Population expansion and genetic structure in Cephalocereus nizandensis (Cactaceae), a microendemic cactus of rocky outcrops of the  Tehuantepec basin, Mexico

Background and aims – Cephalocereus nizandensis is a microendemic columnar cactus that grows isolated in xerophytic enclaves associated with rocky outcrops in the Isthmus of Tehuantepec, in the south of Mexico. Its demographic history and genetic structure were assessed to determine the main events that shaped its current restricted distribution.Material and methods – Chloroplast intergenic sequences of 40 individuals and inter simple sequence repeats (ISSRs) of 45 individuals from four isolated populations were used to estimate haplotypic and nucleotide diversity, using expected heterozygosity and the Shannon index. AMOVA, population pair-wise FST, and Bayesian clustering analyses were performed to explore the genetic structure. Demographic history was estimated with neutrality tests, mismatch distribution analysis, and Bayesian skyline plots. Phylogenetic relationships and divergence times were determined using a median joining network and a Bayesian molecular clock.Key results – C. nizandensis has a high diversity and moderate genetic differentiation. The lowest elevation locality was found to be the most genetically distinct. The species has undergone a process of population expansion that began 150,000 years ago and has remained without evidence of a population contraction in the transition from the Pleistocene to the Holocene (11,700 years ago).Conclusions – C. nizandensis presents moderate but significant genetic differentiation, which may be due to an early divergence of its populations. Currently observed levels of genetic diversity are the result of historical maintenance of high population sizes and a population expansion approximately in the last 150,000 years, which was sustained independently of the climatic fluctuations of the Early Quaternary, due in part to the stability of the rocky habitat.

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

ZooKeys ◽

10.3897/zookeys.830.30586 ◽

2019 ◽

Vol 830 ◽

pp. 127-144 ◽

Cited By ~ 2

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.

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The Genomic Basis of the Genetic Differentiation and Local Adaptive Evolution of Pampus Echinogaster based on SLAF-seq

10.21203/rs.3.rs-640424/v1 ◽

2021 ◽

Author(s):

Yuan Li ◽

Fangrui Lou ◽

Hai Li ◽

Rui Wang ◽

Zizi Cai ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Population Expansion ◽

Nucleotide Polymorphisms ◽

Stress Reactions ◽

Long Distance ◽

Evolutionary Mechanisms ◽

Inflammatory Reactions ◽

Genomic Study

Abstract Background: Factors such as climate change (especially ocean warming) and overfishing have led to a decline in the supply of Pampus echinogaster and a trend of decreasing age. Exploring the genetic structure and local adaptive evolutionary mechanisms is crucial for the management of P. echinogaster. Results: This population genomic study of nine geographical populations of P. echinogaster in China was conducted by specific-locus amplified fragment sequencing (SLAF-seq). A total of 935,215 SLAF tags were obtained, and the average sequencing depth of the SLAF tags was 20.80×. After filtering, a total of 46,187 high-consistency genome-wide single nucleotide polymorphisms (SNPs) were detected. Based on all SNPs, the overall genetic diversity among the nine P. echinogaster populations was high. The Shantou population had the lowest genetic diversity, and the Tianjin population had the highest. Meanwhile, the population genetic structure based on all SNPs revealed significant gene exchange and insignificant genetic differentiation between the nine P. echinogaster populations. Based on pairwise genetic differentiation (FST), we further screened 1,852 outlier SNPs that might have been affected by habitat selection and annotated SLAF tags containing these 1,852 outlier SNPs using Blast2GO. The annotation results showed that the genomic sequences at the outlier SNPs were mainly related to material metabolism, ion transport, breeding, stress response, and inflammatory reactions, which may be related to the adaptation of P. echinogaster to different environmental conditions (such as water temperature and salinity) in different sea areas.Conclusions: The high genetic similarity of nine P. echinogaster populations may have been caused by the population expansion after the last glacial period, the lack of balance between migration and genetic drift, and the long-distance diffusion of eggs and larvae. We suspected that variation of these genes associated with material metabolism, ion transfer, breeding, stress reactions, and inflammatory reactions were critical for adaptation to spatially heterogeneous temperatures in natural P. echinogaster populations.

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Population Genetic Structure of Ornate Threadfin Bream (Nemipterus hexodon) in Thailand

Tropical Life Sciences Research ◽

10.21315/tlsr2021.32.1.4 ◽

2021 ◽

Vol 32 (1) ◽

pp. 61-80

Author(s):

Verakiat Supmee ◽

◽

Apirak Songrak ◽

Juthamas Suppapan ◽

Pradit Sangthong ◽

...

Keyword(s):

Genetic Structure ◽

Population Genetic Structure ◽

Genetic Information ◽

Population Genetic ◽

Demographic History ◽

Haplotype Diversity ◽

Population Expansion ◽

Andaman Sea ◽

Gulf Of Thailand ◽

The Gulf Of Thailand

Ornate threadfin bream (Nemipterus hexodon) is an economically important fishery species in Southeast Asia. In Thailand, N. hexodon decreased dramatically due to overexploitation for commercial purposes. To construct an effective sustainable management plan, genetic information is necessary. Thus, in our study, the population genetic structure and demographic history of N. hexodon were investigated using 419 bp of the mitochondrial DNA sequence in cytochrome oxidase subunit I gene (mtDNA COI). A total of 142 samples was collected from nine localities in the Gulf of Thailand (Chonburi, Samut Songkhram, Surat Thani, Nakhon Si Thammarat, Songkhla), and the Andaman Sea (Satun, Trang, Krabi, Phang Nga). Fourteen polymorphic sites defined 18 haplotypes, revealing a high haplotype diversity and low nucleotide diversity among nine localities. The Analysis of molecular variance (AMOVA) analysis, pairwise FST, and minimum spanning network result revealed that the genetic structure of N. hexodon was separated into two populations: the Gulf of Thailand and the Andaman Sea population. The genetic structure of N. hexodon can be explained by a disruption of gene flow from the geographic barrier and the Pleistocene isolation of the marine basin hypothesis. Neutrality tests, Bayesian skyline analysis, mismatch distribution, and the estimated values of population growth suggested that N. hexodon had experienced a population expansion. The genetic information would certainly help us gain insight into the population genetic structure of N. hexodon living on the coast of Thailand.

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Unraveling the genetic structure of the coconut scale insect pest (Aspidiotus rigidus Reyne) outbreak populations in the Philippines

10.1101/726919 ◽

2019 ◽

Author(s):

Joeselle M. Serrana ◽

Naoto Ishitani ◽

Thaddeus M. Carvajal ◽

Billy Joel M. Almarinez ◽

Alberto T. Barrion ◽

...

Keyword(s):

Genetic Structure ◽

Genetic Differentiation ◽

Demographic History ◽

Insect Pest ◽

Scale Insect ◽

The Philippines ◽

Geographic Region ◽

Invasive Pest ◽

Economic Losses ◽

History Of

AbstractThe Philippines suffered from a devastating outbreak of the coconut scale insect pest, Aspidiotus rigidus Reyne inflicting significant economic losses to the country’s coconut industry. Despite the massive outbreak, little is known about the population and dispersal history of this invasive pest in the Philippines. Here, we examined the genetic diversity, structure and demographic history of A. rigidus sampled from localities with reported outbreaks from 2014 to 2017. We analyzed the genetic structure of seven A. rigidus outbreak populations using mitochondrial COI and nuclear EF-1α markers. Both markers and all methods of population genetic structure analyses indicate clear differentiation among the A. rigidus populations separating the northern (i.e., Luzon provinces) from the southern (i.e., Basilan and Zamboanga Peninsula) regions of the Philippines. Very low or no genetic differentiation was observed within and amongst the populations per geographic region indicating two unrelated outbreak events of the pest originating from two genetically uniform populations isolated in each respective region. Historical data supports the resurgence of an established A. rigidus population in the south which could have been driven by sudden climatic changes or human-induced habitat imbalance. Given no historical information, we disregard the possible resurgence from the northern population and infer that the outbreak could have resulted from a recent introduction of a non-native A. rigidus in the region. Our study provides valuable information on the genetic differentiation of the two A. rigidus groups that would be useful for developing and implementing biological control strategies against this pest in the Philippines.

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Genetic structure of the grey side-gilled sea slug (Pleurobranchaea maculata) in coastal waters of New Zealand

10.1101/239855 ◽

2017 ◽

Author(s):

Yeşerin Yıldırım ◽

Marti J. Anderson ◽

Selina Patel ◽

Craig D. Millar ◽

Paul B. Rainey

Keyword(s):

New Zealand ◽

Genetic Structure ◽

Sequence Data ◽

Demographic History ◽

Population Expansion ◽

Haplotype Network ◽

Founding Population ◽

Mtdna Sequence ◽

Expansion Time ◽

History Of

AbstractPleurobranchaea maculatais a rarely studied species of the Heterobranchia found throughout the south and western Pacific – and recently recorded in Argentina – whose population genetic structure is unknown. Interest in the species was sparked in New Zealand following a series of dog deaths caused by ingestions of slugs containing high levels of the neurotoxin tetrodotoxin. Here we describe the genetic structure and demographic history ofP. maculatapopulations from five principle locations in New Zealand based on extensive analyses of 12 microsatellite loci and theCOIandCytBregions of mitochondrial DNA (mtDNA). Microsatellite data showed significant differentiation between northern and southern populations with population structure being associated with previously described regional variations in tetrodotoxin concentrations. However, mtDNA sequence data did not support such structure, revealing a star-shaped haplotype network with estimates of expansion time suggesting a population expansion in the Pleistocene era. Inclusion of publicly available mtDNA sequence from Argentinian sea slugs did not alter the star-shaped network. We interpret our data as indicative of a single founding population that fragmented following geographical changes that brought about the present day north-south divide in New Zealand waters. Lack of evidence of cryptic species supports data indicating that differences in toxicity of individuals among regions are a consequence of differences in diet.

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Diversity and genetic structure of Ornithogalum L. (Hyacinthaceae) populations as revealed by RAPD-PCR markers

Genetika ◽

10.2298/gensr1501275a ◽

2015 ◽

Vol 47 (1) ◽

pp. 275-288

Author(s):

Andrijana Andric ◽

Natasa Kocis-Tubic ◽

Milica Rat ◽

Dragana Obreht-Vidakovic

Keyword(s):

Genetic Structure ◽

Genetic Differentiation ◽

Population Genetic ◽

Random Amplified Polymorphic Dna ◽

Genetic Distances ◽

Shannon Index ◽

Similarity Coefficients ◽

Additional Tool ◽

Population Genetic Differentiation ◽

Rapd Pcr

Random amplified polymorphic DNA (RAPD) PCR method was used to assess the level of diversity and genetic structure in Ornithogalum L. populations from Serbia and Hungary with the main goal of improving the knowledge of this genus in the given region. The material was collected from 19 populations and identified as two morphologically similar and phylogenetically close taxa: O. umbellatum L. 1753 and O. divergens Boreau 1887. All ten RAPD primers used for the analysis gave PCR products, with length between 3000bp and 300bp. There were 101 amplified fragments in total; number of polymorphic bands per primer varied between seven and 13. Percentage of polymorphic loci was 96% in total and 12% in average in each population. Genetic variation statistics for all loci also showed that genetic diversity for all populations was 0.29 and Shannon index 0.45, while mean values for these parameters calculated for each population were 0.04 and 0.06, respectively. Analysis of molecular variance demonstrated high population genetic differentiation; however Mantel test showed no significant correlation between geographic distances of populations and genetic distances expressed through population pairwise FST. UPGMA dendrogram based on Jaccard genetic similarity coefficients showed subclustering and principal coordinate analysis based on Nei and Li coefficients of genetic distances indicated grouping. Analysis of populations genetic structure was in accordance with these results and clearly separated populations of O. umbellatum from O. divergens. RAPDs proved to be a reliable and rapid method suitable for distinguishing genetic differentiation in Ornithogalum, thus could be applied as a useful additional tool in resolving taxonomic problems.

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High genetic diversity and strong genetic structure of Strongyllodes variegatus populations in oilseed rape production areas of China

10.21203/rs.3.rs-19659/v3 ◽

2020 ◽

Author(s):

HaiXia Zhan ◽

ZhongPing Hao ◽

Rui Tang ◽

LiNi Zhu ◽

JingJiang Zhou ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Oilseed Rape ◽

Demographic History ◽

Insect Pest ◽

Distribution Analysis ◽

Geographical Distance ◽

Geographical Regions ◽

Genetic Diversity And Structure ◽

Production Areas

Abstract Background: Strongyllodes variegatus (Fairmaire) is a major insect pest of oilseed rape in China. Despite its economic importance, the contribution of its population genetics in the development of any suitable protection control strategy for the management of oilseed rape crops is poorly studied. It is a much urgent need to prevent its spread to the rest of the world. Results: Using the sequences of mitochondrial DNA cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) as genetic markers, we analyzed the population genetic diversity and structure of 437 individuals collected from 15 S. variegates populations located in different oilseed rape production areas in China. In addition, we estimated the demographic history using neutrality test and mismatch distribution analysis. The high level of genetic diversity was detected among the COI and Cytb sequences of S. variegates. The population structure analyses strongly suggested three distinct genetic and geographical regions in China with limited gene flow. The Mantel test showed that the genetic distance was greatly influenced by the geographical distance. The demographic analyses showed that S. variegates had experienced population fluctuation during the Pleistocene Epoch, which was likely to be related to the climatic changes.Conclusion: Overall, these results demonstrate that the strong genetic structure of S. variegates populations in China, which is attributed by the isolation through the geographical distance among populations, their weak flight capacity and subsequent adaptation to the regional ecological conditions.

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Genomic differentiation in an endemic Philippine genus (Aves: Sarcophanops) owing to geographical isolation on recently disassociated islands

Biological Journal of the Linnean Society ◽

10.1093/biolinnean/blaa143 ◽

2020 ◽

Vol 131 (4) ◽

pp. 814-821

Author(s):

Luke C Campillo ◽

Joseph D Manthey ◽

Robert C Thomson ◽

Peter A Hosner ◽

Robert G Moyle

Keyword(s):

Population Structure ◽

Genetic Structure ◽

Genetic Differentiation ◽

Deep Structure ◽

Island Population ◽

Geographical Isolation ◽

Isolated Populations ◽

Genetic Sampling ◽

Genome Wide ◽

Species Analysis

Abstract Phylogeographical studies of Philippine vertebrates have demonstrated that genetic variation is broadly partitioned by Pleistocene island aggregation. Contemporary island discontinuity is expected to influence genetic differentiation but remains relatively undocumented, perhaps because the current episode of island isolation started in relatively recent times. We investigated inter- and intra-island population structure in a Philippine endemic bird genus (Sarcophanops) to determine whether genetic differentiation has evolved during the recent period of isolation. We sequenced thousands of genome-wide restriction site associated DNA (RAD) markers from throughout the Mindanao group to assess fine-scale genetic structure across islands. Specifically, we investigated patterns of gene flow and connectivity within and between taxonomic and geographical bounds. A previous assessment of mitochondrial DNA detected deep structure between Sarcophanops samarensis and a sister species, Sarcophanops steerii, but was insufficient to detect differentiation within either species. Analysis of RAD markers, however, revealed structure within S. samarensis between the islands of Samar/Leyte and Bohol. This genetic differentiation probably demonstrates an effect of recent geographical isolation (after the Last Glacial Maximum) on the genetic structure of Philippine avifauna. We suggest that the general lack of evidence for differentiation between recently isolated populations is a failure to detect subtle population structure owing to past genetic sampling constraints, rather than the absence of such structure.

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Unraveling the Genetic Structure of the Coconut Scale Insect Pest (Aspidiotus rigidus Reyne) Outbreak Populations in the Philippines

Insects ◽

10.3390/insects10110374 ◽

2019 ◽

Vol 10 (11) ◽

pp. 374

Author(s):

Joeselle M. Serrana ◽

Naoto Ishitani ◽

Thaddeus M. Carvajal ◽

Billy Joel M. Almarinez ◽

Alberto T. Barrion ◽

...

Keyword(s):

Genetic Structure ◽

Genetic Differentiation ◽

Demographic History ◽

Insect Pest ◽

Scale Insect ◽

The Philippines ◽

Geographic Region ◽

Invasive Pest ◽

Economic Losses ◽

History Of

Despite the fact that massive outbreaks of the coconut scale insect pest, Aspidiotus rigidus Reyne (Hemiptera: Diaspididae) are inflicting significant economic losses to the Philippines’ coconut industry, little is known about the population and dispersal history of this invasive pest in the country. Here, we examined the genetic diversity, structure and demographic history of A. rigidus sampled from localities with reported outbreaks from 2014 to 2017. We analyzed the genetic structure of the outbreak populations using mitochondrial COI and nuclear EF-1α markers. Both markers and all methods of population genetic structure analyses indicate clear differentiation among the A. rigidus populations separating the north from the southern regions of the Philippines. Very low or no genetic differentiation was observed within and amongst the populations per geographic region indicating two unrelated outbreak events of the pest originating from two genetically uniform populations isolated in each respective region. Historical data supports the resurgence of an established A. rigidus population in the south which could have been driven by sudden climatic changes or human-induced habitat imbalance. Our study provides valuable information on the genetic differentiation of the two A. rigidus groups that would be useful for developing and implementing biological control strategies against this pest in the Philippines.

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Genetic and Metabolomic Differentiation of Physalis Ixocarpa Brot. Populations in Michoacan State, Mexico

10.21203/rs.3.rs-585240/v1 ◽

2021 ◽

Author(s):

Ariana Martínez-Vega ◽

Ernesto Oregel-Zamudio ◽

Ignacio García ◽

Vinicio Villalpando-Arteaga ◽

Jesus Torres

Keyword(s):

Genetic Structure ◽

Genetic Differentiation ◽

Native Species ◽

Genetic Resource ◽

Fruit Size ◽

Aromatic Aldehydes ◽

Organoleptic Properties ◽

Metabolomic Fingerprinting ◽

Intergenic Sequences ◽

Signatures Of Selection

Abstract Physalis ixocarpa Brot. is a native species that is consumed in many localities of the Cienega-Chapala in Mexico's Michoacan state. These fruits are cultivated and collected into traditional maize crops. The fruits are similar to P. Philadelphica, but the differences are in the fruit size and organoleptic properties (flavor, sweetness). According to antecedents of domestication that this zone represents in Mexico, is possible that P. ixocarpa shows incipient differentiation signals in genetic structure and metabolomic fingerprinting. Our objective was find evidences of genetic and metabolomic differentiation among populations of P. ixocarpa in the Cienega-Chapala. We used the sequencing of the chloroplast intergenic sequences psbJ – petA and trnL – rpL32, and the metabolomic fingerprinting by GC-MS. The results showed that exist genetic differentiation (FST) and signatures of selection (Fu's Fs' neutrality test) among populations. Moreover the metabolomic fingerprinting showed differences among populations and an increase of aldehydes, aromatic aldehydes, ester, and alcohols related with organoleptic properties of P. ixocarpa. We conclude that P. ixocarpa is an important genetic resource with signatures of differentiation in the Cienega-Chapala, Michoacan state, Mexico that eventually could be related with domestication signatures.

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