Lisa E. Wallace

Bayesian approaches for the analysis of population genetic structure: an example from Platanthera leucophaea (Orchidaceae)

We describe four extensions to existing Bayesian methods for the analysis of genetic structure in populations: (i) use of beta distributions to approximate the posterior distribution of f and θB; (ii) use of an entropy statistic to describe the amount of information about a parameter derived from the data; (iii) use of the Deviance Information Criterion (DIC) as a model choice criterion for determining whether there is evidence for inbreeding within populations or genetic differentiation among populations; and (iv) use of samples from the posterior distributions for f and θB derived from different data sets to determine whether the estimates are consistent with one another. We illustrate each of these extensions by applying them to data derived from previous alloyzme and random amplified polymorphic DNA surveys of an endangered orchid, Platanthera leucophaea, and we conclude that differences in θB from the two data sets may represent differences in the underlying mutational processes.

A comparison of two methods of calculating GST, a genetic measure of population differentiation

G(ST) is a genetic statistic describing differentiation of populations and has frequently been compared with Hamrick and Godts (1989) review of the plant literature. We show here that some comparisons may be inappropriate if G(ST) was calculated in a different way than that used by Hamrick and Godt (HG). An alternative method advocated by Nei is mathematically different from the HG technique, occasionally resulting in different G(ST) values. We reviewed 695 studies that appeared between 1990 and September 1999 that cited Hamrick and Godt (1989) and found that many of these calculated G(ST) according to Neis method (46%), with the majority of these papers (61%) including comparisons to Hamrick and Godts review. We suggest that if G(ST) estimates are compared across studies, it is most appropriate to calculate them the same way. However, we found that in most cases, the magnitude of difference in G(ST) values was small, suggesting that qualitative comparisons of G(ST) estimates between most studies are probably valid. Nevertheless, we have identified theoretical and empirical situations in which large differences in G(ST) values are likely to arise. Thus, we advise future investigators to carefully consider which method to use in calculating G(ST) for a given data set.

CONSERVATION GENETICS AND TAXONOMIC STATUS OF THE RARE KENTUCKY LADY'S SLIPPER : CYPRIPEDIUM KENTUCKIENSE (ORCHIDACEAE)

Cypripedium kentuckiense is a recently described rare orchid found in Arkansas (predominantly) and in eight other states. Much debate has focused on whether this taxon should be recognized as a distinct species or considered to be an extreme manifestation of the variability present in the widespread taxon Cypripedium parviflorum var. pubescens. In this study, 12 isozyme loci were analyzed for 14 populations of C. parviflorum var. pubescens and eight populations of C. kentuckiense. These data were used to examine the genetic similarity of these taxa, assess whether isozyme data support the continued recognition of C. kentuckiense as a distinct species, and assess whether a newly discovered disjunct Virginia population of C. kentuckiense is genetically isolated from other C. kentuckiense populations. The isozyme data revealed that the two taxa are very closely related with a high interspecific genetic identity. However, C. kentuckiense populations contain a subset of the variation present in C. parviflorum var. pubescens, and they have expected levels of heterozygosity that are one-quarter that of C. parviflorum var. pubescens populations. Cypripedium kentuckiense also possesses one widespread unique allele and a unique multilocus genotype. These data suggest that C. kentuckiense should be recognized as a distinct species, possibly of recent origin from C. parviflorum. Lastly, the isozyme data support the hypothesis that gene flow between the Virginia population and other populations of C. kentuckiense has been restricted.

The cost of inbreeding in Platanthera leucophaea (Orchidaceae)

Fragmentation and isolation are expected to have a considerable impact on viability and recruitment in populations of rare species. Platanthera leucophaea (Orchidaceae), a rare orchid, currently exists in a fragmented landscape of its natural habitat. Floral morphology suggests this species is predominantly outcrossing, but surveys of allozyme diversity suggest high, variable levels of inbreeding in populations (F(IS) = -0.078 to 1.0). This study examines the potential cost of inbreeding and the extent to which inbreeding depression can vary temporally and in populations of different size and genetic structure. Flowers were pollinated by hand in one large population and one small population over three seasons. Seed set, seed mass, and seed viability were compared among self-, outcross-, and open-pollinated fruits. Seed set was greater than 50% in both populations for all years of study. High levels of inbreeding depression were detected in seed viability but not in seed mass in both populations. However, the magnitude of inbreeding depression differed over years and between populations, a pattern that reflects differing environmental conditions and variable evolutionary and demographic histories. Consequently, conservation of this species will be most successful if outcrossing is promoted in populations by maximizing population size and genetic variability.

Geographic patterns of genetic diversity from the native range of Cactoblastis cactorum (Berg) support the documented history of invasion and multiple introductions for invasive populations

Spread of the invasive cactus-feeding moth Cactoblastis cactorum has been well documented since its export from Argentina to Australia as a biocontrol agent, and records suggest that all non-native populations are derived from a single collection in the moth’s native range. The subsequent global spread of the moth has been complex, and previous research has suggested multiple introductions into North America. There exists the possibility of additional emigrations from the native range in nursery stock during the late twentieth century. Here, we present mitochondrial gene sequence data (COI) from South America (native range) and North America (invasive range) to test the hypothesis that the rapid invasive spread in North America is enhanced by unique genetic combinations from isolated portions of the native range. We found that haplotype richness in the native range of C. cactorum is high and that there was 90% lower richness in Florida than in Argentina. All Florida C. cactorum haplotypes are represented in a single, well-defined clade, which includes collections from the reported region of original export from Argentina. Thus, our data are consistent with the documented history suggesting a single exportation of C. cactorum from the eastern region of the native range. Additionally, the presence of geographic structure in three distinct haplotypes within the same clade across Florida supports the hypothesis of multiple introductions into Florida from a location outside the native range. Because the common haplotypes in Florida are also known to occur in the neighboring Caribbean Islands, the islands are a likely source for independent North American colonization events. Our data show that rapid and successful invasion within North America cannot be attributed to unique genetic combinations. This suggests that successful invasion of the southeastern US is more likely the product of a fortuitous introduction into favorable abiotic conditions and/or defense responses of specific Opuntia hosts, rapid adaptation, or a release from native enemies.

Spatial genetic structure and frequency of interspecific hybridization in Platanthera aquilonis and P. dilatata (Orchidaceae) occurring in sympatry

Knowledge of genetic structure at different scales is necessary for evaluating the importance of interactions between the genome and environment and for inferring underlying processes that bring about evolutionary diversification. Here, genetic and morphological variation was assessed for 154 individuals of Platanthera aquilonis and P. dilatata in Maine, using RAPD and PCR-RFLP markers and measurements of five morphological traits to determine the prevalence of interspecific hybrids and underlying spatial genetic structure of the population. Both species co-mingled in the population, but clumping was observed. Platanthera aquilonis was more abundant, but genetic variation was lower (polymorphic loci [40%], expected heterozygosity [0.137]) than that of P. dilatata (P(p) = 72%; H(e) = 0.245). Interspecific hybrids were rare (eight individuals), and morphology was not consistently reliable for determining hybrid status even though the species differed significantly in several traits. Spatial autocorrelation analyses showed significant genetic structure at small distances for both species, most likely due to restricted seed dispersal. Platanthera aquilonis did not exhibit a pattern of spatial genetic structure consistent with other selfing species. This suggests that the species is facultative autogamous, which allows for limited production of hybrid individuals and reduces the strength of spatial genetic structure relative to P. dilatata.

Contrasting Allozyme Diversity Between Northern and Southern Populations of Cypripedium parviflorum (Orchidaceae): Implications for Pleistocene Refugia and Taxonomic Boundaries

Abstract Allozyme and morphological analyses were conducted to test speculation and recently published taxonomy concerning northern versus southern variation in the Cypripedium parviflorum complex. Allozyme analyses of 40 populations from 10 states revealed marked differences in genetic variation between northern and southern populations of var. pubescens, and between var. makasin and var. parviflorum. For both comparisons, the northern populations from previously glaciated regions generally contain more genetic variation and larger estimated population sizes than do their southern counterparts. These results are in contrast to most published findings on other taxa that report higher levels of genetic variation in populations near glacial refugia compared to conspecifics from previously glaciated territory. To explain the data in our paper, we suggest the existence of a northern refugium for C. parviflorum in a periglacial environment that contained abundant habitat for this species. This region could have served as a genetically diverse source of propagules for colonizing newly deglaciated territory. Conversely, populations in the heavily forested south may have remained relatively small and isolated throughout glaciation, promoting genetic drift and the loss of genetic variation. Lastly, var. makasin differs from the other two varieties in mottling and coloration of the dorsal sepal, and in pubescence on the uppermost, nonphotosynthetic sheathing leaf. These data are consistent with previous hypotheses of northern versus southern differentiation in C. parviflorum, and support recognition of newly restored var. makasin. Communicating Editor: Jeff H. Rettig

A review of the prevalence, utility, and caveats of using chloroplast simple sequence repeats for studies of plant biology.

Microsatellites occur in all plant genomes and provide useful markers for studies of genetic diversity and structure. Chloroplast microsatellites (cpSSRs) are frequently targeted because they are more easily isolated than nuclear microsatellites. Here, we quantified the frequency and uses of cpSSRs based on a literature review of over 400 studies published 1995–2013. These markers are an important and economical tool for plant biologists and continue to be used alongside modern genomics approaches to study genetic diversity and structure, evolutionary history, and hybridization in native and agricultural species. Studies using species-specific primers reported a greater number of polymorphic loci than those employing universal primers. A major disadvantage to cpSSRs is fragment size homoplasy; therefore, we documented its occurrence at several cpSSR loci within and between species of Acmispon (Fabaceae). Based on our empirical data set, we recommend targeted sequencing of a subset of samples combined with fragment genotyping as a cost-efficient, data-rich approach to the use of cpSSRs and as a test of homoplasy. The availability of genomic resources for plants aids in the development of primers for new study systems, thereby enhancing the utility of cpSSRs across plant biology.

Genetic divergence does not predict change in ornament expression among populations of stalk-eyed flies.

Stalk‐eyed flies (Diptera: Diopsidae) possess eyes at the ends of elongated peduncles, and exhibit dramatic variation in eye span, relative to body length, among species. In some sexually dimorphic species, evidence indicates that eye span is under both intra‐ and intersexual selection. Theory predicts that isolated populations should evolve differences in sexually selected traits due to drift. To determine if eye span changes as a function of divergence time, 1370 flies from 10 populations of the sexually dimorphic species, Cyrtodiopsis dalmanni and Cyrtodiopsis whitei, and one population of the sexually monomorphic congener, Cyrtodiopsis quinqueguttata, were collected from Southeast Asia and measured. Genetic differentiation was used to assess divergence time by comparing mitochondrial (cytochrome oxidase II and 16S ribosomal RNA gene fragments) and nuclear (wingless gene fragment) DNA sequences for c. five individuals per population. Phylogenetic analyses indicate that most populations cluster as monophyletic units with up to 9% nucleotide substitutions between populations within a species. Analyses of molecular variance suggest a high degree of genetic structure within and among the populations; > 97% of the genetic variance occurs between populations and species while < 3% is distributed within populations, indicating that most populations have been isolated for thousands of years. Nevertheless, significant change in the allometric slope of male eye span on body length was detected for only one population of either dimorphic species. These results are not consistent with genetic drift. Rather, relative eye span appears to be under net stabilizing selection in most populations of stalk‐eyed flies. Given that one population exhibited dramatic evolutionary change, selection, rather than genetic variation, appears to constrain eye span evolution.

Molecular Evidence for Allopolyploid Speciation and Recurrent Origins in Platanthera huronensis (Orchidaceae)

The origin of the polyploid orchid Platanthera huronensis was inferred from variation at 305 intersimple sequence repeat (ISSR) and RAPD loci and cpDNA RFLP patterns generated from amplification and digestion of two noncoding regions, rpl16 intron and trnT‐trnF region. Morphological intermediacy indicates that P. huronensis is likely an allopolyploid derivative of Platanthera dilatata and Platanthera aquilonis, and this hypothesis is supported by the data presented in this study. Nearly all of the bands found in P. huronensis were also identified in P. dilatata and/or P. aquilonis, to the exclusion of the other putative parental species examined. Nevertheless, phenotypic patterns of ISSR and RAPD bands were not strictly additive in P. huronensis, which reflects evolutionary divergence since initial formation of polyploid lineages or origin from parental populations that were not sampled. An analysis of cpDNA RFLP patterns revealed five unique haplotypes in P. huronensis and a high degree of geographic structuring. Western samples were more similar to P. dilatata while eastern samples were identical to P. aquilonis in cpDNA RFLP pattern. Collectively, these differences point to multiple independent origins and complex evolutionary histories in extant polyploid lineages. Because P. huronensis is morphologically and genetically distinct from other closely related species, its continued recognition at the rank of species is warranted.