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.

Vulnerability of megapodes (Megapodiidae, Aves) to climate change and related threats

2018 ◽  
Vol 45 (4) ◽  
pp. 396-406 ◽  
Author(s):  
PAUL M. RADLEY ◽  
ROBERT A. DAVIS ◽  
RENÉ W.R.J. DEKKER ◽  
SHAUN W. MOLLOY ◽  
DAVID BLAKE ◽  
...  
Keyword(s):  
Climate Change ◽  
Gene Flow ◽  
Life Histories ◽  
Population Level ◽  
Genetic Connectivity ◽  
Future Research ◽  
Mean Annual Temperature ◽  
Climate Variables ◽  
Microbial Decomposition ◽  
Anthropogenic Habitat

SUMMARYAspects of species life histories may increase their susceptibility to climate change. Owing to their exclusive reliance on environmental sources of heat for incubation, megapodes may be especially vulnerable. We employed a trait-based vulnerability assessment to weigh their exposure to projected climate variables of increasing temperatures, fluctuating rainfall and sea level rise and their biological sensitivity and capacity to adapt. While all 21 species were predicted to experience at least a 2 °C increase in mean annual temperature, 12 to experience a moderate or greater fluctuation in rainfall and 16 to experience rising seas, the most vulnerable megapodes are intrinsically rare and range restricted. Species that employ microbial decomposition for incubation may have an adaptive advantage over those that do not and may be more resilient to climate change. The moderate microclimate necessary for mound incubation, however, may in some areas be threatened by anthropogenic habitat loss exacerbated by warmer and seasonally drier conditions. As with many avian species, little is known about the capacity of megapodes to adapt to a changing climate. We therefore recommend that future research efforts investigate megapode fecundity, gene flow and genetic connectivity at the population level to better determine their adaptive capacity.

A temporal perspective on population structure and gene flow in Atlantic salmon (Salmo salar) in Newfoundland, Canada

2010 ◽  
Vol 67 (2) ◽  
pp. 225-242 ◽  
Author(s):  
Friso P. Palstra ◽  
Daniel E. Ruzzante
Keyword(s):  
Population Dynamics ◽  
Population Structure ◽  
Gene Flow ◽  
Atlantic Salmon ◽  
Salmo Salar ◽  
Environmental Changes ◽  
Population Connectivity ◽  
Temporal Perspective ◽  
Atlantic Salmon Salmo Salar ◽  
Contemporary Gene Flow

Studying population structure and gene flow patterns on temporal scales facilitates an evaluation of the consequences of demographic, physical, and environmental changes on the stability and persistence of populations. Here, we examine temporal genetic variation within and among Atlantic salmon ( Salmo salar ) rivers in Newfoundland and Labrador, Canada, using samples collected over a period of six decades (1951–2004). Our objective was to evaluate temporal changes in population connectivity associated with the closure of a commercial marine fishery. Despite demographic instability, we find that population structure remained temporally stable over more than 50 years. However, age structure can affect results when not taken into consideration, particularly in populations of large effective size where genetic drift is not strong. Where weak signals of genetic differentiation did not complicate analyses, contemporary migration was often asymmetric, yet low, suggesting patterns of intermittent gene flow. Nevertheless, we find some links between changes in population dynamics and contemporary gene flow. These findings may therefore imply that management decisions impacting the contemporary population dynamics of individual Atlantic salmon rivers can also affect the genetic stability of this species as a whole.

scholarly journals The formation of avian montane diversity across barriers and along elevational gradients

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
José Martín Pujolar ◽  
Mozes P. K. Blom ◽  
Andrew Hart Reeve ◽  
Jonathan D. Kennedy ◽  
Petter Zahl Marki ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Differentiation ◽  
Bird Species ◽  
Geographic Area ◽  
Effective Population ◽  
Tropical Mountains ◽  
Mountainous Regions ◽  
Pleistocene Climate ◽  
Genome Wide ◽  
Population Sizes

AbstractTropical mountains harbor exceptional concentrations of Earth’s biodiversity. In topographically complex landscapes, montane species typically inhabit multiple mountainous regions, but are absent in intervening lowland environments. Here we report a comparative analysis of genome-wide DNA polymorphism data for population pairs from eighteen Indo-Pacific bird species from the Moluccan islands of Buru and Seram and from across the island of New Guinea. We test how barrier strength and relative elevational distribution predict population differentiation, rates of historical gene flow, and changes in effective population sizes through time. We find population differentiation to be consistently and positively correlated with barrier strength and a species’ altitudinal floor. Additionally, we find that Pleistocene climate oscillations have had a dramatic influence on the demographics of all species but were most pronounced in regions of smaller geographic area. Surprisingly, even the most divergent taxon pairs at the highest elevations experience gene flow across barriers, implying that dispersal between montane regions is important for the formation of montane assemblages.

scholarly journals Asymmetrical gene flow in five co-distributed syngnathids explained by ocean currents and rafting propensity

2020 ◽  
Vol 287 (1926) ◽  
pp. 20200657 ◽  
Author(s):  
Laura D. Bertola ◽  
J. T. Boehm ◽  
Nathan F. Putman ◽  
Alexander T. Xue ◽  
John D. Robinson ◽  
...  
Keyword(s):  
Gene Flow ◽  
Ocean Circulation ◽  
Habitat Preferences ◽  
Population Level ◽  
Ocean Currents ◽  
Genetic Connectivity ◽  
Dispersal Ability ◽  
Genome Wide ◽  
Near Shore ◽  
Species Specific

Ocean circulation driving macro-algal rafting is believed to serve as an important mode of dispersal for many marine organisms, leading to predictions on population-level genetic connectivity and the directionality of effective dispersal. Here, we use genome-wide single nucleotide polymorphism data to investigate whether gene flow directionality in two seahorses ( Hippocampus ) and three pipefishes ( Syngnathus ) follows the predominant ocean circulation patterns in the Gulf of Mexico and northwestern Atlantic. In addition, we explore whether gene flow magnitudes are predicted by traits related to active dispersal ability and habitat preference. We inferred demographic histories of these co-distributed syngnathid species, and coalescent model-based estimates indicate that gene flow directionality is in agreement with ocean circulation data that predicts eastward and northward macro-algal transport. However, the magnitude to which ocean currents influence this pattern appears strongly dependent on the species-specific traits related to rafting propensity and habitat preferences. Higher levels of gene flow and stronger directionality are observed in Hippocampus erectus , Syngnathus floridae and Syngnathus louisianae , which closely associated with the pelagic macro-algae Sargassum spp., compared to Hippocampus zosterae and the Syngnathus scovelli / Syngnathus fuscus sister-species pair, which prefer near shore habitats and are weakly associated with pelagic Sargassum . This study highlights how the combination of population genomic inference together with ocean circulation data can help explain patterns of population structure and diversity in marine ecosystems.

scholarly journals Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean

2021 ◽  
Vol 12 ◽  
Author(s):  
Sammy Wambua ◽  
Hadrien Gourlé ◽  
Etienne P. de Villiers ◽  
Oskar Karlsson-Lindsjö ◽  
Nina Wambiji ◽  
...  
Keyword(s):  
Coral Reef ◽  
Indian Ocean ◽  
Coral Reefs ◽  
Microbial Communities ◽  
Environmental Changes ◽  
Human Impacts ◽  
Anthropogenic Impacts ◽  
Future Research ◽  
Molecular Monitoring ◽  
Cross Sectional

Coral reefs face an increased number of environmental threats from anthropomorphic climate change and pollution from agriculture, industries and sewage. Because environmental changes lead to their compositional and functional shifts, coral reef microbial communities can serve as indicators of ecosystem impacts through development of rapid and inexpensive molecular monitoring tools. Little is known about coral reef microbial communities of the Western Indian Ocean (WIO). We compared taxonomic and functional diversity of microbial communities inhabiting near-coral seawater and sediments from Kenyan reefs exposed to varying impacts of human activities. Over 19,000 species (bacterial, viral and archaeal combined) and 4,500 clusters of orthologous groups of proteins (COGs) were annotated. The coral reefs showed variations in the relative abundances of ecologically significant taxa, especially copiotrophic bacteria and coliphages, corresponding to the magnitude of the neighboring human impacts in the respective sites. Furthermore, the near-coral seawater and sediment metagenomes had an overrepresentation of COGs for functions related to adaptation to diverse environments. Malindi and Mombasa marine parks, the coral reef sites closest to densely populated settlements were significantly enriched with genes for functions suggestive of mitigation of environment perturbations including the capacity to reduce intracellular levels of environmental contaminants and repair of DNA damage. Our study is the first metagenomic assessment of WIO coral reef microbial diversity which provides a much-needed baseline for the region, and points to a potential area for future research toward establishing indicators of environmental perturbations.

scholarly journals Novel genomic resources for shelled pteropods: a draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Le Qin Choo ◽  
Thijs M. P. Bal ◽  
Marvin Choquet ◽  
Irina Smolina ◽  
Paula Ramos-Silva ◽  
...  
Keyword(s):  
Related Species ◽  
Environmental Changes ◽  
Draft Genome ◽  
Genomic Variation ◽  
Genetic Connectivity ◽  
Model Organisms ◽  
Focal Species ◽  
Genomic Resources ◽  
Target Capture ◽  
Genome Wide

Abstract Background Pteropods are planktonic gastropods that are considered as bio-indicators to monitor impacts of ocean acidification on marine ecosystems. In order to gain insight into their adaptive potential to future environmental changes, it is critical to use adequate molecular tools to delimit species and population boundaries and to assess their genetic connectivity. We developed a set of target capture probes to investigate genetic variation across their large-sized genome using a population genomics approach. Target capture is less limited by DNA amount and quality than other genome-reduced representation protocols, and has the potential for application on closely related species based on probes designed from one species. Results We generated the first draft genome of a pteropod, Limacina bulimoides, resulting in a fragmented assembly of 2.9 Gbp. Using this assembly and a transcriptome as a reference, we designed a set of 2899 genome-wide target capture probes for L. bulimoides. The set of probes includes 2812 single copy nuclear targets, the 28S rDNA sequence, ten mitochondrial genes, 35 candidate biomineralisation genes, and 41 non-coding regions. The capture reaction performed with these probes was highly efficient with 97% of the targets recovered on the focal species. A total of 137,938 single nucleotide polymorphism markers were obtained from the captured sequences across a test panel of nine individuals. The probes set was also tested on four related species: L. trochiformis, L. lesueurii, L. helicina, and Heliconoides inflatus, showing an exponential decrease in capture efficiency with increased genetic distance from the focal species. Sixty-two targets were sufficiently conserved to be recovered consistently across all five species. Conclusion The target capture protocol used in this study was effective in capturing genome-wide variation in the focal species L. bulimoides, suitable for population genomic analyses, while providing insights into conserved genomic regions in related species. The present study provides new genomic resources for pteropods and supports the use of target capture-based protocols to efficiently characterise genomic variation in small non-model organisms with large genomes.

scholarly journals Reduced Global Genetic Differentiation of Exploited Marine Fish Species

2020 ◽  
Author(s):  
Miguel Gandra ◽  
Jorge Assis ◽  
Manuel Ramos Martins ◽  
David Abecasis
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Marine Fish ◽  
Fish Species ◽  
Population Differentiation ◽  
Environmental Changes ◽  
Meta Analysis ◽  
Genetic Connectivity

Abstract Knowledge on genetic structure is key to understand species connectivity patterns and to define the spatiotemporal scales over which conservation management plans should be designed and implemented. The distribution of genetic diversity (within and among populations) greatly influences species ability to cope and adapt to environmental changes, ultimately determining their long-term resilience to ecological disturbances. Yet, the drivers shaping connectivity and structure in marine fish populations remain elusive, as are the effects of fishing activities on genetic subdivision. To investigate these questions, we conducted a meta-analysis and compiled genetic differentiation data (FST/ΦST estimates) for more than 170 fish species from over 200 published studies globally distributed. We modeled the effects of multiple life-history traits, distance metrics, and methodological factors on observed population differentiation indices and specifically tested whether any signal arising from different exposure to fishing exploitation could be detected. Although the myriad of variables shaping genetic structure makes it challenging to isolate the influence of single drivers, results showed a significant correlation between commercial importance and genetic structure, with widespread lower population differentiation in commercially exploited species. Moreover, models indicate that variables commonly used as proxy for connectivity, such as larval pelagic duration, might be insufficient, and suggest that deep-sea species may disperse further. Overall, these results contribute to the growing body of knowledge on marine genetic connectivity and suggest a potential effect of commercial fisheries on the homogenization of genetic diversity, highlighting the need for additional research focused on dispersal ecology to ensure long-term sustainability of exploited marine species.

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.

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