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 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 Genetic population structure of the monogenean parasite Gyrodactylus thymalli and its host European grayling (Thymallus thymallus) in a large Norwegian lake

Hydrobiologia ◽  
2020 ◽  
Author(s):  
Ruben Alexander Pettersen ◽  
Claudia Junge ◽  
Kjartan Østbye ◽  
Tor Atle Mo ◽  
Leif Asbjørn Vøllestad
Keyword(s):  
Genetic Structure ◽  
Evolutionary Biology ◽  
Isolation By Distance ◽  
Genetic Structuring ◽  
Thymallus Thymallus ◽  
Homing Behavior ◽  
Genetic Population ◽  
Monogenean Parasite ◽  
European Grayling ◽  
Genetic Clusters

Abstract Understanding how populations are structured in space and time is a central question in evolutionary biology. Parasites and their hosts are assumed to evolve together, however, detailed understanding of mechanisms leading to genetic structuring of parasites and their hosts are lacking. As a parasite depends on its host, studying the genetic structure of both parasite and host can reveal important insights into these mechanisms. Here, genetic structure of the monogenean parasite Gyrodactylus thymalli and its host the European grayling (Thymallus thymallus) was investigated in 10 tributaries draining into the large Lake Mjøsa in Norway. The population genetic structure of spawning grayling was studied using microsatellite genotyping, while G. thymalli was studied by sequencing a mitochondrial DNA gene (dehydrogenase subunit 5). Two main genetic clusters were revealed in grayling, one cluster comprising grayling from the largest spawning population, while the remaining tributaries formed the second cluster. For both taxa, some genetic differentiation was observed among tributaries, but there was no clear isolation-by-distance signature. The structuring was stronger for the host than for the parasite. These results imply that moderate to high levels of gene flow occur among the sub-populations of both taxa. The high parasite exchange among tributaries could result from a lack of strong homing behavior in grayling as well as interactions among individual fish outside of the spawning season, leading to frequent mixing of both host and parasite.

Dispersal patterns and population structure in a small marsupial, Antechinus agilis, from two forests analysed using microsatellite markers

2002 ◽  
Vol 50 (4) ◽  
pp. 325 ◽  
Author(s):  
F. J. L. Kraaijeveld-Smit ◽  
D. B. Lindenmayer ◽  
A. C. Taylor
Keyword(s):  
Population Structure ◽  
Isolation By Distance ◽  
Habitat Characteristics ◽  
Assignment Test ◽  
Dispersal Patterns ◽  
Genetic Structuring ◽  
Capture Site ◽  
Eastern Australia ◽  
Antechinus Agilis ◽  
One Year

Juvenile male agile antechinus (Antechinus agilis) are thought to disperse immediately after they leave the nest, whereas females are philopatric. However, no genetic data are available to support a hypothesis of male-biased dispersal, and the possible effects of habitat characteristics on dispersal are not known. We used five microsatellite loci to describe the dispersal patterns and population structure of A. agilis at two different forested sites (Mt Donna Buang and Mt Disappointment in central Victoria, south-eastern Australia). Within each site, DNA samples were collected from individuals from different trapping grids (four grids in Mt Donna Buang, collected over two years, and seven grids at Mt Disappointment, collected over one year). To assess levels of genetic structuring among the populations, Fst values (the proportion of genetic variance among populations) were calculated for each site and sex separately, and a test for isolation by distance was performed. Overall, Fst values were low, and did not increase with distance, and this may be the result of high levels of gene flow for both sexes at both sites, at least on the scale of less than 10 km. To investigate microsatellite patterns at a finer scale, we calculated pair-wise relatedness values separately for sites, years and sexes. By comparing these values for animals within and between grids, evidence was found for male-biased dispersal. A genetic assignment test provided further evidence for this: males were more likely to be assigned to grids other than their capture site. Most females had high assignment values for their capture site, although some of the females may have been immigrants. This result could be due to inaccuracies in the assignment test, or due to a higher frequency of dispersal of females than previously thought. The sex-biased dispersal was less pronounced at Mt Disappointment than at Mt Donna Buang. This may be related to the level of disturbance: logging patches, roads and fire-breaks (grass strips) disrupt the forest at Mt Disappointment more than at Mt Donna Buang.

scholarly journals Characterisation of the Mitochondrial Genome and the Phylogeographic Structure of Blue Cod (Parapercis colias)

2021 ◽  
Author(s):  
◽  
Hayden Murray Smith
Keyword(s):  
New Zealand ◽  
Genetic Structure ◽  
Mitochondrial Genome ◽  
Control Region ◽  
Fish Species ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Phylogeographic Structure ◽  
Genetic Population ◽  
Biological Trait

<p>This thesis primarily addresses the genetic population structure of blue cod (Parapercis colias) in the New Zealand Exclusive Economic Zone, within which approximately 2800 Tonnes of the endemic fish are harvested annually. Several regions with traditionally healthy blue cod stocks have recently experienced localised depletion due to over-exploitation. This highlights the importance for a clearer understanding of the genetic structure of the species in order to maximise the potential for the fishery to be managed sustainably. Also covered within this thesis are characteristics of the blue cod's mitochondrial genome, and development of a set of genetic tools that can improve the level of understanding for several important fisheries species in New Zealand waters. Chapter two focuses on the characterisation of the blue cod mitochondrial genome, with the use of second-generation sequencing providing the first fully documented sequence for this species. The blue cod mitochondrial genome is identical in organisation to several other documented fish species' mitochondrial genomes, with no unexpected results. Also dealt with in Chapter two is the development and implementation of a set of generic control region primers, designed primarily for use on commercially important inshore New Zealand fish species. Nine of the eleven species which the primer was tested on had the targeted region successfully amplified, though heteroplasmy may be present in at least four species. Chapter three reports the bulk of this research, with the phylogeographic structure of blue cod investigated. Samples were taken from the pectoral and pelvic fins of blue cod from 14 sites around New Zealand. A total of 475 sequences were taken from the hypervariable 5' end of the control region, with each sequence 491 bp in length. The null hypothesis of genetic homogeneity throughout their distribution was rejected, with significant differentiation observed between mainland New Zealand and Chatham Island samples. While pairwise differences between mainland New Zealand sampling sites was limited, a significant trend of isolation by distance was observed. A demographic population expansion occurred more steeply and more recently in mainland populations, with a slower growth curve in Chatham Island populations. With a trend of isolation by distance present between mainland sampling sites, it is suggested that further investigations are made, utilising genetic markers capable of resolving deeper patterns of genetic structure within the population (e.g. microsatellites, SNP's). Finally, Chapter four summarises and contextualises the results from the research components of this thesis, discussing management implications and potential threats to both the commercial and recreational blue cod fishery. A key area of focus for this section is the genetic and demographic risk that the population may face with continued targeting of larger individuals, given the biological trait of protogynous hermaphroditism in the species.</p>

scholarly journals Looking through glassfish: marine genetic structure in an estuarine species

2008 ◽  
Vol 59 (7) ◽  
pp. 627 ◽  
Author(s):  
Courtenay E. Mills ◽  
Wade L. Hadwen ◽  
Jane M. Hughes
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
New South ◽  
Geographic Distance ◽  
Genetic Structuring ◽  
The North ◽  
South Wales ◽  
High Dispersal ◽  
Eastern Australia ◽  
Atp8 Gene

Through the use of mitochondrial DNA (ATP8 gene), the prediction of intermediate genetic structuring was investigated in two species of estuarine glassfish (Ambassis marianus and Ambassis jacksoniensis) (Perciformes : Ambassidae) to determine the possibility of a generalised ‘estuarine’ genetic structure. Individuals were collected from estuaries in eastern Australia between Tin Can Bay (Queensland) in the north and Kempsey (New South Wales) in the south. Analysis of the haplotype frequencies found in this region suggested panmictic populations with star-like phylogenies with extremely high levels of genetic diversity, but with no correlation between geographic distance and genetic distance. Non-significant FST and ΦST suggested extensive dispersal among estuaries. However, Tajima’s D and Fu’s FS values suggest ‘mutation–genetic drift equilibrium’ has not been reached, and that population expansions occurring 262 000 (A. marianus) and 300 000 (A. jacksoniensis) years ago may obscure any phylogeographic structuring or isolation by distance. The finding of panmixia was contrary to the prediction of genetic structuring intermediate between that of marine fish (shallowly structured) and freshwater fish (highly structured), suggesting high dispersal capabilities in these species.

scholarly journals Characterisation of the Mitochondrial Genome and the Phylogeographic Structure of Blue Cod (Parapercis colias)

2021 ◽  
Author(s):  
◽  
Hayden Murray Smith
Keyword(s):  
New Zealand ◽  
Genetic Structure ◽  
Mitochondrial Genome ◽  
Control Region ◽  
Fish Species ◽  
Isolation By Distance ◽  
Population Expansion ◽  
Phylogeographic Structure ◽  
Genetic Population ◽  
Biological Trait

<p>This thesis primarily addresses the genetic population structure of blue cod (Parapercis colias) in the New Zealand Exclusive Economic Zone, within which approximately 2800 Tonnes of the endemic fish are harvested annually. Several regions with traditionally healthy blue cod stocks have recently experienced localised depletion due to over-exploitation. This highlights the importance for a clearer understanding of the genetic structure of the species in order to maximise the potential for the fishery to be managed sustainably. Also covered within this thesis are characteristics of the blue cod's mitochondrial genome, and development of a set of genetic tools that can improve the level of understanding for several important fisheries species in New Zealand waters. Chapter two focuses on the characterisation of the blue cod mitochondrial genome, with the use of second-generation sequencing providing the first fully documented sequence for this species. The blue cod mitochondrial genome is identical in organisation to several other documented fish species' mitochondrial genomes, with no unexpected results. Also dealt with in Chapter two is the development and implementation of a set of generic control region primers, designed primarily for use on commercially important inshore New Zealand fish species. Nine of the eleven species which the primer was tested on had the targeted region successfully amplified, though heteroplasmy may be present in at least four species. Chapter three reports the bulk of this research, with the phylogeographic structure of blue cod investigated. Samples were taken from the pectoral and pelvic fins of blue cod from 14 sites around New Zealand. A total of 475 sequences were taken from the hypervariable 5' end of the control region, with each sequence 491 bp in length. The null hypothesis of genetic homogeneity throughout their distribution was rejected, with significant differentiation observed between mainland New Zealand and Chatham Island samples. While pairwise differences between mainland New Zealand sampling sites was limited, a significant trend of isolation by distance was observed. A demographic population expansion occurred more steeply and more recently in mainland populations, with a slower growth curve in Chatham Island populations. With a trend of isolation by distance present between mainland sampling sites, it is suggested that further investigations are made, utilising genetic markers capable of resolving deeper patterns of genetic structure within the population (e.g. microsatellites, SNP's). Finally, Chapter four summarises and contextualises the results from the research components of this thesis, discussing management implications and potential threats to both the commercial and recreational blue cod fishery. A key area of focus for this section is the genetic and demographic risk that the population may face with continued targeting of larger individuals, given the biological trait of protogynous hermaphroditism in the species.</p>

Genetic isolation by distance and localized fjord population structure in Pacific cod (Gadus macrocephalus): limited effective dispersal in the northeastern Pacific Ocean

2009 ◽  
Vol 66 (1) ◽  
pp. 153-166 ◽  
Author(s):  
Kathryn Maja Cunningham ◽  
Michael Francis Canino ◽  
Ingrid Brigette Spies ◽  
Lorenz Hauser
Keyword(s):  
Population Structure ◽  
Pacific Ocean ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Puget Sound ◽  
Pacific Cod ◽  
Genetic Population ◽  
Pacific Cod Gadus Macrocephalus ◽  
Gadus Macrocephalus ◽  
Northeastern Pacific

Genetic population structure of Pacific cod, Gadus macrocephalus , was examined across much of its northeastern Pacific range by screening variation at 11 microsatellite DNA loci. Estimates of FST (0.005 ± 0.002) and RST (0.010 ± 0.003) over all samples suggested that effective dispersal is limited among populations. Genetic divergence was highly correlated with geographic distance in an isolation-by-distance (IBD) pattern along the entire coastal continuum in the northeastern Pacific Ocean (~4000 km; r2 = 0.83), extending from Washington State to the Aleutian Islands, and over smaller geographic distances for three locations in Alaska (~1700 km; r2 = 0.56). Slopes of IBD regressions suggested average dispersal distance between birth and reproduction of less than 30 km. Exceptions to this pattern were found in samples taken from fjord environments in the Georgia Basin (the Strait of Georgia (Canada) and Puget Sound (USA)), where populations were differentiated from coastal cod. Our results showed population structure at spatial scales relevant to fisheries management, both caused by limited dispersal along the coast and by sharp barriers to migration isolating smaller stocks in coastal fjord environments.

scholarly journals Whole-genome SNP analysis elucidates the genetic population structure and diversity of Acrocomia species

2020 ◽  
Author(s):  
Brenda G. Díaz ◽  
Maria I. Zucchi ◽  
Alessandro. Alves-Pereira ◽  
Caléo P. de Almeida ◽  
Aline C. L. Moraes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Structure ◽  
Genetic Relationships ◽  
Geographical Area ◽  
Taxonomic Classification ◽  
Genomic Diversity ◽  
Productive Capacity ◽  
Snp Analysis ◽  
Genetic Population

AbstractAcrocomia (Arecaceae) is a genus widely distributed in tropical and subtropical America that has been achieving economic interest due to the great potential of oil production of some of its species. In particular A. aculeata, due to its vocation to supply oil with the same productive capacity as the oil palm even in areas with water deficit. Although eight species are recognized in the genus, the taxonomic classification based on morphology and geographic distribution is still controversial. Knowledge about the genetic diversity and population structure of the species is limited, which has limited the understanding of the genetic relationships and the orientation of management, conservation, and genetic improvement activities of species of the genus. In the present study, we analyzed the genomic diversity and population structure of seven species of Acrocomia including 117 samples of A. aculeata covering a wide geographical area of occurrence, using single nucleotide Polymorphism (SNP) markers originated from Genotyping By Sequencing (GBS). The genetic structure of the Acrocomia species were partially congruent with the current taxonomic classification based on morphological characters, recovering the separation of the species A. aculeata, A. totai, A. crispa and A. intumescens as distinct taxonomic groups. However, the species A. media was attributed to the cluster of A. aculeata while A. hassleri and A. glauscescens were grouped together with A. totai. The species that showed the highest and lowest genetic diversity were A. totai and A. media, respectively. When analyzed separately, the species A. aculeata showed a strong genetic structure, forming two genetic groups, the first represented mainly by genotypes from Brazil and the second by accessions from Central and North American countries. Greater genetic diversity was found in Brazil when compared to the other countries. Our results on the genetic diversity of the genus are unprecedented, as is also establishes new insights on the genomic relationships between Acrocomia species. It is also the first study to provide a more global view of the genomic diversity of A. aculeata. We also highlight the applicability of genomic data as a reference for future studies on genetic diversity, taxonomy, evolution and phylogeny of the Acrocomia genus, as well as to support strategies for the conservation, exploration and breeding of Acrocomia species and in particular A. aculeata.

scholarly journals Population structure of the New Zealand whelk, Cominella glandiformis (Gastropoda: Buccinidae), suggests sporadic dispersal of a direct developer

2020 ◽  
Vol 130 (1) ◽  
pp. 49-60
Author(s):  
Kirsten M Donald ◽  
Graham A McCulloch ◽  
Ludovic Dutoit ◽  
Hamish G Spencer
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
New Zealand ◽  
Genetic Structure ◽  
Geographic Area ◽  
Null Alleles ◽  
Phylogeographic Structure ◽  
Large Geographic Area ◽  
Oceanic Currents ◽  
Minimal Evidence

Abstract We examined phylogeographic structure in the direct-developing New Zealand endemic intertidal mud whelk, Cominella glandiformis. Two hundred and ninety-six whelks from 12 sites were collected from sheltered shores around New Zealand’s four largest islands (North Island, South Island, Stewart Island and Chatham Island), encompassing the geographical range of this species. Despite being direct developers, gene flow among C. glandiformis populations may occur over short distances by adult floating, and over larger distances by rafting of egg masses. Primers were developed to amplify variable microsatellite regions at six loci. All loci were variable, with 8–34 alleles/loci. Observed and expected heterozygosities were high across all alleles, with minimal evidence of null alleles. The average number of alleles varied from 3.5 (Chatham Island) to 7.5 (Waitemata Harbour). Strong genetic structure was evident, with distinct ‘eastern’ and ‘western’ groups. Each group extended over a large geographic area, including regions of unsuitable habitat, but were linked by oceanic currents. We suggest that the intraspecific geographic genetic structure in C. glandiformis has arisen due a combination of ocean currents (promoting gene flow between geographically distant regions) and upwelling areas (limiting gene flow between certain regions).

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