Mitochondrial genome sequences of Artemia tibetiana and Artemia urmiana: assessing molecular changes for high plateau adaptation

Temporal genetic variation mediated by climate change-induced salinity decline, a study on Artemia (Crustacea: Anostraca) from Kyêbxang Co, a high altitude salt lake on the Qinghai-Tibet Plateau

The Qinghai-Tibet Plateau is one of the areas the richest in salt lakes and Artemia sites. As a result of climate warming and wetting, the areas of salt lakes on the plateau have been increasing, and the salinities have decreased considerably since 1990s. However, the impact of salinity change on the genetic diversity of Artemia is still unknown. Kyêbxang Co is the highest (4620 m above sea level) salt lake currently with commercial harvesting of Artemia resting eggs in the world, and harbors the largest Artemia population on the plateau. Its salinity had dropped from ∼67 ppt in 1998 to ∼39 ppt in 2019. Using 13 microsatellite markers and the mitochondrial cytochrome oxidase submit I (COI) gene, we analyzed the temporal changes of genetic diversity, effective population size and genetic structure of this Artemia population based on samples collected in 1998, 2007 and 2019. Our results revealed a steady decline of genetic diversity and significant genetic differentiation among the sampling years, which may be a consequence of genetic drift and the selection of decreased salinity. A decline of effective population size was also detected, which may be relative to the fluctuation in census population size, skewed sex ratio, and selection of the declined salinity. In 2007 and 2019, the Artemia population showed an excess of heterozygosity and significant deviation from Hardy-Weinberg Equilibrium (p < 0.001), which may be associated with the heterozygote advantage under low salinity. To comprehensively understand the impact of climate warming and wetting on Artemia populations on the plateau, further investigation with broad and intensive sampling are needed.

Comparative mitogenomic analysis of subterranean and surface amphipods (Crustacea, Amphipoda) with special reference to the family Crangonyctidae

Mitochondrial genomes play important roles in studying genome evolution, phylogenetic analyses, and species identification. Amphipods (Class Malacostraca, Order Amphipoda) are one of the most ecologically diverse crustacean groups occurring in a diverse array of aquatic and terrestrial environments globally, from freshwater streams and lakes to groundwater aquifers and the deep sea, but we have a limited understanding of how habitat influences the molecular evolution of mitochondrial energy metabolism. Subterranean amphipods likely experience different evolutionary pressures on energy management compared to surface-dwelling taxa that generally encounter higher levels of predation and energy resources and live in more variable environments. In this study, we compared the mitogenomes, including the 13 protein-coding genes involved in the oxidative phosphorylation (OXPHOS) pathway, of surface and subterranean amphipods to uncover potentially different molecular signals of energy metabolism between surface and subterranean environments in this diverse crustacean group. We compared base composition, codon usage, gene order rearrangement, conducted comparative mitogenomic and phylogenomic analyses, and examined evolutionary signals of 35 amphipod mitogenomes representing 13 families, with an emphasis on Crangonyctidae. Mitogenome size, AT content, GC-skew, gene order, uncommon start codons, location of putative control region (CR), length of rrnL and intergenic spacers differed between surface and subterranean amphipods. Among crangonyctid amphipods, the spring-dwelling Crangonyx forbesi exhibited a unique gene order, a long nad5 locus, longer rrnL and rrnS loci, and unconventional start codons. Evidence of directional selection was detected in several protein-encoding genes of the OXPHOS pathway in the mitogenomes of surface amphipods, while a signal of purifying selection was more prominent in subterranean species, which is consistent with the hypothesis that the mitogenome of surface-adapted species has evolved in response to a more energy demanding environment compared to subterranean amphipods. Overall, gene order, locations of non-coding regions, and base-substitution rates points to habitat as an important factor influencing the evolution of amphipod mitogenomes.

Population genetics of Artemia urmiana species complex (Crustacea, Anostraca): A group with asymmetrical dispersal and gene flow mediated by migratory waterfowl

Bird-mediated dispersal of resting eggs is the main mechanism for Artemia dispersal among catchments. The bisexual populations of Artemia urmiana species complex, which is here considered to be a collection of Artemia genetically close to the so-called "Western Asian Lineage", are mostly distributed in central and western Asia (i.e., in regions falling into the Central Asian Flyway of migratory birds) and live in diversified habitats. Little is known about the genetic relationships among these populations. Aiming to understand the population genetic characteristics and the roles of migratory birds on the dispersal and gene flow of this Artemia group, we evaluated the genetic diversity, genetic differentiation, and gene flow among 14 populations, with their altitudes ranging from 540 to 4870 m above sea level, using 13 microsatellite markers. Almost all populations exhibited high genetic diversity and heterozygote excess, which may be a consequence of combined effects of dispersal and hybridization. The global genetic differentiation (FST) value was 0.092, the pairwise FST values were 0.003-0.246. Discriminant analysis of principal components identified three genetic clusters, consisting of Urmia Lake (Iran), Zhundong (Xinjiang, China), and 12 Qinghai-Tibet Plateau populations, respectively. The among-population genetic differentiation seems to be a consequence of isolation by distance and adaptation to diversified habitats induced by altitudinal gradient. Historical gene flows are asymmetrical, and show an evolutionary source-sink dynamics, with Jingyu Lake (Xinjiang, China) population being the major source. These results support our hypothesis that in Qinghai-Tibet Plateau and surrounding areas the bird-mediated dispersal of Artemia may be biased towards from north to south and/or from higher altitude to lower altitude.

Stronger evidence for relaxed selection than adaptive evolution in high-elevation animal mtDNA

Mitochondrial (mt) genes are the subject of many adaptive hypotheses due to the key role of mitochondria in energy production and metabolism. One widespread adaptive hypothesis is that selection imposed by life at high elevation leads to the rapid fixation of beneficial alleles in mtDNA, reflected in the increased rates of mtDNA evolution documented in many high-elevation species. However, the assumption that fast mtDNA evolution is caused by positive, rather than relaxed purifying selection has rarely been tested. Here, we calculated the dN/dS ratio, a metric of nonsynonymous substitution bias, and explicitly tested for relaxed selection in the mtDNA of over 700 species of terrestrial vertebrates, freshwater fishes, and arthropods, with information on elevation and latitudinal range limits, range sizes, and body sizes. We confirmed that mitochondrial genomes of high-elevation taxa have slightly higher dN/dS ratios compared to low-elevation relatives. High-elevation species tend to have smaller ranges, which predict higher dN/dS ratios and more relaxed selection across species and clades, while absolute elevation and latitude do not predict higher dN/dS. We also find a positive relationship between body mass and dN/dS, supporting a role for small effective population size leading to relaxed selection. We conclude that higher mt dN/dS among high-elevation species is more likely to reflect relaxed selection due to smaller ranges and reduced effective population size than adaptation to the environment. Our results highlight the importance of rigorously testing adaptive stories against non-adaptive alternative hypotheses, especially in mt genomes.

Conflicts in Mitochondrial Phylogenomics of Branchiopoda, with the First Complete Mitogenome of Laevicaudata (Crustacea: Branchiopoda)

Conflicting phylogenetic signals are pervasive across genomes. The potential impact of such systematic biases may be reduced by phylogenetic approaches accommodating for heterogeneity or by the exclusive use of homoplastic sites in the datasets. Here, we present the complete mitogenome of Lynceus grossipedia as the first representative of the suborder Laevicaudata. We employed a phylogenomic approach on the mitogenomic datasets representing all major branchiopod groups to identify the presence of conflicts and concordance across the phylogeny. We found pervasive phylogenetic conflicts at the base of Diplostraca. The homogeneity of the substitution pattern tests and posterior predictive tests revealed a high degree of compositional heterogeneity among branchiopod mitogenomes at both the nucleotide and amino acid levels, which biased the phylogenetic inference. Our results suggest that Laevicaudata as the basal clade of Phyllopoda was most likely an artifact caused by compositional heterogeneity and conflicting phylogenetic signal. We demonstrated that the exclusive use of homoplastic site methods combining the application of site-heterogeneous models produced correct phylogenetic estimates of the higher-level relationships among branchiopods.

The complete mitochondrial genome of the Arctic fairy shrimp Branchinectapaludosa (Müller, 1788) (Anostraca, Branchinectidae) from Sirius Passet, North Greenland

Here we report the complete mitochondrial genome of the Arctic fairy shrimp, Branchinectapaludosa (Müller, 1788) (Anostraca, Branchinectidae), which was collected in the High Arctic of North Greenland. A complete 16,059 bp mitochondrion of B.paludosa was sequenced and assembled with the Illumina next generation sequencing platform. The B.paludosa mitogenome contains 13 PCGs, 22 tRNAs and 2 rRNA genes that are commonly observed in most metazoans and shows the conserved gene arrangement pattern of Anostraca. Our results of the phylogenomic analysis are consistent with the previous phylogenetic relationship, based on nuclear 18S ribosomal DNA. The B.paludosa mitogenome will be useful for understanding the geographical distribution and phylogenetic relationship of anostracans.

Comparative Mitogenomic Analyses and New Insights into the Phylogeny of Thamnocephalidae (Branchiopoda: Anostraca)

Thamnocephalidae, a family of Anostraca which is widely distributed on all continents of the world except Antarctica, currently consists of six genera and approximately 63 recognized species. The relationships among genera in Thamnocephalidae and the monophyly of Thamnocephalidae, determined using morphological characteristics or gene markers, remain controversial. In order to address the relationships within Thamnocephalidae, we sequenced Branchinella kugenumaensis mitogenomes and conducted a comparative analysis to reveal the divergence across mitogenomes of B. kugenumaensis. Using newly obtained mitogenomes together with available Anostracan genomic sequences, we present the most complete phylogenomic understanding of Anostraca to date. We observed high divergence across mitogenomes of B. kugenumaensis. Meanwhile, phylogenetic analyses based on both amino acids and nucleotides of the protein-coding genes (PCG) provide significant support for a non-monophyletic Thamnocephalidae within Anostraca, with Asian Branchinella more closely related to Streptocephalidae than Australian Branchinella. The phylogenetic relationships within Anostraca were recovered as follows: Branchinectidae + Chirocephalidae as the basal group of Anostraca and halophilic Artemiidae as a sister to the clade Thamnocephalidae + Streptocephalidae. Both Bayesian inference (BI)- and maximum likelihood (ML)-based analyses produced identical topologies.

The complete mitochondrial genome of Artemia persimilis Piccinelli and Prosdocimi, 1968 (Crustacea: Anostraca)

In the study, we report the complete mitochondrial genome of Artemia persimilis Piccinelli and Prosdocimi, 1968 for the first time. The mitochondrial genome of A. persimilis is 15,436 bp in length, with the typical structure of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and 2 ribosomal RNA genes, and a non-coding control region (CR). Phylogenetic analysis showed that A. persimilis was at the basal position among the bisexual Artemia species, which revealed that A. persimilis is likely to be an ancestral clade. The present study could provide effective resources for population genetics study, as well as germplasm conservation in Artemia.

Complete mitochondrial genomes of three fairy shrimps from snowmelt pools in Japan

Background

Fairy shrimps belong to order Anostraca, class Branchiopoda, subphylum Crustacea, and phylum Arthropoda. Three fairy shrimp species (Eubranchipus uchidai, E. asanumai, and E. hatanakai) that inhabit snowmelt pools are currently known in Japan. Whole mitochondrial genomes are useful genetic information for conducting phylogenetic analyses. Mitochondrial genome sequences for Branchiopoda members are gradually being collated.

Results

Six whole mitochondrial genomes from the three Eubranchipus species are presented here. Eubranchipus species share the anostracan pattern of gene arrangement in their mitochondrial genomes. The mitochondrial genomes of the Eubranchipus species have a higher GC content than those of other anostracans. Accelerated substitution rates in the lineage of Eubranchipus species were observed.

Conclusion

This study is the first to obtain whole mitochondrial genomes for Far Eastern Eubranchipus species. We show that the nucleotide sequences of cytochrome oxidase subunit I and the 16S ribosomal RNA of E. asanumai presented in a previous study were nuclear mitochondrial DNA segments. Higher GC contents and accelerated substitution rates are specific characteristics of the mitochondrial genomes of Far Eastern Eubranchipus. The results will be useful for further investigations of the evolution of Anostraca as well as Branchiopoda.

The complete mitochondrial genome of Artemia salina Leach, 1819 (Crustacea: Anostraca)

In the study, the complete mitochondrial genome of Artemia salina was reported for the first time. The mitochondrial genome of A. salina is 15,762 bp in length, with the typical structure of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes, and a major non-coding region (CR). Phylogenetic analysis showed that A. salina has a much closer relationship with A. persimilis compared to other Artemia species. The complete cp genome sequence of A. salina reported here provided an essential resource for further population genetics research and germplasm conservation on Artemia.

Convergent Adaptation in Mitochondria of Phylogenetically Distant Birds: Does it Exist?

In a wide range of taxa, proteins encoded by mitochondrial genomes are involved in adaptation to lifestyle that requires oxygen starvation or elevation of metabolism rate. It remains poorly understood to what extent adaptation to similar conditions is associated with parallel changes in these proteins. We search for a genetic signal of parallel or convergent evolution in recurrent molecular adaptation to high altitude, migration, diving, wintering, unusual flight abilities, or loss of flight in mitochondrial genomes of birds. Developing on previous work, we design an approach for the detection of recurrent coincident changes in genotype and phenotype, indicative of an association between the two. We describe a number of candidate sites involved in recurrent adaptation in ND genes. However, we find that the majority of convergence events can be explained by random coincidences without invoking adaptation.

Settling taxonomic and nomenclatural problems in brine shrimps, Artemia (Crustacea: Branchiopoda: Anostraca), by integrating mitogenomics, marker discordances and nomenclature rules

High morphological plasticity in populations of brine shrimp subjected to different environmental conditions, mainly salinity, hindered for centuries the identification of the taxonomic entities encompassed within Artemia. In addition, the mismatch between molecular and morphological evolution rates complicates the characterization of evolutionary lineages, generating taxonomic problems. Here, we propose a phylogenetic hypothesis for Artemia based on two new complete mitogenomes, and determine levels of congruence in the definition of evolutionary units using nuclear and mtDNA data. We used a fossil of Artemia to calibrate the molecular clock and discuss divergence times within the genus. The hypothesis proposed herein suggests a more recent time frame for lineage splitting than previously considered. Phylogeographic analyses were performed using GenBank available mitochondrial and nuclear markers. Evidence of gen e flow, identified through discordances between nuclear and mtDNA markers, was used to reconsider the specific status of some taxa. As a result, we consider Artemia to be represented by five evolutionary units: Southern Cone, Mediterranean-South African, New World, Western Asian, and Eastern Asian Lineages. After an exhaustive bibliographical revision, unavailable names for nomenclatural purposes were discarded. The remaining available names have been assigned to their respective evolutionary lineage. The proper names for the evolutionary units in which brine shrimps are structured remain as follows: Artemia persimilis Piccinelli & Prosdocimi, 1968 for the Southern Cone Lineage, Artemia salina (Linnaeus, 1758) for the Mediterranean-SouthAfrican Lineage, Artemia urmiana Günther, 1899 for the Western Asian Lineage, and Artemia sinica Cai, 1989 for the Eastern Asian Lineage. The name Artemia monica Verrill, 1869 has nomenclatural priority over A. franciscana Kellogg, 1906 for naming the New World Lineage. New synonymies are proposed for A. salina (= C. dybowskii Grochowski, 1896 n. syn., and A. tunisiana Bowen & Sterling, 1978 n. syn.), A. monica (= A. franciscana Kellogg, 1906 n. syn., and A. salina var. pacifica Sars, 1904 n. syn.); A. urmiana (= B. milhausenii Fischer de Waldheim, 1834 n. syn., A. koeppeniana Fischer, 1851 n. syn., A. proxima King, 1855 n. syn., A. s. var. biloba Entz, 1886 n. syn., A. s. var. furcata Entz, 1886 n. syn., A. asiatica Walter, 1887 n. syn., A. parthenogenetica Bowen & Sterling, 1978 n. syn., A. ebinurica Qian & Wang, 1992 n. syn., A. murae Naganawa, 2017 n. syn., and A. frameshifta Naganawa & Mura, 2017 n. syn.). Internal deep nuclear structuring within the A. monica and A. salina clades, might suggest the existence of additional evolutionary units within these taxa.

Reanalysis and Revision of the Complete Mitochondrial Genome of Artemia urmiana Günther, 1899 (Crustacea: Anostraca)

In the previously published mitochondrial genome sequence of Artemia urmiana (NC_021382 [JQ975176]), the taxonomic status of the examined Artemia had not been determined, due to parthenogenetic populations coexisting with A. urmiana in Urmia Lake. Additionally, NC_021382 [JQ975176] has been obtained with pooled cysts of Artemia (0.25 g cysts consists of 20,000–25,000 cysts), not a single specimen. With regard to coexisting populations in Urmia Lake, and intra- and inter-specific variations in the pooled samples, NC_021382 [JQ975176] cannot be recommended as a valid sequence and any attempt to attribute it to A. urmiana or a parthenogenetic population is unreasonable. With the aid of next-generation sequencing methods, we characterized and assembled a complete mitochondrial genome of A. urmiana with defined taxonomic status. Our results reveal that in the previously published mitogenome (NC_021382 [JQ975176]), tRNA-Phe has been erroneously attributed to the heavy strand but it is encoded in the light strand. There was a major problem in the position of the ND5. It was extended over the tRNA-Phe, which is biologically incorrect. We have also identified a partial nucleotide sequence of 311 bp that was probably erroneously duplicated in the assembly of the control region of NC_021382 [JQ975176], which enlarges the control region length by 16%. This partial sequence could not be recognized in our assembled mitogenome as well as in 48 further examined specimens of A. urmiana. Although, only COX1 and 16S genes have been widely used for phylogenetic studies in Artemia, our findings reveal substantial differences in the nucleotide composition of some other genes (including ATP8, ATP6, ND3, ND6, ND1 and COX3) among Artemia species. It is suggested that these markers should be included in future phylogenetic studies.

Complete Mitogenome of a Leaf-Mining Buprestid Beetle, Trachys auricollis, and Its Phylogenetic Implications

A complete mitogenome of Trachys auricollis is reported, and a mitogenome-based phylogenetic tree of Elateriformia with all protein-coding genes (PCGs), rRNAs, and tRNAs is presented for the first time. The complete mitochondrial genome of T. auricollis is 16,429 bp in size and contains 13 PCGs, two rRNA genes, 22 tRNA genes, and an A + T-rich region. The A + T content of the entire genome is approximately 71.1%, and the AT skew and GC skew are 0.10 and -0.20, respectively. According to the the nonsynonymous substitution rate to synonymous substitution rates (Ka/Ks) of all PCGs, the highest and lowest evolutionary rates were observed for atp8 and cox1, respectively, which is a common finding among animals. The start codons of all PCGs are the typical ATN. Ten PCGs have complete stop codons, but three have incomplete stop codons with T or TA. As calculated based on the relative synonymous codon usage (RSCU) values, UUA(L) is the codon with the highest frequency. Except for trnS1, all 22 tRNA genes exhibit typical cloverleaf structures. The A + T-rich region of T. auricollis is located between rrnS and the trnI-trnG-trnM gene cluster, with six 72-bp tandem repeats. Both maximum likelihood (ML) and Bayesian (BI) trees suggest that Buprestoidea is close to Byrrhoidea and that Buprestoidea and Byrrhoidea are sister groups of Elateroidea, but the position of Psephenidae is undetermined. The inclusion of tRNAs might help to resolve the phylogeny of Coleoptera.

Mitochondrial genome diversity and evolution in Branchiopoda (Crustacea)

BACKGROUND

The crustacean class Branchiopoda includes fairy shrimps, clam shrimps, tadpole shrimps, and water fleas. Branchiopods, which are well known for their great variety of reproductive strategies, date back to the Cambrian and extant taxa can be mainly found in freshwater habitats, also including ephemeral ponds. Mitochondrial genomes of the notostracan taxa Lepidurus apus lubbocki (Italy), L. arcticus (Iceland) and Triops cancriformis (an Italian and a Spanish population) are here characterized for the first time and analyzed together with available branchiopod mitogenomes.

RESULTS

Overall, branchiopod mitogenomes share the basic structure congruent with the ancestral Pancrustacea model. On the other hand, rearrangements involving tRNAs and the control region are observed among analyzed taxa. Remarkably, an unassigned region in the L. apus lubbocki mitogenome showed a chimeric structure, likely resulting from a non-homologous recombination event between the two flanking trnC and trnY genes. Notably, Anostraca and Onychocaudata mitogenomes showed increased GC content compared to both Notostraca and the common ancestor, and a significantly higher substitution rate, which does not correlate with selective pressures, as suggested by dN/dS values.

CONCLUSIONS

Branchiopod mitogenomes appear rather well-conserved, although gene rearrangements have occurred. For the first time, it is reported a putative non-homologous recombination event involving a mitogenome, which produced a pseudogenic tRNA sequence. In addition, in line with data in the literature, we explain the higher substitution rate of Anostraca and Onychocaudata with the inferred GC substitution bias that occurred during their evolution.

The Complete Mitogenome of Falco amurensis (Falconiformes, Falconidae), and a Comparative Analysis of Genus Falco

In this study, we sequenced the complete mitogenome of Falco amurensis (Falconiformes, Falconidae). The F. amurensis mitogenome is 17,464 bp long, and contains 37 genes, including 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs, and two non-coding regions (control region and pseudo-control region). Most PCGs initiate with ATG and terminate with TAA. atp8 exhibits the highest evolutionary rate, with cox1 showing the lowest. rrnS and rrnL contain three domains with 46 helices and six domains with 59 helices, respectively. All tRNAs have a typical cloverleaf secondary structure, except that trnS(agy) lacks the dihydrouracil arm. The control region is located between trnT and trnP and the pseudo-control between trnE and trnF. Phylogenetic relationships of 23 species from Falconiformes were analyzed based on the nucleotide sequences of the 13 PCGs and two rRNAs. The results support Falco as a monophyletic taxon, and F. amurensis has a close relationship with the clade containing F. cherrug/F. rusticolus/F. peregrinus.

Positive Selection Drove the Adaptation of Mitochondrial Genes to the Demands of Flight and High-Altitude Environments in Grasshoppers

The molecular evolution of mitochondrial genes responds to changes in energy requirements and to high altitude adaptation in animals, but this has not been fully explored in invertebrates. The evolution of atmospheric oxygen content from high to low necessarily affects the energy requirements of insect movement. We examined 13 mitochondrial protein-coding genes (PCGs) of grasshoppers to test whether the adaptive evolution of genes involved in energy metabolism occurs in changes in atmospheric oxygen content and high altitude adaptation. Our molecular evolutionary analysis of the 13 PCGs in 15 species of flying grasshoppers and 13 related flightless grasshoppers indicated that, similar to previous studies, flightless grasshoppers have experienced relaxed selection. We found evidence of significant positive selection in the genes ATP8, COX3, ND2, ND4, ND4L, ND5, and ND6 in flying lineages. This results suggested that episodic positive selection allowed the mitochondrial genes of flying grasshoppers to adapt to increased energy demands during the continuous reduction of atmospheric oxygen content. Our analysis of five grasshopper endemic to the Tibetan Plateau and 13 non-Tibetan grasshoppers indicated that, due to positive selection, more non-synonymous nucleotide substitutions accumulated in Tibetan grasshoppers than in non-Tibetan grasshoppers. We also found evidence for significant positive selection in the genes ATP6, ND2, ND3, ND4, and ND5 in Tibetan lineages. Our results thus strongly suggest that, in grasshoppers, positive selection drives mitochondrial genes to better adapt both to the energy requirements of flight and to the high altitude of the Tibetan Plateau.

Adaptive evidence of mitochondrial genomes in Dolycoris baccarum (Hemiptera: Pentatomidae) to divergent altitude environments

Given mitochondrion is the 'energy and oxygen usage factories', adaptive signatures of mitochondrial genes have been extensively investigated in vertebrates from different altitudes, but few studies focus on insects. Here, we sequenced the complete mitochondrial genome (mitogenome) of Dolycoris. baccarum living in the Tibetan Plateau (DBHC, ∼3200 m above sea level (asl)) and conducted a detailed comparative analysis with another D. baccarum mitogenome (DBQY) from relatively low altitude (∼1300 m asl). All the 37 mitochondrial genes were highly conserved and under purifying selection, except for two mitochondrial protein-coding genes (MPCGs) (atp6 and nad5) that showed positively selected signatures. We therefore further examined non-synonymous substitutions in atp6 and nad5, by sequencing more individuals from three populations with different altitudes. We found that these non-synonymous substitutions were polymorphic in these populations, likely due to relaxed selection constraints in different altitudes. Purifying selection in all mitochondrial genes may be due to their functional importance for the precision of ATP production usually. Length difference in mitochondrial control regions between DBHC and DBQY was also conversed at the population level, indicating that sequence size adjustments in control region may be associated with adaptation to divergent altitudes. Quantitatively real-time PCR analysis for 12 MPCGs showed that gene expression patterns had a significant change between the two populations, suggesting that expression levels of MPCGs could be modulated by divergent environmental pressures (e.g. oxygen content and ambient temperature). These results provided an important guide for further uncovering genetic mechanisms of ecological adaptation in insects.

Diversification of mitochondrial genome of Daphnia galeata (Cladocera, Crustacea): Comparison with phylogenetic consideration of the complete sequences of clones isolated from five lakes in Japan

To characterize genetic diversity and gene flow among Daphnia galeata populations, the complete nucleotide (nt) sequences of the mitochondrial (mt) DNAs of D. galeata clones isolated from five lakes in Japan (Lakes Shirakaba, Suwa, Kizaki, Kasumigaura, and Biwa) were determined. Comparison of non-synonymous (amino acid altering) substitution rates with synonymous substitution rates of D. galeata mt protein-coding genes demonstrated that ATPase8 and COI genes were the most and least susceptible, respectively, to the evolutional forces selecting the aa substitutions. Several non-synonymous substitutions were found in ATPase8 and ATPase6 even in the comparison that no synonymous substitution was found. Comparison of the total number of nt variations among the mt DNAs suggested the phylogenetic relationship ((((Shirakaba/Suwa, Kizaki), Kasumigaura), Biwa), D. pulex). Maximum-likelihood analysis using the total nt sequences of mt protein-coding genes confirmed this relationship with bootstrap values higher than 98%. All the mtDNAs of the analyzed Japanese D. galeata clones contained a control region of essentially the same structure that is distinct from those of the previously reported European Daphnia species of the D. longispina complex. The two control regions of different structures spread among mtDNAs of the Japanese and European Daphnia species, respectively, probably after the divergence of the Japanese D. galeata under different selection pressures associated with their habitats.

The complete mitogenome of the fairy shrimp Phallocryptus tserensodnomi (Crustacea: Anostraca: Thamnocephalidae)

The sequence of the mitochondrial genome (mitogenome) of the fairy shrimp Phallocryptus tserensodnomi Alonso & Ventura 2013 (Crustacea: Anostraca: Thamnocephalidae) has been determined. It is 16,493 bp with an AT-content of 65.4%, which encodes information of the typical 37 genes as all other metazoan mitogenomes. Both AT-content and putative control region of the genome show moderate values among all mitogenomes of the Branchiopoda sequenced to date. The mitochondrial gene order shows the same arrangement with the Artemiidae which is different from the pancrustacean ancestral pattern, due to translocation and inversion of two tRNA genes. Our results will provide important materials for not only phylogenetic but also biogeographic studies of the Anostraca.

The complete mitogenome of the freshwater fairy shrimp Streptocephalus sirindhornae (Crustacea: Anostraca: Streptocephalidae)

In this study, we amplified, sequenced and analyzed the complete mitogenome of the freshwater fairy shrimp Streptocephalus sirindhornae (Crustacea: Anostraca: Streptocephalidae). The full-length of the S. sirindhornae mitogenome is a circular molecule of 16,887 bp in size with an A + T content of 64.5%. It has the largest putative control region (2794 bp) with the lowest A + T content (62.6%) for all determined branchiopod mitogenomes. The genome consisted of 37 genes that are involved in the respiration chain as well as the mitochondrial translation system. The S. sirindhornae mitogenome exhibits an identical gene arrangement as the Artemia pattern, which shows translocation and inversion of two transfer-RNA genes compared to the pancrustacean ancestral pattern. This is by far the first determined mitogenome of a freshwater fairy shrimp. The results of our study will provide significant data for reconstructing the consensus Branchiopoda tree of life.

Comparative mitochondrial genomics and phylogenetic relationships of the Crossoptilon species (Phasianidae, Galliformes)

BACKGROUND

Phasianidae is a family of Galliformes containing 38 genera and approximately 138 species, which is grouped into two tribes based on their morphological features, the Pheasants and Partridges. Several studies have attempted to reconstruct the phylogenetic relationships of the Phasianidae, but many questions still remain unaddressed, such as the taxonomic status and phylogenetic relationships among Crossoptilon species. The mitochondrial genome (mitogenome) has been extensively used to infer avian genetic diversification with reasonable resolution. Here, we sequenced the entire mitogenomes of three Crossoptilon species (C. harmani, C. mantchuricum and C. crossoptilon) to investigate their evolutionary relationship among Crossoptilon species.

RESULTS

The complete mitogenomes of C. harmani, C. mantchuricum and C. crossoptilon are 16682 bp, 16690 bp and 16680 bp in length, respectively, encoding a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a putative control region. C. auritum and C. mantchuricum are more closely related genetically, whereas C. harmani is more closely related to C. crossoptilon. Crossoptilon has a closer relationship with Lophura, and the following phylogenetic relationship was reconstructed: ((Crossoptilon + Lophura) + (Phasianus + Chrysolophus)). The divergence time between the clades C. harmani-C. crossoptilon and C. mantchuricum-C. auritum is consistent with the uplift of the Tibetan Plateau during the Tertiary Pliocene. The Ka/Ks analysis showed that atp8 gene in the Crossoptilon likely experienced a strong selective pressure in adaptation to the plateau environment.

CONCLUSIONS

C. auritum with C. mantchuricum and C. harmani with C. crossoptilon form two pairs of sister groups. The genetic distance between C. harmani and C. crossoptilon is far less than the interspecific distance and is close to the intraspecific distance of Crossoptilon, indicating that C. harmani is much more closely related to C. crossoptilon. Our mito-phylogenomic analysis supports the monophyly of Crossoptilon and its closer relationship with Lophura. The uplift of Tibetan Plateau is suggested to impact the divergence between C. harmani-C. crossoptilon clade and C. mantchuricum-C. auritum clade during the Tertiary Pliocene. Atp8 gene in the Crossoptilon species might have experienced a strong selective pressure for adaptation to the plateau environment.