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Abstract
Genetic markers have provided plant ecologists with a method of assessing levels of genetic relatedness among individuals and populations. In recent years a number of techniques based on DNA sequence variation have been developed to complement allo- zyme methods that are already widely used. Some of these new markers are more variable than protein-based markers, allowing more precise estimates of genetic differences among individuals and populations. Other DNA-based markers are based on organelle genomes that are inherited uniparentally. These cytoplasmic markers can provide a method for as- sessing the separate effects of seed and pollen dispersal on gene flow within and among populations and species. Studies of hybrid populations have been facilitated by the devel- opment of inferential techniques for assessing levels of selection and patterns of intro- gression between species. Genetic markers have also been used to describe mating patterns within populations and to examine the ecological and genetic mechanisms that contribute to variation in selfing and reproductive success. Integration of ecological methods with genetic marker techniques continues to provide novel approaches to the study of evolu- tionary processes in plant populations.
... The following few pages provide a short history of some of these methods, with their applications in primate conservation. 1986; Rogers, 1989; Shimada, 1998; Grobler and Matlala, 2002; Li et al., 2003), plants (Cruzan, 1998) to microorganisms (Monis et al., 1999; Souza et al., 1999). These molecular markers are enzymatic proteins, products of coding DNA, which can be viewed through enzyme-specific staining reactions after said proteins are run through an agarose or polyacrilamide gel, a process called gel electrophoresis. ...
... Allozymes are known as co-dominant genetic markers with a low mutation rate. The low mutation rate of allozymes influences the effectiveness of this method when working with small populations or sample sizes during conservation genetic studies (Cruzan, 1998; Selkoe and Toonen, 2006). A negative aspect of using allozymes in conservation genetic studies is the requirement of large sample sizes for adequate protein extraction for analysis, which is especially difficult to obtain when working with wild populations (Di Foire, 2003), as some samples (liver, muscle, eye) must be collected invasively or lethally. ...
... Despite the negative points of this method, allozymes were used in a range of genetic studies. This is in part due to the cost-effectiveness of using this method as well as the low level of training needed (Hedrick and Miller, 1992; Cruzan, 1998). ...
Vervet monkeys (Chlorocebus aethiops) are one of the most widely distributed
primate species in Africa. The aim of this study was to determine the level of genetic
differentiation among conspecific vervet monkey populations in the south-eastern
regions of South Africa, as part of a bigger project to determine levels of
differentiation across South Africa. For this purpose, samples were taken from four
localities in the Free State Province (Soetdoring Nature Reserve (NR), Gariep Dam
NR, Sandveld NR and the Parys area), four Eastern Cape locations (Tsolwana NR,
Baviaanskloof NR, Shamwari Private Game Reserve (PGR) and the Nelson Mandela
Metropolitan University (NMMU) campus, Port Elizabeth), three Kwa-Zulu Natal
location (St. Lucia area) and one Limpopo Province locality. Genetic differentiation
was quantified using sequence data from a portion of the mtDNA control region.
Twelve Haplotypes were identified within the total sample group. The nucleotide
diversity for each grouping was calculated over all loci. Nucleotide diversity ranged
from 0 to 0.038% ±0.02. Haplotype frequencies distribution among samples was
calculated. An analysis of Molecular Variance (AMOVA) test was conducted and
population pairwise F
values were estimated. The AMOVA test revealed that the
majority of the genetic diversity occurred among the different groups (52.5%), with
only 4.9% of the variation found within populations. The populations were assigned
to groups according to geographic origins. The pairwise analysis identified
significant levels of genetic variation among populations, with an average F
ST
value
of 0.851. These haplotypes were found to coincide with the geographical borders of
Provinces. A ML tree was constructed using the haplotype data, and results showed
clustering corresponding to geographical borders. A phylogenetic network was
constructed, and this showed clustering similar to that found with the ML tree
analysis. According to these results it is clear that there is genetic structuring among
vervet monkey populations in South Africa. This clustering of populations can be
potentially explained by female philopatry and geographical barriers. Female
philopatry is a well known occurrence amongst Cercopithecine primates. The
occurrence of geographical barriers, such as rivers and mountains had influence on
migration rates and genetic structuring. This clustering pattern observed with
mtDNA analysis contradicts results from previous studies working with nuclear DNA markers. This can be caused by various factors. Except for female philopatry
having an effect on mtDNA differentiation patterns, it should be noted that the faster
evolutionary rate of mtDNA vs. nuclear DNA can also cause different genetic
patterns. The effective population size of mtDNA is also four-fold smaller than that of
nuclear genes, and will also cause skewed results when comparing mtDNA data with
nuclear DNA data. No reliable recommendations can be made toward the release of
rehabilitated vervet monkeys, as further analysis is needed. It is thus suggested to
use both genetic markers in follow-up studies. An increase in sample size from a
broader geographical range is also recommended. In addition to further work on
patterns of genetic variation, the adaptive significance of observed genetic
differences should also be investigated.
... Sequential pollination is usually defined as foreign and conspecific pollen grains being deposited on stigmas at different times (Snow et al. , 2000) and it frequently occurs under natural conditions (Arnold et al. , 1993). Sequential pollination is thought to have a strong effect on the siring ability of the different pollen types (Smith, 1970;Cruzan, 1998;Snow et al. , 2000). Studies further indicate that conspecific pollen preference often occurs both in mixed and in sequential pollination, and this phenomenon was actually observed by Darwin (for review see Arnold, 1997). ...
... Nevertheless, our knowledge on the effects that influence pollen performance in sequential pollination have is still limited. Studies using modern technology, particularly molecular markers, can help us to understand more fully the effect of sequential pollination on siring ability (Cruzan, 1998). ...
... In this study pollen germination and pollen tube growth in the mixed pollination were significantly lower than those in the foreign and conspecific pollinations, indicating the existence of interspecific competition. However, the low pollen germination and pollen tube growth could also be attributed to pollen tube attrition (inhibitory effect from style tissue) or variation in growth rates (scramble effect) (Cruzan, 1998). The attrition rate of pollen tubes can be determined by comparing the number of pollen tubes at the base of styles with that across mid-styles in the foreign and conspecific pollinations. ...
Post‐pollination competition is reported here in cultivated rice ( Oryza sativa ) and a perennial wild rice ( O. rufipogon ) to investigate the occurrence of crop‐to‐wild gene flow.
Wild and cultivated rice (variety Minghui‐63) were grown in a common garden in Hunan province, China, and crop‐specific genetic markers were used to detect hybridization following hand‐pollinations. Using 11 sequential pollination treatments, the effects of the relative timing of pollination on the success of foreign pollen was investigated.
Foreign pollen from the crop resulted in lower pollen germination, fewer pollen tubes per style, and a significant reduction of seed set, demonstrating a disadvantage of foreign pollen even in the absence of pollen competition. When 1 : 1 pollen mixtures were applied, only 2% of the resulting seeds were hybrids, revealing a much stronger disadvantage of foreign pollen when competing with conspecific pollen. Testing the effects of the relative timing of pollination on the success of foreign pollen suggested that conspecific pollen is often more successful than foreign pollen. Nonetheless, hybridization is possible following the deposition of pollen mixtures, especially when foreign pollen arrives earlier than conspecific pollen.
Pollen competition between wild and cultivated rice could slow the rate of crop‐to‐wild gene flow, but even if pollen competition was ubiquitous it would not prevent gene flow from the crop.
... Our specific goals are to (i) review some of the key markers that are used to inform biogeographic analyses (including their advantages and limitations); (ii) illustrate their application to inherently biogeographic questions, with examples drawn from studies conducted by scientists in a diversity of fields; and (iii) identify fertile liaisons between biogeographers and scholars in other areas of geography, as well as in other disciplines, whose collaboration could be richly informed by the incorporation of genetic analyses. Our intent is not to provide a comprehensive treatment of the wide array of molecular markers available, or the breadth of questions addressable with molecular approaches; in-depth reviews of the use of molecular markers are available elsewhere (Cruzan 1998;DeYoung and Honeycutt 2005;Ouborg et al. 1999;Parker et al. 1998;Schaal et al. 1998;Shaw et al. 2005, forthcoming;Sunnucks 2000). Instead, our intent is to introduce basic concepts concerning molecular markers that are relevant to biogeography and to discuss selected questions that are made possible by the use of molecular tools. ...
... Even though methods that examine DNA directly (i.e. most other markers) have become widespread in the last decade or so, allozyme analysis remains a straightforward and cost-effective way to determine levels of genetic diversity and the distribution of genetic variation within and among populations (Avise 1994;Cruzan 1998). Allozymes are co-dominant markers; their chief disadvantage is that they may underestimate genetic variability, because they reveal only mutations that are involved in synthesis of the proteins examined (DeYoung and Honeycutt 2005). ...
The last decade has seen tremendous increases in the variety and cost-efficiency of markers available to investigate genetic questions. Molecular markers have been used in a number of biogeographic studies; however, most of this work has been done by scholars in fields other than geography, despite the inherently spatial nature of questions many authors have addressed. This article calls for greater contribution by geographers to this body of work. We begin with a primer that reviews several of the most commonly used molecular markers available today. Next, we illustrate the use of those markers with biogeographic studies in two areas that have a long-standing tradition within geography: paleoenvironmental reconstruction and human-biota interactions. Finally, we identify areas where genetic approaches can greatly expand our biogeographic horizons, including collaborative work with geographers in other subdisciplines, as well as with scholars in other fields.
... However, there are a host of drawbacks. The main drawback of this approach is that it does not yield high levels of polymorphisms, which are needed to classify a large number of genotypes in a population (Cruzan, 1998), since enzyme activity is necessary to research a small number of loci (Beebee and Rowe, 2004). As a result, DNA-based approaches often replace or act in combination with allozymes in order to generate more polymorphisms. ...
Plant Ecogenomics offers a valuable introduction to plant ecology from a genomics point of view. The editors present a thorough foundation and summary of modern approaches, methodologies, research goals, and evidence of plant ecology in the modern genomic era. They also present important updated information on the most recent knowledge of the different aspects of plant populations.
The volume begins with a general overview of the various approaches to unravelling the genetic basis underlying fundamental responses of plants to their natural environments. It also describes in detail the concepts, aims, and approaches of plant ecological genomics along with the genomic tools embraced by ecologists for mining various ecological problems. Recent advances and breakthroughs made in molecular markers along with their applications in plant ecogenomic studies are shared, and specific applications, techniques, and tools are described as well, such advanced molecular techniques, next-generation sequencing, eDNA metabarcoding, among others.
The authors look at community and ecosystem responses in the form of phylogenetic systematics and the theory and methodology for inferring phylogenetic trees or cladograms, including parsimony, Bayesian, and maximum likelihood methods. The employability of QTL analysis and reverse genetics in plant ecogenomics is discussed. Other topics include the role of eco-genomics in conservation and management, models to study the population structure along with the genetic basis of speciation and adaptation in plants, and more.
The volume looks at how genetic variability is assessed with the help of various available tools and how effective they are in the conservation of important plant species. Inbreeding and genetic load and the role of ecogenomics in landscape genetic restoration are covered as well.
This volume offers a rich store of information on the interdisciplinary field of ecological genomics that will be valuable for molecular biologists, ecologists, as well as for researchers, scientists, and faculty and students in related areas.
... According to Cruzan (1998) one of the essential steps necessary to the determine the location of a disease resistance gene is to find DNA markers that are genetically linked with the resistance gene in order to identify its chromosomal location, a procedure known as genetic mapping. A genetic or linkage map is like a road map of an organism's chromosome using molecular markers. ...
Wheat stripe rust, caused by Puccinia striiformis, is a common disease that was found primarily in the Pacific Northwest prior to 1990, with occasional minor outbreaks in the eastern wheat regions. A physiological adaptation to higher temperatures that occurred around 1990 led to stripe rust becoming a major disease problem in the Gulf Coast. Race (pathotype) changes have occurred several times since 2000, resulting in cultivars with previously effective resistance genes becoming susceptible. The cultivar LA 841, developed by the LSU AgCenter, has remained resistant to all races of stripe rust in the area for over 15 years. It contains the gene cluster Lr37/Yr17/Sr38 with Yr17, conferring broad-spectrum stripe rust resistance until recent years, when new races of stripe rust became virulent on Yr17. LA841 has remained resistant after Yr17 has lost its effectiveness, which indicates that LA 841 contains alternate/additional stripe rust resistance genes. Our objective was to determine the genetics of the resistance in LA 841. A mapping population consisting of 192 F2 progeny derived from a cross between the resistant line LA 841 and susceptible line NC06BGTAG12, was genotyped with 216 polymorphic SSR and AFLP markers. The F2:3 progeny was phenotyped for their reaction to stripe rust in replicated trials at three locations: Winnsboro, Louisiana; Plains, Georgia; and Fayetteville, Arkansas. Three QTL were identified - two on the short arm of chromosome 2A and one on chromosome 3B which together explained 43.2% of the total variation for stripe rust resistance. The QTL on chromosome 3B was flanked by SSR markers Barc164 and Barc1044. One QTL on the 2A chromosome was flanked by SSR markers gwm 636 and gwm 359 while the other QTL on the same chromosome was flanked by gwm 359 and AFLP marker gcg 800-2. Yr17, located on the short arm of chromosome 2A, is most likely the QTL closest to marker gwm 636, which is linked to the gene. This QTL explained 8.6% of the variation but has a LOD value of 11.2, which is the highest of the three. The QTL with the largest effect was found in the short arm of chromosome 2A, which accounted for 22% of the variation and had an LOD value of 9.8. The QTL on chromosome 3B explained 13% of the variation and has a LOD value of 2.7, just over the threshold of 2.5. Identification of new QTL linked to resistance genes is important in breeding programs for disease resistance due to the constant adaptation of pathogens which overcome previously effective resistance genes.
... However, because the sample size and total amount of bands could influence the percentage of polymorphic bands value, other parameters that based on the frequency of polymorphic bands, such as Shannon's index of diversity and Simpson's index of diversity, are more suitable in estimating genetic variability (Cruzan 1998). The average of Shannon's index of diversity in the cultivars as studied is 0.44 (Table 3) indicating a relatively high degree of diversity among the tea population. ...
... However, environmental factors as well as the developmental stage of the plant influence such traits. DNA based markers provide more detailed genetic information to either the increased variability of loci or the greater number of the available loci (Cruzan, 1998;Ashley and Dow, 1994). These markers have successfully been used to estimate levels of relatedness among the individuals, studies of mating systems, and successful establishment in natural population. ...
... Although, most studies of P. merkusii were provided by isozyme analysis (Changtragoon and Finkeldey, 1995;Suwarni et al., 1999;Siregar and Hattemer, 2004;Thao et al., 2013), DNA markers such as simple sequence repeat (ISS), inter simple sequence repeat (ISSR), RAPDs have been used successfully used for analysis of pines populations (Alrababah et al., 2011;Marquardt et al., 2007;Mariette et al., 2001;Nurtjahjaningsih et al., 2007;Navascues and Emerson, 2007;Gauli et al., 2009;Thao et al., 2013;Thomas et al., 1999;Zhang et al., 2005). RAPD markers are useful tools to analyze the genetic diversity within and between plant populations (Fritsch and Rieseberg, 1996;Cruzan, 1998). Many species have been assessed using marker such as Gentianella germanica (Fischer and Matthies, 1998), rice (Qian et al., 2001) as well as pines (Alrababah et al., 2011;Lee et al., 2002;Xia et al., 2001;Zhang et al., 2005). ...
Pinus merkusii is an important species in Vietnam with many economic and biological contributions. The information on diversity within and between populations of a species is necessary for plantation programs, breeding and conservation strategies. Genetic diversity of three Vietnamese populations (NA, QB and QN) was analyzed using the random amplified polymorphic DNA (RAPD) markers. Nine RAPD primers produced 82 markers, 77 of which were polymorphic with 93.9% of polymorphism. The results showed higher genetic variation within populations (72%) than between populations (28%) and low Nei’s genetic differentiation index among populations (0.1867). The populations also clustered based on PCoA analysis where cluster I included NA and QB populations and Cluster II, the QN population. These results suggest that P. merkusii populations in Vietnam is necessary to develop the genetic resources.
... The study of genetic variation in plant populations was greatly facilitated by the development of protein based on markers i.e. allozymes over three decades ago (Hamrick and Godt, 1990). Allozyme markers remain the most useful tool for addressing many questions in plant population biology (Cruzan, 1998), although the development of DNA-based markers (Khandka et al., 1997) has revolutionized this field in recent years owing to their higher levels of polymorphism and because they are thought to be less subject to selection (Jenczewski et al., 1999). ...
Ten wheat (Triticum aestivum L.) cultivars were used in the present study, five Egyptian wheat namely, (E1) Sakha 93, (E2) Giza 168, (E3) Gemmiza 9; (E4) Shakha 94 and (E5) Egypt1 and five Yemeni wheat, (Y1) Behoth14, (Y2) Sonalica, (Y3) Acsadgahran, (Y4) Kaaalhakl and (Y5) Local wheat. Grain samples were obtained from Field Crops Research Institute, Agriculture Research Center, Giza, Egypt and Agricultural Researches Extinction authority (The Regional Agricultural Researches for Central Highland) in Yemeni Morphological, biochemical and molecular markers were used to detect the genetic relationship between all cultivars, also we study the effect of different salt levels on seedling performance as tool for calculate the genetic diversity between the Egyptian and Yemeni wheat cultivars. The results indicated that there are high significant variations with and within all wheat cultivars.
... Chloroplast DNA (cpDNA) markers revealed that the Ocoee and Hiwassee River populations are genetically divergent and that gene flow through seed dispersal is limited (Cruzan and Estill, 2001). However, cpDNA markers can be of limited usefulness for studies of population structure resulting from the low levels of intraspecific variation in chloroplast genomes (Cruzan, 1998). ...
Pityopsis ruthii is an endangered species endemic to the Hiwassee and Ocoee Rivers in Tennessee. As part of a recovery effort focused on P. ruthii, vegetative propagation and in vitro multiplication and seed germination techniques were developed. Plants were vegetatively propagated using greenhouse stock plants and wild-collected stems. Rooting occurred with and without auxin treatments but was greatest when 0.1% indole-3-butyric acid (IBA) talc was applied to the vegetative cuttings; rooting was lowest when flowering stems were used. Pro-Mix BX substrate provided the most consistent rooting. In vitro multiplication was accomplished by the removal of lateral shoots from in vitro-grown plants that were rooted on Murashige and Skoog (MS0) basal medium with 270 clones produced from a single individual after 4 months. Nineteen clones were transplanted and secured with bonded fiber matrix into their natural habitat and 14 survived for 1 year. To avoid genetic swamping of native populations with the introduction of large numbers of genetically identical individuals through clonal propagation, seed-based propagation efforts were explored. Open-pollinated seeds were collected, disinfested and germinated, and seedlings established on MS medium. Seeds were submersed in 70% ethanol for 1 minute and briefly flamed. Seeds were surface-sterilized in a range [10% to 50% (v/v)] Clorox® bleach solutions with vigorous shaking for 20 minutes, rinsed three times in sterile water, and germinated on MS0. Removal of pappus from seeds was required for successful disinfestations, but the bleach concentration was not critical. Successful propagation is a step toward the conservation and recovery of P. ruthii and should allow future reintroduction projects.
... Past limitations such as partly represented genetic diversity and the effect of natural selection on distribution of diversity associated with pedigree and morphological data, along with physiological and cytological markers, have been largely circumvented by the development of DNA markers (Soltis et al., 1992;Kidwell et al., 1994;Cruzan, 1998;Ghérardi et al., 1998) such as RFLPs (Botstein et al., 1980;Tavoletti et al., 1996;Pupilli et al., 2000), RAPDs (Williams et al., 1990), AFLPs (Zabeau & Vos, 1993;Julier et al., 2003) and SSRs (Tautz, 1989;Morgante & Olivieri, 1993;Provan et al., 1999). Their applicability could be extended in determining heterotic groups and identifying parents (Brummer, 1999). ...
Genetic variation in ten indigenous populations of Medicago sativa from Azerbaijan was investigated by randomly amplified polymorphic DNA (RAPD) analysis. A total of 80 and 78 fragments were scored using ten arbitrary primers for individual and bulk analysis, respectively. The percentage of polymorphic loci was 67.95% for bulk analysis whereas for individual-based analysis it was 100%. In spite of the low gene diversity, the bulk analysis was highly efficient in discriminating among populations based on genetic distances. Analysis of molecular variance (AMOVA) showed that approximately 80% of the total genetic variation was attributable to intrapopulation variance. However, measurements of Φ{phonetic} st (F statistics analog) were significant for all pairwise population comparisons. The within-populations considerable variation was expected due to the allogamy and autotetraploidy of alfalfa. Based on the differentiation among groups, the coancestry coefficient was the most effective in clustering populations. Among the four surveyed eco-geological traits, elevation of the region has affected populations' genetic structure more severely than any other. However, no significant differentiation between groups was observed.
... Molecular markers and more elaborate bio-informatic models allowed the development of multilocus approaches (Cruzan 1998). The multilocus approach uses information from all genotypes across various loci, better reflecting the true amount of crossing in open-pollinated populations (Ritland 2002). ...
Knowledge about patterns of variation in the mating system of partially allogamous species is essential for germplasm management. To elucidate patterns of variation, we tested two different types of cultivars, one locally adapted to the area and the other more widely adapted, in two different European agro-ecological conditions to help in developing effective germplasm management strategies. Agro-ecological conditions were: two locations and winter cultivars in southwest Europe; and five locations and spring cultivars in
northeast Europe. We analysed enzyme polymorphisms and applied multilocus biometrical models to determine mating system parameters. Outcrossing ranged from 0.14 to 0.72. These results were strongly influenced by agro-ecological conditions. Southwestern cultivars showed a consistently higher outcrossing
rate than did northeastern cultivars. No significant differences were found among local and widely adapted
cultivar outcrossing rates under northeastern conditions. However, under southwestern conditions, we found a tendency to higher selfing rates in the local cultivars than in the more widely adapted ones. Based on the degree of variation among the mating systems of faba bean cultivars, serious genetic erosion is a threat if the same regeneration and management protocols are used for all genebank accessions. Our data not only provide useful information to help in developing effective strategies for germplasm regeneration but also for the development of pre-breeding strategies and landrace enhancement.
... Estos marcadores también permiten describir los patrones genéticos que se dan en las poblaciones, así como analizar su estatus ecológico. Y proveen información que contribuye a dilucidar los procesos evolutivos de las poblaciones de plantas y a orientar las estrategias de conservación de las especies (Cruzan 1998 ...
El género Smilax es un grupo taxonómicamente complicado, por lo que se consideró necesario incursionar en el análisis bioquímico (isoenzimas) y molecular (RAPD) para aclarar el panorama filogenético de las “especies” que tradicionalmente se han clasificado como S. vanilliodora y S. regelli, con fines de explotación futura de sus ingredientes activos. Los resultados obtenidos con las pruebas de las condiciones de las electroforesis para especies de Smilax son satisfactorios. Tanto los buffers de extracción como los de electroforesis utilizados permiten el análisis poblacional con este tipo de muestras. El análisis de distancias genéticas resultado de las electroforesis no indican al menos alguna relación de grupo, de acuerdo con la clasificación inicial. Una relación que pareciera indicar el dendograma se refiere, sobre todo, a las muestras colectadas en el bosque, las cuales tendieron a formar un solo grupo independiente: si eran S. regelli o S. vanilliodora (según clasificación morfológica inicial). Los resultados obtenidos con PAPD, específicamente con los imprimadores CO-01, A-09, A-01, E-01 y E-03, no permiten establecer diferencias entre las supuestas especies diferentes de S. vanilliodora y S. regelli, lo que está de acuerdo con lo propuesto por Ferrufino (2003), quien considera que S. regelli es probablemente un isolectotipo de S. grandifolia y la descarta como otra especie del género.
... microsatellites and restriction fragment length polymorphism [RFLP]) while the percent polymorphic loci will be higher in dominant markers (e.g. amplified frequency length polymorphisms [AFLPs] and randomly amplified polymorphic DNA [RAPD]) (reviewed in Cruzan 1998;Parker et al. 1998). If population bottlenecks have been severe and too recent for sufficient mutation accumulation, diversity estimates based on different molecular markers could be more similar (Butcher et al. 1998). ...
The purpose of his research was to describethe organization of genetic variation in thefederally endangered plant taxon Eriogonumovalifolium var. vineum using allozymes. Such information can help prioritize sites andmanagement choices for capturing andmaintaining genetic variation and can reducethe number of populations necessary to committo conservation, thus reducing costs andconflicts with competing land uses. Information on genetic diversity patterns alsoprovides insight into evolutionary anddemographic history of a taxon which canprovide means to assess future risk of erosionof diversity. Similar to other Eriogonumovalifolium varieties, E. ovalifoliumvar. vineum is diverse atboth the taxon (proportion of polymorphic loci[P] = 0.55 and alleles per locus [A] =5.45 [SD = 2.5]) and population (P = 0.56 [SD =0.11] and A = 2.68 [SD = 0.35]) levels. Gene diversity (H
e) withinpopulations averaged 0.19 (SD = 0.03). Wefound some evidence for limited clonalreproduction within populations. Populationswere moderately differentiated from one another(ΘS = 0.14) and showed moderatedeviations from Hardy-Weinberg equilibriumwithin populations (f = 0.14 and F =0.19). Mean Nei's genetic distance (D)among all pairs of populations was 0.02. Populations with high levels of multiplemeasures of genetic diversity, high levels ofdifferentiation, and low levels of apparentinbreeding are suggested as conservationpriorities.
... Because they are codominant, it is possible for SSRs to distinguish homozygotes and heterozygotes. They are also highly variable and relatively easy to analyze, and they occur regularly throughout the genome (Frankel et al., 1995; Cruzan, 1998; Susol et al., 2000; Zane et al., 2002; Squirrell et al., 2003). Microsatellies are two to six nucleotide motifs that are repeated many times in tandem and display high dissimilarity in repeat number among individuals. ...
Phaedranassa viridiflora (Amaryllidaceae) is an endemic and endangered plant restricted to the Northern Andes in Ecuador. It is known in three locations where it is sympatric with other Phaedranassa species. Phaedranassa viridiflora is the only species of the genus with yellow flowers. We analyzed 13 microsatellite loci to elucidate the genetic structure of the populations of P. viridiflora. Our results pro-vided the first evidence of natural hybridization in the genus (between P. viridiflora and P. dubia in the Pululahua crater of northern Ecuador). The central and southern populations did not show hybridization. Genetic diversity was the highest in the Pululahua population. Central and southern populations have a higher proportion of clones than Pululahua. Bayesian and cluster analysis suggest that the yellow flower type evolved at least three times along the Ecuadorean Andes. In contrast to other Phaedranassa species, Phaedranassa viridiflora shows lower genetic diversity, which is likely related to a vegetative reproductive strategy.
... allozymes) over three decades ago (Loveless and Hamrick, 1984;Hamrick and Godt, 1990). Allozyme markers remain the most useful tool for addressing many questions in plant population biology (Cruzan, 1998), although the development of DNA-based markers (Karp et al., 1996;Khandka et al., 1997) has revolutionized this field in recent years owing to their higher levels of polymorphism and because they are thought to be less subject to selection (Jenczewski et al., 1999). RAPD markers are essentially unlimited in number and usually very polymorphic. ...
There is much concern over the high mortality of many populations of Acacia raddiana, a keystone tree species in the Negev desert of Israel. We used random amplified polymorphic DNA (RAPD) to assess patterns of genetic variation within and among 12 populations of A. raddiana from the Arava (Syrian–African Rift) valley and western Negev. A high level of genetic polymorphism was recorded within populations. An analysis of molecular variance (AMOVA) showed that about 59.4% of total genetic variance occurred among populations, which is considerably greater population differentiation than that recorded for other outbreeding species. Cluster and principal coordinates analyses and AMOVA indicate that the western Negev and Arava valley populations are highly differentiated. We suggest that there may have been two invasions of A. raddiana into Israel: one across the northern Sinai/Gaza Strip area into the western Negev, with some plants reaching the Dead Sea and a second invasion across the southern part of the Sinai peninsula, or even from Saudi Arabia, up to the Arava valley. From the conservation point of view, each population should be conserved separately because they are genetically highly differentiated and loss of any one population would lead to a dramatic loss of genetic variation. The mixing of genetically distinct populations may give rise to outbreeding depression (particularly because of GXE interactions). An obvious first step to the maintenance of this species' genetic diversity is the separate management of the western Negev and Arava valley populations because of their different evolutionary histories.
... For example, the inheritance of frond thickness in L. japonica was proven to be a quantitative characteristic with continuous variation (Zhang and Fang 1980), whereas in practice it was hard to keep the characteristic for several generations. Recently, the application of the random amplified polymorphic DNA (RAPD) technique has offered a promising marker system for detecting the genetic diversity in a population and it is useful in conservation genetics (Cruzan 1998;Sheng et al. 2004). Phycological applications of RAPD include the characterization of genetic variation (Dutcher and Kapraun 1994;Ho et al. 1995;Alberto et al. 1997;Yotsukura et al. 2001;He et al. 2003), the identification of hybrids (Patwary et al. 1993;Patwary and van der Meer 1994), and the analysis of phylogenetic relationships (van Oppen et al. 1994). ...
Molecular markers were used to identify and assess cultivars of Laminaria Lamx. and to delineate their phylogenetic relationships. Random amplified polymorphic DNA (RAPD) analysis was used for detection. After screening, 11 primers were selected and they yielded 133 bands in all, of which approximately 99.2% were polymorphic. The genetic distances between gametophytes ranged from 0.412 to 0.956. Two clusters were formed with the unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on the simple matching coefficient. All cultivars of Laminaria japonica Aresch. used for breeding in China fell into one cluster. L. japonica from Japan, L. saccharina (L.) Lam., and L. angustata Kjellm. formed the other cluster and showed higher genetic variation than L. japonica from China. Nuclear ribosomal DNA (rDNA) sequences, including internal transcribed spacers (ITS 1 and ITS2) were studied and aligned. The nucleotides of the sequences ranged from 634 to 668, with a total of 692 positions including ITS1, ITS2, and the 5.8S coding region. The phylogenetic tree obtained by the neighbor-joining method favored, to some extent, the results revealed by RAPD analysis. The present study indicates that RAPD and ITS analyses could be used to identify and assess Laminaria germplasm and to distinguish some species and, even intraspecies, in Laminaria.
(Managing editor: Ya-Qin HAN)
... Population geneticists commonly use cytoplasmic markers, for estimating the relative seed and pollen dispersal within and among populations (Cruzan, 1998). ...
Plants are distinguished among eukaryotes in possessing two DNA-containing organelles, the mitochondrion and the plastid, whereas, most eucaryotes contain only the mitochondrial genome. Recently, both organelles are used efficiently in population studies as plant geneticists developed molecular techniques that facilitated the study of plant diversity and evolution. In this paper, some comparisons among organelle and nuclear DNA, their mode of inheritance, examples of their use in genetic investigation of natural plant populations and the different sampling strategies for both markers were provided. The availability of completely sequenced genomes facilitated the development of markers (for example, consensus cp DNA markers). The use of the organelle markers as a tool in intra-specific studies of plant populations, can aid in clarifying their complex behavior by studying their respective distribution area and population dynamics such as in several phylogeography studies. Such studies can help in suggesting conservation management strategies in future for the populations under study.
... Developments in molecular techniques are making genetic markers more effective for measurement of relatedness and population structure, and are widening the scope of their application in ecology (Cruzan 1998;Snow & Parker 1998). Likewise, genetic markers have been of great impact in the field of quantitative genetics, mainly for identifying chromosomal segments or individual genes underlying a quantitative trait (Lynch & Walsh 1998). ...
This paper presents a perspective of how inferred relatedness, based on genetic marker data such as microsatellites or amplified fragment length polymorphisms (AFLPs), can be used to demonstrate quantitative genetic variation in natural populations. Variation at two levels is considered: among pairs of individuals within populations, and among pairs of subpopulations within a population. In the former, inferred pairwise relatedness, combined with trait measures, allow estimates of heritability ‘in the wild’. In the latter, estimates of QST are obtained, in the absence of known heritabilities, via estimates of pairwise FST. Estimators of relatedness based on the ‘Kronecker operator’ are given. Both methods require actual variation of relationship, a rarely studied aspect of population structure, and not necessarily present. Some conditions for appropriate population structures in the wild are identified, in part through a review of recent studies.
... The estimation of plant mating systems, or the pattern of genetic relatedness among mating individuals, is best achieved via the use of genetic markers (Ritland 1983Ritland , 2002). Traditionally isozymes have been utilized for this purpose (Brown & Allard 1970; Cruzan 1998), but their low levels of polymorphism confer little information regarding relatedness, reflecting high probabilities of gene 'identity-by-state' relative to gene 'identity-bydescent' . Microsatellite markers, with their high allelic diversity, have much closer correspondence between gene state and gene identity. ...
The high variability of microsatellite markers has allowed more powerful and novel inferences regarding mating systems. We show that the many alleles at microsatellite loci allow a different approach for estimating a mating system that uses four-gene coefficients of relationship; the four genes are those possessed by two progeny at a single locus. We estimated the mating system in four Mimulus taxa sampled from California, USA, all of which display inbreeding floral syndromes: Mimulus nasutus, Mimulus micranthus, Mimulus nudatus and Mimulus laciniatus. For each taxa, 20 progeny pairs were assayed for nine microsatellite loci. Substantial amounts of selfing were found, ranging from 64% to 92% across the taxa. Parent inbreeding coefficients were high (range 70%) in two taxa, and in these two taxa both facets of correlated matings (correlation of selfing and of outcrossed paternity) were also much higher (range 50–80%) than in the other two taxa. This association between correlated matings and levels of selfing has not been previously demonstrated. Microsatellites allow new approaches for mating system inference, but at the disadvantage of higher genotyping costs and potential biases resulting from null alleles.
... Following this estimate, we would expect that genetically identical individuals of the two species formed by clonal growth could be found in their natural habitats. In other words, genetically identical ramets should be identifiable in the populations of L. virgaurea and L. sagitta under natural conditions (in grasslands) using molecular tools, because all the individuals originating from a genet (directly and from its ramets) should share the identical genotype (Hartl and Clark 1997;Cruzan 1998) provided that clonal growth of the two species is realized irrespective of their growing conditions. However, the RAPD analysis based on the 201 clear and consistent bands did not reveal any genetically identical individuals in any of the populations of L. virgaurea and L. sagitta. ...
Ligularia virgaurea, L. sagitta and L. przewalskii are noxious weeds that are widely distributed in psychro-grasslands in the east of Qinghai-Tibet Plateau of China. However, little is known about reproductive modes and genetic diversity in the populations of L. virgaurea and L. sagitta under different environmental conditions, although such information is available for L. przewalskii. In this study, two experiments were conducted to examine the ex situ clonal growth of these weeds, and to determine the effects of reproductive modes on the diversity of their populations, using random amplified polymorphic DNA (RAPD) analysis. Transplanted seedlings of L.
sagitta and L. virgaurea showed considerable clonal growth by forming rhizomes and ramets. The RAPD analysis showed that all individuals collected from natural populations were genetically different, indicating that no individuals originated from clonal growth. It is concluded that L. virgaurea and L. sagitta have the capacity for clonal growth, but the expression of their clonality is constrained by their growing conditions in natural grasslands. Sexual reproduction plays the major role in their population diversity in natural habitats, which requires that the control measures for these weeds should be targeted at the sexually reproducing populations.
Context Red clover (Trifolium pratense L.) is an important legume forage in temperate agricultural zones. Evaluation of self- and cross-pollination fertility is important for setting up an effective breeding-program scale. However, the outcrossing rate of red clover under open-pollination conditions is not certain. Development of a reliable and time-saving marker system is needed to quantify and characterise outcrossing rates. Aim We aimed to develop a duplex PCR-based protocol based on a genome-wide simple sequence repeat (SSR) screen, and to determine the outcrossing rate of red clover under open-pollination environments. Methods We screened 209 SSR markers with pooled DNA samples of 60 plants from 20 red clover accessions, and selected 185 SSR markers that produced clear scorable bands for testing with 24 individual DNA samples to determine polymorphism. We selected 70 primer pairs, and then assembled a core set of 24 loci into 12 sets of duplex markers, which were used for outcrossing behaviour analysis of 60 maternal parents and their respective 22 half-sib progenies. Key results Mean polymorphic information content (PIC) for the 70 markers was 0.490 (range 0.117–0.878). Minimum, mean and maximum PIC values for the 24 markers constituting the 12 duplexes were 0.226, 0.594 and 0.781, respectively. The outcrossing rate was identified as 99.4% for red clover in a natural environment. Conclusion We successfully developed a duplex SSR-based PCR protocol consisting of 24 markers. This SSR system was applied to determine the outcrossing rate of red clover in a natural environment.
Nilgirianthus ciliatus is of interest for its extensive applications in Ayurvedic medicine. The study focuses on the assessment of genetic diversity and phylogenetic relationships in N. ciliatus populations to aid conservation of this species at risk of extinction. Thirty five inter simple sequence repeats (ISSR) and thirty random amplified polymorphic DNA (RAPD) markers were employed in PCR yielding 298 and 99 bands, respectively. Using ISSR markers, bands of 200–3500 bp were obtained and accounted for 77.0% of polymorphism observed. The polymorphism information content (PIC) and resolving power (Rp) values were 0.59 and 20.8, respectively. RAPD analysis resulted in 99 total bands of which 89 were polymorphic (89.9%). The PIC value for RAPD was 0.61 and Rp value was 18.8. The two different cluster analyses (UPGMA and Neighbor Joining) and principal component analysis showed the genetic variation among the populations. Clustering of N. ciliatus populations from different geographical regions in distinct groups can be a good sign for clear separation that is supported by high bootstrap values. Overall, both ISSR and RAPD analyses were valuable for identifying genetic variations and phylogenetic relationships in N. ciliatus populations at the DNA level and these differences provides the basic knowledge for better conservation management policies and genetic identification of the different geographical populations of this plant.
Advancement in the field of molecular biology has led to the development of various molecular markers which has revolutionized our understanding of the organization and evolution of plant genomes. Detection of genetic variation in plants offers an opportunity to understand the molecular basis of several biological phenomena. The reliability and efficiency of restriction digestion and polymerase chain reaction based random DNA markers have already proved their utility in taxonomical, evolutionary and ecological studies of plants. Progresses in the field of genomics and transcriptomics have enabled plant researchers to develop molecular markers derived from exon region of the genome which are termed as genic molecular markers (GMMs). GMMs are the part of the cDNA/EST sequences that mainly characterize the functional part of the genome. Next-generation DNA sequencing has also significantly contributed towards development of microRNA specific novel functional markers at the DNA level. This review focuses on the technical aspects of different molecular markers and their applications in the genome analysis.
Masting, or mast seeding, is the synchronous seed production in certain years by a population of plants (Kelly 1994). The reproductive activity of plants in forests often fluctuates considerably between years, and flowering and fruit production are synchronised over long distances (Koenig and Knops 1998, 2000, Koenig et al. 1999). Mast seeding has clear disadvantages such as higher density-dependent mortality of seedlings and lost opportunities for reproduction (Waller 1979). In addition, field observations suggest that seed production fluctuates more than the level that can be explained by climate-mediated variation in resource availability (Büsgen and Münch 1929). Two major questions arise from ecological studies on masting: Why is masting evolutionarily favoured regardless of apparent disadvantages? How do plants allocate resources to realise variable flowering efforts in a way synchronised over different individuals? A family of resource budget models that have recently been studied provides answers to both questions: on the physiological mechanism by which plants may successfully generate such intermittent and synchronous reproduction (Isagi et al. 1997, Satake and Iwasa 2000, 2002a, b) and on the conditions for which masting is adaptive (Rees et al. 2002, Tachiki and Iwasa 2008). Resource budget models assume that plants accumulate resources every year and set flowers and fruits at a rate limited by pollen availability when the stored resources exceed a reproductive threshold level. The model predicts that individual plants flower intermittently when their resources are depleted after heavy flowering and fruiting, and that synchrony emerges in self-organised fashion by coupling through the need to receive outcross pollen from other plants (Satake and Iwasa 2000).
The variable and synchronous production of seeds by plant populations is called masting or mast seeding and is observed in diverse forests (Kelly 1994). Many flowers and fruits are produced one year (called a mast year) but little reproductive activity occurs during the several subsequent years until the next mast year (Herrera et al. 1998, Koening and Knops 1998, 2000, Koening et al. 1999). The variance in the reproductive activity of trees between years is large. It cannot be simply a result of environmental fluctuation in annual productivity (Tamura and Hiura 1998). Many studies on masting have focused on adaptive significance (Kelly and Sork 2002). A popular hypothesis is the predator satiation theory - that is, seed predators starve during non-mast years, while they are unable to consume all the seeds during mast years (Janzen 1971, Silvertown 1980, Nilsson and Wästljung 1987, van Schaik et al. 1993). An alternative but not mutually exclusive hypothesis is pollination efficiency: in mast years, trees receive a lot of outcross pollen, which may improve fruiting success compared with reproduction in non-mast years (Nilsson and Wästljung 1987, Smith et al. 1990, van Schaik et al. 1993, Shibata et al. 1998, Kelly et al. 2001, Rees et al. 2002, Satake and Bjørnstad 2004).
In contrast with the fundamental ecological expectation that similarity induces competition and loss of species, temporal dynamics allows similar species to co-occur. In fact, the coexistence of similar species contributes significantly to species diversity and could affect ecosystem response to climate change. However, because temporal processes take place over time, they have often been a challenge to document or even to identify. Temporal Dynamics and Ecological Process brings together studies that have met this challenge and present two specific aspects of temporal processes: reproductive scheduling and the stable coexistence of similar species. By using plants to extract general principles, these studies uncover deep ties between temporal niche dynamics and the above central ecological issues, thereby providing a better understanding of what drives temporal processes in nature. Written by leading scientists in the field, this title will be a valuable source of reference to research ecologists and those interested in temporal ecology.
Over 50 years ago, Hutchinson (1941) noted that variation in environmental conditions could alter the outcome of competition. One implication of his observation was that environmental fluctuations could promote coexistence, allowing many species to persist in a habitat where all but one would be excluded under constant conditions. By the end of the 1980s, Chesson and colleagues had clearly described the theoretical requirements for coexistence via the storage effect (Chesson and Warner 1981, Warner and Chesson 1985, Chesson and Huntly 1989). Yet despite the long history of these ideas, relatively few direct empirical tests of the storage effect exist. Studies from a variety of natural ecosystems provide partial evidence for the storage effect (Pake and Venable 1995, 1996, Kelly and Bowler 2002, Descamps-Julien and Gonzalez 2005, Facelli et al. 2005, Kelly et al. 2008), but tests of all the required conditions or quantification of the strength of the effect are much rarer (Cáceres 1997, Adler et al. 2006, 2009, Angert et al. 2009). The lack of rigorous case studies limits our ability to generalise about the role of the temporal storage effect in maintaining diversity. We know that multiple coexistence mechanisms will operate in different communities, but currently we cannot say where the storage effect makes an especially important contribution. This information will be essential for understanding the consequences of expected increases in climate variability (Karl and Trenberth 2003, Jain et al. 2005, Salinger 2005, Allan and Soden 2008), which could impact species diversity in systems where the storage effect is important (Adler and Drake 2008). Understanding the influence of the storage effect on coexistence across a variety of ecosystems is therefore a prerequisite for anticipating future changes in species diversity.
Plant communities are structured in time as well as space. Their component species may differ in the timing of establishment, growth and reproduction both within and between years, creating temporal differences in relative abundances. Under appropriate conditions, temporal differences among co-occurring species can allow their coexistence (Grubb 1977, Chesson and Huntly 1997, Higgins et al. 2000, Kelly and Bowler 2002, 2005, Chesson et al. 2004, Schwinning et al. 2004, Adler et al. 2006). Whether or not temporal differences are responsible for the coexistence of any given pair or set of species, temporal niches are a fundamental part of community structure. Understanding this aspect of community structure is becoming even more important as we are called upon to interpret and to predict responses of communities to climate change (Dukes and Mooney 1999, Walther et al. 2002, Fischlin et al. 2007). In this study we examine temporal variation in population dynamics in a set of eight co-occurring herbaceous perennials. In addition to examining temporal variation in population sizes (densities), we use simple population dynamic models to provide estimates of temporal variation in equilibrium population density. Because actual densities lagged equilibrium population densities, the latter were more useful for comparing the temporal niches of different species and for relating temporal variation in precipitation to population dynamics. The degree of lag itself can be interpreted as a measure of the intensity of density-dependent population regulation, and variation in the degree of lag as another aspect of a species’ temporal niche.
In the last decade, a diverse array of new molecular tools has become available for various types of genetic studies at the population and higher levels. The rate at which these techniques are being developed far outpaces their competent incorporation into studies of population biology. Furthermore, in many cases, statistical methods for analysing novel genetic data have yet to be formulated (Parker et al. 1998). Nevertheless, in many areas of population and evolutionary biology, rapid progress is being made because newly available markers can identify individuals, populations, genetic strains, or closely related species. Thus, it is becoming increasingly important for population biologists to be able to understand and evaluate molecular data, and to know which molecular techniques are appropriate fnr solving their own research questions. Genetic markers have been subject to several recent reviews (Cruzan 1998, Geburek 1997, Haig 1998, Karp and Edwards 1997, Parker et al. 1998, Strauss et al. 1992a, Vekemans and Jacquemart 1997). However, these earlier works did not consider certain properties of genetic markers such as genomic origin and coding function or focused only on special applications such as biosystematics (Strauss et al. 1992a) or genome mapping (Staub et al. 1996, Strauss et al. 1992b). In cur present contribution, we present a brief review of currently available genetic markers and their applications in various areas of population biology with emphasis on the type of analysed DNA sequences.
The genetic diversity of re-established population of endangered species Allium angulosum L. was tested as a one part of rescue program. Founder individuals were picked in Chropyně - Záříčí area (North Moravia, Czech Republic) and new population was set in Protected Landscape Area Litovelské Pomoravi (North Moravia, Czech Republic). The task was whether the newly founded population was made by representative individuals to cover (include) the genetic variability of source (mother) population. Items were tested with variability assay of six isozyme systems (G-6-PDH, AAT, PGM, EST, ACP, PGI) using discontinuous polyacrylamide gel electrophoresis (PAGE). The method stated relatively sufficient level of variability on condition that new population would be raised to prevent genetic changes. Application of more tests checking the genetic diversity within population could be useful during reintroduction and management of endangered plant species.
Studies of genetic variation in wild populations usually are designed to identify the processes causing microevolutionary change. The availability of easily accessible, locus-specific genetic markers is crucial to this endeavor. Such markers have been widely available for only 30 years, but since the mid-1960s several major technological advances have given rise to a variety of new methods for measuring genetic variation. Accompanying these advances has been an exponential growth in the number of studies reporting population genetic variation in a wide variety of organisms. Our goal in this paper is to discuss the utility of various molecular markers for addressing microevolutionary questions. We have chosen to emphasize the questions themselves rather than the techniques per se. We hope that this will demonstrate how each technique can be applied successfully to a variety of studies, and that the question being addressed will to some extent dictate which technique is employed. Just as the choice of gene sequence in molecular phylogenetic analyses depends on the age of the lineage under investigation, the appropriate molecular marker for microevolutionary studies depends on the amount of genetic variation needed to elucidate a particular phenomenon. We have concentrated on recently developed DNA markers rather than on isozymes, not because we believe the former are more valuable, but because some readers may be less familiar with DNA methods than they are with protein electrophoresis. Familiarity with isozyme methods is due in large part to previous reviews of the application of protein electrophoresis in evolutionary studies (e.g., see Soltis and Soltis, 1989).
Trees and shrubs define the physical and biological frameworks of many of the world’s dominant terrestrial ecosystems. Their structural and functional importance also contributes to their being both understudied and over exploited. They are understudied because their sizes and life spans are typically much greater than our own, which makes them difficult subjects for experimentally-tidy studies. They are overexploited because we have too often treated the wood they yield as a resource to be extracted, and have been unwilling to invest the economic and intellectual resources needed to develop plantation forests in many parts of the world.
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This chapter focuses on the history, evolutionary role, and the phylogenetic impact of gene transfer through introgressive hybridization. The rudimentary understanding of hybridization and heredity demonstrated by ancient humans was largely lost until late in the 17th century. The possibility of gene transfer through introgression was not recognized until early in the 20th century, but its evolutionary importance has been debated ever since. The role of introgression in adaptive evolution is more difficult to assess, however, because advantageous alleles spread quickly, making it difficult to catch the introgression of favorable alleles in action. Nonetheless, molecular marker surveys indicate that introgression is widespread in both plants and animals. Thus, horizontal gene transfer and hybridization represent viable alternative explanations for discordance between gene lineages and organismal pedigrees. The model therefore, predicts that selection in the hybrid zone will be largely exogenous, that diagnostic characters should exhibit clinal variation if the zone occurs along an ecotone, and that only a subset of favored hybrid genotypes are likely to be common in the hybrid zone.
Plant mating systems can vary significantly in both space and time, influencing a range of demographic and genetic processes critical for the persistence of plant populations. Spatial and temporal mating-system variations were investigated in Banksia cuneata (A. S. George), a rare bird-pollinated shrub occurring in a highly fragmented landscape. Substantial variation in the mating system was observed, with the magnitude of temporal variation within a population often as high as the level of spatial variation among populations within a season. A significant reduction in outcrossing rates and increased temporal variation in both outcrossing rates and correlated paternity were observed in disturbed populations. Doubling of the paternal neighbourhood and a trend to increased outcrossing rate was found after augmentation of a disturbed population where population size was increased from 57 to 214 adult plants. A large increase in the fixation index for seeds compared with adults was observed in all populations, with the magnitude of the difference showing temporal and spatial uniformity. We suggest that temporal mating-system variation warrants increased consideration, not only in assessing the effects of habitat fragmentation on plant populations, but also in the design and establishment of successful translocation, augmentation and restoration programs.
Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) methods were applied to detect genetic variation of 20 bulking samples and two individually sampled populations of Oryza granulata (Nees et Am. ex Watt.) from China (M5 from Hainan Province and M27 from Yunnan Province). For the bulking sampled populations, 20 RAPD and 12 ISSR primers generated 209 and 122 bands, of which 134 (64.11%) and 89 (72.95%) were polymorphic respectively. For population M5, 146 and 95 bands were generated with 21.48% and 34.78% being polymorphic (PPB). For population M27, 151 (PPB = 17.22%) and 94 (PPB = 19.15%) bands of RAPD and ISSR were obtained. The results indicated that the level of genetic variation of O. granulata was lower than other species detected in the genus Oryza. UPGMA cluster based on genetic similarity and principle component analyses (PCA) based on band patterns divided the populations into two groups corresponding to their sources, which revealed that the majority of genetic variation of O. granulata occurred between Hainan and Yunnan. Consequently, more populations of the species should be considered for a reasonable conservation management. Comparison between the two marker systems showed that ISSR was better than RAPD in terms of reproducibility and ability of detecting genetic polymorphism. Mantel test revealed that the goodness of fit between them was significant (r = 0.917, t = 12.718) when detecting genetic diversity at species level, but was poor at population level (r < 0.200). The discrepancy was considered as the facts that different fragments were targeted by RAPD and ISSR, and that evolutionary process of O. granulata varied at different hierarchical levels.
In contrast with the fundamental ecological expectation that similarity induces competition and loss of species, temporal dynamics allows similar species to co-occur. In fact, the coexistence of similar species contributes significantly to species diversity and could affect ecosystem response to climate change. However, because temporal processes take place over time, they have often been a challenge to document or even to identify. Temporal Dynamics and Ecological Process brings together studies that have met this challenge and present two specific aspects of temporal processes: reproductive scheduling and the stable coexistence of similar species. By using plants to extract general principles, these studies uncover deep ties between temporal niche dynamics and the above central ecological issues, thereby providing a better understanding of what drives temporal processes in nature. Written by leading scientists in the field, this title will be a valuable source of reference to research ecologists and those interested in temporal ecology.
Thinopyrum intermedium is an important species with potential utilization value in breeding of wheat. In this study, the non-coding intergenic region of trnH-psbA was investigated to assess the genetic diversity and infer the maternal origin within T. intermedium accessions. Eleven haplotypes were distinguished among the thirty-five accessions of T. intermedium. They showed a relatively low nucleotide diversity (π) of 0.00473 ± 0.00037 and a moderately high haplotype diversity (Hd) of 0.733 ± 0.061. In the phylogenetic analysis, all accessions of T. intermedium were positioned into two clades, which corresponded to the different diploid donors. These results suggested that there were two phylogenetically divergent maternal donors in T. intermedium.
Thinopyrum intermedium is an important species with potential utilization value in breeding of wheat. In this study, the non-coding intergenic region of trnH-psbA was investigated to assess the genetic diversity and infer the maternal origin within T. intermedium accessions. Eleven haplotypes were distinguished among the thirty-five accessions of T. intermedium. They showed a relatively low nucleotide diversity (π) of 0.00473 ± 0.00037 and a moderately high haplotype diversity (Hd) of 0.733 ± 0.061. In the phylogenetic analysis, all accessions of T. intermedium were positioned into two clades, which corresponded to the different diploid donors. These results suggested that there were two phylogenetically divergent maternal donors in T. intermedium.
The recent development of a number of molecular markers has provided new approaches to the analysis of biogeographic patterns and underlying evolutionary processes. After a brief overview of selected molecular markers, we discuss lines of biogeographic inquiry involving genetic analysis where geographers can potentially make the greatest contribution. Examples from our own genetically-based biogeographic research are provided. These include examination of spatial patterns of genetic variation, inferences about paleoenvironmental conditions, determination of evolutionary relationships, and analysis of genetic effects of human activity.
Many trees in mature forests show intermittent reproduction. Intensive flowering and seed production occur only once in several years, often synchronized over a long distance. In a previous paper, we showed that the limitation of fruit production by the outcross pollen availability can bring about synchronized reproduction of trees in a constant environment, assuming that pollen availability depends on the mean flowering intensity of the trees. However, pollen exchange normally occurs within a distance much shorter than the extent of the whole forest. We studied a coupled map lattice, in which each tree engages in the chaotic dynamics of energy reserve level, but different trees are coupled by pollen exchange with neighbors. We first derived a relation between two statistics of spatial covariance (dynamic spatial covariance and snapshot spatial covariance). A strong synchronization of tree reproduction can develop over the whole forest that may be orders of magnitude larger than the distance of direct pollen exchange between trees. The fluctuation is close to a cycle with a period of two years. The model of local coupling always generates non-uniform spatial patterns, but the enhanced spatial covariance caused by the spatial heterogeneity is restricted to a short range, only a few times larger than the spatial range of direct interaction. When pollen exchange occurs beyond the nearest neighbors, the local spatial pattern becomes proportionally larger, but the condition for synchronization of the whole forest and its magnitude are the same as for the case with the nearest neighbor pollen exchange. When a fraction of the seeds are sired by globally dispersed pollen and the rest are sired by local pollen, long-range synchronization can occur for a wide-parameter region, and trees may engage in a fluctuation with a masting interval longer than two years. We discuss alternative explanations for the long-range synchronization of beech forests.
Butea monosperma (Lam.) Taub. (English. Flame of the forest) belonging to the family Fabaceae, is an anthropogenic tree of several castes and also a very useful tree for both local people and pharmaceutical industry. This valuable tree needs attention for the characterization of its genetic diversity, protection and cultivation. The present work describes randomly amplified polymorphic DNA (RAPD) analysis to assess the genetic divergence among 16 Butea accessions collected from four agro-ecological regions of India (nine agro-climatic sub zones), coverring five states (Uttarakhand, Uttar Pradesh, Rajasthan, Madhya Pradesh and Karnataka). Out of the 30 ten mer random primers used for studying genetic divergence, 12 were polymorphic, generating a total of 145 amplification products with an average of 12 products per polymorphic primer and an estimated mean gene diversity of 0.43. Genetic relationships among accessions were evaluated by generating a similarity matrix based on Jaccard's coefficient ranging from 0.53 to 0.79. The phenetic dendrogram generated by UPGMA analysis grouped accessions into four clusters. Primer 5, 12 and 16 were found most informative based on their resolving power and their potential to differentiate all the accessions. The degree of genetic variation detected among the 16 accessions with RAPD analysis suggested that RAPD could be used for studying genetic diversity in Butea. The study also demonstrated that Butea germplasm collected from different agro-ecological regions showed no isolation based on sub- climatic zones as the accessions collected from different sub-climatic zones grouped together in the genetic tree.
Population size and habitat disturbance are key factors likely to shape the mating system of populations in disturbed and fragmented landscapes. They would be expected to influence the availability and behaviour of the pollinator, the ability to find mates in self-incompatible species, inbreeding in self-compatible species and the size of the pollen pool. These in turn might be expected to influence key variables critical for population persistence such as seed production, seed germination and seedling fitness. Here we investigate mating-system variation in six rare species, i.e. Banksia cuneata, B. oligantha, Lambertia orbifolia (Proteaceae), Verticordia fimbrilepis subsp. fimbrilepis, Eucalyptus rameliana (Myrtaceae), Acacia sciophanes (Mimosaceae), and two common species, i.e. Calothamnus quadrifidus (Myrtaceae) and Acacia anfractuosa. All seven species are animal-pollinated relatively long-lived woody shrubs with mixed-mating systems. Population variation in mating-system parameters was investigated in relation to population size and habitat disturbance. We show that although the mating system will vary depending on pollination biology and life-history, as populations get smaller and habitat disturbance increases there is a trend towards increased inbreeding, smaller effective sizes of paternal pollen pools and greater variation in outcrossing among plants. From the species investigated in this study we have found that changes in the mating system can be useful indicators of population processes and can give valuable insight into the development of conservation strategies for the persistence of plant species following anthropogenic disturbance and landscape fragmentation.
Rapid progress is being made in many areas of forest population genetics owing to the newly available molecular techniques and the fast growth of genomic and sequence data. This paper reviews the currently available genetic markers and their applications in studies on gene diversity, population structure and differentiation, gene flow, introgression, phylogeny and gene evolution. Various marker-based population analyses have highlighted the evolutionary history of many tree species. However, up to now, genetic markers have not fulfilled the expectations for studies on the adaptive variation and the effects of natural selection on forest tree populations. Studies based on integrated and extensive genome sampling, especially the coding regions of the genome, in combination with adaptive traits can potentially improve this situation. This would provide us with a comprehensive knowledge of the evolutionary mechanisms shaping the population changes, both adaptive and neutral.
Allozyme studies have been widely used to estimate genetic variation and to describe genetic structure in natural populations. In many cases, the genetic diversity of recently established populations is generally lower than that of central populations. In addition, the genetic composition of an invasive species is influenced by its history of introduction as well as its ecological characters. Ageratina altissima (L.) R. King & H. Robinson (white snake root) is a perennial herb native to the eastern United States and Canada, and is currently receiving much attention for its rapid invasion of the Korean forests. Starch gel electrophoresis was used to assess the genetic variability at 11 putative loci in seven introduced populations of A. altissima in Seoul. Populations of A. altissima maintained lower levels of allozyme diversity (expected heterozygosity = 0.063) than those reported for other taxa with similar ecological traits. The degree of differentiation observed among A. altissima populations was considerably low. It is suggested that the populations were recently established from only a few founders via dispersal by human activities, resulting in the loss of genetic variation.
Senna multijuga is a pioneer tropical tree species that occurs mainly in the Brazilian Atlantic forest. We investigated the mating system of two populations of S. multijuga, one located in a reserve area (RD1) and the other (RD2) about 15 km away. The mating system parameters were estimated using the mixed mating model (software MLTR). The two populations had significantly different outcrossing rates, with population RD2 having a high rate (t m = 0.838) and population RD1, a lower rate (t m = 0.540). The values of t s were different between the two populations and also lower than those of t m . Significant t m -t s estimates indicated that biparental inbreeding contributed to the apparent selfing rate in these populations. The correlation of paternity was significant in population RD2 (r p = 0.309), suggesting that the progeny were more closely related than inferred by the observed outcrossing rate. The estimates of correlation of paternity, biparental inbreeding and the significant differences in pollen and ovule allele frequencies indicated that population RD2 is genetically substructured. For a pioneer species such as S. multijuga, selfing can be an important strategy for occupying open areas.
— The level and distribution of genetic variation is thought to be affected primarily by the size of individual populations and by gene flow among populations. Although the effects of population size have frequently been examined, the contributions of regional gene flow to levels of genetic variation are less well known. Here I examine the effects of population size and the number of neighboring populations (metapopulation density) on the distribution and maintenance of genetic diversity in an endemic herbaceous perennial. Reductions in the proportion of polymorphic loci and the effective number of alleles per locus were apparent for many populations with a census size of less than 100 individuals, but no effects of population size on levels of inbreeding were detected. I assess the effects of regional population density on levels of diversity and inbreeding using stepwise regression analysis of metapopulation diameter (i.e., the size of a circle within which population density is estimated). This procedure provides a spatially explicit evaluation of the effects of metapopulation size on population genetic parameters and indicates the critical number of neighboring populations (fragmentation threshold) for the regional maintenance of genetic diversity. Stepwise regression analyses revealed fragmentation thresholds at two levels; at a scale of 2 km, where small metapopulations resulted in greater levels of selfing or sibling mating, and at a scale of 8 km, where metapopulation size was positively associated with higher levels of genetic diversity. I hypothesize that the smaller fragmentation threshold may reflect higher levels of selfing in isolated populations because of the absence of pollinators. The larger threshold probably indicates the maximum distance over which pollen dispersal rates are high enough to counteract genetic drift. This study demonstrates that the regional distribution of populations can be an important factor for the long-term maintenance of genetic variation.
— We use chloroplast DNA (cpDNA) variation and nested clade phylogeographic analyses to infer the historical processes that have contributed to the high level of morphological and ecological diversification present in a group of herbaceous perennials (the Piriqueta caroliniana complex) in North America and the Bahamas. The presence of morphologically distinct and intercompatible varieties (morphotypes) that can be distinguished based on suites of taxonomic characters (e.g., leaf shape, pubescence type, stature) and contrasting habitat affinities (from marshes to dry pinelands and sand scrub) makes this group particularly appropriate for studies of intraspecific diversification. To examine the distribution of haplotypes among populations, we sampled 467 individuals from 55 locations in Florida, Georgia, and the northern Bahamas (Grand Bahama and Abaco) and screened each individual for cpDNA variation using restriction fragment length polymorphism (RFLP) and heteroduplex analyses. We develop a one-step haplotype phylogeny for this group and use the geographic distributions of haplotypes and clades to test specific phylogeographic hypotheses using the methods developed by Templeton and his colleagues (Templeton 1998). In general, the distribution of haplotypes was strongly influenced by limited dispersal distances, with the more recently derived haplotypes having much lower levels of dispersion and lower frequencies in populations than the ancestral haplotypes. The patterns of clade and haplotype dispersion and displacement and the distribution of morphotypes imply at least three cases of long-distance dispersal and one case of historical fragmentation. The historical patterns inferred for populations of Piriqueta are consistent with known biogeographical events, historical vegetation change, and the concordant patterns of multiple Pleistocene refugia that have been observed for a number of other taxa in southeastern North America.
We investigated the effects that habitat variation has on the structure and dynamics of a hybrid zone between two closely related crickets in Connecticut. A collecting protocol was developed in which crickets were sampled from characteristic habitats on either side of the hybrid zone and from two distinct habitat types within the zone. Presumptive pure Gryllus pennsylvanicus were sampled from fields in northwestern Connecticut and represent "inland" populations. "Pure" Gryllus firmus were sampled from beaches along the coast and represent the "coastal" populations. Crickets from within the hybrid zone were sampled from two different soil types: the "loam" populations from loamy soils and the "sand" populations from sandy soils. Moreover, an attempt was made to identify closely adjacent sand and loam localities to determine the scale of habitat variation and its possible effects on hybrid-zone structure. In general, there was little variation in morphological traits or in allozyme and mtDNA genotype frequencies among localities from within each of the four habitat types. Between each of the closely situated sand and loam localities within the hybrid zone, however, there were very significant differences in each of these sets of markers. In addition, crickets from hybrid-zone populations were tested for reproductive isolation. The asymmetric outcome of hybrid crosses that exists across the zone (Harrison, 1983) also exists on a finer ecological scale within the zone. Thus, this hybrid zone is a mosaic of strikingly differentiated populations. The dynamics of hybrid zones with mosaic structures are discussed in contrast to the traditional clinal models. The data are also discussed in light of the semipermeable nature of species boundaries. The extent to which a species boundary is permeable varies not only from one genetic marker to the next, but also with the ecological and geographic context of species interaction.
In this study we examine the cytoplasmic inheritance patterns of an interspecific hybridizing population of Fremont and narrowleaf cottonwoods, using mitochondrial DNA. Three mitochondrial probes showing polymorphisms were used to distinguish between trees of known nuclear inheritance. Every tree screened had only one cytoplasmic genotype, either Fremont or narrowleaf. Thus, these results demonstrate that mitochondria are uniparentally inherited in these trees. Previous studies of the nuclear inheritance of this interspecific hybridizing population of cottonwood trees indicated an asymmetry in the frequency of parental genes. Using mitochondrial markers we tested one hypothesis potentially responsible for this asymmetric distribution (i.e., trees of mixed genotypes will be sterile or will not survive if their cytoplasm is derived from one or the other parent). Our results, however, show that both Fremont and narrowleaf mitochondrial markers are found in trees with mixed nuclear genotypes. Thus, nuclear-cytoplasmic incompatibilities do not appear to account for the asymmetric distribution of nuclear genotypes within the hybrid swarm. An alternative explanation for the observed asymmetric distribution of nuclear genotypes is advanced. Although nuclear-cytoplasmic incompatibilities do not appear to explain the asymmetric distribution of nuclear alleles within the hybrid zone, nonrandom associations between nuclear and cytoplasmic genotypes do exist. For example, all F1 hybrids had Fremont mitochondrial genotypes. Furthermore, backcrosses between F1 hybrid and narrowleaf trees have a higher than expected proportion of heterozygous loci and a higher than expected proportion of Fremont mitochondria. We propose that seeds, seedlings, or trees with high proportions of heterozygous loci are at a disadvantage unless they also have the Fremont mitochondrial genotype. While it is generally difficult to infer dynamic processes from static patterns, studies such as ours enable one to gain new insights to the dynamics of plant hybrid zones. A hybridization pattern of decreasingly complex backcrosses as one proceeds from higher to lower elevation within the hybrid swarm, a residue of Fremont cytoplasmic DNA within the pure narrowleaf population, and the unidirectional nature of these crosses suggest that the narrowleaf population may be spreading down the canyon and the Fremont population receding. The eventual fate of the hybrid zone, in relation to these processes, is discussed.
SPECIATION is the process whereby populations acquire sufficient genetic differences to become reproductively isolated1. Since Darwin it has been recognized that the tempo and mode of specia-tion are greatly influenced by the number and magnitude of genetic changes required for reproductive isolation2-6, but detailed genetic studies have been limited to a few taxa such as Drosophila7. Genome mapping techniques now widely adopted in plant8,9 and animal10,11 breeding make it possible to investigate the genetic basis of reproductive isolating mechanisms in natural populations. Here we use this approach to map eight floral traits in two sym-patric monkeyflower species that are reproductively isolated owing to pollinator preference by bumblebees or hummingbirds. For each trait we found at least one quantitative trait locus accounting for more than 25% of the phenotypic variance. This suggests that genes of large effect can contribute to speciation.
Previous workers have obtained evidence suggesting that, under natural conditions, Papaver dubium reproduces by mixed selfing and random mating, the contribution of selfing being substantial. In order to obtain a more quantitative estimate of the amount of selfing, a small number of plants, homozygous or heterozygous for the recessive (flower colour) mutant, magenta, were raised among a large number of wild-type homozygotes and allowed to open pollinate. Progenies raised from these recessive homozygotes and from the heterozygotes, provided estimates of the degree of selfing. Results showed that the degree of selfing varies significantly, both between plants and between different flowers on the same plant. The estimates of average selfing obtained lay between 71 and 81 per cent, the estimates being about the same in two different years. In view of these and earlier results, it was concluded that a high degree of selfing obtains in natural populations of P. dubium; the degree of selfing being sufficiently large to have an important effect on the genetical structure of such populations.
From a study of the geographic occurrences of contemporary hybridization among North American animals, it has become apparent that most of the hybrids are produced in a few relatively localized zones, with little hybridizing in the vast areas between these zones of mixing. The hybrids tend to be at least moderately fertile and therefore to be a source of significant gene exchange between the typically allopatric pairs of species and semispecies. There is a wide variety of consequences from this introgression, with greater or lesser influence on the parental populations, and large portions of the fauna and probably flora are involved. An appropriate term for such a belt of interfaunal and interfloral linkage is suture-zone.1
Ten enzyme systems were investigated by electrophoresis in two species of Typha from the southeastern United States. Analysis of 74 populations of T latifolia and 52 of T domingensis revealed no intraspecific biochemical polymorphisms nor any evidence for hybridization. The species were distinct from one another (Ī = .60) but well within the range for congeneric comparisons. The lack of intraspecific variability may be related to reproductive structure and drift, undetected variability at regulator loci, or electrophoretic bias.
Outcrossing rates in natural populations of Lupinus nanus Dougl. have been found to vary from nearly zero to nearly 100 percent (Harding and Horovitz, 1969; Harding, 1970). These studies were based primarily on a group of northern populations of subspecies apricus (Elliott, Harding, and Mankinen; paper VI). The purposes of this paper are (1) to report estimates of outcrossing for the other subspecies of L. nanus , (2) to report estimates of outcrossing for the closely related species, L. bicolor, L. affinis, L. polycarpus , and L. pachylobus , (3) to discuss the relationship between these estimates of outcrossing and autofertility, and (4) to discuss the relationship between outcrossing and phenotypic and genotypic variability maintained in populations.
We have mapped genes causing life-history trade-offs, and they behave as predicted by ecological theory. Energetic and quantitative-genetic models suggest a trade-off between age and size at first reproduction. Natural selection favored plants that flower early and attain large size at first reproduction. Response to selection was opposed by a genetic trade-off between these two components of fitness. Two quantitative-trait loci (QTLs) influencing flowering time were mapped in a recombinant inbred population of Arabidopsis. These QTLs also influenced size at first reproduction, but did not affect growth rate (resource acquisition). Substitutions of small chromosomal segments, which may represent allelic differences at flowering time loci, caused genetic trade-offs between life-history components. One QTL explained 22% of the genetic variation in flowering time. It is within a few centiMorgans (cM) of the gigantea (GI) locus, and may be allelic with GI. Sixteen percent of the genetic variation was explained by another QTL, FDR1 near 18 cM on chromosome II, which does not correspond to any previously identified flowering-time locus. These life-history genes regulate patterns of resource allocation and life-history trade-offs in this population.
We examined mtDNA and nuclear allozyme genotypes in hybrid populations formed from interbreeding of westslope cutthroat trout (Oncorhynchus clarki lewisi) and Yellowstone cutthroat trout (O. c. bouvieri). These subspecies show substantial genetic divergence (Nei's D = 0.30; mtDNA P = 0.02). Diagnostic alleles at multiple nuclear loci and two distinct mtDNA haplotypes segregate in the hybrids. Nuclear and mtDNA genotypes are largely randomly associated, although there is slight disequilibrium in both nuclear and cytonuclear measures in some samples. Consistent positive gametic disequilibria for three pairs of nuclear loci confirm one previously reported linkage, and indicate two more. Allele frequencies provide no evidence for selection on individual chromosome segments. However, westslope mtDNA haplotype frequencies exceed westslope nuclear allele frequencies in all samples. This may be explained by differences in the frequency of occurrence of reciprocal F1 matings, by viability, fertility, or sex ratio differences in the progeny of reciprocal matings, or by weak selection on mtDNA haplotypes.
Heterostyly has been viewed as both an antiselfing device and a mechanism that increases the proficiency of pollen transfer between plants. We used experimental manipulation of the morph structure of garden populations of self-compatible, tristylous Eichhornia paniculata to investigate the function of floral polymorphism. Outcrossing rates (t), levels of intermorph mating (d), and morph-specific male and female reproductive success were compared in replicate trimorphic and monomorphic populations. In trimorphic populations, t and d averaged 0.81 (2 SE = 0.03) and 0.77 (2 SE = 0.03) respectively, with no difference in either parameter among morphs. Ninety-five percent of outcrossed seeds were therefore the result of intermorph fertilizations. Male reproductive success of the long-styled morph was low, especially in comparison with plants of the short-styled morph. Outcrossing rates for each morph were higher in trimorphic than monomorphic populations where t averaged 0.71 (2 SE = 0.01), 0.30 (2 SE = 0.04) and 0.43 (2 SE = 0.1) for the long-, mid-, and short-styled morphs, respectively. Seed set was lower in monomorphic populations, particularly those composed of the L morph, reflecting reduced pollen deposition. Floral polymorphism therefore increased both outcrossing rate and fecundity but the magnitude of the differences varied among morphs. If the ancestral condition in heterostylous groups resembled the L morph, as has been suggested, data from this study suggests that the selective basis for the establishment of floral polymorphism could have been increased pollen transfer rather than higher levels of outcrossing.
The evolutionary dynamics of recessive or slightly dominant lethal mutations in partially self-fertilizing plants are analyzed using two models. In the identity-equilibrium model, lethals occur at a finite number of unlinked loci among which genotype frequencies are independent in mature plants. In the Kondrashov model, lethals occur at an infinite number of unlinked loci with identity disequilibrium produced by partial selfing. If the genomic mutation rate to (nearly) recessive lethal alleles is sufficiently high, such that the mean number of lethals (or lethal equivalents) per mature plant maintained at equilibrium under complete outcrossing exceeds 10, selective interference among loci creates a sharp discontinuity in the mean number of lethals maintained as a function of the selfing rate. Virtually no purging of the lethals occurs unless the selfing rate closely approaches or exceeds a threshold selfing rate, at which there is a precipitous drop in the mean number of lethals maintained. Identity disequilibrium lowers the threshold selfing rate by increasing the ratio of variance to mean number of lethals per plant, increasing the opportunity for selection. This theory helps to explain observations on plant species that display very high inbreeding depression despite intermediate selfing rates.
Flower production is the major determinant of pollen yield and an important component in pollinator attraction. Consequently differences among plants in flower production are expected to have a substantial impact on their relative success at fathering seed. We examined this prediction using one natural and three structured populations of wild radish. We found that a plant's relative success, at fathering seed on another plant in the population (male fertility) increased with flower production. Nonetheless, the increase in fertility exhibited a diminishing marginal gain, with the relationship varying among populations. The relationship between the estimates of total number of seeds sired and flower production varied substantially among the populations examined, ranging from a weakly linear to strongly negative quadratic. Not surprisingly, the spatial structure of the population with respect to seed yield had a powerful effect on the total number of seeds sired because male fertility decreased exponentially with intermate distance. Thus exponential relationship occurred in all populations examined. Other covariates important to male fertility were flower color, time, the specific identity of the male parent, and male by female interaction. The identity of the male parent consistently accounted for a large portion of the variation in male fertility, indicating that other unmeasured features of the plant influenced its success.
The importance of hybridization in speciation is emphasized by listing most of the known intergeneric hybrids in flowering plants and including a figure (23,675) of all the known hybrids including interspecife ones. No claims are made that the list is complete or absolutely accurate. Some of the strong points regarding hybridization as a process are given. In addition, it is pointed out that hybrids, throughout the range, show both dominance and intermediacy, some possess normal meiosis and many are highly or partially fertile.
1. In experimental populations of self-compatible, tristylous Eichhornia paniculata plants of the long-styled morph (L) consistently sire fewer seeds on the mid-styled morph (M) than do plants of the short-styled morph (S). This mating asymmetry results in gender differences between the L and S morphs. 2. Observations of pollinators and floral manipulations of genetically marked plants in experimental populations were used to evaluate three potential causes of differential siring success: pollinators prefer the S morph leading to higher male success; long styles interfere with pollen pick-up by insect visitors; and pollen from long-level anthers of the S morph sires more seeds on the M morph than pollen from short-level anthers of the L morph. 3. Visitation by pollinators did not differ significantly among morphs. Excision of styles failed to increase the siring ability of the L morph on the M morph. After removal of non-mid-level anthers from the L and S morphs, no difference in siring ability was detected. Thus long-level anthers provided increased male fitness. This could occur either because pollen transfer from long-level anthers exceeds pollen transfer from short-level anthers or because long-level pollen has greater post-pollination siring success on mid-styles that does short-level pollen. 4. Differences in floral architecture may predispose morphs of heterostylous plants to differential success as male parents. Architectural constraints on male performance imposed by the placement of female and male organs within flowers may be of general importance for floral evolution.
Floral features, such as inflorescence size, that lead to increased insect visitation without a concomitant increase in seed production are viewed as adaptations to enhance the probability of fathering seeds on other plants. In tests of this "pollen donation hypothesis,' male reproductive success has usually been measured indirectly by flower production, pollinator visitation, or pollen removal. The pollen donation hypothesis was tested directly by quantifying the number of seeds sired by individual genotypes in a natural population of poke milkweed in SW Virginia. Multiple paternity was low within fruits, a fact which allowed the authors to use genotypes of progeny arrays to identify a unique pollen parent for 85% of the fruits produced in the population. Seeds sired (male success) and seeds produced (female success) were significantly correlated with flower number per plant. While the number of pollinaria removed, the usual estimator of male success in milkweeds, was highly correlated with numbers of seeds sired, it was even more highly correlated with numbers of seeds produced. Plants with many flowers did not behave primarily as males; individuals with the highest total reproductive success contributed equally as males and females. -from Authors
Flowers frequently receive both self (S) and outcross (OC) pollen, but S pollen often sires proportionally fewer seeds. Failure of S pollen can reflect evolved mechanisms that promote outcrossing and/or inbreeding depression expressed during seed development. The relative importance of these two processes was investigated in Aquilegia caerulea, a self-compatible perennial herb. In the field I performed single-donor (S or OC) and mixed-donor (S plus OC) pollinations to compare the relative success of both pollen types at various stages from pollen germination to seed maturity. Single-donor S pollinations produced significantly fewer and lighter seeds (x̄ decrease 12% and 3%, respectively) than OC pollinations. Abortion rates differed by an average of 38% whereas fertilization rates differed by only 5%, indicating that most differences in seed number arose postzygotically. This suggests that inbreeding depression was responsible for most failure of S pollen. One prezygotic effect measured was that 10% fewer S than OC pollen tubes reached ovaries after 42 hr, suggesting S pollen might fertilize proportionately fewer ovules after mixed pollination. Using allozyme markers, I found mixed-donor pollinations produced significantly more and heavier outcrossed than selfed seeds. However, the proportion of selfed seed, fertilized ovules, and aborted seeds for mixed-donor fruits were each predictable from pollen performance in singledonor fruits, suggesting that differential paternity is best explained by inbreeding depression during seed development. Even given these similarities between mixed- and single-donor fruits in the relative performance ors and OC pollen, both individual seed weight and seed set were significantly higher in multiply-sired fruits.
Within a broad (>200 km wide) hybrid zone involving three parapatric species of Aesculus, we observed coincident clines in allele frequency for 6 of 14 electrophoretic loci. The cooccurrence of alleles characteristic of A. pavia, A. sylvatica, and A. flava was used to estimate genetic admixtures in 48 populations involving various hybrids between these taxa in the southeastern United States. High levels of allelic polymorphism (up to 40% greater than the parental taxa) were observed in hybrid populations and also in some populations bordering the hybrid zone. A detailed analysis of a portion of the hybrid zone involving A. pavia and A. sylvatica revealed a highly asymmetrical pattern of gene flow, predominantly from Coastal Plain populations of A. pavia into Piedmont populations of A. sylvatica. Computer simulations were used to generate expected genotypic arrays for parental, F1, and backcross individuals, which were compared with natural populations using a character index scoring system. In these comparisons, hybrid individuals could be distinguished from either parent, but F1 and backcross progeny could not be distinguished from each other. Most hybrid populations were found to include hybrids and one of the parental taxa, but never both parents. Three populations appeared to be predominantly hybrids with no identifiable parental individuals. Hybrids occurred commonly at least 150 km beyond the range of A. pavia, but usually not more than 25 km beyond the range of A. sylvatica. Introgression, suggested by genetically hybrid individuals and significant gene admixtures of two or more species in populations lacking morphological evidence of hybridization, may extend the hybrid zone further in both directions. The absence of one or both parental species from hybrid populations implies a selective disadvantage to parentals in the hybrid zone and/or that hybridization has occurred through long-distance gene flow via pollen, primarily from A. pavia into A. sylvatica. Long-distance pollen movement in plants may generate hybrid zones of qualitatively different structure than those observed in animals, where gene flow involves dispersal of individuals.
The ground crickets Allonemobius fasciatus and A. socius meet in a mosaic hybrid zone that stretches from New Jersey at least as far west as Illinois. Within mixed populations from the contact zone, "pure" species individuals predominate. To determine whether hybrids are less viable than pure-species individuals, and to assess whether the high proportion of pure-species individuals in mixed populations results from hybrid inviability, we performed a cohort analysis. In this study, five mixed populations from the hybrid zone were each sampled three to five times from the fall of 1986 to the spring of 1988. Individuals were assigned to one of three categories based on their genotypes: A. socius (individuals harboring only alleles unique to A. socius), hybrid (individuals with alleles unique to both species), and A. fasciatus (individuals harboring only alleles unique to A. fasciatus). This sampling and measurement scheme permitted monitoring of the proportion of hybrid individuals in a population over time. The results were fairly consistent. The relative survival of A. socius was greater than the relative survival of members of the other two groups in four of the five populations. The relative viability of A. fasciatus was greater than that of hybrids in one population, approximately equal to that of hybrids in two populations, and less than that of hybrids in two populations. These results not only shed light on an important component of fitness, viability from hatching to adulthood, but they demonstrate that loss of hybrid individuals during the course of the field season will not explain deviations from random mating expectations present in mixed populations in late summer. The deviations must be due to assortative mating or to a reproductive barrier operating prior to egg hatch.
Allozyme variation was compared in selfing and outcrossing populations of Gilia achilleifolia. A group of selfing populations in the northern part of the distribution and a group of outcrossing populations in the southern part of the distribution contained similar amounts of genetic variation; however, individual selfing populations contained less genetic variation than individual outcrossing populations. Most of this difference was in number of alleles per locus and percent loci polymorphic per population. Selfing populations had higher heterozygote frequencies than expected based on knowledge of their outcrossing rate. Evidence is presented that suggests some of the heterozygosity excess is the result of selection. As selfing and outcrossing populations fall into distinct geographical groups, it was possible to study the apportionment of genetic diversity within each group. The among population component of genetic diversity in the selfing group was larger than that of the outcrossing group. In general, the relationship between breeding system and amount and structuring of genetic variation in G. achilleifolia agrees with theoretical considerations and with comparisons that have been made interspecifically in several plant genera.
Seeds were collected from 23 sites located within a Napa Valley hillside stand of the slender wild oat, Avena barbata. At the time of collection each site was assigned an environmental rating which ranged from mesic to xeric. In seven of the sites (Sites 1-7) seeds were collected from 250 individuals and each site was divided into six subsites. In the other sixteen sites (A-P) seeds were collected at random from a variable number of individuals. Seedlings from each individual were analyzed for five electrophoretically determined enzyme loci. The results indicated that both environmental and allozyme variation was distributed patchily among the collection sites. Furthermore, allelic frequencies were highly correlated with the environmental conditions; i.e., allele frequencies were predicted by the a priori habitat ratings. Similar associations were found between microhabitat and genetic variation in the subdivisions of Sites 1-7, indicating that the physical dimensions of the biologically relevant microhabitats may be quite small. Large interlocus associations of alleles also exist and subsequent analyses demonstrated the existence of significant gametic phase disequilibrium in all of the sites and most of the subsites studied. Two five-locus gametic types were found to predominate throughout the hillside. Both had much higher frequencies than expected assuming no interlocus association (67% observed vs. 15% expected). These two gametes are the same two that predominate in monomorphic mesic and xeric populations of A. barbata. These results and those of previous studies lead us to the conclusion that natural selection has shaped the genetic structure of A. barbata on this hillside. The action of genetic drift, even combined with gene flow, cannot sufficiently explain the associations between the electrophoretic genotypes and the patchily distributed microhabitats. From this study, however, we cannot determine whether selection is acting on the electrophoretic variants directly or just on the genomes which they mark. Given the predominately selfing mating system and the nearness of large monomorphic populations of both genotypes, it is also difficult to distinguish whether selection acts independently at each locus, or whether selection is epistatic. Although we feel that co-adaptation is likely to exist within the genome of A. barbata, we hesitate to claim that the five allozyme loci studied here belong to such a co-adapted complex.
Seeds and seedlings were used to determine the outcrossing rate in a low-density stand of ponderosa pine. Maximum likelihood analysis of the electrophoretic data revealed an outcrossing rate of t = .81 for seeds from the low-density stand, which differed significantly from the outcrossing rate of t = .96 for a normal density stand. The seedlings were the remnant of a larger group which had experienced 35% mortality in the greenhouse. These seedlings had a significantly lower F than the seeds, which suggests that heterozygotes had a survival advantage over more homozygous individuals.
Estimates of inbreeding depression obtained from the literature were used to evaluate the association between inbreeding depression and the degree of self-fertilization in natural plant populations. Theoretical models predict that the magnitude of inbreeding depression will decrease with inbreeding as deleterious recessive alleles are expressed and purged through selection. If selection acts differentially among life history stages and deleterious effects are uncorrelated among stages, then the timing of inbreeding depression may also evolve with inbreeding. Estimates of cumulative inbreeding depression and stage-specific inbreeding depression (four stages: seed production of parent, germination, juvenile survival, and growth/reproduction) were compiled for 79 populations (using means of replicates, N = 62) comprising 54 species from 23 families of vascular plants. Where available, data on the mating system also were collected and used as a measure of inbreeding history A significant negative correlation was found between cumulative inbreeding depression and the primary selfing rate for the combined sample of angiosperms (N = 35) and gymnosperms (N = 9); the correlation was significant for angiosperms but not gymnosperms examined separately The average inbreeding depression in predominantly selfing species (δ = 0.23) was significantly less (43%) than that in predominantly outcrossing species (δ = 0.53). These results support the theoretical prediction that selfing reduces the magnitude of inbreeding depression. Most self-fertilizing species expressed the majority of their inbreeding depression late in the life cycle, at the stage of growth/reproduction (14 of 18 species), whereas outcrossing species expressed much of their inbreeding depression either early, at seed production (17 of 40 species), or late (19 species). For species with four life stages examined, selfing and outcrossing species differed in the magnitude of inbreeding depression at the stage of seed production (selfing δ = 0.05, N = 11, outcrossing δ = 0.32, N = 31), germination (selfing δ = 0.02, outcrossing δ = 0.12), and survival to reproduction (selfing δ = 0.04, outcrossing δ = 0.15), but not at growth and reproduction (selfing δ = 0.21, outcrossing δ = 0.27); inbreeding depression in selfers relative to outcrossers increased from early to late life stages. These results support the hypothesis that most early acting inbreeding depression is due to recessive lethals and can be purged through inbreeding, whereas much of the late-acting inbreeding depression is due to weakly deleterious mutations and is very difficult to purge, even under extreme inbreeding.
Evidence from morphology, distribution patterns, allozyme variation, and meiotic irregularities associated with decreased pollen germinability confirms the existence of a broad hybrid zone involving three parapatric species of Aesculus in the southeastern United States. The overall hybrid zone involving the three species is at least 200 km in width and probably represents the overlap of two hybrid zones: one between A. pavia and A. sylvatica and the other between A. flava and A. sylvatica. Both zones are highly asymmetrical, with hybrid populations occurring primarily in the Piedmont, where A. sylvatica is native. Detailed analyses of the hybrid zone involving A. pavia and A. sylvatica showed that hybrid populations consistently lack one or both of the putative parental species. Morphology and allozyme variation provide similar estimates of the position of the hybrid zone, but allozymes allow the detection of a larger zone than apparent on the basis of morphology. All available evidence is consistent with the hypothesis that extensive introgression has occurred among these species. Nevertheless, allozymic differentiation between these species is insufficient to reject hypotheses other than introgression that could generate the genetic structure observed in hybrid populations. Observations of pollinator activity in populations of A. pavia, A. sylvatica, A. flava, and their hybrids showed that these species share a number of important pollinators, including several species of bumblebees (Bombus) and the ruby-throated hummingbird (Archilochus colubris). Spring migration patterns of the ruby-throated hummingbird coincide closely with the flowering phenology of each of the Aesculus species, suggesting that hummingbirds could be vectors of long-distance pollen dispersal. The lifespan of pollen under field conditions is sufficient to permit transport of pollen in this fashion over distances of tens or hundreds of kilometers. Directional migration and arrival of hummingbirds after peak flowering would enforce a directional pattern of gene flow and could generate an asymmetrical hybrid zone of unusually great width.
A marker-based method for studying quantitative genetic characters in natural populations is presented and evaluated. The method involves regressing quantitative trait similarity on marker-estimated relatedness between individuals. A procedure is first given for estimating the narrow sense heritability and additive genetic correlations among traits, incorporating shared environments. Estimation of the actual variance of relatedness is required for heritability, but not for genetic correlations. The approach is then extended to include isolation by distance of environments, dominance, and shared levels of inbreeding. Investigations of statistical properties show that good estimates do not require great marker polymorphism, but rather require significant variation of actual relatedness; optimal allocation generally favors sampling many individuals at the expense of assaying fewer marker loci; when relatedness declines with physical distance, it is optimal to restrict comparisons to within a certain distance; the power to estimate shared environments and inbreeding effects is reasonable, but estimates of dominance variance may be difficult under certain patterns of relationship; and any linkage of markers to quantitative trait loci does not cause significant problems. This marker-based method makes possible studies with long-lived organisms or with organisms difficult to culture, and opens the possibility that quantitative trait expression in natural environments can be analyzed in an unmanipulative way.
Six variable protein loci and one variable ribosomal DNA restriction site were used for an analysis of population structure in five species of Polistes from Texas. A sample-reuse algorithm was developed that estimated FST, FIS, and ⊘ (the coefficient of kinship) from probabilities of identity. Of the four species analyzed in detail only one, Polistes exclamans, had statistically significant values of FST. These values may reflect natural constraints on successful nesting for migrants of this species. Three of the four species had significant values of FIS and three of the four species had significant values of ⊘. In many cases ⊘ also differed from the expected value under haplodiploidy and random mating. Values of ⊘ did not differ from expectations under haplodiploidy and local inbreeding. These results emphasize that theories of social behavior and evolution based on coefficients of kinship should include some explicit consideration of population structure.
In partially selfing populations, siblings may be correlated for both selfing and paternity. A model of the mating system based upon sampling pairs of progeny from a maternal parent is described. The model separates the correlation of selfing from the correlation of outcrossed paternal alleles and is an approach to paternity analysis suited for larger populations with fewer marker loci. Its parameters determine the components of genetic covariance between sibs and provide information about the average number of fathers in a maternal sibship. Electrophoretic markers were used to obtain estimates of correlated matings for two Mimulus guttatus populations. In both populations, about 50% selfing was observed. For two sibs randomly selected from the same capsule, the correlations of selfing between these sibs were 17% and 12% in the two populations, and the correlations of paternity (the proportion of full-sibs among outcrossed sib-pairs) were 37% and 44%. Sibs from different capsules were not correlated for selfing, and the paternity correlation dropped to near 20% in both populations. However, estimates of correlated matings have high variance, lack statistical independence, and can be difficult to obtain. The use of marker loci with many alleles can alleviate these problems.
The hybrid zone between the Red- and Yellow-shafted Flickers has been stable on the United States Great Plains in historical times. This conclusion is based on multivariate comparisons of historical and contemporary collections from 18 locales. Adaptive speciation theory predicts that the hybrid zone should either become broader or narrower as a result of introgressive hybridization or reinforcement of premating isolating mechanisms. Neither of these predictions was borne out. Despite 10,000-13,000 years of hybridization, mating between subspecies remains indiscriminate. The data are also inconsistent with a dynamicequilibrium hypothesis wherein narrow hybrid zones are maintained by hybrid unfitness. According to this hypothesis, the hybrid zone would probably "flow" unless it was trapped by a population density trough. The hybrid zone does not appear to be associated with such a feature. The data are consistent with a bounded hybrid superiority theory of a hybrid zone, but this is more a question of survival in a process of elimination than a resounding corroboration.
The DNA sequences that code for the 17S, 5.8S, and 25S subunits of the ribosome have been useful in the study of plant evolutionary biology. The coding sequences are evolutionarily conservative and have provided information on systematic relationships among the species within a genus and have also elucidated higher level relationships. The intergenic spacer region of the sequence is highly variable, and variation occurs within populations and individuals. Analysis of intra- and interpopulation variation in rDNA has documented subdivision within populations of Clematis fremontii and population and subspecific differentiation in Phlox divaricata. These studies indicate that rDNA provides a good genetic marker for the study of microevolutionary processes.
Natural populations of the common morning glory (Ipomoea purpurea) in the Southeastern United States are highly polymorphic for corolla color. The morphs range in color from pure white to intense blue and pink. This self-compatible species is primarily pollinated by bumblebees. Insect pollination coupled with the diversity of flower color raises the possibility that mating structure varies among plants depending upon corolla color. Observational data on pollinator behavior in a natural population of I. purpurea over two consecutive years showed (1) assortative mating within color classes due to pollinator constancy; and that (2) white color morphs are visited approximately half as often as would be expected based upon their representation in the population. Subdivision of observational data on the basis of pollinator flight distance, showed little or no constancy in the long distance flights but high constancy in the nearest neighbor pollinations. This suggests that constancy may depend upon flight distance scales rather than on behavioral preference. It is generally assumed in studies of pollinator behavior that the description of pollination events accurately predicts the pattern of genetic transmission in plant populations. To verify this assumption, the transmission of alleles at a polymorphic esterase locus was measured using the mixed mating model. Estimation of the outcrossing rate as a function of maternal flower color showed that white morphs outcrossed less often than the most intensely pigmented morphs. Thus the estimates of outcrossing rate agreed with the predictions from pollinator visits.
A direct estimate of outcrossing was obtained from progenies of pink-flowered and white-flowered plants in a natural population of Clarkia exilis. Dominant phenotypes are expected in the progenies of heterozygotes with a frequency of 1-(1+λ q-λ p)/4 and in the progenies of recessive plants with a frequency of λ p, where λ is the frequency of outcrossing and p is the frequency of the dominant gene. The two expectations were set equal to observed frequencies and the equations were simultaneously solved for λ. A direct measure of natural crossing, λ p, was observed to be 0.036 and the frequency of outcrossing was calculated to be λ = 0.445. This direct method is considered to be advantageous in that it measures outcrossing after possible modifying influences of pollinators, plant density, phenotypic frequency, etc., and measures gene frequency in the pollen pool.
The variety pulchella of the outcrossing annual plant species Gaillardia pulchella consists of two edaphic races in central Texas which are divergent for one morphological and four electrophoretic characters. Reduced pollen stainability in F1 hybrids suggests the races are also divergent in chromosome structure. The recent proliferation of this species on roadsides and in pastures has led to hybridization between these races. An analysis of character variation in three hybrid populations revealed significant clinal variation associated with edaphic ecotones, and the width of these clines was found to vary among characters in a consistent pattern. It is argued that this pattern is the result of different characters experiencing different effective selection regimes, with narrower clines reflecting greater differentials in effective selection. Several mechanisms are discussed by which selection may impede the transgression of alleles across the ecotones in these populations. The results of this study are compared to the results of parallel studies on the autogamous annual species Avena barbata in California, and it is suggested that the difference between these two species in the width of clines separating edaphic ecotypes may be accounted for by their different breeding systems.
A bimodal distribution of outcrossing rates was observed for natural plant populations, with more primarily selfing and primarily outcrossing species, and fewer species with intermediate outcrossing rate than expected by chance. This distrbution is argued to result from selection for the maintenance of outcrossing in historically large, outcrossing populations with substantial inbreeding depression, and from selection for selfing when increased inbreeding, due to pollinator failure or population bottlenecks, reduces the level of inbreeding depression. Few species or populations are fixed at complete selfing or complete outcrossing. A low level of selfing in primarily outcrossing species is unlikely to be selectively advantageous, but will not reduce inbreeding depression to the level where selfing is selectively favored particularly if accompanied by reproductive compensation. Similarly, occasional outcrossing in primarily selfing species is unlikely to regularly provide sufficient heterosis to maintain selection for outcrossing through individual selection. Genetic, morphological and ecological constraints may limit the potential for outcrossing rates in selfers to be reduced below some minimum level. -Authors
Population structure, the physical arrangement of related and unrelated individuals, can have profound effects on the apparent outcrossing rate (\(\hat t\)) in a plant population. However, detailed experimental investigations of the impact of population structure on \(\hat t\) are few. We compared the apparent outcrossing rates of experimental populations of grain sorghum with seed families spatially arranged in stratified and overdispersed treatments. Using alcohol dehydrogenase allozymes as genetic markers, \(\hat t\) was calculated for each of the treatments at two locations over three years. For all six comparisons, the overdispersed treatment yielded significantly larger apparent outcrossing estimates than the stratified treatment. In one case, the difference was over five-fold. Site-specific and time-specific differences were small compared to treatment differences. Whether natural structuring plays a role in altering the effective outcrossing rates of natural populations has been addressed by only a few descriptive studies; structuring effects appear to have an impact in only about half of such studies. The sample is still too small to make any generalizations.
Population structuring can also be of significance in plant breeding programs. Controllable variation in \(\hat t\) values of the magnitude reported herein may be useful in optimizing selection methods for quantitative characters in experimental plant breeding populations. Further work is under way to determine the effects of the variation in apparent outcrossing rates on genetic gains from selection.
The inheritance of organelle DNAs in loblolly pine was studied by using restriction fragment length polymorphisms. Chloroplast DNA from loblolly pine is paternally inherited in pitch pine x loblolly pine hybrids. Mitochondrial DNA is maternally inherited in loblolly pine crosses. The uniparental inheritance of organelle genomes from opposite sexes within the same plant appears to be unique among those higher plants that have been tested and indicates that loblolly pine, and possibly other conifers, must have special mechanisms for organelle exclusion or degradation or both. This genetic system creates an exceptional opportunity for the study of maternal and paternal genetic lineages within a single species.
There has recently been a burgeoning interest in the analysis of paternity patterns for natural populations because of its relevance to population genetic phenomena such as the distance between successful mates, relative male reproductive success and gene flow. In this paper we develop a method of analyzing populational patterns of paternity, the fractional paternity method, and compare its performance to two other commonly used methods of paternity analysis (simple exclusion and the most-likely methods). We show that the fractional method is the most accurate method for determining populational patterns of paternity because it assigns paternity to all progeny examined, and because it avoids biases inherent in the other paternity analysis methods when model assumptions are met. In particular, it avoids a systematic bias of the most-likely paternity assignment method, which has a tendency to over-assign paternity of progeny to certain male parents with a greater than average number of homozygous marker loci. We also demonstrate the effect of linkage of some of the marker loci on paternity assignment, showing how the knowledge of the linkage phase of male and female parents in the population can significantly improve the accuracy of the estimates of populational patterns of paternity. Knowledge of the linkage phase of individuals in a population is usually unknown and difficult to assess without progeny testing, which involves considerable labor. However, we show how the linkage phase of hermaphroditic individuals in a population can be obtained in conjunction with the paternity analysis if progeny can be obtained from each hermaphroditic individual in the population, thereby avoiding the problem of traditional progeny testing. Applications of the fractional paternity approach developed herein should contribute significantly to our understanding of the mating patterns in, and hence the evolution of, natural populations.
Outcrossing rates were estimated in three populations of the gynodioecious species Plantago coronopus by means of electrophoresis of adult plants and their natural progenies. A multilocus estimation procedure was used. Heterogeneity among the pollen-pool allele frequencies did not exist either in space of in time. Differences between populations in mean outcrossing rates were large (range: 0.34-0.93), probably caused by differences in densities of flowering plants. In addition, there was considerable variability between individuals, which was at least partly caused by the presence of male sterility. Population density may, via its influence on outcrossing rates, be a factor influencing the maintenance of male sterile plants in the population. The level of outcrossing in hermaphrodites was not low enough to explain the maintenance of male steriles. Outcrossing rates in two populations, established via progeny analysis, were much lower than calculated with the fixation index, possibly indicating heterozygote advantage in these natural populations.
Analysis of minisatellite DNA sequences, yielding so called DNA "fingerprints", has proven useful in paternity analysis for several different organisms. Here 64 apple seedlings, grown from seeds collected in an orchard with three cultivars, were analyzed using the M13 "fingerprint" probe. Paternity could be determined for 56 of the seedlings, 2 of which were derived through selfing. The analysis was facilitated by the occurrence of a multiallelic locus. The five different fragments determined by this locus migrated to similar positions, whether digesting the DNA with restriction enzymes TaqI or RsaI.
Recently, "DNA fingerprints" have been reported in a wide array of organisms. We used the M13 repeat probe on several genera and species in the angiosperm family Rosaceae. Four apple cultivars could be differentiated when any one of five restriction enzymes was used to analyze minisatellite DNA. Similarly, four individual trees of Prunus serotina (black cherry) exhibited different "fingerprints" with each of four enyzmes. A total of 14 Rubus (blackberries and raspberries) plants representing four species were investigated with two enzymes. Extensive inter-and intraspecific variation was found. However, some closely growing plants had identical "fingerprints", probably due to their being derived through vegetative propagation.
The cloning of white spruce (Picea glauca) mitochondrial DNA homologous to the cytochrome oxidase II and ATPaseα genes of maize is described. These probes were used to define restriction fragment length polymorphisms which distinguish the white, Engelmann (P. engelmannii) and Sitka spruce (P. sitchensis) populations that occur in British Columbia. Analysis of progeny from crosses between the species revealed that mitochondrial DNA was maternally inherited in all cases (32 progeny from five independent crosses). The inheritance of chloroplast DNA was determined using a probe described previously; in this case, all progeny exhibited paternal inheritance (27 progeny from four crosses). Mitochondrial and chloroplast probes were used to test trees from zones of introgression between coastal (Sitka) and interior spruces (white and Engelmann). In most cases mitochondria and chloroplasts within individuals were contributed by different species. The data shows that there is a significant Sitka spruce component in trees east of the coastal watershed in British Columbia.
Randomly amplified polymorphic DNA (RAPD) markers have been used to characterise cocoa clones representing the three main cultivated subpopulations: Criollo, Forastero and Trinitario. The use of single primers of arbitrary nucleotide sequence resulted in the selective amplification of DNA fragments which were unique to the individual cocoa clones studied. The use of a single primer allowed each of the clones evaluated to be unequivocally characterised. The application of RAPD markers for the evaluation of germplasm and cocoa improvement programmes are discussed.
Three Plantago species were surveyed for within- and between-population variation at DNA sequences detected with the M13 minisatellite probe. The levels and patterns of variation detected by this probe correspond to those expected from the mating systems of the species. The highly-selfing species P. major has a relatively low variability of minisatellite sequences within populations and considerable differentiation between populations. The outcrossing species P. lanceolata exhibits higher minisatellite variability within populations and moderate differentiation between populations. P. coronopus, with a mixed mating system, has levels of variation intermediate between P. major and P. lanceolata. The levels of variation within and between populations corresponds, in general, to the levels of allozyme variation determined in an earlier study. Mating system and population structure appear to have a major influence on M13-detected fragment variation.
Diagnostic chloroplast DNA and nuclear ribosomal DNA markers were used to assess the occurrence and the extent of introgression from the common sunflower, Helian- thus annuus, into the cucumber-leaf sunflower, H. debilis ssp. cucumerifolius. Anal- ysis of 11 populations (270 individuals) of H. debilis ssp. cucumerifolius revealed that 193 individuals from nine populations had the chloroplast DNA genotype of H. annuus, whereas only 20 individuals from nine populations had detectable nuclear ribosomal DNA markers of H. annuus. Not only does the introgression of chloroplast DNA genotypes into H. debilis ssp. cucumerifolius appear to occur more readily than that of nuclear genes, but the flow of chloroplast DNA genotypes is greater than that previously documented in the opposing direction (into H. annuus). It is speculated that the differential, asymmetric gene flow observed in H. debilis ssp. cucumerifolius results from the greater abundance of H. annuus in the area of sympatry coupled with strong selection against "annuus" nuclear genes.