scholarly journals Species Delimitation of the Eisenia nordenskioldi Complex (Oligochaeta, Lumbricidae) Using Transcriptomic Data

2020 ◽  
Vol 11 ◽  
Author(s):  
Sergei V. Shekhovtsov ◽  
Aleksandra A. Shipova ◽  
Tatiana V. Poluboyarova ◽  
Gennady V. Vasiliev ◽  
Elena V. Golovanova ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Coi Gene ◽  
Southeastern Part ◽  
Genetic Lineages ◽  
Transcriptomic Data ◽  
Its Phylogeny ◽  
Eisenia Nordenskioldi ◽  
Very High ◽  
Large Distribution ◽  
High Diversity

Eisenia nordenskioldi (Eisen, 1879) is the only autochthonous Siberian earthworm with a large distribution that ranges from tundra to steppe and broadleaved forests. This species has a very high morphological, ecological, karyological, and genetic diversity, so it was proposed that E. nordenskioldi should be split into several species. However, the phylogeny of the complex was unclear due to the low resolution of the methods used and the high diversity that should have been taken into account. We investigated this question by (1) studying the diversity of the COI gene of E. nordenskioldi throughout its range and (2) sequencing transcriptomes of different genetic lineages to infer its phylogeny. We found that E. nordenskioldi is monophyletic and is split into two clades. The first one includes the pigmented genetic lineages widespread in the northern and western parts of the distribution, and the second one originating from the southern and southeastern part of the species' range and representing both pigmented and non-pigmented forms. We propose to split the E. nordenskioldi complex into two species, E. nordenskioldi and Eisenia sp. 1 (aff. E. nordenskioldi), corresponding to these two clades. The currently recognized non-pigmented subspecies E. n. pallida will be abolished as a polyphyletic and thus a non-natural taxon, while Eisenia sp. 1 will be expanded to include several lineages earlier recognized as E. n. nordenskioldi and E. n. pallida.

scholarly journals Molecular Analysis Reveals a High Diversity of Anopheline Mosquitoes in Yanomami Lands and the Pantanal Region of Brazil

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1995
Author(s):  
Teresa Fernandes Silva-do-Nascimento ◽  
Jordi Sánchez-Ribas ◽  
Tatiane M. P. Oliveira ◽  
Brian Patrick Bourke ◽  
Joseli Oliveira-Ferreira ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Indigenous Communities ◽  
Coi Gene ◽  
Single Linkage ◽  
Operational Taxonomic Units ◽  
As Species ◽  
Species Groups ◽  
Gene Data ◽  
Anopheline Mosquitoes ◽  
High Diversity

Identifying the species of the subfamily Anophelinae that are Plasmodium vectors is important to vector and malaria control. Despite the increase in cases, vector mosquitoes remain poorly known in Brazilian indigenous communities. This study explores Anophelinae mosquito diversity in the following areas: (1) a Yanomami reserve in the northwestern Amazon Brazil biome and (2) the Pantanal biome in southwestern Brazil. This is carried out by analyzing cytochrome c oxidase (COI) gene data using Refined Single Linkage (RESL), Assemble Species by Automatic Partitioning (ASAP), and tree-based multi-rate Poisson tree processes (mPTP) as species delimitation approaches. A total of 216 specimens collected from the Yanomami and Pantanal regions were sequenced and combined with 547 reference sequences for species delimitation analyses. The mPTP analysis for all sequences resulted in the delimitation of 45 species groups, while the ASAP analysis provided the partition of 48 groups. RESL analysis resulted in 63 operational taxonomic units (OTUs). This study expands our scant knowledge of anopheline species in the Yanomami and Pantanal regions. At least 18 species of Anophelinae mosquitoes were found in these study areas. Additional studies are now required to determine the species that transmit Plasmodium spp. in these regions.

scholarly journals Investigating the Parasitoid Community Associated with the Invasive Mealybug Phenacoccus solenopsis in Southern China

Insects ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 290
Author(s):  
Hua-Yan Chen ◽  
Hong-Liang Li ◽  
Hong Pang ◽  
Chao-Dong Zhu ◽  
Yan-Zhou Zhang
Keyword(s):  
Biological Control ◽  
Species Delimitation ◽  
Southern China ◽  
Insect Pest ◽  
Integrated Approach ◽  
Molecular Data ◽  
Coi Gene ◽  
Morphological Examination ◽  
Accurate Identification ◽  
Phenacoccus Solenopsis

The cotton mealybug Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae), is an emerging invasive insect pest in China. Hymenopteran parasitoids are the key organisms for suppressing populations of P. solenopsis in the field, and therefore could be used as biological agents. Accurate identification of the associated parasitoids is the critical step to assess their potential role in biological control. In this study, we facilitated the identification of the parasitoid composition of P. solenopsis using an integrated approach of species delimitation, combining morphology with molecular data. Eighteen Hymenoptera parasitoid species belonging to 11 genera of four families are recognized based on morphological examination and molecular species delimitation of the mitochondrial cytochrome c oxidase 1 (COI) gene and the 28S rDNA using the automatic barcode gap discovery (ABGD) and the Bayesian Poisson tree processes model (bPTP). Among these species, eight species are primary parasitoids with Aenasius arizonensis (Girault) (Hymenoptera: Encyrtidae) being the dominant taxon, while the other 10 species are probably hyperparasitoids, with a prevalence of Cheiloneurus nankingensis Li & Xu (Hymenoptera: Encyrtidae). These results indicate that parasitoid wasps associated with P. solenopsis from China are diverse and the integrated taxonomic approach applied in this study could enhance the accurate identification of these parasitoids that should be assessed in future biological control programs.

scholarly journals Genetic Structure of Field Populations of Begomoviruses and of Their Vector Bemisia tabaci in Pakistan

2003 ◽  
Vol 93 (11) ◽  
pp. 1422-1429 ◽  
Author(s):  
Belén Simón ◽  
José Luis Cenis ◽  
Francisco Beitia ◽  
Saif Khalid ◽  
Ignacio M. Moreno ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Bemisia Tabaci ◽  
Random Amplified Polymorphic Dna ◽  
Southeast Asian ◽  
Coi Gene ◽  
Cotton Leaf ◽  
Reading Frame ◽  
Genetic Lineages ◽  
The Family ◽  
Whitefly Vector

The genetic structure of field populations of begomoviruses and their whitefly vector Bemisia tabaci in Pakistan was analyzed. Begomoviruses and B. tabaci populations were sampled from different crops and weeds in different locations in Punjab and Sindh provinces, in areas where cotton leaf curl disease (CLCuD) occurs or does not occur. Phylogenetic analysis based on nucleotide sequences of the intergenic region in the viral DNA-A provided evidence of two clusters of isolates: viruses isolated from species in the family Malvaceae, and viruses isolated from other dicotyledon families. Analysis of the capsid protein (CP) open reading frame grouped isolates into three geographical clusters, corresponding to isolates collected in Punjab, Sindh, or both provinces. Random amplified polymorphic DNA analyses of the B. tabaci population showed that intrapopulation diversity was high at both the local and regional scales. Sequence analysis of the mitocondrial cytochrome oxydase I (mt COI) gene showed that the B. tabaci population was structured into at least three genetic lineages corresponding to the previously described Indian, Southeast Asian, and Mediterranean-African clades. The Indian clade was present only in Punjab, the Mediterranean-African only in Sindh, and the Southeast Asian in both provinces. B. tabaci haplotypes of the Indian clade were found only in the Punjab, where CLCuD occurs. Hence, the geographical distribution of virus and vector genotypes may be correlated, because similar phylogenetic relationships were detected for the viral CP and the vector mt COI genes.

scholarly journals Fish Identification based on Partial Fragments of The Mitochondrial COI Subunit I Gene

2021 ◽  
Vol 322 ◽  
pp. 01038
Author(s):  
Tuah N. M. Wulandari
Keyword(s):  
Phylogenetic Tree ◽  
Coi Gene ◽  
Local Alignment ◽  
Mtdna Sequences ◽  
Mitochondrial Coi ◽  
Search Tool ◽  
Very High ◽  
I Gene

The mtDNA sequences revealed that several of the fish studied were Hampala macrolepidota and Barbonymus gonionotus. The objective of this research was to learn the pattern of COI gene in mtDNA and establish a phylogenetic tree. Basic Local Alignment Search Tool-nucleotide (BLASTn) confirmed that Barbonymus gonionotus froma the Ranau Lake, South Sumatera has 100% matching ranges to the species from Memberamo River (Indonesia), India, Bangladesh, Thailand (Mae Khlong), Indo-Myanmar, and Malaysia_1. The lowest closeness (98.76%) is related to species from Thailand (Lower Ing). The Blast investigation appears us that the level of familiarity was very high, it is coming to 98-100% in Barbonymus gonionotus. Hampala macrolepidota had 100% matching ranges to the species from Indonesia (SouthaSumatera_1) and Vietnam. They had 99.05%-99.84% closeness from Malaysia_1,2&3, Indonesia (South Sumatera_2&3, Java and Bali_1,2&3).

Evolution and Expansion of Flowering Plants

2000 ◽  
Vol 6 ◽  
pp. 209-232 ◽  
Author(s):  
Scott L. Wing
Keyword(s):  
Large Scale ◽  
Terrestrial Ecosystems ◽  
Taxonomic Diversity ◽  
Climatic Conditions ◽  
Flowering Plants ◽  
Terrestrial Vegetation ◽  
Earth History ◽  
Very High ◽  
High Diversity ◽  
Environmental Disruption

Flowering plants are a classic example of a group arising late in Earth history and yet achieving very high diversity, abundance, and ecological and morphological variety in a great array of environments and climatic conditions on all continents. Thus, the success of flowering plants raises basic questions about how new lineages become inserted into existing terrestrial ecosystems. To what degree did flowering plants replace older lineages competitively, and to what extent did their expansion depend on large-scale environmental disruption or extinction of older groups? Is the higher taxonomic diversity of flowering plants a consequence of higher rates of speciation, lower rates of extinction, or both? Have flowering plants expanded the total area and range of habitats occupied by terrestrial vegetation? What were the effects of the diversification and spread of flowering plants on the structure of habitats and the types of resources available to terrestrial heterotrophs?

Multi-instar descriptions of cave dwelling Erythraeidae (Trombidiformes: Parasitengona) employing an integrative approach

Zootaxa ◽  
2019 ◽  
Vol 4717 (1) ◽  
pp. 137-184 ◽  
Author(s):  
SAMUEL GEREMIAS DOS SANTOS COSTA ◽  
HANS KLOMPEN ◽  
LEOPOLDO FERREIRA DE OLIVEIRA BERNARDI ◽  
LUCIANA CARDOSO GONÇALVES ◽  
DANTE BATISTA RIBEIRO ◽  
...  
Keyword(s):  
Life Cycle ◽  
Cytochrome Oxidase ◽  
Molecular Analysis ◽  
Species Delimitation ◽  
Morphological Changes ◽  
Molecular Data ◽  
Coi Gene ◽  
Integrative Approach ◽  
Larval Instars ◽  
Individual Host

The life cycle of Parasitengona includes major morphological changes precluding an instar association based only on the morphology. This makes rearing and/or molecular data necessary to associate the heteromorphic instars. Most of the described species are known from either post larval instars or larva. Following a previous study on Palearctic Erythraeidae, in the present study the instar association was made through an integrative approach including rearing trials and molecular analysis of the cytochrome oxidase I (COI) gene with the Bayesian Generalized Mixed Yule Coalescent (bGMYC) algorithm for species delimitation. Two new cave dwelling Erythraeidae (Trombidiformes: Parasitengona) species are described Lasioerythraeus jessicae sp. nov. and Leptus sidorchukae sp. nov. including all active instars. Additionally, a complete description of the previously unknown adults of Charletonia rocciai Treat & Flechtmann, 1979 is provided with notes on the larva and deutonymph. We also demonstrate experimentally that Ch. rocciai larvae are not attached to the same individual host during the entire feeding stage. We discuss the presence of troglomorphisms in Le. sidorchukae sp. nov.; and the distribution of the species. 

scholarly journals Effects of genetic polymorphism in Pit1, GH, GHR and KCN3 on milk yield and body weight of Khuzestan (Iran) water buffaloes

2019 ◽  
Vol 32 (2) ◽  
pp. 107-116 ◽  
Author(s):  
Meysam Ahmadzadeh ◽  
Farzad Rashidi ◽  
Hamed Amirpour Najafabadi ◽  
Amir Jaferian ◽  
Shahin Eghbalsaied
Keyword(s):  
Body Weight ◽  
Milk Production ◽  
Genetic Information ◽  
Water Buffaloes ◽  
Khuzestan Province ◽  
Strategic Plans ◽  
Ghr Gene ◽  
Pcr Rflp ◽  
Very High ◽  
High Diversity

Background: Genetic information is necessary to devise strategic plans aimed to improve the genetic merit of buffalos. Objective: To assess the effect of genetic polymorphisms in GH, Pit-1, GHR, GHRHR, and KCN3 genes on milk production and body weight of Khuzestan water buffaloes. Methods: Blood samples were collected from 60 buffaloes from the Khuzestan province, Iran. Using the PCR-RFLP technique, the amplified and digested fragments of GH/AluI, GHR/AluI, GHRHR/ HaeIII, Pit1/HinfI, and KCN3/HindIII were genotyped. Results: All animals were monomorphic for GHRHR. The frequency of mutant alleles for GH, GHR, KCN3, and Pit1 was 47.5, 74.2, 49.2, and 51.7%, respectively. There were significant differences (p<0.0001) in the genotypic frequencies of GH, GHR, and Pit1 between high and low milk-yielding buffaloes. The GH (p=0.0002), GHR (p<0.0001) and Pit1 (p<0.0001) polymorphisms also had significant effects on body weight. Sequencing results revealed the presence of C496A, G495A, G498A and C1501T SNPs in the GH, and G1702T in the GHR gene of Khuzestan buffalos. Conclusion: This study highlights the importance of GH, GHR, and Pit1 on milk production and body weight of Khuzestan buffaloes. The results suggest that devising an integrated breeding plan in Khuzestan water buffalos can considerably benefit from the very high diversity in candidate genes.Keywords: animal breeding, casein, genetic variation, growth hormone, milk production, SNP. ResumenAntecedentes: La información genética es necesaria para diseñar planes estratégicos con el objeto de mejorar el mérito genético de los búfalos. Objetivo: Evaluar el efecto de los polimorfismos genéticos en los genes GH, Pit-1, GHR, GHRHR y KCN3 sobre la producción láctea y peso corporal de búfalos de agua de la provincia de Juzestán, Iran. Métodos: Se recolectaron 60 muestras de sangre de búfalos de la provincia de Juzestán, en Irán. Los fragmentos amplificados y digeridos de GH/AluI, GHR/AluI, GHRHR/HaeIII, Pit1/HinfI y KCN3/HindIII fueron clasificados genotípicamente, utilizando la técnica PCR-RFLP. Resultados: Todos los animales fueron monomórficos para el gen GHRHR. La frecuencia alélica de alelos mutantes para los genes GH, GHR, KCN3 y Pit1 fue 47,5, 74,2, 49,2 y 51,7%, respectivamente. Se encontraron diferencias significativas (p<0,0001) en las frecuencias genotípicas de GH, GHR y Pit1 entre búfalos de alta y baja producción. El efecto del polimorfismo GH (p=0,0002), GHR (p<0,0001) y Pit1 (p<0,0001) también fue significativo para peso corporal. Los resultados de la secuenciación revelaron la presencia de SNPs C496A, G495A, G498A y C1501T en GH, y G1702T en el gen GHR. Conclusiones: Este estudio resalta la importancia de los genes GH, GHR y Pit1 sobre la producción de leche y el peso corporal de búfalos de Juzestán. Los resultados sugieren que la elaboración de un plan de cruzamiento integrado en búfalos de agua de Juzestán puede beneficiarse considerablemente de la gran diversidad de genes candidatos.Palabras clave: caseína, hormona del crecimiento, producción de leche, reproducción animal, SNP, variación genética. ResumoAntecedentes: Determinação informações genéticas é o passo crítico para elaborar planos estratégicos com o objetivo de melhorar o mérito genético dos búfalos. Objetivo: Avaliar o efeito de polimorfismos genéticos nos genes GH, Pit-1, GHR, GHRHR e KCN3 na produção de leite e no peso corporal dos búfalos de água do Cuzistão, Irã. Métodos: Amostras de sangue foram coletadas de 60 búfalos da província de Cuzistão, no Irã. Utilizando a técnica PCR-RFLP, os fragmentos amplificados e digeridos de GH/AluI, GHR/AluI, GHRHR/HaeIII, Pit1/HinfI e KCN3/HindIII foram genotipados. Resultados: Todos os animais eram monomórficos para o gene GHRHR. A freqüência alélica de alelos mutantes para os genes GH, GHR, KCN3 e Pit1 foi 47,5, 74,2, 49,2 e 51,7%, respectivamente. Uma diferença significativa (p<0,0001) foi encontrada nas freqüências genotípicas de os genes GH, GHR e Pit1 entre búfalos de alta e baixa produção. O efeito do polimorfismo GH (p=0,0002), GHR (p<0,0001) e Pit1 (p<0,0001) também foi significativo para o peso corporal. Os resultados da sequenciação revelaram a presença de SNPs C496A, G495A, G498A e C1501T no GH, e G1702T no gene GHR dos buffalos do Cuzistão. Conclusões: Este estudo destacou a importância da GH, GHR e Pit1 na produção de leite e no peso corporal de buffalos do Cuzistão. Os resultados sugerem que a elaboração de um plano de melhoramiento genético integrado em búfalos de água do Cuzistão pode beneficiar consideravelmente da grande diversidade de genes candidatos.Palavras-chave: caseína, hormônio do crescimento, produção de leite, reprodução animal, SNP, variação genética.

Increasing our knowledge of Brazilian bamboos: two new species of Chusquea subg. Rettbergia (Bambusoideae, Poaceae)

Phytotaxa ◽  
2014 ◽  
Vol 161 (3) ◽  
pp. 201 ◽  
Author(s):  
Aline Costa Mota ◽  
REYJANE PATRÍCIA DE OLIVEIRA ◽  
LYNN G. CLARK
Keyword(s):  
New Species ◽  
Atlantic Forest ◽  
Conservation Status ◽  
Minas Gerais ◽  
Foliage Leaf ◽  
Ecological Aspects ◽  
Two New Species ◽  
Woody Bamboos ◽  
Very High ◽  
High Diversity

Brazil includes a very high diversity of bamboos, but this diversity is far from completely known. We increase the list of Brazilian woody bamboos by describing two new species of Chusquea, which belong to subgenus Rettbergia. Chusquea ciliatifolia sp. nov. differs from other species of this subgenus by its mottled culms, distinctly ciliate margins of the foliage leaf blades and pilose synflorescences; and C. mirabilis sp. nov. by the presence of branches with sericeous girdles. Both C. ciliatifolia and C. mirabilis occur exclusively in the Atlantic Forest, from the states of Bahia and Minas Gerais, known only from five and three populations, respectively. Comments on morphology, taxonomic relationships, ecological aspects, and conservation status of these new species are provided.

Integrating DNA barcodes and morphology for species delimitation in theCorynoneuragroup (Diptera: Chironomidae: Orthocladiinae)

2013 ◽  
Vol 104 (1) ◽  
pp. 65-78 ◽  
Author(s):  
F.L. Silva ◽  
S. Wiedenbrug
Keyword(s):  
Dna Markers ◽  
Species Delimitation ◽  
Pupal Stage ◽  
Coi Gene ◽  
Morphological Divergence ◽  
Dna Barcodes ◽  
Morphological Criteria ◽  
Species Groups ◽  
Excellent Tool ◽  
Eleven Species

AbstractIn this study, we use DNA barcodes for species delimitation to solve taxonomic conflicts in 86 specimens of 14 species belonging to theCorynoneuragroup (Diptera: Chironomidae: Orthocladiinae), from the Atlantic Forest, Brazil. Molecular analysis of cytochrome c-oxidase subunit I (COI) gene sequences supported 14 cohesive species groups, of which two similar groups were subsequently associated with morphological variation at the pupal stage. Eleven species previously described based on morphological criteria were linked to DNA markers. Furthermore, there is the possibility that there may be cryptic species within theCorynoneuragroup, since one group of species presented internal grouping, although no morphological divergence was observed. Our results support DNA-barcoding as an excellent tool for species delimitation in groups where taxonomy by means of morphology is difficult or even impossible.

On the evolution of plant secondary chemical diversity

1991 ◽  
Vol 333 (1267) ◽  
pp. 273-280 ◽  
Keyword(s):  
Biological Activity ◽  
Plant Defence ◽  
Secondary Compounds ◽  
Chemical Diversity ◽  
High Biological Activity ◽  
Active Compounds ◽  
Low Probability ◽  
Secondary Chemical ◽  
Very High ◽  
High Diversity

A common-sense evolutionary scenario predicts that well-defended plants should have a moderate diversity of secondary compounds with high biological activity. We contend that plants actually contain a very high diversity of mostly inactive secondary compounds. These patterns result because compounds arising via mutation have an inherently low probability of possessing any biological activity. Only those plants that make a lot of compounds will be well defended because only high diversity confers a reasonable probability of producing active compounds. Inactive compounds are retained, not eliminated, because they increase the probability of producing new active compounds. Plants should therefore have predictable metabolic traits maximizing secondary chemical diversity while minimizing cost. Our hypothesis has important implications to the study of the evolution of plant defence.

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