New deep learning-based methods for visualizing ecosystem properties using environmental DNA metabarcoding data DOI Open Access
Letizia Lamperti, Théophile Sanchez,

Sara Si Moussi

et al.

Authorea (Authorea), Journal Year: 2023, Volume and Issue: unknown

Published: April 15, 2023

1. Metabarcoding of environmental DNA (eDNA) has recently improved our understanding biodiversity patterns in marine and terrestrial ecosystems. However, the complexity these data prevents current methods to extract analyze all relevant ecological information they contain. Therefore, modeling could greatly benefit from new providing better dimensionality reduction clustering. 2. Here we present two deep learning-based that combine different types neural networks ordinate eDNA samples visualize ecosystem properties a two-dimensional space: first is based on variational autoencoders (VAEs) second metric learning (DML). The strength lies combination several inputs: number sequences found for each molecular operational taxonomic unit (MOTU), together with genetic sequence detected MOTU within an sample. 3. Using three datasets, show represent well indicators latent richness per sample, α-diversity ꞵ-diversity between samples. We nonlinear are at extracting features datasets while avoiding major biases associated eDNA. Our outperform traditional dimension such as Principal Component Analysis, t-distributed Stochastic Neighbour Embedding, Uniform Manifold Approximation Projection reduction. 4. results suggest provide more efficient way structure metabarcoding data, thereby improving their interpretation thus monitoring.

Language: Английский

Corridors and barriers to marine connectivity around southern Africa DOI Creative Commons
Christophe Lett,

BS Malauene,

Thierry B. Hoareau

et al.

Marine Ecology Progress Series, Journal Year: 2023, Volume and Issue: 731, P. 105 - 127

Published: April 26, 2023

Detailed knowledge on connectivity, i.e. the exchange of marine organisms among geographically separated populations, is essential for effective spatial planning strategies and design protected areas (MPAs) in coastal ecosystems. Coastal waters around southern Africa are characterized by complex oceanographic processes that strongly influence challenging management Here we reviewed connectivity studies conducted across 25° latitude both southeastern southwestern sides based biophysical modelling, ecological molecular approaches, identified 7 corridors 8 barriers recognized to a variety vertebrate invertebrate taxa commercial interest. These were generally consistent studies, species methodological reflected bioregion breaks. Nevertheless, life history traits appear be important understanding why some may notable stages not others. Our review underlines value including from different disciplines order have broad view and, particular, complementarity larval-dispersal models seascape genetics emphasized. The this represent baselines critically assess existing MPAs prioritize new efforts mitigate human impacts

Language: Английский

Citations

12
Large-scale environmental signals in seagrass blue carbon stocks are hidden by high variability at local scales DOI
Andrew Ndhlovu,

Janine B. Adams,

Sophie von der Heyden

et al.

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 921, P. 170917 - 170917

Published: Feb. 15, 2024

Language: Английский

Citations

4
Biogeography of the Iranian snakes DOI Creative Commons
Naeim Moradi,

Ulrich Joger,

Soheila Shafiei Bafti

et al.

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(10), P. e0309120 - e0309120

Published: Oct. 16, 2024

The events of the Cenozoic era such as mountain formation caused Iran to become one most amazing biodiversity hotspots in world today. This pioneering study on Iranian snake biogeography integrates historical and ecological analyses. A phylogeographic review traces speciation dispersal, while cluster analysis with a new checklist assesses faunistic similarities within its surroundings. Jaccard Sorenson indices generate similarity dendrograms, Indicator Species Analysis pinpoints regional key species, Endemism index calculates endemism rates, enriching our knowledge Iran’s species diversity. Phylogeographic analyses identify four biogeographical corridors for ingress into Iran: Arabian region through southwestern Iran, Western Asian mountainous transition zone via northwestern Turanian northeastern Indus River Valley southeastern eastern Iran. Dendrogram divides fauna three groups. first group associates western Zagros Khuzestan Sahara regions. second links Kopet Dagh Turkmen Steppe region, Central Plateau Baluchistan region. third connects northwest highlands, Alborz mountains, Caspian Sea coasts Mountain zone. validates broad biogeographic patterns ecoregional associations indicator analysis, providing finer resolution. like Platyceps najadum Hyrcanian mixed forests exemplify alignment, mountains exhibit unique faunal indicators, indicating species-level divergence. Shared indicators among widespread ecoregions reflect habitat continuity; exclusive emphasize distinctiveness. Despite endemic prevalence, they seldom act significant due various factors. Our research confirms Mountains, Plain, Persian Gulf diversity hotspots, marked by higher richness compared other

Language: Английский

Citations

3
Connectivity and genetic structure of marine fish populations DOI

Filip Volckaert,

Paolo Momigliano

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 239 - 255

Published: Jan. 1, 2025

Language: Английский

Citations

0
Understanding marine biodiversity patterns and drivers: The fall of Icarus DOI Creative Commons
Roberto Danovaro

Marine Ecology, Journal Year: 2024, Volume and Issue: unknown

Published: May 30, 2024

Abstract Biodiversity patterns are fundamental in our understanding of the distribution life, ecosystem function, and conservation. In this concept analysis, A survey existing knowledge on marine biodiversity drivers across latitudes, longitudes, depths indicates that none postulated represent a rule. The paradigm latitudinal gradients or bathymetric diversity vary biogeographic regions components, kingdoms, body sizes. same holds true for hypothesized longitudinal cost‐offshore patterns. Food availability temperature influence all life forms appear to be most relevant factors shaping biodiversity. However, these interact with many other variables such as spatial heterogeneity, ecological physical processes creating complex mosaic limits any prediction. Climate change, its implications global primary productivity rise, can one major influences future Understanding emphasizes need complete census next decade. effort must use advanced technologies, develop holistic approaches promote integration morphological‐ genetic‐based taxonomy explore organisms size classes, at large scales habitat types, particularly open ocean deep‐sea ecosystems. Without basic knowledge, coupled identification observed patterns, we will unable fill gaps crucial developing adequate conservation measures scale.

Language: Английский

Citations

2
New deep learning‐based methods for visualizing ecosystem properties using environmental DNA metabarcoding data DOI Creative Commons
Letizia Lamperti, Théophile Sanchez,

Sara Si Moussi

et al.

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 23(8), P. 1946 - 1958

Published: Sept. 13, 2023

Environmental DNA (eDNA) metabarcoding provides an efficient approach for documenting biodiversity patterns in marine and terrestrial ecosystems. The complexity of these data prevents current methods from extracting analyzing all the relevant ecological information they contain, new may provide better dimensionality reduction clustering. Here we present two deep learning-based that combine different types neural networks (NNs) to ordinate eDNA samples visualize ecosystem properties a two-dimensional space: first is based on variational autoencoders second metric learning. strength our lies combination inputs: number sequences found each molecular operational taxonomic unit (MOTU) detected their corresponding nucleotide sequence. Using three datasets, show accurately represent several indicators latent MOTU richness per sample, sequence α-diversity Jaccard's β-diversity between samples. We nonlinear are at features datasets while avoiding major biases associated with eDNA. Our outperform traditional dimension such as Principal Component Analysis, t-distributed Stochastic Neighbour Embedding, Nonmetric Multidimensional Scaling Uniform Manifold Approximation Projection reduction. results suggest NNs more way structure data, thereby improving interpretation thus monitoring.

Language: Английский

Citations

5
Reptile richness and genetic divergence patterns were shaped by current and past climate in and around the Irano‐Anatolian global biodiversity hotspot: Implications for conservation DOI Creative Commons
Masoud Yousefi, Anooshe Kafash, Michaël P. J. Nicolaï

et al.

Diversity and Distributions, Journal Year: 2022, Volume and Issue: 28(12), P. 2637 - 2647

Published: Aug. 4, 2022

Abstract Aim The Irano‐Anatolian biodiversity hotspot is among the least‐known hotspots on earth. In this study, we aim to map richness and genetic divergence of lizards in its surrounding areas identify most important determinants patterns. Location Iran Turkey (Irano‐Anatolian hotspot). Methods Here, mapped distribution 211 lizard species using existing occurrence data generated first pattern two countries high diversity hotspot. We also identified Results showed that Zagros Mountains, Central Iranian Plateau northern Persian Gulf have highest richness. Plateau, regions around Lut Desert Jazmourian Plain total Iran. Alborz Kopet Dag mountains south western parts average divergence. annual temperature was predictor richness, change velocity influential determinant pattern. Much our surprise, with are located outside Main conclusions This study patterns associated current past climate. particular, highlights legacy climate changes species‐rich genetically diverse So conservation efforts concentrated inside may not benefit conservation. Thus, future studies programs should consider areas.

Language: Английский

Citations

8
Integrating environmental, evolutionary, and socioeconomic vulnerability to future-proof coastal conservation planning DOI
Erica S. Nielsen, Maria Beger, Romina Henriques

et al.

Biological Conservation, Journal Year: 2023, Volume and Issue: 286, P. 110302 - 110302

Published: Sept. 23, 2023

Language: Английский

Citations

4
The Effect of Spatio‐Temporal Sampling and Biological Replication on the Detection of Kelp Forest Fish Communities Using eDNA Metabarcoding DOI Creative Commons

Kira‐Lee Courtaillac,

Jannes Landschoff, Kelvin L. Hull

et al.

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(5)

Published: Sept. 1, 2024

ABSTRACT Environmental DNA (eDNA) metabarcoding surveys can support the acquisition of extensive biodiversity data to ecosystem monitoring and conservation actions. However, optimization eDNA project design is essential capture spatio‐temporal heterogeneity signals maximize diversity detection. In this study, we developed a system‐specific approach detect fish communities in kelp forests, by analyzing fine‐scale patterns at two sites along South African coastline, as well testing effect biological replication pooling replicates on species At each site, samples were collected stations shoreline depth zones, was repeated time points (24 h apart). We detected 113 operational taxonomic units (OTUs) across 32 families, but fewer than 20% OTUs could be assigned species, indicating that barcode reference libraries need drastically improved. significant differences small spatial scales (< 600 m) points, suggesting best site's patterns, should multiple times within least 24 h. To ~80% community, including some low abundance minimum four appear sufficient. addition, higher number (76 vs. 65) found individual any pools. prior sequencing still valuable broad‐scale for offset decrease resolution with benefit accumulating comprehensive from increased sampling efforts over time. As pilot investigation into how forest‐associated communities, study provides basis optimizing coastal eDNA‐based southern Africa strengthens development long‐term programs better management

Language: Английский

Citations

1
Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa DOI Creative Commons
Sarah Forde, Sophie von der Heyden, Alan Le Moan

et al.

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: unknown

Published: June 8, 2023

Genomic information can aid in the establishment of sustainable management plans for commercially exploited marine fishes, aiding long-term conservation these resources. The southern African hakes (Merluccius capensis and M. paradoxus) are valuable demersal fishes with similar distribution ranges but exhibiting contrasting life histories. Using a comparative framework based on Pool-Seq genome-wide SNP data, we investigated whether evolutionary processes that shaped extant patterns diversity divergence shared among two congeneric or unique to each one. Our findings revealed paradoxus show levels diversity, despite different census sizes life-history features. In addition, shows three highly structured geographic populations across Benguela Current region (one northern Benguela), no consistent genome-environment associations detected. contrast, although population structure outlier analyses suggested panmixia paradoxus, reconstruction its demographic history presence an Atlantic-Indian Ocean subtle substructuring pattern. Therefore, it appears might be composed by connected populations, one Atlantic southwest Indian Ocean. reported low genomic as well newly discovered genetically distinct both hake species thus assist informing improving important Merluccius.

Language: Английский

Citations

1