Comparative analysis of phenotypic and genotypic diversity among plantain landraces (Musa spp., AAB group)

Genetic diversity amongst 76 plantain landraces has been studied using RAPD analysis at two levels of intensity and compared with groupings based on phenotypic indices and morphotype. There was a good correlation (R²=0.78) between estimates of genetic diversity based on 76 RAPD bands and 164 RAPD bands. However, there was a poor correlation between RAPD-based estimates of genetic diversity and a phenotypic index based on agronomic characters. There was also a poor correlation between RAPD analyses and morphotype group (based on bunch type and stature). These results suggest that the traditional designations of plantain landraces based on morphotype do not provide a true reflection of overall genetic divergence. Similarly, classification systems using phenotypic indices based on agronomic characters may not provide accurate taxonomic differentiation. The level of genetic divergence within morphogroups based on bunch type suggests that True Horn plantains are derived from False Horn plantains which in turn are derived from French plantains. Genetic divergence was found to be generally quite low within the plantain landrace genepool, which is consistent with the proposed evolution of this germplasm through somatic mutation of a relatively small number of introductions. However, putative synonyms/duplicates have been shown to be genetically distinct. In contrast, a group of 12 landraces have been identified that are highly distinct from one another (showing 20–35% dissimilarity). Fertile members of this group may be useful for generating genetically diverse 2x and 4x breeding populations that can be used in breeding secondary triploid hybrid plantain varieties. Received: 8 January 2000 / Accepted: 2 March 2000     

Phenotypic Diversity and Patterns of Variation in West and Central African Plantains (Musa Spp., AAB group Musaceae)

Plantains (Musa spp., AAB group) are an important food crop and an integral component of the farming systems in the lowland humid forest zone of West and Central Africa. A group of 24 plantain cultivars, representing the major variability in West Africa, was evaluated for nine quantitative characters. The association between growth and yield parameters in this African plantain germplasm was examined to determine if the pattern of quantitative variation in inflorescence and vegetative traits agreed with taxonomic groupings based on inflorescence type and plant size. Phenotypic correlations between these traits were calculated. Giant cultivars were taller, their pseudostem thicker, and they flowered much later than medium-sized cultivars. Giant cultivars produced more foliage, resulting in heavier bunches with more hands and fruits. Groupings that resulted following principal component analysis (PCA) supported conventional taxonomic groupings of plantains. PC A was based mainly on time to flowering, pseudostem height, and number of fruits. The last two traits, in combination with the number of hermaphrodite flowers and the persistence of the male bud, sufficed to group plantain cultivars.     

The Plantain Proteome,a Focus on Allele Specific Proteins Obtained from Plantain Fruits

Proteomics has been applied with great potential to elucidate molecular mechanisms in plants. This is especially valid in the case of non‐model crops of which their genome has not been sequenced yet, or is not well annotated. Plantains are a kind of cooking bananas that are economically very important in Africa, India, and Latin America. The aim of this work was to characterize the fruit proteome of common dessert bananas and plantains and to identify proteins that are only encoded by the plantain genome. We present the first plantain fruit proteome. All data are available via ProteomeXchange with identifier PXD005589. Using our in‐house workflow, we found 37 alleles to be unique for plantain covered by 59 peptides. Although we do not have access (yet) to whole‐genome sequencing data from triploid banana cultivars, we show that proteomics is an easily accessible complementary alternative to detect different allele specific SNPs/SAAPs. These unique alleles might contribute toward the differences in the metabolism between dessert bananas and plantains. This dataset will stimulate further analysis by the scientific community, boost plantain research, and facilitate plantain breeding.     

Growth Parameters of Yield of Plantain (Musa cv. AAB)

The performance of the crop plant and the ‘ratoon’plant (lateral shoot succeeding the harvested main shoot) of65 medium-sized False Horn plantains (Musa cv. AAB) was studiedby measuring vegetative and inflorescence (bunch) parameters.From significant regressions between different parameters itappears that taller pseudostems produce leaves at a faster rate,flower earlier and produce heavier infructescences which needmore time to mature. A high yield is determined by vigorousinitial growth of the planted sucker (lateral root). Beforeflowering, there is no sink competition between ratoon and mainpseudostem growth, and fast-growing main pseudostems are accompaniedby fast-growing ratoons. After flowering, competition occursbetween the fructifying inflorescence, a preferential sink andthe ratoon. The results indicate that plantain should not beconsidered as an annual crop. Growth, development, production parameters, bananas, plantains     

Compilation of morphological and molecular data,a necessity for taxonomy: The case of Hormogaster abbatissae sp. n. (Annelida,Clitellata, Hormogastridae)

Conflict among data sources can be frequent in evolutionary biology, especially in cases where one character set poses limitations to resolution. Earthworm taxonomy, for example, remains a challenge because of the limited number of morphological characters taxonomically valuable. An explanation to this may be morphological convergence due to adaptation to a homogeneous habitat, resulting in high degrees of homoplasy. This sometimes impedes clear morphological diagnosis of species. Combination of morphology with molecular techniques has recently aided taxonomy in many groups difficult to delimit morphologically. Here we apply an integrative approach by combining morphological and molecular data, including also some ecological features, to describe a new earthworm species in the family Hormogastridae, Hormogaster abbatissae sp. n., collected in Sant Joan de les Abadesses (Girona, Spain). Its anatomical and morphological characters are discussed in relation to the most similar Hormogastridae species, which are not the closest species in a phylogenetic analysis of molecular data. Species delimitation using the GMYC method and genetic divergences with the closest species are also considered. The information supplied by the morphological and molecular sources is contradictory, and thus we discuss issues with species delimitation in other similar situations. Decisions should be based on a profound knowledge of the morphology of the studied group but results from molecular analyses should also be considered.     

Molecules and morphology: Congruence of data inColumnea (Gesneriaceae)

The cladistic analysis and comparison of molecular and morphological data has been the source of much recent debate. In this study, independent analyses of molecular and morphological data fromColumnea L. sects.Pentadenia andStygnanthe (Gesneriaceae) are compared. Comparative methods include consensus, visually comparing trees from independent analyses and combined data analysis. Consensus methods provided little resolution. Comparison of trees obtained from the independent analyses revealed some differences although the trees are highly similar. However, a combined analysis found that the level of incongruence between the two data sets was low. The tree resulting from the combined data has aspects of both the morphological and molecular trees despite the larger number of molecular characters. In addition, the combined data tree has greater resolution than either of the two data sets singly, indicating that the two types of data are congruent, and complementary to each other.     

Using Morphological,Molecular and Climatic Data to Delimitate Yews along the Hindu Kush-Himalaya and Adjacent Regions

Background

Despite the availability of several studies to clarify taxonomic problems on the highly threatened yews of the Hindu Kush-Himalaya (HKH) and adjacent regions, the total number of species and their exact distribution ranges remains controversial. We explored the use of comprehensive sets of morphological, molecular and climatic data to clarify taxonomy and distributions of yews in this region.

Methodology/Principal Findings

A total of 743 samples from 46 populations of wild yew and 47 representative herbarium specimens were analyzed. Principle component analyses on 27 morphological characters and 15 bioclimatic variables plus altitude and maximum parsimony analysis on molecular ITS and trnL-F sequences indicated the existence of three distinct species occurring in different ecological (climatic) and altitudinal gradients along the HKH and adjacent regions Taxus contorta from eastern Afghanistan to the eastern end of Central Nepal, T. wallichiana from the western end of Central Nepal to Northwest China, and the first report of the South China low to mid-elevation species T. mairei in Nepal, Bhutan, Northeast India, Myanmar and South Vietnam.

Conclusion/Significance

The detailed sampling and combination of different data sets allowed us to identify three clearly delineated species and their precise distribution ranges in the HKH and adjacent regions, which showed no overlap or no distinct hybrid zone. This might be due to differences in the ecological (climatic) requirements of the species. The analyses further provided the selection of diagnostic morphological characters for the identification of yews occurring in the HKH and adjacent regions. Our work demonstrates that extensive sampling combined with the analysis of diverse data sets can reliably address the taxonomy of morphologically challenging plant taxa.     

Morphological and genetic diversity of the family Azollaceae inferred from vegetative characters and RAPD markers

Family Azollaceae has seven species with a controversial taxonomy. The identification of species without reproductive structures relies on vegetative characters but some are variable, leading to misinterpretations. The molecular methods may be helpful, but until now, they did not provide a conclusive Azolla taxonomy. Therefore, we studied the family Azollaceae at vegetative and molecular levels. Analysis of vegetative, random amplified polymorphic DNA (RAPD) and combined data showed a comparable grouping of the Azolla species in two main clusters: cluster I, referred to as section Rhizosperma (A. pinnata and A. nilotica) and cluster II, referred to as section Azolla (A. filiculoides, A. microphylla, A. caroliniana and A. mexicana), with the exception of A. rubra, which clustered differently depending on the method. All the Azolla species were distinguished by the 13 polymorphic vegetative characters, the 211 RAPD markers or the combined data, with the latest showing the highest discrimination. The Shannon Index diversity was greater with RAPD (2.276) than with vegetative characters (0.054), highlighting the higher discriminating power of the molecular data. The partitioning of diversity was, as expected, high among species for all the types of data and low within species, with the lowest diversity obtained for morphological data. Both data sets (vegetative and RAPD) allowed the distinction of all the species and their clustering into sections Rhizosperma and Azolla, suggesting this as the most correct for this family. The dendrogram from the combined data was the most accurate, highlighting the benefit of integrating different types of data to study the family Azollaceae.     

Components of morphological variation in Baikalian endemial cyclopid Acanthocyclops signifer complex from different localities

Use of traditional methods for morphological studies only permits the analysis of a small part of the information embodied in morphological structures. Besides comparing populations using the mean values of characters which allows one to estimate their morphological similarity, analysis of variation among individuals within a population can be informative. Variation among individuals consists of factorial and stochastic components. The factorial component is an upper estimate of genetic heterogeneity and thus permits one to evaluate the population's adaptability. The stochastic component (estimated by fluctuating asymmetry, i.e. random deviations from perfect bilateral symmetry), being a measure of developmental stability, is an indicator of a population's fitness. Assessment of measurement error is necessary for assessment of the true value of the stochastic component and for selection of the most informative characters. Such analysis allows one to extract additional information from morphological data in comparison with methods traditionally used on copepods. This approach was applied to an analysis of morphological variation in the study of the Baikalian endemic cyclopoid Acanthocyclops signifer (Mazepova) from three different isolated localities. Characters typically used in studies of taxonomy of this group are considered here. Measurement error was rather high (more than 50% of the stochastic component), which can be explained by technical difficulties of measuring the characters. All populations differ in the mean values of the characters. This shows the taxonomic heterogeneity of this group and reveals the necessity of its taxonomic revision. Populations also differ in the level of stochastic and factorial components of the total variance. The data are interpreted from the point of view of taxonomy and the possible evolution of the group.     

A Duplex PCR Assay for the Detection of Ralstonia solanacearum Phylotype II Strains in Musa spp.

Banana wilt outbreaks that are attributable to Moko disease-causing strains of the pathogen Ralstonia solanacearum (Rs) remain a social and economic burden for both multinational corporations and subsistence farmers. All known Moko strains belong to the phylotype II lineage, which has been previously recognized for its broad genetic basis. Moko strains are paraphyletic and are distributed among seven related but distinct phylogenetic clusters (sequevars) that are potentially major threats to Musaceae, Solanaceae, and ornamental crops in many countries. Although clustered within the Moko IIB-4 sequevar, strains of the epidemiologically variant IIB-4NPB do not cause wilt on Cavendish or plantain bananas; instead, they establish a latent infection in the vascular tissues of plantains and demonstrate an expanded host range and high aggressiveness toward Solanaceae and Cucurbitaceae. Although most molecular diagnostic methods focus on strains that wilt Solanaceae (particularly potato), no relevant protocol has been described that universally detects strains of the Musaceae-infecting Rs phylotype II. Thus, a duplex PCR assay targeting Moko and IIB-4NPB variant strains was developed, and its performance was assessed using an extensive collection of 111 strains representing the known diversity of Rs Moko-related strains and IIB-4NPB variant strains along with certain related strains and families. The proposed diagnostic protocol demonstrated both high accuracy (inclusivity and exclusivity) and high repeatability, detected targets on either pure culture or spiked plant extracts. Although they did not belong to the Moko clusters described at the time of the study, recently discovered banana-infecting strains from Brazil were also detected. According to our comprehensive evaluation, this duplex PCR assay appears suitable for both research and diagnostic laboratories and provides reliable detection of phylotype II Rs strains that infect Musaceae.     

The utility of morphological characters in gastropod phylogenetics: an example from the Calyptraeidae

Organismal taxonomy is often based on a single or a small number of morphological characters. When they are morphologically simple or known to be plastic, we may not have great confidence in the taxonomic conclusions of analyses based on these characters. For example, calyptraeid gastropod shells are well known for their simplicity and plasticity, and appear to be subject to frequent evolutionary convergences, but are nevertheless the basis for calyptraeid taxonomy. In a case like this, knowing how the pattern of relationships inferred from morphological features used in traditional taxonomy compares to the patterns of relationships inferred from other morphological characters or DNA sequence data would be useful. In this paper, I examine the relative utility of traditional taxonomic characters (shell characters), anatomical characters and molecular characters for reconstructing the phylogeny of calyptraeid gastropods. The results of an ILD test and comparisons of the recovered tree topologies suggest that there is conflict between the DNA sequence data and the morphological data. Very few of the nodes recovered by the morphological data were recovered by any other dataset. Despite this conflict, the inclusion of morphological data increased the resolution and support of nodes in the topology recovered from a combined dataset. The RIs and CIs of the morphological data on the best estimate topology were not any worse than these indices for the other datasets. This analysis demonstrates that although analyses can be misled by these convergences if morphological characters are used alone, these characters contribute significantly to the combined dataset.  © 2003 The Linnean Society of London . Biological Journal of the Linnean Society , 2003, 78 , 541–593.     

The use of nuclear DNA molecular markers for studying speciation and systematics as exemplified by the “Lacerta agilis complex” (Sauria: Lacertidae)

Four types of nuclear DNA markers identified by the taxonprint, RAPD, and IMP (Inter-MIR-PCR) methods, and the nucleotide sequences of satellite DNA monomers have been used to analyze the molecular genetic similarity between some populations, subspecies, and species of lizards combined into the group Lacerta s. str., as well as representatives of some other genera. The notions on the systematics and phylogeny of this group based on morphological and zoogeographic criteria have been compared to the conclusions based on molecular genetic data. The genus and species subdivisions of populations based on nuclear molecular markers and morphological characters generally agree with each other, the degree of genetic differences being correlated with the taxonomy suggested by zoomorphologists. The degree of differences between the subspecies of one of the species studied, Lacerta agilis, varies depending on the molecular markers used: according to the results of RAPD analysis, all subspecies substantially differ from one another, the variation within populations being small; with respect to other markers, the differences are smaller and not equivalent. The existence of the so-called eastern and western clades of this species earlier assumed by other researchers on the basis of mtDNA and morphological data has been confirmed. There are no distinct gradations exceeding individual variation in 14 populations of L. agilis exigua (the eastern clade) with respect to IMP markers, although these populations inhabit a vast area from the Ural Mountains to the Kabardino-Balkar Republic (the Caucasus). These data suggest that the subspecies has been rapidly spreading northwards since the Pleistocene glaciation (about 15,000 years ago).     

Dung Beetle and Terrestrial Mammal Diversity in Forests, Indigenous Agroforestry Systems and Plantain Monocultures in Talamanca, Costa Rica

In order to explore the importance of indigenous agroforestry systems for biodiversity conservation, we compared the abundance, species richness and diversity of dung beetles and terrestrial mammals across a gradient of different land use types from agricultural monocultures (plantains) to agroforestry systems (cocoa and banana) and forests in the BriBri and Cabécar indigenous reserves in Talamanca, Costa Rica. A total of 132,460 dung beetles of 52 species and 913 tracks of 27 terrestrial mammal species were registered. Dung beetle species richness and diversity were greatest in the forests, intermediate in the agroforestry systems and lowest in the plantain monocultures, while dung beetle abundance was greatest in the plantain monocultures. The number of mammal tracks per plot was significantly higher in forests than in plantain monocultures, whereas mammal species richness was higher in forests than in either cocoa agroforestry systems or plantain monocultures. Species composition of both terrestrial mammals and dung beetles also varied across the different land use types. Our study indicates that indigenous cocoa and banana agroforestry systems maintain an intermediate level of biodiversity (which is less than that of the original forest but significantly greater than that of plantain monocultures) and provide suitable habitat for a number of forest-dependent species. Although the agroforestry systems appear to serve as favorable habitats for many terrestrial mammal species, their potential positive contribution to mammal conservation is being offset by heavy hunting pressure in the reserves. As in other agricultural landscapes, the conservation of biodiversity in Talamanca will depend not only on maintaining the existing forest patches and reducing the conversion of traditional agroforestry systems to monocultures, but also on reducing hunting pressure.     

Weighting against homoplasy improves phylogenetic analysis of morphological data sets

The problem of character weighting in cladistic analysis is revisited. The finding that, in large molecular data sets, removal of third positions (with more homoplasy) decreases the number of well supported groups has been interpreted by some authors as indicating that weighting methods are unjustified. Two arguments against that interpretation are advanced. Characters that collectively determine few well‐supported groups may be highly reliable when taken individually (as shown by specific examples), so that inferring greater reliability for sets of characters that lead to an increase in jackknife frequencies may not always be warranted. But even if changes in jackknife frequencies can be used to infer reliability, we demonstrate that jackknife frequencies in large molecular data sets are actually improved when downweighting characters according to their homoplasy but using properly rescaled functions (instead of the very strong standard functions, or the extreme of inclusion/exclusion); this further weakens the argument that downweighting homoplastic characters is undesirable. Last, we show that downweighting characters according to their homoplasy (using standard homoplasy‐weighting methods) on 70 morphological data sets (with 50–170 taxa), produces clear increases in jackknife frequencies. The results obtained under homoplasy weighting also appear more stable than results under equal weights: adding either taxa or characters, when weighting against homoplasy, produced results more similar to original analyses (i.e., with larger numbers of groups that continue being supported after addition of taxa or characters), with similar or lower error rates (i.e., proportion of groups recovered that subsequently turn out to be incorrect). Therefore, the same argument that had been advanced against homoplasy weighting in the case of large molecular data sets is an argument in favor of such weighting in the case of morphological data sets. © The Willi Hennig Society 2008.     

Genetic Diversity of Twelve Switchgrass Populations Using Molecular and Morphological Markers

Switchgrass (Panicum virgatum L.) is a warm season, C₄ perennial grass native to most of North America with numerous applications, including use as a bioenergy feedstock species. To date, no studies on genetic diversity in switchgrass have been conducted that use both molecular and morphological markers. The objectives of this study were to assess genetic diversity and determine differences among and between 12 switchgrass populations grown in New Jersey by examining both morphological and molecular characteristics, and to determine whether morphological, molecular, and/or combined data sets can detect ecotype and/or geographical differences at the population level. Twelve plants from each population were characterized with 16 switchgrass expressed sequence tag-simple sequence repeat markers (EST-SSRs) and seven morphological characters. Data was analyzed using GenAlEx and Unweighted Pair-Group Method of Averages (UPGMA) cluster analysis. Most (64%) of the molecular variation in switchgrass populations exists among individuals within populations, with lesser amounts between populations (36%). Upland and lowland populations were distinguished in all three data sets. Some eastern US and midwestern US populations were distinct in all three data sets. Similarities were observed between all three data sets indicating molecular markers may be useful for identifying morphological differences or other adaptive traits. The combined data set was the most useful in differentiating populations based on geography and found separation between midwestern and eastern upland populations. The results indicate that the combination of morphological and molecular markers may be useful in future applications such as genetic diversity studies, plant variety protection, cultivar identification, and/or identifying geographic origin.     

Taxonomy of Mechanitis (F.) (Lepidoptera: Nymphalidae) from the West Colombian Andes: an Integrative Approach

Species identification in the butterfly genus Mechanitis (F.) (Lepidoptera: Nymphalidae) becomes difficult when it is based only on wing color patterns, a common practice in butterfly taxonomy. Difficulties in Mechanitis taxonomy are related to the widespread mimicry and polymorphism among species belonging to this genus. Species recognition and inventories of Mechanitis genus in geographic areas as the Andean region of Colombia are of particular interest and the use of more than one character for taxonomic identification is desirable. In this study, we included morphological, ecological, and mitochondrial DNA data to identify the occurring species in this region. Species of Mechanitis were studied from ecological, morphological, and molecular perspectives considering host plant identification, oviposition behavior, and life cycles under laboratory conditions. Immature morphology, patterns of wing color, and genital structures of adults were also studied. The genetic barcoding region of the cytochrome oxidase I mitochondrial gene was sequenced and used to verify the limits between species previously defined by the other characters and to validate its usefulness for species delimitation in this particular genus. The integrative approach combining independent datasets successfully allowed species identification as compared to the approach based on a single dataset. Three well-differentiated species were found in the studied region, Mechanitis menapis (Hewitson), Mechanitis polymnia (Linnaeus), and Mechanitis lysimnia (Fabricius). New valuable characters that could improve taxonomic identification in this genus are considered.     

Genetic diversity in an African plantain core collection using AFLP and RAPD markers

Fifteen AFLP primer pairs (EcoRI+3 and MseI+3) and 60 10-mer RAPD primers were used to detect polymorphisms and assess genetic relationships in a sample of 25 plantains from diverse parts of Western and Central Africa. The discriminatory power of the AFLP technique was greater than that of the RAPD technique, since the former produced markers with greater polymorphic information content (PIC) than the latter. Hence, AFLP analysis appeared to be a more-powerful approach for identifying genetic differences among plantain accessions. In this regard, significant genetic diversity within the plantains was shown by the unweighted pair-group method of arithmetic averages (UPGMA) and the multidimensional principal coordinate (PCO) analyses. The AFLP-derived clusters indicated closer relationships between similar inflorescence types than the RAPD-derived clusters. A small group of cultivars from Cameroon were separated from the bulk of other plantains, suggesting that Cameroon may harbour accessions with useful or rare genes for widening the genetic base of breeding populations derived from the plantains. A greater effort should be directed at collecting and characterizing plantain cultivars from Cameroon.