Vegetation analysis of the subalpine beech forest on the upper forest line in the Julian Alps (NW Slovenia and NW Italy) and in the northern Dinaric Alps

Abstract Using hierarchical clustering with unweighted pair-group method with arithmetic mean (UPGMA) we arranged 603 phytosociological relevés of beech forests on the present upper forest line, mainly from the Julian Alps and the Trnovo Forest Plateau (we also included the relevés from the Karawanks and the Kamnik Alps), into 32 clusters. Based on their analysis and comparison with previously described similar (alti)montane-subalpine beech communities we classified most of the relevés into the association Polysticho lonchitis-Fagetum and its new subassociations ericetosum carneae, cardaminetosum trifoliae, luzuletosum niveae, luzuletosum luzuloidis, calamagrostietosum variae, allietosum victorialis, adoxetosum moschatellinae, stellarietosum nemorum and several new variants. The altitude of the studied stands is predominantly 1400 to 1550 m (the upper line is at 1660 m); they occur at all aspects, frequently on steep and very steep slopes, mainly on limestone and dolomite limestone, the predominant soil type is rendzina. These stands are species rich (on average 61 species per relevé, altogether more than 500 vascular plants) and have many species in common with the stands of associations Rhododendro hirsuti-Fagetum and Rhodothamno-Laricetum.

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Phytosociological analysis of European larch forests in the Southeastern Alps

Hacquetia ◽

10.2478/hacq-2018-0004 ◽

2018 ◽

Vol 17 (2) ◽

pp. 247-519

Author(s):

I. Dakskobler ◽

A. Seliškar ◽

A. Rozman

Keyword(s):

Beech Forest ◽

Forest Types ◽

Altitudinal Belt ◽

Surface Areas ◽

Average Linkage ◽

Larch Forests ◽

Julian Alps ◽

Phytosociological Relevés ◽

Forest Line ◽

Stable Development

Abstract Using the (unweighted) average linkage clustering (UPGMA) method we classified 458 phytosociological relevés of Larix decidua forests in the Southeastern Alps into 25 clusters. Based on their analysis we described the following new subassociations: Rhodothamno-Laricetum deciduae geetosum rivalis, sorbetosum chamaemespili, piceetosum abietis, adoxetosum moschatellinae, cystopteridetosum fragilis, cyclaminetosum purpurascentis, dryadetosum octopetalae and sorbetosum ariae. The selected method proved adequate in identifying the differences between larch stands on potential subalpine spruce and beech sites, and larch forests on the upper forest line, as well as the differences between initial larch stages on the upper forest line and more stable development stages on better developed soils on promontories and ledges above the upper beech forest line. Larch forests occur mainly in the altitudinal belt between (1,500) 1,600 and 1,800 (1,900) m, on shady aspects and slopes that are steeper than 30°. They are some of the best preserved forest types in the Southeastern Alps, on smaller surface areas (Macesnje above the Beli Potok valley in the Julian Alps) even virgin forests, and their role as biotopes is exceptional.

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Zbiorowiska namułkowe z klasy Isoëto-Nanojuncetea Br.-Bl. et Tx. 1943 w Polsce [Occurrence of the Isoëto-Nanojuncetea-class communities in Poland]

Monographiae Botanicae ◽

10.5586/mb.1997.001 ◽

2014 ◽

Vol 80 ◽

pp. 1-59 ◽

Cited By ~ 3

Author(s):

Agnieszka Popiela

Keyword(s):

Western Europe ◽

Group Method ◽

Numerical Classification ◽

Character Species ◽

Pair Group ◽

Open Questions ◽

Phytosociological Relevés ◽

Complete Catalogue ◽

Made In

The Isoëto-Nanojuncetea-class includes short-lived and ephemerical communities occurring on temporarily flooded places in Western, Southern and Central Europe and Northern Africa. Results of the numerical classification of 739 phytosociological releves of the communities occurring in Poland are presented and discussed. Ali the releves were made in accordance with the principles of the BRAUN-BLANQUET school of syntaxonomy. The calculations were performed using NCLAS program of the SYN-TAX IV package. The JACCARD formuła and the unweighted pair-group method, using arithmetic averages (UPGMA) were applied. There is a strong habitat and floristic differentation of the communities of the Isoëto-Nanojuncetea-class occurring in Poland. The results of the numerical classification indicate that, the distuinguished communities belong to two alliances: the Radiolion linoidis (Rivas Goday 1961) Pietsch 1965 (for associations occurring on synanthropic localities like stubble fields) and the Elatini-Eleocharition ovatae Pietsch 1965 (for communities growing on bottoms of dried ponds and exposed river or lakę banks). The distinguished communities arę phytosociologically characterized on basis of 223 selected releves. These arę: Spergulario-Illecebretum verticillati, Ranunculo-Myosuretum minimi, Centaurium pulchellum-Pottia truncata-commumiy, Heleocharetum ovatae, Cyperetum flavescentis and Cyperus fuscus-Limosella aquatica-commumiy. The study focused on: (1) attempting to solve the problem of phytosociological classification for the communities occurring in Poland, (2) preparing a complete catalogue of them and (3) giving the full list of character species (also among bryophytes) of distinguished syntaxa. It has led to finding out the relation between the communities occurring in Poland and the associations of Western Europe. The problem of the naturality of certain distinguished associations was discussed. The paper gives also some open questions demanding further studies and some suggestions of methods to be applied.

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Phytosociological study of submontane genistoid scrub communities from the Southeastern Balkans

Acta Botanica Croatica ◽

10.37427/botcro-2020-017 ◽

2020 ◽

Vol 79 (2) ◽

pp. 170-184

Author(s):

Georgi Kunev ◽

Rossen Tzonev ◽

Ioannis Tsiripidis ◽

Kalina Pachedjieva

Keyword(s):

Correspondence Analysis ◽

Detrended Correspondence Analysis ◽

Group Method ◽

Ecological Structure ◽

New Associations ◽

Habitat Area ◽

Pair Group ◽

Phytosociological Relevés ◽

Unweighted Pair Group Method ◽

Phytosociological Study

Genista lydia Boiss. is an endemic Balkan-Anatolian species which forms rare communities in the territory of south Bulgaria and northeast Greece. They are spread exclusively on acidic, siliceous substrates. This study presents new data on their distribution, floristic and ecological structure and phytosociological affinities. The research is based on 156 phytosociological relevés. Unweighted pair–group method with arithmetic averages (UPGMA) was employed and a detrended correspondence analysis (DCA) was performed prior to the syntaxonomical decision. Three new associations and the new alliance Genistion lydiae have been described and classified within the order Lavandulo stoechadis-Hypericetalia olympici Mucina in Mucina et al. 2016 of the class Cisto-Lavanduletea stoechadis Br.-Bl. in Br.-Bl. et al. 1940. The study has also emphazised the potential threats concerning a decline of the habitat area and proposed some conservation measures.

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Genetic Diversity Among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

Sustainability ◽

10.3390/su13126830 ◽

2021 ◽

Vol 13 (12) ◽

pp. 6830

Author(s):

Murat Guney ◽

Salih Kafkas ◽

Hakan Keles ◽

Mozhgan Zarifikhosroshahi ◽

Muhammet Ali Gundesli ◽

...

Keyword(s):

Genetic Diversity ◽

Plant Genetic Resources ◽

Juglans Regia ◽

Genetic Distances ◽

Mean Value ◽

Central Anatolia ◽

Group Method ◽

Arithmetic Average ◽

Pair Group ◽

Principal Coordinates

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

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Genome-Wide Identification and Development of LTR Retrotransposon-Based Molecular Markers for the Melilotus Genus

Plants ◽

10.3390/plants10050890 ◽

2021 ◽

Vol 10 (5) ◽

pp. 890

Author(s):

Zifeng Ouyang ◽

Yimeng Wang ◽

Tiantian Ma ◽

Gisele Kanzana ◽

Fan Wu ◽

...

Keyword(s):

Group Method ◽

Ltr Retrotransposon ◽

Ltr Retrotransposons ◽

Important Data ◽

Breeding Programs ◽

Upgma Dendrogram ◽

Pair Group ◽

Medicinal Value ◽

Genome Wide ◽

Melilotus Albus

Melilotus is an important genus of legumes with industrial and medicinal value, partly due to the production of coumarin. To explore the genetic diversity and population structure of Melilotus, 40 accessions were analyzed using long terminal repeat (LTR) retrotransposon-based markers. A total of 585,894,349 bp of LTR retrotransposon sequences, accounting for 55.28% of the Melilotus genome, were identified using bioinformatics tools. A total of 181,040 LTR retrotransposons were identified and classified as Gypsy, Copia, or another type. A total of 350 pairs of primers were designed for assessing polymorphisms in 15 Melilotus albus accessions. Overall, 47 polymorphic primer pairs were screened for their availability and transferability in 18 Melilotus species. All the primer pairs were transferable, and 292 alleles were detected at 47 LTR retrotransposon loci. The average polymorphism information content (PIC) value was 0.66, which indicated that these markers were highly informative. Based on unweighted pair group method with arithmetic mean (UPGMA) dendrogram cluster analysis, the 18 Melilotus species were classified into three clusters. This study provides important data for future breeding programs and for implementing genetic improvements in the Melilotus genus.

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Genetic diversity in table grapes based on RAPD and microsatellite markers

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2011000900010 ◽

2011 ◽

Vol 46 (9) ◽

pp. 1035-1044 ◽

Cited By ~ 9

Author(s):

Patrícia Coelho de Souza Leão ◽

Sérgio Yoshimitsu Motoike

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Genetic Relationships ◽

Similarity Index ◽

Genetic Distances ◽

Table Grape ◽

Group Method ◽

Molecular Characteristics ◽

Table Grapes ◽

Pair Group

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.

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Molecular Diversity and Genetic Relatedness of Candida albicans Isolates from Birds in Hungary

Mycopathologia ◽

10.1007/s11046-021-00527-3 ◽

2021 ◽

Vol 186 (2) ◽

pp. 237-244

Author(s):

M. Domán ◽

L. Makrai ◽

Gy. Lengyel ◽

R. Kovács ◽

L. Majoros ◽

...

Keyword(s):

Candida Albicans ◽

Molecular Diversity ◽

Genetic Relatedness ◽

Group Method ◽

Pair Group ◽

Degree Of Separation ◽

Avian Origin ◽

Species Specific ◽

Sequence Types ◽

Unweighted Pair Group Method

AbstractThe molecular epidemiology of Candida albicans infections in animals has been rarely studied. In this study, multilocus sequence typing was used to characterise the genetic diversity and population structure of 24 avian origin C. albicans isolates collected from different birds with candidiasis and compared to human isolates. Fourteen diploid sequence types (DSTs) including six new DSTs were determined. Cluster analysis revealed that isolates grouped into 8 clades. Bird isolates mainly belonged to minor clades and Clade 15 with DST 172 was the most common (11 isolates; 45.8%). The remaining isolates were clustered into Clade 7 (5 isolates; 20.8%), Clade 10 (4 isolates; 16.6%), Clade 8 (2 isolates; 8.3%), Clade 4 (1 isolate; 4.2%) and Clade 16 (1 isolate; 4.2%). Unweighted pair group method with arithmetic averages (UPGMA) and eBURST analyses showed that the genetic construction of avian origin C. albicans population is fairly diverse. Although species-specific lineages were not found, some degree of separation in the evolution of bird and human strains could be observed.

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Null expectation of spatial correlograms under a stochastic process of genetic divergence with small sample sizes

Genetics and Molecular Biology ◽

10.1590/s1415-47572000000400007 ◽

2000 ◽

Vol 23 (4) ◽

pp. 739-743 ◽

Cited By ~ 1

Author(s):

Mariana Pires de Campos Telles ◽

José Alexandre Felizola Diniz-Filho

Keyword(s):

Stochastic Process ◽

Genetic Divergence ◽

Isolation By Distance ◽

Genetic Distances ◽

Small Sample ◽

Group Method ◽

Gene Frequencies ◽

Exponential Relationship ◽

Local Populations ◽

Pair Group

An Ornstein-Uhlenbeck process was used to simulate the exponential relationship between genetic divergence and geographic distances, as predicted by stochastic processes of population differentiation, such as isolation-by-distance, stepping-stone or coalescence models. These simulations were based only on the spatial coordinates of the local populations that defined a spatial unweighted pair-group method using arithmetic averages (UPGMA) link among them. The simulated gene frequency surfaces were then analyzed using spatial autocorrelation procedures and Nei's genetic distances, constructed with different numbers of variables (gene frequencies). Stochastic divergence in space produced strong spatial patterns at univariate and mutivariate levels. Using a relatively small number of local populations, the correlogram profiles varied considerably, with Manhattan distances greater than those defined by other simulation studies. This method allows one to establish a range of correlogram profiles under the same stochastic process of spatial divergence, thereby avoiding the use of unnecessary explanations of genetic divergence based on other microevolutionary processes.

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Genetic analysis of a heritage variety collection

Plant Genetic Resources ◽

10.1017/s1479262118000448 ◽

2018 ◽

Vol 17 (03) ◽

pp. 232-244 ◽

Cited By ~ 2

Author(s):

J. M. Preston ◽

B. V. Ford-Lloyd ◽

L. M. J. Smith ◽

R. Sherman ◽

N. Munro ◽

...

Keyword(s):

Genetic Analysis ◽

Group Method ◽

Niche Markets ◽

Principal Coordinates Analysis ◽

Pair Group ◽

Landrace Diversity ◽

Principal Coordinates ◽

Length Polymorphisms ◽

Seed Saving ◽

History Of

AbstractLandraces (including heritage varieties) are an important agrobiodiversity resource offering considerable value as a buffer against crop failures, as a crop for niche markets, and as a source of diversity for crop genetic improvement activities underpinning future food security. Home gardens are reservoirs of landrace diversity, but some of the accessions held in them are vulnerable or threatened with extinction. Those associated with seed saving networks have added security, for example, ca. 800 varieties are stored in the Heritage Seed Library (HSL) of Garden Organic, UK. In this study, Amplified Fragment Length Polymorphisms-based genetic analysis of accessions held in the HSL was used to (a) demonstrate the range of diversity in the collection, (b) characterize accessions to aid collection management and (c) promote broader use of the collection. In total, 171 accessions were included from six crops: Vicia faba L., Pisum sativum L., Daucus carota L., Cucumis sativus L., Lactuca sativa L. and Brassica oleracea L. var. acephala (DC.) Metzq. Average expected heterozygosity ranged from 0.18 to 0.28 in D. carota; 0.02–0.18 in P. sativum; 0.05–0.18 in L. sativa; 0.15–0.26 in B. oleracea var. acephala; 0.15–0.37 in C. sativus and 0.07–0.36 in V. faba. Genetic diversity and Fst values generally reflected the breeding system and cultivation history of the different crops. Comparisons of the diversity found in heritage varieties with that found in commercial varieties did not show a consistent pattern. Principal coordinates analysis and Unweighted Pair Group Method with Arithmetic Mean cluster analysis were used to identify four potential duplicate accession pairs.

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Optimal use of SSR markers for varietal identification of upland cotton

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2015000700007 ◽

2015 ◽

Vol 50 (7) ◽

pp. 571-581 ◽

Cited By ~ 1

Author(s):

Guilherme da Silva Pereira ◽

Ana Luíza Ramos Cazé ◽

Michelle Garcia da Silva ◽

Vanessa Cavalcante Almeida ◽

Fernanda Oliveira da Cunha Magalhães ◽

...

Keyword(s):

Genetic Distance ◽

Ssr Markers ◽

Polymorphic Information Content ◽

Group Method ◽

Discrimination Power ◽

Arithmetic Average ◽

Pair Group ◽

Varietal Identification ◽

The World ◽

The Mean

Abstract: The objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the varieties. Initially, 92 SSR markers were genotyped in 20 Brazilian cotton cultivars. Of this total, 38 loci were polymorphic, two of which were amplified by one primer pair; the mean number of alleles per locus was 2.2. The values of polymorphic information content (PIC) and discrimination power (DP) were, on average, 0.374 and 0.433, respectively. The mean genetic distance was 0.397 (minimum of 0.092 and maximum of 0.641). A panel of 96 varieties originating from different regions of the world was assessed by 21 polymorphic loci derived from 17 selected primer pairs. Among these varieties, the mean genetic distance was 0.387 (minimum of 0 and maximum of 0.786). The dendrograms generated by the unweighted pair group method with arithmetic average (UPGMA) did not reflect the regions of Brazil (20 genotypes) or around the world (96 genotypes), where the varieties or lines were selected. Bootstrap resampling shows that genotype identification is viable with 19 loci. The polymorphic markers evaluated are useful to perform varietal identification in a large panel of cotton varieties and may be applied in studies of the species diversity.

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