Microsatellites retain phylogenetic signals across genera in eucalypts (Myrtaceae)

Abstract

The utility of microsatellites (SSRs) in reconstructing phylogenies is largely confined to studies below the genus level, due to the potential of homoplasy resulting from allele size range constraints and poor SSR transferability among divergent taxa. The eucalypt genus Corymbia has been shown to be monophyletic using morphological characters, however, analyses of intergenic spacer sequences have resulted in contradictory hypotheses-showing the genus as either equivocal or paraphyletic. To assess SSR utility in higher order phylogeny in the family Myrtaceae, phylogenetic relationships of the bloodwood eucalypts Corymbia and related genera were investigated using eight polymorphic SSRs. Repeat size variation using the average square and Nei's distance were congruent and showed Corymbia to be a monophyletic group, supporting morphological characters and a recent combination of the internal and external transcribed spacers dataset. SSRs are selectively neutral and provide data at multiple genomic regions, thus may explain why SSRs retained informative phylogenetic signals despite deep divergences. We show that where the problems of size-range constraints, high mutation rates and size homoplasy are addressed, SSRs might resolve problematic phylogenies of taxa that have diverged for as long as three million generations or 30 million years.

Microsatellite allele length variations in inter-specific hybrids of Eucalyptus

“…Microsatellite allele sequencing results of parents and their hybrids show almost same repeat type, corroborating the earlier results in eucalypt species (Ochieng et al 2007, He et al 2012. Variations in fl anking regions and repeat numbers refl ect the occurrence of mutational processes in both the repeat and fl anking regions.…”

Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus

“…The vagaries of phylogenies built using Tribe Leptospermeae a single gene were clearly apparent because, in subsequent studies using microsatellites, nuclear and/or plastid DNA sequence, Corymbia and Angophora were monophyletic sister groups (Ochieng et al 2007a, b;Parra-O et al 2006. This work led to the discovery of multiple nuclear ribosomal pseudogenes within the eucalypt group with differing phylogenetic signals revealed by their ITS sequence potentially complicating phylogenetic reconstruction through comparison of paralogous sequences (Bayly and Ladiges 2007;Bayly et al 2008;Ochieng et al 2007a). Monophyly of Corymbia was evident with a non-functional paralogue of ITS (Bayly et al 2008) but not with the functional form sequenced by Steane et al (2002).…”

“…However, this is the level at which molecular phylogenetics and population genetics (see Section "Molecular population genetics") intersect, with continuous variation often occurring between closely related taxa. Population genetic approaches are increasingly being used to resolve the phylogenetic affinities and differentiation of species, particularly at the intra-series levels (e.g., Byrne 2008;Cook et al 2008;Drummond et al 2000;McKinnon et al 2005;McKinnon et al 2008;Ochieng et al 2007a;Percy et al 2008). In eucalypts, the frequent occurrence of geographic replacement series involving closely related taxa argues for recent speciation through allopatric processes Byrne 2008;Ladiges 1997).…”

Phylogenomics of the green ash eucalypts (Myrtaceae): a tale of reticulate evolution and misidentification

“…et al 2006Parra-O. et al , 2009Ochieng et al 2007b). However, although standard DNA markers have successfully been used to resolve relationships at higher taxonomic levels within Eucalyptus, these have generally been unsuccessful in resolving relationships among closely related species (McKinnon et al 2008).…”