PMID- 31015986
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20231011
IS  - 2045-7758 (Print)
IS  - 2045-7758 (Electronic)
IS  - 2045-7758 (Linking)
VI  - 9
IP  - 7
DP  - 2019 Apr
TI  - Dissimilarity of individual microsatellite profiles under different mutation 
      models: Empirical approach.
PG  - 4038-4054
LID - 10.1002/ece3.5032 [doi]
AB  - Microsatellites (simple sequence repeats, SSRs) still remain popular molecular 
      markers for studying neutral genetic variation. Two alternative models outline 
      how new microsatellite alleles evolve. Infinite alleles model (IAM) assumes that 
      all possible alleles are equally likely to result from a mutation, while stepwise 
      mutation model (SMM) describes microsatellite evolution as stepwise adding or 
      subtracting single repeat units. Genetic relationships between individuals can be 
      analyzed in higher precision when assuming the SMM scenario with allele size 
      differences as a proxy of genetic distance. If population structure is not 
      predetermined in advance, an empirical data analysis usually includes (a) 
      estimating proximity between individual SSR profiles with a selected 
      dissimilarity measure and (b) determining putative genetic structure of a given 
      set of individuals using methods of clustering and/or ordination for the obtained 
      dissimilarity matrix. We developed new dissimilarity indices between SSR profiles 
      of haploid, diploid, or polyploid organisms assuming different mutation models 
      and compared the performance of these indices for determining genetic structure 
      with population data and with simulations. More specifically, we compared SMM 
      with a constant or variable mutation rate at different SSR loci to IAM using data 
      from natural populations of a freshwater bryozoan Cristatella mucedo (diploid), 
      wheat leaf rust Puccinia triticina (dikaryon), and wheat powdery mildew Blumeria 
      graminis (monokaryon). We show that inferences about population genetic structure 
      are sensitive to the assumed mutation model. With simulations, we found that 
      Bruvo's distance performs generally poorly, while the new metrics are capturing 
      the differences in the genetic structure of the populations.
FAU - Kosman, Evsey
AU  - Kosman E
AUID- ORCID: 0000-0002-6121-063X
AD  - Institute for Cereal Crops Improvement Tel Aviv University Tel Aviv Israel.
FAU - Jokela, Jukka
AU  - Jokela J
AD  - ETH Zurich, Department of Environmental Systems Science Institute of Integrative 
      Biology (IBZ) Zurich Switzerland.
AD  - EAWAG Aquatic Ecology Dubendorf Switzerland.
LA  - eng
SI  - Dryad/10.5061/dryad.1b8n2b4
PT  - Journal Article
DEP - 20190319
PL  - England
TA  - Ecol Evol
JT  - Ecology and evolution
JID - 101566408
PMC - PMC6467862
OTO - NOTNLM
OT  - Bruvo's distance
OT  - SSR markers
OT  - genetic dissimilarity of individuals
OT  - infinite alleles model
OT  - population structure
OT  - stepwise mutation model
COIS- The authors declare no conflict of interest.
EDAT- 2019/04/25 06:00
MHDA- 2019/04/25 06:01
PMCR- 2019/04/01
CRDT- 2019/04/25 06:00
PHST- 2019/01/17 00:00 [received]
PHST- 2019/01/21 00:00 [accepted]
PHST- 2019/04/25 06:00 [entrez]
PHST- 2019/04/25 06:00 [pubmed]
PHST- 2019/04/25 06:01 [medline]
PHST- 2019/04/01 00:00 [pmc-release]
AID - ECE35032 [pii]
AID - 10.1002/ece3.5032 [doi]
PST - epublish
SO  - Ecol Evol. 2019 Mar 19;9(7):4038-4054. doi: 10.1002/ece3.5032. eCollection 2019 
      Apr.