scholarly journals Wireworm (Coleoptera: Elateridae) genomic analysis reveals putative cryptic species, population structure, and adaptation to pest control

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Kimberly R. Andrews ◽  
Alida Gerritsen ◽  
Arash Rashed ◽  
David W. Crowder ◽  
Silvia I. Rondon ◽  
...  
Keyword(s):  
Population Structure ◽  
Cryptic Species ◽  
Control Strategies ◽  
Genomic Analysis ◽  
Morphological Characters ◽  
Preliminary Evidence ◽  
Agricultural Pests ◽  
Agricultural Field ◽  
Species Complexes ◽  
Species Population

AbstractThe larvae of click beetles (Coleoptera: Elateridae), known as “wireworms,” are agricultural pests that pose a substantial economic threat worldwide. We produced one of the first wireworm genome assemblies (Limonius californicus), and investigated population structure and phylogenetic relationships of three species (L. californicus, L. infuscatus, L. canus) across the northwest US and southwest Canada using genome-wide markers (RADseq) and genome skimming. We found two species (L. californicus and L. infuscatus) are comprised of multiple genetically distinct groups that diverged in the Pleistocene but have no known distinguishing morphological characters, and therefore could be considered cryptic species complexes. We also found within-species population structure across relatively short geographic distances. Genome scans for selection provided preliminary evidence for signatures of adaptation associated with different pesticide treatments in an agricultural field trial for L. canus. We demonstrate that genomic tools can be a strong asset in developing effective wireworm control strategies.

Resolution of three cryptic agricultural pests (Ceratitis fasciventris, C. anonae, C. rosa, Diptera: Tephritidae) using cuticular hydrocarbon profiling

2014 ◽  
Vol 104 (5) ◽  
pp. 631-638 ◽  
Author(s):  
L. Vaníčková ◽  
M. Virgilio ◽  
A. Tomčala ◽  
R. Břízová ◽  
S. Ekesi ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Species Identification ◽  
Cuticular Hydrocarbon ◽  
Fruit Fly ◽  
Agricultural Pests ◽  
Species Complexes ◽  
Cryptic Species Complex ◽  
Males And Females ◽  
Ceratitis Fasciventris ◽  
Tephritid Fruit Flies

AbstractDiscrimination of particular species within the species complexes of tephritid fruit flies is a very challenging task. In this fruit-fly family, several complexes of cryptic species have been reported, including the African cryptic species complex (FAR complex). Cuticular hydrocarbons (CHCs) appear to be an excellent tool for chemotaxonomical discrimination of these cryptic species. In the present study, CHC profiles have been used to discriminate among three important agricultural pests from the FAR complex, Ceratitis fasciventris, Ceratitis anonae and Ceratitis rosa. Hexane body surface extracts of mature males and females were analyzed by two-dimensional gas chromatography with mass spectrometric detection and differences in CHC profiles between species and sexes tested through multivariate statistics and compared with species identification by means of microsatellite markers. Quantitative as well as qualitative CHC profile differences between sexes and species are reported. The CHC profiles consisted of a mixture of linear, internally methyl-branched and mono-, di- and tri-unsaturated alkanes. Twelve compounds were pinpointed as potential chemotaxonomical markers. The present study shows that presence or absence of particular CHCs might be used in the chemical diagnosis of the FAR complex. Moreover, our results represent an important first step in the development of a useful chemotaxonomic tool for cryptic species identification of these important agricultural pests.

scholarly journals The genus Oligonychus Berlese (Acari, Prostigmata, Tetranychidae): taxonomic assessment and a key to subgenera, species groups, and subgroups

ZooKeys ◽  
2021 ◽  
Vol 1079 ◽  
pp. 89-127
Author(s):  
Hafiz Muhammad Saqib Mushtaq ◽  
Fahad Jaber Alatawi ◽  
Muhammad Kamran ◽  
Carlos Holger Wenzel Flechtmann
Keyword(s):  
Cryptic Species ◽  
Spider Mite ◽  
Morphological Characters ◽  
Species Complexes ◽  
As Species ◽  
Generic Character ◽  
Species Groups ◽  
Doubtful Species ◽  
Species Inquirendae ◽  
Mite Genus

A comprehensive taxonomic assessment of the most agriculturally important and highly diverse spider mite genus, Oligonychus Berlese (Acari: Tetranychidae) was performed. The sub-generic division, species groups, doubtful species, species complexes and the interpretation of a key generic character are discussed. Based on the orientation of the male aedeagus, only two subgenera, namely Oligonychus Berlese (aedeagus downturned) and Reckiella Tuttle & Baker (aedeagus upturned), are valid in the genus Oligonychus. The subgenera Homonychus Wainstein, Metatetranychoides Wainstein, and Wainsteiniella Tuttle & Baker are considered to be synonyms of the subgenus Oligonychus, whereas the subgenus Pritchardinychus Wainstein is proposed as a synonym of the subgenus Reckiella. Moreover, based on female morphological characters, four species groups (coffeae, exsiccator, iseilemae, and peruvianus) and 11 species subgroups (aceris, biharensis, coffeae, comptus, exsiccator, gossypii, iseilemae, peruvianus, pritchardi, smithi, and subnudus) are suggested in the subgenera Oligonychus and Reckiella. Fourteen Oligonychus species are proposed as species inquirendae, and potential cryptic species complexes in the genus Oligonychus are briefly highlighted. It is agreed that the clunal seta h1 is always absent, while the para-anal setae h2 and h3 are always present in the genus Oligonychus. A key to subgenera, species groups, and species subgroups of the genus Oligonychus is provided.

Comparative Analysis of Genetic and Morphological Variation within the Platanthera hyperborea Complex (Orchidaceae)

2020 ◽  
Vol 45 (4) ◽  
pp. 767-778
Author(s):  
Eranga Wettewa ◽  
Nick Bailey ◽  
Lisa E. Wallace
Keyword(s):  
North America ◽  
Diploid Species ◽  
Morphological Characters ◽  
Evolutionary Patterns ◽  
Founding Population ◽  
Multiple Origins ◽  
Geographic Structure ◽  
Species Complexes ◽  
Nuclear Its ◽  
Cryptic Taxa

Abstract—Species complexes present considerable problems for a working taxonomy due to the presence of intraspecific variation, hybridization, polyploidy, and phenotypic plasticity. Understanding evolutionary patterns using molecular markers can allow for a more thorough assessment of evolutionary lineages than traditional morphological markers. In this study, we evaluated genetic diversity and phylogenetic patterns among taxa of the Platanthera hyperborea (Orchidaceae) complex, which includes diploid (Platanthera aquilonis) and polyploid (Platanthera hyperborea, P. huronensis, and P. convallariifolia) taxa spanning North America, Greenland, Iceland, and Asia. We found that three floral morphological characters overlap among the polyploid taxa, but the diploid species has smaller flowers. DNA sequence variation in a plastid (rpL16 intron) and a nuclear (ITS) marker indicated that at least three diploid species have contributed to the genomes of the polyploid taxa, suggesting all are of allopolyploid origin. Platanthera convallariifolia is most like P. dilatata and P. stricta, whereas P. huronensis and P. hyperborea appear to have originated from crosses of P. dilatata and P. aquilonis. Platanthera huronensis, which is found across North America, has multiple origins and reciprocal maternal parentage from the diploid species. By contrast, P. hyperborea, restricted to Greenland and Iceland, appears to have originated from a small founding population of hybrids in which P. dilatata was the maternal parent. Geographic structure was found among polyploid forms in North America. The area of Manitoba, Canada appears to be a contact zone among geographically diverse forms from eastern and western North America. Given the geographic and genetic variation found, we recommend continued recognition of four green-flowered species within this complex, but caution that there may be additional cryptic taxa within North America.

scholarly journals Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Fehintola V. Ajogbasile ◽  
Adeyemi T. Kayode ◽  
Paul E. Oluniyi ◽  
Kazeem O. Akano ◽  
Jessica N. Uwanibe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Control Strategies ◽  
Population Diversity ◽  
Parasite Population ◽  
Nested Polymerase Chain Reaction ◽  
Public Health Burden ◽  
Genetic Diversity And Structure

Abstract Background Malaria remains a public health burden especially in Nigeria. To develop new malaria control and elimination strategies or refine existing ones, understanding parasite population diversity and transmission patterns is crucial. Methods In this study, characterization of the parasite diversity and structure of Plasmodium falciparum isolates from 633 dried blood spot samples in Nigeria was carried out using 12 microsatellite loci of P. falciparum. These microsatellite loci were amplified via semi-nested polymerase chain reaction (PCR) and fragments were analysed using population genetic tools. Results Estimates of parasite genetic diversity, such as mean number of different alleles (13.52), effective alleles (7.13), allelic richness (11.15) and expected heterozygosity (0.804), were high. Overall linkage disequilibrium was weak (0.006, P < 0.001). Parasite population structure was low (Fst: 0.008–0.105, AMOVA: 0.039). Conclusion The high level of parasite genetic diversity and low population structuring in this study suggests that parasite populations circulating in Nigeria are homogenous. However, higher resolution methods, such as the 24 SNP barcode and whole genome sequencing, may capture more specific parasite genetic signatures circulating in the country. The results obtained can be used as a baseline for parasite genetic diversity and structure, aiding in the formulation of appropriate therapeutic and control strategies in Nigeria.

scholarly journals Co-occurring cryptic species pose challenges for conservation: a case study of the African dwarf crocodile (Osteolaemusspp.) in Cameroon

Oryx ◽  
2014 ◽  
Vol 49 (4) ◽  
pp. 584-590 ◽  
Author(s):  
Nicole L. Smolensky
Keyword(s):  
Cryptic Species ◽  
Conservation Status ◽  
Taxonomic Revision ◽  
Single Species ◽  
Conservation Strategies ◽  
Encounter Rates ◽  
Distribution Maps ◽  
Species Complexes ◽  
Threatened Taxa ◽  
Population Structures

AbstractThe conservation status of threatened taxa may be obfuscated by the detection of cryptic species complexes, in both vertebrate and invertebrate species. African dwarf crocodiles (Osteolaemusspp.) are hunted throughout their range but their conservation status is unknown. Few population assessments have been carried out and there has been a taxonomic revision of the number of species in the genus. The similar morphologies ofOsteolaemus tetraspisandOsteolaemus osbornipose a challenge for conservation in Cameroon, where they are still managed as a single species. Nocturnal spotlight surveys were conducted in three regions during August–November 2010 and December 2011–February 2012 to provide population assessments ofO. tetraspisandO. osborniand raise awareness of the two species in Cameroon. The mean encounter rates ofO. tetraspisandO. osborniwere 1.02 ± SD 1.34 (65 individuals in 39 surveys) and 0.61 ± SD 0.38 (three in four surveys) crocodiles per km, respectively. TheO. tetraspispopulation comprised juveniles predominantly and had a male-biased sex ratio. The fewO. osbornidetected comprised both adults and juveniles. Both species are threatened in Cameroon, based on low encounter rates, young population structures and the threats of habitat loss and hunting pressure. This study provides distribution maps and serves as a baseline to quantify population trends and inform conservation strategies.

scholarly journals Genome-wide characterization of genetic diversity and population structure of Valeriana officinalis L.

2019 ◽  
Author(s):  
Maja Boczkowska ◽  
Katarzyna Bączek ◽  
Olga Kosakowska ◽  
Anna Rucińska ◽  
Wiesław Podyma ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Genomics ◽  
Natural Populations ◽  
Valeriana Officinalis ◽  
Wild Populations ◽  
Genetic Fingerprint ◽  
Genome Wide ◽  
Species Population ◽  
Outcrossing Species

Abstract Background: Valeriana officinalis L. is one of the most important medicinal plant with a mild sedative, nervine, antispasmodic and relaxant effect. Despite a substantial number of studies on this species, population genomics has not yet been analyzed. The main aim of this study was: characterization of genetic variation of natural populations of V. officinalis in Poland and comparison of variation of wild populations and the cultivated form using Next Generation Sequencing based DArTseq technique. We also would like to establish foundations for genetic monitoring of the species in the future and to develop genetic fingerprint profile for samples deposited in gene bank and in natural sites in order to assess the degree of their genetic integrity and population structure preservation in the future.Results: The major and also the most astounding result of our work is the low level of observed heterozygosity of individual plants from natural populations despite the fact that the species is widespread in the studied area. Inbreeding, in naturally outcrossing species such as valerian, decreases the reproductive success. The analysis of the population structure indicated the potential presence of metapopulation in a broad area of Poland and the formation of a distinct gene pool in Bieszczady Mountains. The results also indicate the presence of individuals of the cultivated form in natural populations in the region where the species is cultivated for the needs of the pharmaceutical industry and this could lead to structural and genetic imbalance in wild populations.Conclusions: The DArTseq technology can be applied effectively in genetic studies of V. officinalis. The genetic variability of wild populations is in fact significantly lower than assumed. Individuals from the cultivated population are found in the natural environment and their impact on wild populations should be monitored.

scholarly journals A review on the distribution, abundance, residency, survival and population structure of coastal bottlenose dolphins in Argentina

10.5597/00233 ◽  
2018 ◽  
Vol 12 (1-2) ◽  
pp. 2-16 ◽  
Author(s):  
Els Vermeulen ◽  
Ricardo Bastida ◽  
Leonardo G. Berninsone ◽  
Pablo Bordino ◽  
Mauricio Failla ◽  
...  
Keyword(s):  
Population Structure ◽  
Bottlenose Dolphins ◽  
Grey Literature ◽  
Southwest Atlantic ◽  
Sympatric Distribution ◽  
Present Information ◽  
Species Population ◽  
Region Data ◽  
Survival And Reproduction ◽  
Available Information

Although bottlenose dolphins Tursiops truncatus are among the most common delphinid species, global population trends remain poorly understood. To improve the knowledge of the species in the Southwest Atlantic Ocean, thispaper reviews all available data related to the distribution and occurrence, abundance, residency and ranging patterns, group size and composition, survival and reproduction and population structure of the coastal bottlenose dolphin in Argentina. Most information proved to be scattered in time and space. Based on the available data, total abundance of coastal bottlenose dolphins in Argentina appears to be low. Data show sightings decreased notably since the 1990s in the northern province of Buenos Aires and the province of Chubut, with the species having disappeared completely from the former region. Data also indicated that two genetically and morphologically distinct coastal populations occur in Argentinean coastal waters, with a sympatric distribution in the provinces of Río Negro and Chubut. One is an isolated ‘Evolutionary Signifcant Unit’ within the larger Southwest Atlantic, whereas the other population appears to be genetically related to the Southwest Atlantic offshore ecotype. In the absence of more substantial data, the present information is pertinent to our scientifc knowledge of the species in the country, collating all published information as well as information from grey literature and previously unpublished data. However, the available information appears to remain insufcient to explain the apparent decline in sightings and to assess the remaining abundance nationwide accurately. Therefore, we strongly recommend increased research efforts for an in-depth assessment of the species’ population status in Argentina.

scholarly journals Age, growth and population structure of invasive lionfish (Pterois volitans/miles) in northeast Florida using a length-based, age-structured population model

2016 ◽  
Author(s):  
Eric G Johnson ◽  
Mary Katherine Swenarton
Keyword(s):  
Population Structure ◽  
Life History ◽  
Control Strategies ◽  
Ecological Impacts ◽  
Pterois Volitans ◽  
Structured Population Model ◽  
Western Atlantic ◽  
Short Period ◽  
Age Structured ◽  
Negative Impacts

The effective management of invasive species requires a detailed understanding of the invader’s life history. This information is essential for modeling population growth and predicting rates of expansion, quantifying ecological impacts and assessing the efficacy of removal and control strategies. Indo-Pacific lionfish ( Pterois volitans/miles ) have rapidly invaded the western Atlantic, Gulf of Mexico and Caribbean Sea with documented negative impacts on native ecosystems. To better understand the life history of this species, we developed and validated a length-based, age-structured model to investigate age, growth and population structure in northeast Florida. The main findings of this study were: (1) lionfish exhibited rapid growth with seasonal variation in growth rates, (2) distinct cohorts were clearly identifiable in the length-frequency data suggesting that lionfish arerecruiting during a relatively short period in summer, and (3) the majority of lionfish were less than two years old with no lionfish older than 3 years of age, possibly as a result of an ontogenetic shift to deeper water, which may provide a reservoir of spawning biomass not accessible to recreational or commercial spearfishing.

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