Two nematodes (Nematoda: Diplogastridae, Rhabditidae) from the invasive millipede Chamberlinius hualienensis Wang, 1956 (Diplopoda, Paradoxosomatidae) on Hachijojima Island in Japan

Millipedes may cause unexpected damage when they are introduced to new locations, becoming invaders that leave behind their old parasites and predators. Therefore, it was interesting to find numerous rhabditid nematodes within the gut of the invasive phytophagous millipede Chamberlinius hualienensis Wang, 1956 (Diplopoda, Paradoxosomatidae) from Hachijojima (Japan) in November, 2014. This millipede originated in Taiwan but was discovered in Japan in 1986. The nematodes were identified as juvenile Oscheius rugaoensis (Zhang et al., 2012) Darsouei et al., 2014 (Rhabditidae), and juvenile and adult Mononchoides sp. (Diplogastridae) based on images, morphometrics, and sequences of 18S and 28S rDNA. A novel short 28S sequence of a separate population of Oscheius necromenus SB218 from Australian millipedes was also included in a phylogenetic comparison of what can now be characterized as a species complex of millipede-associated Oscheius. The only other nematode associates of millipedes belong to Rhigonematomorpha and Oxyuridomorpha, two strictly parasitic superorders of nematodes. These nematode identifications represent new geographic and host associations.

Millipedes may cause unexpected damage when they are introduced to new locations, becoming invaders that leave behind their old parasites and predators. Therefore, it was interesting to find numerous rhabditid nematodes within the gut of the invasive phytophagous millipede Chamberlinius hualienensis Wang, 1956 (Diplopoda, Paradoxosomatidae) from Hachijojima (Japan) in November, 2014. This millipede originated in Taiwan but was discovered in Japan in 1986. The nematodes were identified as juvenile Oscheius rugaoensis (Zhang et al., 2012) Darsouei et al., 2014 (Rhabditidae), and juvenile and adult Mononchoides sp. (Diplogastridae) based on images, morphometrics, and sequences of 18S and 28S rDNA. A novel short 28S sequence of a separate population of Oscheius necromenus SB218 from Australian millipedes was also included in a phylogenetic comparison of what can now be characterized as a species complex of millipede-associated Oscheius. The only other nematode associates of millipedes belong to Rhigonematomorpha and Oxyuridomorpha, two strictly parasitic superorders of nematodes. These nematode identifications represent new geographic and host associations.

Method for producing transgenic bovine embryos from in vitro matured and fertilized oocytes

Microinjection and in vitro culture procedures were developed to produce transgenic bovine embryos after in vitro fertilization of in vitro matured oocytes. In Experiment I, zygotes were subjected to pronuclear microinjection of DNA 18 or 24 h following addition of spermatozoa to oocytes. Microinjections were performed in either Hepes-buffered TCM-199 or modified Dulbecco's phosphate-buffered saline without glucose. Viability of embryos was similar at both injection times and for both media, as determined by morphological evaluation after culturing embryos in vitro for 10 d. In Experiment II, microinjected embryos were cultured 1) in rabbit oviducts, 2) in vitro in a 5% CO(2) in air, or 3) in a 5% CO(2) / 5% O(2) / 90% N(2) incubator. There were no significant differences between the 2 in vitro culture environments. The in vitro culture systems supported development of embryos significantly better than the rabbit oviducts; 33% of cleaved ova developed to blastocysts in vitro vs 10% in vivo; 98% of transferred ova were recovered from the rabbit oviducts. From both experiments, 6 of 92 blastocysts were positive for the microinjected DNA as determined by a polymerase chain reaction followed by gel electrophoresis.

Differentially expressed genes in aortic smooth muscle cells from atherosclerosis-susceptible and atherosclerosis-resistant pigeons

Susceptibility to spontaneous atherosclerosis in the White Carneau (WC-As) pigeon shows autosomal recessive inheritance. Aortic smooth muscle cells (SMC) cultured from susceptible WC-As and resistant Show Racer (SR-Ar) pigeons exhibit developmental and degenerative features corresponding to the respective SMC at atherosclerosis-prone sites in vivo. We used representational difference analysis to identify differentially expressed genes between WC-As and SR-Ar aortic SMC. Total RNA was extracted from cultured primary SMC of each breed, converted to double-stranded cDNA, followed by direct comparison in reciprocal representational difference analysis experiments. Difference products were cloned, sequenced, and identified by BLAST against the chicken genome. Six putative biochemical pathways were distinctly different between breeds with genes involved in energy metabolism and contractility exhibiting the most striking disparity. Genes associated with glycolysis and a synthetic SMC phenotype were expressed in WC-As cells. In contrast, SR-Ar cells expressed genes indicative of oxidative phosphorylation and a contractile SMC phenotype. In WC-As cells, the alternatives of insufficient ATP production limiting contractile function or the lack of functional contractile elements downregulating ATP synthesis cannot be distinguished due to the compressed in vitro versus in vivo developmental time frame. However, the genetic potential for effectively coupling energy production to muscle contraction present in the resistant SR-Ar was lacking in the susceptible WC-As.

Shifting patterns of natural variation in the nuclear genome of caenorhabditis elegans

Background

Genome wide analysis of variation within a species can reveal the evolution of fundamental biological processes such as mutation, recombination, and natural selection. We compare genome wide sequence differences between two independent isolates of the nematode Caenorhabditis elegans (CB4856 and CB4858) and the reference genome (N2).

Results

The base substitution pattern when comparing N2 against CB4858 reveals a transition over transversion bias (1.32:1) that is not present in CB4856. In CB4856, there is a significant bias in the direction of base substitution. The frequency of A or T bases in N2 that are G or C bases in CB4856 outnumber the opposite frequencies for transitions as well as transversions. These differences were not observed in the N2/CB4858 comparison. Similarly, we observed a strong bias for deletions over insertions in CB4856 (1.44: 1) that is not present in CB4858. In both CB4856 and CB4858, there is a significant correlation between SNP rate and recombination rate on the autosomes but not on the X chromosome. Furthermore, we identified numerous significant hotspots of variation in the CB4856-N2 comparison.

In both CB4856 and CB4858, based on a measure of the strength of selection (k_a/k_s), all the chromosomes are under negative selection and in CB4856, there is no difference in the strength of natural selection in either the autosomes versus X or between any of the chromosomes. By contrast, in CB4858, k_a/k_s values are smaller in the autosomes than in the X chromosome. In addition, in CB4858, k_a/k_s values differ between chromosomes.

Conclusions

The clear bias of deletions over insertions in CB4856 suggests that either the CB4856 genome is becoming smaller or the N2 genome is getting larger. We hypothesize the hotspots found represent alleles that are shared between CB4856 and CB4858 but not N2. Because the k_a/k_s ratio in the X chromosome is higher than the autosomes on average in CB4858, purifying selection is reduced on the X chromosome.

Familial correlations, segregation analysis, and nongenetic correlates of soy isoflavone-metabolizing phenotypes

Particular intestinal bacteria metabolize the soy isoflavone daidzein to equol and O-desmethylangolensin (O-DMA), metabolites that can be identified in urine. Individuals that harbor bacteria capable of producing equol or O-DMA are known as equol producers (approximately 30%-50% of the population) and O-DMA producers (approximately 80%-90% of the population), respectively. The equol-producer phenotype has been associated with sex hormone-related outcomes in several studies. However, the bacteria responsible for these phenotypes have not yet been identified and factors that influence the manifestation of these phenotypes are not well understood. To evaluate familial clustering of and nongenetic factors associated with these phenotypes, 410 individuals from 112 families participated in phenotyping (3-day soy challenge and Day 4 spot urine collection). In segregation analyses of the equol-producer phenotype, the Mendelian dominant model provided the most parsimonious fit to the data, suggesting that the pattern of inheritance of the equol-producer phenotype is consistent with an autosomal dominant trait. This phenotype was positively associated with education (p trend = 0.01), but not with sex, smoking, or several dietary factors. Results of the segregation analyses of the O-DMA-producer phenotype were inconclusive; no other models provided a more parsimonious fit to the data than the general model. This phenotype was inversely associated with age in a nonlinear model (p = 0.01), positively associated with age- and sex-adjusted height (odds ratio [OR] 10-cm increase = 0.38, 95% confidence interval [CI] = 0.15, 0.95) and body mass index (kg/m(2)) (OR = 0.91, 95% CI = 0.85, 0.96), but not with sex, education, smoking, or several dietary factors. These results suggest the equol-producer phenotype may be under some degree of genetic control and that there are likely other environmental factors not evaluated in the present analysis that contribute to both of these phenotypes. These results provide a foundation for further work to refine our understanding of heritable and environmental determinants of daidzein-metabolizing phenotypes.

Evolution of Parasitism in Insect-transmitted Plant Nematodes

Nematode-insect associations have evolved many times in the phylum Nematoda, but these lineages involve plant parasitism only in the Secernentean orders Aphelenchida and Tylenchida. In the Aphelenchida (Aphelenchoidoidea), Bursaphelenchus xylophilus (Pine wood nematode), B. cocophilus (Red ring or Coconut palm nematode) (Parasitaphelenchidae), and the many potential host-specific species of Schistonchus (fig nematodes) (Aphelenchoididae) nematode-insect interactions probably evolved independently from dauer-forming, mycophagous ancestors that were phoretically transmitted to breeding sites of their insect hosts in plants. Mycophagy probably gave rise to facultative or obligate plant-parasitism because of opportunities due to insect host switches or peculiarities in host behavior. In the Tylenchida, there is one significant radiation of insect-associated plant parasites involving Fergusobia nematodes (Fergusobiinae: Neotylenchidae) and Fergusonina (Fergusoninidae) flies as mutualists that gall myrtaceous plant buds or leaves. These dicyclic nematodes have different phases that are parasitic in either the insect or the plant hosts. The evolutionary origin of this association is unclear.

Comparative survey of early embryogenesis of Secernentea (Nematoda), with phylogenetic implications

Insight into the evolution of class Secernentea (Nematoda) for the purpose of providing a phylogenetic context for the model Caenorhabditis elegans is being gained from the use of molecular character sets. Such phylogenies provide a framework for mapping the evolution of diversity in some early-development characters for 70 species and 19 families of Secernentea. These characters include (i) whether AB and P1 blastomeres initially develop at the same (synchronous) or different (asynchronous) rates, (ii) whether AB and P1 are initially aligned along the linear axis of the embryo (tandem pattern) or obliquely (rhomboidal pattern), and (iii) whether the founder germ cell, P4, is established early, i.e., by the sixth cleavage, or later. Evolutionary polarity of characters was evaluated through outgroup comparisons. From our data the following inferences are made. The derived character, late establishment of P4, evolved primarily in the ancestor of the monophyletic groups Diplogastrina, Rhabditina, and Panagrolaimidae. Asynchronous development is convergent, defining one clade of Tylenchina as well as Cephalobina, and also arising independently in Aphelenchina. The rhomboidal embryo is ancestral to the tandem-pattern embryo that defines a second clade of Tylenchina. Early-embryo characters are congruent with the polyphyly of Cephalobina and Aphelenchina, as has been demonstrated by molecular phylogenies. Many aspects of early embryogenesis, rather than being highly conserved, evolve at a rate appropriate to defining taxa within Secernentea.

High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans

Mutations in the mitochondrial genome have been implicated in numerous human genetic disorders and offer important data for phylogenetic, forensic, and population genetic studies. Using a long-term series of Caenorhabditis elegans mutation accumulation lines, we performed a wide-scale screen for mutations in the mitochondrial genome that revealed a mutation rate that is two orders of magnitude higher than previous indirect estimates, a highly biased mutational spectrum, multiple mutations affecting coding function, as well as mutational hotspots at homopolymeric nucleotide stretches.

Phylogenetic Analysis of Geographically Diverse Radopholus similis via rDNA Sequence Reveals a Monomorphic Motif

The nucleic acid sequences of rDNA ITS1 and the rDNA D2/D3 expansion segment were compared for 57 burrowing nematode isolates collected from Australia, Cameroon, Central America, Cuba, Dominican Republic, Florida, Guadeloupe, Hawaii, Nigeria, Honduras, Indonesia, Ivory Coast, Puerto Rico, South Africa, and Uganda. Of the 57 isolates, 55 were morphologically similar to Radopholus similis and seven were citrus-parasitic. The nucleic acid sequences for PCR-amplified ITS1 and for the D2/D3 expansion segment of the 28S rDNA gene were each identical for all putative R. similis. Sequence divergence for both the ITS1 and the D2/D3 was concordant with morphological differences that distinguish R. similis from other burrowing nematode species. This result substantiates previous observations that the R. similis genome is highly conserved across geographic regions. Autapomorphies that would delimit phylogenetic lineages of non-citrus-parasitic R. similis from those that parasitize citrus were not observed. The data presented herein support the concept that R. similis is comprised of two pathotypes-one that parasitizes citrus and one that does not.

Nuclear and Mitochondrial DNA Sequence Diversity in the Antarctic Nematode Scottnema lindsayae

A nematode, Scottnema lindsayae, is the dominant metazoan found in soils of the McMurdo Dry Valleys, Antarctica. The distribution of S. lindsayae is patchy within and between these dry valleys; nevertheless, it is unclear to what extent these populations are genetically isolated. We investigated genetic diversity in this nematode using nuclear and mitochondrial gene sequences that encode ribosomal RNA. In 169 nematodes surveyed, only one variable site was found in each of two different expansion segments of nuclear rRNA. While most nematodes have only one sequence type, some nematodes were found to contain a mixture of both sequences. No fixed differences in nuclear sequences were observed between populations. This pattern of nuclear variation is most consistent with a single species of nematode defined morphologically as S. lindsayae. For mitochondrial DNA sequences, we found 10 variable positions defining 12 haplotypes among 188 nematodes surveyed. While all observed haplotypes are closely related, significant differences in haplotype frequencies were observed between geographically defined populations. The nuclear and mitochondrial variation suggests populations of S. lindsayae represent a single polymorphic species with some restriction of gene flow between geographic populations.

Evolution of vulva development in the Cephalobina (Nematoda)

Ventral cord and vulva development are analyzed in a large sample of nematode species of the suborder Cephalobina. We find a specific range of evolutionary variations at distinct developmental steps. (1) Unlike Caenorhabditis elegans and relatives, the vulva is formed from the four precursor cells P(5-8).p or, exceptionally, from P(6, 7).p only. (2) The vulval competence group is restricted to these four cells or is larger. (3) The fates of more anterior and posterior Pn.p cells vary between closely related species (mostly cell death versus epidermal fate). (4) The mechanism of vulval cell fate patterning varies within a single genus, even between strains of the same species. (5) We describe the first example of a vulval cell lineage that is asymmetric between the anterior and the posterior sides of the vulva. For a selection of the investigated taxa, phylogenetic trees were constructed in order to map vulval characters and infer evolutionary polarities. We can conclude that in this group, death of the Pn.p cells probably constitutes a derived character state compared to a syncytial fate. Rhabditophanes sp. and Strongyloides ratti are placed as sister taxa, probably sharing an exclusive common ancestor in which the number of precursor cells forming the vulva was reduced from four to two.

Morphological, molecular and biological characterization of Mehdinema alii (Nematoda: Diplogasterida) from the decorated cricket (Gryllodes sigillatus)

The nematode Mehdinema alii was recovered from the decorated cricket Gryllodes sigillatus (Walker). Morphometric comparisons are presented from 3 populations. The nematode is characterized by dense arrays of spines on the cuticle of the anterior half of the body and a highly elongate, tubular stoma with a dorsal denticle in the glottoid region. Females have a protruding vulva. Young females are amphidelphic, but the anterior ovary disappears in older females bearing multiple developing juveniles. The male is monorchic with asymmetrically placed genital papillae, distally fused spicules, and a highly complex gubernaculum bearing 2 cuticularized thorns that protrude through a separate, postcloacal opening. Adult nematodes are located primarily in the hindgut, whereas juveniles or dauers occur mainly in the genital chamber of both male and female crickets. Male crickets are significantly more likely to be infected than females. This male-biased infection may be linked to the venereal transmission mechanism of the dauers. Although morphologically unusual in many respects, placement of M. alii in Diplogasterida is supported by both the morphology of the anterior digestive tract as well as analysis of its 18S rDNA sequence. These sequence data suggest that M. alii groups most closely with members of the Cylindrocorporidae.

A molecular evolutionary framework for the phylum Nematoda

Nematodes are important: parasitic nematodes threaten the health of plants, animals and humans on a global scale; interstitial nematodes pervade sediment and soil ecosystems in overwhelming numbers; and Caenorhabditis elegans is a favourite experimental model system. A lack of clearly homologous characters and the absence of an informative fossil record have prevented us from deriving a consistent evolutionary framework for the phylum. Here we present a phylogenetic analysis, using 53 small subunit ribosomal DNA sequences from a wide range of nematodes. With this analysis, we can compare animal-parasitic, plant-parasitic and free-living taxa using a common measurement. Our results indicate that convergent morphological evolution may be extensive and that present higher-level classification of the Nematoda will need revision. We identify five major clades within the phylum, all of which include parasitic species. We suggest that animal parasitism arose independently at least four times, and plant parasitism three times. We clarify the relationship of C. elegans to major parasitic groups; this will allow more effective exploitation of our genetic and biological knowledge of this model species.

Embryonic axis specification in nematodes: evolution of the first step in development

In 1828, von Baer proposed that the early stages of development must be the most conserved [1]. Others have since countered that the middle stages of development are the most conserved [2]. To address whether the earliest step in pattern formation can evolve, we have examined how asymmetry along the antero-posterior (AP) axis is generated in various nematode species. AP asymmetry is specified in Caenorhabditis elegans at fertilization by the sperm, which directs a cytoplasmic rearrangement that segregates critical factors such as the P granules to one side of the uncleaved embryo [3,4]. We found that AP asymmetry is generated differently in another nematode species: the sperm is not used to specify AP asymmetry, there are no signs of cytoplasmic movements, and P granules are segregated differently. Despite these differences, development from the two-cell stage is remarkably similar in the two species. We have reconstructed the evolutionary history of these mechanisms by analyzing the development of 30 nematode species and mapping the results onto a molecular phylogeny of the nematodes [5]. The results suggest that a new mechanism for axis specification evolved in an ancestor of some of the relatives of C. elegans. We conclude that this fundamental step in development can evolve without affecting other aspects of development.

An evolutionary framework for the study of developmental evolution in a set of nematodes related to Caenorhabditis elegans

Nematodes are known to be a useful system for studies of comparative development. Here we perform a molecular phylogenetic analysis to allow for the independent interpretation of the developmental and morphological changes observed among a selected set of nematode species. Our molecular phylogenetic analysis is based on coding regions of the genes for RNA polymerase II, the small subunit rRNA and an expansion segment of the large subunit rRNA. Sequences were compared from five species in the family (Rhabditidae) that includes the developmental model organism Caenorhabditis elegans and from an outgroup taxon Aduncospiculum halicti (Diplogasterina). The phylogenetic analysis does not support the monophyly of the subfamily Mesorhabditinae and identifies the unnamed strain PS1010 as a sister taxon of C. elegans despite its morphologically divergent buccal capsule. On the basis of the inferred framework, we can begin to interpret the evolution of vulval development and of morphological differences among these nematode species.

DNA sequences from formalin-fixed nematodes: integrating molecular and morphological approaches to taxonomy

To effectively integrate DNA sequence analysis and classical nematode taxonomy, we must be able to obtain DNA sequences from formalin-fixed specimens. Microdissected sections of nematodes were removed from specimens fixed in formalin, using standard protocols and without destroying morphological features. The fixed sections provided sufficient template for multiple polymerase chain reaction-based DNA sequence analyses.

The buccal capsule of Aduncospiculum halicti (Nemata: Diplogasterina): an ultrastructural and molecular phylogenetic study

The buccal capsule of Aduncospiculum halicti (Diplogasterina) is compared with that of Zeldia punctata (Cephalobina) and Caenorhabditis elegans (Rhabditina). Characters are mapped on an independent DNA-based phylogenetic tree (inferred from RNA polymerase II and rDNA sequences) to test evolutionary hypotheses. Irrespective of dimorphism, the buccal capsule wall of A. halicti consists of an anterior to posterior series of six cuticular structures classically termed rhabdions. These are defined according to their internal differentiations, discontinuities in profiles, and underlying tissues. Homologies of rhabdions 1 and 2 in A. halicti are proposed on the basis of position and association with adjacent tissues, consistent with those of Cephalobina and Rhabditina. Rhabdion 3 is associated with radial epithelial cells as is the mesorhabdion in C. elegans; this contrasts with Z. punctata, where a rhabdion in a similar position is associated with radial muscle cells. Dorsal and subventral teeth in A. halicti comprise rhabdions 4 and 5; this may be homologous with a corresponding region in Z. punctata but contrasts with C. elegans, where the corresponding region consists of a single metarhabdion. These characters, when mapped on the sequence-based tree, suggest that A. halicti and Diplogasterina share with C. elegans and other Rhabditina derived characters, including a mesorhabdion associated with epithelial cells, but retain some apparently primitive features shared with Cephalobina.

A molecular evolutionary framework for eukaryotic model organisms

BACKGROUND

Implicit in the characterization of a model organism is the hope that insights into its biology can be extended to other species. For this hope to be fulfilled, the phylogenetic position of the model organism within a larger evolutionary framework must be known. We focus here on major model organisms of developmental genetics and cell biology. We first consider the positions of the nematode Caenorhabditis elegans and the arthropod Drosophila melanogaster within a phylogeny of the major advanced metazoan groups. Then we consider the evolutionary relationships between fungi (represented by Saccharomyces cerevisiae and Schizosaccharomyces pombe), plants, and animals.

RESULTS

We show, by a direct comparison with small subunit ribosomal RNA (18 S rRNA), that RNA polymerase II is an appropriate molecule for addressing the phylogenetic branchings in the early evolution of eukaryotes. The results from the analyses of newly determined and previously published sequences of the two largest subunits of RNA polymerase II suggest the following. Firstly, that plants and animals share a last common ancestor that excludes fungi, the lineage of which originated earlier. Secondly, that the lineage leading to the nematode Caenorhabditis elegans diverged earlier from the Metazoa than the lineages of arthropods, deuterostomes, annelids and molluscs. Finally, that deuterostomes arose from within protostomes.

CONCLUSIONS

RNA polymerase II is well-suited for the elucidation of the evolutionary relationships among eukaryotes. We emphasize the implications of our results for other biological disciplines in addition to molecular evolution, as a phylogenetic framework allows predictions and inferences to be made about the existence of fundamental biological mechanisms elucidated in model organisms.

Phylogenetic analysis of the Coscoroba coscoroba using mitochondrial srRNA gene sequences

In order to study the phylogenetic relationships among Coscoroba, goose, and swan lineages, sequences for the complete mitochondrial small ribosomal RNA (srRNA) gene were determined from five waterfowl species. Parsimony and distance analyses support the branching of Coscoroba prior to the divergence of geese and swans, and maximum likelihood analyses give almost equal support to that pattern and to the sister group relationship between Coscoroba and swans. The monophyly of the geese was confirmed at a statistically significant level. In sequence comparisons among waterfowl, transitions increase linearly with transversions, and so we conclude that the lack of complete resolution of Coscoroba's position is not due to sequence saturation alone, but also reflects relatively close branching times.

The marsupial mitochondrial genome and the evolution of placental mammals

The entire nucleotide sequence of the mitochondrial genome of the American opossum, Didelphis virginiana, was determined. Two major features distinguish this genome from those of other mammals. First, five tRNA genes around the origin of light strand replication are rearranged. Second, the anticodon of tRNA(Asp) is posttranscriptionally changed by an RNA editing process such that its coding capacity is altered. When the complete protein-coding region of the mitochondrial genome is used as an outgroup for placental mammals it can be shown that rodents represent an earlier branch among placental mammals than primates and artiodactyls and that artiodactyls share a common ancestor with carnivores. The overall rates of evolution of most of the mitochondrial genome of placentals are clock-like. Furthermore, the data indicate that the lineages leading to the mouse and rat may have diverged from each other as much as 35 million years ago.

Transgenic cattle resulting from biopsied embryos: expression of c-ski in a transgenic calf

Producing transgenic cattle by microinjection of DNA into pronuclei has been inefficient and costly, in large part because of the cost of maintaining numerous nontransgenic pregnancies to term. We designed a system for early identification of transgenic embryos in which biopsies of embryos were assayed by polymerase chain reaction for presence of the transgene before embryo transfer. A total of 2555 embryos were microinjected with one of two DNA constructs. Of the 533 embryos biopsied, 112 were judged to be potentially transgenic and were transferred nonsurgically to recipients, resulting in production of 29 putative transgenic fetuses. One fetus and one calf (7% of offspring) were subsequently shown to be definitively transgenic. The calf was transgenic for a chicken c-ski cDNA, and several months after birth developed dramatic muscular hypertrophy followed by muscle degeneration. This phenotype was associated with expression of high levels of mRNA from the transgene.

A recent origin of marmots

The complete mitochondrial cytochrome b genes from four ground squirrels, a marmot, and a tree squirrel were sequenced and compared. A level of divergence three times lower than expected based on fossil evidence was found between the marmot and the ground squirrels. The observed divergence was similar to that found within the ground squirrels and is consistent with a recent divergence of marmots (Marmota) from true ground squirrels (Spermophilus).

Effects of cumulus cells on culture of bovine embryos derived from oocytes matured and fertilized in vitro

Bovine zygotes derived from oocytes matured and fertilized in vitro were cultured in vitro. In Exp. 1, zygotes were vortexed to remove cumulus cells and then cultured in oviduct epithelial cell-conditioned TCM-199 medium with or without added cumulus cells. Embryos cultured without cumulus cells developed to blastocysts significantly less often than those cultured with added cumulus cells, 3 vs 38% of cleaved ova (P < .05). Co-culture of embryos with cumulus cells during the first 48 h only, or for the duration of the culture period, resulted in development rates similar to those of controls that were not vortexed. In Exp. 2, denuded zygotes were centrifuged (15,850 x g, 3 min) at room temperature to facilitate visualization of pronuclei. Centrifuged zygotes were either placed directly into conditioned medium for culture (with or without added cumulus cells) or DNA was first microinjected into their cytoplasm or a pronucleus. All microinjected embryos were co-cultured with added cumulus cells. Centrifugation and microinjection did not reduce viability significantly when embryos were co-cultured with cumulus cells. Development was reduced significantly when embryos were cultured without cumulus cells. Thus, when oviduct epithelial cell-conditioned medium was used, cumulus cell co-culture was beneficial during the early cleavage stages of in vitro-derived zygotes, including those that received DNA microinjection.

Mitochondrial DNA-like sequence in the nuclear genome of an akodontine rodent

Initial amplification and sequencing of a 366-bp fragment of the cytochrome b gene by a conserved primer pair (MVZ 03 and MVZ 04) revealed a nonfunctional copy of the gene with two deletions (one of which is 17 bp in length and the other of which is 3 bp in length) in Chroeomys jelskii, a South American akodontine rodent. By means of an alternative primer to MVZ 03--namely, MVZ 05--from the region of the tRNA for glutamic acid, a functional copy of cytochrome b was subsequently amplified. Both primer pairs amplify functional sequence when applied to purified mitochondrial DNA (mtDNA). Restriction-endonuclease digestion of purified mtDNA from C. jelskii did not reveal any additional sets of bands that would suggest heteroplasmy in the mitochondrial genome. When probed with both functional and nonfunctional gene fragments, MboI restriction digests revealed the same pattern, providing further evidence that the nonfunctional copy must be located in the nucleus. Observed differences in the mitochondrial and nuclear sequences from two populations are consistent with a faster rate of change in mtDNA than in nuclear DNA.

Rearrangements of mitochondrial transfer RNA genes in marsupials

The nucleotide sequences of the mitochondrial origin of light-strand replication and the five tRNA genes surrounding it were determined for three marsupials. The region was found to be rearranged, leaving only the tRNA(Tyr) gene at the same position as in placental mammals and Xenopus. Distribution of the same rearranged genotype among two marsupial families indicates that the events causing the rearrangements took place in an early marsupial ancestor. The putative mitochondrial light-strand origin of replication in marsupials contains a hairpin structure similar to other vertebrate origins and; in addition, extensive flanking sequences that are not found in other vertebrates. Sequence comparisons among the marsupials as well as placentals indicate that the tRNA(Tyr) gene has been evolving under more constraints than the other tRNA genes.

Mode and tempo of molecular evolution in the nematode caenorhabditis: cytochrome oxidase II and calmodulin sequences

Through direct sequencing methods, the mitochondrial gene for cytochrome oxidase subunit two (CO II) and the single-copy nuclear gene for calmodulin were compared among strains of Caenorhabidits elegans and two other Caenorhabditis species (C. remanei and C. briggsae). In addition the CO II sequence was determined from a distantly related nematode, Steinernema intermedii. Among the 11 strains of C. elegans tested, there are four types of CO II gene, arising from two major lineages. Levels of intraspecific difference in the CO II gene are low (less than 2.0%) compared to the extraordinary divergence between congeneric species, which is about 50% when corrected for multiple hits. Concordant with the increase in divergence between taxa is a change in the pattern of substitution from a strong transition bias (24 transitions compared to two transversions) within species to a substitution pattern that appears to reflect the base composition of the mitochondrial genome when more divergent nematodes are compared. The base composition of the Caenorhabditis CO II gene is strongly biased toward A + T at all three positions of codons and appears to constrain the amino acid composition of the protein. Both the CO II and calmodulin genes show extreme conservation of amino acid sequences. When the accumulation of changes at silent sites in the two genes is compared among strains, it becomes evident that the mitochondrial gene is changing faster than the nuclear gene.

Spatial and temporal continuity of kangaroo rat populations shown by sequencing mitochondrial DNA from museum specimens

The advent of direct sequencing via the polymerase chain reaction (PCR) has opened up the possibility of molecular studies on museum specimens. Here we analyze genetic variation in populations over time by applying PCR to DNA extracted from museum specimens sampled from populations of one species over the last 78 years. Included in this study were 43 museum specimens of the Panamint kangaroo rat Dipodomys panamintinus from localities representing each of three geographically distinct subspecies. These specimens were originally collected and prepared as dried skins in 1911, 1917, or 1937. For each specimen, a 225-bp segment of the mitochondrial genome was sequenced. These mitochondrial DNA sequences were compared to those of 63 specimens collected at the same localities in 1988. The three subspecies were nearly completely distinct. Only 2 of the 106 individuals shared mitochondrial types between subspecies. For all three localities, the diversity levels were maintained between the two temporal samples. The concordance observed between the two temporally separate phylogenies supports the use of museum specimens for phylogenetic inference. This study demonstrates the accuracy and routine nature of the use of museum specimens in the analysis of mitochondrial sequence variation in natural populations and, importantly, that a temporal aspect can now be added to such studies.

Intraspecific sequence variation in the mitochondrial genome of rainbow trout (Oncorhynchus mykiss)

We examined the sequence of a 2214 base pair HindIII fragment from the mitochondrial genome of six rainbow trout. The fragment encodes four proteins and two tRNAs. Sequences for two fish from a single locality were identical. Those from separate localities differed by from 1 to 7 nucleotide substitutions. Of 13 variable sites, 12 were synonymous and 1 led to a conservative amino acid substitution. Transitions accounted for 12 of the 13 variants. In contrast to interspecific comparisons (Thomas and Beckenbach. 1989. J. Mol. Evol. 29: 233-245), the intraspecific divergence estimates based on sequence are less than those estimated from restriction fragment analysis, suggesting a complex, dynamic process for the accumulation of variation in the mitochondrial genome.

Length heteroplasmy of sturgeon mitochondrial DNA: an illegitimate elongation model

Extensive length polymorphism and heteroplasmy (multiple forms within an individual) of the D-loop region are observed in mitochondrial DNA of the white sturgeon (Acipenser transmontanus). The nucleotide sequence of this region, for both a short and a long form, shows that the differences are due to variable numbers of a perfect 82-bp direct repeat. We propose a model for the replicative origin of length differences, involving a competitive equilibrium between the heavy strand and the D-loop strand. This model suggests that frequent misalignment in the repeat region prior to elongation, facilitated by a stable secondary structure in the displaced strand, can explain both the polymorphism and heteroplasmy in this species.

Shifting constraints on tRNA genes during mitochondrial DNA evolution in animals

During the evolution of echinoderm mitochondrial (mt) DNA, a transfer RNA gene lost its tRNA function and became part of a protein-coding gene. To examine the evolutionary consequences of this event, we sequenced 961 bp of mtDNA in five sea urchin species. This enabled us to build a tree relating the mtDNAs and use it for analyzing the pattern and process of evolutionary substitutions in the former leucine tRNA gene, which now is a 5' extension of the gene for NADH dehydrogenase subunit 5 (ND5). This 5' extension is now evolving at the same rate and under the same protein-coding constraints as the rest of ND5. The adjacent (upstream) serine tRNA gene, however, has been evolving at a reduced rate, consistent with the possibility that it has assumed a punctuation role in processing of the primary transcript that was once fulfilled by the former leucine tRNA gene.

Variation in salmonid mitochondrial DNA: evolutionary constraints and mechanisms of substitution

Sequence comparisons were made from 2214 bp of mitochondrial DNA cloned from six Pacific salmonid species. These sequences include the genes for ATPase subunit 6, cytochrome oxidase subunit 3, NADH dehydrogenase subunit 3, NADH dehydrogenase subunit 4L, tRNA(GLY), and tRNA(ARG). Variation is found at 338 silent and 12 nonsilent positions of protein coding genes and 10 positions in the two tRNA sequences. A single 3-bp length difference was also detected. In all pairwise comparisons the sequence divergence observed in the fragment was higher than that previously predicted by restriction enzyme analysis of the entire molecule. The inferred evolutionary relationship of these species is consistent between methods. The distribution of silent variation shows a complex pattern with greatly reduced variation at the junctions of genes. The variation in the tRNA sequences is concentrated in the DHU loop. The close relationship of these species and extensive sequence analyzed allows for an analysis of the spectrum of substitutions that includes the frequencies of all 12 possible substitutions. The observed spectrum of substitutions is related to potential pathways of spontaneous substitution. The salmonid sequences show an extremely high ratio of silent to replacement substitutions. In addition the amino acid sequences of the four proteins coded in this fragment show a consistently high level of identity with the Xenopus sequences. Taken together these data are consistent with a slower rate of amino acid substitution among the cold-blooded vertebrates when compared to mammals.

Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers

With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing were possible using unpurified mtDNA from nanogram samples of fresh specimens and microgram amounts of tissues preserved for months in alcohol or decades in the dry state. The bird and fish sequences evolve with the same strong bias toward transitions that holds for mammals. However, because the light strand of birds is deficient in thymine, thymine to cytosine transitions are less common than in other taxa. Amino acid replacement in a segment of the cytochrome b gene is faster in mammals and birds than in fishes and the pattern of replacements fits the structural hypothesis for cytochrome b. The unexpectedly wide taxonomic utility of these primers offers opportunities for phylogenetic and population research.

Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers

With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing were possible using unpurified mtDNA from nanogram samples of fresh specimens and microgram amounts of tissues preserved for months in alcohol or decades in the dry state. The bird and fish sequences evolve with the same strong bias toward transitions that holds for mammals. However, because the light strand of birds is deficient in thymine, thymine to cytosine transitions are less common than in other taxa. Amino acid replacement in a segment of the cytochrome b gene is faster in mammals and birds than in fishes and the pattern of replacements fits the structural hypothesis for cytochrome b. The unexpectedly wide taxonomic utility of these primers offers opportunities for phylogenetic and population research.