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

Phylogeographic 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 relatively recently. We investigated inter- and intra-island population structure in a Philippine endemic bird genus (Sarcophanops) to determine if genetic differentiation has evolved during the recent period of isolation. We sequenced thousands of genome-wide 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 geographic bounds. A previous assessment of mitochondrial DNA detected deep structure between Sarcophanops samarensis and sister species, S. 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 likely demonstrates an effect of recent geographic isolation (post-LGM) on the genetic structure of Philippine avifauna. We suggest that the general lack of evidence for differentiation between recently isolated islands is a failure to detect subtle population structure due to past genetic sampling constraints, rather than the absence of such structure.

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

10.7287/peerj.preprints.27546 ◽

2019 ◽

Author(s):

Luke 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 ◽

Geographic Isolation ◽

Recent Period ◽

Genetic Sampling ◽

Genome Wide ◽

Species Analysis

Phylogeographic 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 relatively recently. We investigated inter- and intra-island population structure in a Philippine endemic bird genus (Sarcophanops) to determine if genetic differentiation has evolved during the recent period of isolation. We sequenced thousands of genome-wide 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 geographic bounds. A previous assessment of mitochondrial DNA detected deep structure between Sarcophanops samarensis and sister species, S. 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 likely demonstrates an effect of recent geographic isolation (post-LGM) on the genetic structure of Philippine avifauna. We suggest that the general lack of evidence for differentiation between recently isolated islands is a failure to detect subtle population structure due to past genetic sampling constraints, rather than the absence of such structure.

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A differential expression of pyrethroid resistance genes in the malaria vector Anopheles funestus across Uganda is associated with patterns of gene flow

PLoS ONE ◽

10.1371/journal.pone.0240743 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0240743

Author(s):

Maurice Marcel Sandeu ◽

Charles Mulamba ◽

Gareth D. Weedall ◽

Charles S. Wondji

Keyword(s):

Population Structure ◽

Gene Flow ◽

Genetic Structure ◽

Genetic Differentiation ◽

Insecticide Resistance ◽

Pyrethroid Resistance ◽

Anopheles Funestus ◽

Metabolic Resistance ◽

Transcription Analysis ◽

Genome Wide

Background Insecticide resistance is challenging the effectiveness of insecticide-based control interventions to reduce malaria burden in Africa. Understanding the molecular basis of insecticides resistance and patterns of gene flow in major malaria vectors such as Anopheles funestus are important steps for designing effective resistance management strategies. Here, we investigated the association between patterns of genetic structure and expression profiles of genes involved in the pyrethroid resistance in An. funestus across Uganda and neighboring Kenya. Methods Blood-fed mosquitoes An. funestus were collected across the four localities in Uganda and neighboring Kenya. A Microarray-based genome-wide transcription analysis was performed to identify the set of genes associated with permethrin resistance. 17 microsatellites markers were genotyped and used to establish patterns of genetic differentiation. Results Microarray-based genome-wide transcription profiling of pyrethroid resistance in four locations across Uganda (Arua, Bulambuli, Lira, and Tororo) and Kenya (Kisumu) revealed that resistance was mainly driven by metabolic resistance. The most commonly up-regulated genes in pyrethroid resistance mosquitoes include cytochrome P450s (CYP9K1, CYP6M7, CYP4H18, CYP4H17, CYP4C36). However, expression levels of key genes vary geographically such as the P450 CYP6M7 [Fold-change (FC) = 115.8 (Arua) vs 24.05 (Tororo) and 16.9 (Kisumu)]. In addition, several genes from other families were also over-expressed including Glutathione S-transferases (GSTs), carboxylesterases, trypsin, glycogenin, and nucleotide binding protein which probably contribute to insecticide resistance across Uganda and Kenya. Genotyping of 17 microsatellite loci in the five locations provided evidence that a geographical shift in the resistance mechanisms could be associated with patterns of population structure throughout East Africa. Genetic and population structure analyses indicated significant genetic differentiation between Arua and other localities (FST>0.03) and revealed a barrier to gene flow between Arua and other areas, possibly associated with Rift Valley. Conclusion The correlation between patterns of genetic structure and variation in gene expression could be used to inform future interventions especially as new insecticides are gradually introduced.

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Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

10.21203/rs.3.rs-779119/v1 ◽

2021 ◽

Author(s):

Guai-qiang Chai ◽

Yizhong Duan ◽

Peipei Jiao ◽

Zhongyu Du ◽

Furen Kang

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Association Studies ◽

Natural Populations ◽

Principal Component ◽

Nucleotide Polymorphisms ◽

Future Design ◽

Ammopiptanthus Nanus ◽

Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

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Population structure of Opisthorchis felineus (Trematoda) and its second intermediate hosts — cyprinid fishes in the Ob-Irtysh focus of opisthorchiasis, based on allozyme data

Helminthologia ◽

10.2478/s11687-014-0246-3 ◽

2014 ◽

Vol 51 (4) ◽

pp. 309-317 ◽

Cited By ~ 2

Author(s):

O. Zhigileva ◽

V. Ozhireľev ◽

T. Stepanova ◽

T. Moiseenko

Keyword(s):

Population Structure ◽

Genetic Structure ◽

Genetic Differentiation ◽

Population Genetic Structure ◽

Population Genetic ◽

Allozyme Variation ◽

Intermediate Hosts ◽

Opisthorchis Felineus ◽

Cyprinid Fishes ◽

Low Levels

AbstractGenetic variability of West Siberian populations of Opisthorchis felineus and two species of cyprinid fish, its second intermediate hosts, was studied by isozyme analysis. Low levels of allozyme variation and genetic differentiation in O. felineus from the Ob-Irtysh focus of opisthorchiasis were detected. The proportion of polymorphic loci was 21.1 %, the average observed heterozygosity (Hobs) was 0.008, and expected heterozygosity (Hexp) was 0.052. For most loci in O. felineus deficit of heterozygotes (FIS = 0.7424) was observed. A comparison of population genetic structure of fish and parasites showed they were not congruent. Estimates of genetic differentiation of the parasite were smaller than for the fish — its intermediate host. Migration and population structure of the second intermediate hosts do not play an important role in formation of the population-genetic structure of O. felineus in the Ob-Irtysh focus of opisthorchiasis.

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Spatial and temporal genetic structure of the New Zealand scallop Pecten novaezelandiae: A multidisciplinary perspective

10.26686/wgtn.17009846.v1 ◽

2021 ◽

Author(s):

◽

Catarina Nunes Soares Silva

Keyword(s):

Population Structure ◽

Genetic Variation ◽

New Zealand ◽

Genetic Structure ◽

Genetic Differentiation ◽

Marine Species ◽

Effective Management ◽

Spatial And Temporal Scales ◽

Marine Connectivity ◽

Management And Conservation

<p>Knowledge about the population genetic structure of species and the factors shaping such patterns is crucial for effective management and conservation. The complexity of New Zealand’s marine environment presents a challenge for management and the classification of its marine biogeographic areas. As such, it is an interesting system to investigate marine connectivity dynamics and the evolutionary processes shaping the population structure of marine species. An accurate description of spatial and temporal patterns of dispersal and population structure requires the use of tools capable of incorporating the variability of the mechanisms involved. However, these techniques are yet to be broadly applied to New Zealand marine organisms. This study used genetic markers to assess the genetic variation of the endemic New Zealand scallop, Pecten novaezelandiae, at different spatial and temporal scales. A multidisciplinary approach was used integrating genetic with environmental data (seascape genetics) and hydrodynamic modelling tools. P. novaezelandiae supports important commercial, recreational and customary fisheries but there is no previous information about its genetic structure. Therefore, twelve microsatellite markers were developed for this study (Chapter 2). Samples (n=952) were collected from 15 locations to determine the genetic structure across the distribution range of P. novaezelandiae. The low genetic structure detected in this study is expected given the recent evolutionary history, the large reproductive potential and the pelagic larval duration of the species (approximately 3 weeks). A significant isolation by distance signal and a degree of differentiation from north to south was apparent, but this structure conflicted with some evidence of panmixia. A latitudinal genetic diversity gradient was observed that might reflect the colonisation and extinction events and insufficient time to reach migration-drift equilibrium during a recent range expansion (Chapter 3). A seascape genetic approach was used to test for associations between patterns of genetic variation in P. novaezelandiae and environmental variables (three geospatial and six environmental variables). Although the geographic distance between populations was an important variable explaining the genetic variation among populations, it appears that levels of genetic differentiation are not a simple function of distance. Evidence suggests that some environmental factors such as freshwater discharge and suspended particulate matter can be contributing to the patterns of genetic differentiation of P. novaezelandiae in New Zealand (Chapter 4). Dispersal of P. novaezelandiae was investigated at a small spatial and temporal scale in the Coromandel fishery using genetic markers integrated with hydrodynamic modelling. For the spatial analysis, samples (n=402) were collected in 2012 from 5 locations and for the temporal analysis samples (n=383) were collected in 2012 and 2014 from 3 locations. Results showed small but significant spatial and temporal genetic differentiation, suggesting that the Coromandel fishery does not form a single panmictic unit with free gene flow and supporting a model of source-sink population dynamics (Chapter 5). The importance of using multidisciplinary approaches at different spatial and temporal scales is widely recognized as a means to better understand the complex processes affecting marine connectivity. The outcomes of this study highlight the importance of incorporating these different approaches, provide vital information to assist in effective management and conservation of P. novaezelandiae and contribute to our understanding of evolutionary processes shaping population structure of marine species.</p>

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Brown banded bamboo shark (Chiloscyllium punctatum) shows high genetic diversity and differentiation in Malaysian waters

Scientific Reports ◽

10.1038/s41598-021-94257-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kean Chong Lim ◽

Amy Yee-Hui Then ◽

Alison Kim Shan Wee ◽

Ahemad Sade ◽

Richard Rumpet ◽

...

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Population Structure ◽

Genetic Structure ◽

Genetic Differentiation ◽

Fishery Management ◽

Peninsular Malaysia ◽

Fine Scale ◽

Nadh Dehydrogenase Subunit 2 ◽

Bamboo Shark

AbstractThe demersal brown banded bamboo shark Chiloscyllium punctatum is a major component of sharks landed in Malaysia. However, little is known about their population structure and the effect of high fishing pressure on these weak swimming sharks. Both mitochondrial DNA control region (1072 bp) and NADH dehydrogenase subunit 2 (1044 bp) were used to elucidate the genetic structure and connectivity of C. punctatum among five major areas within the Sundaland region. Our findings revealed (i) strong genetic structure with little present day mixing between the major areas, (ii) high intra-population genetic diversity with unique haplotypes, (iii) significant correlation between genetic differentiation and geographical distance coupled with detectable presence of fine scale geographical barriers (i.e. the South China Sea), (iv) historical directional gene flow from the east coast of Peninsular Malaysia towards the west coast and Borneo, and (v) no detectable genetic differentiation along the coastline of east Peninsular Malaysia. Genetic patterns inferred from the mitochondrial DNA loci were consistent with the strong coastal shelf association in this species, the presence of contemporary barriers shaped by benthic features, and limited current-driven egg dispersal. Fine scale population structure of C. punctatum highlights the need to improve genetic understanding for fishery management and conservation of other small-sized sharks.

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Spatial and temporal genetic structure of the New Zealand scallop Pecten novaezelandiae: A multidisciplinary perspective

10.26686/wgtn.17009846 ◽

2021 ◽

Author(s):

◽

Catarina Nunes Soares Silva

Keyword(s):

Population Structure ◽

Genetic Variation ◽

New Zealand ◽

Genetic Structure ◽

Genetic Differentiation ◽

Marine Species ◽

Effective Management ◽

Spatial And Temporal Scales ◽

Marine Connectivity ◽

Management And Conservation

<p>Knowledge about the population genetic structure of species and the factors shaping such patterns is crucial for effective management and conservation. The complexity of New Zealand’s marine environment presents a challenge for management and the classification of its marine biogeographic areas. As such, it is an interesting system to investigate marine connectivity dynamics and the evolutionary processes shaping the population structure of marine species. An accurate description of spatial and temporal patterns of dispersal and population structure requires the use of tools capable of incorporating the variability of the mechanisms involved. However, these techniques are yet to be broadly applied to New Zealand marine organisms. This study used genetic markers to assess the genetic variation of the endemic New Zealand scallop, Pecten novaezelandiae, at different spatial and temporal scales. A multidisciplinary approach was used integrating genetic with environmental data (seascape genetics) and hydrodynamic modelling tools. P. novaezelandiae supports important commercial, recreational and customary fisheries but there is no previous information about its genetic structure. Therefore, twelve microsatellite markers were developed for this study (Chapter 2). Samples (n=952) were collected from 15 locations to determine the genetic structure across the distribution range of P. novaezelandiae. The low genetic structure detected in this study is expected given the recent evolutionary history, the large reproductive potential and the pelagic larval duration of the species (approximately 3 weeks). A significant isolation by distance signal and a degree of differentiation from north to south was apparent, but this structure conflicted with some evidence of panmixia. A latitudinal genetic diversity gradient was observed that might reflect the colonisation and extinction events and insufficient time to reach migration-drift equilibrium during a recent range expansion (Chapter 3). A seascape genetic approach was used to test for associations between patterns of genetic variation in P. novaezelandiae and environmental variables (three geospatial and six environmental variables). Although the geographic distance between populations was an important variable explaining the genetic variation among populations, it appears that levels of genetic differentiation are not a simple function of distance. Evidence suggests that some environmental factors such as freshwater discharge and suspended particulate matter can be contributing to the patterns of genetic differentiation of P. novaezelandiae in New Zealand (Chapter 4). Dispersal of P. novaezelandiae was investigated at a small spatial and temporal scale in the Coromandel fishery using genetic markers integrated with hydrodynamic modelling. For the spatial analysis, samples (n=402) were collected in 2012 from 5 locations and for the temporal analysis samples (n=383) were collected in 2012 and 2014 from 3 locations. Results showed small but significant spatial and temporal genetic differentiation, suggesting that the Coromandel fishery does not form a single panmictic unit with free gene flow and supporting a model of source-sink population dynamics (Chapter 5). The importance of using multidisciplinary approaches at different spatial and temporal scales is widely recognized as a means to better understand the complex processes affecting marine connectivity. The outcomes of this study highlight the importance of incorporating these different approaches, provide vital information to assist in effective management and conservation of P. novaezelandiae and contribute to our understanding of evolutionary processes shaping population structure of marine species.</p>

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Phylogeography and limited distribution of the endangered freshwater crayfish, Euastacus urospinosus

Australian Journal of Zoology ◽

10.1071/zo15006 ◽

2015 ◽

Vol 63 (4) ◽

pp. 236

Author(s):

Charlotte R. Hurry ◽

Daniel J. Schmidt ◽

Jane M. Hughes

Keyword(s):

Population Structure ◽

Genetic Structure ◽

Sequence Data ◽

Species Conservation ◽

Freshwater Crayfish ◽

Isolated Populations ◽

Lowland Streams ◽

High Level ◽

Conservation Plans ◽

High Elevations

Conservation plans can benefit from understanding patterns of genetic structure because many endangered species are spatially fragmented. In particular, headwater species in high elevations are expected to exhibit a high level of population structure, as dispersal through lowland streams may be limited. Euastacus urospinosus is an endangered freshwater crayfish that, until recently, was thought to have a distribution of just 200 km2. In the current study, we identified a total of 26 locations for this species across a 1225 km2 region spanning the Brisbane and Mary River catchments of south-east Queensland, Australia. We then used mitochondrial DNA sequence data to investigate the population structure and the phylogeographic divergence between four uplands. We found significant population differentiation for this species, which conforms to the headwater model of genetic structure. Further, we found that fragmentation between these uplands is most likely historical, as the first divergence between lineages dated back 2.1 million years. Overall, we found no reason to remove the conservation rating of ‘endangered’ for this species. Conservation plans should seek to preserve the genetic integrity of these uplands by considering them to be genetically distinct and isolated populations.

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Genetic Divergence between Two Sympatric Ecotypes of Phalaenopsis pulcherrima on Hainan Island

Diversity ◽

10.3390/d13090446 ◽

2021 ◽

Vol 13 (9) ◽

pp. 446

Author(s):

Xiangyu Hu ◽

Siren Lan ◽

Xiqiang Song ◽

Fusun Yang ◽

Zhe Zhang ◽

...

Keyword(s):

Genetic Structure ◽

Genetic Differentiation ◽

Reproductive Isolation ◽

Hainan Island ◽

Nutrient Content ◽

Soil Conditions ◽

Island Population ◽

Ecological Differentiation ◽

Ecotypic Differentiation ◽

High Level

Ecotypes are the result of ecological differentiation at the early stages of speciation. Adaptation to soil conditions offers arguably the best examples of local adaptation in plants. Two sympatric ecotypes, with either a red or green abaxial leaf surface, were found without clear geographical isolation in Phalaenopsis pulcherrima, a Southeast Asia endemic and endangered orchid. The soil of the red leaf ecotype has a higher water content and nutrient content than the green ecotype. What is the genetic structure of the two ecotypes? Is there complete or partial reproductive isolation between the two ecotypes? In this work, leaf reflection of the two ecotypes in P. pulcherrima were compared, to illustrate their difference in leaf color. The genetic differentiation between two ecotypes was examined, using ISSR and SRAP markers to determine the genetic structure of the populations. Our results showed that the green ecotype had reflectance spectrum peaks at 530 nm and 620 nm, while in the red ecotype, the peak at 530 nm was absent. A total of 165 ISSR and SRAP loci showed a high level of genetic diversity within the green ecotype, and analyses of the population structure revealed two genetic clusters that corresponded to the red and green ecotypes. The percentage of variation between the two ecotypes (24.55%) was greater than the percentage of variation among the populations (16.54%)—indicating partial reproductive isolation, high genetic differentiation, and that ecological differentiation has been more important than geographical barriers among populations within ecotypes. Most pairwise FST values between the populations within either ecotype on Hainan Island were less than 0.15; however, the FST between both the Thai and Malaysian populations and the Hainan Island population was greater than 0.25, due to South China sea isolation. Ecotypic differentiation is an important part of speciation; therefore, we must take into account the axes along which lineages sort, when formulating protection strategies.

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