Population genetic structure and assessment of allochronic divergence in the Macoun’s Arctic (Oeneis macounii) butterfly

<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>

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

10.7287/peerj.preprints.3284v1 ◽

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.

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

10.26686/wgtn.16997824.v1 ◽

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>

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Genome wide sequencing provides evidence of adaptation to heterogeneous environments for the ancient relictual Circaeaster agrestis (Circaeasteraceae, Ranunculales)

10.1101/2020.01.14.902643 ◽

2020 ◽

Author(s):

Xu Zhang ◽

Yanxia Sun ◽

Jacob B. Landis ◽

Jianwen Zhang ◽

Linsen Yang ◽

...

Keyword(s):

Genetic Structure ◽

Local Adaptation ◽

Environmental Heterogeneity ◽

Isolation By Distance ◽

Population Divergence ◽

Heterogeneous Environments ◽

List Type ◽

Biotic And Abiotic Stress ◽

Association Analyses ◽

Genome Wide

SummaryInvestigating the interaction between environmental heterogeneity and local adaptation is critical to understand the evolutionary history of a species, providing the premise for studying the response of organisms to rapid climate change. However, for most species how exactly the spatial heterogeneity promotes population divergence and how genomic variations contribute to adaptive evolution remain poorly understood.We examine the contributions of geographical and environmental variables to population divergence of the relictual, alpine herb Circaeaster agrestis, as well as genetic basis of local adaptation using RAD-seq and plastome data.We detected significant genetic structure with an extraordinary disequilibrium of genetic diversity among regions, and signals of isolation-by-distance along with isolation-by-resistance. The populations were estimated to begin diverging in the late Miocene, along with a possible ancestral distribution of the Hengduan Mountains and adjacent regions. Both environmental gradient and redundancy analyses revealed significant association between genetic variation and temperature variables. Genome-environment association analyses identified 16 putatively adaptive loci related to biotic and abiotic stress resistance.Our genome wide data provide new insights into the important role of environmental heterogeneity in shaping genetic structure, and access the footprints of local adaptation in an ancient relictual species, informing conservation efforts.

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

10.7287/peerj.preprints.3284 ◽

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.

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Significant genetic structure despite high vagility revealed through mitochondrial phylogeography of an Australian freshwater turtle (Chelodina longicollis)

Marine and Freshwater Research ◽

10.1071/mf14102 ◽

2015 ◽

Vol 66 (11) ◽

pp. 1045 ◽

Cited By ~ 2

Author(s):

K. Hodges ◽

S. Donnellan ◽

A. Georges

Keyword(s):

Life History ◽

Gene Flow ◽

Genetic Structure ◽

Life History Traits ◽

Isolation By Distance ◽

Phylogeographic Structure ◽

Freshwater Turtle ◽

Freshwater Species ◽

Chelodina Longicollis ◽

Australian Freshwater

Restriction to the freshwater environment plays a dominant role in the population genetic structure of freshwater fauna. In taxa with adaptations for terrestriality, however, the restrictions on dispersal imposed by drainage divides may be overcome. We investigate the mitochondrial phylogeographic structure of the eastern long-necked turtle (Chelodina longicollis), a widespread Australian freshwater obligate with strong overland dispersa\l capacity and specific adaptations to terrestriality. We predict that such characteristics make this freshwater species a strong candidate to test how life-history traits can drive gene flow and interbasin connectivity, overriding the constraining effects imposed by hydrological boundaries. Contrary to expectations, and similar to low-vagility freshwater vertebrates, we found two ancient mitochondrial haplogroups with clear east–west geographic partitioning either side of the Great Dividing Range. Each haplogroup is characterised by complex genetic structure, demographically stable subpopulations, and signals of isolation by distance. This pattern is overlaid with signatures of recent gene flow, likely facilitated by late Pleistocene and ongoing anthropogenic landscape change. We demonstrate that the divergent effects of landscape history can overwhelm the homogenising effects of life-history traits that connect populations, even in a highly vagile species.

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Spatial Patterns of Chloroplast DNA and Cone Morphology Variation within Populations of a Pinus banksiana-Pinus contorta Sympatric Region

The American Naturalist ◽

10.1086/285209 ◽

1991 ◽

Vol 138 (1) ◽

pp. 156-170 ◽

Cited By ~ 25

Author(s):

David B. Wagner ◽

Zhong-Xu Sun ◽

Diddahally R. Govindaraju ◽

Bruce P. Dancik

Keyword(s):

Chloroplast Dna ◽

Spatial Patterns ◽

Pinus Banksiana ◽

Pinus Contorta ◽

Cone Morphology

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Genetic Relationships of Cory's Shearwater: Parentage, Mating Assortment, and Geographic Differentiation Revealed by DNA Fingerprinting

The Auk ◽

10.1093/auk/117.3.651 ◽

2000 ◽

Vol 117 (3) ◽

pp. 651-662 ◽

Cited By ~ 1

Author(s):

Corinne Rabouam ◽

Vincent Bretagnolle ◽

Yves Bigot ◽

Georges Periquet

Keyword(s):

Genetic Variation ◽

Genetic Structure ◽

Dna Fingerprinting ◽

Genetic Relatedness ◽

Isolation By Distance ◽

Genetic Relationships ◽

Cory’S Shearwater ◽

Genetic Structure Of Populations ◽

The Social ◽

Calonectris Diomedea

Abstract We used DNA fingerprinting to assess genetic structure of populations in Cory's Shearwater (Calonectris diomedea). We analyzed mates and parent-offspring relationships, as well as the amount and distribution of genetic variation within and among populations, from the level of subcolony to subspecies. We found no evidence of extrapair fertilization, confirming that the genetic breeding system matches the social system that has been observed in the species. Mates were closely related, and the level of genetic relatedness within populations was within the range usually found in inbred populations. In contrast to previous studies based on allozymes and mtDNA polymorphism, DNA fingerprinting using microsatellites revealed consistent levels of genetic differentiation among populations. However, analyzing the two subspecies separately revealed that the pattern of genetic variation among populations did not support the model of isolation by distance. Natal dispersal, as well as historic and/or demographic events, probably contributed to shape the genetic structure of populations in the species.

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

Hydrobiologia ◽

10.1007/s10750-020-04431-7 ◽

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.

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