scholarly journals Towards the unravelling of the slug <i>A. ater–A. rufus</i> complex (Gastropoda Arionidae): new genetic approaches

Web Ecology ◽  
2018 ◽  
Vol 18 (2) ◽  
pp. 115-119 ◽  
Author(s):  
María L. Peláez ◽  
Antonio G. Valdecasas ◽  
Daniel Martinez ◽  
Jose L. Horreo
Keyword(s):  
Pest Control ◽  
Phylogenetic Relationships ◽  
Genetic Distances ◽  
Mitochondrial Genes ◽  
Wild Plants ◽  
Species Status ◽  
Conservation Policies ◽  
Specific Species ◽  
Arion Rufus

Abstract. The genus Arion includes several slug species, some of which are considered to be a pest to both cultivated and wild flora. Within this genus, the Arion ater complex comprises two different morphological forms: Arion rufus and A. ater, but there is no consensus about their species status. Their phylogenetic relationships have been recently solved, both of them belonging to different phylogenetic clades, but their species status is still unclear (as different clades are not always different species). For this reason, the aim of this study was to precisely identify these species status by employing the up-to-date multi-rate Poisson tree processes (mPTP) methodology as well as the classic methodology of genetic distances, both of which have three different mitochondrial genes. Results confirmed that both A. ater and A. rufus are independent evolutionary clades, and the high genetic distances between them (K2P distances ranged between 9.1 and 16.4 %, depending on genes) together with mPTP analyses, supported the idea that the clades correspond to different species. Results will be useful for the classification of these specific species as well as for developing proper pest control methodologies and conservation policies in both cultivated and wild plants.

Genetic evidence supports Sylvilagus mansuetus (Lagomorpha: Leporidae) as a subspecies of S. bachmani

Zootaxa ◽  
2016 ◽  
Vol 4196 (2) ◽  
pp. 289
Author(s):  
SERGIO TICUL ÁLVAREZ-CASTAÑEDA ◽  
CONSUELO LORENZO
Keyword(s):  
Phylogenetic Relationships ◽  
Morphological Traits ◽  
Nuclear Gene ◽  
Sister Group ◽  
Genetic Distances ◽  
Mitochondrial Genes ◽  
The Other ◽  
Cyt B ◽  
San Jose ◽  
Allopatric Distribution

Since Sylvilagus bachmani (Lagomorpha: Leporidae) from the Baja California Peninsula and S. mansuetus from San Jose Island, Mexico, display an allopatric distribution and are closely related, their taxonomy is unclear. The phylogenetic relationships among specimens of both species were evaluated using two mitochondrial genes (Cyt b, COI) and the beta-fibrinogen nuclear gene intron 7 (β-fib I7). The genetic analyses revealed that S. mansuetus was included within the S. bachmani clade as the sister-group of S. b. cerrosensis. The genetic distances among S. b. cerrosensis and mansuetus were relatively low (1.3% with Cyt b), similar to intraspecific distances observed within other species of Sylvilagus. We consider mansuetus to be a subspecies of S. bachmani, and the morphological traits previously used to differentiate the two taxa should be used to distinguish S. b. mansuetus from the other subspecies of S. bachmani. 

Intra- or inter-specific difference in genotypes of Caligus elongatus Nordmann 1832?

2008 ◽  
Vol 53 (1) ◽  
Author(s):  
Øivind Øines ◽  
Thomas Schram
Keyword(s):  
Species Differences ◽  
Morphological Characters ◽  
Genetic Distances ◽  
Mitochondrial Genes ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Specific Difference ◽  
Species Status ◽  
Lower Range ◽  
Crustacean Species

AbstractTwo mitochondrial and one nuclear genetic marker were used to study the phylogenetic position of the two reported CO1-genotypes of Caligus elongatus in a group of closely related caligid parasites. Molecular analysis of the two mitochondrial genes (CO1 and 16S), indicate genetic distances of the two C. elongatus genotypes in the lower range of distances previously reported between other crustacean species, but higher than comparable reported within-species differences. Analyses of nuclear 18S sequences indicate no detectable differentiation between these genotypes, but may be due to expected differences in the resolution of these genetic markers. Investigation of two of three selected morphological characters reveals phenotypes supporting the division based on the molecular division. The species status on the two C. elongatus genotypes cannot be drawn conclusively, although the molecular and morphological data presented here suggests the presence of sibling species.

scholarly journals Mitochondrial DNA Phylogeny of Babblers (Timaliidae)

The Auk ◽  
2003 ◽  
Vol 120 (1) ◽  
pp. 35-54
Author(s):  
Alice Cibois
Keyword(s):  
Mitochondrial Dna ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Molecular Data ◽  
Mitochondrial Genes ◽  
Dna Phylogeny ◽  
Traditional Classification ◽  
Phylogenetic Hypotheses

Abstract The systematics of the babblers (Timaliidae) and related members of the Old World insectivorous passerines have been particularly difficult. To clarify our understanding of this group, phylogenetic relationships were constructed using sequences of three mitochondrial genes (cytochrome b, rRNA 12S and 16S). The results indicated that several species traditionally placed among babblers, the shrike babblers (Pteruthius) and the Gray-chested Thrush Babbler (Kakamega poliothorax), are not related to the Timaliidae, but belong to other passerine groups. Furthermore, the phylogenetic hypotheses inferred from molecular data suggest that the babblers assemblage includes two other oscine taxa traditionally considered to be distantly related, Sylvia (Sylviidae) and Zosterops (Zosteropidae). The polyphyly of several babbler genera is discussed, with particular attention to the laughingthrushes (genera Garrulax and Babax) for which the phylogeny is compared to previous hypotheses of relationships. Results from different tests under the maximum-parsimony and maximum-likelihood criteria indicate the rejection of the hypothesis of monophyly for the laughingthrushes group. Thus, the molecular phylogeny challenges the traditional classification of the Timaliidae.

scholarly journals Phylogenetic relationships and subgeneric classification of European Ephedrus species (Hymenoptera, Braconidae, Aphidiinae)

ZooKeys ◽  
2019 ◽  
Vol 878 ◽  
pp. 1-22 ◽  
Author(s):  
Korana Kocić ◽  
Andjeljko Petrović ◽  
Jelisaveta Čkrkić ◽  
Milana Mitrović ◽  
Željko Tomanović
Keyword(s):  
Molecular Markers ◽  
Phylogenetic Relationships ◽  
Taxonomic Status ◽  
Species Group ◽  
Genetic Distances ◽  
Junior Synonym ◽  
Valid Species ◽  
Morphological Studies ◽  
Species Groups

In this study two molecular markers were used to establish taxonomic status and phylogenetic relationships of Ephedrus subgenera and species distributed in Europe. Fifteen of the nineteen currently known species have been analysed, representing three subgenera: Breviephedrus Gärdenfors, 1986, Lysephedrus Starý, 1958 and Ephedrus Haliday, 1833. The results of analysis of COI and EF1α molecular markers and morphological studies did not support this classification. Three clades separated by the highest genetic distances reported for the subfamily Aphidiinae on intrageneric level. Ephedrus brevis is separated from persicae and plagiator species groups with genetic distances of 19.6 % and 16.3 % respectively, while the distance between persicae and plagiator groups was 20.7 %. These results lead to the conclusion that the traditional subgeneric classification of Ephedrus needs revision. Species from persicae species group are raised to subgenus level as Fovephedrus Chen, 1986 and Lysephedrussyn. nov. is assigned as a junior synonym of subgenus Ephedrus. Key for identification of Ephedrus subgenera is provided. Ephedrus hyadaphidis Kocić &amp; Tomanović sp. nov. is described and several species are confirmed as valid species for the first time. Furthermore, two species are synonymised: E. dysaphidissyn. nov. as a junior synonym of E. cerasicola and E. blattnyisyn. nov. as a junior synonym of E. plagiator.

OPTIMALISASI PERAN PEMDA DALAM MENGATASI KENDALA PELAKSANAAN KONSERVASI KEANEKARAGAMAN HAYATI DI DAERAH (STUDI KASUS PROVINSI BENGKULU)

2020 ◽  
Vol 15 (2) ◽  
Author(s):  
Antung Deddy Radiansyah
Keyword(s):  
Local Government ◽  
Biodiversity Conservation ◽  
Local Governments ◽  
Central Government ◽  
Wild Plants ◽  
Regional Government ◽  
Conservation Areas ◽  
Conservation Area ◽  
Conservation Policies

Gaps in biodiversity conservation management within the Conservation Area that are the responsibility of the central government and outside the Conservation Areas or as the Essential Ecosystems Area (EEA) which are the authority of the Regional Government, have caused various spatial conflicts between wildlife /wild plants and land management activities. Several obstacles faced by the Local Government to conduct its authority to manage (EEA), caused the number and area of EEA determined by the Local Government to be still low. At present only 703,000 ha are determined from the 67 million ha indicated by EEA. This study aims to overview biodiversity conservation policies by local governments and company perceptions in implementing conservation policies and formulate strategies for optimizing the role of Local Governments. From the results of this study, there has not been found any legal umbrella for the implementation of Law number 23/ 2014 related to the conservation of important ecosystems in the regions. This regulatory vacuum leaves the local government in a dilemma for continuing various conservation programs. By using a SWOT to the internal strategic environment and external stratetegic environment of the Environment and Forestry Service, Bengkulu Province , as well as using an analysis of company perceptions of the conservation policies regulatary , this study has been formulated a “survival strategy” through collaboration between the Central Government, Local Governments and the Private Sector to optimize the role of Local Government’s to establish EEA in the regions.Keywords: Management gaps, Essential Ecosystems Area (EEA), Conservation Areas, SWOT analysis and perception analysis

scholarly journals Phylogenetic relationships among accessions in Citrus and related genera based on the insertion polymorphism of the CIRE1 retrotransposon

2020 ◽  
Vol 5 (1) ◽  
pp. 243-251
Author(s):  
Akira Horibata ◽  
Tsuneo Kato
Keyword(s):  
Phylogenetic Relationships ◽  
Sweet Orange ◽  
Point Of View ◽  
Insertion Polymorphism ◽  
Navel Orange ◽  
Citrus Germplasm ◽  
Outgroup Species ◽  
Blood Orange

AbstractA total of 145 accessions of the genus Citrus and related genera, maintained in the Conservation Garden for Citrus Germplasm at the Experimental Farm of Kindai University, Yuasa, Wakayama, Japan, were examined for their phylogenetic relationships. The present classification was conducted using an inter-retrotransposon amplified polymorphism (IRAP) method based on the insertion polymorphism of a retrotransposon, CIRE1, identified in C. sinensis. The objective of this study was to evaluate the applicability of the IRAP method for citrus classification. The constructed dendrogram showed that the 145 accessions and two outgroup species were successfully classified into five major clades. A large number of C. sinensis accessions were divided into three traditional groups, navel orange, sweet orange, and blood orange, almost corresponding to the sub-clades in the dendrogram. Several other accessions belonging to the same species, and also many hybrid cultivars from crossbreeding, were localized into the respective sub-clades or near positions in the dendrogram. Several unclassified accessions could also be located in the dendrogram, suggesting novel relationships with other accessions. It was concluded that the IRAP method based on CIRE1 insertion polymorphism was suitable for the classification of citrus from a molecular point of view.

scholarly journals Novel Comprehensive Molecular and Ecological Study Introducing Coastal Mud Shrimp (Solenocera Crassicornis) Recorded at the Gulf of Suez, Egypt

2020 ◽  
Vol 9 (1) ◽  
pp. 9
Author(s):  
Eman M. Abbas ◽  
Fawzia S. Ali ◽  
Mohammed G. Desouky ◽  
Mohamed Ashour ◽  
Ahmed El-Shafei ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Phylogenetic Relationships ◽  
Genetic Distances ◽  
Larval Rearing ◽  
Gulf Of Suez ◽  
Commercial Catch ◽  
Monthly Total ◽  
Wet Weight ◽  
Commercially Important ◽  
The Relationship

Solenocera crassicornis is a commercially important shrimp of the Solenoceridae family. The current study investigated the morphology, molecular identification, phylogenetic relationships, and population dynamics of S. crassicornis in Egypt. Samples were collected monthly (total, 1722; male = 40.19%, wet weight, 0.89–10.77 g; female = 59.81%, wet weight, 1.55–19.24 g) from Al-Attaka commercial catch in the Gulf of Suez in the Red Sea. Two barcode markers, 18S rRNA and cytochrome c oxidase subunit I (COI), were used for molecular identification. COI partial sequences were used to construct the phylogenetic relationships among different species of genus Solenocera and to infer the origin of the studied Solenocera crassicornis. The applied molecular markers successfully identified the studied species to the species level. The genetic distances among S. crassicornis sequences from different countries revealed the Indo-West Pacific origin of S. crassicornis. The relationship between total length (TL) and total weight (TW) was TW = 0.035TL2.275 and r2 = 0.805 for males and TW = 0.007TL3.036 and r2 = 0.883 for females, indicating that females were heavier than males. Despite its social and economic relevance in the area, information on the hatching, larval rearing, and farming of S. crassicornis is scarce and requires future studies under Egyptian conditions.

Species delimitation in the leaf beetle genus Macroplea (Coleoptera, Chrysomelidae) based on mitochondrial DNA, and phylogeographic considerations

2006 ◽  
Vol 37 (4) ◽  
pp. 467-479 ◽  
Author(s):  
Gregor Kölsch ◽  
Bo Vest Pedersen ◽  
Olof Biström
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Species Delimitation ◽  
Mitochondrial Gene ◽  
Leaf Beetle ◽  
Genetic Distances ◽  
Amino Acid Substitutions ◽  
Species Status ◽  
Leaf Beetles ◽  
Gene Coding

AbstractThe genus Macroplea Samouelle, 1819 is a group of highly specialized aquatic leaf beetles occurring in the Palaearctic. Since the members of this genus are morphologically very similar, we addressed the question of species identification and delimitation by analysing the second half of the mitochondrial gene coding for the cytochrome oxidase I (COI) subunit. Species limits are inferred from the multimodal frequency distribution of genetic distances between specimens: low genetic distances within a species are clearly set apart from distances between species. The species status of the hitherto controversial species M. japana (Jacoby, 1885) is confirmed. The pattern of nucleotide and amino acid substitutions is discussed in the light of functional domains of the COI molecule. Although the data are preliminary, the results provide new data on the distribution of the species. Together with the phylogenetic analysis they allow for a discussion of the phylogeography of the genus.

scholarly journals Sequence Analysis and Classification of Apparent Recombinant Begomoviruses Infecting Tomato in the Nile and Mediterranean Basins

2005 ◽  
Vol 95 (5) ◽  
pp. 549-555 ◽  
Author(s):  
C. M. Fauquet ◽  
S. Sawyer ◽  
A. M. Idris ◽  
J. K. Brown
Keyword(s):  
Sequence Analysis ◽  
Phylogenetic Relationships ◽  
Tomato Yellow Leaf ◽  
Viral Diseases ◽  
Yellow Leaf ◽  
Recombination Hotspots ◽  
Molecular Biodiversity ◽  
Leaf Curl Virus ◽  
Leaf Curl

Numerous whitefly-transmitted viral diseases of tomato have emerged in countries around the Nile and Mediterranean Basins the last 20 years. These diseases are caused by monopartite geminiviruses (family Gemini viridae) belonging to the genus Begomovirus that probably resulted from numerous recombination events. The molecular biodiversity of these viruses was investigated to better appreciate the role and importance of recombination and to better clarify the phylogenetic relationships and classification of these viruses. The analysis partitioned the tomato-infecting begomoviruses from this region into two major clades, Tomato yellow leaf curl virus and Tomato yellow leaf curl Sardinia virus. Phylogenetic and pairwise analyses together with an evaluation for gene conversion were performed from which taxonomic classification and virus biodiversity conclusions were drawn. Six recombination hotspots and three homogeneous zones within the genome were identified among the tomatoinfecting isolates and species examined here, suggesting that the recombination events identified were not random occurrences.

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