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A preliminary evaluation of the ancestry of a putative Sabal hybrid (Arecaceae: Coryphoideae), and the description of a new nothospecies, Sabal × brazoriensis
Abstract
In a coastal plain forest in eastern Texas, USA, occurs a population of a putative Sabal hybrid, one of few native, putative
palm hybrids in the continental USA. Robust plants with large trunks, they are morphologically dissimilar to the much
smaller and acaulescent plants of S. minor, with which they co-occur. The only other large Sabal species in the USA are
S. mexicana and S. palmetto, with S. mexicana native only to Texas. Using Amplified Fragment Length Polymorphisms
(AFLPs), we sampled several plants of the putative hybrid and its possible parents in order to evaluate its possible hybrid
origin. UPGMA, principal coordinate analysis, and Bayesian analyses indicated that it seems to be a hybrid, but an old
one, with clear genetic distinctiveness. However, these results also suggest a closer affinity of the putative hybrid with S.
minor and S. palmetto than with S. mexicana, excluding the latter species from possible parentage. Results also suggest
that S. minor, despite its wide morphological diversity, is a clearly coherent species with minimal evidence of
introgression, except for Mexican material that appears to be introgressed with S. mexicana. Sabal palmetto may also
possess a complicated genetic history not necessarily reflected in its morphology
... Adding to the challenge, many morphological traits can vary widely within a species (Zona, 1990). To date, there has been very little assessment of molecular variation within and among Sabal species (but see Goldman et al., 2011). Zona's cladogram, based on 22 morphological characters, generally groups species by geographical proximity; the species within the USA form a clade and a large group of Mexican/Yucatan/South American species are placed sister to the Caribbean and Bermudan species. ...
... Trinity isoforms were assessed using the RSEM pipeline and removed if they had no read support or less than 1% of a component's total reads. The Velvet contigs were assembled using a hash size of 31, as determined by VelvetOptimiser (Gladman & Seemann, 2012), and were further extended into intron sequence using SSAKE (Warren et al., 2007). The Trinity and Columbus-Velvet assemblies for each species were then merged using CAP3 (95% identity over 20 bp) (Huang & Madan, 1999). ...
With the increasing availability of high-throughput sequencing, phylogenetic analyses are no longer constrained by the limited availability of a few loci. Here, we describe a sequence capture methodology, which we used to collect data for analyses of diversification within Sabal (Arecaceae), a palm genus native to the south-eastern USA, Caribbean, Bermuda and Central America. RNA probes were developed and used to enrich DNA samples for putatively low copy nuclear genes and the plastomes for all Sabal species and two outgroup species. Sequence data were generated on an Illumina MiSeq sequencer and target sequences were assembled using custom workflows. Both coalescence and supermatrix analyses of 133 nuclear genes were used to estimate species trees relationships. Plastid genomes were also analysed, yielding generally poor resolution with regard to species relationships. Species relationships described in both nuclear gene and plastome sequences largely reflect the biogeography of the group and, to a lesser extent, previous morphology-based hypotheses. Beyond the biological implications, this research validates a high-throughput methodology for generating a large number of genes for coalescence-based phylogenetic analyses in plant lineages.
... Although the genus Sabal is defined by several morphological attributes, the resolution of species relationships within this genus has been limitedly investigated due to the wide variability of informative characters/morphological traits within a species. 22 To date, limited studies have been conducted to assess the molecular variation within and among Sabal species. 23 Therefore, this study aimed to evaluate the genetic relationships and assess the level of polymorphism among the four Sabal species (S. yapa, S. palmetto, S. causiarum and S. blackburniana), using two efficient functional marker systems (SCoT and CBDP). ...
This work aimed to evaluate the anti-androgenic activity of S. blackburniana Glazebrook, S. causiarum (O. F. Cook) Becc, and S. palmetto (Walter) Lodd. Ex Schult fruit extracts in rats using Hershberger assay. Furthermore, to annotate secondary metabolites using LC-HRMS technique, to investigate underlying mechanisms responsible for 5-α-reductase inhibitory activity in silico and to compare cytotoxic effects in vitro against human prostatic stromal myofibroblast (WPMY-1) and human benign prostatic hyperplasia (BPH-1) cell lines using MTT, 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (spectrophotometrically). The results showed significant anti-androgenic implications with varying degrees, markedly decreased sex organ weights, reduction in testosterone and increase in LH and FSH serum levels. Genetic diversity study ensured the correct genotype and revealed outperformance of SCoT compared with CBDP markers to interpret polymorphism among selected species. S. blackburniana exhibited selective cytotoxic activity against BPH-1 compared to finasteride. Molecular docking of 59 dereplicated metabolites belonging to various chemical classes revealed that helasaoussazine, pinoresinol and tetra-O-caffeoylquinic acid are the top inhibitors of 5-α-reductase-2. Our study provides an insight into the anti-androgenic activity of selected species of Egyptian Sabal supported by docking study for the first time, demonstrates safety toward liver and kidney and highlights a new potential therapeutic candidate for anti-androgenic related disease such as benign prostatic hyperplasia.
... The modeled current ranges for the five palm species closely mirrored published range maps (Henderson et al., 1995;Zona, 2000), (Goldman, Klooster, & Griffith, 2011). ...
Palms (Arecaceae) are a relatively speciose family and provide materials for food, construction, and handicraft, especially in the tropics. They are frequently used as paleo‐indicators for megathermal climates, and therefore, it is logical to predict that palms will benefit from predicted warmer temperatures under anthropogenic climate change. We created species distribution models to explore the projected ranges of five widespread southeastern North American palm species (Rhapidophyllum hystrix, Sabal etonia, Sabal minor, Sabal palmetto, and Serenoa repens) under four climate change scenarios through 2070. We project that the amount of habitat with >50% suitability for S. etonia will decline by a median of 50% by 2070, while the amount of habitat with >50% suitability S. minor will decline by a median of 97%. In contrast, the amount of suitable habitat for Rhapidophyllum hystrix will remain stable, while the amount of suitable habitat for Serenoa repens will slightly increase. The projected distribution for S. palmetto will increase substantially, by a median of approximately 21% across all scenarios. The centroid of the range of each species will shift generally north at a median rate of 23.5 km/decade. These five palm species have limited dispersal ability and require a relatively long time to mature and set fruit. Consequently, it is likely that the change in the distribution of these palms will lag behind the projected changes in climate. However, Arecaceae can modify physiological responses to heat and drought, which may permit these palms to persist as local conditions become increasingly inappropriate. Nonetheless, this plasticity is unlikely to indefinitely prevent local extinctions.
... Sabal Adans.-the palmetto-is a New World genus with 17 recognized species (Zona, 1990, Goldman et al. 2012, Griffith et al. 2017). Boldingh's Florae (1913, 1914 did not include any Sabal in the Leeward Antilles. ...
A new palm species, Sabal lougheediana, is described and illustrated. This critically endangered island endemic, native solely to Bonaire, is characterized by a compact crown of leaves, erect leaf segments, distinctive leaf scars, and frequently vascularized fiber bundles in leaflet transection. Detail on history, morphology, range, habitat, and conservation status is presented, along with a diagnostic key.
... Whole genome dominant marker AFLP (amplified fragment length polymorphism; Vos et al. 1995) is an effective molecular technique for examining hybrids and determin- ing their affiliation to parental species ( Bonin et al. 2007), as documented in particular case studies such as Kirk et al. (2004), Minder et al. (2007), Segarra-Moragues et al. (2007), Hersch-Green & Cronn (2009), Goldman et al. (2011), Cires et al. (2012) and Szczepaniak et al. (2016). Another efficient method for examining hybrids, which is mostly used when the parental species differ in ploidy level, is flow cytometry ( Suda et al. 2007b), as documented in case studies such as Bureš et al. (2003), Morgan- Richards et al. (2004), Suda et al. (2007a), Kúr et al. (2016) and Macková et al. (2017). ...
In this study we describe a new nothospecies, Cirsium ×sudae Michálková et Bureš, a homoploid hybrid between two rare Alpine species, C. carniolicum and C. greimleri. Hybrid status was confirmed for four morphologically intermediate individuals, found in the Ennstal Alps, Austria (three of them were F1 hybrids and one a backcross with C. carniolicum). We used amplified fragment length polymorphism (AFLP) to confirm affiliation to the parental species and exclude the potential contribution of other sympatric species. In addition, we used flow cytometry to confirm the diploid status of this hybrid. The newly assessed genome size of this hybrid is 2C = 1.99±0.03 pg, and for C. carniolicum 2C = 2.03±0.04 pg.
... Related Species: There is one hybrid from Texas, S. x brazoriensis which is probably the offspring of S. minor and S. palmetto (Goldman et al. 2011). ...
To many tribes in the southeast Sabal minor (Jacq.) Pers. Dwarf Palmetto is a very important plant that was used as a medicine, survival food, building use, mats, baskets, brooms,blowguns and other artwork. Many years ago The house structures of the Houma, Choctaw, Chitimacha and other tribes were thatched with overlapping dwarf palmetto leaves which shed the rain and insulated the homes (Figure 3).(Stork 1881; Swanton 1946; 2001). Walls were also lined with the leaves.
... Due to the fact that our data include both the quantitative and qualitative measurements, the Mann-Whitney U-test was conducted (Hollander & Wolfe 1999) in order to determine statistical significance of morphological differences between two species pairs, D. crinitus and D. pseudocrinitus, and D. orientalis and D. pseudocrinitus. It seems that the use of multivariate statistical algorithms is an important strategy for simultaneously analyzing multiple measurements of a group of taxa under investigation (Mráz et al. 2005, Goldman et al. 2011, Jiang et al. 2013. Henderson (2006) indicated that if a data matrix consists of both qualitative and quantitative characters, it is appropriate for analysis using multidimensional scaling analysis (MDS). ...
A new species from southwest of Bojnord, NE of Iran is described and illustrated here as Dianthus pseudocrinitus (Caryophyllaceae). This species is morphologically similar to D. crinitus subsp. turcomanicus, but can be distinguished from the latter by bract number, width of lower and upper leaves, margin of thickness of outermost bracts, length of calyx, length and width of anther, branches of stem, type of sheath of lower leaf, and tip shape of petal fimbria. The new species is also similar to D. orientalis subsp. stenocalyx in terms of floral characters, but they differ by several non- overlapping morphological characters. Results obtained from the morphological data are consistent with those obtained from the molecular phylogenetic trees based on sequences of the two copies of DFR1 gene, confirming phylogenetic affinity of the new species to D. crinitus subsp. turcomanicus.
With more than 2,600 species and 181 genera, palms (Arecaceae) are one of the
most diverse and widely distributed plant families in tropical environments (Baker and Dransfield, 2016). Although they make up a modest portion of the above-ground biomass in most neotropical forests (DeWalt and Chave, 2004), their contribution increases in places where palms are dominant (Muscarella et al., 2020). In the Amazon forests, palms are hyperdominant elements(ter Steege et al., 2013). Their sheer abundance secures them a key role in forest function and forest structure (Boukili and Chazdon, 2017). Palms provide food for a wide variety of animal species (Onstein et al., 2017), including key resources for frugivores, which in turn disperse canopy trees that store most of the carbon in mature forests (Bello et al., 2015). Many human groups value palms and use them as raw material for building, food, drink, clothing, fuel, and medicine (Sylvester et al., 2012).
Palms tissues stretch the limits of plant cells to reach tree-like heights while
preserving mechanical stability and long-term function using only apical meristems
(Tomlinson, 2006). Little is known about the functional mechanisms governing
palms’ adaptation to environmental gradients, despite their ecological significance
and distinctive morphological and physiological structure. Here, we summarize the
functional role of palms from a variety of perspectives, which concentrate on the
analysis of functional traits and their influence on adaptation to environmental gradients. Contributions are grouped into the analysis of functional traits and conservation issues.
Under the old taxon Principes, palms were once the Princes of the Kingdom Plantae. First on Engler’s list, they occupy a cherished place to botanists, and remain treasured centerpieces of many gardens. In turn, botanic gardens have put forward a decades-long effort to conserve these widely admired plants, keeping a number of palm species from extinction. Living palm collections also have critical value for comparative ecological studies. In this paper we highlight successful ex situ conservation programs for palms, review how the promising new field of collections genetics can guide ex situ conservation of palms, conduct a family-wide gap analysis for living collections in the Arecaceae, and provide an in-depth case study of ex situ conservation of the genus Sabal. These analyses highlight ways in which gardens can advance palm conservation following four recommendations: collect, cultivate, communicate, and collaborate.
Thesis (Ph. D.)--Claremont Graduate School, 1989. Includes bibliographical references (leaves 177-192). Photocopy.
Despite its relatively recent introduction to Africa, cassava (Manihot esculenta Crantz) has become a major food crop adapted to a wide range of agro-ecologies that is grown by millions of small-holding farmers of sub-Saharan Africa (SSA), owing to its remarkable tolerance to an array of biotic and abiotic stresses. Its economic importance is expected to grow further as evidenced by global consideration of cassava as an alternative source of renewable energy (biofuel) that prompted genome sequencing initiative of the crop. To address the evolving demand for new cultivars with unique traits such as high quality and quantity starch, high protein and high carotene content, breeders seek to broaden the genetic base of the breeding pool. Secondly, there is a dire need to develop alternative mapping populations such as doubled haploid (DH) to enhance the efficiency of molecular breeding. Towards these goals, we launched a project to cross cassava (Manihot esculenta) with castor bean (Ricinus communis L.). As a first step of validation of hybridization, different types of molecular markers (RAPD, AFLP, and SSR) were screened to distinguish cassava, castor and the putative hybrids at the DNA level. Only few of the RAPD and SSR primers screened showed that some hybrids might have combined alleles from both parents. Some of the primers revealed a castor-specific band that was absent in both cassava and the hybrid. In AFLP analysis, some primer combinations detected both castor and cassava specific bands in the hybrid. However, these data were not consistent with most hybrids and results are inconclusive. In the latest approach, we used bioinformatics tools to design a castor specific sequence tagged site (STS) primer. Preliminary results show that castor-specific STS primer pairs could not amplify products in the putative hybrids while cassava-specific primers amplify the products. Comparison of relative nuclear DNA content with flow cytometry showed that hybrids have similar DNA content with cassava suggesting that the tested genotypes may not be true hybrids. Further crossing and testing of hybrids, including reciprocals and a panel of cassava and castor clones will continue. The development of markers to verify such wide crosses, once confirmed by cytological analysis and morphological characterization, opens an opportunity to use DH mapping populations thereby accelerating the development of saturated linkage map in cassava, with the possibility of introgressing novel traits of commercial value from castor to cassava.
ABSTRACT Comparative morphology, AFLP fingerprinting and trnL-F region sequencing were used to investigate the origin of an unknown member of the Sorbus latifolia group with weakly lobed leaves and large fruits, discovered at Naas near the River Severn, Gloucestershire. Samples of the unknown hybrid, the three putative parents S. aria, S. rupicola and S. torminalis, and from S. × vagensis, the primary diploid hybrid between S.aria and S. torminalis, were analysed. Morphological analysis of leaf characters showed that the unknown hybrid fell between S. ariaand S. torminalis. Genetic fingerprints were obtained using AFLP, and two primer combinations gave 109 bands, 84 of which were polymorphic. Both hybrids showed additivity between S.torminalis and ,S. aria/S. rupicola. Sorbus torminalis was ,one parent of both ,hybrids. The presence of twelve unique bands in S. rupicola(compar ed to only three bands in S. aria) indicate that S. ariais probably the other parent in both hybrids. Sequences for the trnL-F region of plastid DNA indicate that S. torminalis was the female parent of both hybrids. As the two hybrids thus appear to result from hybridisation between the same parents and the hybridisation took place in the same direction, we include the unknown hybrid within S. × vagensis. KEYWORDS: AFLP, Sorbus aria, S. rupicola, S. torminalis, S. × vagensis, trnL-F region sequencing,
The Galapagos endemic plants Scalesia aspera, Scalesia crockeri, and Scalesia pedunculata (Asteraceae) grow in distinct parts of Santa Cruz Island. Between them lie morphologically intermediate populations. The putative hybridization of the three species was investigated by means of morphological (leaf characters) and molecular (amplified fragment length polymorphism) measures. The results suggest that the intermediate populations are interspecific hybrids. Artificial hybrids were also made by crossing S. crockeri and S. pedunculata manually. We thus document that reproductive barriers are incomplete and that gene flow occurs between the three different species of Scalesia.
We report the first confirmed occurrence in Britain of Orchis ¥ angusticruris Franch. ex Rouy, a hybrid between two
closely related orchid species of anthropomorphic Orchis (O. purpurea Huds. ¥ O. simia Lam.) that hybridize
frequently in Continental Europe. Seven individual hybrids, most likely F1 plants representing a single interspecific
pollination event, first flowered with both parents in May 2006 at a nature reserve in the Chiltern Hills near
Goring, Oxfordshire. Univariate and multivariate morphometric analyses (43 characters plus 12 indices), internal
transcribed spacer sequencing, plastid microsatellites and amplified fragment length polymorphism (AFLP)
analyses together readily separate the parents and confirm that O. purpurea was the ovule parent and O. simia
the pollen parent, presumably reflecting the greater frequency and/or later flowering period of the latter at the site.
This study reinforces a more general observation that, in most orchids, the ovule parent contributes substantially
more to the hybrid phenotype than does the pollen parent, perhaps reflecting cytoplasmic inheritance. In contrast,
the hybrids are placed closer to O. simia than to O. purpurea in the AFLP tree. Apparently recent arrivals, the few
O. purpurea plants at Goring contrast genetically with the two other small populations of this species known in
the Chilterns, but rather are consistent with relatively uncommon Continental populations. This suggests that the
plants may have been deliberately introduced at Goring by man, although transport from the Continent in
high-level air currents cannot be ruled out. The Goring population of O. simia is likely to have become genetically
impoverished through (1) preferential removal of many relatively fit plants to herbaria in the 19th century and/or
(2) a catastrophic population crash in the first half of the 20th century. However, both our re-examination of
herbarium specimens and our population genetic data indicate past hybridization among anthropomorphic Orchis
species occurring naturally in the Chilterns. Thus, we tentatively recommend retention of the hybrid plants at
Goring, despite their likely anthropogenic origin from Continental material and the partial viability of their pollen
and seeds, which offers opportunities for future introgression. Although the Goring hybrids broadly resemble
morphologically O. militaris, another anthropomorphic Orchis still found at two Chiltern localities, sufficient
morphological and molecular differences were observed to strongly refute our initial hypothesis that O. militaris
could have originated through hybridization between ancestors that resembled O. purpurea and O. simia. The
comparatively complex genetic properties evident in both O. simia and O. purpurea merit further study. © 2008
The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 157, 687–711.
Millions of Nearctic-Neotropical landbirds move through the coastal forests of the Gulf of Mexico each spring and autumn as they migrate across and around the gulf. Migration routes in the gulf region are not static—they shift year to year and season to season according to prevailing wind patterns. Given the dynamic nature of migration routes, coastal forests around the Gulf of Mexico potentially can provide important stopover habitat to en route migrants. The coastal forests from the Florida Keys to the Yucatan Peninsula include a wide range of habitat types that we have classified as 19 broad community types. From literature reviews, we determined that the majority of these coastal habitats have been lost or degraded due to the effects of development, agriculture, livestock graz- ing, timber industry activities, and the spread of exotic species. The continued loss and degradation of coastal forests pose a risk to migrating birds, and thus we need to develop a conservation strategy that maximizes the suitability of the remaining forested patches around the gulf. An effective conservation strategy will require considerations at the gulf-wide, regional, landscape and habitat levels. These considerations should include mi- grant movement and landfall patterns, migrant use of inland versus coastal fringe stopover sites, the creation of landscape mosaics that incorporate patch size and inter-patch distance, and the availability of within- habitat resources.
Human activities can promote increased hybridization in the genus Eucalyptus with potentially detrimental consequences for the persistence of rare species. However, many hybrid combinations have not
been investigated with combined use of genetic markers and morphology. We assessed the efficiency of the STRUCTURE program
and morphological intermediacy for identifying hybrids between the uncommon tree, Eucalyptus aggregata, which putatively hybridizes with the common congeners, E.rubida and E.viminalis in south-eastern Australia. We sampled 1,005 seedlings across 27 populations, all seedlings were genotyped at 6 allozyme
loci and scored for 22 stem and leaf characters. Both marker sets confirmed that E.aggregata is hybridizing with both E.rubida and E.viminalis. Allozymes revealed hybrids from E.aggregata trees in 88% of populations and hybrids comprised 7.3% of all seedlings. Both genetics and morphology indicated that ~50%
were likely to be F1 hybrids, and both simulations and morphological characteristics indicated that the remainder were mostly backcrosses. Morphological
analysis correctly distinguished 71% of F1 hybrids from parentals and was least accurate when dealing with potential backcrosses (50% success). Hence, techniques using
genetic data (no prior information) and the assessment of appropriate admixture thresholds through simulations provided the
most accurate estimates of hybrid frequency. In this study, potential introgression and the high frequency of hybrids in small
populations (~30%), suggests that hybridization should be considered in the management and conservation of E.aggregata.
A new hybrid palm, ×Attabignya minarum, from the Rio São Francisco Valley of Minas Gerais, Brazil is described. It is a natural hybrid betweenAttalea compta Mart. andOrbignya oleifera Burret and is quite common in the area studied. Most of the morphological characters of the hybrid are intermediate between
those of the parent species. A notable exception is the number of fruits produced; ×Attabignya minarum produces more fruits per panicle than either parent species. This is the first report of hybridization betweenOrbignya andAttalea and may shed light on the status ofOrbignya, considered by some to be synonymous withAttalea.
Formulae are given for estimators for the parameters F, θ, f (FIT, FST, FIS) of population structure. As with all such estimators, ratios are used so that their properties are not known exactly, but they have been found to perform satisfactorily in simulations. Unlike the estimators in general use, the formulae do not make assumptions concerning numbers of populations, sample sizes, or heterozygote frequencies. As such, they are suited to small data sets and will aid the comparisons of results of different investigators. A simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure.
The utility of the PCR-based AFLP technique (polymerase chain reaction; amplified fragment length polymorphisms) was explored in elucidating details of polyploid evolution in the Eurasian orchid genus Dactylorhiza. We emphasized Swedish taxa but also included some material from the British Isles and elsewhere in Europe. Three different sets of primers, amplifying different subsets of restriction fragments, independently revealed similar patterns for relationships among the Dactylorhiza samples investigated. The AFLP data support the general picture of polyploid evolution in Dactylorhiza, i.e., that allotetraploid derivatives have arisen repeatedly as a result of hybridization beween the two parental groups D. incarnata s.l. (sensu lato; diploid marsh orchids) and the D. maculata group (spotted orchids). Within the incarnata s.l. group, morphologically defined varieties were interdigitated. The D. maculata group consisted of two distinct subgroups, one containing autotetraploid D. maculata subsp. maculata and the other containing diploid D. maculata subsp. fuchsii. Allotetraploids showed a high degree of additivity for the putative parental genomes, and relationships among them were partly correlated to morphologically based entities, but also to geographic distribution. Thus, allotetraploid taxa from the British Isles clustered together, rather than with morphologically similar plants from other areas.
The orchid genus Calopogon R.Br. (Orchidaceae), native to eastern North America and the northern Caribbean, currently contains five species and up to three varieties. Using nuclear internal transcribed spacer (ITS) ribosomal DNA sequences, amplified fragment length polymorphisms (AFLPs), chloroplast DNA restriction fragments, and chromosome counts, we present a phylogenetic and taxonomic study of the genus. Calopogon multiflorus and C. pallidus are consistently sister species, but the relationships of C. barbatus, C. oklahomensis, and C. tuberosus are not as clear. In the ITS analysis C. oklahomensis is sister to C. barbatus, whereas it is sister to C. tuberosus in the plastid restriction fragment analysis. Furthermore, all species were found to have chromosome numbers of 2n = 38 and 40, with the exception of the putatively hybrid-derived C. oklahomensis with 2n = 114 and 120. The hexaploidy of the latter, plus the discrepancy in its position between the ITS and plastid restriction fragment trees, could suggest that it is of hybrid origin. However, the presence of unique morphological and molecular characters might indicate that it is either an ancient hybrid or not of hybrid derivation at all. Finally, using these molecular methods all taxa appear to generally be discrete groups, with the exception of C. tuberosus vars. latifolius and tuberosus, the former of which is best combined with the latter.
Hybridization and polyploidization are exceedingly important processes because both influence the ecological envelope and evolutionary trajectory of land plants. These processes are frequently invoked for Castilleja (Indian paintbrushes) as contributors to morphological and genetic novelty and as complicating factors in species delimitations. Here, we provide a detailed analysis of morphological and genetic evidence for hybridization in a well-characterized hybrid swarm involving three broadly sympatric species (C. miniata, C. rhexiifolia, C. sulphurea) in western Colorado. Field-classified hybrids are present at high frequencies at these sites and show morphological intermediacy to and segregate for chloroplast DNA haplotypes with C. rhexiifolia and C. sulphurea. Contrarily, DNA content and AFLP variation show that field-classified hybrids are not recent hybrids but a distinctive fourth taxon. Actual hybrids (plants showing admixture ≥10% for two genotypic groups) comprised 13% of our sample, with most admixture involving C. rhexiifolia, C. sulphurea, and the unknown taxon. The identity of the field-classified "hybrids" remains unknown; they either represent a stabilized hybrid species or a species with uncharacteristically high diversity for color alleles. This study highlights the importance of examining concordance and discordance between morphology, cytology, and genetic criteria to understand the complex evolutionary history of diverse groups such as Castilleja.
Admixture between genetically divergent populations facilitates genomic studies of the mechanisms involved in adaptation, reproductive isolation, and speciation, including mapping of the loci involved in these phenomena. Little is known about how pre- and postzygotic barriers will affect the prospects of "admixture mapping" in wild species. We have studied 93 mapped genetic markers (microsatellites, indels, and sequence polymorphisms, ∼60,000 data points) to address this topic in hybrid zones of Populus alba and P. tremula, two widespread, ecologically important forest trees. Using genotype and linkage information and recently developed analytical tools we show that (1) reproductive isolation between these species is much stronger than previously assumed but this cannot prevent the introgression of neutral or advantageous alleles, (2) unexpected genotypic gaps exist between recombinant hybrids and their parental taxa, (3) these conspicuous genotypic patterns are due to assortative mating and strong postzygotic barriers, rather than recent population history. We discuss possible evolutionary trajectories of hybrid lineages between these species and outline strategies for admixture mapping in hybrid zones between highly divergent populations. Datasets such as this one are still rare in studies of natural hybrid zones but should soon become more common as high throughput genotyping and resequencing become feasible in nonmodel species.
The Columbia Bottomlands, a Southern floodplain forest formation on the upper Texas coast, historically covered over 283,000 ha but has since been reduced to 25% of its former extent. The importance of this regional ecosystem as critical stopover and staging habitat for Nearctic-Neotropical migratory landbirds gave rise to the Columbia Bottomlands Conservation Plan, an active land acquisition and conservation program administered by the U.S. Fish and Wildlife Service and its governmental and non-governmental partners. The Plan seeks to establish an integrated network of protected tracts as representative examples of the regional landscape, and thus conserve ecosystem integrity, function, heterogeneity, and biological diversity. We describe the Conservation Plan and its progress to date, and we summarize data on the plant composition of a typical preserved tract. Vegetation sampling at the Dance Bayou Unit, a mature forest remnant, revealed a mosaic of species composition across habitats varying in microtopography, soil type, and flooding pattern. The Dance Bayou study is a formative step in developing guidelines for future plant inventories, for site characterization in aid of land acquisition, and for restoration targets. As threats from urban development accelerate, intensified efforts may be needed to reach the Conservation Plan goal of protecting 10% of the original ecosystem extent.
Natural Phytophthora hybrids (P. nicotianae x P. cactorum) infecting loquat in Peru and Taiwan were characterized with AFLP (amplified fragment length polymorphism) markers, the internal transcribed spacer (ITS) region and the phenol acid carboxylase gene (Pheca) and inheritance of the mitochondrial cytochrome oxidase I gene (coxI). AFLP profiles of two Taiwanese isolates recovered in 1995 were polymorphic in approximately 50% of the fragments whereas five Peruvian isolates, recovered 2002-2003 and 2007, showed no genotypic variation. Sequencing analysis of the cloned ITS region resulted in the identification of sequences with high homology to either P. nicotianae (99%) or P. cactorum (97%). Direct sequence analysis of the Pheca gene revealed 13 heterozygous sites suggesting the presence of both P. nicotianae and P. cactorum genes in P. hybrids isolates. Melting analyses of coxI suggested that all seven Phytophthora hybrids inherited the mitochondrial DNA from P. nicotianae. Our results suggest that Phytophthora hybrids from Peru might have originated from a single hybridization event and that the two isolates from Taiwan might have originated through different hybridization events. The Peruvian hybrids appear to have persisted at least 3 y at three locations. Possible factors influencing the population structure of Phytophthora hybrids infecting loquat are discussed.
A novel DNA fingerprinting technique called AFLP is described. The AFLP technique is based on the selective PCR amplification
of restriction fragments from a total digest of genomic DNA. The technique involves three steps: (i) restriction of the DNA
and ligation of oligonucleotide adapters, (ii) selective amplification of sets of restriction fragments, and (iii) gel analysis
of the amplified fragments. PCR amplification of restriction fragments is achieved by using the adapter and restriction site
sequence as target sites for primer annealing. The selective amplification is achieved by the use of primers that extend into
the restriction fragments, amplifying only those fragments in which the primer extensions match the nucleotides flanking the
restriction sites. Using this method, sets of restriction fragments may be visualized by PCR without knowledge of nucleotide
sequence. The method allows the specific co-amplification of high numbers of restriction fragments. The number of fragments
that can be analyzed simultaneously, however, is dependent on the resolution of the detection system. Typically 50—100 restriction
fragments are amplified and detected on denaturing polyacrylamide gels. The AFLP technique provides a novel and very powerful
DNA fingerprinting technique for DNAs of any origin or complexity.
Restriction site variation of chloroplast DNA was analyzed in nine of the eleven currently recognized species of Caryota. Phylogenetic relationships were estimated and used to examine biogeographic patterns in the genus. Analysis of 49 populations of Caryota and six species from the putative outgroup genera Arenga and Wallichia demonstrated low levels of inter- and intraspecific variation as seen in other groups of palms and long-lived perennials. A total of 796 restriction sites representing 4,752 bp (ca. 4.0%) of the chloroplast genome was detected with 75 sites (9.4% of the total) showing phylogenetically informative variation. Phylogenetic analysis identified three main clades, each with one widespread variable species and one or more geographically restricted species. Hybridization was suggested as a probable explanation for patterns of variation detected in several instances of species sympatry. Biogeographic patterns among the three principal clades are largely congruent with Wallace's 1910 Line or Huxley's Line. The Maxima clade consists of three species restricted to the west of Huxley's Line. The Mitis clade consists of two species found west Huxley's Line and on the island of Sulawesi. The Rumphiana clade includes four species distributed, with one exception, to the east of Huxley's Line and on the border islands of Borneo and Palawan. The economically important C. urens, the errant member of the Rumphiana clade, has a distribution disjunct to India and Sri Lanka, possibly a reflection of early human introduction, cultivation, and subsequent natural dispersal into local forests.
Schoenoplectus samples from the Rivers Arun, Medway, Tamar and Thames were studied using AFLP genetic fingerprinting to test hypotheses concerning the origin of hybrids of S. triqueter with S. lacustris and S. tabernaemontani. Schoenoplectus lacustris and S. tabernaemontani were shown to be only distantly related, and therefore it is appropriate that they be treated as two distinct species rather than as two subspecies of S. lacustris, as recommended by some authorities. S. lacustris was excluded as a possible parent in all potential hybrids studied from all rivers, and evidence of additivity was found between the fingerprints of S. tabernaemontani and S. triqueter in all cases. Material collected as pure species turned out to be of hybrid origin in two cases, and identification of the hybrids and S. tabernaemontani appears to be difficult as a result of phenotypic plasticity. Conservation implications of the results and areas of possible future work are discussed.
Multivariate analyses of qualitative and quantitative characters taken from herbarium specimens of Calyptrogyne H. Wendl. (Palmae), together with analysis of geographic distributions, reveals 27 groups of specimens. Application of the Phylogenetic Species/Subspecies Concept to these groups gives 18 species and 13 subspecies, giving a total of 27 taxa in the genus. Eight species (C. tutensis, C. fortunensis, C. sanblasensis, C. baudensis, C. deneversii, C. coloradensis, C. panamensis, C. osensis) and seven subspecies (C. costatifrons subsp. occidentalis, C. costatifrons subsp. dariensis, C. allenii subsp. centralis, C. panamensis subsp. centralis, C. panamensis subsp. tutensis, C. panamensis subsp. occidentalis, C. ghiesbreghtiana subsp. hondurensis) are new, and two new combinations are made (C. ghiesbreghtiana subsp. spicigera, C. ghiesbreghtiana subsp. glauca). These taxa are distributed from southern Mexico to northwestern Colombia, with the greatest diversity in western Panama.
Publisher Summary This chapter describes a filter hybridization approach for mapping chloroplast DNA (cpDNA) restriction sites along with several strategies for generating restriction fragments for use as hybridization probes. Approaches for visualizing and mapping cpDNAs that are difficult or impossible to isolate in very pure form are also discussed. The chloroplast genome is densely packed with genes and many of them have been isolated and sequenced. Chloroplast gene products identified thus far function either in photosynthesis or as components of the chloroplast protein synthesizing system. The basic strategy for mapping by overlap hybridization is to hybridize each one of a set of restriction fragments that together cover an entire chloroplast genome to replica membranes containing various single and double digests of total cpDNA. Three classes of individually purified cpDNA restriction fragments that can be used as hybridization probes are homologous, uncloned fragments; homologous, cloned fragments; and heterologous, cloned fragments. Procedures to obtain each class of probe fragments and the relative merits of each class are discussed.
Scirpus × mariqueter Tang & F.T. Wang (CYPERACEAE) is a pioneer plant of the tidal zone of estuaries of East Asia. Amplified fragment length polymorphisms (AFLP) were used to infer the relationship between S. × mariqueter and its putative progenitors, Scirpus planiculmis F. Schmidt and Scirpus triqueter L. The genetic distance between S. × mariqueter and S. triqueter was much higher than that between S. × mariqueter and S. planiculmis, and samples of S. × mariqueter and those of S. planiculmis did not form a monophyletic group, while the S. triqueter group formed a distinct monophyletic group. However, we also detected an apparent clustering of individuals of S. × mariqueter and S. planiculmis separately. Our results disprove the hybrid origin of S. × mariqueter and rather suggest that it is more closely related to S. planiculmis.
Approaches to determining the number of components to interpret from principal components analysis were compared. Heuristic procedures included: retaining components with eigenvalues (Xs) > 1 (i.e., Kaiser-Guttman criterion); components with bootstrapped Xs > 1 (bootstrapped Kaiser-Guttman); the scree plot; the broken-stick model; and components with Xs totalling to a fixed amount of the total variance. Statistical ap- proaches included: Bartlett's test of sphericity; Bartlett's test of homogeneity of the cor- relation matrix, Lawley's test of the second X; bootstrapped confidence limits on successive Xs (i.e., significant differences between Xs); and bootstrapped confidence limits on eigen- vector coefficients (i.e., coefficients that differ significantly from zero). All methods were compared using simulated data matrices of uniform correlation structure, patterned ma- trices of varying correlation structure and data sets of lake morphometry, water chemistry, and benthic invertebrate abundance. The most consistent results were obtained from the broken-stick model and a combined measure using bootstrapped Xs and associated eigen- vector coefficients. The traditional and bootstrapped Kaiser-Guttman approaches over- estimated the number of nontrivial dimensions as did the fixed-amount-of-variance model. The scree plot consistently estimated one dimension more than the number of simulated dimensions. Bartlett's test of sphericity showed inconsistent results. Both Bartlett's test of homogeneity of the correlation matrix and Lawley's test are limited to testing for only one and two dimensions, respectively.
Two species of palo santo trees are distributed in the Galápagos archipelago, the native Bursera graveolens and the endemic Bursera malacophylla (Burseraceae). However, a zone of individuals morphologically intermediate between the two exists on northern Santa Cruz Island and south-eastern Santiago Island, suggesting that they may not be reproductively isolated. Here we review the species' distributional and morphological differences and test for evidence of hybridization between the two species using DNA sequence and AFLP data. We find that the species lack distinguishing synapomorphies across the five nuclear and plastid regions examined. Population assignment tests and population genetic analyses of AFLP data indicate that genetically similar palo santo individuals (N = 87), including putative hybrids, partition into two genealogical groups that do not uniformly correspond to island- or taxon-based membership. Furthermore, genotypic admixture levels among morphologically intermediate individuals do not indicate widespread hybridization. Thus, we recommend recognizing the endemic palo santo taxon as B. graveolens subspecies malacophylla (B.L.Rob.) A. Weeks & Tye comb. & stat. nov. in light of its close genetic relationship to B. graveolens subsp. graveolens and its distinctive morphology and distribution. Future research should quantify phenotypic variation in palo santo populations as another means for understanding the basis of morphological differences between the subspecies. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 161, 396–410.
Contact zones between recently diverged taxa offer unique opportunities to test whether the forms are reproductively isolated and therefore distinct species. The Pacific-slope flycatcher Empidonax difficilis and Cordilleran flycatcher Empidonax occidentalis are closely related taxa that were officially separated into two species in 1989, a treatment that has been controversial due to reports of phenotypically intermediate birds across the southern interior of British Columbia and Alberta. We present the first analysis of molecular variation across this region, in order to determine whether there is genetic introgression between the taxa. Allopatric populations of Pacific-slope and Cordilleran flycatchers belong to distinct mitochondrial clades, and all of the individuals sampled in interior southwestern Canada have the Pacific-slope haplotype. In contrast, variation in nuclear DNA (AFLPs) indicates hybridization between Pacific-slope and Cordilleran flycatchers in this region. We suggest that the discordance between the mitochondrial and nuclear markers most likely results from stochastic loss of Cordilleran mitochondrial haplotype lineages facilitated by asymmetries in mating due to earlier arrival and greater abundance of Pacific-slope flycatchers in the contact zone. The discovery of hybridization between Pacific-slope and Cordilleran flycatchers in southwestern Canada may call into question the decision to split them into two species. On the other hand, allopatric populations are genetically distinct in both mitochondrial and nuclear DNA, and the hybridization might not affect populations outside of the contact zone. This study highlights the importance of employing multiple genetic markers in studies of contact zones between closely related species.
Solanum gourlayi and Solanum spegazzinii, wild potatoes endemic to Argentina, possess desirable traits for breeding. In periodical regenerations of accessions, variability
was detected for morphology and breeding barriers. The persistence of these populations in nature was evaluated after more
than 20years. Both species were observed in all visited sites, along with other wild and cultivated potatoes. Chromosome
numbers coincided with the originally reported, except for one population of Solanum gourlayi, with diploid and tetraploid cytotypes. The accompanying flora and environmental conditions revealed important alterations
as the result of road construction, excessive stocking rates and overgrazing. Principal coordinate and cluster analyses and
an AMOVA using AFLP data of three original accessions and the corresponding new accessions revealed high molecular variability
and extensive overlapping. Plant grouping of accessions occurred at a distance of 0.58 for S. gourlayi, 0.62 for S. spegazzinii and 0.67 for both species. The role of natural hybridization and sexual polyploidization in the evolution of sympatric populations
of wild potatoes is discussed.
Sabal miamiensis, a species endemic to the Miami pinelands of south Florida, is described and illustrated. It is shown to be morphologically
and ecologically distinct fromS. etonia andS. palmetto.
Ophrys orchids mimic the female sex pheromones of their pollinator species to attract males for pollination. Reproductive isolation in Ophrys is based on the selective attraction of only a single pollinator species. A change of floral odour can result in the attraction of a new pollinator species that acts as an isolation barrier towards other sympatrically occurring Ophrys species. Ophrys lupercalis, Ophrys bilunulata, and Ophrys fabrella grow sympatrically and bloom consecutively on Majorca and are pollinated by three species of Andrena. We investigated variation of phenotypic and genotypic flower traits, aiming to study the role of the floral odour for reproductive isolation and speciation. Using chemical and electrophysiology (gas chromatography coupled with an electroantennographic detector) methods, we show that the three Ophrys species use the same odour compounds for pollinator attraction, but in different proportions. A comparison of the floral odour bouquets in a multivariate analysis revealed a clear grouping of plants from the same species, although with an overlap between species. A comparison of the same plants using molecular markers gave a contrasting result. Although O. lupercalis and O. fabrella were genetically well separated, plants of O. bilunulata did not form a distinct group but were similar to either O. lupercalis or O. fabrella. Our data indicate gene flow and hybridization to occur between O. bilunulata and O. lupercalis as well as between O. bilunulata and O. fabrella. All plants of O. bilunulata, despite having different genotypes, showed a very similar floral odour. This reflects a strong selective pressure by the pollinating males. The overlap of genotypes of O. bilunulata and O. fabrella supports our hypothesis that O. fabrella diverged from O. bilunulata by scent variation and the attraction of a new pollinator species, Andrena fabrella.
A measure of genetic distance (D) based on the identity of genes between populations is formulated. It is defined as D = -logeI, where I is the normalized identity of genes between two populations. This genetic distance measures the accumulated allele differences per locus. If the rate of gene substitution per year is constant, it is linearly related to the divergence time between populations under sexual isolation. It is also linearly related to geographical distance or area in some migration models. Since D is a measure of the accumulated number of codon differences per locus, it can also be estimated from data on amino acid sequences in proteins even for a distantly related species. Thus, if enough data are available, genetic distance between any pair of organisms can be measured in terms of D. This measure is applicable to any kind of organism without regard to ploidy or mating scheme.
Previous systematic treatments of the neotropical palm genus Hyospathe have recognized from two to 18 species. An explicit, quantitative, repeatable sequence of operations for delimiting and testing groups of specimens and applying species concepts is carried out. Multivariate statistical analysis of morphological data is used to delimit and test groups of specimens. Cluster analysis is used to distinguish between characters and traits. Analysis of qualitative and quantitative characters reveals six groups of specimens, and the Phylogenetic Species Concept is applied to these groups. Two species, H. peruviana Henderson and H. frontinensis Henderson, are described as new. One of the specimen groups is large and widespread, and six geographically separate subgroups can be recognized within it. These subgroups can be distinguished by one or more significantly different quantitative characters. A Phylogenetic Subspecies Concept is applied to these subgroups. Three subspecies, H. elegans subsp. costaricensis Henderson, H. elegans subsp. sanblasensis Henderson, and H. elegans subsp. tacarcunensis Henderson are described as new, and two new combinations are made: H. elegans subsp. sodiroi (Dammer ex Burret) Henderson and H. elegans subsp. concinna (H. E. Moore) Henderson. One subspecies occurring in the Amazon region is complex morphologically and is not resolved by the methods used here.
Thesis (Ph. D.)--Tulane University, 1989. Includes bibliographical references (leaves 190-211). Microfilm. s
The decrease of successive eigenvalues in some principal component analysis of 20 variates and 44 individuals, is compared with that of the ‘broken stick’ model, where a fixed length is broken at random into a number of segments.In the real analysis, the two first eigenvalues stay distinctly above the model values, indicating the occurrence of factors acting on the variables. Residual variance seems partitioned between other axes, according to a model which approaches the broken stick. The adjustment is not perfect, since an unknown part of the random variance also contributes to the first eigenvalues. The model, however, allows an empirical determination of the number of significant vectors.
Dominant markers such as amplified fragment length polymorphisms (AFLPs) provide an economical way of surveying variation at many loci. However, the uncertainty about the underlying genotypes presents a problem for statistical analysis. Similarly, the presence of null alleles and the limitations of genotype calling in polyploids mean that many conventional analysis methods are invalid for many organisms. Here we present a simple approach for accounting for genotypic ambiguity in studies of population structure and apply it to AFLP data from whitefish. The approach is implemented in the program structure version 2.2, which is available from http://pritch.bsd.uchicago.edu/structure.html.