An Approach to Population and Evolutionary Genetic Theory for Genes in Mitochondria and Chloroplasts, and Some Results

We developed population genetic theory for organelle genes, using an infinite alleles model appropriate for molecular genetic data, and considering the effects of mutation and random drift on the frequencies of selectively neutral alleles. The effects of maternal inheritance and vegetative segregation of organelle genes are dealt with by defining new effective gene numbers, and substituting these for 2N(e) in classical theory of nuclear genes for diploid organisms. We define three different effective gene numbers. The most general is N(lambda), defined as a function of population size, number of organelle genomes per cell, and proportions of genes contributed by male and female gametes to the zygote. In many organisms, vegetative segregation of organelle genomes and intracellular random drift of organelle gene frequencies combine to produce a predominance of homoplasmic cells within individuals in the population. Then, the effective number of organelle genes is N(eo), a simple function of the numbers of males and females and of the maternal and paternal contributions to the zygote. Finally, when the paternal contribution is very small, N( eo) is closely approximated by the number of females, N( f). Then if the sex ratio is 1, the mean time to fixation or loss of new mutations is approximately two times longer for nuclear genes than for organelle genes, and gene diversity is approximately four times greater. The difference between nuclear and organelle genes disappears or is reversed in animals in which males have large harems. The differences between nuclear and organelle gene behavior caused by maternal inheritance and vegetative segregation are generally small and may be overshadowed by differences in mutation rates to neutral alleles. For monoecious organisms, the effective number of organelle genes is approximately equal to the total population size N. We also show that a population can be effectively subdivided for organelle genes at migration rates which result in panmixis for nuclear genes, especially if males migrate more than females.     

Habitat loss and fragmentation reduce effective gene flow by disrupting seed dispersal in a neotropical palm

Habitat loss and fragmentation often reduce gene flow and genetic diversity in plants by disrupting the movement of pollen and seed. However, direct comparisons of the contributions of pollen vs. seed dispersal to genetic variation in fragmented landscapes are lacking. To address this knowledge gap, we partitioned the genetic diversity contributed by male gametes from pollen sources and female gametes from seed sources within established seedlings of the palm Oenocarpus bataua in forest fragments and continuous forest in northwest Ecuador. This approach allowed us to quantify the separate contributions of each of these two dispersal processes to genetic variation. Compared to continuous forest, fragments had stronger spatial genetic structure, especially among female gametes, and reduced effective population sizes. We found that within and among fragments, allelic diversity was lower and genetic structure higher for female gametes than for male gametes. Moreover, female gametic allelic diversity in fragments decreased with decreasing surrounding forest cover, while male gametic allelic diversity did not. These results indicate that limited seed dispersal within and among fragments restricts genetic diversity and strengthens genetic structure in this system. Although pollen movement may also be impacted by habitat loss and fragmentation, it nonetheless serves to promote gene flow and diversity within and among fragments. Pollen and seed dispersal play distinctive roles in determining patterns of genetic variation in fragmented landscapes, and maintaining the integrity of both dispersal processes will be critical to managing and conserving genetic variation in the face of continuing habitat loss and fragmentation in tropical landscapes.     

Mitochondrial gene segregation in mammals: is the bottleneck always narrow?

Summary The segregation of a heteroplasmic silent polymorphism in the mitochondrial ND6 gene has been followed in a human maternal lineage comprising eight individuals and spanning three generations. Heteroplasmy persisted in all eight maternally related family members. More importantly, the frequencies of the two alleles showed relatively little variation among individuals or between generations. In contrast to the findings in other mammalian lineages, the present results indicate relatively slow mitochondrial gene segregation. A narrow bottleneck in the number of mitochondrial DNA (mtDNA) molecules, which occurs at some stage of oogenesis, has been advanced to explain rapid mammalian mitochondrial gene segregation. It is suggested here that the segregation of mitochondrial genes may be more complex than initially envisaged, and that models need to be developed that account for both rapid and slow segregation. One possibility, which reconciles both physical and genetic studies of mammalian mtDNA, is that the unit of mitochondrial segregation is the organelle itself, each containing multiple mtDNA molecules.     

LIGHT AND ELECTRON MICROSCOPIC OBSERVATIONS OF PREFERENTIAL DESTRUCTION OF CHLOROPLAST AND MITOCHONDRIAL DNA AT EARLY MALE GAMETOGENESIS OF THE ANISOGAMOUS GREEN ALGA DERBESIA TENUISSIMA (CHLOROPHYTA)1

Gametogenesis in male and female gametophytes was studied by light microscopy and EM in the dioecious multinucleate green alga Derbesia tenuissima (Moris & De Notaris) P. Crouan & H. Crouan, where male and female gametes differ in size. Gametogenesis was divided into five stages: 32 h (stage 1), 24 h (stage 2), 16 h (stage 3), 8 h (stage 4), and 0.5 h (stage 5) before gamete release. At stage 1, the first sign of gametogenesis observed was the aggregation of gametophyte protoplasm to form putative gametangia. At stage 2, gametangia were separated from the vegetative protoplasm of gametophytes. Morphological changes of nuclei and organelles occurred at this early stage of male gametogenesis, and organelle DNA degenerated. At stage 3, male organelle DNA had completely degenerated, whereas in female gametangia, organelle DNA continued to exist in both chloroplasts and mitochondria. Gametogenesis was almost completed at stage 4 and fully at stage 5. Small male gametes had a DNA‐containing nucleus and a large mitochondrion and one or several degenerated chloroplasts. The mitochondria and plastids were devoid of DNA. The large female gametes had a nucleus and multiple organelles, all of which contained their own DNA. Thus, degeneration of chloroplast DNA along with morphological changes of organelles occurred at male gametogenesis in anisogamous green algae (Bryopsis and D. tenuissima), in contrast with previous studies in isogamous green algae (Chlamydomonas, Acetabularia caliculus, and Dictyosphaeria cavernosa) in which degeneration of chloroplast DNA occurred after zygote formation.     

The relative contributions of seed and pollen dispersal to gene flow and genetic diversity in seedlings of a tropical palm

Seed and pollen dispersal shape patterns of gene flow and genetic diversity in plants. Pollen is generally thought to travel longer distances than seeds, but seeds determine the ultimate location of gametes. Resolving how interactions between these two dispersal processes shape microevolutionary processes is a long‐standing research priority. We unambiguously isolated the separate and combined contributions of these two dispersal processes in seedlings of the animal‐dispersed palm Oenocarpus bataua to address two questions. First, what is the spatial extent of pollen versus seed movement in a system characterized by long‐distance seed dispersal? Second, how does seed dispersal mediate seedling genetic diversity? Despite evidence of frequent long‐distance seed dispersal, we found that pollen moves much further than seeds. Nonetheless, seed dispersal ultimately mediates genetic diversity and fine‐scale spatial genetic structure. Compared to undispersed seedlings, seedlings dispersed by vertebrates were characterized by higher female gametic and diploid seedling diversity and weaker fine‐scale spatial genetic structure for female gametes, male gametes and diploid seedlings. Interestingly, the diversity of maternal seed sources at seed deposition sites (N _em) was associated with higher effective number of pollen sources (N _ep), higher effective number of parents (N _e) and weaker spatial genetic structure, whereas seed dispersal distance had little impact on these or other parameters we measured. These findings highlight the importance maternal seed source diversity (N _em) at frugivore seed deposition sites in driving emergent patterns of fine‐scale genetic diversity and structure.     

Reproductive strategy, clonal structure and genetic diversity in populations of the aquatic macrophyte Sparganium emersum in river systems

Many aquatic and riparian plant species are characterized by the ability to reproduce both sexually and asexually. Yet, little is known about how spatial variation in sexual and asexual reproduction affects the genotypic diversity within populations of aquatic and riparian plants. We used six polymorphic microsatellites to examine the genetic diversity within and differentiation among 17 populations (606 individuals) of Sparganium emersum, in two Dutch-German rivers. Our study revealed a striking difference between rivers in the mode of reproduction (sexual vs. asexual) within S. emersum populations. The mode of reproduction was strongly related to locally reigning hydrodynamic conditions. Sexually reproducing populations exhibited a greater number of multilocus genotypes compared to asexual populations. The regional population structure suggested higher levels of gene flow among sexually reproducing populations compared to clonal populations. Gene flow was mainly mediated via hydrochoric dispersal of generative propagules (seeds), impeding genetic differentiation among populations even over river distances up to 50 km. Although evidence for hydrochoric dispersal of vegetative propagules (clonal plant fragments) was found, this mechanism appeared to be relatively less important. Bayesian-based assignment procedures revealed a number of immigrants, originating from outside our study area, suggesting intercatchment plant dispersal, possibly the result of waterfowl-mediated seed dispersal. This study demonstrates how variation in local environmental conditions in river systems, resulting in shifting balances of sexual vs. asexual reproduction within populations, will affect the genotypic diversity within populations. This study furthermore cautions against generalizations about dispersal of riparian plant species in river systems.     

Biosystematic study ofSedum L. subgenusAizoon (Crassulaceae)

Chromosome numbers of 114 individuals from twelve populations ofSedum aizoon L. var.aizoon (Crassulaceae) are reported. They include 37 different chromosome numbers ranging from 2n=71 to 124. Although the chromosome number variation has been found in all populations examined, no correlation with geographical distribution could not be found. Various kinds of meiotic irregularities, i.e., multivalents, univalents, chromosome lagging, and polysporous “tetrad” formation have been found. These irregularities lead to the formation of gametes with various chromosome numbers. All aneuploid plants set seeds and seem to reproduce sexually. The extensive aneuploidy in var.aizoon seems to be caused by the unequal chromosome segregation in meiosis and the subsequent fertilization of gametes with various chromosome numbers.     

Organelle Gene Diversity under Migration, Mutation, and Drift: Equilibrium Expectations, Approach to Equilibrium, Effects of Heteroplasmic Cells, and Comparison to Nuclear Genes

We developed stochastic population genetic theory for mitochondrial and chloroplast genes, using an infinite alleles model appropriate for molecular genetic data. We considered the effects of mutation, random drift, and migration in a finite island model on selectively neutral alleles. Recurrence equations were obtained for the expectation of gene diversities within zygotes, within colonies, and between colonies. The variables are number and sizes of colonies, migration rates, sex ratios, degree of paternal transmission, number of germ line cell divisions, effective number of segregating organelle genomes, and mutation rate. Computer solutions of the recurrence equations were used to study the approach to equilibrium. Gene diversities equilibrate slowly, while GST, used to measure population subdivision, equilibrates rapidly. Approximate equilibrium equations for gene diversities and GST can be obtained by substituting Neo and me, simple functions of the numbers of breeding or migrating males and females and of the degree of paternal transmission, for the effective numbers of genes and migration rates in the corresponding equations for nuclear genes. The approximate equations are not valid when the diversity within individuals is large compared to that between individuals, as is often true for the D-loop of animal mtDNA. We used the exact equations to verify that organelle genes often show more subdivision than nuclear genes; however, we also identified the range of breeding and migrating sex ratios for which population subdivision is greater for nuclear genes. Finally, we show that gene diversities are higher for nuclei than for organelles over a larger range of sex ratios in a subdivided population than in a panmictic population.     

Vegetative segregation of mitochondria in yeast: Estimating parameters using a random model

Summary Yeast zygotes which are heteroplasmic for mitochondrial genes reproduce vegetatively to form clones of diploid progeny which are homoplasmic. This vegetative segregation of mitochondrial genes has been interpreted in terms of a random distribution of mitochondria or mitochondrial genomes between mother and bud at cell division. We have developed equations which permit calculation of the number of segregating units in the zygote and the number of those units which enter the bud, assuming that segregation of the units is genetically random and numerically variable or equal. Use of the equations requires data from partial pedigree analyses: we isolate zygotes, separate the first bud, then determine the frequency of mitochondrial alleles among the progeny of mother cells whose first buds were homoplasmic. Application of this method to data from five crosses suggests that most zygotes have a small number of segregating units (usually less than a dozen) and only one or two enter the first bud. Analysis of the frequency of buds which are nearly but not quite homoplasmic indicates that the segregating units may be mitochondria or portions thereof which include many mitochondrial genomes, all the genomes in a unit being genetically identical in most but not all cases. These results are compatible with, but do not prove, the hypothesis of random vegetative segregation of mitochondria.     

The inheritance of heteroplasmy in guppies

Guppies Poecilia reticulata from the Rio Grande, Trinidad are heteroplasmic; individuals possess up to nine different-sized mtDNA haplotypes. A PCR survey of mtDNA length variation that included mothers and embryos suggests that a large number of mitochondrial genomes (possibly within a much smaller number of organelles) pass from one generation to the next.     

Cytological evidence of biparental inheritance of plastids and mitochondria inPelargonium

Summary Based on the organelle differences between egg and sperm cells inPelargonium hortorum, the zygote, proembryo, and endosperm were examined under the transmission electron microscope. Plastids and mitochondria in the egg cell are significantly different from those of the sperm cell. Egg plastids are starch-containing and less electron dense. They appear circular, elliptical irregular elongate in sections. Sperm cell plastids are relatively electrondense, mostly cup-shaped or dumbbell and devoid of starch granules. Mitochondria of the egg cell are giant and mostly cup-shaped while sperm mitochondria are smaller and usually circular in section. Double fertilization is completed by 24 h after pollination and the pollen tube can be seen in the degenerated synergid. In the zygote, plastids and mitochondria from male and female gametes can be distinguished by their characteristic differences. Moreover, paternal and maternal organelles appear to be distributed at random in the zygote. Aside from the pollen tube and its released starch granules, there is no enucleated cytoplasmic body in the degenerated synergid. Two days after pollination, the zygote undergoes one transverse division to form a 2-celled proembryo which consists of one larger vacuolated basal cell and one smaller densely cytoplasmic apical cell. Paternal and maternal organelles can be detected in both cells of the proembryo and also in the endosperm at this stage. From these results, it can be concluded that plastids and mitochondria from both male and female gametes have been transmitted into the apical cell of the proembryo and most probably to the following generation.Abbreviations TEM transmission electron microscope - DAPI 4,6-diamidino-2-phenylindole - RFLP restriction fragment length polymorphism     

Mitochondrial DNA Length Variation and Heteroplasmy in Populations of White Sturgeon (Acipenser Transmontanus)

Southern blot analysis was used to quantify the extent of mtDNA D-loop length variation in two populations of white sturgeon, Acipenser transmontanus. Over 42% of individuals were heteroplasmic for up to six different mtDNA length variants attributable to varying copy numbers of an 82-bp repeat sequence. Chi-square analyses revealed that the frequencies of length genotypes and the incidence of heteroplasmy were significantly different between Fraser and Columbia River sturgeon populations but not between restriction site haplotypes. Heteroplasmic fish have, on average, higher copy number than homoplasmic fish. Forty-five of 101 homoplasmic individuals carry only a single copy of the repeat, while none of the 73 heteroplasmic fish has the single repeat as the predominant variant. On the basis of differences in frequency distributions of copy number within and between fish, we suggest that (1) heteroplasmy is maintained by high recurrent mutation of multiple copy genomes, favoring increased copy number and (2) the mutation pressure toward higher copy number heteroplasmy is partially offset by selection to reduced genome size and segregation to the homoplasmic condition.     

THE ULTRASTRUCTURE OF DERBESIA TENUISSIMA (DE NOTARIS) CROUAN. I. ORGANIZATION OF THE GAMETOPHYTE PROTOPLAST,GAMETANGIUM, AND GAMETANGIAL PORE1,2,3

The fine structure of vegetative and reproductive gametophytes of Derbesia tenuissima is described. Development of the gametangium and release of the gametes progress as follows: (1) In initial stages of gametangium formation, prior to 24 hr before gamete release, there is an accumulation and proliferation of nuclei, chloroplasts, and other organelles. (2) This is followed by separation of the gametangium from the rest of the plant by a gametangial membrane; segregation of organelles into gametes has begun by 12 hr before release and the process is completed by 2.5 hr before release. (3) Enzymatic wall dissolution of the pore area occurs between 2.5 and, 12 hr before normal lights-on time. (4) The release mechanism appears to be an instantaneous light-induced increase in lurgor pressure rupturing the weakened pore area, of the wall and causing a forcible expulsion of the gametes. (5) Following release, the pore is sealed by organellar debris and the gametangial membrane. Additional wall layers are presumed to be laid down internal to the plugged pore by the vegetative protoplasm which migrates into the area.     

Effects of demographic parameters on metapopulation size and persistence: an analytical stochastic model

An analytical stochastic metapopulation model is developed. It describes how individuals will be distributed among patches as a function of density-dependent birth, death and emigration rates, and the probability of successful dispersal. The model includes demographic stochasticity, but not catastrophes, environmental stochasticity or variation in patch size and suitability. All patches are equally likely to be colonized by migrants. The model predicts: (a) mean and variance of the number of individuals per patch; (b) probability distribution of individuals per patch; (c) mean number of individuals in transit; and (d) turn-over rate and expected persistence time of a single patch. The model shows that (a) dispersal rates must be intermediate in order to ensure metapopulation persistence; (b) the mean number of individuals per patch is often well below the carrying capacity; (c) long transit times and/or high mortality during dispersal reduce the mean number of individuals per patch; (d) density-dependent emigration responses will usually increase metapopulation size and persistence compared with density-independent dispersal; (e) an increase in the per capita net growth rate can both increase and decrease metapopulation size and persistence depending on whether dispersal rates are high or low; (f) density-independent birth, death, and emigration rates lead to a spatial pattern described by the negative binomial distribution.     

Segregation of mitochondrial genomes in a heteroplasmic lineage with Leber hereditary optic neuroretinopathy.

Relatively little is known about the factors maintaining mitochondrial DNA (mtDNA) sequence diversity in humans. A detailed understanding of the transmission genetics of mtDNA has been partly hampered by the lack of evidence for heteroplasmic individuals. Among families with Leber hereditary optic neuroretinopathy, we found a maternal lineage with individuals heteroplasmic for a single nucleotide change, and we were able to follow the segregation of polymorphic mitochondrial genomes over 3 generations. The results show that rapid segregation can occur but also that the level of heteroplasmy can be maintained from one generation to another. In this family the disease phenotype is associated with the mtDNA sequence change, confirming the involvement of the mutation in the disease.     

Rapid mitochondrial DNA segregation in primate preimplantation embryos precedes somatic and germline bottleneck

The timing and mechanisms of mitochondrial DNA (mtDNA) segregation and transmission in mammals are poorly understood. Genetic bottleneck in female germ cells has been proposed as the main phenomenon responsible for rapid intergenerational segregation of heteroplasmic mtDNA. We demonstrate here that mtDNA segregation occurs during primate preimplantation embryogenesis resulting in partitioning of mtDNA variants between daughter blastomeres. A substantial shift toward homoplasmy occurred in fetuses and embryonic stem cells (ESCs) derived from these heteroplasmic embryos. We also observed a wide range of heteroplasmic mtDNA variants distributed in individual oocytes recovered from these fetuses. Thus, we present here evidence for a previously unknown mtDNA segregation and bottleneck during preimplantation embryo development, suggesting that return to the homoplasmic condition can occur during development of an individual organism from the zygote to birth, without a passage through the germline.     

Photographs of Fertilization in the Smaller Species of Trichonympha

SYNOPSIS. The photographs illustrate male and female gametes before fertilization, several progressive stages in the entrance of the male gamete into the cytoplasm of the female, cytoplasmic fusion of gametes, loss of extranuclear organelles of male gamete, retention of extranuclear organelles of female gamete, movement of pronucleus of male gamete to that of female, progressive stages in fusion of pronuclei, and the formation of the zygote which possesses the extranuclear organelles of the female gamete. Some abortive attempts at fertilization, resulting from failure of gametes to differentiate, are shown.     

DECOUPLING OF SHORT‐ AND LONG‐DISTANCE DISPERSAL PATHWAYS IN THE ENDEMIC NEW ZEALAND SEAWEED CARPOPHYLLUM MASCHALOCARPUM (PHAEOPHYCEAE,FUCALES)1

The processes that produce and maintain genetic structure in organisms operate at different timescales and on different life‐history stages. In marine macroalgae, gene flow occurs through gamete/zygote dispersal and rafting by adult thalli. Population genetic patterns arise from this contemporary gene flow interacting with historical processes. We analyzed spatial patterns of mitochondrial DNA variation to investigate contemporary and historical dispersal patterns in the New Zealand endemic fucalean brown alga Carpophyllum maschalocarpum (Turner) Grev. Populations bounded by habitat discontinuities were often strongly differentiated from adjoining populations over scales of tens of kilometers and intrapopulation diversity was generally low, except for one region of northeast New Zealand (the Bay of Plenty). There was evidence of strong connectivity between the northern and eastern regions of New Zealand’s North Island and between the North and South Islands of New Zealand and the Chatham Islands (separated by 650 km of open ocean). Moderate haplotypic diversity was found in Chatham Islands populations, while other southern populations showed low diversity consistent with Last Glacial Maximum (LGM) retreat and subsequent recolonization. We suggest that ocean current patterns and prevailing westerly winds facilitate long‐distance dispersal by floating adult thalli, decoupling genetic differentiation of Chatham Island populations from dispersal potential at the gamete/zygote stage. This study highlights the importance of encompassing the entire range of a species when inferring dispersal patterns from genetic differentiation, as realized dispersal distances can be contingent on local or regional oceanographic and historical processes.     

Dispersal response to climate change: scaling down to intraspecific variation

Range shift, a widespread response to climate change, will depend on species abilities to withstand warmer climates. However, these abilities may vary within species and such intraspecific variation can strongly impact species responses to climate change. Facing warmer climates, individuals should disperse according to their thermal optimum with consequences for species range shifts. Here, we studied individual dispersal of a reptile in response to climate warming and preferred temperature using a semi‐natural warming experiment. Individuals with low preferred temperatures dispersed more from warmer semi‐natural habitats, whereas individuals with higher preferred temperatures dispersed more from cooler habitats. These dispersal decisions partly matched phenotype‐dependent survival rates in the different thermal habitats, suggesting adaptive dispersal decisions. This process should result into a spatial segregation of thermal phenotypes along species moving ranges which should facilitate local adaptation to warming climates. We therefore call for range shift models including intraspecific variation in thermal phenotype and dispersal decision.     

Seed dispersal in both space and time is necessary for plant diversity maintenance in fragmented landscapes

Metacommunity theory emphasizes that seed dispersal not only limits but equally maintains plant diversity, though the latter receives little empirical attention. Discerning the temporal and spatial components of seed dispersal and understanding how their interaction shapes fragmented communities and maintains their diversity may be pivotal to further our ecological understanding of spatial and temporal seed dispersal and its implications for landscape‐scale conservation management. To investigate the relative importance of spatial and temporal seed dispersal and their roles in maintaining plant diversity, the herb layer and seed bank of grassland communities were inventoried in 77 sites across abandoned and intact rotational grazing networks in a 100 km² fragmented grassland landscape in the Stockholm archipelago (Baltic Sea, Sweden). Besides analysing alpha‐ and beta‐diversity patterns, nestedness analyses connect deterministic community changes and diversity losses with dispersal‐related life‐history traits and habitat specialization to identify the mechanism driving community changes and maintaining local diversity. The loss of rotational grazing networks caused community diversity declines via non‐random extinctions of spatially and temporally poor dispersers, particularly among grassland specialists. Temporal seed dispersal halted further community disassembly, maintaining diversity in the abandoned grazing networks. Spatial dispersal within the intact grazing networks was found to be an overriding, homogenizing agent conserving diversity in both the herb layer and seed bank. This empirical evidence establishes how spatial and temporal seed dispersal interact to maintain diversity in fragmented landscapes. Poorly connected grasslands appear limited by spatial dispersal, yet are maintained by temporal seed dispersal. In fragmented landscapes where grazing networks are rarely present, temporal rather than spatial seed dispersal may be more important in maintaining species diversity, since effective spatial dispersal may be significantly diminished. The grazing network's efficacy at boosting spatial dispersal and upholding community diversity presents a powerful management tool to conserve local and regional species diversity.