Mitochondrial genome of the critically endangered Baer’s Pochard, Aythya baeri, and its phylogenetic relationship with other Anatidae species

Liu, Dawei; Zhou, Yihong; Fei, Yi-Ling; Chun-ping, Xie; Hou, Sen

doi:10.1038/s41598-021-03868-7

Cited by 10 publications

(6 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The complete mitochondrial genome sequence of A. marila is a typical closed-circular molecule with a size of 16,617 bp and has been deposited in GenBank under the accession number OP326610. The mitochondrial genome contents of A. marila are similar to those of most other published Aythya, which includes 37 genes [36], 13 PCGs, 22 tRNAs, 2 rRNAs (rrnL and rrnS), and a control region (D-loop) (Figure 1). Among the 37 fragment genes, a PCG (ND6) and 8 tRNA genes (tRNA-Ala, tRNA-Cys, tRNA-Glu, tRNA-Gln, tRNA-Asn, tRNA-Pro, tRNA-Ser2, and tRNA-Tyr) were located on the light strand (L-strand), whereas the CR and the remaining 28 genes were located on the heavy strand (H-strand).…”

Section: Genome Structure and Compositionsupporting

confidence: 63%

See 1 more Smart Citation

Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Aythya marila

Zhang

Xia

Gao

et al. 2023

Genes

View full text Add to dashboard Cite

Aythya marila is a large diving duck belonging to the family Anatidae. However, the phylogenetic relationship among these Aythya species remains unclear due to the presence of extensive interspecific hybridization events within the Aythya genus. Here, we sequenced and annotated the complete mitochondrial genome of A. marila, which contained 22 tRNAs, 13 protein-coding genes (PCGs), 2 ribosomal RNAs, and 1 D-loop, with a length of 16,617 bp. The sizes of the PCGs ranged from 297 to 1824 bp and were all, except for ND6, located on the heavy chain (H). ATG and TAA were the most common start and termination codons of the 13 PCGs, respectively. The fastest- and slowest-evolving genes were ATP8 and COI, respectively. Codon usage analysis indicated that CUA, AUC, GCC, UUC, CUC, and ACC were the six most frequent codons. The nucleotide diversity values indicated a high level of genetic diversity in A. marila. FST analysis suggested a widespread gene exchange between A. baeri and A. nyroca. Moreover, phylogenetic reconstructions using the mitochondrial genomes of all available Anatidae species showed that, in addition to A. marila, four major clades among the Anatidae (Dendrocygninae, Oxyurinae, Anserinae, and Anatinae) were closely related to A. fuligula. Overall, this study provides valuable information on the evolution of A. marila and new insights into the phylogeny of Anatidae.

show abstract

Section: Genome Structure and Compositionsupporting

confidence: 63%

“…The most frequently used codons (amino acids) were CUA (317), AUC (208), GCC (173), UUC (167), CUC (166), and ACC (156). Except for Trp and Met, all amino acids have their preferred codons, which is a unique feature of A. marila compared to other Aythya species identified to date [ 36 ].…”

Section: Resultsmentioning

confidence: 99%

Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Aythya marila

Zhang

Xia

Gao

et al. 2023

Genes

View full text Add to dashboard Cite

show abstract

“…Mitochondrial DNA (mtDNA) has specific characteristics such as a simple structure, maternal inheritance, rapid evolutionary speed, and almost no recombination, making it the best molecular genetic marker for studying a species' origin, evolution, and classification [14]. mtDNA is a type of DNA that exists in all animal cells.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Genetic Diversity and Population Structure of Endemic Endangered Goose (Anser cygnoides) Breeds Based on Mitochondrial CYTB

Qi,

Fan,

et al. 2024

Animals

View full text Add to dashboard Cite

The analysis of the genetic diversity and historical dynamics of endemic endangered goose breeds structure has attracted great interest. Although various aspects of the goose breed structure have been elucidated, there is still insufficient research on the genetic basis of endemic endangered Chinese goose breeds. In this study, we collected blood samples from Lingxiang White (LX), Yan (YE), Yangjiang (YJ), Wuzong (WZ), Xupu (XP), and Baizi (BZ) geese (Anser cygnoides) and used Sanger sequencing to determine the partial sequence of the cytochrome b (CYTB) gene in a total of 180 geese. A total of 117 polymorphic sites were detected in the 707 bp sequence of the mtDNA CYTB gene after shearing and correction, accounting for approximately 16.55% of the entire sequence. The AT content (51.03%) of the processed sequence was slightly higher than the GC content (48.97%), indicating a preference for purine bases. The YJ, YE, and WZ breeds had the highest population genetic diversity, with a haplotype diversity greater than 0.9 (Hd > 0.9) and average population nucleotide difference of 8.01 (K > 8.01). A total of 81 haplotypes were detected and divided into six major branches. Among the six goose breeds, there were frequent genetic exchanges among LX, YJ, YE, and WZ geese (Nm > 15.00). We analyzed the distribution of base-mismatch differences in goose breeds and tested their historical dynamics for neutrality in Tajima’s D and Fu’s Fs. For YJ and WZ geese, Tajima’s D > 0, but the difference was not significant (p > 0.05). The actual values for the two breeds exhibited multimodal Poisson distributions. The population patterns of the WZ and YJ geese are purportedly relatively stable, and the breeds have not experienced population expansions or bottleneck effects, which is consistent with the neutrality test results. This study provides new insights into the diverse genetic origins and historical dynamics that sustain endemic endangered goose breeds.

show abstract

“…According to the literature, during the breeding season, they primarily inhabited the Amur and Ussuri river basins in the Russian Far East and Northeast China. In the winter migration period, they were mainly observed in eastern and southern China, India, Bangladesh, and Myanmar [26]. Their diet primarily comprises aquatic plants like Ceratophyllum demersum, Potamogeton crispus, Najas marina, as well as tender leaves from plants like Nelumbo nucifera, Typha orientalis, and Sagittaria trifolia.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Suitable Habitats for Birds Based on MaxEnt and Google Earth Engine—A Case Study of Baer’s Pochard (Aythya baeri) in Baiyangdian, China

Tian,

Huo,

et al. 2023

Remote Sensing

View full text Add to dashboard Cite

The combined impacts of rapid urbanization and climate change pose significant threats to global biodiversity. To counter these threats, the establishment of appropriate habitats is becoming pivotal for species preservation. Due to positive ecological interventions, Baer’s Pochard (Aythya baeri), a critically endangered avian species per the International Union for Conservation of Nature (IUCN) classification, has made a remarkable resurgence in the wetlands of Baiyangdian (BYD). BYD, located in Xiong’an New Area, central North China, is the largest wetland and an ideal habitat for rare bird species. Our study focuses on identifying ideal habitats within BYD to further its conservation. To this end, unmanned aerial vehicles (UAV) integrated with GPS functionalities were utilized to collect occurrence data for the species. Furthermore, the Google Earth Engine (GEE) provided access to high-resolution, real-time satellite imagery. Our model exhibited substantial reliability, reflected by area under the curve (AUC) values of 0.917 and 0.934 for breeding and migration periods, respectively. During the breeding phase, the prime habitat for Baer’s Pochard spans 162 km2, predominantly encompassing regions like Xiaobaiyangdian (XBYD), Zhaozadian (ZZD), Damaidian (DMD), and Shaochedian (SCD). Factors such as Distance to towns and Landcover predominantly influence breeding habitat selection. In the migration phase, ideal regions covered an expanse of 124 km2, highlighting areas like northern and eastern SCD, the northwestern side of Datian Village (DTV) and Beitian Village (BTV) Fuhe Wetland (FHW), and Xiaoyihe Wetland (XYHW). The predominant determinants for migration habitat are Distance to towns and Wetness. These insights offer a fundamental foundation for the conservation and management strategies of Baer’s Pochard in BYD, presenting a roadmap for future conservation endeavors.

show abstract

Mitochondrial genome of the critically endangered Baer’s Pochard, Aythya baeri, and its phylogenetic relationship with other Anatidae species

Cited by 10 publications

References 53 publications

Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Aythya marila

Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Aythya marila

Analysis of Genetic Diversity and Population Structure of Endemic Endangered Goose (Anser cygnoides) Breeds Based on Mitochondrial CYTB

Evaluation of Suitable Habitats for Birds Based on MaxEnt and Google Earth Engine—A Case Study of Baer’s Pochard (Aythya baeri) in Baiyangdian, China

Contact Info

Product

Resources

About