Recombinant Mitochondrial Genomes Reveal Recent Interspecific Hybridization between Invasive Salangid Fishes

Abstract

The interspecific recombination of the mitochondrial (mt) genome, if not an experimental artifact, may result from interbreeding of species with broken reproductive barriers, which, in turn, is a frequent consequence of human activities including species translocations, habitat modifications, and climate change. This issue, however, has not been addressed for Protosalanx chinensis and other commercially important and, simultaneously, invasive salangid fishes that were the product of successful aquaculture in China. To assess the probability of interspecific hybridization, we analyzed the patterns of diversity and recombination in the complete mitochondrial (mt) genomes of these fishes using the GenBank resources. A sliding window analysis revealed a non-uniform distribution of the intraspecific differences in P. chinensis with four highly pronounced peaks of divergence centered at the COI, ND4L-ND4, and ND5 genes, and also at the control region. The corresponding divergent regions in P. chinensis show a high sequence similarity (99–100%) to the related salangid fishes, Neosalanx tangkahkeii and N. anderssoni. This observation suggests that the divergent regions of P. chinensis may represent a recombinant mitochondrial DNA (mtDNA) containing mt genome fragments belonging to different salangid species. Indeed, four, highly significant (pairwise homoplasy index test, P < 0.00001) signals of recombination have been revealed at coordinates closely corresponding to the divergent regions. The recombinant fragments are, however, not fixed, and different mt genomes of P. chinensis are mosaic, containing different numbers of recombinant events. These facts, along with the high similarity or full identity of the recombinant fragments between the donor and the recipient sequences, indicate a recent interspecific hybridization between P. chinensis and two Neosalanx species. Alternative hypotheses, including taxonomical misidentifications, sequence misalignments, DNA contamination, and/or artificial PCR recombinants, are not supported by the data. The recombinant fragments revealed in our study represent diagnostic genetic markers for the identification and distinguishing of hybrids, which can be used to control the invasive dynamics of hybrid salangid fishes.

Purifying selection and intraspecies recombination may drive the speciation in Crassostrea: evidence from complete mitochondria sequence ofCrassostrea hongkongensisand comparative genomic analysis

“…However, several intraspecies recombination events were observed during this analysis. This type of phenomenon was also noticed during the study of salangid fishes (Balakirev, 2022). Only four out of seven species of Crassostrea actively engaged during recombination.…”

“…This recombination also leads to hybridization followed by the emergence of sub-species within the lineage (Ladoukakis & Zouros, 2017). Recently, several recombination events were observed within the mtDNA of salangid fishes that led to inter-specific hybridization (Balakirev, 2022).…”

“…This recombination also leads to hybridization followed by the emergence of sub-species within the lineage (Ladoukakis & Zouros, 2017). Recently, several recombination events were observed within the mtDNA of salangid fishes that led to inter-specific hybridization (Balakirev, 2022). The recombination generally occurs through homologous recombination (intermolecular) or non-homologous recombination (intramolecular) during the recent stages of spermatogenesis (Kraytsberg et al, 2004).…”

“…The recombination generally occurs through homologous recombination (intermolecular) or non-homologous recombination (intramolecular) during the recent stages of spermatogenesis (Kraytsberg et al, 2004). Furthermore, repeats are also considered a hot spot for recombination within the mitochondria of plants, animals, and yeast (Balakirev, 2022; Gantenbein et al, 2005; Tsaousis et al, 2005). Therefore, we searched for the presence of recombination within the mtDNA of Crassostrea.…”

“…However, its information within Crassostrea is limited. Furthermore, both inter and intraspecific recombination observed in several animals, that regulate speciation (Balakirev, 2022; Gantenbein et al, 2005; Tsaousis et al, 2005). However, in Crassostrea, no information is still available concerning the recombination process.…”