<scp>genotype</scp>and<scp>genodive</scp>: two programs for the analysis of genetic diversity of asexual organisms

Meirmans, Patrick G.; Tienderen, Peter H. van

doi:10.1111/j.1471-8286.2004.00770.x

Cited by 1,788 publications

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References 11 publications

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“…AMOVA was performed using GenoDive 2.0b11 (Meirmans & Van Tienderen, 2004) which allows the calculation of a FST analogue coefficient of differentiation, standardized according to the level of intra-population variation, so that the (Meirmans, 2006). To avoid confusion, this ratio is hereafter referred to as FST'.…”

Section: Statistical Analysesmentioning

confidence: 99%

Spatial genetic structure across a hybrid zone between European rabbit subspecies

Alda

Doadrio

2014

Preprint

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View the peer-reviewed version (peerj.com/articles/582), which is the preferred citable publication unless you specifically need to cite this preprint.Alda F, Doadrio I. 2014. Spatial genetic structure across a hybrid zone between European rabbit subspecies. PeerJ 2:e582 https://doi.org/10.7717/peerj.582 S p a t i a l g e n e t i c s t r u c t u r e a c r o s s a h y b r i d z o n e b e t we e n E u r o p e a n r a b b i t s u b s p e c i e sT h e I b e r i a n P e n i n s u l a i s t h e o n l y r e g i o n i n t h e wo r l d wh e r e t h e t wo e x i s t i n g s u b s p e c i e s o f t h e E u r o p e a n r a b b i t ( Or y c t o l a g u s c u n i c u l u s ) n a t u r a l l y o c c u r a n d h y b r i d i z e . I n t h i s s t u d y we e x p l o r e t h e r e l a t i v e r o l e s o f h i s t o r i c a l a n d c o n t e mp o r a r y p r o c e s s e s i n s h a p i n g t h e s p a t i a l g e n e t i c s t r u c t u r e o f t h e r a b b i t a c r o s s i t s n a t i v e d i s t r i b u t i o n r a n g e , a n d h o w t h e y d i ff e r e n t l y a ff e c t e a c h s u b s p e c i e s a n d t h e h y b r i d z o n e . F o r t h a t p u r p o s e mu l t i l o c u s g e n o t y p e s a n d mi t o c h o n d r i a l DNA d a t a we r e o b t a i n e d f o r 7 7 1 r a b b i t s a c r o s s mo s t o f t h e s p e c i e s ' d i s t r i b u t i o n r a n g e i n S p a i n . Nu c l e a r ma r k e r s d e fi n e d a h i e r a r c h i c a l g e n e t i c s t r u c t u r e fi r s t l y c o mp r i s e d b y t wo g e n e t i c g r o u p s , l a r g e l y c o n g r u e n t wi t h t h e mi t o c h o n d r i a l l i n e a g e s a n d s u b s p e c i e s d i s t r i b u t i o n s ( O. c . a l g i r u s a n d O. c . c u n i c u l u s ) , wh i c h we r e s u b s e q u e n t l y s u b d i v i d e d i n t os e v e n g e n e t i c g r o u p s p r o b a b l y s h a p e d b y e n v i r o n me n t a l o r e c o l o g i c a l f a c t o r s . Ge o g r a p h i c d i s t a n c e a l o n e e me r g e d a s a n i mp o r t a n t f a c t o r e x p l a i n i n g g e n e t i c d i ff e r e n t i a t i o n a c r o s s t h e wh o l e r a n g e , wi t h o u t t h e n e e d t o i n v o k e f o r t h e e ff e c t f o r g e o g r a p h i c a l b a r r i e r s . T h u s , wh e n c o n s i d e r i n g t h e o v e r a l l g e n e t i c s t r u c t u r e , d i ff e r e n c e s a t a l o c a l l e v e l s e e m t o b e o f g r e a t e r i mp o r t a n c e . T h e s i g n i fi c a n t l y p o s i t i v e s p a t i a l c o r r e l a t i o n u p t o a d i s t a n c e o f o n l y 1 0 0 k m s u p p o r t e d t h i s h y p o t h e s i s . Ho we v e r , n o r t h e r n p o p u l a t i o n s o f O. c . c u n i c u l u s s h o we d mo r e s p a t i a l g e n e t i c s t r u c t u r e a n d d i ff e r e n t i a t i o n t h a n O. c . a l g i r u s , wh i c h c o u l d b e d u e t o l o c a l g e o g r a p h i c b a r r i e r s , l i mi t e d r e s o u r c e s , s o i l t y p e a n d / o r s o c i a l b e h a v i o u r s l i mi t i n g d i s p e r s a l .T h e h y b r...

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Section: Statistical Analysesmentioning

confidence: 99%

Spatial genetic structure across a hybrid zone between European rabbit subspecies

Alda

Doadrio

2014

Preprint

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“…A clone is defined if at least two individuals had the same genotype. The total and effective number of genotypes (1/sum of genotype frequencies) per population were calculated using the programmes Genotype v. 1.2 and Genodive v. 1.1 (Meirmans & van Tienderen 2004; Table 2). …”

Section: Microsatellite Analysismentioning

confidence: 99%

Genetic variability and morphology of tri- and tetraploid members of the Sorbus aria complex in northern Bavaria

Feulner¹,

Weig²,

Paule³

et al. 2017

Preslia

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. (2017): Genetic variability and morphology of tri-and tetraploid members of the Sorbus aria complex in northern Bavaria. -Preslia 89: 275-290.The Sorbus aria complex in the Franconian Jura, northern Bavaria, consists of the sexual diploid S. aria s. str. and putative apomictic polyploids, among them S. collina and S. danubialis. Here, the genetic and cytotypic structure of the S. aria complex and the proportion of clonal versus variable genotypes with a special focus on S. collina are studied using nuclear microsatellite markers, flow cytometry and multivariate morphometrics. In the Franconian Jura the tetraploid S. collina is the most frequent taxon in the S. aria complex. It consists of six closely related clones and a high number of unique genotypes, which were found in 70% of the populations studied. Morphologically, most of the clones and the unique tetraploid genotypes are not significantly differentiated. Therefore, all of them could be assigned to S. collina. Mechanisms that could result in the high number of genotypes within S. collina are accumulations of mutations, remnant sexuality, multiple polyploidization events and backcrossing. The results show that S. collina is a genetically quite variable facultative apomictic taxon. Triploids were identified sporadically and the microsatellites pointed to an origin from repeated hybridization events between diploid S. aria s. str. and S. collina. K e y w o r d s:

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“…Strains with the same multilocus microsatellite genotype (MLMG) were considered as a clone or haplotype, as determined by GENODIVE, version 2.0b23 (Meirmans and van Tienderen 2004), and only one representative of each haplotype was selected per population to construct clone-corrected data sets that were used for downstream analysis. Indicators of genotypic diversity estimated included (i) number of genotypes per population; (ii) clonal fraction, calculated as 1 _ (number of different genotypes within the population)/(total number of isolates within the population) (Zhan et al 2003); (iii) the Simpson's diversity index (Si), which was estimated as Si = 1 _ åP 2 r (r = 1 to s), where P r is the relative abundance of the rth genotype at the population (1 represents infinite diversity and 0 no diversity) (He and Hu 2005); and (iv) the genotypic distribution over populations (evenness) (Stoddart and Taylor 1988).…”

Section: Methodsmentioning

confidence: 99%

Spatial Genetic Structure of Coffee-Associated Xylella fastidiosa Populations Indicates that Cross Infection Does Not Occur with Sympatric Citrus Orchards

et al. 2017

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genotypeandgenodive: two programs for the analysis of genetic diversity of asexual organisms

Cited by 1,788 publications

References 11 publications

Spatial genetic structure across a hybrid zone between European rabbit subspecies

Spatial genetic structure across a hybrid zone between European rabbit subspecies

Genetic variability and morphology of tri- and tetraploid members of the Sorbus aria complex in northern Bavaria

Spatial Genetic Structure of Coffee-Associated Xylella fastidiosa Populations Indicates that Cross Infection Does Not Occur with Sympatric Citrus Orchards

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