scholarly journals Structure and phylogeography of two tropical predators, spinner ( Stenella longirostris ) and pantropical spotted ( S. attenuata ) dolphins, from SNP data

2018 ◽  
Vol 5 (4) ◽  
pp. 171615 ◽  
Author(s):  
Matthew S. Leslie ◽  
Phillip A. Morin
Keyword(s):  
Population Structure ◽  
Pacific Ocean ◽  
Nuclear Dna ◽  
Population Level ◽  
Genetic Connectivity ◽  
Nucleotide Polymorphisms ◽  
Stenella Longirostris ◽  
Spinner Dolphin ◽  
Spinner Dolphins ◽  
Almost All

Little is known about global patterns of genetic connectivity in pelagic dolphins, including how circumtropical pelagic dolphins spread globally following the rapid and recent radiation of the subfamily delphininae. In this study, we tested phylogeographic hypotheses for two circumtropical species, the spinner dolphin ( Stenella longirostris ) and the pantropical spotted dolphin ( Stenella attenuata ), using more than 3000 nuclear DNA single nucleotide polymorphisms (SNPs) in each species. Analyses for population structure indicated significant genetic differentiation between almost all subspecies and populations in both species. Bayesian phylogeographic analyses of spinner dolphins showed deep divergence between Indo-Pacific, Atlantic and eastern tropical Pacific Ocean (ETP) lineages. Despite high morphological variation, our results show very close relationships between endemic ETP spinner subspecies in relation to global diversity. The dwarf spinner dolphin is a monophyletic subspecies nested within a major clade of pantropical spinner dolphins from the Indian and western Pacific Ocean populations. Population-level division among the dwarf spinner dolphins was detected—with the northern Australia population being very different from that in Indonesia. In contrast to spinner dolphins, the major boundary for spotted dolphins is between offshore and coastal habitats in the ETP, supporting the current subspecies-level taxonomy. Comparing these species underscores the different scale at which population structure can arise, even in species that are similar in habitat (i.e. pelagic) and distribution.

scholarly journals A whole-genome scan for association with invasion success in the fruit fly Drosophila suzukii using contrasts of allele frequencies corrected for population structure

2019 ◽  
Author(s):  
Laure Olazcuaga ◽  
Anne Loiseau ◽  
Hugues Parrinello ◽  
Mathilde Paris ◽  
Antoine Fraimout ◽  
...  
Keyword(s):  
Population Structure ◽  
Genome Wide Association Study ◽  
Evolutionary Model ◽  
Population Level ◽  
Allele Frequencies ◽  
Invasion Success ◽  
Nucleotide Polymorphisms ◽  
Drosophila Suzukii ◽  
A Genome ◽  
Invasive Status

AbstractEvidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or suppressed. Here we characterized the genome response of the spotted wing drosophila Drosophila suzukii during the worldwide invasion of this pest insect species, by conducting a genome-wide association study to identify genes involved in adaptive processes during invasion. Genomic data from 22 population samples were analyzed to detect genetic variants associated with the status (invasive versus native) of the sampled populations based on a newly developed statistic, we called C2, that contrasts allele frequencies corrected for population structure. This new statistical framework has been implemented in an upgraded version of the program BayPass. We identified a relatively small set of single nucleotide polymorphisms (SNPs) that show a highly significant association with the invasive status of populations. In particular, two genes RhoGEF64C and cpo, the latter contributing to natural variation in several life-history traits (including diapause) in Drosophila melanogaster, contained SNPs significantly associated with the invasive status in the two separate main invasion routes of D. suzukii. Our methodological approaches can be applied to any other invasive species, and more generally to any evolutionary model for species characterized by non-equilibrium demographic conditions for which binary covariables of interest can be defined at the population level.

scholarly journals RADseq analyses reveal concordant Indian Ocean biogeographic and phylogeographic boundaries in the reef fish Dascyllus trimaculatus

2019 ◽  
Vol 6 (5) ◽  
pp. 172413 ◽  
Author(s):  
E. M. Salas ◽  
G. Bernardi ◽  
M. L. Berumen ◽  
M. R. Gaither ◽  
L. A. Rocha
Keyword(s):  
Indian Ocean ◽  
Red Sea ◽  
Arabian Sea ◽  
Population Level ◽  
Western Indian Ocean ◽  
Genetic Connectivity ◽  
Nucleotide Polymorphisms ◽  
Population Genetic Analysis ◽  
Outlier Loci ◽  
Biogeographic Provinces

Population genetic analysis is an important tool for estimating the degree of evolutionary connectivity in marine organisms. Here, we investigate the population structure of the three-spot damselfish Dascyllus trimaculatus in the Red Sea, Arabian Sea and Western Indian Ocean, using 1174 single nucleotide polymorphisms (SNPs). Neutral loci revealed a signature of weak genetic differentiation between the Northwestern (Red Sea and Arabian Sea) and Western Indian Ocean biogeographic provinces. Loci potentially under selection (outlier loci) revealed a similar pattern but with a much stronger signal of genetic structure between regions. The Oman population appears to be genetically distinct from all other populations included in the analysis. While we could not clearly identify the mechanisms driving these patterns (isolation, adaptation or both), the datasets indicate that population-level divergences are largely concordant with biogeographic boundaries based on species composition. Our data can be used along with genetic connectivity of other species to identify the common genetic breaks that need to be considered for the conservation of biodiversity and evolutionary processes in the poorly studied Western Indian Ocean region.

scholarly journals GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Yu Wan ◽  
Ryan R. Wick ◽  
Justin Zobel ◽  
Danielle J. Ingle ◽  
Michael Inouye ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Level ◽  
R Package ◽  
Whole Genome Sequencing Data ◽  
Nucleotide Polymorphisms ◽  
Network Approach ◽  
Sequencing Data ◽  
Association Tests ◽  
Novel Approach ◽  
Antimicrobial Resistance Genes

Abstract Background Horizontal gene transfer contributes to bacterial evolution through mobilising genes across various taxonomical boundaries. It is frequently mediated by mobile genetic elements (MGEs), which may capture, maintain, and rearrange mobile genes and co-mobilise them between bacteria, causing horizontal gene co-transfer (HGcoT). This physical linkage between mobile genes poses a great threat to public health as it facilitates dissemination and co-selection of clinically important genes amongst bacteria. Although rapid accumulation of bacterial whole-genome sequencing data since the 2000s enables study of HGcoT at the population level, results based on genetic co-occurrence counts and simple association tests are usually confounded by bacterial population structure when sampled bacteria belong to the same species, leading to spurious conclusions. Results We have developed a network approach to explore WGS data for evidence of intraspecies HGcoT and have implemented it in R package GeneMates (github.com/wanyuac/GeneMates). The package takes as input an allelic presence-absence matrix of interested genes and a matrix of core-genome single-nucleotide polymorphisms, performs association tests with linear mixed models controlled for population structure, produces a network of significantly associated alleles, and identifies clusters within the network as plausible co-transferred alleles. GeneMates users may choose to score consistency of allelic physical distances measured in genome assemblies using a novel approach we have developed and overlay scores to the network for further evidence of HGcoT. Validation studies of GeneMates on known acquired antimicrobial resistance genes in Escherichia coli and Salmonella Typhimurium show advantages of our network approach over simple association analysis: (1) distinguishing between allelic co-occurrence driven by HGcoT and that driven by clonal reproduction, (2) evaluating effects of population structure on allelic co-occurrence, and (3) direct links between allele clusters in the network and MGEs when physical distances are incorporated. Conclusion GeneMates offers an effective approach to detection of intraspecies HGcoT using WGS data.

Descriptive parameters of pulsed calls for the spinner dolphin, Stenella longirostris, in the Fernando de Noronha Archipelago, Brazil

2008 ◽  
Vol 88 (6) ◽  
pp. 1093-1097 ◽  
Author(s):  
Marcos R. Rossi-Santos ◽  
José Martins da Silva ◽  
Flavio Lima Silva ◽  
Emygdio L.A. Monteiro-Filho
Keyword(s):  
Visual Inspection ◽  
Maximum Frequency ◽  
Acoustic Parameters ◽  
Call Duration ◽  
Minimum Frequency ◽  
Stenella Longirostris ◽  
Spinner Dolphin ◽  
Fernando De Noronha ◽  
Spinner Dolphins ◽  
Southern Atlantic Ocean

The aim of this work is to describe the repertoire of calls utilized by the spinner dolphins (Stenella longirostris) in the southern Atlantic Ocean. We measured four acoustic parameters of the fundamental frequency of each call: (i) duration; (ii) frequency amplitude; (iii) minimum frequency; and (iv) maximum frequency. We also classified calls by their shape contour by visual inspection of the spectrograms. The obtained values for call duration were 0.046 to 2.08 seconds (mean 0.433, standard deviation (SD) 0.433), amplitude of 0.13 to 2.01 kHz (mean of 0.36, SD 0.29), minimum frequency of 0.22 to 1.80 (mean 0.55, SD 0.29), maximum frequency of 0.46 to 7.50 (mean 1.00, SD 0.89). We classified 73 calls by spectral contour, identifying six basic types of discernible calls, showing heterogeneity among the call types, with C1, C2 and C3 calls presenting higher frequencies, 21, 30 and 23%, respectively. We found that the calls of S. longirostris in the Fernando de Noronha Archipelago are more diverse and complex than previously recognized for spinner dolphins and further studies worldwide can reinforce the broad use of this sound for the species repertoire.

scholarly journals Mitogenomic differentiation in spinner (Stenella longirostris) and pantropical spotted dolphins (S. attenuata) from the eastern tropical Pacific Ocean

2016 ◽  
Author(s):  
Leslie Matthew S. ◽  
Archer Frederick I. ◽  
Morin Phillip A.
Keyword(s):  
Pacific Ocean ◽  
Haplotype Diversity ◽  
Morphological Diversity ◽  
Tropical Pacific ◽  
Tropical Pacific Ocean ◽  
Eastern Tropical Pacific ◽  
Stenella Longirostris ◽  
Snp Data ◽  
Subspecies Level ◽  
Spinner Dolphins

AbstractSpinner dolphins (Stenella longirostris) and spotted dolphins (S. attenuata) show high intraspecific morphological diversity and endemic subspecies in the eastern tropical Pacific Ocean (ETP). Previous studies of mitochondrial DNA (mtDNA) have found low genetic differentiation among most of these groups, possibly due to demographic factors, ongoing gene flow, and/or recent divergence. These species were heavily depleted due to bycatch in the ETP yellowfin tuna fishery. Because population structure is important for accurate management of the recovery of these species, we collected whole mitochondrial genome sequences from 104 spinner and 76 spotted dolphins to test structure hypotheses at multiple hierarchical levels. Our results showed significant differences between subspecies of spotted (FST: 0.0125; P = 0.0402) and spinner dolphins (FST: 0.0133; P = 0.034), but no support for the division of existing offshore stocks of spotted dolphins or Tres Marias spinner dolphins. We compare these results to previous results of genome-wide nuclear SNP data and suggest high haplotype diversity, female dispersal, male philopatry, or relative power of the two datasets explains the differences observed. Our results further support a genetic basis for biologically meaningful management units at the subspecies level, and provide a critical component to mitigating historical and continued fishery interactions.

Mitochondrial and microsatellite DNA analyses of harbour seal population structure in the northeast Pacific Ocean

1999 ◽  
Vol 77 (6) ◽  
pp. 930-943 ◽  
Author(s):  
Theresa M Burg ◽  
Andrew W Trites ◽  
Michael J Smith
Keyword(s):  
British Columbia ◽  
Population Structure ◽  
Pacific Ocean ◽  
Nuclear Dna ◽  
Puget Sound ◽  
Mitochondrial Control Region ◽  
Single Individual ◽  
The Pacific ◽  
Harbour Seals ◽  
The Pacific Ocean

The genetic diversity and population structure of harbour seals (Phoca vitulina richardsi) along the coasts of British Columbia and parts of Alaska were investigated using both mitochondrial DNA (mtDNA) and nuclear DNA. A 475-bp fragment of the mitochondrial control region was amplified and sequenced from 128 animals. Sixty variable sites defined 72 mtDNA haplotypes with pairwise nucleotide differences as high as 5%. Fifty-eight haplotypes were represented by a single individual, and shared haplotypes were generally restricted to a small geographic range. Phylogenetic reconstruction revealed two distinct populations comprising (i) southern British Columbia and (ii) northern British Columbia - southeast Alaska. Furthermore, the order of the clades suggests that the Pacific Ocean was colonized at least twice, 670 000 and 380 000 years ago. Haplotypes from the first invasion are restricted to a small number of seals around southern Vancouver Island. Analyses of five polymorphic microsatellite loci showed significant differences between the populations of southern British Columbia and northern British Columbia - Alaska. Migration rates for males based on microsatellite data (3-22 seals/generation) were higher than those obtained for females from mtDNA data (0.3 females/generation). Combining all the DNA data collected to date suggests that there are at least three populations of harbour seals in the Pacific composed of seals from (i) Japan, Russia, Alaska, and northern British Columbia, (ii) southern British Columbia and Puget Sound, Washington, and (iii) the outer coasts of Washington, Oregon, and California. The data do not support the existence of two subspecies of harbour seals in the Pacific Ocean.

Spinner dolphin (Stenella longirostris) resting habitat in Samadai Reef (Egypt, Red Sea) protected through tourism management

2008 ◽  
Vol 89 (1) ◽  
pp. 211-216 ◽  
Author(s):  
Giuseppe Notarbartolo-di-Sciara ◽  
Mahmoud H. Hanafy ◽  
Moustafa M. Fouda ◽  
Ayman Afifi ◽  
Marina Costa
Keyword(s):  
Red Sea ◽  
Core Habitat ◽  
Tourism Management ◽  
Stenella Longirostris ◽  
Spinner Dolphin ◽  
The Mean ◽  
Red Sea Coast ◽  
Spinner Dolphins ◽  
Governmental Management ◽  
Sea Coast

The daily presence of spinner dolphins,Stenella longirostris, inside a small reef offshore the Red Sea coast of southern Egypt was monitored from January 2004 to January 2006. Observations indicated marked seasonal and daily variations in the use of the reef as a resting and socializing area by the dolphins, consistent during the two years of monitoring. Overall, the mean number of dolphins present in the reef at any day was 39.2 (SD = 39.34, range 0–210), with the lowest presence in February to April and the highest in June. Similar to other populations of this species in other oceans, dolphins entered the reef between daybreak and mid-morning, and started exiting during the afternoon hours. Although calves were seen in all seasons, a sharp peak was observed in June. Monitoring data provided indications relevant to governmental management efforts, which were implemented in 2004 to ensure that the dolphins could continue using the reef for their resting needs while a sustainable, respectful tourist activity is allowed in a designated zone of the reef adjacent to the dolphins' core habitat.

scholarly journals Underlying microevolutionary processes parallel macroevolutionary patterns in ancient Neotropical Mountains

2020 ◽  
Author(s):  
Marcos Vinicius Dantas-Queiroz ◽  
Tami da Costa Cacossi ◽  
Bárbara Simões Santos Leal ◽  
Cleber Juliano Neves Chaves ◽  
Thais N. C. Vasconcelos ◽  
...  
Keyword(s):  
Population Structure ◽  
Nuclear Dna ◽  
Environmental Changes ◽  
Isolation By Distance ◽  
Population Level ◽  
Isolated Populations ◽  
Climatic Fluctuations ◽  
Espinhaço Range ◽  
The Past ◽  
Isolation By Environment

ABSTRACTAimThe exceptional species-richness associated with mountains worldwide is linked to the fragmented topography of these areas, responsible for constantly isolating populations during periods of climatic fluctuations. Consequently, endemism and spatial turnover in mountains are very high and few species are widespread among entire mountain ranges, precluding population-level studies that help understanding how macroevolutionary patterns were shaped. Here, we used the bromeliad Vriesea oligantha, a species endemic to, but widespread in, one of the most species-rich ancient montane areas in the globe, the Espinhaco Range, to test how environmental changes over time may have acted on the evolutionary history of this taxon, contributing to understanding how montane macroevolutionary patterns were shaped. Through analyses of plastidial and nuclear DNA of V. oligantha, we dated its origin and intraspecific diversification, and estimated the genetic diversity, structure and migration rates among populations. Using climatic and geographic variables, we modeled suitable areas for the present and the past, estimating corridors between isolated populations. We also used demographic analyses to estimate ancient population dynamics of V. oligantha. Finally, we tested whether climatic variables or geographical distance explain the observed population structure. The origin and intraspecific diversification of V. oligantha are related to early climatic oscillations during the Plio-Pleistocene. This species has a high population structure due to its low pollen and seed dispersibility. The analysis of species distribution modeling estimated corridors between populations in the past, whereas the structure of V. oligantha results from both models of isolation by distance and isolation by environment. The phylogeographic patterns of Vriesea oligantha reflect previously recognized spatial and temporal macroevolutionary patterns in the Espinhaco Range, providing insights into how microevolutionary processes may have given rise to this astonishing mountain biodiversity.

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