scholarly journals Comparative Genetic Analysis of Invasive Fall Armyworm Populations Provides Evidence for Population Expansion in India

2020 ◽  
Author(s):  
Nishtha Nayyar ◽  
Gracy Ramasamy ◽  
Ashika Thotambyl ◽  
Mohan Govindasamy ◽  
Mohan Muthugounder ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Fall Armyworm ◽  
Western Hemisphere ◽  
Coi Gene ◽  
Polymorphism Analysis ◽  
Distribution Analysis ◽  
Maize Production ◽  
The World

Abstract Fall Armyworm (FAW), Spodoptera frugiperda, is a polyphagous pest capable of feeding over 80 plant species and was indigenous to Western Hemisphere until recently. Within a span of four years, FAW has established itself throughout most of the regions in Africa and Asia incurring significant losses in maize production. Owing to its revamped distribution range, it would be prudent to analyse the ensuing genetic changes and study the emerging phylogeographic patterns across the world. In this regard, we would like to provide a current snapshot of genetic diversity of FAW in India after two years of the initial introduction and compare it with the worldwide diversity in order to trace the origins and evolutionary trajectories of FAW in India.We have investigated around 145 FAW samples from different regions in India for strain identity and polymorphism analysis on the basis of partial mitochondrial cytochrome oxidase I (COI) gene sequences. Apart from the ancestral rice and corn strain haplotype, our study demonstrates the presence of 19 more haplotypes unique to India at a haplotype diversity of 0.498. We were also able to record the occurrence of inter-strain hybrid haplotypes of rice and corn strain in India. Regional heterogeneity within Indian populations seems to be quite low representative of extensive migration of FAW within India. Distribution analysis of pairwise differences and rejection of neutrality tests suggest that the FAW population in India is undergoing expansion. However, the scenario is much different for rest of the invaded regions like Africa and other Asian countries where FAW still appear to evolve neutrally. Our data is consistent with the findings suggesting a recent and common origin for invasive FAW populations in Asia and Africa, with significant population structure observed in Indian populations.This study reports the highest genetic diversity for Indian FAW populations till date and identifies India as the emerging hotspot for expansion of COIA rice haplotypes across the world. The findings will be useful to track the subsequent evolution of FAW and would have important ramifications for FAW behaviour and composition throughout the world.

scholarly journals Population structure and genetic diversity of invasive Fall Armyworm after 2 years of introduction in India

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
N. Nayyar ◽  
R. G. Gracy ◽  
T. R. Ashika ◽  
G. Mohan ◽  
R. S. Swathi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Haplotype Diversity ◽  
Fall Armyworm ◽  
Western Hemisphere ◽  
Coi Gene ◽  
Polymorphism Analysis ◽  
Distribution Analysis ◽  
Maize Production ◽  
Multiple Introductions ◽  
The World

AbstractFall Armyworm (FAW), Spodoptera frugiperda, is a polyphagous pest capable of feeding over 80 plant species and was indigenous to the Western Hemisphere. Within a span of 4 years, FAW has established itself throughout most of the regions in Africa and Asia causing significant losses in maize production. Owing to its revamped distribution range, it would be prudent to analyze the ensuing genetic changes and study the emerging phylogeographic patterns across the world. In this regard, we would like to provide a current snapshot of genetic diversity of FAW in India 2 years after the initial introduction and compare it with the worldwide diversity in order to trace the origins and evolutionary trajectories of FAW in India. We have investigated around 190 FAW samples from different regions in India for strain identity and polymorphism analysis on the basis of partial mitochondrial cytochrome oxidase I (COI) gene sequences. Apart from the ancestral rice and corn strain haplotype, our study demonstrates the presence of 14 more haplotypes unique to India at a haplotype diversity of 0.356. We were also able to record inter-strain hybrid haplotypes of rice and corn strains in India. Regional heterogeneity within Indian populations seems to be quite low representative of extensive migration of FAW within India. Distribution analysis of pairwise differences and rejection of neutrality tests suggest that the FAW population in India might be undergoing expansion. Our data is consistent with the findings suggesting a recent and common origin for invasive FAW populations in Asia and Africa, and does not indicate multiple introductions to India. This study reports the highest genetic diversity for Indian FAW populations to date and will be useful to track the subsequent evolution of FAW in India. The findings would have important ramifications for FAW behavior and composition throughout the world.

scholarly journals Population genetic structure of Marbled Rockfish, Sebastiscus marmoratus (Cuvier, 1829), in the northwestern Pacific Ocean

ZooKeys ◽  
2019 ◽  
Vol 830 ◽  
pp. 127-144 ◽  
Author(s):  
Lu Liu ◽  
Xiumei Zhang ◽  
Chunhou Li ◽  
Hui Zhang ◽  
Takashi Yanagimoto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic ◽  
Fishery Management ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Northwestern Pacific ◽  
Distribution Analysis ◽  
Recent Population Expansion

Sebastiscusmarmoratus is an ovoviviparous fish widely distributed in the northwestern Pacific. To examine the gene flow and test larval dispersal strategy of S.marmoratus in Chinese and Japanese coastal waters, 421 specimens were collected from 22 localities across its natural distribution. A 458 base-pair fragment of the mitochondrial DNA (mtDNA) control region was sequenced to examine genetic diversity and population structure. One-hundred-six variable sites defined 166 haplotypes. The populations of S.marmoratus showed high haplotype diversity with a range from 0.8587 to 0.9996, indicating a high level of intrapopulation genetic diversity. Low non-significant genetic differentiation was estimated among populations except those of Hyogo, Behai, and Niiigata, which showed significant genetic differences from the other populations. The demographic history examined by neutrality tests, mismatch distribution analysis, and Bayesian skyline analysis suggested a sudden population expansion dating to the late Pleistocene. Recent population expansion in the last glacial period, wide dispersal of larvae by coastal currents, and the homogeneity of the environment may have important influences on the population genetic pattern. Knowledge of genetic diversity and genetic structure will be crucial to establish appropriate fishery management of S.marmoratus.

scholarly journals Phylogeography of the Brittle Star Ophiura sarsii Lütken, 1855 (Echinodermata: Ophiuroidea) from the Barents Sea and East Atlantic

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 40
Author(s):  
Evgeny Genelt-Yanovskiy ◽  
Yixuan Li ◽  
Ekaterina Stratanenko ◽  
Natalia Zhuravleva ◽  
Natalia Strelkova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Barents Sea ◽  
Haplotype Diversity ◽  
Brittle Star ◽  
The Arctic ◽  
Coi Gene ◽  
High Genetic Diversity ◽  
Svalbard Archipelago ◽  
Mitochondrial Coi ◽  
The Barents Sea

Ophiura sarsii is a common brittle star species across the Arctic and Sub-Arctic regions of the Atlantic and the Pacific oceans. Ophiurasarsii is among the dominant echinoderms in the Barents Sea. We studied the genetic diversity of O.sarsii by sequencing the 548 bp fragment of the mitochondrial COI gene. Ophiurasarsii demonstrated high genetic diversity in the Barents Sea. Both major Atlantic mtDNA lineages were present in the Barents Sea and were evenly distributed between the northern waters around Svalbard archipelago and the southern part near Murmansk coast of Kola Peninsula. Both regions, and other parts of the O.sarsii range, were characterized by high haplotype diversity with a significant number of private haplotypes being mostly satellites to the two dominant haplotypes, each belonging to a different mtDNA clade. Demographic analyses indicated that the demographic and spatial expansion of O.sarsii in the Barents Sea most plausibly has started in the Bølling–Allerød interstadial during the deglaciation of the western margin of the Barents Sea.

scholarly journals Influence of Quaternary environmental changes on mole populations inferred from mitochondrial sequences and evolutionary rate estimation

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Azusa Nakamoto ◽  
Masashi Harada ◽  
Reiko Mitsuhashi ◽  
Kimiyuki Tsuchiya ◽  
Alexey P. Kryukov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Environmental Changes ◽  
Late Quaternary ◽  
Population Expansion ◽  
Rapid Expansion ◽  
Dependent Manner ◽  
Distribution Analysis ◽  
Land Bridge ◽  
Mismatch Distribution Analysis ◽  
Expansion Event

AbstractQuaternary environmental changes fundamentally influenced the genetic diversity of temperate-zone terrestrial animals, including those in the Japanese Archipelago. The genetic diversity of present-day populations is taxon- and region-specific, but its determinants are poorly understood. Here, we analyzed cytochrome b gene (Cytb) sequences (1140 bp) of mitochondrial DNA (mtDNA) to elucidate the factors determining the genetic variation in three species of large moles: Mogera imaizumii and Mogera wogura, which occur in central and southern mainland Japan (Honshu, Shikoku, and Kyushu), and Mogera robusta, which occurs on the nearby Asian continent. Network construction with the Cytb sequences revealed 10 star-shaped clusters with apparent geographic affinity. Mismatch distribution analysis showed that modes of pairwise nucleotide differences (τ values) were grouped into five classes in terms of the level, implying the occurrence of five stages for rapid expansion. It is conceivable that severe cold periods and subsequent warm periods during the late Quaternary were responsible for the population expansion events. The first and third oldest events included island-derived haplotypes, indicative of the involvement of land bridge formation between remote islands, hence suggesting an association of the ends of the penultimate (PGM, ca. 130,000 years ago) and last (LGM, ca. 15,000 years ago) glacial maxima, respectively. Since the third event was followed by the fourth, it is plausible that the termination of the Younger Dryas and subsequent abrupt warming ca. 11,500 years ago facilitated the fourth expansion event. The second event most likely corresponded to early marine isotope stage (MIS) 3 (ca. 53,000 years ago) when the glaciation and subsequent warming period were predicted to have influenced biodiversity. Utilization of the critical times of 130,000, 53,000, 15,000, and 11,500 years ago as calibration points yielded evolutionary rates of 0.03, 0.045, 0.10 and 0.10 substitutions/site/million years, respectively, showing a time-dependent manner whose pattern was similar to that seen in small rodents reported in our previous studies. The age of the fifth expansion event was calculated to be 5800 years ago with a rate of 0.10 substitutions/site/million years ago during the mid-Holocene, suggestive of the influence of humans or other unspecified reasons, such as the Jomon marine transgression.

scholarly journals Genetic Diversity in the mtDNA control region and population structure of Chrysichthys nigrodigitatus from selected Nigerian rivers: Implications for conservation and aquaculture

2016 ◽  
Vol 24 (2) ◽  
pp. 85-97 ◽  
Author(s):  
Sylvanus A. Nwafili ◽  
Tian-Xiang Gao
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Control Region ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Recent Population Expansion ◽  
Base Pair Fragment ◽  
Population Structures ◽  
High Level

Abstract The genetic diversity and population structure of Chrysichthys nigrodigitatus were evaluated using a 443 base pair fragment of the mitochondrial control region. Among the eight populations collected comprising 129 individuals, a total of 89 polymorphic sites defined 57 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the eight populations were 0.966±0.006 and 0.0359±0.004, respectively. Analysis of molecular variance showed significant genetic differentiation among the eight populations (FST =0.34; P < 0.01). The present results revealed that C. nigrodigitatus populations had a high level of genetic diversity and distinct population structures. We report the existence of two monophyletic matrilineal lineages with mean genetic distance of 10.5% between them. Non-significant negative Tajima’s D and Fu’s Fs for more than half the populations suggests that the wild populations of C. nigrodigitatus underwent a recent population expansion, although a weak one since the late Pleistocene.

Effects of habitat fragmentation on the genetic diversity and differentiation of Dendrolimus punctatus (Lepidoptera: Lasiocampidae) in Thousand Island Lake, China, based on mitochondrial COI gene sequences

2018 ◽  
Vol 109 (1) ◽  
pp. 62-71 ◽  
Author(s):  
K. Lv ◽  
J.-R. Wang ◽  
T.-Q. Li ◽  
J. Zhou ◽  
J.-Q. Gu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Habitat Fragmentation ◽  
Geographic Distance ◽  
Haplotype Diversity ◽  
Shape Index ◽  
Coi Gene ◽  
Fragmented Landscape ◽  
Dispersal Capacity ◽  
Island Populations ◽  
High Dispersal

AbstractThousand Island Lake (TIL) is a typical fragmented landscape and an ideal model to study ecological effects of fragmentation. Partial fragments of the mitochondrial cytochrome oxidase subunit I gene of 23 island populations of Dendrolimus punctatus in TIL were sequenced, 141 haplotypes being identified. The number of haplotypes increased significantly with the increase in island area and shape index, whereas no significant correlation was detected between three island attributes (area, shape and isolation) and haplotype diversity. However, the correlation with number of haplotypes was no longer significant when the ‘outlier’ island JSD (the largest island) was not included. Additionally, we found no significant relationship between geographic distance and genetic distance. Geographic isolation did not obstruct the gene flow among D. punctatus populations, which might be because of the high dispersal capacity of this pine moth. Fragmentation resulted in the conversion of large and continuous habitats into isolated, small and insular patches, which was the primary effect on the genetic diversity of D. punctatus in TIL. The conclusion to emphasize from our research is that habitat fragmentation reduced the biological genetic diversity to some extent, further demonstrating the importance of habitat continuity in biodiversity protection.

scholarly journals Genetic Diversity and Population Genetics of Mosquitoes (Diptera: Culicidae:Culexspp.) from the Sonoran Desert of North America

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Edward Pfeiler ◽  
Carlos A. Flores-López ◽  
Jesús Gerardo Mada-Vélez ◽  
Juan Escalante-Verdugo ◽  
Therese A. Markow
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
North America ◽  
Sonoran Desert ◽  
Phylogenetic Analyses ◽  
Gene Segment ◽  
Population Expansion ◽  
The Other ◽  
Coi Gene ◽  
Unidentified Species

The population genetics and phylogenetic relationships ofCulexmosquitoes inhabiting the Sonoran Desert region of North America were studied using mitochondrial DNA and microsatellite molecular markers. Phylogenetic analyses of mitochondrial cytochromecoxidase subunit I (COI) from mosquitoes collected over a wide geographic area, including the Baja California peninsula, and mainland localities in southern Arizona, USA and Sonora, Mexico, showed several well-supported partitions corresponding toCx. quinquefasciatus, Cx. tarsalis,and two unidentified species,Culexsp. 1 and sp. 2.Culex quinquefasciatuswas found at all localities and was the most abundant species collected.Culex tarsaliswas collected only at Tucson, Arizona and Guaymas, Sonora. The two unidentified species ofCulexwere most abundant at Navojoa in southern Sonora. Haplotype and nucleotide diversities in the COI gene segment were substantially lower inCx. quinquefasciatuscompared with the other three species. Analysis of molecular variance revealed little structure among seven populations ofCx. quinquefasciatus, whereas significant structure was found between the two populations ofCx. tarsalis. Evidence for an historical population expansion beginning in the Pleistocene was found forCx. tarsalis. Possible explanations for the large differences in genetic diversity betweenCx. quinquefasciatusand the other species ofCulexare presented.

scholarly journals Genetic differentiation among Parastichopus regalis populations from Western Mediterranean Sea: potential effects of its fishery and current connectivity.

2015 ◽  
Vol 16 (3) ◽  
pp. 489 ◽  
Author(s):  
C. MAGGI ◽  
M. GONZÁLEZ-WANGÜEMERT
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Haplotype Diversity ◽  
Western Mediterranean ◽  
Mediterranean Coast ◽  
Morphological Data ◽  
Coi Gene ◽  
Fixation Index ◽  
Morphological Description ◽  
Western Mediterranean Sea

Parastichopus regalis (Cuvier, 1817) is the most expensive seafood product on the catalonian market (NE Spain), with prices around 130 €/Kg (fresh weight). Despite its ecological and economic importance, biological and genetic information on this sea cucumber species is scarce. We provided the first insight on the genetic structure of P. regalis using sequences of cytochrome oxidase I (COI) and 16S genes, as well as a morphological description of its populations. Individuals were collected in six locations along the Spanish Mediterranean coast, including an area under fishery pressure (Catalonia). We found high haplotype diversity and low nucleotide diversity for both genes, with higher levels of genetic diversity observed on COI gene. Population pairwise fixation index (FST), AMOVA and correspondence analysis (CA) based on COI, revealed significant genetic differentiation among some locations. However, further analysis using nuclear markers (e.g. microsatellites) would be necessary to corroborate these results. Moreover, the genetic and morphological data may indicate fishery effects on the Catalonian population with decrease of the size and weight average and lower genetic diversity compared to locations without fishery pressure. For an appropriate management of this species, we suggest: 1) an accurate assessment of the stocks status along the Spanish coasts; 2) the study of the reproductive cycle of this target species and the establishment of a closed fishery season according to it; 3) the founding of protected areas (i.e. not take zones) to conserve healthy populations and favour the recruitment on the nearby areas.

scholarly journals Short Communication: Genetic diversity of scalloped hammerhead sharks (Sphyrna lewini) landed in Muncar Fishing Port, Banyuwangi

2019 ◽  
Vol 20 (4) ◽  
pp. 1154-1159 ◽  
Author(s):  
FAQIH AKBAR ALGHOZALI ◽  
DIAH PERMATA WIJAYANTI ◽  
AGUS SABDONO
Keyword(s):  
Genetic Diversity ◽  
Short Communication ◽  
Polymerase Chain Reaction Amplification ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Fishing Ground ◽  
Sphyrna Lewini ◽  
Scalloped Hammerhead ◽  
Hammerhead Sharks ◽  
Longline Fisheries

Abstract. Alghozali FA, Wijayanti DP, Sabdono A. 2019. Short Communication: Genetic diversity of scalloped hammerhead sharks (Sphyrna lewini) landed in Muncar Fishing Port, Banyuwangi. Biodiversitas 20: 1154-1159. The majority of sharks caught in Indonesian fisheries were bycatch products from the tuna longline fisheries, but some regions in Indonesia fish the sharks as their main target. One of these regions is located in Muncar, Banyuwangi, which fishes the endangered Scalloped Hammerhead sharks (Sphyrna lewini) as target species. This research aimed to study the genetic diversity of the endangered Scalloped Hammerhead sharks landed in Muncar Fishing Port, Banyuwangi. Genetic analysis was done through PCR (Polymerase Chain Reaction) amplification and sequencing of the mitochondrial DNA COI (Cytochrome Oxidase subunit I) gene. Out of the 37 samples collected, 30 were successfully amplified and sequenced.The results showed moderate haplotype diversity (Hd: 0,582 ± 0,079) and low nucleotide diversity (π: 0,00392± 0,0024) with five haplotypes (h) and 26 polymorphic sites (S). Tajima’s D neutrality model values indicated a population expansion event. Two different clades were determined through phylogenetic analysis and by GenBank sequences comparison. These results provided basic information and present status of the Scalloped Hammerhead sharks population genetically within the fishing ground (Makassar Strait-Kangean Islands).

scholarly journals Diversitas Genetika dan Identifikasi Jenis Kelamin Burung Pelikan (Pelecanus conspicillatus Temminck, 1824) di Penangkaran Taman Margasatwa Ragunan Jakarta

2021 ◽  
Vol 17 (2) ◽  
pp. 105-114
Author(s):  
Anik Budhi Dharmayanthi ◽  
Achmad Muchsinin ◽  
Afriana Pulungan ◽  
Moch Syamsul Arifin Zein
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Bird Populations ◽  
Low Genetic Diversity ◽  
In Captivity ◽  
D Loop ◽  
Haplotype 1

Pelicans (Pelecanus conspicillatus) is one of the wild species that have a widely distribution. This bird has been successfully bred in Ragunan Zoo, Jakarta. The indicator of inbreeding in the captive population is shown by the decrease of nucleotide diversity and number of haplotypes. The result of genetic diversity analysis using D-loop fragment sequences showed low genetic diversity with nucleotide diversity (p) = 0.00064 ± 0.00010 and haplotype diversity (Hd) = 0.532 ± 0.061 in Pelecanus conspicillatus populations in the Ragunan Zoo. However, negative Fu's Fs value (-3,246) indicates population expansion. We found that there were seven haplotypes in bird populations in the captivity: haplotype 1, 2 and 3 consist of 43 individuals (65.15%), five individuals (7.57%), and 14 individuals (21.21%), respectively. For each haplotype 4, 5, 6 and 7 is only represented by one individual of Pelecanus conspicillatus (1.51%). The sex ratio of males to females is 1: 8.86 with four males identified as haplotype 1, and one male on haplotypes 3, 5 and 7, respectively. Genetic diversity data of the population is an important way for designing long-term plans and goals in efforts to maintain genetic diversity of the Pelecanus conspicillatus population in captivity.

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