Development and characterization of microsatellite markers for two dioecious Ficus species

Patterns of Genomic Diversity in a Fig-Associated Close Relative of Caenorhabditis elegans

The evolution of reproductive mode is expected to have profound impacts on the genetic composition of populations. At the same time, ecological interactions can generate close associations among species, which can in turn generate a high degree of overlap in their spatial distributions. Caenorhabditis elegans is a hermaphroditic nematode that has enabled extensive advances in developmental genetics. Caenorhabditis inopinata, the sister species of C. elegans, is a gonochoristic nematode that thrives in figs and obligately disperses on fig wasps. Here, we describe patterns of genomic diversity in C. inopinata. We performed RAD-seq on individual worms isolated from the field across three Okinawan island populations. C. inopinata is about five times more diverse than C. elegans. Additionally, C. inopinata harbors greater differences in diversity among functional genomic regions (such as between genic and intergenic sequences) than C. elegans. Conversely, C. elegans harbors greater differences in diversity between high-recombining chromosome arms and low-recombining chromosome centers than C. inopinata. FST is low among island population pairs, and clear population structure could not be easily detected among islands, suggesting frequent migration of wasps between islands. These patterns of population differentiation appear comparable with those previously reported in its fig wasp vector. These results confirm many theoretical population genetic predictions regarding the evolution of reproductive mode and suggest C. inopinata population dynamics may be driven by wasp dispersal. This work sets the stage for future evolutionary genomic studies aimed at understanding the evolution of sex as well as the evolution of ecological interactions.

Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species

The obligate pollination mutualism between figs (Ficus, Moraceae) and pollinator wasps (Agaonidae, Hymenoptera) is a classic example of cospeciation. However, examples of phylogenetic incongruencies between figs and their pollinators suggest that pollinators may speciate by host shifting. To investigate the mechanism of speciation by host shifting, we examined the phylogenetic relationships and population genetic structures of six closely related fig species and their pollinators from southern China and Taiwan-Ryukyu islands using various molecular markers. The results revealed 1) an extraordinary case of pollinator sharing, in which five distinct fig species share a single pollinator species in southern China; 2) two types of copollination, namely, sympatric copollination by pollinator duplication or pollinator migration, and allopatric copollination by host migration and new pollinator acquisition; 3) fig species from southern China have colonized Taiwan repeatedly and one of these events has been followed by host shifting, reestablishment of host specificity, and pollinator speciation, in order. Based on our results, we propose a model for pollinator speciation by host shifting in which the reestablishment of host-specificity plays a central role in the speciation process. These findings provide important insights into understanding the mechanisms underlying pollinator speciation and host specificity in obligate pollination mutualism.

Phylogenetic and population genetic analyses reveal mechanisms of pollinator sharing, copollination and speciation by host-shift in fig-wasp mutualism.

Development and characterization of microsatellite loci for Ficus hirta (Moraceae)

PREMISE OF THE STUDY

Microsatellite primers were developed to investigate population genetic structure in Ficus hirta (Moraceae).

METHODS AND RESULTS

Sixteen microsatellite primers were developed and optimized for F. hirta using Illumina paired-end sequencing of pre-receptive and receptive developmental-phase female flowers. Out of 16 primers, nine were found to be polymorphic in four populations of F. hirta. Alleles per locus ranged from two to 15 across the 94 F. hirta individuals, while within-population observed and expected heterozygosity per locus ranged from 0.000 to 0.955 and from 0.000 to 0.882, respectively. In addition, the 16 primers were tested in 29 additional Ficus species, with all found to amplify in at least 11 of these species and with most amplifying in a majority of the species.

CONCLUSIONS

This set of microsatellite primers is the first specifically developed for F. hirta and will facilitate studies of genetic diversity within and genetic differentiation among populations of Ficus species.

Genetic structure and hybridization in the species group of Ficus auriculata: can closely related sympatric Ficus species retain their genetic identity while sharing pollinators?

Obligate mutualistic nursery pollination systems between insects and plants have led to substantial codiversification involving at least some parallel cladogenesis, as documented in Yucca, Ficus and Phyllanthaceae. In such systems, pollinators are generally species specific thus limiting hybridization and introgression among interfertile host species. Nevertheless, in the three systems, cases of one insect pollinating several plant species are reported. In most cases, host plants sharing pollinators are allopatric. However, in the case of the species group of Ficus auriculata, forms may co-occur over large parts of their range. We show here that the species group of F. auriculata is constituted by four well-defined genetic entities that share pollinators. We detected hybrids in nature mainly when both parental forms were growing nearby. Controlled crosses showed that F1 offspring could be successfully backcrossed. Hence, despite sharing pollinators and despite hybrid viability, the different forms have preserved their genetic and morphological identity. We propose that ecological differentiation among forms coupled with limited overlap of reproductive season has facilitated the maintenance of these interfertile forms. As such, establishment of pollinator host specificity may not be a prerequisite for sympatric diversification in Ficus.

Nuclear and chloroplast DNA phylogeography of Ficus hirta: obligate pollination mutualism and constraints on range expansion in response to climate change

This study uses a phylogeographic approach to investigate how interspecific interactions in an obligate pollination mutualism enhance or constrain dispersal and the range distributions of species through time. Fifteen populations of Ficus hirta, a bird-dispersed fig pollinated by a species-specific fig wasp, were sampled from Thailand to the northern limits of the tropical forest in China. These populations were assayed for six nuclear microsatellite loci and two intergenic chloroplast DNA sequences. Analyses of range expansion and genetic clustering indicated a relatively slow rate of range expansion from two or more southern glacial refugia. Low nuclear differentiation, combined with high interpopulation differentiation, and phylogeographic structuring of chloroplast variation indicated that seed dispersal has had a greater constraint than obligate interactions with fig wasps on the rate of post-glacial range expansion. This study is the first to investigate the phylogeographic history of a widely distributed southeast Asian tropical plant whose distribution extends to the northern limits of tropical forest habitat in China. It is also the first study of Ficus utilizing molecular data to evaluate whether species-specific pollination is a limitation or an aid to range expansion in response to climate change.

Pollinator-mediated reproductive isolation among dioecious fig species (Ficus, Moraceae)

The extent of isolation among closely related sympatric plant species engaged in obligate pollination mutualisms depends on the fitness consequences of interspecies floral visitation. In figs (Ficus), interspecific gene flow may occur when pollinating wasps (Agaonidae) visit species other than their natal fig species. We studied reproductive isolation in a clade of six sympatric dioecious fig species in New Guinea. Microsatellite genotyping and Bayesian clustering analysis of the fig community indicated strong reproductive barriers among sympatric species. A total of 1-2% of fig populations consisted of hybrid individuals. A new experimental method of manipulating fig wasps investigated the reproductive consequences of conspecific and heterospecific pollinator visitation for both mutualists. Fig wasps introduced to Ficus hispidioides pollinated and oviposited in receptive figs. Seed development and seedling growth were largely comparable between conspecific and heterospecific crosses. Heterospecific pollinator fitness, however, was significantly less than that of conspecific pollinators. Heterospecific pollinators induced gall formation but offspring did not develop to maturity in the new host. Selection on pollinators maintaining host specificity appears to be an important mechanism of contemporary reproductive isolation among these taxa that could potentially influence their diversification.

Development and characterization of microsatellite loci in dioecious figs (Ficus, Moraceae)

PREMISE OF THE STUDY

Microsatellite markers for dioecious fig species, Ficus bernaysii King (section Sycocarpus), Ficus pachyrrhachis K. Schum. & Lauterb. (section Sycocarpus), and Ficus copiosa Steud. (section Sycidium) were developed to estimate gene flow among closely related fig species.

METHODS AND RESULTS

Loci were developed from tri- and tetranucleotide-enriched genomic libraries. The six most repeatable and scorable loci for F. bernaysii and F. pachyrrhachis were characterized in 50 individuals each of five species from section Sycocarpus. Four primer pairs from F. copiosa were screened in 50 individuals each of two species from section Sycidium. Observed heterozygosity ranged from 0.53 to 0.93 in loci developed from F. bernaysii, 0.25 to 0.86 in loci developed from F. pachyrrhachis, and 0.68 to 0.87 in loci developed from F. copiosa.

CONCLUSIONS

Amplification across the two Ficus sections was observed in seven of the ten total primer pairs.

Transferability and characterization of microsatellite markers in two Neotropical Ficus species

Microsatellite markers were transferred and characterized for two Neotropical fig tree species, Ficus citrifolia and Ficus eximia. Our study demonstrated that microsatellite markers developed from different subgenera of Ficus can be transferred to related species. In the present case, 12 of the 15 primer pairs tested (80%) were successfully transferred to both of the above species. Eleven loci were polymorphic when tested across 60 F. citrifolia and 60 F. eximia individuals. For F. citrifolia, there were 4 to 15 alleles per locus, whereas expected heterozygosities ranged from 0.31 to 0.91. In the case of F. eximia, this was 2 to 12 alleles per locus and expected heterozygosities from 0.42 to 0.87.