A novel mitochondrial genome of Arborophila and new insight into Arborophila evolutionary history

Abstract

The lineage of the Bar-backed Partridge (Arborophila brunneopectus) was investigated to determine the phylogenetic relationships within Arborophila as the species is centrally distributed within an area covered by the distributions of 22 South-east Asian hill partridge species. The complete mitochondrial genome (mitogenome) of A. brunneopectus was determined and compared with four other hill partridge species mitogenomes. NADH subunit genes are radical in hill partridge mitogenomes and contain the most potential positive selective sites around where variable sites are abundant. Together with 44 other mitogenomes of closely related species, we reconstructed highly resolved phylogenetic trees using maximum likelihood (ML) and Bayesian inference (BI) analyses and calculated the divergence and dispersal history of Arborophila using combined datasets composed of their 13-protein coding sequences. Arborophila is reportedly be the oldest group in Phasianidae whose ancestors probably originated in Asia. A. rufipectus shares a closer relationship with A. ardens and A. brunneopectus compared to A. gingica and A. rufogularis, and such relationships were supported and profiled by NADH dehydrogenase subunit 5 (ND5). The intragenus divergence of all five Arborophila species occurred in the Miocene (16.84~5.69 Mya) when there were periods of climate cooling. We propose that these cooling events in the Miocene forced hill partridges from higher to lower altitudes, which led to geographic isolation and speciation. We demonstrated that the apparently deleterious +1 frameshift mutation in NADH dehydrogenase subunit 3 (ND3) found in all Arborophila is an ancient trait that has been eliminated in some younger lineages, such as Passeriformes. It is unclear of the biological advantages of this elimination for the relevant taxa and this requires further investigation.

The complete mitochondrial genome of Black-streaked Scimitar Babbler Pomatorhinus dedekeni (Passeriformes: Timaliidae)

“…Among these genes, ND6 and eight tRNA genes (tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNA-Ser, tRNA-Glu, and tRNA-Pro) located on the light strand (L-strand), whereas other genes located on the heavy strand (H-strand). The insertion of an extra cytosine at position 147 of the ND3 protein-coding sequence and pseudo-control region as in many birds (Song et al 2015;Yan et al 2017;Jiang et al 2019) were not found in P. dedekeni mitogenome.…”

The complete mitochondrial genome of Indian Cuckoo Cuculus micropterus (Aves: Cuculiformes)

“… 1998 ; Yan et al. 2017 ). However, the base in C. micropterus is replaced by a single ‘A’, which is consistent with the result of some other species of Cuculidae like Cuculus canorus bakeri (Qiu et al.…”

“…The PCGs have four types of termination codon, including TAA for COX2, ND3, ND4L, ND6, ATP6, ATP8 and Cytb; AGA for ND1 and ND5; AGG for COX1; and an incomplete stop codon T for ND2, ND4, and COX3. It is found that some birds have an extra single 'C' insertion in ND3 (Mindell et al 1998;Yan et al 2017). However, the base in C. micropterus is replaced by a single 'A', which is consistent with the result of some other species of Cuculidae like Cuculus canorus bakeri (Qiu et al 2019), C. poliocephalus (Wang et al 2016) and Eudynamys taitensis (Pratt et al 2009).…”

The complete mitochondrial genome of Robin Accentor Prunella rubeculoides (Passeriformes: Prunellidea)

“…Some birds have been found to have single insertion mutations in ND3, but the P. rubeculoides has WOC (without extra Cytosine) ND3 (Yan et al. 2017 ). Unlike these mitochondrial genomes of many other bird, which have a pseudo—control region (Song et al.…”

“…The PCGs have six types of termination codon, including TAA for ATP8, ND3, ND4 and Cytb, TAG for ATP6, AGA for ND1 and ND5, AGG for COX1, 'T--' for COX2, COX3, ND4 and ND6, and 'TA-' for ND2. Some birds have been found to have single insertion mutations in ND3, but the P. rubeculoides has WOC (without extra Cytosine) ND3 (Yan et al 2017). Unlike these mitochondrial genomes of many other bird, which have a pseudo-control region (Song et al 2015), the mitochondrial…”