DNA-based species delimitation in algae

Abstract

Given the problems of species delimitation in algae using morphology or sexual compatibility, molecular data are becoming the standard for delimiting species and testing their traditional boundaries. The idea that species are separately evolving metapopulation lineages, along with theoretical progress in phylogenetic and population genetic analyses, has led to the development of new methods of species delimitation. We review these recent developments in DNA-based species delimitation methods, and discuss how they have changed and continue to change our understanding of algal species boundaries. Although single-locus approaches have proven effective for a first rapid and large-scale assessment of species diversity, species delimitation based on single gene trees falls short due to gene tree-species tree incongruence, caused by confounding processes like incomplete lineage sorting, trans-species polymorphism, hybridization and introgression. Data from unlinked loci and multi-species coalescent methods, which combine principles from phylogenetics and population genetics, may now be able to account for these complicating factors. Several of these methods also provide statistical support regarding species boundaries, which is important because speciation is a process and therefore uncertainty about precise species boundaries is inevitable in recently diverged lineages.

Genetic diversity in chrysophytes: Comparison of different gene markers

“…In phylogenetic studies, gene markers like the SSU rRNA gene, sometimes in combination with other markers, are regularly used to reveal phylogenetic relationships (Jo et al 2013;Škaloud et al 2014). Our results confirm previous results that the SSU offers good phylogenetic resolution on genus level, but is in part too conserved to differentiate between closely related lineages as already reported from different other organisms (Piganeau et al 2011;leliaert et al 2014; showed that the COI region is suitable to distinguish Dinobryon divergens from D. bavaricum strains, which is nearly impossible based on SSU rRNA gene analyses. Our analyses confirmed the high degree of variation for chrysophytes.…”

“…The application of molecular markers for distinguishing protist species and/or assessing diversity patterns in different environments is nowadays an established method (krienitz & Bock 2012;leliaert et al 2014). In phylogenetic studies, gene markers like the SSU rRNA gene, sometimes in combination with other markers, are regularly used to reveal phylogenetic relationships (Jo et al 2013;Škaloud et al 2014).…”

Symbiodinium necroappetenssp. nov. (Dinophyceae): an opportunist ‘zooxanthella’ found in bleached and diseased tissues of Caribbean reef corals

“…Theoretically, most members of a species should share the same dominant rDNA sequences, assuming our understanding about the mechanism of concerted evolution is correct (Dover, 1986). However, concerted evolution (under a stochastic model) may conservatively maintain the dominant rDNA sequence in the genomes of individuals that form distinct populations which diverged ecologically and evolutionarily long ago (Leliaert et al, 2014). Recent phylogeographic evidence based on independent genetic markers indicate that ITS rDNA can evolve slowly and require many millions of years before nucleotide sequence differences (in the dominant intragenomic variants) arise between two species (Thornhill et al, 2014).…”

Progress on research on rodents and rodent-borne zoonoses in South-east Asia

“…This estimated number of species is in agreement with the number of species described for this part of mainland South-east Asia (Thailand, Laos, Cambodia), with some exceptions (see Musser and Carleton 2005), in particular within the Berylmys and Rattus genera or Crunomys diversion. However, regardless of the method used, species delimitation depends on the evolutionary history of the species group and may fail due to incomplete lineage sorting, trans-species polymorphism, hybridisation and introgression (Leliaert et al 2014).…”