Population genomic evidence for radiative divergence of four Orychophragmus (Brassicaceae) species in eastern Asia

Abstract

Radiation rather than bifurcating divergence has been inferred through a number of phylogenetic analyses using different DNA fragments. However, such inferences have rarely been tested by examining alternative hypotheses based on population genomic data. In this study, we sequenced the transcriptomes of 32 individuals from 13 populations of four Orychophragmus spp. (Brassicaceae) to investigate their divergence history. Cluster and population structure analyses recovered four distinct genetic clusters without any genetic mixture. Most orthologous genes produced unresolved bifurcating interspecific relationships with a star phylogeny. The resolved gene trees were highly inconsistent with each another in reconstructing interspecific relationships. Population genomic analyses suggested unexpectedly high genetic divergence and a lack of gene flow between the four species. We examined radiation vs. bifurcating divergence between these four species based on coalescent modelling tests of population genomic data. Our statistical tests supported a radiation of these species from a common ancestor at almost the same time, rejecting stepwise bifurcating interspecific divergence with time. This nearly simultaneous radiation was dated to the Quaternary, during which climate changes are suggested to have promoted species diversity in eastern Asia. Our results highlight the importance of population genomic data and statistical tests in deciphering interspecific relationships and tracing the divergence histories of closely related species.

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“…Affinities: Leptospermum repo belongs to the northern Te Ika a Maui / North Island clade of L. scoparium s. l. (Buys et al, 2019;Koot et al in sub.). Those plants (L. scoparium var.…”

“…Collectively then, the various Aotearoa / New Zealand flora treatments of Leptospermum scoparium s. l. have retained the impression of a highly variable and morphologically "plastic" species, initially worthy of further infraspecific taxonomic segregation but now apparently not. In part, this modern view reflects the conservative approach to species limits adopted by Joseph Dalton Hooker and Thomas Cheeseman, whilst the treatment meted out by Allan (1961) seems to have been strongly influenced by his mentor Leonard Cockayne, an opinionated, politically astute though rather forceful botanist (Thomson, 1983(Thomson, , 2021; de Lange, 2019). Cockayne had by the early 1900s developed a strong dislike of taxonomy, taxonomic concepts and most Aotearoa / New Zealand based taxonomists (Cockayne, 1917b(Cockayne, , 1919(Cockayne, , 1926Moore, 1967;Thomson, 1983Thomson, , 1990Thomson, , 2021de Lange, 2019) such that he was happy to relegate the Leptospermum scoparium varieties established by Aiton, Hooker, and Kirk to mere "footnotes" in the annals of that species, though notably he retained his own contribution to the taxonomic resolution of that species variation, var.…”

“…The question is why did Cockayne have this view? The answer lies in the fact that while Cockayne had little interest in taxonomy, he exerted a strong influence on how he felt the discipline should be practised in Aotearoa / New Zealand (Cockayne, 1926;Moore, 1967;Thomson, 1990;de Lange, 2019), central to this was his view that taxonomic conclusion must result from a comprehensive analysis not only of morphological variation but also whether that variation was represented by "true breeding races" (Cockayne, 1917a(Cockayne, , 1919(Cockayne, , 1926. For Leptospermum scoparium then, Cockayne felt that the variation people were describing, required formal testing using what he called "experimental taxonomy" whereby the stability of characters in a plant were tested by cultivation.…”

“…Now that Leptospermum scoparium has significant economic value (McDonald et al, 2018;Taunton, 2021), there is increased interest in resolving whether the species (in the strict sense) is endemic to Aotearoa / New Zealand or not. Buys et al (2019) undertook a limited Fig. 1.…”

“…scoparium (c) (AK191319; "Waikato peat bog") on the basis that it is now threatened and that its taxonomic status needed resolution (de Lange et al, 2018). The inclusion of this race within the northern Te Ika a Maui / North Island clade of Buys et al (2019) suggests a relationship to Leptospermum scoparium var. incanum, and two other races L. aff.…”