Genomic variation patterns of subspecies defined by phenotypic criteria: Analyses of the mangrove species complex, Avicennia marina

Abstract

Subspecies is used to designate taxa below species but above geographical populations. What patterns of genomic variation are expected if taxa are designated as subspecies? In this study, we carry out such a survey on the mangrove tree Avicennia marina (Forssk.) Vierh. of the Indo-West Pacific coasts. This species has three subspecies, distinguished by morphological traits and geographical distribution. We collected samples from 16 populations (577 individuals) covering all three subspecies and sequenced 94 nuclear genes. We reveal comprehensive genetic divergence among subspecies, generally higher than among geographical populations within subspecies. The level of genetic diversity differs among the three subspecies, possibly hinting at a degree of separation among their gene pools. We observed that divergence varies from locus to locus across the genome. A small portion of the genome is most informative about subspecies delineation, whereas the rest is undifferentiated or slightly differentiated, hinting at uneven gene flow and incomplete isolation. The three subspecies likely split simultaneously with gene flow among lineages. This reticulate evolution results in some discordance between morphology and genetics in areas of population contact. In short, A. marina subspecies show species-like patterns in some respects and population-like patterns in others. We propose that the subspecies designated in A. marina are informative in predicting genetic divergences and useful in making conservation decisions.

Population subdivision promoted by a sea‐level‐change‐driven bottleneck: A glimpse from the evolutionary history of the mangrove plant Aegiceras corniculatum

“…mucronata (Yan et al, 2016), Av . marina (Wang et al, 2021), Sonneratia alba (Yang et al, 2017), S . caseolaris (Yang et al, 2016), Ceriops tagal (Huang et al, 2012), C .…”

“…He et al validated the accuracy of this method to infer haplotypes by sequencing individuals using the Sanger method. The details associated with using this method have been described in a previous publication (Wang et al, 2021). We obtained 392 gene segments, among which 84 gene segments were longer than 300 bp.…”

“…Genetic discontinuity between the Indian ocean and Pacific Ocean sides of Sundaland has been observed in R. apiculata (Guo et al, 2016), R. mucronata (Yan et al, 2016), Av. marina (Wang et al, 2021), Sonneratia alba (Yang et al, 2017), S. caseolaris (Yang et al, 2016), Ceriops tagal (Huang et al, 2012), C. decandra (Huang et al, 2008), Xylocarpus species , Lumnitzera racemosa (Li et al, 2016), Bruguiera gymnorhiza (Minobe et al, 2010;Urashi et al, 2013), Excoecaria agallocha , Heritiera littoralis (Banerjee et al, 2020), Scaevola taccada (Banerjee et al, 2021) and Acanthus ilicifolus (Guo et al, 2020). In this study, the Malay Peninsula was again identified to isolate populations of Ae.…”

“…Such pattern has been observed in the species of R. apiculata (Guo et al, 2016), R. stylosa (Yan et al, 2016), S. alba (Yang et al, 2017), S. caseolaris (Yang et al, 2016), Av. marina (Wang et al, 2021), C. tagal (Huang et al, 2008(Huang et al, , 2012, C. decandra (Huang et al, 2008), X. granatum , and L. racemosa (Li et al, 2016). This water barrier appears less dominant that populations of several species are not isolated, e.g.…”

“…Northeastern Borneo and surrounding populations in S. alba (Yang et al, 2017) and Av. marina (Wang et al, 2021). Such population structures in the smaller geographical ranges are highly likely generated by a bottleneck process.…”