Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae)

Abstract

The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded species: M. excelsa, widespread from West to East Africa, and M. regia, endemic to West Africa. We combined information from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences, and morphological systematics to identify significant evolutionary units and infer their evolutionary and biogeographical history. We detected five geographically coherent genetic clusters using nSSRs and three levels of genetic differentiation. First, one West African cluster matched perfectly with the morphospecies M. regia that formed a monophyletic clade at both DNA sequences. Second, a West African M. excelsa cluster formed a monophyletic group at plastid DNA and was more related to M. regia than to Central African M. excelsa, but shared many haplotypes with the latter at nuclear DNA. Third, three Central African clusters appeared little differentiated and shared most of their haplotypes. Although gene tree paraphyly could suggest a single species in Milicia following the phylogenetic species concept, the existence of mutual haplotypic exclusivity and nonadmixed genetic clusters in the contact area of the two taxa indicate strong reproductive isolation and, thus, two species following the biological species concept. Molecular dating of the first divergence events showed that speciation in Milicia is ancient (Tertiary), indicating that long-living tree taxa exhibiting genetic speciation may remain similar morphologically.

Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences – a case study in the tree genus Milicia

“…Both species are wind pollinated and seeds are dispersed by bats and parrots [25]. Genetic evidence showed that they constitute two reproductively isolated groups despite existence of paraphyly in M. excelsa [26]. In West Africa, M. regia is considered as an endangered species due to overexploitation for timber production and deforestation, and is listed as a vulnerable species by the IUCN [24].…”

“…These 435 individuals were genotyped at seven nuclear microsatellites following [26] and at 67 biallelic nuclear SNP loci. These SNP markers were developed using an approach of the Thünen Institute for Forest Genetics (TIFG).…”

“…In a subset of 190 individuals, we further sequenced two intergenic regions of the plastid genome, psbA-trnH and trnC-ycf6, and one genic region of the nuclear genome, At103 , the only polymorphic region observed among 12 tested gene regions in Milicia [37]. The protocol for sequencing is described in [26]. …”

“…Phylogeographical and phylogenetical investigations by [25, 26] confirmed the existence of two morphologically similar species: M. regia , found West Africa from Senegal to Ghana, and M. excelsa , found from West to East Africa and part of Austral Africa. Several lines of evidence suggest that our current phylogeographic knowledge might be incomplete.…”

“…First, relying on morphological characterization, the renowned botanist Auguste Chevalier claimed that M. regia naturally occurs in some parts of Gabon [27]. Second, East Africa was poorly represented in [26] while it might harbour genetically original populations, as reported in other widely distributed African plant species (e.g. [28, 29]).…”