| 1. |
- Zamora, Juan Carlos, et al.
(författare)
-
Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
-
Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
-
Tidskriftsartikel (refereegranskat)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
|
|
| 2. |
- Baker, J., et al.
(författare)
-
On the establishment of a mutant
- 2020
-
Ingår i: Journal of Mathematical Biology. - : Springer Science and Business Media LLC. - 0303-6812 .- 1432-1416. ; 80, s. 1733-1757
-
Tidskriftsartikel (refereegranskat)abstract
- How long does it take for an initially advantageous mutant to establish itself in a resident population, and what does the population composition look like then? We approach these questions in the framework of the so called Bare Bones evolution model (Klebaner et al. in J Biol Dyn 5(2):147-162, 2011. https://doi.org/ 10.1080/ 17513758.2010.506041) that provides a simplified approach to the adaptive population dynamics of binary splitting cells. As the mutant population grows, cell division becomes less probable, and it may in fact turn less likely than that of residents. Our analysis rests on the assumption of the process starting from resident populations, with sizes proportional to a large carrying capacity K. Actually, we assume carrying capacities to be a(1)K and a(2)K for the resident and the mutant populations, respectively, and study the dynamics for K -> infinity. We find conditions for the mutant to be successful in establishing itself alongside the resident. The time it takes turns out to be proportional to log K. We introduce the time of establishment through the asymptotic behaviour of the stochastic nonlinear dynamics describing the evolution, and show that it is indeed 1/rho log K, where rho is twice the probability of successful division of the mutant at its appearance. Looking at the composition of the population, at times 1/rho log K + n, n is an element of Z(+), we find that the densities (i.e. sizes relative to carrying capacities) of both populations follow closely the corresponding two dimensional nonlinear deterministic dynamics that starts at a random point. We characterise this random initial condition in terms of the scaling limit of the corresponding dynamics, and the limit of the properly scaled initial binary splitting process of the mutant. The deterministic approximation with random initial condition is in fact valid asymptotically at all times 1/rho log K + n with n is an element of Z.
|
|
| 3. |
- Chigansky, P., et al.
(författare)
-
What can be observed in real time PCR and when does it show?
- 2018
-
Ingår i: Journal of Mathematical Biology. - : Springer Science and Business Media LLC. - 0303-6812 .- 1432-1416. ; 76:3, s. 679-695
-
Tidskriftsartikel (refereegranskat)abstract
- Real time, or quantitative, PCR typically starts from a very low concentration of initial DNA strands. During iterations the numbers increase, first essentially by doubling, later predominantly in a linear way. Observation of the number of DNA molecules in the experiment becomes possible only when it is substantially larger than initial numbers, and then possibly affected by the randomness in individual replication. Can the initial copy number still be determined? This is a classical problem and, indeed, a concrete special case of the general problem of determining the number of ancestors, mutants or invaders, of a population observed only later. We approach it through a generalised version of the branching process model introduced in Jagers and Klebaner (J Theor Biol 224(3):299-304, 2003. doi: 10.1016/S0022-5193(03) 001668), and based on Michaelis-Menten type enzyme kinetical considerations from Schnell and Mendoza (J Theor Biol 184(4):433-440, 1997). A crucial role is played by the Michaelis-Menten constant being large, as compared to initial copy numbers. In a strange way, determination of the initial number turns out to be completely possible if the initial rate v is one, i.e all DNA strands replicate, but only partly so when v < 1, and thus the initial rate or probability of succesful replication is lower than one. Then, the starting molecule number becomes hidden behind a "veil of uncertainty". This is a special case, of a hitherto unobserved general phenomenon in population growth processes, which will be adressed elsewhere.
|
|
| 4. |
|
|
| 5. |
|
|
| 6. |
|
|
