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

Characterization of Complete Mitochondrial Genome and Phylogeny of Three Echeneidae Species

Species of the family Echeneidae are renowned for their capacity to adhere to various hosts using a sucking disc. This study aimed to examine the mitochondrial genome characteristics of three fish species (Echeneis naucrates, Remora albescens, and Remora remora) within the family Echeneidae and determine their phylogenetic relationships. The findings revealed that the mitochondrial genome lengths of the three species were 16,611 bp, 16,648 bp, and 16,623 bp, respectively, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a D-loop region. Most PCGs utilized ATG as the initiation codon, while only cox I used the GTG as the initiation codon. Additionally, seven genes employed incomplete termination codons (T and TA). The majority of PCGs in the three species displayed negative AT-skew and GC-skew values, with the GC-skew amplitude being greater than the AT-skew. The Ka/Ks ratios of the 13 PCGs did not exceed 1, demonstrating these species had been subjected to purification selection. Furthermore, only tRNA-Ser (GCT) lacked the D arm, while other tRNAs exhibited a typical cloverleaf secondary structure. Bayesian inference (BI) and maximum likelihood (ML) methods were utilized to construct a phylogenetic tree of the three species based on the 13 PCGs. Remora remora was identified as a distinct group, while R. osteochir and R. brachyptera were classified as sister taxa. This study contributes to the mitochondrial genome database of the family Echeneidae and provides a solid foundation for further systematic classification research in this fish group.

Complete Mitochondrial Genomes of Pluvialis fulva and Charadrius dubius with Phylogenetic Analysis of Charadriiformes

BACKGROUND

Plovers (Charadriidae), within the order of Charadriiformes, a group of modern birds distributed worldwide, are a frequent subject of molecular phylogenetic studies. While research on mitochondrial genome (mitogenome) variation within the family Charadriidae, especially intraspecific variation, is limited. Additionally, the monophyly of Charadrius and the phylogenetic placement of Pluvialis remain contentious. Nevertheless, recent studies utilizing complete mitogenomes from available databases to construct phylogenetic trees for Charadriidae and Charadriiformes remain scarce.

METHODS

This study aims to explore mitogenome variation within Charadrius dubius and clarify the phylogenetic placement of Pluvialis fulva. We sequenced the complete mitogenome of six C. dubius and one P. fulva, and all additional available mitogenomes were integrated within Charadriiformes. The average complete mitogenome length of C. dubius is 16,889 bp, and P. fulva is 16,859 bp.

RESULTS

Our results support the suggestion that the monophyly of Charadrius and P. fulva is nested within Charadriidae. The phylogenetic analysis of Charadriiformes based on mitogenomes strongly supports the recognition of three major shorebird clades: Charadrii, Lari and Scolopaci, with Lari and Scolopaci identified as sister clades.

CONCLUSIONS

Our study reinforces the credibility of the inferred evolutionary relationships within Charadriidae and Charadriiformes.

Characterization of the Complete Mitogenome of the Ring-Necked Pheasant Phasianus colchicus (Galliformes: Phasianidae) and Systematic Implications for Phasianinae Phylogenetics

BACKGROUND

Phasianidae mitogenomes exhibit significant structural variations critical for understanding evolution and subspecies divergence. However, annotations of these features in some pheasant species remain limited. This study aimed to enhance understanding of Phasianidae mitogenomes and their evolutionary patterns.

METHODS

A comparative analysis of complete mitogenomes from Phasianus colchicus, Phasianus versicolor, and 22 other accipitrids was conducted, examining codon usage, rRNA structures, selective pressures, phylogenetics, and structural variations.

RESULTS

The mitogenome of P. colchicus is 16,696 bp, comprising 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region, with a base composition of A: 30.61%, T: 25.26%, C: 30.85%, and G: 13.28%. Phylogenetic analysis revealed P. colchicus and P. versicolor are closely related, with the following relationship: ((Phasianus + Chrysolophus) + (Crossoptilon + Lophura)). Divergence timing aligns with the Tibetan Plateau uplift during the Tertiary Pliocene. Ka/Ks analysis suggests the CO I, CO II, CO III, ND1, ND4L, and ND6 genes in Phasianus underwent strong selective pressure for plateau adaptation.

CONCLUSIONS

The study confirms Phasianus monophyly and its close relationship with Chrysolophus. Adaptation-related selective pressures on the CO I, CO II, CO III, ND1, ND4L, and ND6 genes highlight its role in plateau environments, offering valuable insights into pheasant phylogeny.

Sturnidae sensu lato Mitogenomics: Novel Insights into Codon Aversion, Selection, and Phylogeny

The Sturnidae family comprises 123 recognized species in 35 genera. The taxa Mimidae and Buphagidae were formerly treated as subfamilies within Sturnidae. The phylogenetic relationships among the Sturnidae and related taxa (Sturnidae sensu lato) remain unresolved due to high rates of morphological change and concomitant morphological homoplasy. This study presents five new mitogenomes of Sturnidae sensu lato and comprehensive mitogenomic analyses. The investigated mitogenomes exhibit an identical gene composition of 37 genes-including 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes-and one control region (CR). The most important finding of this study is drawn from CAM analyses. The surprisingly unique motifs for each species provide a new direction for the molecular species identification of avian. Furthermore, the pervasiveness of the natural selection of PCGs is found in all examined species when analyzing their nucleotide composition and codon usage. We also determine the structures of mt-tRNA, mt-rRNA, and CR structures of Sturnidae sensu lato. Lastly, our phylogenetic analyses not only well support the monophyly of Sturnidae, Mimidae, and Buphagidae, but also define nine stable subclades. Taken together, our findings will enable the further elucidation of the evolutionary relationships within Sturnidae sensu lato.

Complete Mitochondrial Genome of Four Peristediidae Fish Species: Genome Characterization and Phylogenetic Analysis

The systematic revision of the family Peristediidae remains an unresolved issue due to their diverse and unique morphology. Despite the popularity of using mitochondrial genome research to comprehensively understand phylogenetic relationships in fish, genetic data for peristediid fish need to be included. Therefore, this study aims to investigate the mitochondrial genomic characteristics and intra-family phylogenetic relationships of Peristediidae by utilizing mitochondrial genome analysis. Therefore, this study aims to investigate the phylogenetic relationship of Peristediidae by utilizing mitochondrial genome analysis. The mitochondrial genome of four species of Peristediidae (Peristedion liorhynchus, Satyrichthys welchi, Satyrichthys rieffeli, and Scalicus amiscus) collected in the East China Sea was studied. The mitochondrial gene sequence lengths of four fish species were 16,533 bp, 16,526 bp, 16,527 bp, and 16,526 bp, respectively. They had the same mitochondrial structure and were all composed of 37 genes and one control region. Most PCGs used ATG as the start codon, and a few used GTG as the start codon. An incomplete stop codon (TA/T) occurred. The AT-skew and GC-skew values of 13 PCGs from four species were negative, and the GC-skew amplitude was greater than that of AT-skew. All cases of D-arm were found in tRNA-Ser (GCT). The Ka/Ks ratio analysis indicated that 13 PCGs were suffering purifying selection. Based on 12 PCGs (excluding ND6) sequences, a phylogenetic tree was constructed using Bayesian inference (BI) and maximum likelihood (ML) methods, providing a further supplement to the scientific classification of Peristediidae fish. According to the results of divergence time, the four species of fish had apparent divergence in the Early Cenozoic, which indicates that the geological events at that time caused the climax of species divergence and evolution.

High-quality genome assembly of a C. crossoptilon and related functional and genetics data resources

There are four species in the Crossoptilon genus inhibiting at from very low to very high altitudes across China, and they are in varying levels of danger of extinction. To better understand the genetic basis of adaptation to high altitudes and genetic changes due to bottleneck, we assembled the genome (~1.02 Gb) of a white eared pheasant (WT) (Crossoptilon crossoptilon) inhibiting at high altitudes (3,000~7,000 m) in northwest of Yunnan province, China, using a combination of Illumina short reads, PacBio long reads and Hi-C reads, with a contig N50 of 19.63 Mb and only six gaps. To further provide resources for gene annotation as well as functional and population genetics analyses, we sequenced transcriptomes of 20 major tissues of the WT individual and re-sequenced another 10 WT individuals and a blue eared pheasant (Crossoptilon auritum) individual inhabiting at intermediate altitudes (1,500~3,000 m). Our assembled WT genome, transcriptome data, and DNA sequencing data can be valuable resources for studying the biology, evolution and developing conservation strategies of these endangered species.

Complete Mitochondrial Genome and Phylogenetic Analysis of Tarsiger indicus (Aves: Passeriformes: Muscicapidae)

Tarsiger indicus (Vieillot, 1817), the White-browed Bush Robin, is a small passerine bird widely distributed in Asian countries. Here, we successfully sequenced its mitogenome using the Illumina Novaseq 6000 platform (Illumina, San Diego, CA, USA) for PE 2 × 150 bp sequencing. Combined with other published mitogenomes, we conducted the first comprehensive comparative mitogenome analysis of Muscicapidae birds and reconstructed the phylogenetic relationships between Muscicapidae and related groups. The T. indicus mitogenome was 16,723 bp in size, and it possessed the typical avian mitogenome structure and organization. Most PCGs of T. indicus were initiated strictly with the typical start codon ATG, while COX1 and ND2 were started with GTG. RSCU statistics showed that CUA, CGA, and GCC were relatively high frequency in the T. indicus mitogenome. T. cyanurus and T. indicus shared very similar mitogenomic features. All 13 PCGs of Muscicapidae mitogenomes had experienced purifying selection. Specifically, ATP8 had the highest rate of evolution (0.13296), whereas COX1 had the lowest (0.01373). The monophylies of Muscicapidae, Turdidae, and Paradoxornithidae were strongly supported. The clade of ((Muscicapidae + Turdidae) + Sturnidae) in Passeriformes was supported by both Bayesian Inference and Maximum likelihood analyses. The latest taxonomic status of many passerine birds with complex taxonomic histories were also supported. For example, Monticola gularis, T. indicus, and T. cyanurus were allocated to Turdidae in other literature; our phylogenetic topologies clearly supported their membership in Muscicapidae; Paradoxornis heudei, Suthora webbiana, S. nipalensis, and S. fulvifrons were formerly classified into Muscicapidae; we supported their membership in Paradoxornithidae; Culicicapa ceylonensis was originally classified as a member of Muscicapidae; our results are consistent with a position in Stenostiridae. Our study enriches the genetic data of T. indicus and provides new insights into the molecular phylogeny and evolution of passerine birds.

Comparison of Endogenous Alpharetroviruses (ALV-like) across Galliform Species: New Distant Proviruses

The Genus Alpharetrovirus contains viruses pathogenic mainly for chickens, forming the Avian Sarcoma and Leukosis Virus group (ASLV). Cells of most Galliform species, besides chickens, contain genetic elements (endogenous retroviruses, ERVs) that could recombine with other alpharetroviruses or express proteins, complementing defective ASLV, which may successfully replicate and cause disease. However, they are quite unknown, and only ALV-F, from ring-necked pheasants, has been partially published. Upon scrutiny of 53 genomes of different avian species, we found Alpharetrovirus-like sequences only in 12 different Galliformes, including six full-length (7.4-7.6 Kbp) and 27 partial sequences. Phylogenetic studies of the regions studied (LTR, gag, pol, and env) consistently resulted in five almost identical clades containing the same ERVs: Clade I (presently known ASLVs); Clade II (Callipepla spp. ERVs); Clade IIIa (Phasianus colchicus ERVs); Clade IIIb (Alectoris spp. ERVs); and Clade IV (Centrocercus spp. ERVs). The low pol identity scores suggested that each of these Clades may be considered a different species. ORF analysis revealed that putatively encoded proteins would be very similar in length and domains to those of other alpharetroviruses and thus potentially functional. This will undoubtedly contribute to better understanding the biology of defective viruses, especially in wild Galliformes, their evolution, and the danger they may represent for other wild species and the poultry industry.

Taxonomic Status and Phylogenetic Relationship of the Charadriidae Family Based on Complete Mitogenomes

Background

The Charadriiformes provide a good source for researching evolution owing to their diverse distribution, behavior, morphology, and ecology. However, in the Charadrii, family-level relationships remain understudied, and the monophyly of Charadriidae is also a subject of controversy.

Methods

In the present study, we generated complete mitogenomes for two species, Charadrius leschenaultii and Charadrius mongolus, which were found to be 16,905 bp and 16,844 bp in length, respectively. Among the 13 protein codon genes, we observed variation in the rate of non-synonymous substitution rates, with the slowest rate found in COI and the fastest rate observed in ATP8. The Ka/Ks ratio for all Charadriidae species was significantly lower than one, which inferred that the protein-coding genes underwent purifying selection.

Results

Phylogenetic analysis based on the genes of Cyt b, 12S and ND2 revealed that the genus Pluvialis is the sister group of three families (Haematopodidae, Ibidorhynchidae, Recurvirostridae). However, the phylogenetic analysis based on complete mitogenomes indicated that the genus Pluvialis is within the Charadriidae family.

Conclusion

This study highlights the importance of carefully selecting the number of genes used to obtain accurate estimates of the species tree. It also suggests that relying on partial mtDNA genes with fast-evolving rates may lead to misleading results when resolving the Pluvialis sister group. Future research should focus on sequencing more mitogenomes at different taxonomic levels to gain a better understanding of the features and phylogenetic relationships within the Charadriiformes order.

The draft genome of the Temminck's tragopan (Tragopan temminckii) with evolutionary implications

BACKGROUND

High-quality genome data of birds play a significant role in the systematic study of their origin and adaptive evolution. The Temminck's tragopan (Tragopan temminckii) (Galliformes, Phasianidae), a larger pheasant, is one of the most abundant and widely distributed species of the genus Tragopan, and was defined as class II of the list of national key protected wild animals in China. The absence of a sequenced genome has restricted previous evolutionary trait studies of this taxa.

RESULTS

The whole genome of the Temminck's tragopan was sequenced using Illumina and PacBio platform, and then de novo assembled and annotated. The genome size was 1.06 Gb, with a contig N50 of 4.17 Mb. A total of 117.22 Mb (11.00%) repeat sequences were identified. 16,414 genes were predicted using three methods, with 16,099 (98.08%) annotated as functional genes based on five databases. In addition, comparative genome analyses were conducted across 12 Galliformes species. The results indicated that T. temminckii was the first species to branch off from the clade containing Lophura nycthemera, Phasianus colchicus, Chrysolophus pictus, Syrmaticus mikado, Perdix hodgsoniae, and Meleagris gallopavo, with a corresponding divergence time of 31.43 million years ago (MYA). Expanded gene families associated with immune response and energy metabolism were identified. Genes and pathways associated with plumage color and feather development, immune response, and energy metabolism were found in the list of positively selected genes (PSGs).

CONCLUSIONS

A genome draft of the Temminck's tragopan was reported, genome feature and comparative genome analysis were described, and genes and pathways related to plumage color and feather development, immune response, and energy metabolism were identified. The genomic data of the Temminck's tragopan considerably contribute to the genome evolution and phylogeny of the genus Tragopan and the whole Galliformes species underlying ecological adaptation strategies.

Mitochondrial genome characteristics of six Phylloscopus species and their phylogenetic implication

The mitochondrial genomes of six Phylloscopus species-small insectivores belonging to the Phylloscopidae family-were obtained using the Illumina sequencing platform. The mitogenomes were closed circular molecules 16,922-17,007 bp in size, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two control regions (CR1 and remnant CR2). The gene orders were conserved in 35 sampled Phylloscopus mitogenomes in the GenBank database, with a gene rearrangement of cytb-trnT-CR1-trnP-nad6-trnE-remnant CR2-trnF-rrnS. The average base compositions of the six Phylloscopus mitogenomes were 29.43% A, 32.75% C, 14.68% G, and 23.10% T, with the A+T content slightly higher than that of G+C. ATG and TAA were the most frequent initiating and terminating codons, respectively. Several conserved boxes were identified in CR1, including C-string in domain I; F, E, D, and C boxes, as well as bird similarity and B boxes, in domain II; and CSB1 in domain III. Tandem repeats were observed in remnant CR2 of the Phylloscopus fuscatus and Phylloscopus proregulus mitogenomes. A phylogenetic analysis with maximum likelihood (ML) and Bayesian inference (BI) methods, based on 13 protein-coding genes and two rRNA genes, indicated that the Phylloscopus species was divided into two larger clades, with a splitting time approximately 11.06 million years ago (mya). The taxa of Phylloscopus coronatus/Phylloscopus burkii and Phylloscopus inornatus/P. proregulus were located at the basal position of the different clades. The phylogenetic result of the cox1 gene showed that Seicercus was nested within Phylloscopus. The complete set of mitogenomes of the Phylloscopus species provides potentially useful resources for the further exploration of the taxonomic status and phylogenetic history of Phylloscopidae.

A de novo assembled genome of the Tibetan Partridge (Perdix hodgsoniae) and its high-altitude adaptation

The Tibetan Partridge (Perdix hodgsoniae) is an endemic species distributed in high-altitude areas of 3600-5600 m on the Qinghai-Tibet Plateau. To explore how the species is adapted to the high elevation environment, we assembled a draft genome based on both the Illumina and PacBio sequencing platforms with its population genetics and genomics analysis. In total, 134.74 Gb short reads and 30.81 Gb long reads raw data were generated. The 1.05-Gb assembled genome had a contig N50 of 4.56 Mb, with 91.94% complete BUSCOs. The 17 457 genes were annotated, and 11.35% of the genome was composed of repeat sequences. The phylogenetic tree showed that P. hodgsoniae was located at the basal position of the clade, including Golden Pheasant (Chrysolophus pictus), Common Pheasant (Phasianus colchicus), and Mikado Pheasant (Syrmaticus mikado). We found that 1014, 2595, and 2732 of the 6641 one-to-one orthologous genes were under positive selection in P. hodgsoniae, detected using PAML, BUSTED, and aBSREL programs, respectively, of which 965 genes were common under positive selection with 3 different programs. Several positively selected genes and immunity pathways relevant to high-altitude adaptation were detected. Gene family evolution showed that 99 gene families experienced significant expansion events, while 6 gene families were under contraction. The total number of olfactory receptor genes was relatively low in P. hodgsoniae. Genomic data provide an important resource for a further study on the evolutionary history of P. hodgsoniae, which provides a new insight into its high-altitude adaptation mechanisms.

Characterization of the Complete Mitochondrial Genome of the Spotted Catfish Arius maculatus (Thunberg, 1792) and Its Phylogenetic Implications

The spotted catfish, Arius maculatus (Siluriformes), is an important economical aquaculture species inhabiting the Indian Ocean, as well as the western Pacific Ocean. The bioinformatics data in previous studies about the phylogenetic reconstruction of Siluriformes were insufficient and incomplete. In the present study, we presented a newly sequenced A. maculatus mitochondrial genome (mtDNA). The A. maculatus mtDNA was 16,710 bp in length and contained two ribosomal RNA (rRNA) genes, thirteen protein-coding genes (PCGs), twenty-two transfer RNA (tRNA) genes, and one D-loop region. The composition and order of these above genes were similar to those found in most other vertebrates. The relative synonymous codon usage (RSCU) of the 13 PCGs in A. maculatus mtDNA was consistent with that of PCGs in other published Siluriformes mtDNA. Furthermore, the average non-synonymous/synonymous mutation ratio (Ka/Ks) analysis, based on the 13 PCGs of the four Ariidae species, showed a strong purifying selection. Additionally, phylogenetic analysis, according to 13 concatenated PCG nucleotide and amino acid datasets, showed that A. maculatus and Netuma thalassina (Netuma), Occidentarius platypogon (Occidentarius), and Bagre panamensis (Bagre) were clustered as sister clade. The complete mtDNA of A. maculatus provides a helpful dataset for research on the population structure and genetic diversity of Ariidae species.

Complete mitochondrial genome of little ringed plover Charadrius dubius (Charadriiformes, Charadriidae)

This study encoded the complete mitochondrial genomic sequence of the little ringed plover Charadrius dubius. The mitochondrial genome has a total length of 16,864 bp, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. The nucleotide composition was 23.8% T, 31.6% A, 30.8% C, and 13.8% G. This study provides the basic information on the mitogenome of C. dubius and supports the understanding of mitogenomic information and its phylogenetic relationship within Charadriiformes.

Comparative mitogenomics of the genus Motacilla (Aves, Passeriformes) and its phylogenetic implications

The genus Motacilla belongs to Motacillidae (Passeriformes), where mitochondrial features are poorly understood and phylogeny is controversial. Whole mitochondrial genome (mitogenome) data and large taxon sampling are considered to be ideal strategies to obtain this information. We generated four complete mitogenomes of M.flava, M.cinerea, M.alba and Dendronanthusindicus, and made comparative analyses of Motacilla species combined with mitogenome data from GenBank, and then reconstructed phylogenetic trees based on 37 mitochondrial genes. The mitogenomes of four mitogenome sequences exhibited the same gene order observed in most Passeriformes species. Comparative analyses were performed among all six sampled Motacilla mitogenomes. The complete mitogenomes showed A-skew and C-skew. Most protein-coding genes (PCGs) start with an ATG codon and terminate with a TAA codon. The secondary structures of RNAs were similar among Motacilla and Dendronanthus. All tRNAs except for trnS(agy) could be folded into classic clover-leaf structures. Three domains and several conserved boxes were detected. Phylogenetic analysis of 90 mitogenomes of Passeriformes using maximum likelihood (ML) and Bayesian inference (BI) revealed that Motacilla was a monophyletic group. Among Motacilla species, M.flava and M.tschutschensis showed closer relationships, and M.cinerea was located in a basal position within Motacilla. These data provide important information for better understanding the mitogenomic characteristics and phylogeny of Motacilla.

Domestic chicken diversity: Origin, distribution, and adaptation

Chicken is the most numerous among the domesticated livestock species. Across cultures, religions, and societies, chicken is widely accepted with little or no taboo compared to other domestic animals. Its adaptability to diverse environmental conditions and demonstrated potential for breeding improvement provide a unique genetic resource for addressing the challenges of food security in a world impacted by climatic change and human population growth. Recent studies, shedding new knowledge on the chicken genomes, have helped reconstruct its past evolutionary history. Here, we review the literature concerning the origin, dispersion, and adaptation of domestic chicken. We highlight the role of human and natural selection in shaping the diversity of the species and provide a few examples of knowledge gaps that may be the focus of future research.

A chromosome-level genome assembly of the yellowfin seabream (Acanthopagrus latus; Hottuyn, 1782) provides insights into its osmoregulation and sex reversal

The yellowfin seabream Acanthopagrus latus is the economically most important Sparidae fish in the northern South China Sea. As euryhaline fish, they are perfect model for investigating osmoregulatory mechanisms in teleosts. Moreover, the reproductive biology of hermaphrodites has long been intriguing; however, little information is known about the molecular pathways underlying their sex change. Here, we report a chromosome level reference genome of A. latus generated by employing the PacBio single molecule sequencing technique (SMRT) and high-throughput chromosome conformation capture (Hi-C) technologies. The draft genome of yellowfin seabream was 806 Mb, with 732 Mb scaffolds anchored on 24 chromosomes. The contig N50 and scaffold N50 were 2.6 Mb and 30.17 Mb, respectively. The assembly is of high integrity and includes 92.23% universal single-copy orthologues based on benchmarking universal single-copy orthologs (BUSCO) analysis. A total of 19,631 protein-coding genes were functionally annotated in the reference genome. Moreover, ARRDC3 and GSTA gene families which related to osmoregulation underwent an extensive expansion in two euryhaline sparids fish genomes compared to other teleost genomes. Moreover, integrating sex-specific transcriptome analyses, several genes related to the transforming growth factor beta (TGF-β) signalling pathway involved in sex differentiation and development. This genomic resource will not only be valuable for studying the osmoregulatory mechanisms in estuarine fish and sex determination in hermaphrodite vertebrate species, but also provide useful genomic tools for facilitating breeding of the yellowfin seabream.

Structure and comparative analysis of the mitochondrial genomes of Liolaemus lizards with different modes of reproduction and ploidy levels

Liolaemus is the most specious genus of the Squamata lizards in South America, presenting exceptional evolutionary radiation and speciation patterns. This recent diversification complicates the formal taxonomic treatment and the phylogenetic analyses of this group, causing relationships among species to remain controversial. Here we used Next-Generation Sequencing to do a comparative analysis of the structure and organization of the complete mitochondrial genomes of three differently related species of Liolaemus and with different reproductive strategies and ploidy levels. The annotated mitochondrial genomes of ca. 17 kb are the first for the Liolaemidae family. Despite the high levels of sequence similarity among the three mitochondrial genomes over most of their lengths, the comparative analyses revealed variations at the stop codons of the protein coding genes and the structure of the tRNAs among species. The presence of a non-canonical dihydrouridine loop is a novelty for the pleurodonts iguanians. But the highest level of variability was observed in two repetitive sequences of the control region, which were responsible for most of the length heterogeneity of the mitochondrial genomes. These tandem repeats may be useful markers to analyze relationships of closely related species of Liolaemus and related genera and to conduct population and phylogenetic studies.

Chromosome level assembly reveals a unique immune gene organization and signatures of evolution in the common pheasant

The common pheasant Phasianus colchicus, belonging to the order Galliformes and family Phasianidae, is the most widespread species. Despite a long history of captivity, the domestication of this bird is still at a preliminary stage. Recently, the demand for accelerating its transformation to poultry for meat and egg production has been increasing. In this study, we assembled high quality, chromosome scale genome of the common pheasant by using PacBio long reads, next-generation short reads, and Hi-C technology. The primary assembly has contig N50 size of 1.33 Mb and scaffold N50 size of 59.46 Mb, with a total size of 0.99 Gb, resolving most macrochromosomes into single scaffolds. A total of 23,058 genes and 10.71 Mb interspersed repeats were identified, constituting 30.31% and 10.71% of the common pheasant genome, respectively. Our phylogenetic analysis revealed that the common pheasant shared common ancestors with turkey about 24.7-34.5 million years ago (Ma). Rapidly evolved gene families, as well as branch-specific positively selected genes, indicate that calcium-related genes are potentially related to the adaptive and evolutionary change of the common pheasant. Interestingly, we found that the common pheasant has a unique major histocompatibility complex B locus (MHC-B) structure: three major inversions occurred in the sequence compared with chicken MHC-B. Furthermore, we detected signals of selection in five breeds of domestic common pheasant, several of which are production-oriented.

Characterization of three new mitochondrial genomes of Coraciiformes (Megaceryle lugubris, Alcedo atthis, Halcyon smyrnensis) and insights into their phylogenetics

Coraciiformes contains more than 200 species with great differences on external morphology and life-style. The evolutionary relationships within Coraciiformes and the phylogenetic placement of Coraciiformes in Aves are still questioned. Mitochondrial genome (mitogenome) sequences are popular markers in molecular phylogenetic studies of birds. This study presented the genome characteristics of three new mitogenomes in Coraciiformes and explored the phylogenetic relationships among Coraciiformes and other five related orders with mitogenome data of 30 species. The sizes of three mitogenomes were 17,383 bp (Alcedo atthis), 17,892 bp (Halcyon smyrnensis) and 17,223 bp (Megaceryle lugubris). Each mitogenome contained one control region and 37 genes that were common in vertebrate mitogenomes. The organization of three mitogenomes was identical to the putative ancestral gene order in Aves. Among 13 available Coraciiform mitogenomes, 12 protein coding genes showed indications of negative selection, while the MT-ND6 presented sign of positive selection or relaxed purifying selection. The phylogenetic results supported that Upupidae and Bucerotidae should be separated from Coraciiformes, and that Coraciiformes is more closely related to Piciformes than to Strigiformes, Trogoniformes and Cuculiformes. Our study provide valuable data for further phylogenetic investigation of Coraciiformes.

Complete mitochondrial genome of Iniistius trivittatus and unique variation in two observed inserts between rRNA and tRNA genes in wrasses

BACKGROUND

The family Labridae made up of 519 species in the world. The functional evolution of the feeding-related jaws leaded to differentiation of species, and the pharyngeal jaw apparatus evolved independently, but evolutionary mechanism still remain unaddressed in wrasses. Mitogenomes data can be used to infer genetic diversification and investigate evolutionary history of wrasses, whereas only eight complete mitogenomes in this family have been sequenced to date. Here, we sequenced the complete mitogenomes of Iniistius trivittatus to investigate genetic differentiation among wrasse species.

RESULTS

We sequenced the complete mitogenomes of I. trivittatus using a novel PCR strategy. The I. trivittatus mitogenomes is 16,820 bp in length and includes 13 protein -coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. Compared to eight known mitochondrial genome, 2 additional noncoding regions (lengths of 121 and 107 bp), or so-called inserts, are found in the intergenic regions 12S rRNA - tRNAVal - 16S rRNA. The presumed origin of the two rare inserts is from tRNA- related retrotransposons. Compared with cytochrome b gene, the two insert sequences are highly conserved at the intraspecies level, but they showed significant variation and low similarity (< 70%) at the interspecies level. The insert events were only observed in I. trivittatus by checking the phylogenetic trees based on the complete mitogenomes of Labrida species. This finding provides evidence that in the mitogenomes, retrotransposon inserts result in intraspecific homoplasmy and interspecific heteroplasmy by natural selection and adaptation to various environments.

CONCLUSIONS

This study found additional mitogenome inserts limited in wrasse species. The rRNA genes with inserts might have experienced a selective pressure for adaptation to feeding modes. Such knowledge can enable a better understanding of molecular mechanism underlying morphological evolution in wrasses.

Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast

The whole mitochondrial genome ofLateolabrax maculatus(Cuvier, 1828) was used to investigate the reasons for the observed patterns of genetic differentiation among 12 populations in northern and southern China. The haplotype diversity and nucleotide diversity ofL. maculatuswere 0.998 and 0.00169, respectively. Pairwise FSTvalues between populations ranged from 0.001 to 0.429, correlating positively with geographic distance. Genetic structure analysis and haplotype network analysis indicated that these populations were split into two groups, in agreement with geographic segregation and environment. Tajima’s D values, Fu’s Fs tests and Bayesian skyline plot (BSP) indicated that a demographic expansion event may have occurred in the history ofL. maculatus. Through selection pressure analysis, we found evidence of significant negative selection at the ATP6, ND3, Cytb, COX3, COX2 and COX1 genes. In our hypotheses, this study implied that demographic events and selection of local environmental conditions, including temperature, are responsible for population divergence. These findings are a step forward toward the understanding of the genetic basis of differentiation and adaptation, as well as conservation ofL. maculatus.

The wild species genome ancestry of domestic chickens

BACKGROUND

Hybridisation and introgression play key roles in the evolutionary history of animal species. They are commonly observed within several orders in wild birds. The domestic chicken Gallus gallus domesticus is the most common livestock species. More than 65 billion chickens are raised annually to produce meat and 80 million metric tons of egg for global human consumption by the commercial sector. Unravelling the origin of its genetic diversity has major application for sustainable breeding improvement programmes.

RESULTS

In this study, we report genome-wide analyses for signatures of introgression between indigenous domestic village chicken and the four wild Gallus species. We first assess the genome-wide phylogeny and divergence time across the genus Gallus. Genome-wide sequence divergence analysis supports a sister relationship between the Grey junglefowl G. sonneratii and Ceylon junglefowl G. lafayettii. Both species form a clade that is sister to the Red junglefowl G. gallus, with the Green junglefowl G. varius the most ancient lineage within the genus. We reveal extensive bidirectional introgression between the Grey junglefowl and the domestic chicken and to a much lesser extent with the Ceylon junglefowl. We identify a single case of Green junglefowl introgression. These introgressed regions include genes with biological functions related to development and immune system.

CONCLUSIONS

Our study shows that while the Red junglefowl is the main ancestral species, introgressive hybridisation episodes have impacted the genome and contributed to the diversity of the domestic chicken, although likely at different levels across its geographic range.

Mitochondrial genes associated with pyrethroid resistance revealed by mitochondrial genome and transcriptome analyses in the malaria vector Anopheles sinensis (Diptera: Culicidae)

BACKGROUND

Insecticides are still the main method of mosquito control, but mosquito resistance presents a large obstacle. The function of mitochondrial genes in the evolution of insecticide resistance is still poorly understood. Pyrethroid is the most commonly used insecticide, and Anopheles sinensis is an important malaria vector in China and Southeast Asia. In this study, we investigated the mitochondrial genes associated with pyrethroid resistance through their genetic and expression variation based on analyses of transcriptomes and 36 individuals with resequencing in three geographical populations in China.

RESULTS

The nucleotide diversity (Pi) in 18 resistant individuals was much lower than that in 18 susceptible individuals, which suggests that some sites experienced purifying selection subject to pyrethroid stress. Ka/Ks and amino acid analyses showed that ND4 experienced positive selection and had 23 amino acid mutations due to pyrethroid stress. These mutations might change the ND4 structure and function and thus alter the efficiency of the respiratory chain. ND5 was significantly upregulated, and ATP8 was significantly downregulated in these three pyrethroid resistant populations, which suggests that these two genes function in the production and maintenance of pyrethroid resistance. There are differences in mitochondrial genes involved in pyrethroid resistance among these three populations.

CONCLUSION

This is the first study to reveal the association of mitochondrial genes in the evolution of insecticide resistance through amino acid mutation and expression patterns and can help us further understand insecticide resistance mechanisms. © 2019 Society of Chemical Industry.

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.

Complete mitochondrial genome sequence of the Himalayan Griffon, Gyps himalayensis (Accipitriformes: Accipitridae): Sequence, structure, and phylogenetic analyses

This is the first study to describe the mitochondrial genome of the Himalayan Griffon, Gyps himalayensis, which is an Old World vulture belonging to the family Accipitridae and occurring along the Himalayas and the adjoining Tibetan Plateau. Its mitogenome is a closed circular molecule 17,381 bp in size containing 13 protein-coding genes, 22 tRNA coding genes, two rRNA-coding genes, a control region (CR), and an extra pseudo-control region (CCR) that are conserved in most Accipitridae mitogenomes. The overall base composition of the G. himalayensis mitogenome is 24.55% A, 29.49% T, 31.59% C, and 14.37% G, which is typical for bird mitochondrial genomes. The alignment of the Accipitridae species control regions showed high levels of genetic variation and abundant AT content. At the 5' end of the domain I region, a long continuous poly-C sequence was found. Two tandem repeats were found in the pseudo-control regions. Phylogenetic analysis with Bayesian inference and maximum likelihood based on 13 protein-coding genes indicated that the relationships at the family level were (Falconidae + (Cathartidae + (Sagittariidae + (Accipitridae + Pandionidae))). In the Accipitridae clade, G. himalayensis is more closely related to Aegypius monachus than to Spilornis cheela. The complete mitogenome of G. himalayensis provides a potentially useful resource for further exploration of the taxonomic status and phylogenetic history of Gyps species.

The complete mitochondrial genome of Helan Mountain chukar Alectoris chukar potanini (Galliformes: Phasianidae)

The complete mitochondrial genome of Helan Mountain chukar (Alectoris chukar potanini) was first determined. The genome was 16,685 bp in length, comprising 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a putative control region. The phylogenetic analysis based on the complete mitochondrial genome sequences revealed a close relationship between A. chukar potanini and Tetraogallus tibetanus. This work is expected to provide a set of fundamental data on further genetic studies of this protected species.

The complete mitochondrial genome of Melon thrips, Thrips palmi (Thripinae): Comparative analysis

The melon thrips, Thrips palmi is a serious pest and vector for plant viruses on a wide range of economically important crops. DNA barcoding evidenced the presence of cryptic diversity in T. palmi and that warrants exhaustive molecular studies. Our present study is on decoding the first complete mitochondrial genome of T. palmi (15,333 bp) through next-generation sequencing (NGS). The T. palmi mt genome contains 37 genes, including 13 Protein coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA (tRNAs), and two control regions (CRs). The majority strand of T. palmi revealed 78.29% A+T content, and 21.72% G+C content with positive AT skew (0.09) and negative GC skew (-0.06). The ATN initiation codons were observed in 12 PCGs except for cox1 which have unique start codon (TTG). The relative synonymous codon usage (RSCU) analysis revealed Phe, Leu, Ile, Tyr, Asn, Lys and Met were the most frequently used amino acids in all PCGs. The codon (CGG) which is assigned to Arginine in most insects but absent in T. palmi. The Ka/Ks ratio ranges from 0.078 in cox1 to 0.913 in atp8. We observed the typical cloverleaf secondary structure in most of the tRNA genes with a few exceptions; absence of DHU stem and loop in trnV and trnS, absence of DHU loop in trnE, lack of T-arm and loop in trnN. The T. palmi gene order (GO) was compared with ancestral GO and observed an extensive gene arrangement in PCGs, tRNAs and rRNAs. The cox2 gene was separated from the gene block 'cox2-trnL2' in T. palmi as compared with the other thrips mt genomes, including ancestor GO. Further, the nad1, trnQ, trnC, trnL1, trnV, trnF, rrnS, and rrnL were inversely transpositioned in T. palmi GO. The gene blocks 'trnQ-trnS2-trnD' and 'trnN-trnE-trnS1-trnL1' seems to be genus specific. The T. palmi mt genome contained 24 intergenic spacer regions and 12 overlapping regions. The 62 bp of CR2 shows the similarity with CR1 indicating a possible duplication. The occurrence of multiple CRs in thrips mt genomes seems to be a derived trait which needs further investigation. Although, the study depicted extensive gene rearrangements in T. palmi mt genome, but the negative GC skew reflects only strand asymmetry. Both the ML and BI phylogenetic trees revealed the close relationships of Thrips with Scirtothrips as compared to Frankliniella. Thus, more mt genomes of the diverse thrips species are required to understand the in-depth phylogenetic and evolutionary relationships.

Complete mitogenome of Anopheles sinensis and mitochondrial insertion segments in the nuclear genomes of 19 mosquito species

Anopheles sinensis is a major malarial vector in China and Southeast Asia. The mitochondria is involved in many important biological functions. Nuclear mitochondrial DNA segments (NUMTs) are common in eukaryotic organisms, but their characteristics are poorly understood. We sequenced and analyzed the complete mitochondrial (mt) genome of An. sinensis. The mt genome is 15,418 bp long and contains 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs and a large non-coding region. Its gene arrangement is similar to previously published mosquito mt genomes. We identified and analyzed the NUMTs of 19 mosquito species with both nuclear genomes and mt genome sequences. The number, total length and density of NUMTs are significantly correlated with genome size. About half of NUMTs are short (< 200 bp), but larger genomes can house longer NUMTs. NUMTs may help explain genome size expansion in mosquitoes. The expansion due to mitochondrial insertion segments is variable in different insect groups. PCGs are transferred to nuclear genomes at a higher frequency in mosquitoes, but NUMT origination is more different than in mammals. Larger-sized nuclear genomes have longer mt genome sequences in both mosquitoes and mammals. The study provides a foundation for the functional research of mitochondrial genes in An. sinensis and helps us understand the characteristics and origin of NUMTs and the potential contribution to genome expansion.

Glaciation-based isolation contributed to speciation in a Palearctic alpine biodiversity hotspot: Evidence from endemic species

Organisms are unevenly distributed on earth and the evolutionary drivers of that have puzzled ecologists and evolutionary biologists for over a century. Even though many studies have focused on the mechanisms of unevenly distributed fauna and flora, there remains much to learn about the evolutionary drivers behind biodiversity hotspots. In the Tibetan Plateau and Hengduan Mountains, a biodiversity hotspot in the Palearctic realm, alpine uplift cannot be the driver for recent speciation (<two million years ago), researchers broadly refer to climatic oscillations driven biodiversity, however, the specific individual roles of glaciation and inter-glaciation periods in promoting biodiversity is unclear. The current study focuses on investigating whether recent speciation between two close-related avian species (White eared pheasant, Crossoptilon crossoptilon and Tibetan eared pheasant, C. harmani) was driven by glaciation-based isolation or by dispersal during inter-glaciation. To answer this question, we combined Sanger sequencing and next-generation sequencing technology to estimate population structure, phylogeny, divergence time, demographic history and potential historical distributions for C. crossoptilon and C. harmani, which are endemic to China. We found that the divergence time between these two species and within C. crossoptilon are both during glaciation periods. During glaciation periods, both C. harmani and C. crossoptilon experienced isolated distributions and extreme bottlenecks. The results of this study suggest that glaciation-based isolation contributed to recent speciation in the Tibetan Plateau and Hengduan Mountains, and sheds light on our understanding of the evolutionary mechanisms that contributed to the formation of Palearctic alpine biodiversity hotspots and unevenly distributed species richness pattern.

The mitochondrial genome of the Kentish Plover Charadrius alexandrinus (Charadriiformes: Charadriidae) and phylogenetic analysis of Charadrii

The suborder Charadrii (Aves: Charadriiformes), one of the most species-rich radiations within shorebirds, which contains good source for studies of ecology, behaviour and evolution. The resources of mitogenome have rapidly accumulated in recent years due to the advanced genomic sequencing, while suborder Charadrii's mitogenome has not been well studied. The primary objective of this study was to determine the complete mitogenome sequence of Charadrius alexandrinus, and investigated the evolutionary relationship within Charadrii. The mitogenome of C. alexandrinus were generated by amplification of overlapping Polymerase Chain Reaction (PCR) fragments. In this study, we determined the complete mitogenome sequence of the Kentish Plover Charadrius alexandrinus, and comparative analysed 11 species to illustrate mitogenomes structure and investigated their evolutionary relationship within Charadrii. The Charadrii mitogenomes displayed moderate size variation, the mean size was 16,944 bp (SD = 182, n = 11), and most of the size variation due to mutations in the control region (CR). Nucleotide composition was consistently biased towards AT rich, and the A+T content also varies for each protein-coding genes. The variation in ATP8 and COIII was the highest and lowest respectively. The GC skew was always negative, with the ATP8 had higher value than other regions. The average uncorrected pairwise distances revealed heterogeneity of evolutionary rate for each gene, the COIII, COI and COII have slow evolutionary rate, whereas the gene of ATP8 has the relative fast rate. The highest value of Ks and Ka were ND1 and ATP8, and the ratios of Ka/Ks are lower than 0.27, indicating that they were under purifying selection. Phylogenomic analysis based on the complete mitochondrial genomes strongly supported the monophyly of the suborder Charadrii. This study improves our understanding of mitogenome structure and evolution, and providing further insights into phylogeny and taxonomy in Charadrii. In future, sequencing more mitogenomes from various taxonomic levels will significantly improve our understanding of phylogenetic relationships within Charadrii.

Complete Mitochondrial Genome of Dinorhynchus dybowskyi (Hemiptera: Pentatomidae: Asopinae) and Phylogenetic Analysis of Pentatomomorpha Species

Dinorhynchus dybowskyi (Hemiptera: Pentatomidae: Asopinae) is used as a biological control agent against various insect pests for its predatory. In the present study, the complete mitochondrial genome (mitogenome) of the species was sequenced using the next-generation sequencing technology. The results showed that the mitogenome is 15,952 bp long, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and a control region. Furthermore, the gene order and orientation of this mitogenome are identical to those of most heteropterans. There are 21 intergenic spacers (of length 1-28 bp) and 13 overlapping regions (of length 1-23 bp) throughout the genome. The control region is 1,291 bp long. The start codon of the PCGs is ATN, except cox1 (TTG), and stop codon is TAA, except nad1 (TAG). The 22 tRNAs exhibit a typical cloverleaf secondary structure, except trnS1, which lacks a dihydrouridine (DHU) arm and trnV, where the DHU arm forms a simple loop. The analyses based on nucleotide sequences of the 13 PCGs by Bayesian Inference and maximum likelihood methods. The results support the monophyly of five superfamilies Aradoidea, Pentatomoidea, Pyrrhocoroidea, Lygaeoidea, and Coreoidea. Within Pentatomoidea, the relationship observed is as follows: (Plataspidae + Urostylididae) + (Pentatomidae + (Acanthosomatidae + (Cydnidae + (Scutelleridae + (Dinidoridae + Tessaratomidae))))), and D. dybowskyi was placed in Pentatomidae and close to Eurydema gebleri.

Sequencing and characterization of the complete mitochondrial genome of Japanese Swellshark (Cephalloscyllium umbratile)

To further comprehend the genome features of Cephalloscyllium umbratile (Carcharhiniformes), an endangered species, the complete mitochondrial DNA (mtDNA) was firstly sequenced and annotated. The full-length mtDNA of C. umbratile was 16,697 bp and contained ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region. Each PCG was initiated by an authoritative ATN codon, except for COX1 initiated by a GTG codon. Seven of 13 PCGs had a typical TAA termination codon, while others terminated with a single T or TA. Moreover, the relative synonymous codon usage of the 13 PCGs was consistent with that of other published Carcharhiniformes. All tRNA genes had typical clover-leaf secondary structures, except for tRNA-Ser (GCT), which lacked the dihydrouridine 'DHU' arm. Furthermore, the analysis of the average Ka/Ks in the 13 PCGs of three Carcharhiniformes species indicated a strong purifying selection within this group. In addition, phylogenetic analysis revealed that C. umbratile was closely related to Glyphis glyphis and Glyphis garricki. Our data supply a useful resource for further studies on genetic diversity and population structure of C. umbratile.

Rapid and recent diversification patterns in Anseriformes birds: Inferred from molecular phylogeny and diversification analyses

The Anseriformes is a well-known and widely distributed bird order, with more than 150 species in the world. This paper aims to revise the classification, determine the phylogenetic relationships and diversification patterns in Anseriformes by exploring the Cyt b, ND2, COI genes and the complete mitochondrial genomes (mito-genomes). Molecular phylogeny and genetic distance analyses suggest that the Dendrocygna species should be considered as an independent family, Dendrocygnidae, rather than a member of Anatidae. Molecular timescale analyses suggests that the ancestral diversification occurred during the Early Eocene Climatic Optimum (58 ~ 50 Ma). Furthermore, diversification analyses showed that, after a long period of constant diversification, the median initial speciation rate was accelerated three times, and finally increased to approximately 0.3 sp/My. In the present study, both molecular phylogeny and diversification analyses results support that Anseriformes birds underwent rapid and recent diversification in their evolutionary history, especially in modern ducks, which show extreme diversification during the Plio-Pleistocene (~ 5.3 Ma). Therefore, our study support that the Plio-Pleistocene climate fluctuations are likely to have played a significant role in promoting the recent diversification for Anseriformes.

The role of niche divergence and geographic arrangement in the speciation of Eared Pheasants (Crossoptilon, Hodgson 1938)

One of the most contentious theories in current ecology is the ecological niche conservatism, which is defined as conservatism among closely related species; however, the ecological niche can also be shifted, as documented in several cases. Genetic drift and ecological divergent selection may cause ecological niche divergence. The current study aims to test whether the ecological niche is conserved or divergent and to determine the main factor that drives ecological niche divergence or conservation. We analyzed the phylogenetic relationship, ecological niche model (ENM) and demographic history of Eared Pheasants in the genus Crossoptilon (Galliformes: Phasianidae) to test niche conservatism with respect to different geographically distributed patterns. The phylogenetic relationship was reconstructed using ∗BEAST with mitochondrial cytochrome b (cyt b) and 44 unlinked autosomal exonic loci, and ENMs were reconstructed in MAXENT using an average of 41 occurrence sites in each species and 22 bioclimatic variables. A background similarity test was used to detect whether the ecological niche is conserved. Demographic history was estimated using the isolation with migration (IM) model. We found that there was asymmetric gene flow between the allopatric sister species Crossoptilon mantchuricum and C. auritum and the parapatric sister species C. harmani and C. crossoptilon. We found that ecological niches were divergent, not conserved, between C. mantchuricum and C. auritum, which began to diverge at approximately 0.3 million years ago. However, the ecological niches were conserved between C. crossoptilon and C. harmani, which gradually diverged approximately half a million years ago. Ecological niches can be either conserved or divergent, and ecological divergent selection for local adaptation is probably an important factor that promotes and maintains niche divergence in the face of gene flow. This study provides a better understanding of the role that divergent selection has in the initial speciation process. The platform combined demographic processes and ecological niches to offer new insights into the mechanism of biogeography patterns.

The mitochondrial genome of pin-tailed snipe Gallinago stenura, and its implications for the phylogeny of Charadriiformes

The Charadriiformes, among the most diverse orders of bird, is a good source to research on evolution. The mitochondrial genome sequencing database has rapidly increased in recent years, while Charadriiformes mitogenome has not been well studied. In this research, we determined the complete mitogenome sequence of Gallinago stenura, and comparatively analysed 20 mitogenomes of Charadriiformes. The mitogenomes display moderate size variation, and most of variation due to mutations in the control region. In 13 protein-coding genes, we found: 1. The GC skews are always negative, while the negative AT skews are found in 5 genes, 2. The average uncorrected pairwise distances reveal heterogeneity of evolutionary rate for each gene, 3. The ATG and TAA, respectively, are observed the most commonly start and stop codon. The highest dN/dS is detected for ATP8 (0.16) among Charadriiformes, while the lowest for COI (0.01), indicating that 13 protein-coding genes are evolving under the purifying selection. Predicted secondary structures of tRNAs indicate that the sequences and structures of anticodon, amino acceptor, and TψC arms are highly conserved, and most nucleotide variation is restricted to dihydrouridine arms with obvious indel polymorphisms. A total of 15 conserved sequence boxes were recognized in the control regions, and the 4 bp (5'-AAAC-3') and 7 bp (5'- AAACAAC -3') repeat sequences occurred frequently. Phylogenomic analysis based on the nearly complete mitochondrial genomes strongly supported the monophyly of the order, and the suborder Charadrii is at the basal of Charadriiformes. Moreover, our results well resolved the complexity family-level relationships and clearly depicted the evolutionary processes of Charadriiformes, based on 12 mitochondrial protein-coding genes from 18 families. This study improves our understanding of mitogenomic structure and evolution, which can provide further insights into our understanding of phylogeny and taxonomy in Charadriiformes.

Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda)

BACKGROUND

Whole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups. In the case of decapod crustaceans, several infraorders, including Axiidea (ghost shrimps, sponge shrimps, and mud lobsters) and Caridea (true shrimps) are still under-represented, limiting comprehensive phylogenetic studies that utilize mitogenomic information.

METHODS

Sequence reads from partial genome scans were generated using the Illumina MiSeq platform and mitogenome sequences were assembled from these low coverage reads. In addition to examining phylogenetic relationships within the three infraorders, Axiidea, Gebiidea, and Caridea, we also investigated the diversity and frequency of codon usage bias and mitogenome gene order rearrangements.

RESULTS

We present new mitogenome sequences for five shrimp species from Australia that includes two ghost shrimps, Callianassa ceramica and Trypaea australiensis, along with three caridean shrimps, Macrobrachium bullatum, Alpheus lobidens, and Caridina cf. nilotica. Strong differences in codon usage were discovered among the three infraorders and significant gene order rearrangements were observed. While the gene order rearrangements are congruent with the inferred phylogenetic relationships and consistent with taxonomic classification, they are unevenly distributed within and among the three infraorders.

DISCUSSION

Our findings suggest potential for mitogenome rearrangements to be useful phylogenetic markers for decapod crustaceans and at the same time raise important questions concerning the drivers of mitogenome evolution in different decapod crustacean lineages.

Determining the distribution loss of brown eared-pheasant (Crossoptilon mantchuricum) using historical data and potential distribution estimates

We analyzed the synchronous relationship between forest cover and species distribution to explain the contraction in the distribution range of the brown eared-pheasant (Crossoptilon mantchuricum) in China. Historical resources can provide effective records for reconstructing long-term distribution dynamics. The brown eared-pheasant's historical distribution from 25 to 1947 CE, which included the three provinces of Shaanxi, Shanxi, and Hebei based on this species' habitat selection criteria, the history of the forests, ancient climate change records, and fossil data. The current species distribution covers Shaanxi, Shanxi, and Hebei provinces, as well as Beijing city, while Shanxi remains the center of the distribution area. MaxEnt model indicated that the suitable conditions of the brown eared-pheasant had retreated to the western regions of Shanxi and that the historical distribution area had reduced synchronously with the disappearance of local forest cover in Shanxi. We built a correlative relationship between the presence/absence of brown eared-pheasants and forest coverage and found that forest coverage in the north, northeast, central, and southeast areas of the Shanxi province were all less than 10% in 1911. Wild brown eared-pheasants are stable in the Luliang Mountains, where forest coverage reached 13.2% in 2000. Consequently, we concluded that the distribution of this species is primarily determined by vegetation conditions and that forest cover was the most significant determining factor.

The Mitochondrial Genomes of Aquila fasciata and Buteo lagopus (Aves, Accipitriformes): Sequence, Structure and Phylogenetic Analyses

The family Accipitridae is one of the largest groups of non-passerine birds, including 68 genera and 243 species globally distributed. In the present study, we determined the complete mitochondrial sequences of two species of accipitrid, namely Aquila fasciata and Buteo lagopus, and conducted a comparative mitogenome analysis across the family. The mitogenome length of A. fasciata and B. lagopus are 18,513 and 18,559 bp with an A + T content of 54.2% and 55.0%, respectively. For both the two accipitrid birds mtDNAs, obvious positive AT-skew and negative GC-skew biases were detected for all 12 PCGs encoded by the H strand, whereas the reverse was found in MT-ND6 encoded by the L strand. One extra nucleotide'C'is present at the position 174 of MT-ND3 gene of A. fasciata, which is not observed at that of B. lagopus. Six conserved sequence boxes in the Domain II, named boxes F, E, D, C, CSBa, and CSBb, respectively, were recognized in the CRs of A. fasciata and B. lagopus. Rates and patterns of mitochondrial gene evolution within Accipitridae were also estimated. The highest dN/dS was detected for the MT-ATP8 gene (0.32493) among Accipitridae, while the lowest for the MT-CO1 gene (0.01415). Mitophylogenetic analysis supported the robust monophyly of Accipitriformes, and Cathartidae was basal to the balance of the order. Moreover, we performed phylogenetic analyses using two other data sets (two mitochondrial loci, and combined nuclear and mitochondrial loci). Our results indicate that the subfamily Aquilinae and all currently polytypic genera of this subfamily are monophyletic. These two novel mtDNA data will be useful in refining the phylogenetic relationships and evolutionary processes of Accipitriformes.