Genomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism

Ficus (figs) and their agaonid wasp pollinators present an ecologically important mutualism that also provides a rich comparative system for studying functional co-diversification throughout its coevolutionary history (~75 million years). We obtained entire nuclear, mitochondrial, and chloroplast genomes for 15 species representing all major clades of Ficus. Multiple analyses of these genomic data suggest that hybridization events have occurred throughout Ficus evolutionary history. Furthermore, cophylogenetic reconciliation analyses detect significant incongruence among all nuclear, chloroplast, and mitochondrial-based phylogenies, none of which correspond with any published phylogenies of the associated pollinator wasps. These findings are most consistent with frequent host-switching by the pollinators, leading to fig hybridization, even between distantly related clades. Here, we suggest that these pollinator host-switches and fig hybridization events are a dominant feature of fig/wasp coevolutionary history, and by generating novel genomic combinations in the figs have likely contributed to the remarkable diversity exhibited by this mutualism.

Improved de novo Assembly of the Achlorophyllous Orchid Gastrodia elata

Achlorophyllous plants are full mycoheterotrophic plants with no chlorophyll and they obtain their nutrients from soil fungi. Gastrodia elata is a perennial, achlorophyllous orchid that displays distinctive evolutionary strategy of adaptation to the non-photosynthetic lifestyle. Here in this study, the genome of G. elata was assembled to 1.12 Gb with a contig N50 size of 110 kb and a scaffold N50 size of 1.64 Mb so that it helped unveil the genetic basics of those adaptive changes. Based on the genomic data, key genes related to photosynthesis, leaf development, and plastid division pathways were found to be lost or under relaxed selection during the course of evolution. Thus, the genome sequence of G. elata provides a good resource for future investigations of the evolution of orchids and other achlorophyllous plants.

Effects of landscapes and range expansion on population structure and local adaptation

Understanding the origin and distribution of genetic diversity across landscapes is critical for predicting the future of organisms in changing climates. This study investigated how adaptive and demographic forces have shaped diversity and population structure in Pinus densata, a keystone species on Qinghai-Tibetan Plateau (QTP). We examined the distribution of genomic diversity across the range of P. densata using exome capture sequencing. We applied spatially explicit tests to dissect the impacts of allele surfing, geographic isolation and environmental gradients on population differentiation and forecasted how this genetic legacy may limit the persistence of P. densata in future climates. We found that allele surfing from range expansion could explain the distribution of 39% of the c. 48 000 genotyped single nucleotide polymorphisms (SNPs). Uncorrected, these allele frequency clines severely confounded inferences of selection. After controlling for demographic processes, isolation-by-environment explained 9.2-19.5% of the genetic structure, with c. 4.0% of loci being affected by selection. Allele surfing and genotype-environment associations resulted in genomic mismatch under projected climate scenarios. We illustrate that significant local adaptation, when coupled with reduced diversity as a result of demographic history, constrains potential evolutionary response to climate change. The strong signal of genomic vulnerability in P. densata may be representative for other QTP endemics.

Hybridization in human evolution: Insights from other organisms

During the late Pleistocene, isolated lineages of hominins exchanged genes thus influencing genomic variation in humans in both the past and present. However, the dynamics of this genetic exchange and associated phenotypic consequences through time remain poorly understood. Gene exchange across divergent lineages can result in myriad outcomes arising from these dynamics and the environmental conditions under which it occurs. Here we draw from our collective research across various organisms, illustrating some of the ways in which gene exchange can structure genomic/phenotypic diversity within/among species. We present a range of examples relevant to questions about the evolution of hominins. These examples are not meant to be exhaustive, but rather illustrative of the diverse evolutionary causes/consequences of hybridization, highlighting potential drivers of human evolution in the context of hybridization including: influences on adaptive evolution, climate change, developmental systems, sex-differences in behavior, Haldane's rule and the large X-effect, and transgressive phenotypic variation.

Functional Fc gamma receptor gene polymorphisms and donor-specific antibody-triggered microcirculation inflammation

Fc-dependent effector mechanisms may contribute to antibody-mediated rejection (ABMR), and distinct gene polymorphisms modifying the function of Fc gamma receptors (FcγRs) may influence the capability of donor-specific antibodies (DSAs) to trigger inflammation. To evaluate the relevance of functional FcγR variants in late ABMR, 85 DSA-positive kidney allograft recipients, who were recruited upon antibody screening of 741 prevalent patients, were genotyped for polymorphisms in FcγRIIA (FCGR2A-H/R₁₃₁ ; rs1801274), FcγRIIIA (FCGR3A-V/F₁₅₈ ; rs396991), and FcγRIIIB (FCGR3B-neutrophil antigen 1 ([NA1]/NA2; rs35139848). Individuals with high-affinity FCGR3A-V₁₅₈ alleles (V/V₁₅₈ or V/F₁₅₈ ) showed a higher rate (and extent) of peritubular capillaritis (ptc) in protocol biopsies than homozygous carriers of the lower-affinity allele (ptc score ≥1: 53.6% vs 25.9%; P = .018). Associations were independent of C1q-binding to DSA or capillary C4d. In parallel, there was a trend toward increased macrophage- and injury-repair response-associated transcript subsets. Kidney function over 24 months, however, was not different. In support of a functional role of FcγRIIIA polymorphism, NK92 cells expressing FCGR3A-V₁₅₈ produced >2 times as much interferon gamma upon incubation with HLA antibody-coated cells as those expressing FCGR3A-F₁₅₈ . FcγRIIA and FcγRIIIB polymorphisms were not associated with allograft morphology. Our data suggest that the presence of high-affinity FcγRIIIA variants may favor DSA-triggered microcirculation inflammation.

POLLEN-TUBE COMPETITION, SIRING SUCCESS, AND CONSISTENT ASYMMETRIC HYBRIDIZATION IN LOUISIANA IRISES

Postpollination mechanisms can play an important role in limiting natural hybridization in plants. Reciprocal hand pollination experiments were performed to study these mechanisms in two species of Louisiana iris: Iris brevicaulis and I. fulva. Relative pollen-tube growth rates changed significantly through time, with I. fulva tubes increasingly outperforming I. brevicaulis tubes in both conspecific and heterospecific styles. However, this pattern of change in relative performance was a poor predictor of siring success: the majority of seeds sired by both maternal species was conspecific rather than hybrid. Experimental crosses and field studies show consistent asymmetric hybridization in Louisiana irises, with I. fulva being a more successful father and a more selective mother than both I. brevicaulis and a third species, I. hexagona. The cause of this pattern is not yet clear, but the pattern itself is unusual. Typically, short-styled species tend to be less successful in reciprocal crosses than long-styled relatives, but I. fulva has shorter styles than either I. brevicaulis or I. hexagona. The effects of pollen-tube competition, differential fertilization, and selective abortion in causing this pattern of asymmetric hybridization is discussed.

ECOLOGICAL AND GENETIC ASSOCIATIONS IN AN IRIS HYBRID ZONE

Chloroplast DNA (cpDNA) markers and 12 nuclear (random amplified polymorphic DNA, or RAPD) markers were used to examine the distribution of genetic variation among individuals and the genetic and ecological associations in a hybrid iris population. Plants in the population occurred at various distances from the edge of a bayou in a relatively undisturbed mixed hardwood forest and in an adjacent pasture dominated by herbaceous perennials with interspersed oak and cypress trees. The majority of plants sampled possessed combinations of markers from the different Iris species. Genetic markers diagnostic for Iris fulva and I. brevicaulis occurred at high frequencies, whereas markers diagnostic for I. hexagona were infrequent. For the majority of the nuclear markers, significant levels of cytonuclear disequilibria existed because of intraspecific associations among the markers in both the pasture and the forest. The distribution of nuclear markers among individuals was bimodal; intermediate genotypes were absent and the majority of RAPD markers were associated with their intraspecific cpDNA haplotypes. Strong intraspecific associations existed among RAPD markers in the forest, but associations tended to be weaker in the pasture area. Ecological correlations were detected for all but one of the I. fulva and I. brevicaulis RAPD markers. The ecological associations of hybrids similar to I. brevicaulis resembled associations of I. brevicaulis parental genotypes, suggesting that these hybrid genotypes may be relatively fit in the same habitats. The hybrids similar to I. fulva, however, were distributed in habitats that were unique relative to the parental species. The patterns of genetic and environmental associations along with other available data suggest that (1) only advanced generation hybrids were present in the population; (2) formation of F₁ hybrids among Louisiana irises is rare, leading to sporadic formation of hybrid populations; and (3) selection and assortative mating have contributed to the formation of hybrid genotypes that tend to be similar to parental genotypes. The patterns of ecological and genetic associations detected in this population suggest that assortative mating and environmental and viability selection are important in the structuring and maintenance of this hybrid zone.

EFFECTS OF DIFFERENTIAL POLLEN-TUBE GROWTH ON HYBRIDIZATION IN THE LOUISIANA IRISES

To elucidate the importance of hybridization in evolution, it is necessary to understand the processes that affect hybridization frequency in nature. Here we focus on postpollination, prefertilization isolating mechanisms using two hybridizing species of Louisiana iris as a study system. We compared the effects of differential pollen-tube growth on the frequency of F₁ hybrid formation in experimental crosses between Iris fulva and Iris hexagona. Analyses of seed production in fruits from pure conspecific and heterospecific pollinations revealed that more seeds were produced in the top half than the bottom half of fruits for all four crosses. Heterospecific pollen was applied to flowers of each species at zero to 24 h prior to conspecific pollen, thereby giving a head start to the foreign pollen. Using diagnostic isozyme markers, the frequency of hybrid progeny was examined at the level of the whole fruit and separately for the top and bottom halves of fruits. In both species, the proportion of hybrid seeds per fruit increased significantly with increasing head starts, suggesting that differences in pollen-tube growth rates affect the frequency of hybridization. In I. fulva fruits, the increase in hybrid seeds occurred in both halves of the fruits, but in I. hexagona an increase was only detected in the top half of fruits. These findings are consistent with a model that assumes attrition of pollen tubes due to the greater length of I. hexagona styles. While pollen-tube growth rate appears to be the most important factor affecting hybridization frequency in I. fulva, both pollen-tube growth rate and pollen-tube attrition appear to be important in I. hexagona.

Niche Conservatism for Ecological Preference in the Louisiana iris species complex

Spatial and temporal environmental variation influences evolutionary processes such as divergence among populations and species. Here, we investigate the patterns of niche evolution for the Louisiana irises as well as understanding the phylogenetic relationship between these species. Using BEAST, a species phylogeny was generated for the Louisiana irises in order to test the hypothesis of whether niche conservatism has played an important role for this species complex. Species Distribution Models were constructed for present day distributions to determine the environmental factors, which contribute to species ranges. Tests of niche similarity were performed in order to evaluate if niche conservatism is apparent within this species complex. We demonstrate that the Louisiana iris species complex is a monophyletic clade with I. brevicaulis and I. fulva as being sister to each other. The differences observed among the iris species, in regard to associated environmental factors suggest an effect from these components on the distributions and habitats occupied. Furthermore, tests of niche similarity indicate niche conservatism for all species comparisons. Working at the species level and assessing various factors that can influence differentiation, this study assessed a more complete picture of the ecological and evolutionary history of this species complex across their geographic and ecological range.

Neutral and Selective Processes Drive Population Differentiation for Iris hexagona

Gene flow among widespread populations can be reduced by geographical distance or by divergent selection resulting from local adaptation. In this study, we tested for the divergence of phenotypes and genotypes among 8 populations of Iris hexagona. Using a genotyping-by-sequencing approach, we generated a panel of 750 single nucleotide polymorphisms (SNPs) and used population genetic analyses to determine what may affect patterns of divergence across I. hexagona populations. Specifically, genetic differentiation was compared between populations at neutral and nonneutral SNPs and detected significant differences between the 2 types of markers. We then asked whether loci with the strongest degree of population genetic differentiation were also the loci with the strongest association to morphology or climate differences, allowing us to test if pollinators or climate drive population differentiation or some combination of both. We found 2 markers that were associated with morphology and 1 marker associated with 2 of the environmental variables, which were also identified in the outlier analysis. We then show that the SNPs putatively under selection were positively correlated with both geographic distance and phenotypic distance, albeit weakly to phenotypic distance. Moreover, neutral SNPs were only correlated with geographic distance and thus isolation-by-distance was observed for neutral SNPs. Our data suggest that both deterministic and neutral processes have contributed to the evolutionary trajectory of I. hexagona populations.

Determining population structure and hybridization for two iris species

Identifying processes that promote or limit gene flow can help define the ecological and evolutionary history of a species. Furthermore, defining those factors that make up “species boundaries” can provide a definition of the independent evolutionary trajectories of related taxa. For many species, the historic processes that account for their distribution of genetic variation remain unresolved. In this study, we examine the geographic distribution of genetic diversity for two species of Louisiana Irises, Iris brevicaulis and Iris fulva. Specifically, we asked how populations are structured and if population structure coincides with potential barriers to gene flow. We also asked whether there is evidence of hybridization between these two species outside Louisiana hybrid zones. We used a genotyping-by-sequencing approach and sampled a large number of single nucleotide polymorphisms across these species' genomes. Two different population assignment methods were used to resolve population structure in I. brevicaulis; however, there was considerably less population structure in I. fulva. We used a species tree approach to infer phylogenies both within and between populations and species. For I. brevicaulis, the geography of the collection locality was reflected in the phylogeny. The I. fulva phylogeny reflected much less structure than detected for I. brevicaulis. Lastly, combining both species into a phylogenetic analysis resolved two of six populations of I. brevicaulis that shared alleles with I. fulva. Taken together, our results suggest major differences in the level and pattern of connectivity among populations of these two Louisiana Iris species.

Transcriptome sequencing and phylogenetic analysis of floral and leaf MIKC(C) MADS-box and R2R3 MYB transcription factors from the monocot Iris fulva

The Louisiana Irises serve as an important system for the study of the evolutionary processes of speciation, including reproductive isolation, hybridization, and adaptation. Sequencing methods today allow for the generation of resources key to elucidating the genetic basis of these phenomena. Here we describe the transcriptomes of floral and young leaf tissue from Iris fulva generated by massively parallel pyrosequencing. In order to identify potential candidates for the study of reproductive isolation and adaptation in the Louisiana Irises we phylogenetically analyzed the type II MIKC(C) MADS-box and R2R3 MYB transcription factors expressed in these tissues. A total of 25 Iris MIKC(C) MADS-box genes in 9 clades and 42 Iris R2R3 MYB genes in 19 clades were identified. Through the identification of eudicot and monocot specific clades, these analyses contribute to our understanding of the evolution of these prominent transcription factor families in the angiosperms.

QTL mapping reveals the genetic architecture of loci affecting pre- and post-zygotic isolating barriers in Louisiana Iris

BACKGROUND

Hybridization among Louisiana Irises has been well established and the genetic architecture of reproductive isolation is known to affect the potential for and the directionality of introgression between taxa. Here we use co-dominant markers to identify regions where QTL are located both within and between backcross maps to compare the genetic architecture of reproductive isolation and fitness traits across treatments and years.

RESULTS

QTL mapping was used to elucidate the genetic architecture of reproductive isolation between Iris fulva and Iris brevicaulis. Homologous co-dominant EST-SSR markers scored in two backcross populations between I. fulva and I. brevicaulis were used to generate genetic linkage maps. These were used as the framework for mapping QTL associated with variation in 11 phenotypic traits likely responsible for reproductive isolation and fitness. QTL were dispersed throughout the genome, with the exception of one region of a single linkage group (LG) where QTL for flowering time, sterility, and fruit production clustered. In most cases, homologous QTL were not identified in both backcross populations, however, homologous QTL for flowering time, number of growth points per rhizome, number of nodes per inflorescence, and number of flowers per node were identified on several linkage groups.

CONCLUSIONS

Two different traits affecting reproductive isolation, flowering time and sterility, exhibit different genetic architectures, with numerous QTL across the Iris genome controlling flowering time and fewer, less distributed QTL affecting sterility. QTL for traits affecting fitness are largely distributed across the genome with occasional overlap, especially on LG 4, where several QTL increasing fitness and decreasing sterility cluster. Given the distribution and effect direction of QTL affecting reproductive isolation and fitness, we have predicted genomic regions where introgression may be more likely to occur (those regions associated with an increase in fitness and unlinked to loci controlling reproductive isolation) and those that are less likely to exhibit introgression (those regions linked to traits decreasing fitness and reproductive isolation).

The strange blood: natural hybridization in primates

Hybridization between two closely related species is a natural evolutionary process that results in an admixture of previously isolated gene pools. The exchange of genes between species may accelerate adaptation and lead to the formation of new lineages. Hybridization can be regarded as one important evolutionary mechanism driving speciation processes. Although recent studies have highlighted the taxonomic breadth of natural hybridization in the primate order, information about primate hybridization is still limited compared to that about the hybridization of fish, birds, or other mammals. In primates, hybridization has occurred mainly between subspecies and species, but has also been detected between genera and even in the human lineage. Here we provide an overview of cases of natural hybridization in all major primate radiations. Our review emphasizes a phylogenetic approach. We use the data presented to discuss the impact of hybridization on taxonomy and conservation.

Reticulate evolution: frequent introgressive hybridization among Chinese hares (genus lepus) revealed by analyses of multiple mitochondrial and nuclear DNA loci

BACKGROUND

Interspecific hybridization may lead to the introgression of genes and genomes across species barriers and contribute to a reticulate evolutionary pattern and thus taxonomic uncertainties. Since several previous studies have demonstrated that introgressive hybridization has occurred among some species within Lepus, therefore it is possible that introgressive hybridization events also occur among Chinese Lepus species and contribute to the current taxonomic confusion.

RESULTS

Data from four mtDNA genes, from 116 individuals, and one nuclear gene, from 119 individuals, provides the first evidence of frequent introgression events via historical and recent interspecific hybridizations among six Chinese Lepus species. Remarkably, the mtDNA of L. mandshuricus was completely replaced by mtDNA from L. timidus and L. sinensis. Analysis of the nuclear DNA sequence revealed a high proportion of heterozygous genotypes containing alleles from two divergent clades and that several haplotypes were shared among species, suggesting repeated and recent introgression. Furthermore, results from the present analyses suggest that Chinese hares belong to eight species.

CONCLUSION

This study provides a framework for understanding the patterns of speciation and the taxonomy of this clade. The existence of morphological intermediates and atypical mitochondrial gene genealogies resulting from frequent hybridization events likely contribute to the current taxonomic confusion of Chinese hares. The present study also demonstrated that nuclear gene sequence could offer a powerful complementary data set with mtDNA in tracing a complete evolutionary history of recently diverged species.

Hybrid fitness across time and habitats

There has been considerable debate about the role of hybrids in the evolutionary process. One question has involved the relative fitness of hybrid versus non-hybrid genotypes. For some, the assumption of lower hybrid fitness continues to be integral to their concept of species and speciation. In contrast, numerous workers have suggested that hybrid genotypes might demonstrate higher relative fitness under various environmental settings. Of particular importance in deciding between these opposing hypotheses are long-term analyses coupling ecological and genetic information. Although currently rare, such analyses have provided a test of the fitness of hybrid genotypes across generations and habitats and their role in adaptation and speciation. Here we discuss examples of these analyses applied to viruses, prokaryotes, plants and Darwin's Finches.

Ribosomal RNA-encoding DNA introgression across a narrow hybrid zone between two subspecies of grasshopper

A ribosomal RNA-encoding DNA (rDNA) cloned sequence, consisting of a 0.8-kilobase fragment from the 26S/nontranscribed spacer region, was used to identify diagnostic restriction enzyme fragments that distinguish the Moreton and Torresian subspecies of the grasshopper Caledia captiva. These restriction fragments were then used to study patterns of rDNA variation across a narrow geographical hybrid zone between the two subspecies. The pattern of rDNA variation that emerged after the analysis of over 250 individuals clearly demonstrates the asymmetrical introgression of the Moreton ribosomal RNA genes into the Torresian subspecies. This asymmetric movement of genetic material occurs even though there exists extreme postmating F(2) and backcross inviability between the two subspecies. From our data, as well as those of previous chromosomal and allozymic studies, we are able to support the occurrence of nonrandom processes such as biased gene conversion and/or natural selection. Because the rDNA loci in the Moreton and Torresian individuals are located in different regions on chromosomes 10 and 11, it should be possible to determine the relative contributions of conversion, natural selection, and these sorts of processes to the pattern of introgression of the Moreton rDNA into the Torresian subspecies.

Transmission ratio distortion results in asymmetric introgression in Louisiana Iris

BACKGROUND

Linkage maps are useful tools for examining both the genetic architecture of quantitative traits and the evolution of reproductive incompatibilities. We describe the generation of two genetic maps using reciprocal interspecific backcross 1 (BC1) mapping populations from crosses between Iris brevicaulis and Iris fulva. These maps were constructed using expressed sequence tag (EST)- derived codominant microsatellite markers. Such a codominant marker system allowed for the ability to link the two reciprocal maps, and compare patterns of transmission ratio distortion observed between the two.

RESULTS

Linkage mapping resulted in markers that coalesced into 21 linkage groups for each of the reciprocal backcross maps, presumably corresponding to the 21 haploid chromosomes of I. brevicaulis and I. fulva. The composite map was 1190.0-cM long, spanned 81% of the I. brevicaulis and I. fulva genomes, and had a mean density of 4.5 cM per locus. Transmission ratio distortion (TRD) was observed in 138 (48.5%) loci distributed in 19 of the 21 LGs in BCIB, BCIF, or both BC1 mapping populations. Of the distorted markers identified, I. fulva alleles were detected at consistently higher-than-expected frequencies in both mapping populations.

CONCLUSIONS

The observation that I. fulva alleles are overrepresented in both mapping populations suggests that I. fulva alleles are favored to introgress into I. brevicaulis genetic backgrounds, while I. brevicaulis alleles would tend to be prevented from introgressing into I. fulva. These data are consistent with the previously observed patterns of introgression in natural hybrid zones, where I. fulva alleles have been consistently shown to introgress across species boundaries.

Asymmetric introgressive hybridization among louisiana iris species

In this review, we discuss findings from studies carried out over the past 20+ years that document the occurrence of asymmetric introgressive hybridization in a plant clade. In particular, analyses of natural and experimental hybridization have demonstrated the consistent introgression of genes from Iris fulva into both Iris brevicaulis and Iris hexagona. Furthermore, our analyses have detected certain prezygotic and postzygotic barriers to reproduction that appear to contribute to the asymmetric introgression. Finally, our studies have determined that a portion of the genes transferred apparently affects adaptive traits.

Adaptation by introgression

Both selective and random processes can affect the outcome of natural hybridization. A recent analysis in BMC Evolutionary Biology of natural hybridization between an introduced and a native salamander reveals the mosaic nature of introgression, which is probably caused by a combination of selection and demography.

Reticulate evolution and marine organisms: the final frontier?

The role that reticulate evolution (i.e., via lateral transfer, viral recombination and/or introgressive hybridization) has played in the origin and adaptation of individual taxa and even entire clades continues to be tested for all domains of life. Though falsified for some groups, the hypothesis of divergence in the face of gene flow is becoming accepted as a major facilitator of evolutionary change for many microorganisms, plants and animals. Yet, the effect of reticulate evolutionary change in certain assemblages has been doubted, either due to an actual dearth of genetic exchange among the lineages belonging to these clades or because of a lack of appropriate data to test alternative hypotheses. Marine organisms represent such an assemblage. In the past half-century, some evolutionary biologists interested in the origin and trajectory of marine organisms, particularly animals, have posited that horizontal transfer, introgression and hybrid speciation have been rare. In this review, we provide examples of such genetic exchange that have come to light largely as a result of analyses of molecular markers. Comparisons among these markers and between these loci and morphological characters have provided numerous examples of marine microorganisms, plants and animals that possess the signature of mosaic genomes.

EST and EST-SSR marker resources for Iris

BACKGROUND

Limited DNA sequence and DNA marker resources have been developed for Iris (Iridaceae), a monocot genus of 200-300 species in the Asparagales, several of which are horticulturally important. We mined an I. brevicaulis-I. fulva EST database for simple sequence repeats (SSRs) and developed ortholog-specific EST-SSR markers for genetic mapping and other genotyping applications in Iris. Here, we describe the abundance and other characteristics of SSRs identified in the transcript assembly (EST database) and the cross-species utility and polymorphisms of I. brevicaulis-I. fulva EST-SSR markers among wild collected ecotypes and horticulturally important cultivars.

RESULTS

Collectively, 6,530 ESTs were produced from normalized leaf and root cDNA libraries of I. brevicaulis (IB72) and I. fulva (IF174), and assembled into 4,917 unigenes (1,066 contigs and 3,851 singletons). We identified 1,447 SSRs in 1,162 unigenes and developed 526 EST-SSR markers, each tracing a different unigene. Three-fourths of the EST-SSR markers (399/526) amplified alleles from IB72 and IF174 and 84% (335/399) were polymorphic between IB25 and IF174, the parents of I. brevicaulis x I. fulva mapping populations. Forty EST-SSR markers were screened for polymorphisms among 39 ecotypes or cultivars of seven species - 100% amplified alleles from wild collected ecotypes of Louisiana Iris (I.brevicaulis, I.fulva, I. nelsonii, and I. hexagona), whereas 42-52% amplified alleles from cultivars of three horticulturally important species (I. pseudacorus, I. germanica, and I. sibirica). Ecotypes and cultivars were genetically diverse - the number of alleles/locus ranged from two to 18 and mean heterozygosity was 0.76.

CONCLUSION

Nearly 400 ortholog-specific EST-SSR markers were developed for comparative genetic mapping and other genotyping applications in Iris, were highly polymorphic among ecotypes and cultivars, and have broad utility for genotyping applications within the genus.

Is the new primate genus rungwecebus a baboon?

BACKGROUND

In 2005, a new primate species from Tanzania, the kipunji, was described and recognized as a member of the mangabey genus Lophocebus. However, molecular investigations based upon a number of papionins, including a limited sample of baboons of mainly unknown geographic origin, identified the kipunji as a sister taxon to Papio and not as a member of Lophocebus. Accordingly, the kipunji was separated into its own monotypic genus, Rungwecebus.

METHODOLOGY/PRINCIPAL FINDINGS

We compare available mitochondrial and nuclear sequence data from the voucher specimen of Rungwecebus to other papionin lineages, including a set of geographically proximal (parapatric) baboon samples. Based on mitochondrial sequence data the kipunji clusters with baboon lineages that lie nearest to it geographically, i.e. populations of yellow and chacma baboons from south-eastern Africa, and thus does not represent a sister taxon to Papio. Nuclear data support a Papio+Rungwecebus clade, but it remains questionable whether Rungwecebus represents a sister taxon to Papio, or whether it is nested within the genus as depicted by the mitochondrial phylogeny.

CONCLUSIONS/SIGNIFICANCE

Our study clearly supports a close relationship between Rungwecebus and Papio and might indicate that the kipunji is congeneric with baboon species. However, due to its morphological and ecological uniqueness Rungwecebus more likely represents a sister lineage to Papio and experienced later introgressive hybridization. Presumably, male (proto-)kipunjis reproduced with sympatric female baboons. Subsequent backcrossing of the hybrids with kipunjis would have resulted in a population with a nuclear kipunji genome, but which retained the yellow/chacma baboon mitochondrial genome. Since only one kipunji specimen was studied, it remains unclear whether all members of the new genus have been impacted by intergeneric introgression or rather only some populations. Further studies with additional Rungwecebus samples are necessary to elucidate the complete evolutionary history of this newly-described primate genus.

Review. Genetic exchange and the origin of adaptations: prokaryotes to primates

Data supporting the occurrence of adaptive trait transfer (i.e. the transfer of genes and thus the phenotype of an adaptive trait through viral recombination, lateral gene transfer or introgressive hybridization) are provided in this review. Specifically, we discuss examples of lateral gene transfer and introgressive hybridization that have resulted in the transfer or de novo origin of adaptations. The evolutionary clades in which this process has been identified include all types of organisms. However, we restrict our discussion to bacteria, fungi, plants and animals. Each of these examples reflects the same consequence, namely that the transfer of genetic material, through whatever mechanism, may result in adaptive evolution. In particular, each of the events discussed has been inferred to impact adaptations to novel environmental settings in the recipient lineage.

Characterization and comparative analysis of sequence-specific amplified polymorphisms based on two subfamilies of IRRE retrotransposons in Iris missouriensis (Iridaceae)

DNA markers based on transposable-element polymorphisms are potentially useful alternatives to anonymous fragment-length polymorphisms (AFLPs). We developed the retrotransposon sequence-specific amplified polymorphism (retrotransposon SSAP) technique for the angiosperm Iris missouriensis (Iridaceae) in order to evaluate its use in generating population-genetic markers. Our cloning strategy identified two groups of long-terminal repeat retrotransposons of the IRRE family. Primers homologous to conserved regions of these elements generated repeatable and polymorphic markers. In comparison, the AFLP protocol failed to produce useful markers in our hands in this species. To investigate the distribution and evolutionary tempo of the two retrotransposons, we developed a phylogeny of representative species of subgenus Limniris based on chloroplast sequence. Sequences of both groups of retrotransposons were widespread in Limniris, but we also found evidence of substantial sequence and copy-number evolution since the divergence of I. missouriensis from other Limniris species. We corroborated these results with quantitative real-time PCR estimates of relative copy number. Importantly, the geographic structure of retrotransposon SSAP was strikingly different for the two groups of retrotransposons, indicating that different mutational dynamics and/or selective pressures govern their distribution. Although these primers should be useful for population-genetic studies of Iris missouriensis and other Limniris species, our findings reinforce the need for caution in evaluating transposable-element markers used to analyze the relatedness of populations or cultivars, as very different conclusions may be reached depending on the sequence amplified.

Phylogeography of Iris missouriensis (Iridaceae) based on nuclear and chloroplast markers

We investigated the phylogeography of Iris missouriensis (Iridaceae), which is widely distributed in western North America. We utilized transposon display and DNA sequencing to quantify nuclear and chloroplast genetic structure. Our objectives were (i) to characterize the geographic structure of genetic variation throughout the species range, (ii) to test whether both margins of the range show reduced genetic diversity as predicted by north-south expansion and contraction associated with climate change, and (iii) to determine whether the subspecies Iris missouriensis ssp. longipetala is genetically distinct. We found that genetic diversity was significantly lower in the northern part of the range but was not significantly different between the central and southern regions, indicating greater stability of the southern margin vs. the northern. Among-population differentiation was high (PhiPT=0.52). The largest divisions in each marker set were concordant and separated the southern Rocky Mountains and Basin and Range provinces from the remainder of the range. The boundaries of this phylogeographic break do not coincide with gaps in present-day distributions or phylogeographic breaks identified in other species, and may indicate a measure of reproductive isolation. Consistent with current treatments, we did not find support for the taxonomic placement of I. missourienis ssp. longipetala as a distinct species. Although transposon display has been used to investigate relationships among crop accessions and their wild relatives, to our knowledge, this is the first use of these markers for population-level phylogeography of a nonmodel species and further demonstrates their utility in species recalcitrant to amplified fragment length polymorphism protocols.

QTL ANALYSIS OF FLORAL TRAITS IN LOUISIANA IRIS HYBRIDS

The formation of hybrid zones between nascent species is a widespread phenomenon. The evolutionary consequences of hybridization are influenced by numerous factors, including the action of natural selection on quantitative trait variation. Here we examine how the genetic basis of floral traits of two species of Louisiana Irises affects the extent of quantitative trait variation in their hybrids. Quantitative trait locus (QTL) mapping was used to assess the size (magnitude) of phenotypic effects of individual QTL, the degree to which QTL for different floral traits are colocalized, and the occurrence of mixed QTL effects. These aspects of quantitative genetic variation would be expected to influence (1) the number of genetic steps (in terms of QTL substitutions) separating the parental species phenotypes; (2) trait correlations; and (3) the potential for transgressive segregation in hybrid populations. Results indicate that some Louisiana Iris floral trait QTL have large effects and QTL for different traits tend to colocalize. Transgressive variation was observed for six of nine traits, despite the fact that mixed QTL effects influence few traits. Overall, our QTL results imply that the genetic basis of floral morphology and color traits might facilitate the maintenance of phenotypic divergence between Iris fulva and Iris brevicaulis, although a great deal of phenotypic variation was observed among hybrids.

The genetic architecture of reproductive isolation in Louisiana irises: flowering phenology

Despite the potential importance of divergent reproductive phenologies as a barrier to gene flow, we know less about the genetics of this factor than we do about any other isolating barrier. Here, we report on the genetic architecture of divergent flowering phenologies that result in substantial reproductive isolation between the naturally hybridizing plant species Iris fulva and I. brevicaulis. I. fulva initiates and terminates flowering significantly earlier than I. brevicaulis. We examined line crosses of reciprocal F1 and backcross (BC1) hybrids and determined that flowering time was polygenic in nature. We further defined quantitative trait loci (QTL) that affect the initiation of flowering in each of these species. QTL analyses were performed separately for two different growing seasons in the greenhouse, as well as in two field plots where experimental plants were placed into nature. For BCIF hybrids (BC1 toward I. fulva), 14 of 17 detected QTL caused flowering to occur later in the season when I. brevicaulis alleles were present, while the remaining 3 caused flowering to occur earlier. In BCIB hybrids (BC1 toward I. brevicaulis), 11 of 15 detected QTL caused flowering to occur earlier in the season when introgressed I. fulva alleles were present, while the remaining 4 caused flowering to occur later. These ratios are consistent with expectations of selection (as opposed to drift) promoting flowering divergence in the evolutionary history of these species. Furthermore, epistatic interactions among the QTL also reflected the same trends, with the majority of epistatic effects causing later flowering than expected in BCIF hybrids and earlier flowering in BCIB hybrids. Overlapping QTL that influenced flowering time across all four habitat/treatment types were not detected, indicating that increasing the sample size of genotyped plants would likely increase the number of significant QTL found in this study.

Natural hybridization in primates: one evolutionary mechanism

The role and importance of natural hybridization in the evolutionary histories of animal taxa is still debated. This results largely from a history of zoological investigations that assumed, rather than documented, a limited evolutionary role for this process. However, it is now becoming apparent that, just as for plants, the creative effects of reticulate evolution are widespread in animal taxa as well. This conclusion is supported by the documentation of numerous instances of the formation of new taxa and the genetic enrichment through introgressive hybridization. In the present review, we use primates as a paradigm for how natural hybridization can affect the evolution of species complexes and remains a footprint on genomes. Findings for a number of groups, including basal (e.g. lemurs) and derived (e.g. Old World apes) lineages, demonstrate that introgression and hybrid speciation have caused a reticulate pattern that is still detectable in the, often mosaic, genomes of primates. For example, results from genetic analyses of our own species demonstrate the process of past introgressive hybridization with the progenitors of our sister taxa (i.e. chimpanzees and gorillas) and most likely also our extinct, close relatives in the hominid lineage.

Detecting adaptive trait introgression between Iris fulva and I. brevicaulis in highly selective field conditions

The idea that natural hybridization has served as an important force in evolutionary and adaptive diversification has gained considerable momentum in recent years. By combining genome analyses with a highly selective field experiment, we provide evidence for adaptive trait introgression between two naturally hybridizing Louisiana Iris species, flood-tolerant Iris fulva and dry-adapted I. brevicaulis. We planted reciprocal backcross (BC1) hybrids along with pure-species plants into natural settings that, due to a flooding event, favored I. fulva. As expected, I. fulva plants survived at much higher rates than I. brevicaulis plants. Backcross hybrids toward I. fulva (BCIF) also survived at significantly higher rates than the reciprocal backcross toward I. brevicaulis (BCIB). Survivorship of BCIB hybrids was strongly influenced by the presence of a number of introgressed I. fulva alleles located throughout the genome, while survivorship in the reciprocal BCIF hybrids was heavily influenced by two epistatically acting QTL of opposite effects. These results demonstrate the potential for adaptive trait introgression between these two species and may help to explain patterns of genetic variation observed in naturally occurring hybrid zones.

Genetic mapping of species boundaries in Louisiana irises using IRRE retrotransposon display markers

Genetic mapping studies provide insight into the pattern and extent of genetic incompatibilities affecting hybridization between closely related species. Genetic maps of two species of Louisiana Irises, Iris fulva and I. brevicaulis, were constructed from transposon-based molecular markers segregating in reciprocal backcross (BC1) interspecific hybrids and used to investigate genomic patterns of species barriers inhibiting introgression. Linkage mapping analyses indicated very little genetic incompatibility between I. fulva and I. brevicaulis in the form of map regions exhibiting transmission ratio distortion, and this was confirmed using a Bayesian multipoint mapping analysis. These results demonstrate the utility of transposon-based marker systems for genetic mapping studies of wild plant species and indicate that the genomes of I. fulva and I. brevicaulis are highly permeable to gene flow and introgression from one another via backcrossing.

Loci affecting long-term hybrid survivorship in Louisiana irises: implications for reproductive isolation and introgression

Iris fulva and I. brevicaulis are long-lived plant species known to hybridize where they coexist in nature. Year-to-year survival contributes significantly to overall fitness for both species and their hybrid derivatives, and differences in hybrid survivability may have important consequences to interspecific gene flow in nature. We examined the genetic architecture of long-term survivorship of reciprocal backcross I. fulva x I. brevicaulis hybrids in a common-garden, greenhouse environment. Differences in mortality were found between the two backcross (BC1) hybrid classes, with hybrids crossed toward I. fulva (BCIF) revealing twice the mortality of those hybrids backcrossed toward I. brevicaulis (BCIB). Using genomic scans on two separate genetic linkage maps derived from the reciprocal hybrid populations, we found that hybrid survivorship is influenced by several genetic regions. Multiple interval mapping (MIM) revealed four quantitative trait loci (QTLs) in BCIF hybrids that were significantly associated with survivorship. Introgressed I. brevicaulis DNA increased survivorship at three of the four QTLs. For the fourth QTL, introgressed I. brevicaulis DNA was associated with decreased survivorship. No QTLs were detected in BCIB hybrids; however, single-marker analysis revealed five unlinked loci that were significantly associated with survivorship. At all five markers, survivorship was positively associated with introgressed I. fulva DNA. The present findings have important implications for the evolutionary dynamics of naturally occurring hybrid zones. Regions of the genome that increase survivorship when in a heterozygous (i.e., hybrid) state should have an increased likelihood of passing across species boundaries, whereas those that decrease survivorship will be less likely to introgress.

Contrasting genetic structure of adults and progeny in a Louisiana iris hybrid population

Studies of natural hybridization have suggested that it may be a creative stimulus for adaptive evolution and speciation. An important step in this process is the establishment of fit recombinant genotypes that are buffered from subsequent recombination with unlike genotypes. We used molecular markers and a two-generation sampling strategy to infer the extent of recombination in a Louisiana iris hybrid zone consisting predominantly of Iris fulva-type floral phenotypes. Genotypic diversity was fairly high, indicating that sexual reproduction is frequent relative to clonal reproduction. However, we observed strong spatial genetic structure even after controlling for clonality, which implies a low level of pollen and seed dispersal. We therefore used cluster analysis to explore the hypothesis that the fulva-type hybrids are an admixture of groups between which there has been limited recombination. Our results indicate that several such groups are present in the population and are strongly localized spatially. This spatial pattern is not attributable strictly to a lack of mating opportunities between dissimilar genotypes for two reasons: (1) relatedness of flowering pairs was uncorrelated with the degree of overlap in flowering, and (2) paternity analysis shows that pollen movement among the outcross fraction occurred over large distances, with roughly half of all paternity attributed to pollen flow from outside the population. We also found evidence of strong inbreeding depression, indicated by contrasting estimates of the rate of self-fertilization and the average inbreeding coefficient of fulva-type hybrids. We conclude that groups of similar hybrid genotypes can be buffered from recombination at small spatial scales relative to pollen flow, and selection against certain recombinant genotypes may be as important as or more important than clonal reproduction and inbreeding.

Natural hybridization and the evolution of domesticated, pest and disease organisms

The role of natural hybridization in the evolutionary history of numerous species is well recognized. The impact of introgressive hybridization and hybrid speciation has been documented especially in plant and animal assemblages. However, there remain certain areas of investigation for which natural hybridization and its consequences remain under-studied and under-appreciated. One such area involves the evolution of organisms that positively or negatively affect human populations. In this review, I highlight exemplars of how natural hybridization has contributed to the evolution of (i) domesticated plants and animals; (ii) pests; (iii) human disease vectors; and (iv) human pathogens. I focus on the effects from genetic exchange that may lead to the acquisition of novel phenotypes and thus increase the beneficial or detrimental (to human populations) aspects of the various taxa.