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.

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.

Genetic architecture of floral traits in Iris hexagona and Iris fulva.

The formation of hybrids among closely related species has been observed in numerous plant taxa. Selection by pollinators on floral traits can act as an early reproductive isolating barrier and may be especially important when there is overlap in distribution and flowering time. In this study, we use Quantitative Trait Locus (QTL) mapping based on 293 codominant SNP markers in an F2 population (n = 328) to assess the size, magnitude, and location of the genetic regions controlling floral traits known to be important for pollinator attraction in 2 species of Lousiana Irises, Iris fulva and Iris hexagona. We also evaluate correlations among F2 traits and identify transgression in the hybrid population. Overall, we observe that differences in most floral traits between I. fulva and I. hexagona are controlled by multiple QTLs and are distributed across several linkage groups. We also find evidence of transgression at several QTL, suggesting that hybridization can contribute to generating phenotypic variation, which may be adaptive in rapidly changing environments.

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).

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.

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.

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.

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.

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.

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.

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.

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.

The genetic architecture of reproductive isolation in Louisiana irises: pollination syndromes and pollinator preferences.

In animal-pollinated plants, pollinator preferences for divergent floral forms can lead to partial reproductive isolation. We describe regions of plant genomes that affect pollinator preferences for two species of Louisiana Irises, Iris brevicaulis and Iris fulva, and their artificial hybrids. Iris brevicaulis and I. fulva possess bee and bird-pollination syndromes, respectively. Hummingbirds preferred I. fulva and under-visited both I. brevicaulis and backcrosses toward this species. Lepidopterans preferred I. fulva and backcrosses toward I. fulva, but also under-visited I. brevicaulis and I. brevicaulis backcrosses. Bumblebees preferred I. brevicaulis and F1 hybrids and rarely visited I. fulva. Although all three pollen vectors preferred one or the other species, these preferences did not prevent visitation to other hybrid/parental classes. Quantitative trait locus (QTL) mapping, in reciprocal BC1 mapping populations, defined the genetic architecture of loci that affected pollinator behavior. We detected six and nine QTLs that affected pollinator visitation rates in the BCIb and BCIf mapping populations, respectively, with as many as three QTLs detected for each trait. Overall, this study reflects the possible role of quantitative genetic factors in determining (1) reproductive isolation, (2) the pattern of pollinator-mediated genetic exchange, and thus (3) hybrid zone evolution.

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.

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.

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.

Adaptive Genetic Exchange: A Tangled History of Admixture and Evolutionary Innovation.

Genetic exchange between divergent evolutionary lineages, from introgressive hybridization between locally adapted populations to insertion of retroviral sequences into eukaryotic genomes, has now been documented. The detection of frequent divergence-with-gene-flow contrasts the neo-Darwinian paradigm of largely allopatric diversification. Nevertheless, of even greater significance is the growing wealth of data suggesting that the recipients of the transferred genomic material gain adaptive phenotypes from the donor lineages. This adaptive enrichment is reflected by changes in pathogenicity in viruses and bacteria, the transformation of ecological amplitude in eukaryotes, and adaptive radiations in extremely diverse lineages. Although genetic exchange may produce maladaptive consequences, most of the recently reported examples suggest increases in fitness, and many such adaptive trait transfers have been identified in our own species.

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.

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.