scholarly journals Genomic analyses suggest strong population connectivity over large spatial scales of the commercially important baitworm, Australonuphis teres (Onuphidae)

2020 ◽  
Vol 71 (11) ◽  
pp. 1549
Author(s):  
Amanda Padovan ◽  
Rowan C. Chick ◽  
Victoria J. Cole ◽  
Ludovic Dutoit ◽  
Patricia A. Hutchings ◽  
...  
Keyword(s):  
Gene Flow ◽  
Spatial Scales ◽  
Population Connectivity ◽  
Eastern Coast ◽  
Marine Biodiversity ◽  
Marine Animals ◽  
Long Distance ◽  
South Wales ◽  
Genome Wide ◽  
Eastern Australia

Barriers to dispersal can disrupt gene flow between populations, resulting in genetically distinct populations. Although many marine animals have potential for long-distance dispersal via a planktonic stage, gene flow among populations separated by large geographic distances is not always evident. Polychaetes are ecologically important and have been used as biological surrogates for marine biodiversity. Some polychaete species are used as bait for recreational fisheries, with this demand supporting commercial fisheries for polychaetes to service the retail bait market. However, despite their ecological and economic importance, very little is known about the life history or population dynamics of polychaetes, and few studies have used genetic or genomic approaches to understand polychaete population connectivity. Here, we investigate the population structure of one commonly collected beachworm species used for bait on the eastern coast of Australia, namely, Australonuphis teres, by using genome-wide single-nucleotide polymorphism data. We sampled A. teres from hierarchical nested spatial scales along 900km of the coast in New South Wales. We identified six genetic groups, but there was no clear geographic pattern of distribution. Our results suggest that there is considerable gene flow among the sampled populations. These high-resolution genomic data support the findings of previous studies, and we infer that oceanographic processes promote genetic exchange among polychaete populations in south-eastern Australia.

scholarly journals Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity

2021 ◽  
Author(s):  
Taya L. Forde ◽  
Tristan P. W. Dennis ◽  
O. Rhoda Aminu ◽  
William T. Harvey ◽  
Ayesha Hassim ◽  
...  
Keyword(s):  
Bacillus Anthracis ◽  
Population Genomics ◽  
Spatial Scales ◽  
Genomic Diversity ◽  
Phylogeographic Structure ◽  
Bacterial Disease ◽  
Significant Finding ◽  
Long Distance ◽  
Genome Wide ◽  
Analytical Approaches

AbstractGenomic sequencing has revolutionized our understanding of bacterial disease epidemiology, but remains underutilized for zoonotic pathogens in remote endemic settings. Anthrax, caused by the spore-forming bacterium Bacillus anthracis, remains a threat to human and animal health and rural livelihoods in low- and middle-income countries. While the global genomic diversity of B. anthracis has been well-characterized, there is limited information on how its populations are genetically structured at the scale at which transmission occurs, critical for understanding the pathogen’s evolution and transmission dynamics. Using a uniquely rich dataset, we quantified genome-wide single nucleotide polymorphisms (SNPs) among 73 B. anthracis isolates derived from 33 livestock carcasses sampled over one year throughout the Ngorongoro Conservation Area, Tanzania, an area hyperendemic for anthrax. Genome-wide SNPs distinguished 22 unique B. anthracis genotypes within the study area. However, phylogeographic structure was lacking, as identical SNP profiles were found throughout the study area, likely the result of the long and variable periods of spore dormancy and long-distance livestock movements. Significantly, divergent genotypes were obtained from spatio-temporally linked cases and even individual carcasses. The high number of SNPs distinguishing isolates from the same host is unlikely to have arisen during infection, as supported by our simulation models. This points to an unexpectedly wide transmission bottleneck for B. anthracis, with an inoculum comprising multiple variants being the norm. Our work highlights that inferring transmission patterns of B. anthracis from genomic data will require analytical approaches that account for extended and variable environmental persistence as well as co-infection.ImportancePathogens transmitted between animals and people affect the health and livelihoods of farmers, particularly in developing countries dependent on livestock. Understanding over what distances these pathogens are transmitted and how they evolve is important to inform control strategies towards reducing disease impacts. Information on the circulation of Bacillus anthracis, which causes the often-lethal disease anthrax, is lacking for settings where the disease is commonplace. Consequently, we examined its genetic variability in an area in Tanzania where anthrax is widespread. We found no clear link between how closely cases were sampled and their genetic similarity. We suspect this lack of congruence is primarily driven by large-scale livestock movements, which control efforts should take into consideration. Another significant finding was the co-occurrence of multiple B. anthracis types within individual hosts, suggesting animals are commonly infected with a mixture of variants. This needs to be accounted for when investigating possible connections between cases.

scholarly journals Population structure and dispersal across small and large spatial scales in a direct developing marine isopod

2020 ◽  
Author(s):  
William S. Pearman ◽  
Sarah J. Wells ◽  
Olin K. Silander ◽  
Nikki E. Freed ◽  
James Dale
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Population Genetic ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Population Connectivity ◽  
Clear Pattern ◽  
Small Spatial Scale ◽  
Cook Strait ◽  
Genetic Break

AbstractMarine organisms generally exhibit one of two developmental modes: biphasic, with distinct adult and larval morphology, and direct development, in which larvae resemble adults. Developmental mode is thought to significantly influence dispersal, with direct developers expected to have much lower dispersal potential. However, in contrast to our relatively good understanding of dispersal and population connectivity for biphasic species, comparatively little is known about direct developers. In this study, we use a panel of 8,020 SNPs to investigate population structure and gene flow for a direct developing species, the New Zealand endemic marine isopod Isocladus armatus. On a small spatial scale (20 kms), gene flow between locations is extremely high and suggests an island model of migration. However, over larger spatial scales (600km), populations exhibit a clear pattern of isolation-by-distance. Because our sampling range is intersected by two well-known biogeographic barriers (the East Cape and the Cook Strait), our study provides an opportunity to understand how such barriers influence dispersal in direct developers. Our results indicate that I. armatus exhibits significant migration across these barriers, and suggests that ocean currents associated with these locations do not present a barrier to dispersal. Interestingly, we do find evidence of a north-south population genetic break occurring between Māhia and Wellington, two locations where there are no obvious biogeographic barriers between them. We conclude that developmental life history largely predicts dispersal in intertidal marine isopods. However, localised biogeographic processes can disrupt this expectation.

scholarly journals Hammer Chyme: The Russian-Doll Effect Limits Reconstructing Marine Trophic Food Webs

2021 ◽  
Author(s):  
Mark de Bruyn ◽  
Matteo Barbato ◽  
Joseph D. DiBattista ◽  
Matt K. Broadhurst
Keyword(s):  
Trophic Interactions ◽  
Fishing Effort ◽  
Marine Biodiversity ◽  
Carcharhinus Limbatus ◽  
Dietary Preferences ◽  
South Wales ◽  
Eastern Australia ◽  
Dna Metabarcoding ◽  
The Common ◽  
Species Being

Abstract Increasing fishing effort, including bycatch and discard practices, are impacting marine biodiversity, particularly among slow-to-reproduce taxa such as elasmobranchs, and specifically sharks. While some fisheries involving sharks are sustainably managed, collateral mortalities continue, contributing towards >35% of species being threatened with extinction. To effectively manage shark stocks, life-history information, including resource use/feeding ecologies is pivotal, especially among those species with wide-ranging distributions and habitats. Two cosmopolitan sharks bycaught off eastern Australia are the common blacktip shark (Carcharhinus limbatus; globally classified as Near Threatened) and great hammerhead (Sphyrna mokarran; Critically Endangered). We opportunistically sampled the digestive tracts of these two species and also any whole prey; (termed the ‘Russian-doll’ approach) caught in bather-protection gillnets off northern New South Wales to investigate their regional feeding ecologies and the capacity for DNA metabarcoding to delineate trophic interactions. Sphyrna mokkaran fed predominantly on Myliobatiformes and Rajiformes, but also teleosts, while C. limbatus mostly consumed teleosts, with some inter-specific dietary overlap of prey items. Extensive cross-contamination of predator and prey digestive tracts, likely via the predator’s stomach chyme, was evident from the metabarcoding assays limiting the opportunity to delineate trophic interactions from these data. This Russian-doll effect requires further investigation in DNA metabarcoding studies focused on dietary preferences, but implies any outcomes will need to be interpreted concomitant with traditional visual approaches.

scholarly journals Population Genomics and Lagrangian Modeling Shed Light on Dispersal Events in the Mediterranean Endemic Ericaria zosteroides (=Cystoseira zosteroides) (Fucales)

2021 ◽  
Vol 8 ◽  
Author(s):  
Lauric Reynes ◽  
Didier Aurelle ◽  
Cristele Chevalier ◽  
Christel Pinazo ◽  
Myriam Valero ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Population Genomics ◽  
Spatial Scales ◽  
Seawater Temperature ◽  
Marine Species ◽  
Population Connectivity ◽  
Central Process ◽  
Lagrangian Modeling ◽  
Dispersal Events

Dispersal is a central process that affects population growth, gene flow, and ultimately species persistence. Here we investigate the extent to which gene flow occurs between fragmented populations of the deep-water brown algae Ericaria zosteroides (Turner) Greville (Sargassaceae, Fucales). These investigations were performed at different spatial scales from the bay of Marseille (western Provence) to Corsica. As dispersal of zygotes is shown to be limited over distances beyond a few meters, we used a multidisciplinary approach, based on Lagrangian modeling and population genomics to test the hypothesis that drifting of fertile parts of thallus (eggs on fertile branches), mediated by ocean currents, enable occasional gene flow between populations. Therefore we assessed the respective contribution of oceanographic connectivity, geographical isolation, and seawater temperatures to the genetic structure of this species. The genetic structure was assessed using 10,755 neutral SNPs and 12 outlier SNPs genotyped by dd-RAD sequencing in 261 individuals of E. zosteroides. We find that oceanographic connectivity is the best predictor of genetic structure, while differentiation in outlier SNPs can be explained by the depth of populations, as emphasized by the minimum seawater temperature predictor. However, further investigations will be necessary for clarifying how depth drives adaptive genetic differentiation in E. zosteroides. Our analyses revealed that local hydrodynamic conditions are correlated with the very high divergence of one population in the Bay of Marseille. Overall, the levels of gene flow mediated by drifting were certainly not sufficient to counteract differentiation by local genetic drift, but enough to allow colonization several kilometers away. This study stresses the need to consider secondary dispersal mechanisms of presumed low dispersal marine species to improve inference of population connectivity.

scholarly journals Beyond the Coral Triangle: high genetic diversity and near panmixia in Singapore's populations of the broadcast spawning sea star Protoreaster nodosus

2016 ◽  
Vol 3 (8) ◽  
pp. 160253 ◽  
Author(s):  
Y. C. Tay ◽  
M. W. P. Chng ◽  
W. W. G. Sew ◽  
F. E. Rheindt ◽  
K. P. P. Tun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Marine Invertebrates ◽  
Small Population ◽  
Population Connectivity ◽  
Marine Biodiversity ◽  
Coral Triangle ◽  
Sea Star ◽  
High Genetic Diversity ◽  
Broadcast Spawning ◽  
Genome Wide

The Coral Triangle is widely considered the most important centre of marine biodiversity in Asia while areas on its periphery such as the South China Sea, have received much less interest. Here, we demonstrate that a small population of the knobbly sea star Protoreaster nodosus in Singapore has similarly high levels of genetic diversity as comparable Indonesian populations from the Coral Triangle. The high genetic diversity of this population is remarkable because it is maintained despite decades of continued anthropogenic disturbance. We postulate that it is probably due to broadcast spawning which is likely to maintain high levels of population connectivity. To test this, we analysed 6140 genome-wide single nucleotide polymorphism (SNP) loci for Singapore's populations and demonstrate a pattern of near panmixia. We here document a second case of high genetic diversity and low genetic structure for a broadcast spawner in Singapore, which suggests that such species have high resilience against anthropogenic disturbances. The study demonstrates the feasibility and power of using genome-wide SNPs for connectivity studies of marine invertebrates without a sequenced genome.

scholarly journals Comprehensive Examination of the Determinants of Damage to Houses in Two Wildfires in Eastern Australia in 2013

Fire ◽  
2021 ◽  
Vol 4 (3) ◽  
pp. 44
Author(s):  
Owen F. Price ◽  
Joshua Whittaker ◽  
Philip Gibbons ◽  
Ross Bradstock
Keyword(s):  
New South ◽  
Spatial Scales ◽  
Fire Spread ◽  
Defensible Space ◽  
Forest Modelling ◽  
South Wales ◽  
House Construction ◽  
Eastern Australia ◽  
Active Defence ◽  
Cover Up

Wildfires continue to destroy houses, but an understanding of the complex mix of risk factors remains elusive. These factors comprise six themes: preparedness actions (including defensible space), response actions (including defence), house construction, landscape fuels, topography and weather. The themes span a range of spatial scales (house to region) and responsible agents (householders through government to entirely natural forces). We conducted a statistical analysis that partitions the contribution of these six themes on wildfire impact to houses, using two fires that destroyed 200 houses in New South Wales (Australia) in October 2013 (the Linksview and Mt York fires). We analysed 85 potential predictor variables using Random Forest modelling. The best predictors of impact were whether the house was defended and distance to forest toward the direction of fire spread. However, predictors from all four of the other themes had some influence, including distance to the nearest other burnt house (indicating house-to-house transmission) and vegetation cover up to 40 m from the house. The worst-placed houses (undefended, without adequate defensible space, with burnt houses nearby and with a westerly aspect) were 10 times more likely to be impacted than the best-placed houses in our study. The results indicate that householders are the agents most able to mitigate risk in the conditions experienced in these fires through both preparation and active defence.

scholarly journals An Aboriginal shield collected in 1770 at Kamay Botany Bay: an indicator of pre-colonial exchange systems in south-eastern Australia

Antiquity ◽  
2014 ◽  
Vol 88 (341) ◽  
pp. 883-895 ◽  
Author(s):  
Valerie J. Attenbrow ◽  
Caroline R. Cartwright
Keyword(s):  
New South ◽  
British Museum ◽  
North Coast ◽  
Tropical Species ◽  
Long Distance ◽  
Exchange Networks ◽  
Red Mangrove ◽  
South Wales ◽  
Eastern Australia ◽  
Special Value

A bark shield now in the British Museum can be identified from documentary and pictorial evidence as one collected by Captain Cook during his first voyage to Australia in 1770. Such shields often had special value to their Australian Aboriginal owners and hence might have been exchanged over considerable distances. This particular shield is known to have been collected in Kamay Botany Bay but analysis of the bark of which it is made revealed it to be of red mangrove, a tropical species found today more than 500km distant on the New South Wales north coast. It hence bears valuable testimony to the long-distance exchange networks operating in eastern Australia in the period before the disruption caused by European colonisation.

scholarly journals A Matter of Scale: Population Genomic Structure and Connectivity of Fisheries At-Risk Common Dolphins (Delphinus delphis) From Australasia

2021 ◽  
Vol 8 ◽  
Author(s):  
Andrea Barceló ◽  
Jonathan Sandoval-Castillo ◽  
Karen A. Stockin ◽  
Kerstin Bilgmann ◽  
Catherine R. M. Attard ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Spatial Scales ◽  
Eastern Coast ◽  
Common Dolphin ◽  
Delphinus Delphis ◽  
Multiple Spatial Scales ◽  
Population Genomic ◽  
Common Dolphins ◽  
Australasian Region

An understanding of population structure and connectivity at multiple spatial scales is required to assist wildlife conservation and management. This is particularly critical for widely distributed and highly mobile marine mammals subject to fisheries by-catch. Here, we present a population genomic assessment of a near-top predator, the common dolphin (Delphinus delphis), which is incidentally caught in multiple fisheries across the Australasian region. The study was carried out using 14,799 ddRAD sequenced genome-wide markers genotyped for 478 individuals sampled at multiple spatial scales across Australasia. A complex hierarchical metapopulation structure was identified, with three highly distinct and genetically diverse regional populations at large spatial scales (>1,500 km). The populations inhabit the southern coast of Australia, the eastern coast of Australia, New Zealand, and Tasmania, with the latter also showing a considerable level of admixture to Australia's east coast. Each of these regional populations contained two to four nested local populations (i.e., subpopulations) at finer spatial scales, with most of the gene flow occurring within distances of 50 to 400 km. Estimates of contemporary migration rates between adjacent subpopulations ranged from 6 to 25%. Overall, our findings identified complex common dolphin population structure and connectivity across state and international jurisdictions, including migration and gene flow across the Tasman Sea. The results indicate that inter-jurisdictional collaboration is required to implement conservation management strategies and mitigate fisheries interactions of common dolphins across multiple spatial scales in the Australasian region.

scholarly journals Riverscape genomics of cichlid fishes in the lower Congo: Uncovering mechanisms of diversification in an extreme hydrological regime

2021 ◽  
Author(s):  
Naoko Kurata ◽  
Michael Hickerson ◽  
Sandra Hoffberg ◽  
Ned Gardiner ◽  
Melanie L.J. Stiassny ◽  
...  
Keyword(s):  
Gene Flow ◽  
Spatial Scales ◽  
Hydrological Regime ◽  
High Energy ◽  
Ecological Specialization ◽  
Cichlid Fishes ◽  
Heterogeneous Habitats ◽  
Snp Data ◽  
Genome Wide ◽  
Physical Barriers

Rivers provide excellent models to understand how species diversity is generated and maintained across heterogeneous habitats. The lower Congo River (LCR) consists of a dynamic hydroscape exhibiting extraordinary aquatic biodiversity, endemicity, and ecological specialization. Previous studies have suggested that the numerous high-energy rapids throughout the LCR form physical barriers to gene flow, thus facilitating diversification and speciation, and generating ichthyofaunal diversity. However, this hypothesis has not been fully explored using genome-wide SNPs for fish species distributed across the LCR. In this study, we examined four species of lamprologine cichlids endemic to the LCR, of which three are sequentially distributed along the LCR without range overlap. Using genome-wide SNP data, we tested the hypotheses that high-energy rapids serve as physical barriers to gene flow that generate genetic divergence at inter- and intraspecific levels, and that gene flow occurs primarily in a downstream direction. Our results are consistent with the prediction that the rapids sometimes serve to reduce gene flow, but also suggest that at certain temporal and spatial scales, they may also act as promoters of gene flow. Furthermore, we detected both upstream and downstream gene flow between some populations of Lamprologus tigripictilis as well as hybridization between congeneric species. These results suggest that powerful high-energy rapids may therefore provide occasional multidirectional dispersal opportunities for riverine cichlid fishes, highlighting the complexity of factors driving evolutionary processes in the LCR.

scholarly journals The relative contribution of natural landscapes and human-mediated factors on the connectivity of a noxious invasive weed

2016 ◽  
Author(s):  
Diego F. Alvarado-Serrano ◽  
Megan Van Etten ◽  
Shu-Mei Chang ◽  
Regina S. Baucom
Keyword(s):  
Gene Flow ◽  
Population Differentiation ◽  
Environmental Changes ◽  
Anthropogenic Impacts ◽  
Population Connectivity ◽  
Genetic Connectivity ◽  
Future Research ◽  
Invasive Weed ◽  
Relative Contribution ◽  
Genome Wide

ABSTRACTExamining how the landscape may influence gene flow is at the forefront of understanding population differentiation and adaptation. Such understanding is crucial in light of ongoing environmental changes and the elevated risk of ecosystems alteration. In particular, knowledge of how humans may influence the structure of populations is imperative to allow for informed decisions in management and conservation as well as to gain a better understanding of anthropogenic impacts on the interplay between gene flow, genetic drift and selection. Here we use genome-wide molecular markers to characterize the population genetic structure and connectivity of Ipomoea purpurea, a noxious invasive weed. We likewise assess the interaction between natural and human-driven influences on genetic differentiation among populations. Our analyses find that human population density is an important predictor of pairwise population differentiation, suggesting that the agricultural and/or horticultural trade may be involved in maintaining some level of connectivity across distant agricultural fields. Climatic variation appears as an additional predictor of genetic connectivity in this species. We discuss the implications of these results and highlight future research needed to disentangle the mechanistic processes underlying population connectivity of weeds.

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