Phenetic Analysis Research Articles

Describing intermediate host snails in Kapatagan, Lanao del Norte, Philippines: a phenetic analysis

Describing intermediate host snails in Kapatagan, Lanao del Norte, Philippines: a phenetic analysis

Vertebrate endemism in south-eastern Africa numerically redefines a biodiversity hotspot.

We use numerical methods to explore patterns of vertebrate endemism in south-eastern Africa, refining the boundaries of the intuitively-defined Maputaland-Pondoland-Albany biodiversity hotspot, also proposing a zoogeographic regionalisation. An incidence matrix of 300 vertebrate species endemic to south-eastern Africa sensu lato in 37 operational geographic units were used in (a) phenetic cluster analysis (PCA) using the algorithm of unweighted pair-group method with arithmetic averages (phenetic approach), and (b) parsimony analysis of endemicity (PAE; parsimony approach), in order to numerically evaluate the bioregional delimitations. The analyses provide a valid biogeographical entity 37% larger than the Maputaland-Pondoland-Albany hotspot, but substantially (131%) higher in vertebrate endemicity viz. the Greater Maputaland-Pondoland-Albany (GMPA) region of vertebrate endemism. South-east Africa is recognised as a dominion in the global zoogeographical area hierarchy, with subordinate units including the GMPA province. Various spatially-based measures of endemism were mapped for vertebrate species restricted to the dominion, i.e. endemic to south-eastern Africa sensu stricto. Areas and centres of endemism detected respectively from PAE and PCA, within the south-east Africa dominion also support the refined boundary of the GMPA region of endemism, which provides a better spatial conservation priority compared to the Maputaland-Pondoland-Albany hotspot. Reptiles and amphibians are found to be the main drivers of the overall pattern of endemism, while the pattern in freshwater fish is the most distinctive. Our analyses also indicate a good congruence of the centres of endemism across different terrestrial vertebrate taxa.

Genetic and morphological evidence supports the hybrid status of Adenanthos cunninghamii (now Adenanthos × cunninghamii)

Hybridisation is common among plants and is considered to be an important process in evolution. However, there is much debate as to the role of hybridisation in conservation, particularly whether species of hybrid origin should be protected. In general, conservation policy allows for the protection of hybrids and hybrid progeny if they are shown to be taxonomically distinct, stable and capable of self-perpetuation, and naturally produced. The rare species Adenanthos cunninghamii was suspected to be a hybrid between putative parents, Adenanthos sericeus and Adenanthos cuneatus, as it only occurs where these species co-occur and it displays intermediate and variable morphology. Genetic analysis of A. cunninghamii and the two putative parent species was consistent with this species being a hybrid between A. sericeus and A. cuneatus. Direct analysis of diagnostic loci and phenetic analysis indicated that A. cunninghamii was not genetically uniform and was genetically intermediate between the putative parents. A. cunninghamii is not a distinguishable taxon, morphologically or genetically, and does not produce offspring with morphology within the taxonomic description of the species, thus the species does not satisfy the criteria for protection of hybrids and listing as a rare species in Western Australia.

Spikemoss flora (Selaginella) in Mindanao Island, the Philippines: species composition and phenetic analysis of morphological variations

The genus Selaginella, commonly referred to as spikemosses, is an important component of the Philippines’ lycophytes diversity. Mountain ecosystems in Mindanao island hold diverse species of lycophytes, however the morpho-taxonomy diversity of this group is poorly documented there. The study aimed to determine Selaginella species richness, distribution and phenetic relationships based on morphological characteristics in Mindanao island. Specimens of Selaginella were collected in Mt. Apo, Kidapawan City; Mt. Hamiguitan, Davao Oriental; Mt. Kiamo, Mt. Kitanglad, Mt. Musuan and Mt. Limbawon in Bukidnon; Mt. Timpoong, Camiguin; and Mt. Malindang, Misamis Occidental. The 24 Selaginella species were collected and subjected to numerical phenetic analysis using the PC-ORD program. A total of 11 morphological characters and 44 character states were used in the analyses. Of the 24 species, seven are Philippine endemics, four are potential new species and two species are widely distributed in the areas studied. Results of the phenetic analysis showed four major clusters.

A new species of

We investigated the limits of Lepidosperma congestum R.Br. and a putative new species of Lepidosperma Labill. from Victoria and South Australia. Phenetic analyses (flexible UPGMA agglomerative hierarchical fusion and semi-strong hybrid multidimensional scaling) were conducted on a dataset derived from morphological characters scored from herbarium material. The results of our analyses supported the recognition of a new species, which we describe here as Lepidosperma hispidulum G.T.Plunkett, J.J.Bruhl & K.L.Wilson. Our results clarified the differences among L. congestum, L. laeve R.Br. and L. hispidulum, the first two of which have often been misidentified. We also discuss the distribution, habitat and conservation status of L. hispidulum.

Phenetic and Phylogenetic Analysis of Kocuria palustris and Kocuria rhizophila Strains isolated from Healthy and Thalassemia Persons

Phenetic and Phylogenetic Analysis of Kocuria palustris and Kocuria rhizophila Strains isolated from Healthy and Thalassemia Persons

Phenotypic identification and numerical taxonomy of pigmented bacteria isolated from marine and freshwater aquatic at Yogyakarta, Indonesia

<p class="Abstract"><span class="fontstyle01">Numerical phenetic analysis was used to compare phenotypic data obtained from 6 isolates of pigmented bacteria strains taken from marine and river aquatic. Each strain was tested for 120 characters, analysed using the simple matching (SSM) and Jaccard (SJ) similarity indices with unweighted pair-group method with arithmetic mean (UPGMA) clustering method. All of the strains classified into two clusters, cluster A as marine pigmented bacteria and cluster B as river pigmented bacteria. Differences were observed between the dendrograms derived from the SSM and SJ. Presence of bacteriochlorophyll–a (Bchl–a), carotenoids, as well as other biochemical tests of three marine pigmented strains were in match with key characters of the genera<i> </i></span><span class="fontstyle01" style="font-style: italic;">Roseobacter, Roseateles</span><span class="fontstyle01" style="">, and </span><span class="fontstyle01" style="font-style: italic;">Erythrobacter</span><span class="fontstyle01">. Three of river pigmented strains were identified as </span><span class="fontstyle01" style="font-style: italic;">Xanthobacter</span><span class="fontstyle01" style="font-style: italic;">, </span><span class="fontstyle01" style="font-style: italic;">Flavobacterium</span><span class="fontstyle01" style=""><i>, </i>and </span><span class="fontstyle01" style="font-style: italic;">Pseudomonas</span><span class="fontstyle01"><i>.</i> It was proved that the marine and river pigmented bacteria isolates showed a relative phenotypically distance. It was clearly seen that the phenetic approach was a necessary tool to delimitate and identify the pigmented bacteria from different habitats.</span><o:p></o:p></p>

Schoenus rupicola: a narrowly endemic species distinguished from S. melanostachys (Cyperaceae, Schoeneae) in eastern Australia

Widespread, common species are of limited value for regional biogeographic studies and of least concern for conservation and land management. In contrast, narrow endemics may be informative for such studies and are usually of high conservation priority. A new species is separated from the widespread species Schoenus melanostachys on the basis of phenetic analysis of morphological data, and integrating evidence from culm anatomy, culm and fruit ornamentation, and corroborated by ecological differentiation. Schoenus rupicola Musili & J.J.Bruhl is found on acid volcanics of south-eastern Queensland and north-eastern New South Wales, adding yet another narrow endemic to the suite of species that characterises the McPherson Range and associated igneous outcrops.

Phenetic and cladistic studies help clarify species assemblages in Passiflora section Dysosmia (Passifloraceae)

One of the most enigmatic and unusual groups in the passionflower genus, Passiflora section Dysosmia (Passifloraceae), stands out as a group that is notoriously taxonomically complicated. Phenetic and cladistic analyses of Dysosmia were carried out with representatives from all 21 species currently recognized in the section, in order to delineate morphological groups above the species level. The study was based mainly on vegetative morphological characters and included principal coordinates, non-metric multidimensional scaling, cluster, and cladistic analyses. Results from each analysis reveals that three major species assemblages exist within Dysosmia, corresponding largely to vegetative pubescence and fruit color. The results presented here set the stage for future systematic and phylogenetic studies in Passiflora sect. Dysosmia.

Morphological affinities of Homo naledi with other Plio-Pleistocene hominins: a phenetic approach.

Recent fossil material found in Dinaledi Chamber, South Africa, was initially described as a new species of genus Homo, namely Homo naledi. The original study of this new material has pointed to a close proximity with Homo erectus. More recent investigations have, to some extent, confirmed this assignment. Here we present a phenetic analysis based on dentocranial metric variables through Principal Components Analysis and Cluster Analysis based on these fossils and other Plio-Pleistocene hominins. Our results concur that the Dinaledi fossil hominins pertain to genus Homo. However, in our case, their nearest neighbors are Homo habilis and Australopithecus sediba. We suggest that Homo naledi is in fact a South African version of Homo habilis, and not a new species. This can also be applied to Australopithecus sediba.

Identification among morphologically similar Argyreia (Convolvulaceae) based on leaf anatomy and phenetic analyses

BackgroundThe genus Argyreia Lour. is one of the species-rich Asian genera in the family Convolvulaceae. Several species complexes were recognized in which taxon delimitation was imprecise, especially when examining herbarium materials without fully developed open flowers. The main goal of this study is to investigate and describe leaf anatomy for some morphologically similar Argyreia using epidermal peeling, leaf and petiole transverse sections, and scanning electron microscopy. Phenetic analyses including cluster analysis and principal component analysis were used to investigate the similarity of these morpho-types.ResultsAnatomical differences observed between the morpho-types include epidermal cell walls and the trichome types on the leaf epidermis. Additional differences in the leaf and petiole transverse sections include the epidermal cell shape of the adaxial leaf blade, the leaf margins, and the petiole transverse sectional outline. The phenogram from cluster analysis using the UPGMA method represented four groups with an R value of 0.87. Moreover, the important quantitative and qualitative leaf anatomical traits of the four groups were confirmed by the principal component analysis of the first two components. The results from phenetic analyses confirmed the anatomical differentiation between the morpho-types.ConclusionsLeaf anatomical features regarded as particularly informative for morpho-type differentiation can be used to supplement macro morphological identification.

Comparison and delimitation of the Monopyle bilsaensis ined. complex within Ecuador

KYLEE RADABAUGH, Dept. of Science & Mathematics, Glenville State College, Glenville, WV 26351, and JEREMY KEENE, Dept. of Science & Mathematics, Glenville State College, Glenville, WV 26351. Comparison and delimitation of the Monopyle bilsaensis ined. complex within Ecuador. Monopyle is a genus of herbaceous plants in the family Gesneriaceae. The genus is distributed from Central into northern South America. Recent studies for a revision of the genus have revealed many species complexes that require more in-depth study. Monopyle bilsaensis ined. a new species discovered in northern Ecuador near the Bilsa Biological Station is part of a species complex that has been difficult to delimit. It appears that the species is hybridizing with two other nearby species Monopyle ecuadorensis and Monopyle communis ined. The extensive hybridization between the species has made morphological separation very tedious. In order to separate these species, I am currently using a molecular phylogenetic approach that utilizes both nuclear and chloroplast gene regions to compare the species. The objectives of this research are to study the morphological and molecular characteristics of Monopyle found in Ecuador with special emphasis given to the species complex. A comparison of all the taxa will provide insight into the overall evolution of the group in the area. Future studies of this complex will include a phenetic analysis of taxonomically useful characters to confirm morphological differences in the group.

Weaving through a cryptic species: Comparing the Neotropical ants Camponotus senex and Camponotus textor (Hymenoptera: Formicidae)

Camponotus senex (Fr. Smith 1858) and Camponotus textor Forel, 1899 are commonly confused species in the New World tropics. We provide morphological characteristics based on the larvae and adults, behavioural differences, together with evidence from molecular markers (cuticular hydrocarbon profiles, venom differences, nuclear ribosomal ITS-1, and mtDNA COI sequence comparisons) to separate the two species, demonstrating they are not immediately closely related. In conclusion we suggest new reliable morphological characters which can benefit from deeper phenetic analysis, and support the contextual usefulness of non-morphological tools in resolving sibling ant species.

Taxonomic Studies Using Multivariate Analysis of Eriobotrya Based on Morphological Traits

A phenetic analysis was obtained using numerical taxonomy involving 27 accessories composed of species and varieties of Eriobotrya Lindl. and two related species, Photinia serrulata Lindl., and Rhapiolepis indica Lindl. Principal component analysis (PCA) was used to separate 53 morphological traits. Leaf morphology was essential for the classification of Eriobotrya. Clustering was consistent with traditional taxonomy. Eriobotrya was distinctly separate from its related genera, and when the similarity coefficient was 0.55, the Eriobotrya accessions could be divided into five groups as follows: Group 1: species with small leaf, included E. angustissima Hook. f., E. henryi Nakai, and E. seguinii Cardot ex Guillaumin; Group 2: Species with mid-size and large leaf included E. japonica Lindl., E. malipoensis K.C. Kuan, E. serrata J.E. Vidal, and E. stipularis Craib; Group 3: Species with large leaf distributed in tropical and south subtropical areas, E. elliptica Lindl., E. ellliptica f. peniolata Hook., and E. elliptica var. petelottii Vidal; Group 4: Species with tomentose leaves included E. prinoides Rehder & E.H. Wilson, E.× daduheensis H.Z. Zhang ex W.B. Liao, Q. Fan & M.Y. Ding, E. prinoides var. laotica Vidal, E. salwinensis Hand.-Mass., and E. tengyuehensis W.W. Smith; Group 5: All the remaining species including E. bengalensis Hook. f. bengalensis, E. bengalensis (Roxb.) Hook. f. forma angustifolia (Card.) Vidal E. cavaleriei Rehder, E deflexa Nakai, E. deflexa f. buisanensis Nakia, E. deflexa f. koshunensis, E. fragrans Champ. ex Benth., E. kwangsiensis, E. obovata, and E. potlanei Vidal. Our results were in total agreement with the traditional taxonomy of Eriobotrya classification and provide a foundation for the classification and genetic improvement of loquat germplasm.

Embryo and seedling morphology of some Trigonella L. species (Fabaceae) and their taxonomic importance

The current study aims to evaluate the significance of embryo and seedling characters in the taxonomy of genus Trigonella L. Embryo and seedling morphology of 33 accessions of the genus belonging to 9 sections were examined using stereo-microscopy. Observation showed considerable variations among the studied taxa. The different types of embryos and seedlings were illustrated, compared and analyzed based on morphological characters such as cotyledons shape and colour, radicle shape and position, prophyl leaf shape and margin and their taxonomic importance were discussed. Our phenetic analysis partially supported the sectional classification of section Falcatulae and Foenum-graecum based on existing morphological data. However, section Callicerates seemed to be more closely related to section Cylindricae and not to section Verae, that is not consistent with the phylogenetic analysis and morphological features. Thus, we can say that embryo and seedlings characters are taxonomically important but cannot be used alone for sectional classification of Trigonella.

Cuticular n-alkane in leaves of seven Neotropical species of the family Lecythidaceae: a contribution to chemotaxonomy

ABSTRACT Biosynthesized from very long-chain fatty acid wax precursors, n-alkanes make a valuable contribution to the taxonomy of plants. The alkane components of foliar epicuticles of seven Neotropical species of Lecythidaceae were investigated: Bertholletia excelsa, Cariniana legalis, Couroupita guianensis, Eschweilera alvimii, Eschweilera ovata, Gustavia augusta and Lecythis pisonis. Specimens were collected in the metropolitan area of Recife, Pernambuco, and their n-alkane fractions were analyzed by gas chromatography. The chemical relationships among the species were then evaluated using cophenetic correlation and UPGMA. Among the seven species, a total of 15 n-alkanes, with 21-35 carbon atoms, were identified and formed a consistent group of B. excelsa, C. guianensis, E. ovata, G. augusta, and L. pisonis with n-C31. The greatest similarities were found between B. excelsa and L. pisonis, and between C. guianensis and G. augusta. Nevertheless, a phenetic analysis based on a larger number of species is needed to better understand the chemotaxonomic value of epicuticular n-alkanes within the Lecythidaceae.

KEANEKARAGAMAN KULTIVAR SEMANGKA [<em>Citrullus lanatus</em> (THUNB.) MATSUM. & NAKAI] DI SENTRA SEMANGKA NUSAWUNGU CILACAP

Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is a plant of Cucurbitaceae family which is include in an annual plant. In Indonesia, watermelon has diversity in its cultivar as can be seen from the stem, leaf, flower, and fruit morphology. This research is aimed to find out the diversity and the similarity relationship of watermelon cultivar in Nusawungu, Cilacap. A survey method was used in this research by taking the samples with a random sampling technique (purposive sampling). This research parameter consisted of stem, leaf, flower, and fruit morphology of each watermelon cultivar. Data of watermelon cultivar morphology were analyzed descriptively and then analyzed based on the similarity relationship with UPGMA method (Unweighted Pair Group Method with Arithmetic Mean) using the MEGA 5.05 software. The result of this research showed that there were five watermelon cultivars namely C. lanatus ‘Farmers Giant’, C. lanatus ‘Nina’, C. lanatus ‘Black Orange’, C. lanatus ‘Torpedo’, and C. lanatus ‘Bintang’. There were two groups of watermelons based on phenetic analysis namely group I consisting of C. lanatus ‘Torpedo’, C. lanatus ‘Black Orange’, and C. lanatus ‘Nina’ cultivars, group II consisting of C. lanatus ‘Bintang’ and C. lanatus ‘Farmers Giant’. The closest similarity was between C. lanatus ‘Farmers Giant’ and C. lanatus ‘Bintang’ cultivars with the dissimilarity index of 0,516. While the most distantly related was between C. lanatus ‘Nina’ and C. lanatus ‘Farmers Giant’ cultivars with the dissimilarity index of 2,338.

Taxonomic revision of the genus Tetraglochin (Rosaceae, Rosoideae) and morphometric analysis of its species

Tetraglochin is a small genus distributed along the Andes from Perú to southern Argentina and central Chile, belonging to the family Rosaceae. Systematic studies in Tetraglochin are scarce, and circumscription of some members of this genus is controversial. In order to evaluate the degree of morphological differentiation between the species of this genus, we performed morphometric analyses using multivariate methods (non parametric ANOVA, phenetic analysis and canonical discriminant analysis) including those specimens with intermediate characteristics between T. alata and T. ameghinoi. The phenogram obtained showed two principal clusters; this picture suggested a clear grouping of the specimens of T. alata, T. ameghinoi, T. aff. alata and T. andina. In the canonical discriminant analysis five groups were found and in general terms all individuals of T. alata, T. aff. alata and T. ameghinoi were grouped together. When multivariate analyses were applied almost all specimens could be correctly assigned to its species. However, specimens of T. alata, T. aff. alata and T. ameghinoi , were not well discriminated. Following recent phylogenetic results on the genus, and morphometric analyses perfomed herein for the first time, we present an updated taxonomic revision of Tetraglochin, based on exomorphological, vegetative and reproductive characters, including a key to identify species and varieties, their associated synonymy, full descriptions, geographical distribution and illustrations. As result, a new combination, T. alata var. ameghinoi is proposed, T. alata var. patagonica is reduced to synonymy of T. alata var. alata, and T. paucijugata and T. tragacantha are reduced to synonymy of T. cristata. Lectotypes for Margyricarpus acanthocarpus, Tetraglochin acanthocarpa var. lasiocarpa, var. dasycarpa, var. macropoda and var. lejocarpa are designated. One species, Tetraglochin buxifolia is excluded from the genus.

×Polascontria (Cactaceae), a nothogenus that represents the gene flow between Escontria and Polaskia

Hybridization represents an important mechanism in the diversification of Cactaceae where interspecific barriers are poorly developed. Putative hybrids with an intermediate phenotype between the columnar cacti Escontria chiotilla and Polaskia chichipe were observed in Oaxaca, Mexico. The putative hybrids grow sympatrically with their parents, sharing pollinators and overlapping flowering periods. On the basis of morphological, genetic and molecular studies, we show that a gene flow occurs between E. chiotilla and P. chichipe. Morphological and genetic similarities were used to carry out phenetic analyses, which allowed us to separate the two taxa and the potential hybrids, and cluster them into discrete groups with a high degree of consistency. We also generate artificial hybrids by hand-pollination crosses. These hybrids indicate that there are partial pre- and postzygotic barriers between E. chiotilla and P. chichipe. Backcrosses between parents and hybrids produced viable seeds, suggesting that there is a high potential of introgression with both parents. Taken together, we propose that hybrids observed in the field are the product of cross-pollination between E. chiotilla and P. chichipe. Thus, gene flow between both genera can explain why the genetic independence of these taxa has not kept them reproductively isolated. A complete description and illustrations of a new intergeneric hybrid are provided.

Taxonomic resolution of the Tetratheca hirsuta (Elaeocarpaceae) species complex using an integrative approach

The Tetratheca hirsuta Lindl. species complex from south-west Western Australia is one of the last unresolved complexes in this Australian endemic genus, and comprises the highly variable T. hirsuta, two rare, phrase-named taxa, and the closely allied T. hispidissima Steetz. An integrative approach, incorporating multivariate morphometric analysis and molecular phylogenetic and phenetic analyses of nrDNA (ETS) and cpDNA (ndhF–trnL, rpl16, trnS–trnG5ʹ2S), was used to investigate taxonomic boundaries within the complex. Morphological data showed clear divergence within the complex, and allowed several taxonomically uncertain individuals to be assigned. Phenetic and phylogenetic analyses of ETS showed substantial congruence with morphology, indicating that the groups recognised through morphometric analyses are also genetically divergent. By comparison, the chloroplast regions yielded incongruent gene trees, perhaps owing to incomplete lineage sorting, hybridisation or slow evolution of cpDNA. The present results support the recognition of the following four taxa: a morphologically and geographically expanded T. hispidissima, which is highly divergent from the remainder of the complex, and a closer grouping of T. hirsuta subsp. boonanarring Joyce & R.Butcher subsp. nov., T. hirsuta subsp. viminea (Lindl.) Joyce comb. et stat. nov. and T. hirsuta subsp. hirsuta.