), the only living species of the order Tubulidentata, to the extant eutherian lineages. In order to examine this problem the complete mitochondrial DNA (mtDNA) molecule of the aardvark was sequenced and analysed. The aardvark tRNA-Ser (UCN) differs from that of other mammalian mtDNAs reported and appears to have reversed to the ancestral secondary structure of non-mammalian vertebrates and mitochondrial tRNAs in general. Phylogenetic analysis of 12 concatenated protein-coding genes (3325 amino acids) included the aardvark and 15 additional eutherians, two marsupials and a monotreme. The most strongly supported tree identified the aardvark as a sister group of a clade including the armadillo (Xenarthra) and the Cetferungulata (carnivores, perissodactyls, artiodactyls and cetaceans). By applying three molecular calibration points the divergence between the aardvark and armadillo-cetferungulates was estimated at ca. 90 million years before present.

Molecular timing of primate divergences as estimated by two nonprimate calibration points

The complete mitochondrial DNA (mtDNA) molecule of the hamadryas baboon, Papio hamadryas, was sequenced and included in a molecular analysis of 24 complete mammalian mtDNAs. The particular aim of the study was to time the divergence between Cercopithecoidea and Hominoidea. That divergence, set at 30 million years before present (MYBP) was a fundamental reference for the original proposal of recent hominoid divergences, according to which the split among gorilla, chimpanzee, and Homo took place 5 MYBP. In the present study the validity of the postulated 30 MYBP dating of the Cercopithecoidea/Hominoidea divergence was examined by applying two independent nonprimate molecular references, the divergence between artiodactyls and cetaceans set at 60 MYBP and that between Equidae and Rhinocerotidae set at 50 MYBP. After calibration for differences in evolutionary rates, application of the two references suggested that the Cercopithecoidea/Hominoidea divergence took place >50 MYBP. Consistent with the marked shift in the dating of the Cercopithecoidea/Hominoidea split, all hominoid divergences receive a much earlier dating. Thus the estimated date of the divergence between Pan (chimpanzee) and Homo is 10-13 MYBP and that between Gorilla and the Pan/Homo linage approximately 17 MYBP. The same datings were obtained in an analysis of clocklike evolving genes. The findings show that recalculation is necessary of all molecular datings based directly or indirectly on a Cercopithecoidea/Hominoidea split 30 MYBP.

The complete mitochondrial DNA sequence of the domestic sheep (Ovis aries) and comparison with the other major ovine haplotype

The complete mitochondrial DNA (mtDNA) molecule of the domestic sheep, Ovis aries, was sequenced, together with part of the mtDNA of a specimen representing the other major O. aries haplotype group. The length of the complete ovine mtDNA presented is 16,616 nucleotides (nt). This length is not absolute, however, due to heteroplasmy caused by the occurrence of different numbers of a 75-nt-long tandem repeat in the control region. The sequence data were included in analyses of intraspecific ovine molecular differences, molecular comparisons with bovine mtDNAs, and phylogenetic analyses based on complete mtDNAs. The comparisons with bovine mtDNAs were based on the central domains of the ovine control regions, representing both major ovine haplotype groups, and the corresponding domains of Bos taurus and B. indicus. The comparisons showed that the difference between the bovids was 1.4 times greater than the intraspecific ovine difference. These findings suggest that the strains of wild sheep from which domestic sheep originated were more closely related than were the B. primigenius subspecies which gave rise to B. indicus and B. taurus cattle. Datings based on complete mtDNAs suggest that the bovine and ovine lineages diverged about 30 million years before present. This dating is considerably earlier than that proposed previously.

Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders

The phylogenetic relationship among primates, ferungulates (artiodactyls + cetaceans + perissodactyls + carnivores), and rodents was examined using proteins encoded by the H strand of mtDNA, with marsupials and monotremes as the outgroup. Trees estimated from individual proteins were compared in detail with the tree estimated from all 12 proteins (either concatenated or summing up log-likelihood scores for each gene). Although the overall evidence strongly suggests ((primates, ferungulates), rodents), the ND1 data clearly support another tree, ((primates, rodents), ferungulates). To clarify whether this contradiction is due to (1) a stochastic (sampling) error; (2) minor model-based errors (e.g., ignoring site rate variability), or (3) convergent and parallel evolution (specifically between either primates and rodents or ferungulates and the outgroup), the ND1 genes from many additional species of primates, rodents, other eutherian orders, and the outgroup (marsupials + monotremes) were sequenced. The phylogenetic analyses were extensive and aimed to eliminate the following artifacts as possible causes of the aberrant result: base composition biases, unequal site substitution rates, or the cumulative effects of both. Neither more sophisticated evolutionary analyses nor the addition of species changed the previous conclusion. That is, the statistical support for grouping rodents and primates to the exclusion of all other taxa fluctuates upward or downward in quite a tight range centered near 95% confidence. These results and a site-by-site examination of the sequences clearly suggest that convergent or parallel evolution has occurred in ND1 between primates and rodents and/or between ferungulates and the outgroup. While the primate/rodent grouping is strange, ND1 also throws some interesting light on the relationships of some eutherian orders, marsupials, and montremes. In these parts of the tree, ND1 shows no apparent tendency for unexplained convergences.