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

Abstract

The barn swallow (Hirundo rustica) poses a number of fascinating scientific questions, including the taxonomic status of postulated subspecies. Here, we obtained and assessed the sequence variation of 411 complete mitogenomes, mainly from the European H. r. rustica, but other subspecies as well. In almost every case, we observed subspecies-specific haplogroups, which we employed together with estimated radiation times to postulate a model for the geographical and temporal worldwide spread of the species. The female barn swallow carrying the Hirundo rustica ancestral mitogenome left Africa (or its vicinity) around 280 thousand years ago (kya), and her descendants expanded first into Eurasia and then, at least 51 kya, into the Americas, from where a relatively recent (<20 kya) back migration to Asia took place. The exception to the haplogroup subspecies specificity is represented by the sedentary Levantine H. r. transitiva that extensively shares haplogroup A with the migratory European H. r. rustica and, to a lesser extent, haplogroup B with the Egyptian H. r. savignii. Our data indicate that rustica and transitiva most likely derive from a sedentary Levantine population source that split at the end of the Younger Dryas (YD) (11.7 kya). Since then, however, transitiva received genetic inputs from and admixed with both the closely related rustica and the adjacent savignii. Demographic analyses confirm this species' strong link with climate fluctuations and human activities making it an excellent indicator for monitoring and assessing the impact of current global changes on wildlife.

Keywords: Hirundo rustica subspecies; barn swallow phylogeny; haplogroups; mitogenome.

Fig. 1.

Schematic MP phylogeny of Hirundo rustica mitogenomes. This tree was built using the entire mitogenome coding-region (15,601 bps; nps 1–14,859, nps 16,068–16740, nps 18,075–18,143) of 411 barn swallows. It was rooted using H. angolensis (NC_050287) and H. aethiopica (NC_050293) reference mitogenomes (not displayed). Haplogroups are represented as triangles whose bases are proportional to the number of mitogenomes. HrAM refers to the Hirundo rustica Ancestral Mitogenome. Different colors were assigned only to major branches. Bootstrap values (1000 iterations) are shown. The timeline (log₁₀) at the bottom refers to the Bayesian coalescence times of supplementary table S3, Supplementary Material online. The insets (A) and (B) illustrate the frequencies of the major haplogroups in the different sampling locations. Inset (B) details frequencies in Italy and Switzerland.

Fig. 2.

Schematic MP phylogeny of haplogroup A mitogenomes. This tree was built using the coding regions of 388 mitogenomes belonging to haplogroup A (fig. 1) and was rooted with the available H. angolensis (NC_050287) and H. aethiopica (NC_050293) reference mitogenomes (not displayed). Mitogenomes marked in black are from H. r. transitiva specimens sampled in Israel, the one in white (see also red arrow) is from a H. r. gutturalis sample (no. 258) from China, while all others are from H. r. rustica. Main haplogroup affiliations are shown, with branches colored according to fig. 1. Branch lengths are proportional to the number of nucleotide substitutions. Bootstrap values (1000 iterations) are shown only for the deepest nodes. Six country-specific sub-haplogroups are also shown. They are the oldest found in the reported country. Additional details about samples and mitogenomes are provided in supplementary table S1, Supplementary Material online.

Fig. 3.

MP phylogeny of Hirundo rustica ND2 and CYB gene sequences. This tree includes 155 barn swallows from different subspecies for which both ND2 and CYB gene sequences were available. A total of 119 are from the literature and the remaining were selected from our mitogenome dataset as follows: the first five mitogenomes that we obtained from H. r. rustica (nos. 1, 20, 35, 136, 302) and the one from Formenti et al. (2019) (no. 151), all mitogenomes from the uncommon sub-haplogroups of A (A1b, A2, A3; nos. 383–388) and all mitogenomes belonging to haplogroups B, C and D (nos. 389–411) (supplementary table S1, Supplementary Material online). Sequences encompass 2,075 bps, 1,017 bps of ND2 (nps 3,980–4,996) and 1,058 bps of CYB (nps 13,696–14,753). The tree was rooted using the H. aethiopica and H. angolensis reference mitogenomes. Main haplogroup and sub-haplogroup affiliations are shown. 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. 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.

Fig. 4.

BSP of haplogroup A mitogenomes. The plot considers the 388 haplogroup A mitogenomes listed in supplementary table S1, Supplementary Material online. These include all H. r. rustica mitogenomes and 92% of those from H. r. transitiva. The black line indicates the median estimate of the effective population size and the blue shading shows the 95% highest posterior density limits. The time axis is limited to 50 kya, beyond which the curve remains flat.

Fig. 5.

A model for the geographical and temporal spread of barn swallows. Map showing time divergence and hypothetical splits and diffusion routes of barn swallow haplogroups prior to the Younger Dryas and the subsequent climatic changes. The dashed grey circle indicates the possible homeland of the Hirundo rustica ancestral mitogenome (HrAM), while the other dashed circles indicate zones where two haplogroups are currently found, possibly indicating recent admixture between subspecies. Colors indicate the breeding ranges of the eight postulated barn swallow subspecies, while striped areas indicate wintering ranges (modified from Turner 2006).