Mismatch in the distribution of floral ecotypes and pollinators: insights into the evolution of sexually deceptive orchids

Plants are predicted to show floral adaptation to geographic variation in the most effective pollinator, potentially leading to reproductive isolation and genetic divergence. Many sexually deceptive orchids attract just a single pollinator species, limiting opportunities to experimentally investigate pollinator switching. Here, we investigate Drakaea concolor, which attracts two pollinator species. Using pollinator choice tests, we detected two morphologically similar ecotypes within D. concolor. The common ecotype only attracted Zaspilothynnus gilesi, whereas the rare ecotype also attracted an undescribed species of Pogonothynnus. The rare ecotype occurred at populations nested within the distribution of the common ecotype, with no evidence of ecotypes occurring sympatrically. Surveying for pollinators at over 100 sites revealed that ecotype identity was not correlated with wasp availability, with most orchid populations only attracting the rare Z. gilesi. Using microsatellite markers, genetic differentiation among populations was very low (G_ST = 0.011) regardless of ecotype, suggestive of frequent gene flow. Taken together, these results may indicate that the ability to attract Pogonothynnus has evolved recently, but this ecotype is yet to spread. The nested distribution of ecotypes, rather than the more typical formation of ecotypes in allopatry, illustrates that in sexually deceptive orchids, pollinator switching could occur throughout a species' range, resulting from multiple potentially suitable but unexploited pollinators occurring in sympatry. This unusual case of sympatric pollinators highlights D. concolor as a promising study system for further understanding the process of pollinator switching from ecological, chemical and genetic perspectives.     

What We Think We Know vs. What We Need to Know About Orchid Pollination and Conservation: <Emphasis Type="Italic">Cypripedium</Emphasis> L. as a Model Lineage

While Darwin (1862, 1877) showed that reproductive success in orchid populations depended on adaptive floral morphology coupled with pollinator visitation a more recent review of the literature (Tremblay et al., 2005) confirmed that many out-breeding species are pollinator-limited because most orchid species showing low fecundity also lack rewards. The absence of rewards depresses both pollinator fidelity and the frequency of pollinator visits to an orchid population even though orchid flowers that lack rewards retain the same interlocking floral structures for precise pollinia removal and deposition found in related species that offer rewards. Using the genus, Cypripedium, as a model lineage of non-rewarding flowers this study also shows that the correlation between low fruit set in a Cypripedium sp. and its specific pollinator(s) is insufficient to predict specific frequencies of low fecundity. Annual rates of fruit set often vary broadly between populations of the same species and within the same population over several seasons. We speculate that fruit-set rates also decline when orchid demography and additional biotic and abiotic factors interrupt rates of pollinator activity (pre-zygotic) and fertilization/fruit maturation (post-zygotic). We suggest that that traditional field studies on pollination ecology and breeding systems be combined with data sets recording genetic variation and orchid flower demography in relation to seasonal variation in climate. We also propose that the same information be collected in regard to genetic variation, demography and phenology of populations of known orchid pollinators and co-blooming angiosperm species native to orchid habitats.     

Patterns of genetic and morphometric differentiation in Melitaea (Mellicta) athalia (Lepidoptera: Nymphalidae)

Patterns of genetic and morphometric differentiation were surveyed in Melitaea (Mellicta) athalia populations of the Carpathian Basin. This species has a wide distribution and exists under a wide variety of ecological conditions. It has two ecotypes in Hungary: with either one or two broods per year. It is of particular interest to reveal the main factors driving differentiation patterns in this species. Samples in our study were obtained from five Hungarian and one Transylvanian (Romanian) regions. Enzyme polymorphism, wing characters and male external genitalia were analysed using traditional morphometric methods. Statistical methods were optimized to compare morphological and genetic data. The results of genetic surveys revealed a clear regional pattern of differentiation in M. athalia. Moreover, the results of principal component analysis, Bayesian clustering and the dendrogram all suggested that the regions can be classified into two groups corresponding to the East or West zones of the Carpathian Basin. In contrast, differentiation between the two ecotypes was less expressed in the genetic variation of M. athalia. Results of the analyses conducted on phenotypic variation also suggested a regional pattern for both sets of morphometric characters (wings and external genitalia). At the same time, neither East–West regional division nor ecotype differentiation was detected in the morphometric studies. In sum, our analyses confirmed that both genetic and phenotypic variations of M. athalia exhibit a regional pattern rather than the differentiation between the two ecotypes. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Contrasting levels of genetic diversity between the historically rare orchid Cypripedium japonicum and the historically common orchid Cypripedium macranthos in South Korea

Many terrestrial orchids are historically rare and occur in small, spatially isolated populations. Theory predicts that such species will harbour low levels of genetic variation within populations and will exhibit a high degree of population genetic divergence, primarily as a result of genetic drift. If the origin of the present‐day populations is relatively recent from the same genetically depauperate source population, a complete lack of genetic differentiation between conspecific populations is expected. If a terrestrial orchid was historically common with moderate or high levels of genetic diversity, but has experienced more recent anthropogenic disturbance as a result of over‐collection, it would still exhibit initial levels of genetic variation within populations and a low degree of genetic divergence between populations. To test these predictions, we examined the genetic diversity in six populations (N = 131) of the historically and currently rare Cypripedium japonicum and in four populations (N = 94) of the historically common but now rare C. macranthos from South Korea. Fourteen putative allozyme loci resolved from eight enzyme systems revealed no variation either within or among populations of C. japonicum, which supports the first prediction. In contrast, populations of C. macranthos harboured high levels of genetic variation (mean percentage of polymorphic loci %P = 46.7; mean expected heterozygosity H_e = 0.185) and exhibited a low degree of population genetic divergence (G_ST = 0.059), supporting the second prediction. The lack of genetic variation both within and among conspecific populations of C. japonicum may suggest that populations originated from the same genetically depauperate ancestral population. The high levels of genetic diversity maintained in populations of C. macranthos suggest that the collection‐mediated decrease in the number of individuals is still too recent for long‐term effects on genetic variation. Based on current demographic and genetic data, in situ and ex situ conservation strategies should be provided to preserve genetic variation and to ensure the long‐term survival of the two species in the Korean Peninsula. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 160 , 119–129.     

Floral shape mimicry and variation in sexually deceptive orchids with a shared pollinator

Mimics can have both accurate mimicry and phenotypic variation if deception operates in multiple sensory modes. Australian Tongue orchids (Cryptostylis species) attract their sole pollinator, male Lissopimpla excelsa wasps (Ichneumonidae), by accurately mimicking the scent and colour of female L. excelsa wasps. To test for shape mimicry of female wasps, both traditional and geometric morphometric comparisons were performed with allopatric Cryptostylis ovata and the often sympatric Cryptostylis erecta, Cryptostylis leptochila, and Cryptostylis subulata. Although some floral parts accurately mimicked the female wasp, the overall floral shape differed dramatically among orchid species. The function (if any) of this interspecific shape variation is unknown, although it does not cause character displacement of pollen attachment locations to reduce interspecific pollen transfer. Analyses showed that floral parts involved in pollinia transfer were similarly shaped for three of the four Cryptostylis species and all attach their pollinia to the same location on the pollinator's abdomen. Shape may interact with pollinator behaviour: in the field, pollination rates doubled when two Cryptostylis species were present, regardless of orchid abundances. Perhaps variation in shape hinders pollinator recognition and the avoidance of orchids, similar to scent and colour variation in other sexually deceptive orchid systems. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 469–481.     

A comparative study of allozyme variation of peripheral and central populations of Silene nutans L. (Caryophyllaceae) from Western Europe: implications for conservation

In Belgium, at the western border of its continental distribution range, the perennial herb S. nutans has evolved two parapatric ecotypes (calcicolous or silicicolous), which show contrasted allozyme, morphological and adaptive patterns, and isolating reproductive barriers. We examined allozyme variation in 21 populations close to Belgium (from France and Luxemburg) in relation to their peripheral or central geographical position, and investigated their genetic relationships with the Belgian ecotypes. Both peripheral and central populations showed high genetic variation. They were differentiated from each other, but not in relation to the substrate (calcareous or siliceous). The peripheral and central populations were related to the Belgian silicicolous and calcicolous ecotype, respectively. This suggests an ancient differentiation and different past histories for the Belgian ecotypes, and parapatric speciation processes. This study exemplifies the high evolutionary potential of populations at range peripheries and the need for considering them in conservation strategies.     

Genetic diversity of nectar‐rewarding Platanthera chlorantha and nectarless Cephalanthera rubra

We examined the genetic diversity of two orchid species, the nectar‐rewarding Platanthera chlorantha and the nectarless Cephalanthera rubra, in north‐eastern Poland. We found lower differences in genetic diversity between the species than we expected. The level of genetic variation at species level was lower in C. rubra (P_POL = 14%, A = 1.14 and H_E = 0.060) than in P. chlorantha (P_POL = 25.5%, A = 1.35 and H_E = 0.078). In the majority of populations of both species a high proportion of unique genotypes was noted. The overall F_ST values for all populations were moderate and similar for both species (P. chlorantha: 0.251, P < 0.001; C. rubra: 0.267, P < 0.001). No relationship was found between genetic and geographical distances in either species (P > 0.05, Mantel test). We discuss the breeding systems, small population size and population subdivision as the most important factors affecting the genetic diversity of this species. We suggest that conservation programmes should be initiated to maintain or even increase the fitness and genetic variation of populations of both species. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013 , 171 , 751–763.     

Immigrant and extrinsic hybrid seed inviability contribute to reproductive isolation between forest and dune ecotypes of Epipactis helleborine (Orchidaceae)

Reproductive isolation caused by divergent natural selection arising from differences between ecological environments or ecological interactions represents a major mechanism contributing to speciation, but its relative importance is poorly known. In this study, controlled reciprocal crossings and seed germination experiments were combined with genetic and morphometric analyses to test the hypothesis that previously described differences in mycorrhizal communities between forest and dune ecotypes of Epipactis helleborine were sufficiently strong to create complete reproductive isolation between the two ecotypes. Molecular analyses using 770 SNP markers showed that the two ecotypes were genetically distinct and that populations of the dune ecotype were genetically impoverished compared to populations of the forest ecotype. Morphologically, the two ecotypes were also significantly different, with plants of the dune ecotype generally being smaller than plants of the forest ecotype. The results further showed that immigrant seeds had a significantly lower probability of protocorm formation than native seeds, indicating strong immigrant inviability. Although both ecotypes were able to cross easily and to produce a large number of viable seeds, hybrid seeds showed significantly lower protocorm formation than pure seeds, further contributing to reproductive isolation. Overall, these results indicate that interfertile populations of a widespread orchid adapting to contrasting environments diverge as a consequence of concurrent selection acting against immigrants and hybrids and suggest that mycorrhizal fungi can play a role in the early stages of plant speciation.     

Population history of the terrestrial orchid Cremastra appendiculata var. variabilis from Korea,inferred from levels and distribution of genetic diversity

Cremastra appendiculata var. variabilis is a self‐compatible, insect‐pollinated, terrestrial orchid that is a typical member of the warm‐temperate vegetation in the Korean Peninsula. Here we examine levels and partitioning of allozyme diversity (22 loci) in 12 populations of this orchid to gain insight into its genetic structure and post‐glacial colonization history in Korea. It harboured considerably higher levels of genetic variation within populations (%P = 48.1, A = 1.70 and H_e = 0.217) and lower degree of differentiation among populations (F_ST = 0.068) than those typical of allozyme‐based studies in other terrestrial orchid species. These patterns suggest that extant populations were derived from multiple source populations (i.e. from multiple glacial refugia), although further studies are needed to confirm this scenario. In addition to population history, traits such as high potential of seed dispersal, a mixed mating system and its occurrence in large and continuous populations would have contributed to the current levels and distribution of genetic diversity in Korean populations of C. appendiculata var. variabilis. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 721–732.     

Distribution,habitat disturbance and pollination of the endangered orchid Broughtonia cubensis (Epidendrae: Laeliinae)

The geographical distribution, population structure and pollination ecology are key aspects in the conservation and management of rare orchids. Here, we address these aspects and the main threats affecting the endangered Cuban orchid Broughtonia cubensis. This rewardless orchid is self‐compatible, but pollinator dependent. However, seed production can be negatively affected by insect‐mediated selfing. Three species of small bee (genera Ceratina and Lasioglossum) act as pollinators. As in the case of other nectarless orchids, we detected two species of plant producing large amounts of nectar in the area, the floral morphology of which closely resembles that of B. cubensis. The simultaneous flowering of these species could positively affect the reproductive success of B. cubensis. Nonetheless, the fitness of this orchid in natural conditions is low, possibly related to strong pollen limitation. To the problems arising from reduced fitness is added the fact that its historical distribution range has been greatly reduced in recent years. Throughout this study, we have detected dramatic reductions in the population sizes, in some cases as a result of human plundering, but also as a consequence of hurricanes. Based on the results of this study, we propose some guidelines to manage and conserve this orchid. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 345–357.     

Pollinator shifts between Ophrys sphegodes populations: might adaptation to different pollinators drive population divergence?

Local adaptation to different pollinators is considered one of the possible initial stages of ecological speciation as reproductive isolation is a by‐product of the divergence in pollination systems. However, pollinator‐mediated divergent selection will not necessarily result in complete reproductive isolation, because incipient speciation is often overcome by gene flow. We investigated the potential of pollinator shift in the sexually deceptive orchids Ophrys sphegodes and Ophrys exaltata and compared the levels of floral isolation vs. genetic distance among populations with contrasting predominant pollinators. We analysed floral hydrocarbons as a proxy for floral divergence between populations. Floral adoption of pollinators and their fidelity was tested using pollinator choice experiments. Interpopulation gene flow and population differentiation levels were estimated using AFLP markers. The Tyrrhenian O. sphegodes population preferentially attracted the pollinator bee Andrena bimaculata, whereas the Adriatic O. sphegodes population exclusively attracted A. nigroaenea. Significant differences in scent component proportions were identified in O. sphegodes populations that attracted different preferred pollinators. High interpopulation gene flow was detected, but populations were genetically structured at species level. The high interpopulation gene flow levels independent of preferred pollinators suggest that local adaptation to different pollinators has not (yet) generated detectable genome‐wide separation. Alternatively, despite extensive gene flow, few genes underlying floral isolation remain differentiated as a consequence of divergent selection. Different pollination ecotypes in O. sphegodes might represent a local selective response imposed by temporal variation in a geographical mosaic of pollinators as a consequence of the frequent disturbance regimes typical of Ophrys habitats.     

Reduced genetic variation and strong genetic population structure in the freshwater killifish Valencia letourneuxi (Valenciidae) based on nuclear and mitochondrial markers

The genetic variation of the critically endangered Corfu killifish (Valencia letourneuxi), an endemic freshwater fish species of the western Balkans, was assessed for nine populations sampled in eight water systems in western continental Greece, the Peloponnese and the Ionian Island of Corfu, using mitochondrial and microsatellite markers. The analyses were based on data from three mtDNA regions (D‐loop, COI and 16S rRNA sequences) and 14 microsatellite loci. Samples from the congeneric species Valencia hispanica and the phylogenetically closely related species Aphanius fasciatus were also used in the study as outgroups. Both the mitochondrial and the microsatellite analyses revealed three distinct population groupings associated with the geographical distribution of the populations: one southern group occupying rivers draining to the Patraikos Gulf, the second one including the populations flowing into the Amvrakikos Gulf and the third, more northern group, including the other populations from rivers in Corfu Island and Epirus flowing into the Ionian Sea. Within these groupings there is limited genetic differentiation between populations; in addition, there is reduced intrapopulation genetic variation, evidenced by low heterozygosity values, number of alleles and haplotype diversity. In terms of taxonomic implications and appropriate management actions for conservation, our data suggest that the major population groups should be regarded at least as three distinct conservation units (CUs), with translocation and restocking actions to take place only within the geographical range of the CU concerned. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 334–349.     

Extremely low levels of genetic diversity in the terrestrial orchid Epipactis thunbergii (Orchidaceae) in South Korea: implications for conservation

Levels of allozyme variation, population genetic structure, and fine-scale genetic structure (FSGS) of the rare, both sexually and clonally reproducing terrestrial orchid Epipactis thunbergii were examined for eight ( N  = 734) populations in a 20 × 20-km area in South Korea. Twenty-three putative allozyme loci resolved from 15 enzyme systems were used. Extremely low levels of allozyme variation were found within populations: the mean frequency of polymorphic loci was 3.8% [isocitrate dehydrogenase ( Idh-2 ) with two alleles was polymorphic across populations], the mean number of alleles per locus was 1.04, and the mean expected heterozygosity was 0.013. The overall fixation index was not significantly different from zero ( F _IS = 0.069), although the species is self-compatible. However, a significantly high degree of population differentiation was found between populations at Idh-2 ( F _ST = 0.388) in the studied area. Furthermore, spatial autocorrelation analyses revealed a significant FSGS (up to 3 m) within populations. These observations suggest that the main explanatory factors for the extremely low levels of genetic diversity and the shaping of the population genetic structure of E. thunbergii are genetic drift as a result of a small effective population size, a restricted gene flow, and the isolation of populations. Considering the current genetic structure of E. thunbergii , three guidelines are suggested for the development of conservation strategies for the species in South Korea: (1) protection of habitats of standing populations; (2) prohibition by law of any collection of E. thunbergii ; and (3) protection of nearby pollinator populations, given the fact that fruit set in natural habitats is very low.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 161–169.     

Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior

Understanding the emergence of species through the process of ecological speciation is a central question in evolutionary biology which also has implications for conservation and management. Lake trout (Salvelinus namaycush) is renowned for the occurrence of different ecotypes linked to resource and habitat use throughout North America. We aimed to unravel the fine genetic structure of the four lake trout ecotypes in Lake Superior. A total of 486 individuals from four sites were genotyped at 6822 filtered SNPs using RADseq technology. Our results revealed different extent of morphological and genetic differentiation within the different sites. Overall, genetic differentiation was weak but significant and was on average three times higher between sites (mean F_ST = 0.016) than between ecotypes within sites (mean F_ST = 0.005) indicating higher level of gene flow or a more recent shared ancestor between ecotypes within each site than between populations of the same ecotype. Evidence of divergent selection was also found between ecotypes and/or in association with morphological variation. Outlier loci found in genes related to lipid metabolism and visual acuity were of particular interest in this context of ecotypic divergence. However, we did not find clear indication of parallelism at the genomic level, despite the presence of phenotypic parallelism among some ecotypes from different sampling sites. Overall, the occurrence of different levels of both genomic and phenotypic differentiation between ecotypes within each site with several differentiated loci linked to relevant biological functions supports the presence of a continuum of divergence in lake trout.     

Environmental determinants of genetic diversity in Caragana microphylla (Fabaceae) in northern China

Non‐rewarding orchids rely on various ruses to attract their pollinators. One of the most common is for them to resemble flowers sought by insects as food sources. This can range from generalized food deception to the mimicry of specific sympatric food plants. We investigated the basis of pollinator deception in the European food‐deceptive orchid Traunsteinera globosa, which has unusually compact flowerheads resembling those of sympatric rewarding species of Knautia and Scabiosa (Dipsacaceae), and Valeriana (Caprifoliaceae). Visual signals of T. globosa are similar in both fly and bee vision models to those of the sympatric food plants used in the choice experiments, but scent signals are divergent. Field experiments conducted in Austria and the Czech Republic showed that both naive and experienced (with respect to visitation of T. globosa) insect species approached the orchids at the same rate as food plants, but direct contact with orchid flowers was taxon specific. Flies were most easily duped into probing the orchid, and, in doing so, frequently received and deposited pollinaria, whereas most bees and butterflies avoided landing on orchid flowers. We conclude that T. globosa is a mimic of a guild of fly‐pollinated plants, but the ecological dependence of the orchid on its models remains to be fully tested. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2016, 180 , 269–294.     

Diversification across a heterogeneous landscape

Adaptation to contrasting environments across a heterogeneous landscape favors the formation of ecotypes by promoting ecological divergence. Patterns of fitness variation in the field can show whether natural selection drives local adaptation and ecotype formation. However, to demonstrate a link between ecological divergence and speciation, local adaptation must have consequences for reproductive isolation. Using contrasting ecotypes of an Australian wildflower, Senecio lautus in common garden experiments, hybridization experiments, and reciprocal transplants, we assessed how the environment shapes patterns of adaptation and the consequences of adaptive divergence for reproductive isolation. Local adaptation was strong between ecotypes, but weaker between populations of the same ecotype. F1 hybrids exhibited heterosis, but crosses involving one native parent performed better than those with two foreign parents. In a common garden experiment, F2 hybrids exhibited reduced fitness compared to parentals and F1 hybrids, suggesting that few genetic incompatibilities have accumulated between populations adapted to contrasting environments. Our results show how ecological differences across the landscape have created complex patterns of local adaptation and reproductive isolation, suggesting that divergent natural selection has played a fundamental role in the early stages of species diversification.     

Geographical variation in cone volatile composition among populations of the African cycad Encephalartos villosus

Variation in traits across species distribution ranges is often indicative of diversifying evolution that can lead to speciation. Of particular interest is whether traits vary clinally or abruptly because the latter pattern can be indicative of incipient speciation. Understanding of intraspecific variation in chemical traits is still in its infancy because studies of population variation have tended to focus on morphology or neutral genetic markers. To address these issues, the composition of cone volatile odours was examined in ten populations of the South African cycad Encephalartos villosus across its range in the Eastern Cape and KwaZulu Natal using headspace sampling and analysis by gas chromatography‐mass spectrometry. Because volatiles play a key role in attracting pollinators to cones of Encephalartos cycads and may thus reflect local adaptation to pollinators, pollinator assemblages were also investigated in the ten populations of E. villosus. Volatile compounds from populations in the north of the distribution range were dominated by unsaturated hydrocarbons, whereas, in the southern populations, nitrogen‐containing compound and terpenoids were the major compounds. A shift between southern and northern populations appeared to occur at the Umtamvuna River, where populations had odour profiles with components of both the northern and southern populations. However, one population in the north (Vernon Crookes Nature Reserve) had a quantitatively similar odour profile to the populations in the extreme south of the range. These results reveal strong interpopulation variation in the cone scent of E. villosus, including variation in the relative emission of dominant compounds that may play key functional role in this pollination system. However, pollinator assemblages did not differ across the different populations, which suggest that these patterns were produced by co‐evolution or drift, rather than by pollinator shifts. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 514–527.     

Microsatellite allele sequencing in population analyses of the South American cactophilic species Drosophila antonietae (Diptera: Drosophilidae)

Drosophila antonietae belongs to the Drosophila buzzatii cluster, a cactophilic group of species naturally endemic to South America. Morphological and genetic analyses indicate that its populations are the most homogenous in the cluster and that the diversity observed is mainly a result of variation within populations. Seven polymorphic microsatellite loci were described for this species and used in the present study to investigate the genetic diversity of natural populations of D. antonietae by both length and sequence variation. The study aimed to understand how homoplasy and null alleles affect inferences about the population history of this species and to obtain an accurate interpretation of population inferences where these loci could be applied. The results provide useful information on the interpretation of genetic data derived from the microsatellite loci described for D. antonietae and on evolutionary aspects of cactophilic Drosophila. Importantly, the results indicate that size homoplasy and null alleles do not represent significant problems for the population genetics analyses because the large amount of variability at microsatellite loci compensate the low frequency of these problems in the populations. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 573–584.     

Effects of human disturbance on reproductive success and population viability of Serapias cordigera (Orchidaceae)

Fragmentation of habitats by roads, railroads, fields, buildings and other human activities can affect population size, pollination success and fruit production, especially in plants showing pollinator limitation, such as Mediterranean orchids. In this study, we investigated the effect of human activity on the population dynamics and reproductive success of the orchid Serapias cordigera. Three anthropic and three natural populations were monitored over 14 years (1999–2012), classifying individuals into five stage classes and evaluating reproductive success. Population growth rates differed between anthropic and natural populations. Our results demonstrated that small anthropic populations have lower population viability compared with large natural populations. The proportion of flowering plants, the number of reproductive plants and the percentage of fruits were significantly lower in anthropic than in natural populations. This strong decline in fruit production in populations in urban areas may reflect lower pollination attraction and higher inbreeding in small than in natural populations. Calculation of extinction probabilities showed that the anthropic populations will drop below the survival threshold of 15–20 years. This study highlights that continued monitoring is needed to improve information on population viability and for appropriate conservation management. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 408–420.     

Diversity and population structure of northern switchgrass as revealed through exome capture sequencing

Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype, composed of tetraploid and octoploid accessions, and a southern lowland ecotype, composed of primarily tetraploid accessions. We employed high‐coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single‐nucleotide polymorphisms (SNPs), of which 1 590 653 high‐confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype‐restricted, non‐synonymous SNPs that are predicted to affect the protein function of CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering, which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near‐reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up‐CNVs), 112 630 genes present in fewer copies than in the reference genome (down‐CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland‐specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.