scholarly journals Implications of Genetic Structure for Aquaculture and Cultivar Translocation of the Kelp Ecklonia radiata in Northern New Zealand

2021 ◽  
Vol 8 ◽  
Author(s):  
Jacob Nepper-Davidsen ◽  
Marie Magnusson ◽  
Christopher R. K. Glasson ◽  
Philip M. Ross ◽  
Rebecca J. Lawton
Keyword(s):  
New Zealand ◽  
Genetic Structure ◽  
Isolation By Distance ◽  
Regional Scale ◽  
Brood Stock ◽  
Ecklonia Radiata ◽  
The North ◽  
Genetic Clustering ◽  
Genetic Structure And Diversity ◽  
High Degree

The fast expansion of the global seaweed aquaculture industry has created an interest in translocating seedlings cultivated from wild type brood stock. However, such translocations must be applied with caution as introduced cultivars can reduce genetic structure and diversity of wild populations. An understanding of the genetic structure and connectivity of target species is required to guide decision making around aquaculture translocation activities. In this study we used 14 microsatellite loci in a three-level hierarchical sampling design to analyze the genetic structure and connectivity of the native kelp Ecklonia radiata across 12 sites among four geographic regions (Northland, Bay of Plenty, Gisborne, and Wellington) in the North Island of New Zealand. Our aim was to provide guidance for translocation of cultivars to prevent the introduction of locally absent genotypes of E. radiata. Strong genetic structure and low geneflow were observed at all hierarchical levels, indicating the presence of multiple genetically distinct sub-populations. On a regional scale, high genetic differentiation was found between the Wellington region and the other three regions (FST = 0.407–0.545), and within regions most sites were significantly different (measured by pairwise FST) with high relatedness found between individuals within sites (mean 28.2% ± 0.7 SE). Bayesian modeling and redundancy analysis showed a high degree of genetic clustering and indicate that ocean currents and other factors that have resulted in biogeographical breaks along the coast are likely to be the main factors shaping genetic structure and connectivity of E. radiata on the North Island, rather than isolation by distance. Based on these findings, we recommend that that cultivars of E. radiata should not be translocated outside their area of origin to avoid introducing locally absent genotypes to local sub-populations.

scholarly journals Late Holocene Sediment Deposition in Lake Wairarapa

2021 ◽  
Author(s):  
◽  
Martha Ingrid Trodahl
Keyword(s):  
New Zealand ◽  
Morphological Changes ◽  
Regional Scale ◽  
Hydrological Regime ◽  
Lake Management ◽  
Anthropogenic Influence ◽  
Eastern Shore ◽  
Ecological Value ◽  
The North ◽  
Development Scheme

<p>Lake Wairarapa is a highly modified lacustrine system at the southern end of the North Island, New Zealand. Not only is it situated in a region that is affected by catchment altering natural phenomena such as earthquakes, storms and fire, but both the catchment and hydrology of the lake have also been significantly altered by humans. Polynesian settlers arrived in the area approximately 700BP and proceeded to deforest the lowlands. European settlers began arriving from 1844AD onwards, completing deforestation of the lowlands and Eastern Uplands. In 1964 the Lower Wairarapa Valley Development Scheme was commissioned in an effort to alleviate flooding. This scheme significantly altered the hydrological regime of the lake. Interest in the condition of the lake and associated wetlands, and the realization that it has important recreational, cultural and ecological value, began to develop in the 1990's. This has led to a desire to see the lake restored to a more natural condition while still maintaining its flood protection capabilities. However, the lake has only been monitored over the last several decades. Any evidence of the lakes condition prior to this time is anecdotal and little is known of its natural tendencies and functions. This research has investigated and quantified morphological changes to Lake Wairarapa at the decadal and millenial scale using a combination of aerial photograph analysis, bathymetric survey comparison and lakebed core analysis. Study at these diverse scales has allowed the observed changes to be related to human environmental modification, while also being juxtaposed against natural trajectories of change. It is hoped that this can inform lake management and restoration efforts and provide a benchmark for measuring future changes to the lake, while also addressing wider issues concerning natural versus anthropogenic landscape change at the local and regional scale. The results of this project suggest that the lake has been steadily infilling over the last 6000BP – particularly along the eastern shore. For the two decades after significant hydrological changes to the lake associated with the Lower Wairarapa Valley Development Scheme, the rate of infilling on the eastern shore increased more than tenfold. However, this was accompanied by deepening in other parts of the lake. Today infilling along the eastern shore appears to have returned to natural rates and overall the lake in 2010 is only slightly smaller in volume than in 1975. Longer term anthropogenic influence on the lake and catchment was also evident. In particular Polynesian settlement and subsequent deforestation by fire was apparent in the lakebed cores. This result not only addresses the immediate issue of anthropogenic influence on this particular lacustrine system, but also informs the debate surrounding the dating of Polynesian arrival in New Zealand.</p>

scholarly journals Late Holocene Sediment Deposition in Lake Wairarapa

2021 ◽  
Author(s):  
◽  
Martha Ingrid Trodahl
Keyword(s):  
New Zealand ◽  
Morphological Changes ◽  
Regional Scale ◽  
Hydrological Regime ◽  
Lake Management ◽  
Anthropogenic Influence ◽  
Eastern Shore ◽  
Ecological Value ◽  
The North ◽  
Development Scheme

<p>Lake Wairarapa is a highly modified lacustrine system at the southern end of the North Island, New Zealand. Not only is it situated in a region that is affected by catchment altering natural phenomena such as earthquakes, storms and fire, but both the catchment and hydrology of the lake have also been significantly altered by humans. Polynesian settlers arrived in the area approximately 700BP and proceeded to deforest the lowlands. European settlers began arriving from 1844AD onwards, completing deforestation of the lowlands and Eastern Uplands. In 1964 the Lower Wairarapa Valley Development Scheme was commissioned in an effort to alleviate flooding. This scheme significantly altered the hydrological regime of the lake. Interest in the condition of the lake and associated wetlands, and the realization that it has important recreational, cultural and ecological value, began to develop in the 1990's. This has led to a desire to see the lake restored to a more natural condition while still maintaining its flood protection capabilities. However, the lake has only been monitored over the last several decades. Any evidence of the lakes condition prior to this time is anecdotal and little is known of its natural tendencies and functions. This research has investigated and quantified morphological changes to Lake Wairarapa at the decadal and millenial scale using a combination of aerial photograph analysis, bathymetric survey comparison and lakebed core analysis. Study at these diverse scales has allowed the observed changes to be related to human environmental modification, while also being juxtaposed against natural trajectories of change. It is hoped that this can inform lake management and restoration efforts and provide a benchmark for measuring future changes to the lake, while also addressing wider issues concerning natural versus anthropogenic landscape change at the local and regional scale. The results of this project suggest that the lake has been steadily infilling over the last 6000BP – particularly along the eastern shore. For the two decades after significant hydrological changes to the lake associated with the Lower Wairarapa Valley Development Scheme, the rate of infilling on the eastern shore increased more than tenfold. However, this was accompanied by deepening in other parts of the lake. Today infilling along the eastern shore appears to have returned to natural rates and overall the lake in 2010 is only slightly smaller in volume than in 1975. Longer term anthropogenic influence on the lake and catchment was also evident. In particular Polynesian settlement and subsequent deforestation by fire was apparent in the lakebed cores. This result not only addresses the immediate issue of anthropogenic influence on this particular lacustrine system, but also informs the debate surrounding the dating of Polynesian arrival in New Zealand.</p>

scholarly journals Population genetic structure of New Zealand blue cod (Parapercis colias) based on mitochondrial and microsatellite DNA markers

2021 ◽  
Author(s):  
◽  
Clare Louise Gebbie
Keyword(s):  
New Zealand ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Dna Markers ◽  
Microsatellite Dna ◽  
Population Genetic ◽  
Current Knowledge ◽  
Isolation By Distance ◽  
Genetic Connectivity ◽  
Microsatellite Dna Markers

<p>Parapercis colias (blue cod) is an endemic temperate reef fish that supports an important commercial and recreational fishery in New Zealand. However, concerns have been raised about localized stock depletion, and multiple lines of evidence have suggested P. colias may form several biologically distinct populations within the New Zealand Exclusive Economic Zone. Mark and recapture studies along with otolith and stable isotope studies have indicated that individuals are sedentary with very limited movement beyond the scale of 10-20km. The primary goal of this research was to advance the current knowledge of P. colias population genetic structure. This information can be incorporated into stock assessment models with the aim of improving the management of the P. colias fishery. This study made use of 454 pyrosequencing technology to isolate and develop the first set of microsatellite DNA markers for P. colias. These seven microsatellite loci, along with mitochondrial control region sequences, were used to determine the levels of genetic variation and differentiation between sites around the New Zealand coastline, including the Chatham Islands.  Significant differentiation was observed between the Chatham Islands and mainland New Zealand sample sites, indicating that these two regions form distinct populations. Interpretation of the results for the mainland sites was more complex. Mitochondrial sequence data detected no significant pairwise differentiation between mainland sites, although a pattern of isolation-by-distance was observed. However, evidence for genetic differentiation among mainland sites was weak based on the microsatellite DNA analysis. Although pairwise Gѕт levels were significant in some sites, this was not reflected in principal component analysis or Bayesian structure analysis. It is likely that through long range dispersal, migration is at or above the threshold for genetic connectivity, but below a level necessary for demographic connectivity. This is indicated by both the genetic structure reported here, along with previous studies showing limited dispersal of P. colias.</p>

scholarly journals The Genetic Structure of Populations of the Douglas-Fir Swiss Needle Cast Fungus Nothophaeocryptopus gaeumannii in New Zealand

2019 ◽  
Vol 109 (3) ◽  
pp. 446-455 ◽  
Author(s):  
P. I. Bennett ◽  
I. A. Hood ◽  
J. K. Stone
Keyword(s):  
Population Structure ◽  
New Zealand ◽  
Genetic Structure ◽  
Random Mating ◽  
Douglas Fir ◽  
Needle Cast ◽  
The North ◽  
Genetic Structure Of Populations ◽  
Swiss Needle Cast ◽  
North And South

Swiss needle cast is a foliar disease of Douglas-fir (Pseudotsuga menziesii) that results in premature foliage loss and reduced growth. The causal fungus, Nothophaeocryptopus gaeumannii, was first detected in New Zealand in 1959 and spread throughout the North and South Islands over the following decades. The contemporary genetic structure of the N. gaeumannii population in New Zealand was assessed by analyzing 468 multilocus SSR genotypes (MLGs) from 2,085 N. gaeumannii isolates collected from 32 sites in the North and South Islands. Overall diversity was lower than that reported from native N. gaeumannii populations in the northwestern United States, which was expected given that N. gaeumannii is introduced in New Zealand. Linkage disequilibrium was significantly higher than expected under random mating, suggesting that population structure is clonal. Populations of N. gaeumannii in the North and South Islands were weakly differentiated, and the isolates collected from sites within the islands were moderately differentiated. This suggests that gene flow has occurred between the N. gaeumannii populations in the North and South Islands, and between the local N. gaeumannii populations within each island. Eighteen isolates of N. gaeumannii Lineage 2, which has previously been reported only from western Oregon, were recovered from two sites in the North Island and four sites in the South Island. The most likely explanation for the contemporary distribution of N. gaeumannii in New Zealand is that it was introduced on infected live seedlings through the forestry or ornamental nursery trade, as the fungus is neither seed borne nor saprobic, and the observed population structure is not consistent with a stochastic intercontinental dispersal event.

Colonization routes, microevolutionary genetic structure and conservation concerns in a remote widespread insular endemic grass: the case of the Azorean tussock grass Deschampsia foliosa

2019 ◽  
Vol 191 (3) ◽  
pp. 365-380 ◽  
Author(s):  
Mónica Moura ◽  
Pilar Catálan ◽  
António Brehm ◽  
Miguel Menezes De Sequeira
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
Genetic Data ◽  
Phylogenetic Networks ◽  
Island Populations ◽  
Western Group ◽  
Principal Coordinates ◽  
Clear Differentiation ◽  
Insular Endemic ◽  
Genetic Structure And Diversity

Abstract Population genetic structure and diversity and phylogeographical dispersal routes were assessed for the Azorean endemic grass Deschampsia foliosa using AFLP markers. This species occurs on seven islands in the archipelago and a sampling of populations from the three main geographical groups of islands was used, covering its known distribution. Principal coordinates analyses (PCoAs), Bayesian analyses and phylogenetic networks revealed different degrees of admixture for the central group (C) populations and a clear differentiation for the western group (W) and São Miguel island (in the eastern group, E) populations. The best K values corresponded to nine and 11 genetic groups, which were also confirmed by analysis of molecular variance. A low but significant correlation between genetic data and geography was observed, with most relevant barriers to gene flow generally placed between sub-archipelagos. We suggest a west-to-east isolation by distance dispersal model across an island age continuum with Flores–Corvo (W) and Pico (C) at the extremes of the dispersal path. An alternative scenario, also supported by the genetic data, implies an initial colonization of São Jorge (C), dispersal within C and following bidirectional dispersal to the W and E. The phylogeographical framework detected might be related to island age and to highly destructive volcanic events, and it supports the occurrence of cryptic diversity within D. foliosa. Genetic diversity estimators were highest for Pico island populations (C), lowest for São Miguel (E) and Flores (W) populations, and more divergent for the Corvo population (W). Conservation measures should be taken to preserve the genetic structure found across sub-archipelagos and islands.

scholarly journals Comparing the population structure of the specialist Butler’s gartersnake (Thamnophis butleri) and the generalist eastern gartersnake (Thamnophis sirtalis sirtalis) in Ontario and Michigan

2021 ◽  
Author(s):  
Megan Snetsinger ◽  
Jeffrey Row ◽  
Megan Hazell ◽  
Dennis Plain ◽  
Stephen Lougheed
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
Natural Populations ◽  
Thamnophis Sirtalis ◽  
Dna Microsatellites ◽  
Distance Class ◽  
Population Comparisons ◽  
Underlying Causes ◽  
Habitat Generalist ◽  
Genetic Clustering

Species differing in life history attributes vary in their responses to features within a shared landscape. We evaluated genetic structure of sympatric gartersnake species in Southwestern Ontario, Canada and south-east Michigan, U.S.A., where habitat fragmentation is high due to agriculture and urbanization. We surveyed genetic structure of the habitat specialist, Butler’s gartersnake (Thamnophis butleri; Cope, 1889) and habitat generalist, eastern gartersnake (Thamnophis sirtalis sirtalis; Linnaeus, 1758) using DNA microsatellites. Bayesian clustering, Discriminant Analysis of Principal Components, and pairwise population comparisons revealed genetic differentiation among three major regional clusters of Butler’s gartersnake with evidence of further division within one. Genetic clustering of Butler’s gartersnake suggest that inhospitable habitat limits dispersal. Eastern gartersnakes showed less structure, with assignment tests implying a single genetic cluster. We found positive significant Mantel’s r for both species in the smallest distance class (<15 kms), but significant isolation by distance for Thamnophis butleri only. These findings together imply that connectivity for eastern gartersnakes is less impacted by habitat loss and fragmentation or that we were less able to detect their effects. Our study shows the value of multispecies comparisons in studies seeking to understand the underlying causes of genetic structure in natural populations.

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 Panmixia in the European eel: a matter of time…

2005 ◽  
Vol 272 (1568) ◽  
pp. 1129-1137 ◽  
Author(s):  
Johan Dannewitz ◽  
Gregory E Maes ◽  
Leif Johansson ◽  
Håkan Wickström ◽  
Filip A.M Volckaert ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
North Atlantic ◽  
Isolation By Distance ◽  
Temporal Stability ◽  
Anguilla Anguilla ◽  
European Eel ◽  
Sargasso Sea ◽  
The North ◽  
Temporal Genetic Variation

The European eel ( Anguilla anguilla L.) has been a prime example of the panmixia paradigm because of its extraordinary adaptation to the North Atlantic gyral system, semelparous spawning in the Sargasso Sea and long trans-oceanic migration. Recently, this view was challenged by the suggestion of a genetic structure characterized by an isolation-by-distance (IBD) pattern. This is only likely if spawning subpopulations are spatially and/or temporally separated, followed by non-random larval dispersal. A limitation of previous genetic work on eels is the lack of replication over time to test for temporal stability of genetic structure. Here, we hypothesize that temporal genetic variation plays a significant role in explaining the spatial structure reported earlier for this species. We tested this by increasing the texture of geographical sampling and by including temporal replicates. Overall genetic differentiation among samples was low, highly significant and comparable with earlier studies ( F ST =0.0014; p <0.01). On the other hand, and in sharp contrast with current understandings, hierarchical analyses revealed no significant inter-location genetic heterogeneity and hence no IBD. Instead, genetic variation among temporal samples within sites clearly exceeded the geographical component. Our results provide support for the panmixia hypothesis and emphasize the importance of temporal replication when assessing population structure of marine fish species.

scholarly journals Pronghorn population genomics show connectivity in the core of their range

2020 ◽  
Vol 101 (4) ◽  
pp. 1061-1071
Author(s):  
Melanie E F LaCava ◽  
Roderick B Gagne ◽  
Sierra M Love Stowell ◽  
Kyle D Gustafson ◽  
C Alex Buerkle ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Seasonal Migration ◽  
Gps Tracking ◽  
Landscape Features ◽  
Landscape Modification ◽  
The Core ◽  
Genetic Structure And Diversity

Abstract Preserving connectivity in the core of a species’ range is crucial for long-term persistence. However, a combination of ecological characteristics, social behavior, and landscape features can reduce connectivity among wildlife populations and lead to genetic structure. Pronghorn (Antilocapra americana), for example, exhibit fluctuating herd dynamics and variable seasonal migration strategies, but GPS tracking studies show that landscape features such as highways impede their movements, leading to conflicting hypotheses about expected levels of genetic structure. Given that pronghorn populations declined significantly in the early 1900s, have only partially recovered, and are experiencing modern threats from landscape modification, conserving connectivity among populations is important for their long-term persistence in North America. To assess the genetic structure and diversity of pronghorn in the core of their range, we genotyped 4,949 genome-wide single-nucleotide polymorphisms and 11 microsatellites from 398 individuals throughout the state of Wyoming. We found no evidence of genetic subdivision and minimal evidence of isolation by distance despite a range that spans hundreds of kilometers, multiple mountain ranges, and three interstate highways. In addition, a rare variant analysis using putatively recent mutations found no genetic division between pronghorn on either side of a major highway corridor. Although we found no evidence that barriers to daily and seasonal movements of pronghorn impede gene flow, we suggest periodic monitoring of genetic structure and diversity as a part of management strategies to identify changes in connectivity.

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.

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