Complete mitochondrial genomes provide current refined phylogenomic hypotheses for relationships among ten Hirundo species

Abstract

Hirundo is the most species-rich genus of the passerine swallow family (Hirundinidae) and has a cosmopolitan distribution. Here we report the complete, annotated mitochondrial genomes for 25 individuals from 10 of the 14 extant Hirundo species; these include representatives from four subspecies of the barn swallow, H. rustica. Mitogenomes were conserved in size, ranging from 18,500 to 18,700 base pairs. They all contained 13 protein-coding regions, 22 tRNAs, a control region, and large and small ribosomal subunits. Phylogenetic analysis resolved most of the relationships between the studied species and subspecies which were largely consistent with previously published trees. Several new relationships were observed within the phylogeny that could have only been discovered with the increased amount of genetic material. This study represents the largest Hirundo mitochondrial phylogeny to date, and could serve as a vital tool for other studies focusing on the evolution of the Hirundo genus.

The Mitogenome Relationships and Phylogeography of Barn Swallows (Hirundo rustica)

“…To gain a broader view of the haplogroup distribution in the different subspecies, including some not included in our study, we compared the combined ND2 and CYB gene variation of our mitogenomes with that reported in 119 barn swallow mtDNAs available from previous studies ( Dor et al 2010 , 2012 ; Liu et al 2015 , direct submission; Keepers et al 2016 , direct submission; Smith et al 2018 ; Feng et al 2020 ; Carter et al 2020 ) ( fig. 3 ).…”

“…Colors identify the different subspecies. The numbers on the branches indicate the number of distinguishing mutations while the numbers in parentheses refer to the following publication sources: 1) this study; 2) Carter et al (2020) ; 3) Dor et al (2010) ; 4) Dor et al (2012) ; 5) Liu et al (2015) , direct submission; 6) Keepers et al (2016) , direct submission; 7) Smith et al (2018) ; 8) Feng et al (2020) . Sequences not covering the aforementioned ND2 and CYB gene ranges were not included, as well as sequences that harbored gaps at informative nucleotides.…”

“…Sequences not covering the aforementioned ND2 and CYB gene ranges were not included, as well as sequences that harbored gaps at informative nucleotides. The two mtDNAs forming the rather long sub-branch (6 mutations) within A1a2, one from H. r. savignii , and one from H. r. transitiva ( Carter et al 2020 ), most likely contain erroneous mutations as their mitogenome sequences harbored NUMTs (see Materials and Methods). A similar problem characterizes the H. r. gutturalis sequence KP148840 ( Liu et al 2015 , direct submission) with its 81 mutations branch.…”

“…However, ND2 and CYB sequences are available also for three H. r. tytleri specimens ( Dor et al 2010 ; Carter et al 2020 ), an Asian subspecies that was not included in our survey of entire mitogenomes. The three H. r. tytleri partial mtDNA sequences appear to form a private sub-haplogroup within D1, which we named D1 tytleri ( fig.…”

“…Despite the valuable genetic insights provided by these studies, the assessment of only a rather short segment of the barn swallow mtDNA limits their phylogenetic resolution and the understanding of this species’ origin and spread. A finer phylogenetic resolution can be achieved by sequencing the entire mitogenome, an approach that has been employed for humans and many other animal species ( Achilli et al 2008 , 2012 ; Behar et al 2012 ; Miao et al 2013 ; Morin et al 2015 ; Battaglia et al 2016 ; Barth et al 2017 ; Peng et al 2018 ; Cole et al 2019 ; de Manuel et al 2020 ; Niedziałkowska et al 2021 ) and recently pursued also in H. rustica ( Carter et al 2020 ). Here, we exploited next generation sequencing (NGS) to obtain 411 complete mitogenomes, mainly from the European H. r. rustica , but also from other subspecies.…”