Hybridization and introgression in Carpobrotus spp. (Aizoaceae) in California. II. Allozyme evidence

Morphological evidence has indicated that hybridization and introgression are occurring between Carpobrotus edulis L., a nonindigenous, invasive species in California (Bolus), and its putative native congener, C. chilensis. The identification of allozyme markers has enabled us to quantify hybridization and the extent of introgression between these species. Samples from 20 individuals of each of five morphological types (both parent species and three hybrid phenotypes) were collected from 39 populations along the coast of California from the Mexico to Oregon borders. Ten enzyme systems revealed a total of 17 resolvable loci, eight of which were polymorphic for the genus. Five of the polymorphic loci easily differentiate C. edulis and C. chilensis. Allele frequencies among the morphologically defined types are consistent with estimations of allele frequency changes due to first- and second-generation backcrossing. In comparison to long-lived, herbaceous perennials and widespread species, C. edulis and intermediate types have more variation in their populations (P = 41.73, Ap = 2.11, Ho = 0.246, and P = 38.13, Ap = 2.06, Ho = 0.216, respectively) than C. chilensis (P = 11.76, Ap = 2.00, Ho = 0.082). Indirect estimates of gene flow indicate four of the five morphological types are outcrossing. Gene flow between previously allopatric species may have broad implications if it results in an increase in fitness; further experimentation is needed to determine the ultimate ecological consequences of this phenomenon and its possible threat to limited, remaining natural habitat in California.     

Hybridization and introgression in Carpobrotus spp. (Aizoaceae) in California. I. Morphological evidence

Individuals of the invasive non-native plant species Carpobrotus edulis, its native or naturalized congener C. chilensis, and putative hybrids are found throughout coastal California. This study characterized morphological variation within the genus and assessed the extent of hybridization and direction of introgression between C. edulis and C. chilensis. Twelve randomly selected Carpobrotus individuals from each of 49 sample locations were classified as "C. edulis," "C. chilensis," or one of three intermediate morphotype classes, and compared for clonal, vegetative, and fruit characters. Univariate comparisons showed that C. edulis individuals had deeper mats with more cover within the mat boundary, longer, wider, more serrate leaves, and wider fruits with more carpels than intermediate and C. chilensis morphotype classes. Carpobrotus edulis and intermediates had more lateral branches than did C. chilensis, suggesting that hybrids tend to vary toward C. edulis. Discriminant function analysis (DFA) identified the following characters as discriminating significantly among Carpobrotus groups: leaf length, leaf width, leaf length/width, number of lateral branches, number of carpels, and fruit diameter. Using these characters, DFA correctly classified 98% of apparently pure C. edulis and C. chilensis, but only 76% of all Carpobrotus individuals when putative hybrids were included. Principal components analysis showed that C. edulis and C. chilensis cluster into distinct morphotypes, but that hybrids overlap with both groups, particularly with C. edulis. The genus Carpobrotus in California resembles a large hybrid swarm, with putative hybrids forming a large portion of the overall population and tending to vary toward C. edulis.     

Germination and growth responses of hybridizing Carpobrotus species (Aizoaceae) from coastal California to soil salinity

Germination, growth, and physiological responses of hybridizing Carpobrotus from coastal California to soil salinity were studied. Hybrids are presumably the result of hybridization and introgression between the exotic Carpobrotus edulis, a succulent perennial invading coastal habitats, and the native or long-naturalized C. chilensis. Germination responses were investigated at 0, 10, 20, and 50% seawater. Seedling growth and physiology were compared by irrigating seedlings with solutions of the same seawater concentrations and in low and high nutrients. Germination was inhibited in the presence of salt, but recovered after transferring the seeds to fresh water. Seeds exposed to salt had higher final germination rates than control. Growth of Carpobrotus was slightly enhanced by low seawater concentrations but reduced at high salinity at both nutrient regimes. Leaf cell sap osmolarity increased with increasing soil salinity, and taxa did not differ significantly in this physiological adjustment. Leaf carbon isotope ratios (∂¹³C) ranged from −28 to −22‰ and became less negative at higher salinities, indicating an improved water use efficiency in the seedlings at high salt concentrations. In addition, ∂¹³C values were generally less negative at high than at low nutrients. Differences among taxa were generally small. The results show that salinity affects both establishment and growth of hybridizing Carpobrotus. The overall weak species differences in salt tolerance indicate that the exotic C. edulis can occupy the same sites as C. chilensis in terms of salinity. The similarity of hybrids in their response to salinity suggests that they may contribute to the invasion by Carpobrotus.     

Differences in physiological integration between invasive and noninvasive introduced clonal species of Carpobrotus

AimsClonal growth is associated with invasiveness in introduced plant species, but few studies have compared invasive and noninvasive introduced clonal species to investigate which clonal traits may underlie invasiveness. To test the hypothesis that greater capacity to increase clonal growthviaphysiological integration of connected ramets increases invasiveness in clonal plants, we compared the effects of severing connections on accumulation of mass in the two species of the creeping, succulent, perennial, herbaceous genusCarpobrotusthat have been introduced on sand dunes along the Pacific Coast of northern California, the highly invasive speciesCarpobrotus edulisand the co-occurring, noninvasive speciesCarpobrotus chilensis.     

Using phylogeographic analyses of gene trees to test species status and processes

A gene tree is an evolutionary reconstruction of the genealogical history of the genetic variation found in a sample of homologous genes or DNA regions that have experienced little or no recombination. Gene trees have the potential of straddling the interface between intra- and interspecific evolution. It is precisely at this interface that the process of speciation occurs, and gene trees can therefore be used as a powerful tool to probe this interface. One application is to infer species status. The cohesion species is defined as an evolutionary lineage or set of lineages with genetic exchangeability and/or ecological interchangeability. This species concept can be phrased in terms of null hypotheses that can be tested rigorously and objectively by using gene trees. First, an overlay of geography upon the gene tree is used to test the null hypothesis that the sample is from a single evolutionary lineage. This phase of testing can indicate that the sampled organisms are indeed from a single lineage and therefore a single cohesion species. In other cases, this null hypothesis is not rejected due to a lack of power or inadequate sampling. Alternatively, this null hypothesis can be rejected because two or more lineages are in the sample. The test can identify lineages even when hybridization and lineage sorting occur. Only when this null hypothesis is rejected is there the potential for more than one cohesion species. Although all cohesion species are evolutionary lineages, not all evolutionary lineages are cohesion species. Therefore, if the first null hypothesis is rejected, a second null hypothesis is tested that all lineages are genetically exchangeable and/or ecologically interchangeable. This second test is accomplished by direct contrasts of previously identified lineages or by overlaying reproductive and/or ecological data upon the gene tree and testing for significant transitions that are concordant with the previously identified lineages. Only when this second null hypothesis is rejected is a lineage elevated to the status of cohesion species. By using gene trees in this manner, species can be identified with objective, a priori criteria with an inference procedure that automatically yields much insight into the process of speciation. When one or more of the null hypotheses cannot be rejected, this procedure also provides specific guidance for future work that will be needed to judge species status.     

Genomic regions with a history of divergent selection affect fitness of hybrids between two butterfly species

Speciation is the process by which reproductively isolated lineages arise, and is one of the fundamental means by which the diversity of life increases. Whereas numerous studies have documented an association between ecological divergence and reproductive isolation, relatively little is known about the role of natural selection in genome divergence during the process of speciation. Here, we use genome-wide DNA sequences and Bayesian models to test the hypothesis that loci under divergent selection between two butterfly species (Lycaeides idas and L. melissa) also affect fitness in an admixed population. Locus-specific measures of genetic differentiation between L. idas and L. melissa and genomic introgression in hybrids varied across the genome. The most differentiated genetic regions were characterized by elevated L. idas ancestry in the admixed population, which occurs in L. idas-like habitat, consistent with the hypothesis that local adaptation contributes to speciation. Moreover, locus-specific measures of genetic differentiation (a metric of divergent selection) were positively associated with extreme genomic introgression (a metric of hybrid fitness). Interestingly, concordance of differentiation and introgression was only partial. We discuss multiple, complementary explanations for this partial concordance.     

Genetic variation and possible origins of weedy rice found in California

Control of weeds in cultivated crops is a pivotal component in successful crop production allowing higher yield and higher quality. In rice‐growing regions worldwide, weedy rice (Oryza sativa f. spontanea Rosh.) is a weed related to cultivated rice which infests rice fields. With populations across the globe evolving a suite of phenotypic traits characteristic of weeds and of cultivated rice, varying hypotheses exist on the origin of weedy rice. Here, we investigated the genetic diversity and possible origin of weedy rice in California using 98 simple sequence repeat (SSR) markers and an Rc gene‐specific marker. By employing phylogenetic clustering analysis, we show that four to five genetically distinct biotypes of weedy rice exist in California. Analysis of population structure and genetic distance among individuals reveals diverse evolutionary origins of California weedy rice biotypes, with ancestry derived from indica, aus, and japonica cultivated rice as well as possible contributions from weedy rice from the southern United States and wild rice. Because this diverse parentage primarily consists of weedy, wild, and cultivated rice not found in California, most existing weedy rice biotypes likely originated outside California.     

Genetic variation and phylogeographic structure of Laodelphax striatellus in China based on microsatellite markers

The small brown planthopper (SBPH), Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae), is an important agricultural pest that has caused serious economic losses in the major rice-producing areas of China. To effectively manage this insect pest, we analysed its genetic variation, genetic structure and population demographic history. We used nine nuclear microsatellite loci to investigate the genetic diversity and population genetic structure of SBPH at 43 sampling sites in China. High levels of genetic diversity and genetic differentiation among most populations were detected. Overall, neighbour-joining dendrograms, STRUCTURE and principal coordinate analysis (PCoA) revealed no genetically distinct groups and exhibited an admixed phylogeographic structure in China. Isolation by distance (IBD) and spatial autocorrelation analyses demonstrated no correlation between genetic distance and geographic distance. On the other hand, bottleneck analysis indicated that SBPH populations had not undergone severe bottleneck effects in these regions. This study provides useful data for resolving the genetic relationships and migration patterns of SBPH and thus contributes to developing effective management strategies for this pest.     

Genetic differentiation between two host “races” and two species of cleptoparasitic bees and between their two hosts

In this paper we test the following two hypotheses: (1) that apparently conspecific samples of the cleptoparasitic beeCoelioxys funeraria, differing markedly in size and reared from different host species, do indeed represent one panmictic population; (2) that bees that nest in holes in wood or twigs have higher levels of genetic variation than those nesting in the ground. Based upon 41 loci, the genetic differences between the two samples ofC. funeraria could be explained entirely in terms of sampling error. In contrast, the sympatricC. moesta showed 16 fixed allelic differences from theC. funeraria samples. Similarly, the two hosts ofC. funeraria, Megachile relativa andM. inermis, had 21 fixed allelic differences between them out of 42 presumptive gene loci. Heterozygosities among the wood-nesting bees were not particularly high for Hymenoptera, ranging from 0.045 to 0.054. Comparisons of heterozygosity estimates among bees remain ambiguous as to whether soil nesting confers sufficient environmental buffering effects to reduce possible advantages of heterosis in ground-nesting species.     

A phylogeographic investigation of the hybrid origin of a species of swordtail fish from Mexico

Hybrid speciation may contribute significantly to generating biodiversity, but only a few well‐documented examples for it exist so far that do not involve polyploidization as a mechanism. The swordtail fish, Xiphophorus clemenciae, shows common hallmarks of a hybrid origin and still overlaps in its current geographic distribution with its putative ancestral species (Xiphophorus hellerii and Xiphophorus maculatus). Xiphophorus clemenciae provides an ideal system for investigating the possible continued genetic interactions between a hybrid and its parental species. Here, we use microsatellite and mitochondrial markers to investigate the population structure of these species of swordtails and search for signs of recent hybridization. Individuals were sampled from 21 localities across the known range of X. clemenciae– the Isthmus of Tehuantepec (IT) Mexico, and several environmental parameters that might represent barriers to dispersal were recorded. The hybridization event that gave rise to X. clemenciae appears to be rather ancient, and a single origin is likely. We find negligible evidence for ongoing hybridization and introgression between the putative ancestral species, because they now occupy distinct ecological niches, and a common haplotype is shared by most populations of X. clemenciae. The population structure within these species shows an isolation‐by‐distance (IBD) pattern and genetic differentiation between most populations is significant and high. We infer that tectonic evolution in the Isthmus has greatly restricted gene flow between the southern and central IT populations of X. clemenciae and X. helleriii and provide preliminary information to aid in conservation management of this geographically restricted hybrid species, X. clemenciae.     

Enzyme patterns in two species of Xenopus and their hybrids

Differences in the isozyme patterns of Xenopus laevis and Xenopus mulleri have been utilized to examine the expression of alleles of both species in hybrid animals. Mitochondrial MDH and tetrazolium oxidase phenotypes were examined during the development of non-hybrid embryos of each species and of reciprocal hybrids. Early stages of the hybrids resemble the enzyme phenotype of the maternal parent. Appearance of paternal enzyme takes place just prior to the active feeding tadpole stage for both mitochondrial MDH and oxidase. The maternal effect disappears shortly thereafter in early feeding tadpoles, at which point reciprocal hybrids have identical isozyme patterns. There is no evidence for a predominance of one species over the other. Examination of feeding tadpoles and adult toads indicates that both laevis and mulleri expression is stable. The appearance of paternal mitochondrial MDH does not correspond to the time when other mitochondrial components begin to increase in Xenopus. Multiple bands of MDH in both species and of oxidase in laevis are probably not due to the aggregation of subunits produced by different alleles at the same locus. There is no evidence for the formation of “hybrid” molecules consisting of subunits of both species.     

Molecular variation in Leymus species and populations

Icelandic populations of European lymegrass [Leymus arenarius (L.) Hochst.] were examined using amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) of the major ribosomal genes (18S-5.8S-26S rDNA), in comparison with Alaskan populations of its closely related species L. mollis (Trin.) Pilger. The AFLP profiles emerged as two distinct entities, clearly separating the two species, and based on species-specific bands it was simple to distinguish these two morphologically similar species. The rDNA-RFLPs also differentiated the species. Within species, the Icelandic L. arenarius was more homogeneous than the Alaskan L. mollis, and its variation was dispersed over geographically different populations, suggesting a common gene pool. The variation among the Alaskan L. mollis was more extensive and its interrupted pattern may be the result of gene introgression at subspecies level. Within a 40-year-old population of L. mollis established in Iceland from Alaskan material, the molecular profiles separated old and new genotypes. Both AFLP and rDNA revealed the new genotypes to be extremely similar. This rapid change in allele frequency is thought to be the result of adaptation to a new environment.     

Genetic analysis of natural hybrids between endemic and alien Rubus (Rosaceae) species in Hawai`i

A population of putative hybrids between theendemic Rubus hawaiensis and naturalizedR. rosifolius was discovered inKpahulu Valley, on the island of Maui inthe Hawaiian archipelago. The goal of thisstudy was to molecularly characterize thisnatural hybridization event, investigate themode of hybridization, and determine the malefertility of the hybrid individuals. Bothmorphological and RAPD marker data indicatethat the putative hybrid individuals are theprogeny of R. rosifolius and R.hawaiensis. All 39 hybrid individuals sampledhad the chloroplast DNA haplotype of R.rosifolius. Thus hybridization appears to beasymmetric, with R. rosifolius acting asthe maternal parent. All hybrid individualsassessed for pollen stainability were sterile,and there was no evidence of backcrossing toeither parent. This result suggests thathybrids are of the first filial generation andthat variation among hybrids reflectsdifferences within the parental populations.Sympatric populations of R. hawaiensisand R. rosifolius occur on four islandsand six additional alien species of Rubusare naturalized and sympatric with R. hawaiensisin Hawai`i. Further investigationis merited to assess whether hybridization maypose a threat to the long term viability ofR. hawaiensis. This study highlights theincreasing frequency and negative consequencesof native-alien hybridization and theimportance of maintaining active alien speciescontrol programs in the Hawaiian Islands.     

Genetic variation and relationships of seven sturgeon species and ten interspecific hybrids

Background

Sturgeon cultivation is important for both industry and aquaculture in China. To date, more than 17 species or strains have been farmed for fillets and caviar production. Crossbreeding among different sturgeon species is frequent and the F2 hybrids are fertile. However, large-scale farming can have negative impacts on wild populations i.e. escape of exotic sturgeons and must be taken into consideration. Escape of exotic sturgeons can cause severe ecological problems, including threatening native sturgeon species once the exotic varieties become established or hybridize with native individuals. However, little is known about their genetic resources and variation.

Methods

Genetic diversity and introgression of seven sturgeon species were analyzed using mitochondrial DNA cytochrome oxidase subunit I (COI) and nine microsatellite markers. This study included 189 individuals from seven sturgeon species and 277 individuals from ten lineages of F2 hybrid strains.

Results

MtDNA COI sequences (632 bp long) were generated from 91 individuals across the 17 sturgeon strains and produced 23 different haplotypes. Haplotype diversity was high (h = 0.915 ± 0.015) and nucleotide diversity was low (π = 0.03680 ± 0.00153) in the seven sturgeon species and ten interspecific hybrids. Phylogenetic analyses resulted in almost identical tree topologies, and different haplotype structures were mainly related with sturgeons of different female parents. Analysis of molecular variance revealed that 81.73% of the genetic variance was due to matrilineal differences, while 9.40% resulted from strain variation. Pairwise Fst values obtained with POLYSAT software, were high among strains and ranged from 0.031 to 0.164. Admixture analysis assigned seven distinct groups and ten genotypes of admixed clusters composed of hybrid strains using STRUCTURE when assuming K = 7.

Conclusions

The interspecific mtDNA gene tree corresponded to the expected taxonomic divisions. These relationships were also supported by the results from the microsatellite analysis and contributed to unambiguously identify seven sturgeon species and ten F2 hybrid strains from sturgeon farms in China. Moreover, we found that introgressive hybridization is pervasive, exists in both purebred and hybrid sturgeons, and may reflect widespread mismanagement in sturgeon breeding in China.     

Genetic evidence for species cohesion,substructure and hybrids in spruce

The origin and history of species are shaped by various evolutionary dynamics, including their persistence in the face of potential gene flow from related taxa. In this study, we use broad geographical and taxonomic sampling (2,219 individuals) to establish the distribution of species, hybrids and cryptic genetic variation within the conifer genus Picea (spruce) across western North America. We demonstrate that the six species of spruce in this region are distinguishable based on their genetic composition, and that the more closely related Engelmann spruce (P. engelmannii) and white spruce (P. glauca) have generated numerous and widespread hybrids. These hybrids occur in the central Rocky Mountains, well to the south of the well‐established region of admixture in Canada. Additionally, we provide evidence for subdivision within Engelmann spruce, manifested as a southern Rocky Mountains form, and a northern Rocky Mountain and Cascade mountains (western) form. In the intervening central Rocky Mountains region (forests in Wyoming and adjacent states) we found primarily individuals with admixed ancestry. Following their origin, these species of spruce have interacted repeatedly and in different geographical contexts. Multiple pairs of species have been shown to hybridize, yet the species persist and retain distinguishable compositions. At the same time, large geographical areas exist where hybrids are pervasive. Consequently, spruce provide a case study for the maintenance of species boundaries, particularly for how widespread hybridization need not lead to the collapse and loss of species.     

Chloroplast phylogeography of Iris dichotoma (Iridaceae), a widespread herbaceous species in East Asia

Both a complex topography and climate change have huge impacts on the distribution and genetic structure of extant species. Due to the lack of relevant molecular research, little is definitively known about the phylogeography of herbaceous plants in East Asia. Here we investigate the genetic diversity, population structure and historical population dynamics of Iris dichotoma Pallas, a widespread perennial herbaceous species in northeastern and northern China. Twenty-nine populations, totalling 297 individuals, were sampled throughout the Chinese distributional range of I. dichotoma. The combined sequences of six chloroplast DNA fragments (petA-psbE, rps18-clpp, psbJ-petA, trnD-trnT, rps16 and ndhA) were used to identify 13 haplotypes, of which six were private ones restricted in a single population. Genetic differentiation among I. dichotoma populations, enabled us to infer potential refugia during the glacial period in the Yinshan Mountains–Yanshan Mountains, where high levels of haplotype and nucleotide diversity were detected. The results of a neutral test and mismatch distribution analysis both indicated that I. dichotoma underwent a recent population expansion. In East Asia, postglacial environmental and climatic changes appear to have promoted genetic diversification not only in better-studied woody species, but also in herbaceous ones like I. dichotoma. Future studies of more herbaceous plant species are needed to obtain better insight into how modern temperate biodiversity has developed in East Asia.     

Nucleolar number variation in Hordeum species,their haploids and interspecific hybrids

Nucleolar number variation has been investigated in root tip cells by cytologically determining the number of nucleoli per cell in autoploids and alloploids of Hordeum species, their haploids and interspecific hybrids. The nucleolus organisers in autoploid types of H. vulgare or H. bulbosum did not show any alterations irrespective of the ploidy level. The nucleolar number variation in these species results from a definite pattern of fusion and the maximum number of nucleoli per nucleus corresponds to the number of secondary constrictions. Nucleolus formation in alloploids and interspecific hybrids is impaired on some of the NORs, suggesting differential amphiplasty or nucleolar dominance. A comparison of nucleolar formation in the alloploid species (brachyantherum, arizonicum, procerum and parodii), their haploids, and the interspecific hybrids revealed different degrees of variation from the expected mean and maximum numbers of nucleoli. While the deviations in hybrids between alloploids (H. arizonicum and H. brachyantherum or H. procerum and H. brachyantherum) are marginal, nucleolar dominance is more pronounced in hybrids involving H. vulgare or H. bulbosum as one of the parents and is invariably associated with the disappearance of the secondary constriction(s) from the NOR(s) contributed by one of the parents, and the number of nucleoli is appropriately reduced.