Response to Tibayrenc and Ayala: reproductive clonality in protozoan pathogens – truth or artefact?

Abstract

Tibayrenc and Ayala raised several interesting objections to an opinion piece we recently published in Molecular Ecology (Ramirez & Llewellyn 2014). Our piece examined the value of an alternative perspective to their theory of predominant clonal evolution (PCE) on the prevalence and importance of genetic exchange in parasitic protozoa. In particular, our aim was to establish whether population genetic signatures of clonality in parasites were representative of true biological/evolutionary processes or artefacts of inadequate tools and inappropriate or inadequate sampling. We address Tibayrenc and Ayala's criticisms and make a detailed response. In doing so, we deny the consensus that Tibayrenc and Ayala claim around their views and dismiss much of the language which Tibayrenc and Ayala have introduced to this debate as either arbitrary or inaccurate. We strongly reject accusations that we misunderstood and misquoted the work of others. We do not think the PCE provides a useful framework for understanding existing parasite population structures. Furthermore, on the eve of the population genomic era, we strongly urge Tibayrenc and Ayala to wait for the forthcoming wealth of high-resolution data before considering whether it is appropriate to refine or re-iterate their PCE hypothesis.

Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?

“…This definition is widely accepted by many authors working on general evolution as well as on population genetics and evolution of micropathogens, including protozoa, fungi, bacteria and viruses. Our claim that many authors accept this definition, and accept also the view that selfing/inbreeding is a particular case of clonality (see A Debate in the Debate: Unisex/Selfing/ Inbreeding versus 'Strict' Clonality) is not based mainly on self-citations (Ramírez and Llewellyn, 2015;Rougeron et al, 2015), but rather on the thorough analysis of a large number of articles (Table 2). Many times, authors consider scarcity of recombination, clonality and asexuality as Arnaud-Haond et al…”

“…This is what we have called the 'clonality threshold', beyond which clonal evolution becomes preponderant, that is, efficiently counters the impact of recombination and causes this growing phylogenetic signal. This clonality threshold concept is therefore neither 'pseudoquantitative' nor 'vague', and 'predominant' is not open to 'wide interpretation' either (Ramírez and Llewellyn, 2015). The clonality threshold relies on the observation of a growing phylogenetic signal, which is easy to verify with appropriate data (see later).…”

“…Many examples aimed at challenging the RD model either rely on improper samples or denote a miscomprehension of the model (Ramírez and Llelwellyn, 2014). This model indeed has been considered as largely relying on insufficient samples and being an 'unnecessary oversimplification' (Ramírez and Llewellyn, 2015). However, all models are based on simplifications of diversified situations in which a common denominator can be evidenced.…”

“…3, middle), and that they also undergo predominant clonal evolution. hypothesis) to the RD model, which is definitely not falsified by occasional recombination occurring without erasing PCE features within the nearclades (Ramírez and Llewellyn, 2015). As we have insisted (Tibayrenc and Ayala, 2013), when exploring PCE within each near-clade, it is important to adapt the resolution of the markers and to carefully consider population sizes.…”

“…'far from being a clonal species' (Coscoll a et al, 2011), 'extensive genetic exchange' (Caugant and Maiden, 2009), 'gross' incongruences (between phylogenetic trees) (Messenger et al, 2012), 'widespread genetic exchange' Ramírez and Lllewellyn, 2014), 'intense lateral exchange of genetic information' (Ramírez and Llewellyn, 2015), 'genetic exchange is a fairly common phenomenon' (Lima et al, 2014), 'genetic exchange playing a major role in T. cruzi population structure' (Minning et al, 2011), and others. It is impossible to totally discard such expressions in the scientific literature.…”