Relative strength of fine-scale spatial genetic structure in paternally vs biparentally inherited DNA in a dioecious plant depends on both sex proportions and pollen-to-seed dispersal ratio

Chybicki, Igor J.; Dering, Monika; Iszkuło, Grzegorz; Meyza, Katarzyna; Suszka, Jan

doi:10.1038/hdy.2016.65

Cited by 14 publications

(17 citation statements)

References 48 publications

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“…Among possible biological explanations for such conflicting patterns is hybridization between species with both maternal and paternal organellar inheritance (Govindarajulu et al, 2015). Plants typically have maternal inheritance of both the plastid (Corriveau and Coleman, 1988; Schneider et al, 2015; Van de Paer et al, 2016) and the mitochondrial genome (McCauley, 2013; Shen et al, 2015; Van de Paer et al, 2016), but biparental (Corriveau and Coleman, 1988) as well as paternal inheritance are also reported (McCauley, 2013; Shen et al, 2015; Chybicki et al, 2016). This means that the mitochondrion and the plastome can have different evolutionary histories in a taxon of hybrid origin.…”

Section: Discussionmentioning

confidence: 99%

Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny

Rydin

Wikström

Bremer

2017

American J of Botany

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Today, about 30 years aft er the beginning of the "molecular revolution" of systematics, we have relatively good knowledge of angiosperm evolution and interrelationships among major groups ( APG III, 2009 ). Th ere are, however, still unanswered phylogenetic questions and unresolved nodes. Furthermore, contemporary knowledge of plant phylogeny typically derives from plastid data, which have been widely used for resolving evolutionary relationships. Early phylogenetic studies based on analysis of the rubisco gene rbcL ( Olmstead et al., 1992 ;Chase et al., 1993 ;Bremer et al., 1995 ) inspired, and the availability of universal primers (e.g., Zurawski and Clegg, 1987 ;Taberlet et al., 1991 ) enhanced molecular laboratory work, resulting in numerous phylogenetic studies on land plants during the subsequent decades. Typically, these studies were single-gene or multigene studies, i.e., they were based on one to several gene regions. Following recent developments, new sequencing techniques permit time-and cost-effi cient production of much more data, e.g., entire genomes, but it is nevertheless still not fully clear to what extent phylogenomics can signifi cantly increase our understanding of land plant phylogeny.While it was early recognized that data from the nuclear and mitochondrial genomes are desirable, such data have been much less used for the purpose of resolving evolutionary relationships in plants than have plastid data. Using nuclear genes may pose biological challenges associated with, for example, allelic variation and paralogy, as well as methodological problems with availability of general primers and requirements of fresh plant material (see e.g., Zimmer and Wen, 2012 ). The exception is nuclear ribosomal DNA, which is present in many copies that are assumed to be PREMISE OF THE STUDY:Reconstruction of plant phylogeny has heavily relied on single-gene or multigene plastid data. New sequencing methods have led to an increasing number of studies based on data from the entire plastid, but the mitochondrion has rarely been used to infer plant phylogeny because of an assumed information poverty and demonstrated lateral transfer of mitochondrial gene regions between distantly related species. METHODS:We explored phylogenetic information from the plant mitochondrion using 57 representatives of the species-rich coff ee family as study system and assessed consistency with previous results based (mostly) on plastid data. KEY RESULTS:We showed that the mitochondrial genome can provide structured and statistically signifi cant information on plant phylogeny. While most of our results are consistent with those based on plastid data, some surprising and statistically signifi cant confl icts emerge, and our study demonstrates with striking clarity that the phylogeny of Rubiaceae is far from resolved.CONCLUSIONS: It appears unlikely that confl icts between results retrieved from the diff erent genomic compartments would be restricted to Rubiaceae. Rather, they are probably a general phenomenon and an important facto...

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Section: Discussionmentioning

confidence: 99%

Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny

Rydin

Wikström

Bremer

2017

American J of Botany

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“…The ratio of the regression slopes in nuclear genotypes b b and chloroplast haplotypes b m is thought to depend on the ratio of pollen dispersal area to seed dispersal area (Chybicki et al, ; Hardy & Vekemans, ). The ratio of b m to b b (1 + F IS ) is expected to be 3 when pollen dispersal area is equal to seed dispersal area and to increase as the ratio of pollen dispersal area to seed dispersal area increases (Appendix ).…”

Section: Methodsmentioning

confidence: 99%

“…Assignment of mother plants with identical genotypes of maternal tissues of dispersed seeds directly estimates seed dispersal (Browne, Ottewell, Sork, & Karubian, ; Grivet, Robledo‐Arnuncio, Smouse, & Sork, ). On the other hand, genetic markers with uniparental and biparental inheritance indirectly estimate the contribution of pollen and seed dispersal to gene flow (Chybicki, Dering, Iszkuło, Meyza, & Suszka, ; Ennos, ; Hamilton & Miller, ; Petit, Duminil, & Fineschi, ).…”

Section: Introductionmentioning

confidence: 99%

“…The index Sp calculated from the regression slope and the relatedness between neighbors is often used to compare SGS intensity among populations (Vekemans & Hardy, ). The SGS intensity is expected to differ between genetic markers under different modes of inheritance (Chybicki et al, ). Maternally inherited loci are expected to show higher SGS intensity than biparentally inherited loci due to lower effective population densities and fewer opportunities of gene dispersal in the former loci (Hardy & Vekemans, ; Appendix ).…”

Section: Introductionmentioning

confidence: 99%

“…Maternally inherited loci are expected to show higher SGS intensity than biparentally inherited loci due to lower effective population densities and fewer opportunities of gene dispersal in the former loci (Hardy & Vekemans, ; Appendix ). The ratio of pollen and seed dispersal area can be inferred from the ratio of regression slopes in maternally and biparentally inherited loci (Chybicki et al, ; Appendix ). Because of the low polymorphism of maternally inherited loci within populations, fine‐scale SGS has rarely been compared between genetic markers with maternal and biparental inheritance.…”

Section: Introductionmentioning

confidence: 99%

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Multiscale spatial genetic structure within and between populations of wild cherry trees in nuclear genotypes and chloroplast haplotypes

Nagamitsu

Kato

Kikuchi

et al. 2019

Ecology and Evolution

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Spatial genetic structure (SGS) of plants mainly depends on the effective population size and gene dispersal. Maternally inherited loci are expected to have higher genetic differentiation between populations and more intensive SGS within populations than biparentally inherited loci because of smaller effective population sizes and fewer opportunities of gene dispersal in the maternally inherited loci. We investigated biparentally inherited nuclear genotypes and maternally inherited chloroplast haplotypes of microsatellites in 17 tree populations of three wild cherry species under different conditions of tree distribution and seed dispersal. As expected, interpopulation genetic differentiation was 6–9 times higher in chloroplast haplotypes than in nuclear genotypes. This difference indicated that pollen flow 4–7 times exceeded seed flow between populations. However, no difference between nuclear and chloroplast loci was detected in within‐population SGS intensity due to their substantial variation among the populations. The SGS intensity tended to increase as trees became more aggregated, suggesting that tree aggregation biased pollen and seed dispersal distances toward shorter. The loss of effective seed dispersers, Asian black bears, did not affect the SGS intensity probably because of mitigation of the bear loss by other vertebrate dispersers and too few tree generations after the bear loss to alter SGS. The findings suggest that SGS is more variable in smaller spatial scales due to various ecological factors in local populations.

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Genetic variation of English yew (Taxus baccata L.) in the Bavarian Forest National Park, Germany

Moosavi,

Budde,

Heurich

et al. 2024

Eur J Forest Res

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Taxus baccata L. is a highly valuable species with wide distribution but scattered and locally rare occurrence. Human intervention, including forest management practices and fragmentation, can significantly impact the species’ genetic diversity, structure, and dynamics. In this study, we investigated these factors within T. baccata populations in the Bavarian Forest National Park (NP) in Germany and their implications for conservation. We used 13 EST-SSRs to assess the genetic diversity and structure of the population. Our analysis revealed a scarcity of small-diameter trees, indicating limited natural regeneration over time. However, conservation efforts, like selectively removing competitor species and using protective fencing, have improved growth conditions and promoted seedling emergence. The NP’s natural zone has no active management, which is confined to the development and management zones. Genetic diversity assessments revealed high genetic diversity (He: 0.612 and 0.614 for seedlings and adults, respectively) compared to other studies in Taxus baccata, dispelling concerns of significant inbreeding and showcasing a stable genetic structure. However, significant spatial clustering of related individuals (family structures) in both cohorts and low effective population size in the progeny hints at restricted gene flow, necessitating conservation efforts prioritizing safeguarding and promoting natural regeneration in development and management zones. Limited natural regeneration and the recent decrease in effective population size in the NP populations indicate habitat fragmentation and human interventions. Effective population size estimates emphasize the need for diverse conservation strategies. Conservation efforts should prioritize protecting natural regeneration and enhancing gene flow by actively promoting European yew, e.g., by shelterwood cutting, to ensure the long-term viability of T. baccata in the region outside the NP.

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Relative strength of fine-scale spatial genetic structure in paternally vs biparentally inherited DNA in a dioecious plant depends on both sex proportions and pollen-to-seed dispersal ratio

Cited by 14 publications

References 48 publications

Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny

Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny

Multiscale spatial genetic structure within and between populations of wild cherry trees in nuclear genotypes and chloroplast haplotypes

Genetic variation of English yew (Taxus baccata L.) in the Bavarian Forest National Park, Germany

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