Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates

Genetic Diversity of mtDNA D-loop Polymorphisms in Laotian Native Fowl Populations

Here, we studied the genetic diversity of native fowls in Laos by analyzing a mitochondrial DNA (mtDNA) sequence polymorphism. A 546-bp fragment of the mtDNA D-loop region was sequenced in 129 chickens from the areas of Vientiane, Luang Prabang and Pakse. In total, 29 haplotypes were identified and formed five clades. Haplotype diversity and nucleotide diversity of the native fowls in Laos were 0.85536±0.0172 and 0.010158±0.005555, respectively. Although the Laotian native fowls were distributed across five clades, most of them were clustered in two main clades (A and B), which were originated in China. The other haplotypes were contained in clades D, F, and I, which originated from continental southeast Asia. These results suggest that multiple maternal lineages were involved in the origin of domestic chicken in Laos. Moreover, there appear to be at least two maternal lineages, one from China and the other from the southeast Asian continent.

The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements

BACKGROUND

The animal mitochondrial genome is generally considered to be under selection for both compactness and gene order conservation. As more mitochondrial genomes are sequenced, mitochondrial duplications and gene rearrangements have been frequently identified among diverse animal groups. Although several mechanisms of gene rearrangement have been proposed thus far, more observational evidence from major taxa is needed to validate specific mechanisms. In the current study, the complete mitochondrial DNA of sixteen bird species from the family Ardeidae was sequenced and the evolution of mitochondrial gene rearrangements was investigated. The mitochondrial genomes were then used to review the phylogenies of these ardeid birds.

RESULTS

The complete mitochondrial genome sequences of the sixteen ardeid birds exhibited four distinct mitochondrial gene orders in which two of them, named as "duplicate tRNA(Glu)-CR" and "duplicate tRNAThr-tRNA(Pro) and CR", were newly discovered. These gene rearrangements arose from an evolutionary process consistent with the tandem duplication--random loss model (TDRL). Additionally, duplications in these gene orders were near identical in nucleotide sequences within each individual, suggesting that they evolved in concert. Phylogenetic analyses of the sixteen ardeid species supported the idea that Ardea ibis, Ardea modesta and Ardea intermedia should be classified as genus Ardea, and Ixobrychus flavicollis as genus Ixobrychus, and indicated that within the subfamily Ardeinae, Nycticorax nycticorax is closely related to genus Egretta and that Ardeola bacchus and Butorides striatus are closely related to the genus Ardea.

CONCLUSIONS

The duplicate tRNAThr-CR gene order is found in most ardeid lineages, suggesting this gene order is the ancestral pattern within these birds and persisted in most lineages via concerted evolution. In two independent lineages, when the concerted evolution stopped in some subsections due to the accumulation of numerous substitutions and deletions, the duplicate tRNAThr-CR gene order was transformed into three other gene orders. The phylogenetic trees produced from concatenated rRNA and protein coding genes have high support values in most nodes, indicating that the mitochondrial genome sequences are promising markers for resolving the phylogenetic issues of ardeid birds when more taxa are added.

Complete mitochondrial genome of Palawan peacock-pheasant Polyplectron napoleonis (Galliformes, Phasianidae)

The complete mitochondrial genome of the Palawan peacock-pheasant Polyplectron napoleonis is 16,710 bp and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control-region. All protein-coding genes use the standard ATG start codon, except for cox1 which has GTG start codon. Seven out of 13 PCGs have TAA stop codons, two have AGG (cox1 and nd6), and three PCGs (nd2, cox2 and nd4) have incomplete stop codon of just T- - nucleotide.

Differentiation state-specific mitochondrial dynamic regulatory networks are revealed by global transcriptional analysis of the developing chicken lens

The mature eye lens contains a surface layer of epithelial cells called the lens epithelium that requires a functional mitochondrial population to maintain the homeostasis and transparency of the entire lens. The lens epithelium overlies a core of terminally differentiated fiber cells that must degrade their mitochondria to achieve lens transparency. These distinct mitochondrial populations make the lens a useful model system to identify those genes that regulate the balance between mitochondrial homeostasis and elimination. Here we used an RNA sequencing and bioinformatics approach to identify the transcript levels of all genes expressed by distinct regions of the lens epithelium and maturing fiber cells of the embryonic Gallus gallus (chicken) lens. Our analysis detected more than 15,000 unique transcripts expressed by the embryonic chicken lens. Of these, more than 3000 transcripts exhibited significant differences in expression between lens epithelial cells and fiber cells. Multiple transcripts coding for separate mitochondrial homeostatic and degradation mechanisms were identified to exhibit preferred patterns of expression in lens epithelial cells that require mitochondria relative to lens fiber cells that require mitochondrial elimination. These included differences in the expression levels of metabolic (DUT, PDK1, SNPH), autophagy (ATG3, ATG4B, BECN1, FYCO1, WIPI1), and mitophagy (BNIP3L/NIX, BNIP3, PARK2, p62/SQSTM1) transcripts between lens epithelial cells and lens fiber cells. These data provide a comprehensive window into all genes transcribed by the lens and those mitochondrial regulatory and degradation pathways that function to maintain mitochondrial populations in the lens epithelium and to eliminate mitochondria in maturing lens fiber cells.

Complete mitochondrial genomes of the New World jacanas: Jacana spinosa and Jacana jacana

The New World jacanas, Jacana spinosa (Mexico to Panama and also the West Indies) and Jacana jacana (Panama and South America), are polyandrous freshwater waders that are common throughout the Neotropics. These two species hybridize narrowly at their contact zone in Panama, and as part of a study of the hybrid zone dynamics, we present complete, annotated mitochondrial genomes for both species. The two species have very similar mitochondrial genomes, showing identical gene orders, and differing in size in only two RNA features and the control region, and among protein-coding genes, the two genomes had average uncorrected pairwise divergence of 1.8%, ranging from 0.7% for ND4L and 3.6% for ATP8. However, control region divergence is high (∼ 16%). These mitochondrial genome sequences may be useful tools for understanding jacana hybridization dynamics, especially regarding potential mitonuclear incompatibilities.

Complete mitochondrial genome of Germain's Peacock-Pheasant Polyplectron germaini (Aves, Galliformes, Phasianidae)

The Germain's Peacock-Pheasant Polyplectron germaini (Aves, Galliformes, Phasianidae) is classified as Near Threatened on the IUCN Red List. The complete mitochondrial genome of P. germaini is 16,699 bp, consisting of 13 protein-coding genes, 2 rRNA, 22 tRNA genes and 1 control region. All of the 13 protein-coding genes have ATG as start codon. Eight of the 13 protein-coding genes have TAA as stop codon.

The complete mitochondrial genome of Odontesthes sp. (Atheriniforms, Atherinopsidae)

In this study, the complete mitochondrial genome of Odontesthes sp. has been studied first. The genome is 16,528 bp in length and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and 1 putative control region. The mitochondrial genome of Odontesthes sp. had common features about gene arrangement and tRNA structures compared with those of other teleost fishes. The overall base composition of Odontesthes sp. is T 27.3%, C 29.4%, A 26.0% and G 17.3%, with a slight A+T bias of 53.3%. Meanwhile, the conserved motif 5'-GCCGG-3' was determined in the origin of light-strand replication of Odontesthes sp. The mitochondrial genome of this species would play an important role in the phylogenetics of Atherinopsidae.

Intraspecific rearrangement of duplicated mitochondrial control regions in the Luzon Tarictic Hornbill Penelopides manillae (Aves: Bucerotidae)

Philippine hornbills of the genera Aceros and Penelopides (Bucerotidae) are known to possess a large tandemly duplicated fragment in their mitochondrial genome, whose paralogous parts largely evolve in concert. In the present study, we surveyed the two distinguishable duplicated control regions in several individuals of the Luzon Tarictic Hornbill Penelopides manillae, compare their characteristics within and across individuals, and report on an intraspecific mitochondrial gene rearrangement found in one single specimen, i.e., an interchange between the two control regions. To our knowledge, this is the first observation of two distinct mitochondrial genome rearrangements within a bird species. We briefly discuss a possible evolutionary mechanism responsible for this pattern, and highlight potential implications for the application of control region sequences as a marker in population genetics and phylogeography.

Unusual features of control region and a novel NADH 6 genes in mitochondrial genome of the finespot goby, Chaeturichthys stigmatias (Perciformes, Gobiidae)

In this article, we determined the complete mitogenome of finespot goby Chaeturichthys stigmatias with emphasis on the arranged gene order and gene feature with published Gobiidae species. The C. stigmatias mtDNA was 18,562 bp in length (56.94% AT), and comprised 37 genes (13 protein genes, 2 rRNAs and 22 tRNAs) that was typical for mitochondrial genome of Gobiidae species. Unusually, the NADH 6 gene was very large in length compared with other Gobiidae species. Mitogenome of C. stigmatias had a long putative control region with high AT content (71.28%). Within this sequence, we determined repeat regions, the termination-associated sequence and the conserved sequence block for this region. The origin of L-strand replication in C. stigmatias was located in a cluster of five tRNA genes (WANCY). The conserved motif (5'-GCCGG-3') was also determined at the base of the stem in the tRNA-Cys gene. This study will provide a better understanding of Gobiidae mitogenomes and offer useful information for future studies concerning Gobiidae mitogenome evolution.

Complete mitogenome sequences of four flatfishes (Pleuronectiformes) reveal a novel gene arrangement of L-strand coding genes

Background

Few mitochondrial gene rearrangements are found in vertebrates and large-scale changes in these genomes occur even less frequently. It is difficult, therefore, to propose a mechanism to account for observed changes in mitogenome structure. Mitochondrial gene rearrangements are usually explained by the recombination model or tandem duplication and random loss model.

Results

In this study, the complete mitochondrial genomes of four flatfishes, Crossorhombus azureus (blue flounder), Grammatobothus krempfi, Pleuronichthys cornutus, and Platichthys stellatus were determined. A striking finding is that eight genes in the C. azureus mitogenome are located in a novel position, differing from that of available vertebrate mitogenomes. Specifically, the ND6 and seven tRNA genes (the Q, A, C, Y, S₁, E, P genes) encoded by the L-strand have been translocated to a position between tRNA-T and tRNA-F though the original order of the genes is maintained.

Conclusions

These special features are used to suggest a mechanism for C. azureus mitogenome rearrangement. First, a dimeric molecule was formed by two monomers linked head-to-tail, then one of the two sets of promoters lost function and the genes controlled by the disabled promoters became pseudogenes, non-coding sequences, and even were lost from the genome. This study provides a new gene-rearrangement model that accounts for the events of gene-rearrangement in a vertebrate mitogenome.

Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei)

Background

A skewed assemblage of two epi-, meso- and bathypelagic fish families makes up the order Myctophiformes – the blackchins Neoscopelidae and the lanternfishes Myctophidae. The six rare neoscopelids show few morphological specializations whereas the divergent myctophids have evolved into about 250 species, of which many show massive abundances and wide distributions. In fact, Myctophidae is by far the most abundant fish family in the world, with plausible estimates of more than half of the oceans combined fish biomass. Myctophids possess a unique communication system of species-specific photophore patterns and traditional intrafamilial classification has been established to reflect arrangements of photophores. Myctophids present the most diverse array of larval body forms found in fishes although this attribute has both corroborated and confounded phylogenetic hypotheses based on adult morphology. No molecular phylogeny is available for Myctophiformes, despite their importance within all ocean trophic cycles, open-ocean speciation and as an important part of neoteleost divergence. This study attempts to resolve major myctophiform phylogenies from both mitogenomic sequences and corroborating evidence in the form of unique mitochondrial gene order rearrangements.

Results

Mitogenomic evidence from DNA sequences and unique gene orders are highly congruent concerning phylogenetic resolution on several myctophiform classification levels, corroborating evidence from osteology, larval ontogeny and photophore patterns, although the lack of larval morphological characters within the subfamily Lampanyctinae stands out. Neoscopelidae is resolved as the sister family to myctophids with Solivomer arenidens positioned as a sister taxon to the remaining neoscopelids. The enigmatic Notolychnus valdiviae is placed as a sister taxon to all other myctophids and exhibits an unusual second copy of the tRNA-Met gene – a gene order rearrangement reminiscent of that found in the tribe Diaphini although our analyses show it to be independently derived. Most tribes are resolved in accordance with adult morphology although Gonichthyini is found within a subclade of the tribe Myctophini consisting of ctenoid scaled species. Mitogenomic sequence data from this study recognize 10 reciprocally monophyletic lineages within Myctophidae, with five of these clades delimited from additional rearranged gene orders or intergenic non-coding sequences.

Conclusions

Mitogenomic results from DNA sequences and unique gene orders corroborate morphology in phylogeny reconstruction and provide a likely scenario for the phylogenetic history of Myctophiformes. The extent of gene order rearrangements found within the mitochondrial genomes of myctophids is unique for phylogenetic purposes.

The complete mitochondrial genome of bean goose (Anser fabalis) and implications for anseriformes taxonomy

Mitochondrial DNA plays an important role in living organisms, and has been used as a powerful molecular marker in a variety of evolutionary studies. In this study, we determined the complete mtDNA of Bean goose (Anser fabalis), which is 16,688 bp long and contains 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a control region. The arrangement is similar to that of typical Anseriform species. All protein-coding genes, except for Cyt b, ND5, COI, and COII, start with an ATG codon. The ATG start codon is also generally observed in the 12 other Anseriform species, including 2 Anser species, with sequenced mitochondrial genomes. TAA is the most frequent stop codon, one of three–TAA, TAG, and T- –commonly observed in Anseriformes. All tRNAs could be folded into canonical cloverleaf secondary structures except for tRNA^Ser(AGY) and tRNA^Leu(CUN), which are missing the dihydrouridine (DHU) arm. The control region of Bean goose mtDNA, with some conserved sequence boxes, such as F, E, D, and C, identified in its central domain. Phylogenetic analysis of complete mtDNA data for 13 Anseriform species supports the classification of them into four major branches: Anatinae, Anserinae, Dendrocygninae and Anseranatidae. Phylogenetic analyses were also conducted on 36 Anseriform birds using combined Cyt b, ND2, and COI sequences. The results clearly support the genus Somateria as an independent lineage classified in its own tribe, the Somaterini. Recovered topologies from both complete mtDNA and combined DNA sequences strongly indicate that Dendrocygninae is an independent subfamily within the family Anatidae and Anseranatidae represents an independent family. Based on the results of this study, we conclude that combining ND2, Cyt b, and COI sequence data is a workable solution at present for resolving phylogenetic relationships among Anseriform species in the absence of sufficient complete mtDNA data.

Phylogenetic analysis using d-loop marker of mtDNA of Saudi native chicken strains

This study was carried out to figure the potentiality of d-loop of mitochondrial DNA in discriminating among Saudi native chicken strains and other species of genus Gallus. The first 500 base pairs of d-loop region were amplified and successfully sequenced. The results indicated that native chicken strains and genus Gallus species have a tandem repeat sequence with (14) base units into a two copy. Also, there was clear evidence that the native chickens have a unique tandem repeat sequence with (42) base units as a two copy. Two haplotypes (T) and (C) were observed in native chicken strains. Our research displayed approximately (26) transition substitutions in nucleotide sequences specific for native chicken strains, whereas it was 120 mutant sites in case of other species of Gallus. We found that the genetic divergence between these types of chickens was very low (0.022). The phylogenetic tree revealed that each strain of native chicken belonged to each other with the same cluster. In addition, each strain has its own cluster in some individuals. The results showed that the native chicken strains are closely related to Gallus gallus and its subspecies G. g. spadiceus and G/. g. bankiva.

Chicken domestication: an updated perspective based on mitochondrial genomes

Domestic chickens (Gallus gallus domesticus) fulfill various roles ranging from food and entertainment to religion and ornamentation. To survey its genetic diversity and trace the history of domestication, we investigated a total of 4938 mitochondrial DNA (mtDNA) fragments including 2843 previously published and 2095 de novo units from 2044 domestic chickens and 51 red junglefowl (Gallus gallus). To obtain the highest possible level of molecular resolution, 50 representative samples were further selected for total mtDNA genome sequencing. A fine-gained mtDNA phylogeny was investigated by defining haplogroups A-I and W-Z. Common haplogroups A-G were shared by domestic chickens and red junglefowl. Rare haplogroups H-I and W-Z were specific to domestic chickens and red junglefowl, respectively. We re-evaluated the global mtDNA profiles of chickens. The geographic distribution for each of major haplogroups was examined. Our results revealed new complexities of history in chicken domestication because in the phylogeny lineages from the red junglefowl were mingled with those of the domestic chickens. Several local domestication events in South Asia, Southwest China and Southeast Asia were identified. The assessment of chicken mtDNA data also facilitated our understanding about the Austronesian settlement in the Pacific.

Genetic variability in mitochondrial and nuclear genes of Larus dominicanus (Charadriiformes, Laridae) from the Brazilian coast

Several phylogeographic studies of seabirds have documented low genetic diversity that has been attributed to bottleneck events or individual capacity for dispersal. Few studies have been done in seabirds on the Brazilian coast and all have shown low genetic differentiation on a wide geographic scale. The Kelp Gull is a common species with a wide distribution in the Southern Hemisphere. In this study, we used mitochondrial and nuclear markers to examine the genetic variability of Kelp Gull populations on the Brazilian coast and compared this variability with that of sub-Antarctic island populations of this species. Kelp Gulls showed extremely low genetic variability for mitochondrial markers (cytb and ATPase) and high diversity for a nuclear locus (intron 7 of the β-fibrinogen). The intraspecific evolutionary history of Kelp Gulls showed that the variability found in intron 7 of the β-fibrinogen gene was compatible with the variability expected under neutral evolution but suggested an increase in population size during the last 10,000 years. However, none of the markers revealed evidence of a bottleneck population. These findings indicate that the recent origin of Kelp Gulls is the main explanation for their nuclear diversity, although selective pressure on the mtDNA of this species cannot be discarded.

Rapid characterization of mitochondrial genome rearrangements in Australian songbirds using next-generation sequencing technology

Using next-generation sequencing technology, we describe the complete mitochondrial genomes for 5 Australian passerine birds (Epthianura albifrons, Petroica phoenicea, Petroica goodenovii, Petroica boodang, and Eopsaltria australis). We successfully assemble each mitogenome de novo using just 1/8th of a Roche GL FSX 454 pyrosequencing plate. From the assembled mitogenomes, we identify 2 different mitochondrial gene arrangements in the region spanning 5'-3' from Cytochrome B to 12s RNA. These gene arrangements represent 2 of the 4 known avian mitochondrial gene arrangements. Our results, together with other previously described avian mitogenomes, highlight that certain mitochondrial rearrangements appear to have arisen multiple times.

Determination of mitochondrial cytochrome B gene sequence for red deer (Cervus elaphus) and the differentiation of closely related deer meats

The cytochrome b gene sequence for red deer was determined using the Dye Terminator Cycle Sequencing method and used for identification of deer meat in meat and meat products. Red deer showed a similarity of 94.1, 84.0, 81.1, 85.5 and 85.6% to sika deer (Cervus nippon), bovine, pigs, sheep and goats, respectively. To differentiate the deer meat, oligonucleotide primers RD-1(5'-TCATCGCAGCACTCGCTATAGTACACT-3'), RD-2(5'-ATCTCCAAGTAGGTCTGGTGCGAATAA-3') were designed for the region of the cytochrome b gene of red deer. The PCR amplified 194 bp fragments from red and sika deer, but no fragments from bovine, pig, chicken, sheep, goat, horse and rabbit DNA. Although cooking the meats reduced the PCR products, red deer could still be detected in meat heated at 120 °C. To discriminate between red and sika deer, these PCR products were digested by a restriction enzyme (EcoRI,BamHI,ScaI) and analyzed by 4% agorose gel electrophoresis. As a result, the red deer fragment was digested by EcoRI to 67/127 bp fragments but not by BamHI and ScaI. The sika deer fragment was digested to 48/146 bp and 49/145 bp fragments with the two other enzymes, and thus it is possible to differentiate between the two kinds of deer from the digestion pattern of restriction enzymes.

Coding constraints modulate chemically spontaneous mutational replication gradients in mitochondrial genomes

Distances from heavy and light strand replication origins determine duration mitochondrial DNA remains singlestranded during replication. Hydrolytic deaminations from A->G and C->T occur more on single- than doublestranded DNA. Corresponding replicational nucleotide gradients exist across mitochondrial genomes, most at 3rd, least 2^nd codon positions. DNA singlestrandedness during RNA transcription causes gradients mainly in long-lived species with relatively slow metabolism (high transcription/replication ratios). Third codon nucleotide contents, evolutionary results of mutation cumulation, follow replicational, not transcriptional gradients in Homo; observed human mutations follow transcriptional gradients. Synonymous third codon position transitions potentially alter adaptive off frame information. No mutational gradients occur at synonymous positions forming off frame stops (these adaptively stop early accidental frameshifted protein synthesis), nor in regions coding for putative overlapping genes according to an overlapping genetic code reassigning stop codons to amino acids. Deviation of 3rd codon nucleotide contents from deamination gradients increases with coding importance of main frame 3rd codon positions in overlapping genes (greatest if these are 2^nd position in overlapping genes). Third codon position deamination gradients calculated separately for each codon family are strongest where synonymous transitions are rarely pathogenic; weakest where transitions are frequently pathogenic. Synonymous mutations affect translational accuracy, such as error compensation of misloaded tRNAs by codon-anticodon mismatches (prevents amino acid misinsertion despite tRNA misacylation), a potential cause of pathogenic mutations at synonymous codon positions. Indeed, codon-family-specific gradients are inversely proportional to error compensation associated with gradient-promoted transitions. Deamination gradients reflect spontaneous chemical reactions in singlestranded DNA, but functional coding constraints modulate gradients.

Ratite nonmonophyly: independent evidence from 40 novel Loci

Large-scale multilocus studies have become common in molecular phylogenetics, but the best way to interpret these studies when their results strongly conflict with prior information about phylogeny remains unclear. An example of such a conflict is provided by the ratites (the large flightless birds of southern land masses, including ostriches, emus, and rheas). Ratite monophyly is strongly supported by both morphological data and many earlier molecular studies and is used as a textbook example of vicariance biogeography. However, recent studies have indicated that ratites are not monophyletic; instead, the volant tinamous nest inside the ratites rather than forming their sister group within the avian superorder Palaeognathae. Large-scale studies can exhibit biases that reflect a number of factors, including limitations in the fit of the evolutionary models used for analyses and problems with sequence alignment, so the unexpected conclusion that ratites are not monophyletic needs to be rigorously evaluated. A rigorous approach to testing novel hypotheses generated by large-scale studies is to collect independent evidence (i.e., excluding the loci and/or traits used to generate the hypotheses). We used 40 nuclear loci not used in previous studies that investigated the relationship among ratites and tinamous. Our results strongly support the recent molecular studies, revealing that the deepest branch within Palaeognathae separates the ostrich from other members of the clade, rather than the traditional hypothesis that separates the tinamous from the ratites. To ensure these results reflected evolutionary history, we examined potential biases in types of loci used, heterotachy, alignment biases, and discordance between gene trees and the species tree. All analyses consistently supported nonmonophyly of the ratites and no confounding biases were identified. This confirmation that ratites are not monophyletic using independent evidence will hopefully stimulate further comparative research on paleognath development and genetics that might reveal the basis of the morphological convergence in these large, flightless birds.

Multiple independent origins of mitochondrial control region duplications in the order Psittaciformes

Mitochondrial genomes are generally thought to be under selection for compactness, due to their small size, consistent gene content, and a lack of introns or intergenic spacers. As more animal mitochondrial genomes are fully sequenced, rearrangements and partial duplications are being identified with increasing frequency, particularly in birds (Class Aves). In this study, we investigate the evolutionary history of mitochondrial control region states within the avian order Psittaciformes (parrots and cockatoos). To this aim, we reconstructed a comprehensive multi-locus phylogeny of parrots, used PCR of three diagnostic fragments to classify the mitochondrial control region state as single or duplicated, and mapped these states onto the phylogeny. We further sequenced 44 selected species to validate these inferences of control region state. Ancestral state reconstruction using a range of weighting schemes identified six independent origins of mitochondrial control region duplications within Psittaciformes. Analysis of sequence data showed that varying levels of mitochondrial gene and tRNA homology and degradation were present within a given clade exhibiting duplications. Levels of divergence between control regions within an individual varied from 0-10.9% with the differences occurring mainly between 51 and 225 nucleotides 3' of the goose hairpin in domain I. Further investigations into the fates of duplicated mitochondrial genes, the potential costs and benefits of having a second control region, and the complex relationship between evolutionary rates, selection, and time since duplication are needed to fully explain these patterns in the mitochondrial genome.

Complete mitochondrial genome of Saunders's gull Chroicocephalus saundersi (Charadriiformes, Laridae)

Saunders's gull Chroicocephalus saundersi (Aves, Charadriiformes, Laridae) is a small-sized gull having black-colored head. In this study, the entire mitochondrial genome of C. saundersi is sequenced, which is 16,725 bp in length. The detailed characteristics of the mitochondrial genome are described here.

Leber's hereditary optic neuropathy with the 3434, 9011 mitochondrial DNA point mutation

BACKGROUND

Leber's hereditary optic neuropathy (LHON) contains several well-known mitochondrial DNA (mtDNA) point mutations. We report a case with characteristic clinical manifestations of LHON involving a possible new LHON point mutation.

CASE

A 34-year-old man was diagnosed with LHON. The patient exhibited (1) sudden onset of bilateral visual loss, (2) normal light reflex, and (3) swelling of the peripapillary nerve fiber layer. After subsequent development of bilateral optic disc pallor, we concluded that the patient had LHON. mtDNA analysis was conducted using non-radioisotopic single-strand conformational polymorphism followed by direct sequencing. There was no change in the patient's visual acuity during the 26-month follow-up period.

OBSERVATIONS

The mtDNA point mutations were found at T3434C, G3483A, and V9011A. The confirmed mtDNA substitutions included (1) A-G at nucleotide position 3434, (2) G-A at nucleotide position 3483, and (3) C-T at nucleotide position 9011. The amino acid code at the nucleotide positions 3434 and 9011 was phylogenetically highly conserved.

CONCLUSION

The 3434 and 9011 mtDNA point mutations are candidates for a new LHON mutation.

Evolution of linear mitochondrial genomes in medusozoan cnidarians

In nearly all animals, mitochondrial DNA (mtDNA) consists of a single circular molecule that encodes several subunits of the protein complexes involved in oxidative phosphorylation as well as part of the machinery for their expression. By contrast, mtDNA in species belonging to Medusozoa (one of the two major lineages in the phylum Cnidaria) comprises one to several linear molecules. Many questions remain on the ubiquity of linear mtDNA in medusozoans and the mechanisms responsible for its evolution, replication, and transcription. To address some of these questions, we determined the sequences of nearly complete linear mtDNA from 24 species representing all four medusozoan classes: Cubozoa, Hydrozoa, Scyphozoa, and Staurozoa. All newly determined medusozoan mitochondrial genomes harbor the 17 genes typical for cnidarians and map as linear molecules with a high degree of gene order conservation relative to the anthozoans. In addition, two open reading frames (ORFs), polB and ORF314, are identified in cubozoan, schyphozoan, staurozoan, and trachyline hydrozoan mtDNA. polB belongs to the B-type DNA polymerase gene family, while the product of ORF314 may act as a terminal protein that binds telomeres. We posit that these two ORFs are remnants of a linear plasmid that invaded the mitochondrial genomes of the last common ancestor of Medusozoa and are responsible for its linearity. Hydroidolinan hydrozoans have lost the two ORFs and instead have duplicated cox1 at each end of their mitochondrial chromosome(s). Fragmentation of mtDNA occurred independently in Cubozoa and Hydridae (Hydrozoa, Hydroidolina). Our broad sampling allows us to reconstruct the evolutionary history of linear mtDNA in medusozoans.

PHYLOGENETIC ANALYSES OF FRINGILLIDAE (AVES: PASSERIFORMES) USING MITOCHONDRIAL tRNA GENE SEQUENCES AND SECONDARY STRUCTURE

Fringillidae is a large and diverse family of Passeriformes. So far, however, Fringillidae relationships deduced from morphological features and by a number of molecular approaches have remained unproven. Recently, much attention has been attracted to mitochondrial tRNA genes, whose sequence and secondary structural characteristics have shown to be useful for Acrodont Lizards and deep-branch phylogenetic studies. In order to identify useful phylogenetic markers and test Fringillidae relationships, we have sequenced three major clusters of mitochondrial tRNA genes from 15 Fringillidae taxa. A coincident tree, with coturnix as outgroup, was obtained through Maximum-likelihood method using combined dataset of 11 mitochondrial tRNA gene sequences. The result was similar to that through Neighbor-joining but different from Maximum-parsimony methods. Phylogenetic trees constructed with stem-region sequences of 11 genes had many different topologies and lower confidence than with total sequences. On the other hand, some secondary structural characteristics may provide phylogenetic information on relatively short internal branches at under-genus level. In summary, our data indicate that mitochondrial tRNA genes can achieve high confidence on Fringillidae phylogeny at subfamily level, and stem-region sequences may be suitable only at above-family level. Secondary structural characteristics may also be useful to resolve phylogenetic relationship between different genera of Fringillidae with good performance.

Evolution and connectivity in the world-wide migration system of the mallard: inferences from mitochondrial DNA

Background

Main waterfowl migration systems are well understood through ringing activities. However, in mallards (Anas platyrhynchos) ringing studies suggest deviations from general migratory trends and traditions in waterfowl. Furthermore, surprisingly little is known about the population genetic structure of mallards, and studying it may yield insight into the spread of diseases such as Avian Influenza, and in management and conservation of wetlands. The study of evolution of genetic diversity and subsequent partitioning thereof during the last glaciation adds to ongoing discussions on the general evolution of waterfowl populations and flyway evolution. Hypothesised mallard flyways are tested explicitly by analysing mitochondrial mallard DNA from the whole northern hemisphere.

Results

Phylogenetic analyses confirm two mitochondrial mallard clades. Genetic differentiation within Eurasia and North-America is low, on a continental scale, but large differences occur between these two land masses (F_ST = 0.51). Half the genetic variance lies within sampling locations, and a negligible portion between currently recognised waterfowl flyways, within Eurasia and North-America. Analysis of molecular variance (AMOVA) at continent scale, incorporating sampling localities as smallest units, also shows the absence of population structure on the flyway level. Finally, demographic modelling by coalescence simulation proposes a split between Eurasia and North-America 43,000 to 74,000 years ago and strong population growth (~100fold) since then and little migration (not statistically different from zero).

Conclusions

Based on this first complete assessment of the mallard's world-wide population genetic structure we confirm that no more than two mtDNA clades exist. Clade A is characteristic for Eurasia, and clade B for North-America although some representatives of clade A are also found in North-America. We explain this pattern by evaluating competing hypotheses and conclude that a complex mix of historical, recent and anthropogenic factors shaped the current mallard populations. We refute population classification based on flyways proposed by ornithologists and managers, because they seem to have little biological meaning. Our results have implications for wetland management and conservation, with special regard to the release of farmed mallards for hunting, as well as for the possible transmission of Avian Influenza by mallards due to migration.

Searching for evidence of selection in avian DNA barcodes

The barcode of life project has assembled a tremendous number of mitochondrial cytochrome c oxidase I (COI) sequences. Although these sequences were gathered to develop a DNA-based system for species identification, it has been suggested that further biological inferences may also be derived from this wealth of data. Recurrent selective sweeps have been invoked as an evolutionary mechanism to explain limited intraspecific COI diversity, particularly in birds, but this hypothesis has not been formally tested. In this study, I collated COI sequences from previous barcoding studies on birds and tested them for evidence of selection. Using this expanded data set, I re-examined the relationships between intraspecific diversity and interspecific divergence and sampling effort, respectively. I employed the McDonald-Kreitman test to test for neutrality in sequence evolution between closely related pairs of species. Because amino acid sequences were generally constrained between closely related pairs, I also included broader intra-order comparisons to quantify patterns of protein variation in avian COI sequences. Lastly, using 22 published whole mitochondrial genomes, I compared the evolutionary rate of COI against the other 12 protein-coding mitochondrial genes to assess intragenomic variability. I found no conclusive evidence of selective sweeps. Most evidence pointed to an overall trend of strong purifying selection and functional constraint. The COI protein did vary across the class Aves, but to a very limited extent. COI was the least variable gene in the mitochondrial genome, suggesting that other genes might be more informative for probing factors constraining mitochondrial variation within species.

Complete sequence and gene organization of the mitochondrial genome of scaly-sided merganser (Mergus squamatus) and phylogeny of some Anatidae species

The scaly-sided merganser (Mergus squamatus) is an endangered bird species on the IUCN Red List with the estimated global population of less than 2,500 individuals at present. In the present study, we studied the complete mitochondrial genome (mtDNA) and the phylogenetic of M. squamatus by PCR amplification and GenBank data. The genome was 16,595 bp in length and contained 37 genes (13 protein coding genes, two rRNAs, and 22 tRNAs) and a non-coding control region (D-loop). All protein-coding genes of M. squamatus mtDNA start with a typical ATG codon, except ND1, COI, and COII uses GTG as their initial codon. TAA, T- and TAG as the terminate codon occurred very commonly in the sequence. All tRNA genes can be folded into canonical cloverleaf secondary structure except for tRNA(Ser) (AGY) and tRNA(Leu) (CUN), which lose ''DHU'' arm. The genome sequences had been deposited in GenBank under accession number HQ833701. Based on the concatenated nucleotide sequences of mtDNA genes (Cyt b and D-loop), we reconstructed phylogenetic trees and discussed the phylogenetic relationships among ten Anatidae species. The results are different from the present classification, and we support Lophodytes cucullatus and Mergullus albellus to be members of the genus Mergus.

Full mitochondrial genome sequences of two endemic Philippine hornbill species (Aves: Bucerotidae) provide evidence for pervasive mitochondrial DNA recombination

Background

Although nowaday it is broadly accepted that mitochondrial DNA (mtDNA) may undergo recombination, the frequency of such recombination remains controversial. Its estimation is not straightforward, as recombination under homoplasmy (i.e., among identical mt genomes) is likely to be overlooked. In species with tandem duplications of large mtDNA fragments the detection of recombination can be facilitated, as it can lead to gene conversion among duplicates. Although the mechanisms for concerted evolution in mtDNA are not fully understood yet, recombination rates have been estimated from "one per speciation event" down to 850 years or even "during every replication cycle".

Results

Here we present the first complete mt genome of the avian family Bucerotidae, i.e., that of two Philippine hornbills, Aceros waldeni and Penelopides panini. The mt genomes are characterized by a tandemly duplicated region encompassing part of cytochrome b, 3 tRNAs, NADH6, and the control region. The duplicated fragments are identical to each other except for a short section in domain I and for the length of repeat motifs in domain III of the control region. Due to the heteroplasmy with regard to the number of these repeat motifs, there is some size variation in both genomes; with around 21,657 bp (A. waldeni) and 22,737 bp (P. panini), they significantly exceed the hitherto longest known avian mt genomes, that of the albatrosses. We discovered concerted evolution between the duplicated fragments within individuals. The existence of differences between individuals in coding genes as well as in the control region, which are maintained between duplicates, indicates that recombination apparently occurs frequently, i.e., in every generation.

Conclusions

The homogenised duplicates are interspersed by a short fragment which shows no sign of recombination. We hypothesize that this region corresponds to the so-called Replication Fork Barrier (RFB), which has been described from the chicken mitochondrial genome. As this RFB is supposed to halt replication, it offers a potential mechanistic explanation for frequent recombination in mitochondrial genomes.