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Genomic landscape of subspecies defined by phenotypic criteria:Analyses of the mangrove species complex, Avicennia marina
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  • Zhengzhen Wang,
  • Zixiao Guo,
  • Cairong Zhong,
  • Haomin Lyu,
  • Xinnian Li,
  • Norman Duke,
  • SUHUA SHI
Zhengzhen Wang
Sun Yat-Sen University
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Zixiao Guo
Sun Yat-Sen University
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Cairong Zhong
Hainan Dongzhai Harbor National Nature Reserve
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Haomin Lyu
Sun Yat-Sen University
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Xinnian Li
Sun Yat-Sen University
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Norman Duke
James Cook University
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SUHUA SHI
Sun Yat-sen University
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Abstract

Subspecies designation is widely used to describe taxa below species but above geographical populations. What patterns of genomic variation is expected if taxa are designated as subspecies? In this study, we carry out such a survey on the mangrove tree Avicennia marina 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 while 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. This “ambiguity” is expected at a stage between structured populations and full species, thus the observed patterns strengthen the subspecies designation. We propose that subspecies designation is informative in predicting genomic landscape of divergences and useful in making conservation decisions.