scholarly journals Post-Disturbance Genetic Changes: The Impact of the 2010 Mega-Earthquake and Tsunami on Chilean Sandy Beach Fauna

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Antonio Brante ◽  
Garen Guzmán-Rendón ◽  
Erwin M. Barría ◽  
Marie-Laure Guillemin ◽  
Iván Vera-Escalona ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Adult Survival ◽  
Genetic Changes ◽  
Species Response ◽  
Emerita Analoga ◽  
Mtdna Sequence ◽  
The Impact

Abstract Earthquake/tsunamis can have profound impacts on species and their genetic patterns. It is expected that the magnitude of this impact might depend on the species and the time since the disturbance occurs, nevertheless these assumptions remain mostly unexplored. Here we studied the genetic responses of the crustacean species Emerita analoga, Excirolana hirsuticauda, and Orchestoidea tuberculata to the 27F mega-earthquake/tsunami that occurred in Chile in February 2010. mtDNA sequence analyses revealed a lower haplotype diversity for E. analoga and E. hirsuticauda in impacted areas one month after the 27F, and the opposite for O. tuberculata. Three years after the 27F we observed a recovery in the genetic diversity of E. analoga and E. hirsuticauda and decrease in the genetic diversity in O. tuberculata in 2/3 of sampled areas. Emerita analoga displayed decrease of genetic differentiation and increase in gene flow explained by long-range population expansion. The other two species revealed slight increase in the number of genetic groups, little change in gene flow and no signal of population expansion associated to adult survival, rapid colonization, and capacity to burrow in the sand. Our results reveal that species response to a same disturbance event could be extremely diverse and depending on life-history traits and the magnitude of the effect.

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.

scholarly journals Population structure and demographic history of the chukar partridge Alectoris chukar in China

2013 ◽  
Vol 59 (4) ◽  
pp. 458-474 ◽  
Author(s):  
Sen Song ◽  
Shijie Bao ◽  
Ying Wang ◽  
Xinkang Bao ◽  
Bei An ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
North America ◽  
Demographic History ◽  
Population Expansion ◽  
Northwest China ◽  
Population History ◽  
Extant Species ◽  
History Of ◽  
Chukar Partridge

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

Comparative genetic diversity of Cryptosporidium species causing human infections

Parasitology ◽  
2020 ◽  
Vol 147 (13) ◽  
pp. 1532-1537 ◽  
Author(s):  
Juan C. Garcia-R ◽  
Murray P. Cox ◽  
David T. S. Hayman
Keyword(s):  
Genetic Diversity ◽  
Population Expansion ◽  
Recent Population Expansion ◽  
Cryptosporidium Hominis ◽  
High Genetic Diversity ◽  
Genetic Changes ◽  
Low Genetic Diversity ◽  
Human Infections ◽  
Host Parasite ◽  
Founder Events

AbstractParasites sometimes expand their host range and cause new disease aetiologies. Genetic changes can then occur due to host-specific adaptive alterations, particularly when parasites cross between evolutionarily distant hosts. Characterizing genetic variation in Cryptosporidium from humans and other animals may have important implications for understanding disease dynamics and transmission. We analyse sequences from four loci (gp60, HSP-70, COWP and actin) representing multiple Cryptosporidium species reported in humans. We predicted low genetic diversity in species that present unusual human infections due to founder events and bottlenecks. High genetic diversity was observed in isolates from humans of Cryptosporidium meleagridis, Cryptosporidium cuniculus, Cryptosporidium hominis and Cryptosporidium parvum. A deviation of expected values of neutrality using Tajima's D was observed in C. cuniculus and C. meleagridis. The high genetic diversity in C. meleagridis and C. cuniculus did not match our expectations but deviations from neutrality indicate a recent decrease in genetic variability through a population bottleneck after an expansion event. Cryptosporidium hominis was also found with a significant Tajima's D positive value likely caused by recent population expansion of unusual genotypes in humans. These insights indicate that changes in genetic diversity can help us to understand host-parasite adaptation and evolution.

scholarly journals Genetic diversity and extent of gene flow in the endangered Japanese population of Hodgson's hawk-eagle, Spizaetus nipalensis

2006 ◽  
Vol 16 (2) ◽  
pp. 113-129 ◽  
Author(s):  
SHIGEKI ASAI ◽  
YOSHIHIRO YAMAMOTO ◽  
SATOSHI YAMAGISHI
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Japanese Population ◽  
Isolation By Distance ◽  
Cladistic Analysis ◽  
Variable Region ◽  
Complete Sequence ◽  
Restricted Gene Flow ◽  
Critical Situation ◽  
Mtdna Sequence

The Japanese subspecies of Hodgson's Hawk-eagle, Spizaetus nipalensis orientalis, is considered threatened and has been designated as Endangered by the Japanese government. We determined the complete mitochondrial DNA (mtDNA) sequence of this species and designed a primer set to amplify a highly variable region of mtDNA, part of the control region (CR), based on this complete sequence. Using the primers, we amplified the CR and then determined the haplotypes of 178 samples collected at different sites in Japan. A nested cladistic analysis indicated that gene flow within some clades was restricted. The inference key implied that isolation by distance had caused the restriction of gene flow. Moreover, the ranges of the clades in which restricted gene flow was detected overlapped with the ranges of other clades. These results suggest that there is no fragmental population of Hodgson's Hawk-eagle in Japan and that this species has dispersed within short distances, at least in some lineages. Genetic diversity was high in comparison with other species. Therefore, at least in terms of genetic diversity, the Japanese population of Hodgson's Hawk-eagle is probably not in a critical situation.

scholarly journals Climate change and conservation in a warm North American desert: effect in shrubby plants

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6572 ◽  
Author(s):  
Victoria Sosa ◽  
Israel Loera ◽  
Diego F. Angulo ◽  
Marilyn Vásquez-Cruz ◽  
Etelvina Gándara
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Gene Flow ◽  
North American ◽  
Chihuahuan Desert ◽  
Haplotype Diversity ◽  
Sierra Madre Oriental ◽  
Ecological Resistance ◽  
Sierra Madre ◽  
Shrubby Species

Background Deserts are biologically rich habitats with a vast array of animals and plants adapted to xeric conditions, and most deserts are among the planet’s last remaining areas of total wilderness. Among North American deserts, the Chihuahuan Desert has the highest levels of diversity and endemism. To understand the effect of future climate change on plants distributed in this arid land and propose effective conservation planning, we focused on five endemic shrubby species that characterize the Chihuahuan Desert and used an integrative approach. Methods Ecological niche-based modeling, spatial genetics and ecological resistance analyses were carried out to identify the effect of global warming on the studied five shrubby species. Key areas that need to be preserved were identified taking into account the existing protected areas within the Chihuahuan Desert. Results The extent of future distribution will vary among these species, and on average expansion will occur in the western part of the Chihuahuan Desert. For most species low environmental resistance to gene flow was predicted, while higher future resistance was predicted for one species that would lead to increased population isolation. The highest haplotype diversity was identified in three hotspots. Based on future suitability of habitat and in the haplotype diversity we suggest preserving two hotspots of genetic diversity in the Sierra Madre Oriental, located in areas without protection. The third hotspot was detected in the well preserved Tehuacán-Cuicatlán Man and Biosphere Reserve. Conclusion Global climate change will have an effect in arid adapted plants, favoring expansion in the western of the Chihuahuan Desert however negatively affecting others with high ecological resistance disrupting gene flow. Two hotspots of genetic diversity in the Sierra Madre Oriental should be protected.

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.

scholarly journals Novel Insights Into the Genetic Population Connectivity of Transient Whale Sharks (Rhincodon typus) in Pacific Panama Provide Crucial Data for Conservation Efforts

2021 ◽  
Vol 8 ◽  
Author(s):  
Héctor M. Guzmán ◽  
Caitlin E. Beaver ◽  
Edgardo Díaz-Ferguson
Keyword(s):  
Genetic Diversity ◽  
Gulf Of California ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Population Connectivity ◽  
Region Gene ◽  
Genetic Population ◽  
Regional Patterns ◽  
Rhincodon Typus ◽  
Whale Sharks

The whale shark (Rhincodon typus) is an endangered and highly migratory species, of which solitary individuals or aggregations are observed in oceans worldwide and for which conservation efforts are hindered by a lack of comprehensive data on genetic population connectivity. Tissue samples were collected from wandering whale sharks in Pacific Panama to determine genetic diversity, phylogeographic origin, and possible global and local connectivity patterns using a 700–800 bp fragment of the mitochondrial control region gene. Genetic diversity among samples was high, with five new haplotypes and nine polymorphic sites identified among the 15 sequences. Haplotype diversity (Hd = 0.83) and nucleotide diversity (π = 0.00516) were similar to those reported in other studies. Our sequences, in particular haplotypes PTY1 and PTY2, were similar to those previously reported in the Arabian Gulf and the Western Indian Ocean populations (a novel occurrence in the latter case). Haplotypes PTY3, PTY4, and PTY5 were similar to populations in Mexico and the Gulf of California. In contrast, the only populations to which our Panamanian sequences were genetically dissimilar were those from the Atlantic Ocean. The absence of reference sequences in GenBank from southern sites in the Eastern Tropical Pacific, such as Galapagos (Ecuador), Gorgona and Malpelo Islands (Colombia), and Coco Island (Costa Rica), reduced our capacity to genetically define regional patterns. Genetic differentiation and connectivity were also assessed using an analysis of molecular variance (AMOVA), which showed a similar population structure (five groups) to the neighbor-joining tree. Other population features based on neutrality tests, such as Tajima’s D and Fu’s Fs statistics, showed positive values for Panama of 0.79 and 1.61, respectively. Positive values of these statistics indicate a lack of evidence for population expansion among the sampled individuals. Our results agree with previous reports suggesting that whale sharks can travel over long distances and that transboundary conservation measures may be effective for species protection.

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