J Syst Evol ›› 2022, Vol. 60 ›› Issue (4): 835-847.DOI: 10.1111/jse.12709

• Research Articles • Previous Articles     Next Articles

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

Zheng‐Zhen Wang1,2, Zi‐Xiao Guo1*, Cai‐Rong Zhong3, Hao‐Min Lyu1, Xin‐Nian Li1, Norman C. Duke4, and Su‐Hua Shi1*   

  1. 1 State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat‐sen University, Guangzhou 510275, China
    2 Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
    3 Hainan Dongzhai Harbor National Nature Reserve, Haikou 571129, China
    4 Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University, Townsville, QLD 4811, Australia

    *Authors for correspondence. Zi‐Xiao Guo. E‐mail: guozx8@mail.sysu.edu.cn; Su‐Hua Shi. E‐mail: lssssh@mail.sysu.edu.cn
  • Received:2020-10-31 Accepted:2020-11-18 Online:2020-11-23 Published:2022-07-01


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.

Key words: Avicennia marina, gene flow, mangrove, population genetics, speciation, subspecies