scholarly journals Phylogeography of the banded butterflyfish, Chaetodon striatus, indicates high connectivity between biogeographic provinces and ecosystems in the western Atlantic

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Ana M.R. Liedke ◽  
Hudson T. Pinheiro ◽  
Sergio R. Floeter ◽  
Giacomo Bernardi
Keyword(s):  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Haplotype Network ◽  
Genetic Connectivity ◽  
Rocky Reef ◽  
Recent Population Expansion ◽  
Western Atlantic ◽  
Network Analyses ◽  
Biogeographic Provinces ◽  
The Caribbean

ABSTRACT Among the four butterflyfishes of the genus Chaetodon present in the western Atlantic, the banded butterflyfish Chaetodon striatus has the largest distribution range, spanning 44 degrees of latitude (from Massachusetts, USA to Santa Catarina, Brazil). Although the ecology of the banded butterflyfish has been well studied over its entire range, nothing is known about its phylogeography and how biogeographic barriers structure its populations. To assess the level of genetic connectivity among populations from distinct biogeographic provinces and environmental conditions, we collected samples from seven localities: Puerto Rico, in the Caribbean, and Tamandaré, Salvador, Abrolhos, Trindade Island, Arraial do Cabo and Florianópolis, in Brazil. One nuclear (rag 2) and two mitochondrial (control region and cyt b) molecular markers were sequenced. Our findings are consistent with a recent population expansion, around 30-120 thousand years ago, which was found for all populations. Haplotype network analyses point to the Caribbean as a refugium before the population expansion. Results show no geographic pattern of genetic diversity. Indeed, a lack of population structure was found and no isolation was observed across oceanographic barriers, as well as between coral and rocky reef ecosystems. Furthermore, no directionality in the migration pattern was found among populations. Since ecological and environmental characteristics are very diverse across such a vast geographic range, the lack of genetic differentiation suggests that C. striatus evolved ecological plasticity rather than local adaptation in the western Atlantic.

scholarly journals Demographic history of the fragmented yellowthroated bulbul (Pycnonotus xantholaemus) population in the Deccan Peninsula, India

2020 ◽  
Vol 43 ◽  
pp. 199-207
Author(s):  
A Jha ◽  
K Vasudevan
Keyword(s):  
Demographic History ◽  
Population Decline ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Haplotype Network ◽  
Genetic Connectivity ◽  
Founder Population ◽  
Effective Population ◽  
Genetic Structuring

The yellow-throated bulbul (YTB) is an endemic passerine restricted to scrub forests along hill slopes with exposed rocky outcrops in the Deccan Peninsula, India. It is found in small, discontinuous populations and is vulnerable to extinction due to ongoing habitat loss and subsequent population decline. To assess the genetic connectivity and past demography, we sequenced 1050 nucleotide base pairs of the mitochondrial control region of 60 individuals that represent distinct populations in the geographic range of the species. We recovered 39 haplotypes defined by 81 variable sites. Haplotype diversity was high with low nucleotide diversity, suggesting rapid population growth from a founder population with a small effective population size. The negative values of Tajima’s D and Fu’s Fs and small positive value of Ramos-Onsins and Rozas’ R2 suggest deviation from neutrality and population expansion. The haplotype network and demographic expansion parameters further suggest historical population expansion. Mismatch analysis statistics and Bayesian skyline plots estimate population expansion during the late Pleistocene. Although the species presently occurs in small, disconnected we found no structuring of the population. Dispersal events are the most likely explanation for the absence of genetic structuring in the YTB population. These results represent important data for the design of a conservation plan for this endemic and globally threatened species.

scholarly journals The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4409 ◽  
Author(s):  
‘Ale‘alani Dudoit ◽  
Matthew Iacchei ◽  
Richard R. Coleman ◽  
Michelle R. Gaither ◽  
William E. Browne ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Population Expansion ◽  
Global Scale ◽  
Genetic Connectivity ◽  
Marine Biodiversity ◽  
Posterior Density ◽  
Recent Population Expansion ◽  
Western Atlantic ◽  
Highest Posterior Density

The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ∼120–253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To resolve patterns of divergence and phylogeography of S. hispidus, we surveyed 525 bp of mitochondrial cytochrome c oxidase subunit I (COI) from 198 individuals sampled at 10 locations across ∼27,000 km of the species range. Phylogenetic analyses reveal that S. hispidus has a Western Atlantic lineage and a widely distributed Indo-Pacific lineage, separated by sequence divergence of 2.1%. Genetic diversity is much higher in the Western Atlantic (h = 0.929; π = 0.004) relative to the Indo-Pacific (h = 0.105; π < 0.001), and coalescent analyses indicate that the Indo-Pacific population expanded more recently (95% HPD (highest posterior density) = 60,000–400,000 yr) than the Western Atlantic population (95% HPD = 300,000–760,000 yr). Divergence of the Western Atlantic and Pacific lineages is estimated at 710,000–1.8 million years ago, which does not readily align with commonly implicated colonization events between the ocean basins. The estimated age of populations contradicts the prevailing dispersal route for tropical marine biodiversity (Indo-Pacific to Atlantic) with the oldest and most diverse population in the Atlantic, and a recent population expansion with a single common haplotype shared throughout the vast Indian and Pacific oceans. In contrast to the circumtropical fishes, this diminutive reef shrimp challenges our understanding of conventional dispersal capabilities of marine species.

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 Occurrence of the genus Pseudoboletia (Echinoidea: Toxopneustidae) in the South-Western Atlantic: morphological and molecular approaches

2017 ◽  
Vol 65 (1-1) ◽  
pp. 299 ◽  
Author(s):  
Elinia M. Lopes ◽  
Carlos Eduardo L. Ferreira ◽  
Carlos Renato R. Ventura
Keyword(s):  
Sea Urchins ◽  
Population Expansion ◽  
First Record ◽  
Molecular Data ◽  
Brazilian Coast ◽  
Long Distance ◽  
Recent Population Expansion ◽  
Western Atlantic ◽  
Molecular Approaches ◽  
Morphological And Molecular Data

The genus Pseudoboletia was recently reported off coast of Brazil (Trindade-Martin Vaz insular complex). This study reports the first record of this genus to southern of Brazil in Rio de Janeiro and Santa Catarina coasts. Morphological and molecular data showed that sea urchins from Brazil and São Tomé are the same species, genetically distinct of individuals from Indo-Pacific. However, taxonomic identity of Brazilian species remains as a challenge. Two hypotheses to explain the recent records of this species on Brazilian coast are discussed: a recent natural invasion by long-distance dispersal and a recent population expansion in the Brazilian coast after absence or low density period. Rev. Biol. Trop. 65(Suppl. 1): S299-S308. Epub 2017 November 01. 

scholarly journals Estimating the number of lionfish (Pterois volitans) that colonized the Atlantic Ocean

2017 ◽  
Author(s):  
Jason D Selwyn ◽  
John E Johnson ◽  
Alan M Downey-Wall ◽  
Adam M Bynum ◽  
Rebecca M Hamner ◽  
...  
Keyword(s):  
Atlantic Ocean ◽  
Gulf Of Mexico ◽  
Control Region ◽  
Mitochondrial Control Region ◽  
Aquarium Trade ◽  
Allee Effects ◽  
Pterois Volitans ◽  
Western Atlantic ◽  
Introduction Pathway ◽  
The Caribbean

The invasion of the western Atlantic Ocean by the Indo-Pacific red lionfish (Pterois volitans) has had devastating consequences for marine ecosystems. Estimating the number of colonizing lionfish can be useful in identifying the introduction pathway and can inform policy decisions aimed at preventing similar invasions. It is well-established that at least ten lionfish were initially introduced. However, that estimate has not faced statistical scrutiny and is based solely on the number of haplotypes in the maternally-inherited mitochondrial control region observed in samples from the western Atlantic Ocean. To rigorously estimate the number of lionfish introduced, we used a forward-time, Wright-Fisher, population genetic model of the mitochondrial control region in concert with a demographic life-history model to simulate the invasion. The colonization of the western North Atlantic and subsequent spread to the Caribbean and Gulf of Mexico were modeled as single introductions of 1-800 females, which should conservatively estimate the most likely number of colonizing lionfish relative to a model with multiple introductions. Assuming a balanced sex ratio and no Allee effects, the simulations indicate that the Atlantic population was most likely founded by 118 (54-514, 95% HPD) lionfish from the Indo-Pacific, the Caribbean by 84 (22-328, 95% HPD) lionfish from the Atlantic, and the Gulf of Mexico by at least 114 (no upper bound on 95% HPD) lionfish from the Caribbean. Considering the additional possibilities that (1) multiple Indo-Pacific populations colonized the Atlantic and (2) Allee effects (e.g. 50% reduction in fecundity) plagued the colonists, the most likely number of lionfish increased to 180 (88-416, 95% HPD). These results, in combination with all other published data, support the hypothesis that lionfish were introduced to the Atlantic via the aquarium trade, rather than shipping. The most parsimonious introduction pathway is a single release of lionfish in one location, but it seems likely that a combination of smaller and larger releases from a variety of aquarium trade stakeholders occurred near Miami, Florida. Efforts to prevent future invasions via the aquarium trade should focus on the education of stakeholders and the prohibition of release, with adequate rewards for compliance and penalties for violations.

scholarly journals Estimating the number of lionfish (Pterois volitans) that colonized the Atlantic Ocean

2017 ◽  
Author(s):  
Jason D Selwyn ◽  
John E Johnson ◽  
Alan M Downey-Wall ◽  
Adam M Bynum ◽  
Rebecca M Hamner ◽  
...  
Keyword(s):  
Atlantic Ocean ◽  
Gulf Of Mexico ◽  
Control Region ◽  
Mitochondrial Control Region ◽  
Aquarium Trade ◽  
Allee Effects ◽  
Pterois Volitans ◽  
Western Atlantic ◽  
Introduction Pathway ◽  
The Caribbean

The invasion of the western Atlantic Ocean by the Indo-Pacific red lionfish (Pterois volitans) has had devastating consequences for marine ecosystems. Estimating the number of colonizing lionfish can be useful in identifying the introduction pathway and can inform policy decisions aimed at preventing similar invasions. It is well-established that at least ten lionfish were initially introduced. However, that estimate has not faced statistical scrutiny and is based solely on the number of haplotypes in the maternally-inherited mitochondrial control region observed in samples from the western Atlantic Ocean. To rigorously estimate the number of lionfish introduced, we used a forward-time, Wright-Fisher, population genetic model of the mitochondrial control region in concert with a demographic life-history model to simulate the invasion. The colonization of the western North Atlantic and subsequent spread to the Caribbean and Gulf of Mexico were modeled as single introductions of 1-800 females, which should conservatively estimate the most likely number of colonizing lionfish relative to a model with multiple introductions. Assuming a balanced sex ratio and no Allee effects, the simulations indicate that the Atlantic population was most likely founded by 118 (54-514, 95% HPD) lionfish from the Indo-Pacific, the Caribbean by 84 (22-328, 95% HPD) lionfish from the Atlantic, and the Gulf of Mexico by at least 114 (no upper bound on 95% HPD) lionfish from the Caribbean. Considering the additional possibilities that (1) multiple Indo-Pacific populations colonized the Atlantic and (2) Allee effects (e.g. 50% reduction in fecundity) plagued the colonists, the most likely number of lionfish increased to 180 (88-416, 95% HPD). These results, in combination with all other published data, support the hypothesis that lionfish were introduced to the Atlantic via the aquarium trade, rather than shipping. The most parsimonious introduction pathway is a single release of lionfish in one location, but it seems likely that a combination of smaller and larger releases from a variety of aquarium trade stakeholders occurred near Miami, Florida. Efforts to prevent future invasions via the aquarium trade should focus on the education of stakeholders and the prohibition of release, with adequate rewards for compliance and penalties for violations.

Broad-ranging low genetic diversity among populations of the yellow finger marsh crab Sesarma rectum Randall, 1840 (Sesarmidae) revealed by DNA barcode

Crustaceana ◽  
2017 ◽  
Vol 90 (7-10) ◽  
pp. 845-864
Author(s):  
Raquel C. Buranelli ◽  
Fernando L. Mantelatto
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Dna Barcode ◽  
Population Expansion ◽  
Haplotype Network ◽  
Sudden Expansion ◽  
Restricted Gene Flow ◽  
Western Atlantic

Population genetic studies on marine taxa, specifically in the field of phylogeography, have revealed distinct levels of genetic differentiation in widely distributed species, even though they present long planktonic larval development. A set of factors have been identified as acting on gene flow between marine populations, including physical or physiological barriers, isolation by distance, larval behaviour, and geological and demographic events. In this way, the aim of this study was to analyse the genetic variability among populations of the crab speciesSesarma rectumRandall, 1840 along the western Atlantic in order to check the levels of genetic diversity and differentiation among populations. To achieve this purpose, mtDNA cytochrome-coxidase subunit I (COI) (DNA-barcode marker) data were used to compute a haplotype network and a Bayesian analysis for genetic differentiation, to calculate an Analysis of Molecular Variance (AMOVA), and haplotype and nucleotide diversities. Neutrality tests (Tajima’sDand Fu’s ) were accessed, as well as pairwise mismatch distribution under the sudden expansion model. We found sharing of haplotypes among populations ofS. rectumalong its range of distribution and no significant indication for restricted gene flow between populations separately over 6000 km, supporting the hypothesis of a high dispersive capacity, and/or the absence of strong selective gradients along the distribution. Nevertheless, some results indicated population structure suggesting the presence of two genetic sources (i.e., groups or lineages), probably interpreted as a result of a very recent bottleneck effect due to habitat losses, followed by the beginning of a population expansion.

scholarly journals Chromoblastomycosis in an Endemic Area of Brazil: A Clinical-Epidemiological Analysis and a Worldwide Haplotype Network

2020 ◽  
Vol 6 (4) ◽  
pp. 204
Author(s):  
Daniel Wagner C. L. Santos ◽  
Vania Aparecida Vicente ◽  
Vinicius Almir Weiss ◽  
G. Sybren de Hoog ◽  
Renata R. Gomes ◽  
...  
Keyword(s):  
Population Expansion ◽  
Haplotype Network ◽  
Lower Limbs ◽  
Clinical Aspects ◽  
Recent Population Expansion ◽  
Epidemiological Analysis ◽  
Standard Report ◽  
The Mean ◽  
First Time ◽  
Mean Time

Chromoblastomycosis (CBM) is a neglected implantation mycosis prevalent in tropical climate zones, considered an occupational disease that affects impoverished rural populations. This retrospective study described clinical aspects of CBM in a hyperendemic area in Brazil and constructed a worldwide haplotype network of Fonsecaea spp. strains. The variables were collected from medical records using a standard report form, reporting 191 patients with CBM from Maranhão, Brazil. The mean age was 56.1 years, 168 (88%) patients were male and predominantly farmers (85.8%). The mean time of evolution of the disease until diagnosis was 9.4 years. Lower limbs (81.2%) and upper limbs (14.2%) were the main sites affected. Most patients exhibited verrucous (55%) and infiltrative plaque (48.2%). Fonsecaea spp. were identified in 136 cases and a haplotype network constructed with ITS sequences of 185 global strains revealed a total of 59 haplotypes exhibiting high haplotypic and low nucleotide diversities. No correlation was observed between the different haplotypes of Fonsecaea species and dermatological patterns, severity of disease or geographic distribution inside Maranhão. Data from this area contributed to better understanding the epidemiology of CBM. For the first time, a robust haplotype network with Fonsecaea strains reveals an evolutionary history with a recent population expansion.

scholarly journals High genetic diversity and mixing of coastal horseshoe crabs (Tachypleus gigas) across major habitats in Sundaland, Indonesia

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11739
Author(s):  
Naila Khuril Aini ◽  
Yusli Wardiatno ◽  
Hefni Effendi ◽  
Ali Mashar ◽  
Hawis Madduppa
Keyword(s):  
Dna Sequences ◽  
Horseshoe Crab ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Haplotype Network ◽  
Structured Populations ◽  
Conservation Strategy ◽  
Genetic Connectivity ◽  
High Genetic Diversity ◽  
Geographic Ranges

Species with limited dispersal abilities are often composed of highly genetically structured populations across small geographic ranges. This study aimed to investigate the haplotype diversity and genetic connectivity of the coastal horseshoe crab (Tachypleus gigas) in Indonesia. To achieve this, we collected a total of 91 samples from six main T. gigas habitats: Bintan, Balikpapan, Demak, Madura, Subang, and Ujung Kulon. The samples were amplified using primers for mitochondrial (mt) AT-rich region DNA sequences. The results showed 34 haplotypes, including seven shared and 22 unique haplotypes, across all localities. The pairwise genetic differentiation (FST) values were low (0 to 0.13) and not significantly different (p > 0.05), except among samples from Ujung Kulon-Madura and Kulon-Subang (p < 0.05). Additionally, the 34 analysis of molecular variance (AMOVA) showed the most variation within populations (95.23%) compared to less among populations (4.77%). The haplotype network showed evidence of shared haplotypes between populations. Tajima’s D and Fu’s FS test values indicated a population expansion. Our results showed a low level of differentiation, suggesting a single stock and high connectivity. Therefore, a regionally-based conservation strategy is recommended for the coastal horseshoe crab in Indonesia.

scholarly journals Population Structure of Lutjanus purpureus (Lutjanidae - Perciformes) on the Brazilian coast: further existence evidence of a single species of red snapper in the western Atlantic

2012 ◽  
Vol 84 (4) ◽  
pp. 979-999 ◽  
Author(s):  
Grazielle Gomes ◽  
Iracilda Sampaio ◽  
Horacio Schneider
Keyword(s):  
Population Structure ◽  
Control Region ◽  
Single Species ◽  
Mitochondrial Control Region ◽  
Haplotype Network ◽  
Molecular Data ◽  
Red Snapper ◽  
Brazilian Coast ◽  
Base Pairs ◽  
Western Atlantic

The present study focus on the mitochondrial control region to investigate phylogeographic patterns and population structure in Lutjanus purpureus, and to evaluate the genetic similarity between L. purpureus and L. campechanus. For the initial analysis, 810 base pairs sequence from control region were obtained from 239 specimens of L. purpureus collected from four localities off the Brazilian coast. The results revealed the presence of a single panmictic population characterized by high values of genetic diversity. The 299 base pairs hypervariable portion were used for the combined analysis of L. purpureus and L. campechanus, being 275 haplotypes identified in the 414 specimens. Phylogenetic tree and haplotype network did not indicate phylogeographic substructuring between the two species, but rather an intense intermingling of individuals. Considering their marked morphological similarity, the molecular data presented here indicate that only one species of red snapper exists in the western Atlantic.

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