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

Sara Si Moussi

и другие.

Authorea (Authorea), Год журнала: 2023, Номер unknown

Опубликована: Апрель 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.

Язык: Английский

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

BS Malauene,

Thierry B. Hoareau

и другие.

Marine Ecology Progress Series, Год журнала: 2023, Номер 731, С. 105 - 127

Опубликована: Апрель 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

Язык: Английский

Процитировано

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

и другие.

The Science of The Total Environment, Год журнала: 2024, Номер 921, С. 170917 - 170917

Опубликована: Фев. 15, 2024

Язык: Английский

Процитировано

4
Understanding marine biodiversity patterns and drivers: The fall of Icarus DOI Creative Commons
Roberto Danovaro

Marine Ecology, Год журнала: 2024, Номер unknown

Опубликована: Май 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.

Язык: Английский

Процитировано

3
Biogeography of the Iranian snakes DOI Creative Commons
Naeim Moradi,

Ulrich Joger,

Soheila Shafiei Bafti

и другие.

PLoS ONE, Год журнала: 2024, Номер 19(10), С. e0309120 - e0309120

Опубликована: Окт. 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

Язык: Английский

Процитировано

3
Connectivity and genetic structure of marine fish populations DOI

Filip Volckaert,

Paolo Momigliano

Elsevier eBooks, Год журнала: 2025, Номер unknown, С. 239 - 255

Опубликована: Янв. 1, 2025

Язык: Английский

Процитировано

0
New deep learning‐based methods for visualizing ecosystem properties using environmental DNA metabarcoding data DOI Creative Commons
Letizia Lamperti, Théophile Sanchez,

Sara Si Moussi

и другие.

Molecular Ecology Resources, Год журнала: 2023, Номер 23(8), С. 1946 - 1958

Опубликована: Сен. 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.

Язык: Английский

Процитировано

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

и другие.

Diversity and Distributions, Год журнала: 2022, Номер 28(12), С. 2637 - 2647

Опубликована: Авг. 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.

Язык: Английский

Процитировано

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

и другие.

Biological Conservation, Год журнала: 2023, Номер 286, С. 110302 - 110302

Опубликована: Сен. 23, 2023

Язык: Английский

Процитировано

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

и другие.

Environmental DNA, Год журнала: 2024, Номер 6(5)

Опубликована: Сен. 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

Язык: Английский

Процитировано

1
Conservation Implications of Strong Population Structure Despite Admixture in an Endangered African Seagrass DOI Creative Commons
Charlotte A. Combrink, Romina Henriques, Matthew Jackson

и другие.

Aquatic Conservation Marine and Freshwater Ecosystems, Год журнала: 2024, Номер 34(12)

Опубликована: Дек. 1, 2024

ABSTRACT Zostera capensis is an African seagrass that endangered throughout its range. In South Africa, it solely confined to low wave energy estuarine habitats and characterised by two evolutionary lineages diverge across a biogeographic transition. this study, we sampled plants from five populations span the region of lineage divergence investigated extent overlap. Using 2681 SNP loci, including 32 putative outlier calculated population structure, genomic diversity levels admixture. All were significantly different each other, those < 10 km apart admixture indicate limited dispersal Z. . Every was high inbreeding coefficient (F IS ), suggesting number breeding individuals in population. Given increasing anthropogenic stressors are linked declines meadow cover our study provides strong support require targeted management conservation actions individual avoid further loss unique dynamics safeguard ecosystem services seagrasses provide. Further, evidence significant structure geographically close highlights efforts relying on restoration would risk mixing signatures when transplanting between estuaries. This represents critical challenge using transplants as potential mechanism restoring declining crucial importance preventing extinction.

Язык: Английский

Процитировано

1