scholarly journals First Evidence of Cryptic Species Diversity and Population Structuring of Selaroides leptolepis in the Tropical Western Pacific

2021 ◽  
Vol 8 ◽  
Author(s):  
Lorenzo C. Halasan ◽  
Paul John L. Geraldino ◽  
Hsiu-Chin Lin
Keyword(s):  
Genetic Structure ◽  
Cryptic Species ◽  
Phylogenetic Trees ◽  
Rapid Expansion ◽  
Western Pacific ◽  
Genetic Structuring ◽  
Tropical Western Pacific ◽  
Haplotype Networks ◽  
Population Structuring ◽  
Genetic Structure And Diversity

The yellowstripe scad, Selaroides leptolepis (Carangidae), is an important fish commodity in the Tropical Western Pacific (TWP). It has a latitudinal Pacific range from south of Japan down to northern Australia, with the highest concentration in Southeast Asia. However, its TWP fishing grounds have long been a hotspot of unsustainable exploitations, thus threatening the remaining wild populations. Despite the species’ commercial significance, there is limited understanding of its genetic structure and diversity. Herein, the genetic structure of S. leptolepis was examined using mitochondrial COI and CytB sequences. Both markers denoted significant genetic structuring based on high overall FST values. Hierarchical analysis of molecular variance (AMOVA), maximum likelihood (ML) phylogenetic trees, and median-joining (MJ) haplotype networks strongly supported the occurrence of two allopatrically distributed lineages. These comprised of a widespread Asian lineage and an isolated Australian lineage. Within-lineage distances were low (K2P < 1%) whereas across-lineage distances were remarkably high (K2P > 6%), already comparable to that of interspecific carangid divergences. Haplotype sequence memberships, high genetic variations, and the geographic correlation suggested that the Australian lineage was a putative cryptic species. Historical demographic inferences also revealed that the species experienced rapid expansion commencing on the late Pleistocene, most likely during the end of the Last Glacial Maximum (∼20,000 years ago). The present study encouraged the application of lineage-specific management efforts, as the lineages are experiencing different evolutionary pressures. Overall, accurate knowledge of the species’ genetic distribution is fundamental in protecting its diversity and assuring stock sustainability.

scholarly journals Cryptic species and genetic structure in Didemnum granulatum Tokioka, 1954 (Tunicata: Ascidiacea) from the southern Brazilian coast

2014 ◽  
Vol 74 (4) ◽  
pp. 923-932 ◽  
Author(s):  
JL Bouzon ◽  
SM Vargas ◽  
JF Oliveira Neto ◽  
PH Stoco ◽  
FP Brandini
Keyword(s):  
Spatial Distribution ◽  
Genetic Structure ◽  
Cryptic Species ◽  
Nucleotide Diversity ◽  
Mitochondrial Gene ◽  
Haplotype Diversity ◽  
Single Species ◽  
Brazilian Coast ◽  
Neighbor Joining ◽  
Haplotype Networks

Didemnum granulatum is a colonial fouling ascidian that lives in subtidal substrates, worldwide. It exhibits two morphotypes, orange and beige. In this study, we verified if the color morphotypes and/or the spatial distribution of specimens in different islands might be associated to patterns of genetic structure of a single species, or if they represent distinct cryptic species. Specimens were collected in four islands, along the coast of the Santa Catarina state. A segment of 490 bp from the mitochondrial gene cytochrome c oxidase subunit 1 (COI) was amplified from 45 samples. Twenty-one haplotypes were identified. The total haplotype diversity (0.912) and the total nucleotide diversity (0.044) were high. The global Fst of the populations analyzed was 0.97, with most of the variation occurring between orange and beige groups (82.19%). The variation found between populations within groups was 15.37%, and 2.45% within populations. Haplotype networks and the neighbor-joining tree showed clear genetic divergence between individuals of distinct colors, and between the islands. These evidences strongly support the presence of a complex of two cryptic species for D. granulatum occupying the studied area. Both species were also highly genetically structured between islands, suggesting that the conservation process of these populations is complex.

scholarly journals Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets

2021 ◽  
Author(s):  
Daniele De Luca ◽  
Roberta Piredda ◽  
Diana Sarno ◽  
Wiebe H.C.F. Kooistra
Keyword(s):  
Gene Flow ◽  
Cryptic Species ◽  
Phylogenetic Trees ◽  
Distribution Patterns ◽  
Chaetoceros Curvisetus ◽  
Haplotype Networks ◽  
Species Complexes ◽  
Biogeographic Regions ◽  
Ocean Sampling ◽  
Marine Protists

AbstractMarine protists have traditionally been assumed to be lowly diverse and cosmopolitan. Yet, several recent studies have shown that many protist species actually consist of cryptic complexes of species whose members are often restricted to particular biogeographic regions. Nonetheless, detection of cryptic species is usually hampered by sampling coverage and application of methods (e.g. phylogenetic trees) that are not well suited to identify relatively recent divergence and ongoing gene flow. In this paper, we show how these issues can be overcome by inferring phylogenetic haplotype networks from global metabarcoding datasets. We use the Chaetoceros curvisetus (Bacillariophyta) species complex as study case. Using two complementary metabarcoding datasets (Ocean Sampling Day and Tara Oceans), we equally resolve the cryptic complex in terms of number of inferred species. We detect new hypothetical species in both datasets. Gene flow between most of species is absent, but no barcoding gap exists. Some species have restricted distribution patterns whereas others are widely distributed. Closely related taxa occupy contrasting biogeographic regions, suggesting that geographic and ecological differentiation drive speciation. In conclusion, we show the potential of the analysis of metabarcoding data with evolutionary approaches for systematic and phylogeographic studies of marine protists.

scholarly journals Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4654 ◽  
Author(s):  
Md Rakeb-Ul Islam ◽  
Daniel J. Schmidt ◽  
David A. Crook ◽  
Jane M. Hughes
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Cryptic Species ◽  
Species Complex ◽  
Gene Tree ◽  
Genetic Connectivity ◽  
Phylogeographic Structure ◽  
Genetic Structuring ◽  
Eastern Australia ◽  
Cryptic Species Complex

Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinnidae:Retropinna semoni) is a native fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations towards the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cytbgene. We tested the hypothesis that genetic connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to dispersal. We investigated populations corresponding with two putative cryptic species, SEQ-North (SEQ-N), and SEQ-South (SEQ-S) lineages occurring in south east Queensland drainages. These two groups formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within each clade. In agreement with our hypothesis, highly significant overallFSTvalues suggested that both groups exhibit very low dispersal among rivers (SEQ-SFST= 0.13; SEQ-NFST= 0.27). Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting dispersal may not homogenise populations at the within-river scale. Northern groups in the Australian smelt cryptic species complex exhibit comparatively higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentially susceptible to future conservation threats, and we define eight genetically distinct management units along south east Queensland to guide future conservation management. The present findings at least can assist managers to plan for effective conservation and management of different fish species along coastal drainages of south east Queensland, Australia.

scholarly journals Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex

2017 ◽  
Author(s):  
Md Rakeb-Ul Islam ◽  
Daniel J Schmidt ◽  
David A Crook ◽  
Jane M Hughes
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Cryptic Species ◽  
Isolation By Distance ◽  
Gene Tree ◽  
Phylogeographic Structure ◽  
Genetic Structuring ◽  
River Population ◽  
Genetic Population ◽  
Eastern Australia

Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinninae: Retropinna semoni) is a facultatively diadromous fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations at the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cyt b gene. We tested the hypothesis that connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to potamodromous behaviour. We investigated populations corresponding with two putative cryptic species, the South East Queensland (SEQ), and Central East Queensland (CEQ) lineages. In agreement with our hypothesis, highly significant overall FST values suggested that both groups exhibit very low dispersal among rivers (SEQ FST = 0.13; CEQ FST = 0.30). The two putative cryptic species, formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within clades. Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting potamodromous behaviour does not homogenise populations at the within-river scale. Overall, northern groups in the smelt cryptic species exhibit higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentially susceptible to future conservation threats, and we define eight genetically distinct management units to guide future conservation management.

scholarly journals Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex

2017 ◽  
Author(s):  
Md Rakeb-Ul Islam ◽  
Daniel J Schmidt ◽  
David A Crook ◽  
Jane M Hughes
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Cryptic Species ◽  
Isolation By Distance ◽  
Gene Tree ◽  
Phylogeographic Structure ◽  
Genetic Structuring ◽  
River Population ◽  
Genetic Population ◽  
Eastern Australia

Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinninae: Retropinna semoni) is a facultatively diadromous fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations at the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cyt b gene. We tested the hypothesis that connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to potamodromous behaviour. We investigated populations corresponding with two putative cryptic species, the South East Queensland (SEQ), and Central East Queensland (CEQ) lineages. In agreement with our hypothesis, highly significant overall FST values suggested that both groups exhibit very low dispersal among rivers (SEQ FST = 0.13; CEQ FST = 0.30). The two putative cryptic species, formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within clades. Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting potamodromous behaviour does not homogenise populations at the within-river scale. Overall, northern groups in the smelt cryptic species exhibit higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentially susceptible to future conservation threats, and we define eight genetically distinct management units to guide future conservation management.

scholarly journals Influence of historical and human factors on genetic structure and diversity patterns in peripheral populations: implications for the conservation of Moroccan trout

2020 ◽  
Author(s):  
S Perea ◽  
M Al Amouri ◽  
EG Gonzalez ◽  
L Alcaraz ◽  
A Yahyaoui ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Brown Trout ◽  
Distribution Range ◽  
Peripheral Populations ◽  
List Type ◽  
Genetic Structuring ◽  
Evolutionary Patterns ◽  
Genetic Structure And Diversity ◽  
The Impact

AbstractThe brown trout s.l. has been the focus of numerous phylogeographic and conservation studies due to its socioeconomic importance, its marked genetic and phenotypic differentiation and its broad distribution range. Especially interesting evolutionary patterns are observed for populations occupying peripheral areas of a distribution range, such as in the case of the highly isolated trout populations in Morocco.Continuous stocking programs may conceal natural genetic patterns, making it challenging to discern evolutionary patterns. In Morocco, trout stocking programs have been implemented to increase the genetic diversity of native populations by pooling fish of different origins in the Ras el Ma hatchery (Azrou region) and then stocking them in the different basins. In this study, phylogenetic and phylogeographic patterns, as well as genetic structure and diversity, of Moroccan trout populations were analyzed to evaluate the impact of continuous fish stocking on evolutionary processes in order to better distinguish between natural and human-mediated patterns.Two mitochondrial and nine microsatellite markers were analyzed for all populations along the entire distribution range of brown trout in Morocco. Phylogenetic and phylogeographic analyses rendered two highly divergent evolutionary lineages, one comprising populations in the Drâa Basin and a second grouping the remaining Moroccan populations. Divergence of the Drâa lineage occurred during the Upper Pliocene, whilst differentiation within the second lineage coincided with the onset of the Pleistocene.Genetic structuring among populations was evident. Nevertheless, populations exhibiting higher levels of genetic diversity were those affected by human-mediated processes, making it difficult to associate this diversity with natural processes. In fact, highly geographically isolated, not stocked populations showed the lowest values of genetic diversity. Although stocking management may increase the genetic diversity of these populations, it could also lead to the loss of local adaptive genotypes. Hence, current trout conservation programs should be revised.

scholarly journals LC–MS/MS Analysis of Ciguatoxins Revealing the Regional and Species Distinction of Fish in the Tropical Western Pacific

2021 ◽  
Vol 9 (3) ◽  
pp. 299 ◽  
Author(s):  
Naomasa Oshiro ◽  
Takumi Tomikawa ◽  
Kyoko Kuniyoshi ◽  
Akira Ishikawa ◽  
Hajime Toyofuku ◽  
...  
Keyword(s):  
Fish Species ◽  
The Philippines ◽  
Western Pacific ◽  
Tropical Region ◽  
Northern Coast ◽  
Coastal Regions ◽  
Main Island ◽  
Tropical Western Pacific ◽  
The Pacific ◽  
Fish Samples

Ciguatera fish poisoning (CFP) is one of the most frequently reported seafood poisoning diseases. It is endemic to the tropical region and occurs most commonly in the regions around the Pacific Ocean, Indian Ocean, and Caribbean Sea. The principal toxins causing CFP are ciguatoxins (CTXs). In the Pacific region, more than 20 analogs of CTXs have been identified to date. Based on their skeletal structures, they are classified into CTX1B-type and CTX3C-type toxins. We have previously reported species-specific and regional-specific toxin profiles. In this study, the levels and profiles of CTXs in fish present in the tropical western Pacific regions were analyzed using the liquid chromatography–tandem mass spectrometry (LC–MS/MS) technique. Forty-two fish specimens, belonging to the categories of snappers, groupers, Spanish mackerel, and moray eel, were purchased from various places such as Fiji, the Philippines, Thailand, and Taiwan. Only the fish captured from Fijian coastal waters contained detectable amounts of CTXs. The toxin levels in the fish species found along the coastal regions of the Viti Levu Island, the main island in Fiji, and the toxin profiles were significantly different from those of the fish species present in other coastal regions. The toxin levels and profiles varied among the different fish samples collected from different coastal areas. Based on the toxin levels and toxin profiles, the coast was demarcated into three zones. In Zone-1, which covers the northern coast of the main island and the regions of the Malake Island and Korovau, CTXs in fish were below the detection level. In Zone-2, CTX3C-type toxins were present in low levels in the fish. CTX1B-type and CTX3C-type toxins co-occurred in the fish present in Zone-3. The toxin profiles may have reflected the variation in Gambierdiscus spp.

Understanding introduction history: Genetic structure and diversity of the edible ectomycorrhizal fungus, Suillus luteus, in Patagonia (Argentina)

Mycologia ◽  
2021 ◽  
pp. 1-10
Author(s):  
María Belén Pildain ◽  
Paula Marchelli ◽  
María Marta Azpilicueta ◽  
Cristian Starik ◽  
Carolina Barroetaveña
Keyword(s):  
Genetic Structure ◽  
Ectomycorrhizal Fungus ◽  
Suillus Luteus ◽  
Introduction History ◽  
Genetic Structure And Diversity

scholarly journals Population Genetic Structure Analysis Reveals Decreased but Moderate Diversity for the Oriental Fire-Bellied Toad Introduced to Beijing after 90 Years of Independent Evolution

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1429
Author(s):  
Yang Teng ◽  
Jing Yang ◽  
Guofen Zhu ◽  
Fuli Gao ◽  
Yingying Han ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Structure Analysis ◽  
Phylogenetic Trees ◽  
Molecular Genetic ◽  
Genetic Research ◽  
Haplotype Diversity ◽  
Botanical Garden ◽  
Source Population ◽  
Independent Evolution ◽  
Loop Region

Detailed molecular genetic research on amphibian populations has a significant role in understanding the genetic adaptability to local environments. The oriental fire-bellied toads (Bombina orientalis) were artificially introduced to Beijing from Shandong Province in 1927, and since then, this separated population went through an independent evolution. To explore the differentiation of the introduced population with its original population, this study analyzed the genetic structure of the oriental fire-bellied toad, based on the mitochondrial genome control region and six microsatellite sites. The results showed that the haplotype diversity and nucleotide diversity of the mitochondrial D-loop region partial sequences of the Beijing Botanical Garden population and the Baiwangshan population were lower than those of the Shangdong Kunyushan population. Microsatellite marker analysis also showed that the observed heterozygosity and expected heterozygosity of the Beijing populations were lower than those of the Kunyushan population. The phylogenetic trees and network diagrams of haplotypes indicated that the three populations were not genetically separated. However, the structure analysis showed a genetic differentiation and categorized the sampling individuals into Beijing and Shandong genetic clusters, which indicated a tendency for isolated evolution in the Beijing population. Although the Beijing populations showed a decline in genetic diversity, it was still at a moderate level, which could maintain the survival of the population. Thus, there is no need to reintroduce new individuals from the Kunyushan source population.

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