How, not if, is the question mycologists should be asking about DNA-based typification

Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings chal-lenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants

Costs of Inducible Defence along a Resource Gradient

In addition to having constitutive defence traits, many organisms also respond to predation by phenotypic plasticity. In order for plasticity to be adaptive, induced defences should incur a benefit to the organism in, for example, decreased risk of predation. However, the production of defence traits may include costs in fitness components such as growth, time to reproduction, or fecundity. To test the hypothesis that the expression of phenotypic plasticity incurs costs, we performed a common garden experiment with a freshwater snail, Radix balthica, a species known to change morphology in the presence of molluscivorous fish. We measured a number of predator-induced morphological and behavioural defence traits in snails that we reared in the presence or absence of chemical cues from fish. Further, we quantified the costs of plasticity in fitness characters related to fecundity and growth. Since plastic responses may be inhibited under limited resource conditions, we reared snails in different densities and thereby levels of competition. Snails exposed to predator cues grew rounder and thicker shells, traits confirmed to be adaptive in environments with fish. Defence traits were consistently expressed independent of density, suggesting strong selection from predatory molluscivorous fish. However, the expression of defence traits resulted in reduced growth rate and fecundity, particularly with limited resources. Our results suggest full defence in predator related traits regardless of resource availability, and costs of defence consequently paid in traits related to fitness

Showing defensive traits at increasing snail densities (2, 4, 8, 16 and 24 snails) in treatments with no fish (open squares) and in the presence of fish (closed diamonds).

<p>The effects of shell shape in PC 1 (a) and PC 2 (b). The visualized outline shell shape is on the left side. Positive scores in PC 1 have an outline with a narrow aperture and a long apex and negative scores generates an outline with a wider body whorl and a larger shell opening, as well as a lower apex. For PC 2, a widened second whorl and a narrower aperture generate positive scores, while a narrowing of this area and a widening of the aperture generate negative scores. Size corrected shell crushing resistance (c) and the proportion of snails showing predator avoidance behaviour (d). Values are mean and SE.</p

Showing fitness related traits at increasing snail densities (2, 4, 8, 16 and 24 snails) in treatments with no fish (open squares) and in the presence of fish (closed diamonds).

<p>The dependent variables are: final size of the snails (a), averaged individual fecundity (b), time in days to first reproduction (c). Values are mean and SE.</p

Results showing treatment (control, predator), density (2, 4, 8, 16, 24 snails) and the interaction term treatment×density.

<p>Traits above the dotted line are defensive traits and traits below are more fitness related traits. Bold figures indicate significant effects.</p

Trait correlations for low and high densities.

<p>The low density including 2 snails (a), while the high density encompassing 24 snails (b). Lines designate a significant correlations between traits, and stars indicate P-values: *<0.05; **<0.01; ***<0.001.</p

How, not if, is the question mycologists should be asking about DNA-based typification

Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings chal-lenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.ISSN:1314-4049ISSN:1314-405