Review and simulation of homoplasy and collision in AFLP

Gort, Gerrit; Eeuwijk, F.A. van

doi:10.1007/s10681-011-0368-3

Cited by 3 publications

(4 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Dissimilarity between the results of microsatellite and AFLP analysis may reflect differences in the accuracy of these two molecular markers. Although the wide‐ranging genomic coverage of AFLP markers is useful for uncovering hybrid individuals, AFLP loci can often exhibit size homoplasy (Gort & Eeuwijk, ). This can cause separate loci to be mistakenly grouped together as a single locus, leading to an over‐estimation of the degree of relatedness between individuals (Gort & van Eeuwijk, ).…”

Section: Discussionmentioning

confidence: 99%

“…Although the wide‐ranging genomic coverage of AFLP markers is useful for uncovering hybrid individuals, AFLP loci can often exhibit size homoplasy (Gort & Eeuwijk, ). This can cause separate loci to be mistakenly grouped together as a single locus, leading to an over‐estimation of the degree of relatedness between individuals (Gort & van Eeuwijk, ). It is therefore possible that hybrid individuals identified during AFLP studies of L. rubellus may have resulted from the scoring of homoplasic loci.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Nuclear DNA recapitulates the cryptic mitochondrial lineages ofLumbricus rubellusand suggests the existence of cryptic species in an ecotoxological soil sentinel

Donnelly

Harper

Morgan

et al. 2013

Biol J Linn Soc Lond

View full text Add to dashboard Cite

Mitochondrial DNA analysis has revealed two distinct phylogenetic lineages within the ecotoxological sentinel earthworm model Lumbricus rubellus Hoffmeister, 1843. The existence of these lineages could complicate ecotoxicological studies that use the species as a sentinel for soil contamination testing, as they may respond differently to contamination; however, as mitochondrial haplotypes are not always expected to segregate in the same way as chromosomal DNA in natural populations, we further investigated this issue by using nuclear DNA markers (microsatellites) to measure genetic diversity, differentiation, and gene flow in sympatric populations of the two L. rubellus lineages at two sites in South Wales. Our results show that sympatric populations of the two lineages are more genetically differentiated than geographically distant populations of the same lineage, and Bayesian clustering analysis revealed no evidence of gene flow between the lineages at either site. Additionally, DNA sequencing of these microsatellite loci uncovered substantial differentiation between lineages at homologous flanking regions. Overall our findings indicate a high degree of nuclear genetic differentiation between the two lineages of L. rubellus, implying reproductive isolation at the two study sites and therefore the potential existence of cryptic species. The existence of two cryptic taxa has major implications for the application of L. rubellus as an ecotoxicological sentinel. It may therefore be necessary to consider the lineages as separate taxa during future ecotoxicological studies.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Nuclear DNA recapitulates the cryptic mitochondrial lineages ofLumbricus rubellusand suggests the existence of cryptic species in an ecotoxological soil sentinel

Donnelly

Harper

Morgan

et al. 2013

Biol J Linn Soc Lond

View full text Add to dashboard Cite

show abstract

“…The use of AFLP-marker data deserves discussion because the methodology has gained criticism e.g. due to frequent occurrence of non-homologous fragments with the same amplicon length [ 23 , 24 ]. Study on Nasonia jewel wasp [ 25 ] revealed 41.5% shorter map size when SNP-markers were used instead of RAPD/AFLP markers [ 26 ].…”

Section: Discussionmentioning

confidence: 99%

A high recombination rate in eusocial Hymenoptera: evidence from the common wasp Vespula vulgaris

Sirviö

Johnston

Wenseleers³

et al. 2011

BMC Genet

View full text Add to dashboard Cite

BackgroundHigh recombination rates have previously been detected in two groups of eusocial insects; honeybees and ants. In this study we estimate recombination rate in a eusocial wasp Vespula vulgaris that represents a third phylogenetic lineage within eusocial hymenopterans.ResultsA genetic linkage map of V. vulgaris based on 210 markers shows that the total map length is 2129 cM and the recombination rate is 9.7 cM/Mb (or 103 kb/cM). The present estimate in V. vulgaris is somewhat smaller than in the honeybee Apis mellifera and intermediate between the estimates from two ant species (Acromyrmex echinatior, Pogonomyrmex rugosus). Altogether, the estimates from these eusocial species are higher than in any other insect reported so far.ConlusionsThe four species (V. vulgaris, A. mellifera, A. echinatior, P. rugosus) are characterized by advanced eusociality with large colonies, clear queen-worker dimorphism and well developed task specialization. They also have colonies with a single, normally multiply inseminated (polyandrous) queen. Benefits of genotypic diversity within colonies (e.g. through improved task specialization or pathogen and parasite resistance) may have selected for both polyandry and high recombination rate in such advanced eusocial insects.

show abstract

“…Because Pe , Pco and Pdu are very closely related taxa [ 30 ] [ 34 ] [ 35 ] [ 40 ] and their physical and reproductive barriers are very weak [ 36 ] [ 37 ] [ 38 ], the degree of homoplasy was not expected to significantly increase [ 56 ] [ 57 ] [ 58 ].…”

Section: Methodsmentioning

confidence: 99%

Degree of Hybridization in Seed Stands of Pinus engelmannii Carr. In the Sierra Madre Occidental, Durango, Mexico

et al. 2016

View full text Add to dashboard Cite

Hybridization is an important evolutionary force, because interspecific gene transfer can introduce more new genetic material than is directly generated by mutations. Pinus engelmannii Carr. is one of the nine most common pine species in the pine-oak forest ecoregion in the state of Durango, Mexico. This species is widely harvested for lumber and is also used in reforestation programmes. Interspecific hybrids between P.engelmannii and Pinus arizonica Engelm. have been detected by morphological analysis. The presence of hybrids in P. engelmannii seed stands may affect seed quality and reforestation success. Therefore, the goals of this research were to identify introgressive hybridization between P. engelmannii and other pine species in eight seed stands of this species in Durango, Mexico, and to examine how hybrid proportion is related to mean genetic dissimilarity between trees in these stands, using Amplified Fragment Length Polymorphism (AFLP) markers and morphological traits. Differences in the average current annual increment of putative hybrids and pure trees were also tested for statistical significance. Morphological and genetic analyses of 280 adult trees were carried out. Putative hybrids were found in all the seed stands studied. The hybrids did not differ from the pure trees in vigour or robustness. All stands with putative P. engelmannii hybrids detected by both AFLPs and morphological traits showed the highest average values of the Tanimoto distance, which indicates: i) more heterogeneous genetic material, ii) higher genetic variation and therefore iii) the higher evolutionary potential of these stands, and iv) that the morphological differentiation (hybrid/not hybrid) is strongly associated with the Tanimoto distance per stand. We conclude that natural pairwise hybrids are very common in the studied stands. Both morphological and molecular approaches are necessary to confirm the genetic identity of forest reproductive material.

show abstract

Review and simulation of homoplasy and collision in AFLP

Cited by 3 publications

References 28 publications

Nuclear DNA recapitulates the cryptic mitochondrial lineages ofLumbricus rubellusand suggests the existence of cryptic species in an ecotoxological soil sentinel

Nuclear DNA recapitulates the cryptic mitochondrial lineages ofLumbricus rubellusand suggests the existence of cryptic species in an ecotoxological soil sentinel

A high recombination rate in eusocial Hymenoptera: evidence from the common wasp Vespula vulgaris

Degree of Hybridization in Seed Stands of Pinus engelmannii Carr. In the Sierra Madre Occidental, Durango, Mexico

Contact Info

Product

Resources

About