population connectivity
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2021 ◽  
Author(s):  
Jeremy Larroque ◽  
Julian Wittische ◽  
Patrick M. A. James

Abstract Context Dispersal has a key role in the population dynamics of outbreaking species such as the spruce budworm (Choristoneura fumiferana) as it can synchronize the demography of distant populations and favor the transition from endemic to epidemic states. However, we know very little about how landscape structure influences dispersal in such systems while such knowledge is essential for better forecasting of spatially synchronous population dynamics and to guide management strategies. Objectives We aimed to characterize the spatial environmental determinants of spruce budworm dispersal to determine how these features affect outbreak spread in Quebec (Canada). We then apply our findings to predict expected future landscape connectivity and explore its potential consequences on future outbreaks. Methods We used a machine-learning landscape genetics approach on 447 larvae covering most of the outbreak area and genotyped at 3562 SNP loci to identify the main variables affecting connectivity. Results We found that the connectivity between outbreak populations was driven by the combination of precipitation and host cover. Our forecasting suggests that between the current and next outbreaks, connectivity may increase between Ontario and Quebec, and might decrease in the eastern part, which could have the effect of limiting outbreak spread from Ontario and Quebec to the eastern provinces. Conclusions Although we did not identify any discrete barriers, low connectivity areas might constrain dispersal in the current and future outbreaks and should in turn, be intensively monitored. However, continued sampling as the outbreak progresses is needed to confirm the temporal stability of the observed patterns.


2021 ◽  
Author(s):  
Renata L. Muylaert ◽  
Tigga Kingston ◽  
Jinhong Luo ◽  
Maurício Humberto Vancine ◽  
Nikolas Galli ◽  
...  

Global changes in response to human encroachment into natural habitats and carbon emissions are driving the biodiversity extinction crisis and increasing disease emergence risk. Host distributions are one critical component to identify areas at risk of spillover, and bats act as reservoirs of diverse viruses. We developed a reproducible ecological niche modelling pipeline for bat hosts of SARS-like viruses (subgenus Sarbecovirus), given that since SARS-CoV-2 emergence several closely-related viruses have been discovered and sarbecovirus-host interactions have gained attention. We assess sampling biases and model bats' current distributions based on climate and landscape relationships and project future scenarios. The most important predictors of species distribution were temperature seasonality and cave availability. We identified concentrated host hotspots in Myanmar and projected range contractions for most species by 2100. Our projections indicate hotspots will shift east in Southeast Asia in >2 °C hotter locations in a fossil-fueled development future. Hotspot shifts have implications for conservation and public health, as loss of population connectivity can lead to local extinctions, and remaining hotspots may concentrate near human populations.


PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260344
Author(s):  
Marlis R. Douglas ◽  
Steven M. Mussmann ◽  
Tyler K. Chafin ◽  
Whitney J. B. Anthonysamy ◽  
Mark A. Davis ◽  
...  

Ecological restoration can promote biodiversity conservation in anthropogenically fragmented habitats, but effectiveness of these management efforts need to be statistically validated to determine ’success.’ One such approach is to gauge the extent of recolonization as a measure of landscape permeability and, in turn, population connectivity. In this context, we estimated dispersal and population connectivity in prairie vole (Microtus ochrogaster; N = 231) and meadow vole (M. pennsylvanicus; N = 83) within five tall-grass prairie restoration sites embedded within the agricultural matrix of midwestern North America. We predicted that vole dispersal would be constrained by the extent of agricultural land surrounding restored habitat patches, spatially isolating vole populations and resulting in significant genetic structure. We first employed genetic assignment tests based on 15 microsatellite DNA loci to validate field-derived species-designations, then tested reclassified samples with multivariate and Bayesian clustering to assay for spatial and temporal genetic structure. Population connectivity was further evaluated by calculating pairwise FST, then potential demographic effects explored by computing migration rates, effective population size (Ne), and average relatedness (r). Genetic species assignments reclassified 25% of initial field identifications (N = 11 M. ochrogaster; N = 67 M. pennsylvanicus). In M. ochrogaster population connectivity was high across the study area, reflected in little to no spatial or temporal genetic structure. In M. pennsylvanicus genetic structure was detected, but relatedness estimates identified it as kin-clustering instead, underscoring social behavior among populations rather than spatial isolation as the cause. Estimates of Ne and r were stable across years, reflecting high dispersal and demographic resilience. Combined, these metrics suggest the agricultural matrix is highly permeable for voles and does not impede dispersal. High connectivity observed confirms that the restored landscape is productive and permeable for specific management targets such as voles and also demonstrates population genetic assays as a tool to statistically evaluate effectiveness of conservation initiatives.


2021 ◽  
Vol 8 ◽  
Author(s):  
Anna M. Jażdżewska ◽  
Tammy Horton ◽  
Ed Hendrycks ◽  
Tomasz Mamos ◽  
Amy C. Driskell ◽  
...  

Paralicella tenuipesChevreux, 1908 and Paralicella caperescaShulenberger and Barnard, 1976 are known as widely distributed deep-sea scavenging amphipods. Some recent studies based on genetic data indicated the presence of high intraspecific variation of P. caperesca suggesting it is a species complex. Based on published molecular data from the Pacific and Indian oceans and new material obtained from the North and South Atlantic, we integrated the knowledge on the intraspecific variation and species distribution of the two nominal taxa. The study included analysis of three genes (COI, 16S rRNA, 28S rRNA) and revealed the existence of a single Molecular Operational Taxonomic Unit (MOTU) within P. tenuipes and six different MOTUs forming P. caperesca. The distribution pattern of the recognized lineages varied with three (P. tenuipes, MOTU 1 and MOTU 5 of P. caperesca) being widely distributed. There was evidence of contemporary population connectivity expressed by the share of the same COI haplotypes by individuals from very distant localities. At the same time no signal of recent demographic changes was observed within the studied taxa. The time-calibrated phylogeny suggested the emergence of species to be at the time of Mesozoic/Cenozoic transition that may be associated with global changes of the ocean circulation and deep sea water cooling.


Author(s):  
Juan Antonio Baeza

Whole mitogenomes or short fragments (e.g., 300-700 bp of the cox1 gene) are markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include 'primer walking' or 'long PCR' followed by Sanger sequencing or low-coverage whole genome (LCWGS) sequencing with or without prior mitochondrial enrichment and Illumina sequencing. The aforementioned strategies assemble complete and accurate mitochondrial genomes but are time consuming and/or expensive. In this study, I tested first if mitogenomes can be sequenced from long-read nanopore sequencing data exclusively. Second, I explored the accuracy of the long-read assembled genomes by comparing them to a 'gold' standard reference mitogenome retrieved from the same individualusing Illumina sequencing. LC-WGS using a MinION ONT device and various de-novo and reference-based assembly pipelines did retrieve a complete and highly accurate mitogenome for the Caribbean spiny lobster Panulirus argus. Discordance between each of the long-read assemblies and the reference mitogenome was mostly due to indels at the flanks of homopolymer regions. Although not 'perfect', phylogenetic analyses using entire mitogenomes or a fragment of the cox1 gene demonstrated that mitogenomes assembled using long reads can reliably identify the sequenced specimen as belonging to P. argus and distinguish it from other closely and distantly related species in the same genus, family, and superorder. This study serves as a proof-of-concept for the future implementation of in-situ surveillance protocols using the MinION so to detect mislabeling in P. argus across its supply chain. Mislabeling detection will improve fishery management in this overexploited lobster. This study will additionally aid in decreasing costs for exploring meta-population connectivity in the Caribbean spiny lobster and will aid with the transfer of genomics technology to low-income and developing countries.


2021 ◽  
Vol 8 ◽  
Author(s):  
Jorge Assis ◽  
Pierre Failler ◽  
Eliza Fragkopoulou ◽  
David Abecasis ◽  
Gregoire Touron-Gardic ◽  
...  

Marine Protected Areas (MPAs) must function as networks with sufficient stepping-stone continuity between suitable habitats to ensure the conservation of naturally connected regional pools of biodiversity in the long-term. For most marine biodiversity, population connectivity is mediated by passively dispersed planktonic stages with contrasting dispersal periods, ranging from a few hours to hundreds of days. These processes exert a major influence on whether threatened populations should be conserved as either isolated units or linked metapopulations. However, the distance scales at which individual MPAs are connected are insufficiently understood. Here, we use a biophysical model integrating high-resolution ocean currents and contrasting dispersal periods to predict connectivity across the Network of MPAs in Western Africa. Our results revealed that connectivity differs sharply among distinct ecological groups, from highly connected (e.g., fish and crustacea) to predominantly isolated ecosystem structuring species (e.g., corals, macroalgae and seagrass) that might potentially undermine conservation efforts because they are the feeding or nursery habitats required by many other species. Regardless of their dispersal duration, all ecological groups showed a common connectivity gap in the Bijagós region of Guinea-Bissau, highlighting the important role of MPAs there and the need to further support and increase MPA coverage to ensure connectivity along the whole network. Our findings provide key insights for the future management of the Network of MPAs in Western Africa, highlighting the need to protect and ensure continuity of isolated ecosystem structuring species and identifying key regions that function as stepping-stone connectivity corridors.


2021 ◽  
Author(s):  
◽  
Rachel Boschen

<p>Deep-sea mining is rapidly becoming a reality, yet there are considerable gaps in our knowledge of the seabed assemblages that could be affected by mining activities. Seafloor Massive Sulfide (SMS) mining is expected to remove nearly all organisms in the immediate area and alter the remaining habitat, so that mitigation strategies for SMS mining will most likely need to include the establishment of protected areas to preserve the biodiversity that is lost at mine sites. Prospecting licences have been issued previously for SMS deposits within the New Zealand Exclusive Economic Zone (EEZ), however little is known about the seabed assemblages potentially at risk from SMS mining, particularly with respect to their structure (at multiple spatial scales) and the connectivity of assemblages at different sites. Designing studies to provide this information can be aided by turning to terrestrial, freshwater and shallow marine systems, where the fields of ecological theory, environmental management and conservation theory are better developed (Chapter 1).  Prior to detailed investigations into the assemblage structure and population connectivity of New Zealand SMS deposits, it is essential to understand the global context of SMS mining. This was undertaken through an extensive literature review of SMS deposits, including their geology, seafloor communities, impacts from mining, international and national regulation, and environmental management (Chapter 2).  In order to investigate the large-scale spatial distribution and structure of seafloor assemblages at SMS deposits, three New Zealand seamounts previously licenced for the prospecting phase of SMS mining were surveyed. Video footage from a towed camera was analysed to identify and characterise assemblages, and their association with environmental variation was investigated. Analysis of 249 video samples (each 250 m in length) distributed amongst the three seamounts indicated that SMS deposits support unique assemblages and that there were strong links between assemblage structure and environmental variation at a range of spatial scales. There was also a complex distribution of assemblages amongst the seamounts, suggesting a network of protected areas would be the most effective method for spatial management. Such networks should include sites that support the unique assemblages found in association with SMS deposits (Chapter 3).  The fine-scale distribution and structure of assemblages at SMS deposits was investigated by using data from a single SMS deposit, Proteus 1, and comparing it to a Reference Site selected to have similar size and seabed characteristics to the deposit. Video footage from a Remotely Operated Vehicle (ROV) was used to identify and characterise assemblages, and their association with environmental conditions. Analysis of 153 video samples (each 15 m in length) confirmed the existence of assemblages unique to SMS deposits, and indicated that environmental characteristics specific to the deposit are responsible for the observed patterns of faunal distribution. Although five assemblages were shared between Proteus 1 and the Reference Site, six assemblages were unique to Proteus 1. This suggested that the proposed Reference Site would be inadequate on its own in terms of protecting the biological diversity present at the mine site but could contribute to a network of protected areas (Chapter 4).  The issue of connectivity was addressed by examining the genetic connectivity of populations of the endemic hydrothermal vent mussel, Gigantidas gladius. Universal markers, archived material and off-the-shelf DNA extraction kits were used to investigate a cost effective approach. The assessment utilised variation in 586 base pairs of the mitochondrial cytochrome oxidase I subunit (COI) from 150 individuals in seven populations of G. gladius. Small sample sizes limited the recommendations that could be made for environmental management; however interpretation of the available sequences indicated panmixia with limited genetic structure and high connectivity amongst populations. Central Kermadec Volcanic Arc populations had particularly high haplotypic diversity and migrant exchange, suggesting they could be important for maintaining regional genetic connectivity and would merit inclusion in seabed protection measures (Chapter 5).  Establishing protected areas for biodiversity needs to utilise all of the available information. The integrated findings of this thesis highlight the need for a network of protected seabed areas along the Kermadec Volcanic Arc to help mitigate the impacts of any future SMS mining activities. These networks should be highly connected (as determined by genetic connectivity) and include both active and inactive SMS areas to conserve 1) the endemic vent fauna in active areas and 2) the unique assemblages found in both environments (Chapter 6).</p>


2021 ◽  
Author(s):  
◽  
Rachel Boschen

<p>Deep-sea mining is rapidly becoming a reality, yet there are considerable gaps in our knowledge of the seabed assemblages that could be affected by mining activities. Seafloor Massive Sulfide (SMS) mining is expected to remove nearly all organisms in the immediate area and alter the remaining habitat, so that mitigation strategies for SMS mining will most likely need to include the establishment of protected areas to preserve the biodiversity that is lost at mine sites. Prospecting licences have been issued previously for SMS deposits within the New Zealand Exclusive Economic Zone (EEZ), however little is known about the seabed assemblages potentially at risk from SMS mining, particularly with respect to their structure (at multiple spatial scales) and the connectivity of assemblages at different sites. Designing studies to provide this information can be aided by turning to terrestrial, freshwater and shallow marine systems, where the fields of ecological theory, environmental management and conservation theory are better developed (Chapter 1).  Prior to detailed investigations into the assemblage structure and population connectivity of New Zealand SMS deposits, it is essential to understand the global context of SMS mining. This was undertaken through an extensive literature review of SMS deposits, including their geology, seafloor communities, impacts from mining, international and national regulation, and environmental management (Chapter 2).  In order to investigate the large-scale spatial distribution and structure of seafloor assemblages at SMS deposits, three New Zealand seamounts previously licenced for the prospecting phase of SMS mining were surveyed. Video footage from a towed camera was analysed to identify and characterise assemblages, and their association with environmental variation was investigated. Analysis of 249 video samples (each 250 m in length) distributed amongst the three seamounts indicated that SMS deposits support unique assemblages and that there were strong links between assemblage structure and environmental variation at a range of spatial scales. There was also a complex distribution of assemblages amongst the seamounts, suggesting a network of protected areas would be the most effective method for spatial management. Such networks should include sites that support the unique assemblages found in association with SMS deposits (Chapter 3).  The fine-scale distribution and structure of assemblages at SMS deposits was investigated by using data from a single SMS deposit, Proteus 1, and comparing it to a Reference Site selected to have similar size and seabed characteristics to the deposit. Video footage from a Remotely Operated Vehicle (ROV) was used to identify and characterise assemblages, and their association with environmental conditions. Analysis of 153 video samples (each 15 m in length) confirmed the existence of assemblages unique to SMS deposits, and indicated that environmental characteristics specific to the deposit are responsible for the observed patterns of faunal distribution. Although five assemblages were shared between Proteus 1 and the Reference Site, six assemblages were unique to Proteus 1. This suggested that the proposed Reference Site would be inadequate on its own in terms of protecting the biological diversity present at the mine site but could contribute to a network of protected areas (Chapter 4).  The issue of connectivity was addressed by examining the genetic connectivity of populations of the endemic hydrothermal vent mussel, Gigantidas gladius. Universal markers, archived material and off-the-shelf DNA extraction kits were used to investigate a cost effective approach. The assessment utilised variation in 586 base pairs of the mitochondrial cytochrome oxidase I subunit (COI) from 150 individuals in seven populations of G. gladius. Small sample sizes limited the recommendations that could be made for environmental management; however interpretation of the available sequences indicated panmixia with limited genetic structure and high connectivity amongst populations. Central Kermadec Volcanic Arc populations had particularly high haplotypic diversity and migrant exchange, suggesting they could be important for maintaining regional genetic connectivity and would merit inclusion in seabed protection measures (Chapter 5).  Establishing protected areas for biodiversity needs to utilise all of the available information. The integrated findings of this thesis highlight the need for a network of protected seabed areas along the Kermadec Volcanic Arc to help mitigate the impacts of any future SMS mining activities. These networks should be highly connected (as determined by genetic connectivity) and include both active and inactive SMS areas to conserve 1) the endemic vent fauna in active areas and 2) the unique assemblages found in both environments (Chapter 6).</p>


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