scholarly journals Extensive gene flow among populations of the cavernicolous shrimp at the northernmost distribution margin in the Ryukyu Islands, Japan

2020 ◽  
Vol 7 (10) ◽  
pp. 191731
Author(s):  
Takefumi Yorisue ◽  
Akira Iguchi ◽  
Nina Yasuda ◽  
Masaru Mizuyama ◽  
Yuki Yoshioka ◽  
...  
Keyword(s):  
Gene Flow ◽  
Flow Pattern ◽  
Population Genetic ◽  
High Throughput Sequencing ◽  
Abiotic Factors ◽  
Genotyping By Sequencing ◽  
Flow Patterns ◽  
Ryukyu Islands ◽  
Effective Population ◽  
The Ryukyu Islands

Marine cave habitats in the Ryukyu Islands, Indo-West Pacific, are located at the northern edge of the distribution of many cave-dwelling species. At distribution margins, gene flow is often more restricted than that among core populations due to the smaller effective population size. Here, we used high-throughput sequencing technology to investigate the gene flow pattern among three sampling sites of a marine cave-dwelling species at the margin of its distribution range. We collected individuals of the barbouriid shrimp Parhippolyte misticia from three marine caves in the Ryukyu Islands and performed population genetic analyses by means of multiplexed inter-simple sequence repeat genotyping by sequencing. Based on 62 single-nucleotide polymorphism markers, no clear population structure or directional gene flow pattern was found among the three sites. These results were unexpected because previous studies of other stygobitic shrimps in this region did find significant population genetic structures and northward directional gene flow patterns . Together, these inconsistent findings imply that marine cave-dwelling species in the region have different mechanisms of larval dispersal. Future studies on larval ecology and the biotic and abiotic factors influencing gene flow patterns are needed to clarify the mechanisms underlying the population dynamics of marine cave-dwelling species.

scholarly journals Landscape genomics of an obligate mutualism: discordant population structures between a leafcutter-ant and its fungal cultivars

2018 ◽  
Author(s):  
Chad C. Smith ◽  
Jesse N. Weber ◽  
Alexander S. Mikheyev ◽  
Flavio Roces ◽  
Martin Bollazzi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Abiotic Factors ◽  
Genotyping By Sequencing ◽  
Range Limit ◽  
Range Margin ◽  
Landscape Genomics ◽  
Temperature And Precipitation ◽  
Obligate Mutualism

AbstractTo explore landscape genomics at the range limit of an obligate mutualism, we used genotyping-by-sequencing (ddRADseq) to quantify population structure and the effect of hostsymbiont interactions between the northernmost fungus-farming leafcutter ant Atta texana and its two main types of cultivated fungus. At local scales, genome-wide differentiation between ants associated with either of the two fungal types is greater than the differentiation associated with the abiotic factors temperature and precipitation, suggesting that specific ant-fungus genome-genome combinations may have been favored by selection. For the ant hosts, we found a broad cline of genetic structure across the range, and a reduction of genetic diversity along the axis of range expansion towards the range margin. In contrast, genetic structure was patchy in the cultivated fungi, with no consistent reduction of fungal genetic diversity at the range margins. This discordance in population-genetic structure between ant hosts and fungal symbionts is surprising because the ant farmers co-disperse with their vertically-transmitted fungal symbionts, but apparently the fungi disperse occasionally also through between-nest horizontal transfer or other unknown dispersal mechanisms. The discordance in populationgenetic structure indicates that genetic drift and gene flow differ in magnitude between each partner in this leafcutter mutualism. Together, these findings imply that variation in the strength of drift and gene flow experienced by each mutualistic partner affects adaptation to environmental stress at the range margin, and genome-genome interactions between host and symbiont influences adaptive genetic differentiation of the host during range evolution in this obligate mutualism.

Population genetic structure and gene flow patterns between populations of the Antarctic icefish Chionodraco rastrospinosus

2012 ◽  
Vol 39 (7) ◽  
pp. 1361-1372 ◽  
Author(s):  
Chiara Papetti ◽  
Jose Martin Pujolar ◽  
Massimo Mezzavilla ◽  
Mario La Mesa ◽  
Jennifer Rock ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Flow Patterns ◽  
Antarctic Icefish ◽  
The Antarctic

scholarly journals Pelagic larval duration, growth rate, and population genetic structure of the tidepool snake morayUropterygius micropterusaround the southern Ryukyu Islands, Taiwan, and the central Philippines

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4741
Author(s):  
Wen-Chien Huang ◽  
Jui-Tsung Chang ◽  
Chun Liao ◽  
Atsushi Tawa ◽  
Yoshiyuki Iizuka ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Growth Rates ◽  
Population Genetic ◽  
The Philippines ◽  
Pelagic Larval Duration ◽  
Ryukyu Islands ◽  
Larval Duration ◽  
Otolith Growth

The relationships between pelagic larval duration (PLD) and geographic distribution patterns or population genetic structures of fishes remain obscure and highly variable among species. To further understand the early life history of the tidepool snake morayUropterygius micropterusand the potential relationship between PLD and population genetic structure of this species, otolith microstructure and population genetics based on concatenated mtDNA sequence (cytochromeband cytochrome oxidase subunit I, 1,336 bp) were analyzed for 195 specimens collected from eight locations around the southern Ryukyu Islands, Taiwan, and the central Philippines. Eels with longer PLD and lower otolith growth rates were observed at relatively higher latitudes with lower water temperatures (54.6 ± 7.7 days and 1.28 ± 0.16 µm day−1on Ishigaki Island, Japan, vs. 43.9 ± 4.9 days and 1.60 ± 0.19 µm day−1on Badian, the Philippines), suggesting that leptocephali grew faster and had shortened pelagic periods in warmer waters. Meanwhile, the eels along the southwest coast of Taiwan had relatively longer PLD (57.9 ± 10.5 days), which might be associated with the more complex ocean current systems compared to their counterparts collected along the east coast of Taiwan (52.6 ± 8.0 days). However, the southwestern and eastern Taiwan groups had similar otolith growth rates (1.33 ± 0.19 µm day−1vs. 1.36 ± 0.16 µm day−1). Despite the intergroup variation in PLD, genetic analysis revealed fluent gene flow among the tidepool snake morays in the study regions, implying that intraspecies PLD variation had a weak effect on genetic structure. The leptocephalus stage might have ensured the widespread gene flow among the study areas and leptocephalus growth was likely influenced by regional water temperature.

scholarly journals Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7769 ◽  
Author(s):  
Kenji Takata ◽  
Hiroki Taninaka ◽  
Masanori Nonaka ◽  
Fumihito Iwase ◽  
Taisei Kikuchi ◽  
...  
Keyword(s):  
Structure Analysis ◽  
Deep Sea ◽  
Nuclear Dna ◽  
Genotyping By Sequencing ◽  
Inter Simple Sequence Repeat ◽  
Mitochondrial Haplotype ◽  
Ryukyu Islands ◽  
The Ryukyu Islands ◽  
Principle Coordinate Analysis ◽  
Species Specific

Background Precious corals known as coralliid corals (Anthozoa: Octocorallia) play an important role in increasing the biodiversity of the deep sea. Currently, these corals are highly threatened because of overfishing that has been brought on by an increased demand and elevated prices for them.The deep sea precious corals Pleurocorallium elatius and P. konojoi are distributed in Japanese waters and have distinct morphological features: (1) the terminal branches of the colony form of P. elatius are very fine, while those of P. konojoi are blunt and rounded, (2) the autozooids of P. elatius are arranged in approximately four rows, while those of P. konojoi are clustered in groups. However, previous genetic analysis using mtDNA and nuclear DNA did not indicate monophyly. Therefore, it is important to clarify their species status to allow for their conservation. Methodology We collected a total of 87 samples (60 of Corallium japonicum and 27 of P. konojoi) from around the Ryukyu Islands and Shikoku Island, which are geographically separated by approximately 1,300 km. We used a multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) and obtained 223 SNPs with which to perform STRUCTURE analysis and principle coordinate analysis (PCoA). In addition, two relatively polymorphic mtDNA regions were sequenced and compared. Results P. elatius and P. konojoi share a same mtDNA haplotype, which has been previously reported. However, MIG-seq analysis clearly distinguished the two species based on PCoA and STRUCTURE analysis, including 5% of species-specific fixed SNPs. Conclusion This study indicated that P. elatius and P. konojoi are different species and therefore both species should be conserved separately. Our findings highlight the importance of the conservation of these two species, especially P. elatius, whose population has been dramatically depleted over the last 100 years. The study also demonstrated the effectiveness and robustness of MIG-seq for defining closely related octocoral species that were otherwise indistinguishable using traditional genetic markers (mtDNA and EF).

scholarly journals Geographic population genetic structure and diversity of Sophora moorcroftiana based on genotyping-by-sequencing (GBS)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9609
Author(s):  
Ying Liu ◽  
Fei Yi ◽  
Guijuan Yang ◽  
Yuting Wang ◽  
Ciren Pubu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Population Genetic ◽  
Genotyping By Sequencing ◽  
Mean Value ◽  
Gene Exchange ◽  
Subgroup Ii ◽  
Yarlung Zangbo River ◽  
High Level ◽  
Sophora Moorcroftiana

Sophora moorcroftiana is a perennial leguminous low shrub endemic to the Yarlung Zangbo River basin in Tibet with irreplaceable economic and ecological value. To determine the drivers of evolution in this species, 225 individuals belonging to 15 populations from different geographic locations were sampled, and population genetics was studied using high-throughput genotyping-by-sequencing (GBS). Based on genetic diversity analysis, phylogenetic analysis, principal component analysis, and structure analysis, 15 natural populations were clustered into the following five subgroups: subgroup I (Shigatse subgroup) was located in the upper reaches of the Yarlung Zangbo River with a relatively high level of population genetic variation (means for PIC, Shannon and PI were 0.173, 0.326 and 0.0000305, respectively), and gene flow within the subgroup was also high (mean value for Nm was 4.67). Subgroup II (including Pop 7 and Pop 8; means for PIC, Shannon and PI were 0.182, 0.345 and 0.0000321, respectively), located in the middle reaches of the Yarlung Zangbo River had relatively high levels of gene flow with the populations distributed in the upper and lower reaches. The Nm between subgroup II with subgroups I and III was 3.271 and 2.894, respectively. Considering all the genetic diversity indices Pop 8 had relatively high genetic diversity. Subgroup III (the remaining mixed subgroup of Lhasa and Shannan) was located in the middle reaches of the Yarlung Zangbo River and the means for PIC, Shannon and PI were 0.172, 0.324 and 0.0000303, respectively. Subgroup IV (Nyingchi subgroup), located in the lower reaches of the Yarlung Zangbo River basin, showed a further genetic distance from the other subgroups and the means for PIC, Shannon and PI were 0.147, 0.277 and 0.0000263, respectively. Subgroup V (Nyingchi Gongbu Jiangda subgroup), located in the upper reaches of the Niyang River, had the lowest level of genetic variation (means for PIC, Shannon and PI were 0.106, 0.198 and 0.0000187, respectively) and gene flow with other populations (mean value for Nm was 0.42). According to the comprehensive analysis, the S. moorcroftiana populations generally expanded from upstream to downstream and displayed a high level of genetic differentiation in the populations in the upper and lower reaches. There were high levels of gene exchange between the central populations with upstream and downstream populations, and wind-induced seed dispersal was an important factor in the formation of this gene exchange mode.

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