Diversity

26 pages, 4915 KB

Open AccessArticle

Influence of Arctic Conditions on the Diatom Diversity of Islands Within the Conservation of Arctic Flora and Fauna Region

by Sophia Barinova, Viktor A. Gabyshev, Boris Borisov and Sviatoslav R. Rybnikov

Diversity 2025, 17(12), 808; https://doi.org/10.3390/d17120808 (registering DOI) - 22 Nov 2025

Abstract

The distribution of algal biodiversity is important for better understanding the factors controlling ecosystem functioning in harsh Arctic and sub-Arctic habitats. In this region, diatoms are the most representative and best indicators of environmental parameters. Here, we analyzed the distribution of 1268 diatom [...] Read more.

The distribution of algal biodiversity is important for better understanding the factors controlling ecosystem functioning in harsh Arctic and sub-Arctic habitats. In this region, diatoms are the most representative and best indicators of environmental parameters. Here, we analyzed the distribution of 1268 diatom species across 18 islands within the Conservation of Arctic Flora and Fauna (CAFF) region based on our own and published data. To assess the representativeness of these floras, we examine genus–species associations, a method applicable to future algal flora studies. Diatom diversity is sufficiently high across the islands, with species richness decreasing toward higher latitudes. Species–area relationship models indicate that latitude—and even more so factors describing climatic extremes, like BIO19 (19 standard bioclimatic variables)—affects species richness stronger than islands area, and combined environmental and geographic predictors explain up to 81% of the observed variation. Bioindicator analysis reveals an increase in water pH, content in organic matter, and the number of eutrophic and mixotrophic species southward, which correlates with rising temperatures, as shown by the BIO19 and DHI (Dynamic Habitat Index) environmental indices. The latitudinal distribution of bioindicators demonstrates the ecological response of diatom communities to climatic factors and allows the identification of key indicator groups experiencing optimal conditions. So, island diatom species prefer benthic and planktonic–benthic habitats, well-oxygenated waters with low salinity, and moderate temperatures, which prevail on all islands except Vancouver Island, located outside the CAFF (Conservation of Arctic Flora and Fauna) region. A comparative analysis of bioindicators as a response to Arctic conditions of island diatoms revealed circumpolar similarities, connections with the corresponding parts of the Eurasian and North American continents, as well as similarities in the conditions of the islands closest to the pole. Almost a third of the island diatom list (324 species) was assigned IUCN (International Union for Conservation of Nature) vulnerability categories, 112 of which were in the three most threatened categories (Ex, Cr, and En) with their number increasing southwards, but 944 species have not been evaluated yet. Full article

(This article belongs to the Special Issue The Ecological Functions of Algae in a Changing World: From Fundamentals to Applications)

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21 pages, 6429 KB

Open AccessReview

Current Knowledge and Research Perspectives on Bryophytes in West Africa

by Chabi Ghyslain Kpetikou, Gafarou Agoundé, Gbèwonmèdéa Hospice Dassou, Kolawolé Valère Salako, Gbèkponhami Monique Tossou and Terry Hedderson

Diversity 2025, 17(12), 807; https://doi.org/10.3390/d17120807 - 21 Nov 2025

Abstract

Bryophytes are non-vascular plants comprising mosses, liverworts and hornworts. In West Africa, they are one of the least investigated components of biodiversity, receiving far less attention than vascular plants. This systematic review synthesizes the current knowledge on bryophytes in West Africa and identifies [...] Read more.

Bryophytes are non-vascular plants comprising mosses, liverworts and hornworts. In West Africa, they are one of the least investigated components of biodiversity, receiving far less attention than vascular plants. This systematic review synthesizes the current knowledge on bryophytes in West Africa and identifies gaps and future prospects for advancing bryophytes research. Since the earliest explorations in the 18th century, bryophyte research in West Africa has remained poorly developed, with a noticeable bias toward certain countries over other countries. Over the past four decades, bryophyte research and the number of recorded species have increased. To date, 1175 bryophyte species and infraspecific taxa, representing 320 genera and 120 families, were recorded in the region, of which 6.47% are endemic. This documented diversity surely does not represent the full flora of the region: many species are evidently still undescribed. Another major constraint on advancing knowledge is the scarcity of specialists in the region and the lack of sustained scientific interest and academic focus in the taxonomic group. A priority for advancing knowledge on bryophytes in West Africa is to strengthen taxonomic research to document biodiversity, alongside comprehensive studies on bryophyte diversity and distribution across regions. Full article

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22 pages, 3095 KB

Open AccessArticle

PTL-Inception: Integrating Deep Learning and Taxonomy for Desert Plant Classification

by Yonis Gulzar, Zeynep Ünal, Kadir Şahbaz and Mohannad Alkanan

Diversity 2025, 17(11), 806; https://doi.org/10.3390/d17110806 - 20 Nov 2025

Abstract

Accurate identification of plant species forms the basis of taxonomy, biodiversity assessment, and conservation planning. This requirement is especially urgent in arid ecosystems such as those of Saudi Arabia, where limited rainfall, fragile habitats, and high ecological stress create distinctive but poorly documented [...] Read more.

Accurate identification of plant species forms the basis of taxonomy, biodiversity assessment, and conservation planning. This requirement is especially urgent in arid ecosystems such as those of Saudi Arabia, where limited rainfall, fragile habitats, and high ecological stress create distinctive but poorly documented flora. In this study, a deep learning framework, termed PTL-Inception, was developed to classify desert plants and to provide reliable taxonomic data that can be integrated into biodiversity and phylogenetic studies. A dataset of ten native species was compiled and expanded through augmentation, and several state-of-the-art architectures were tested. InceptionV3 was found to be the most effective baseline, and the network was further modified by incorporating ten additional layers, transfer learning, and hyperparameter tuning. The proposed model achieved an accuracy of 99.46%, with precision and recall values of 99.46% and 99.44%, respectively. Reliability was confirmed through K-fold validation, while early stopping reduced training time with minimal loss of accuracy. Beyond these computational outcomes, the study demonstrates how deep learning can complement traditional taxonomy by producing consistent species-level identifications. The outputs can be combined with spatial and phylogenetic approaches to explore patterns of diversity, endemism, and adaptation in desert ecosystems, thereby supporting conservation strategies and biodiversity management. Full article

(This article belongs to the Special Issue Integrating Spatial Phylogenetic, and Taxonomic Approaches to Understand Plant Biodiversity)

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21 pages, 8814 KB

Open AccessReview

The Impact of Life History Traits and Defensive Abilities on the Invasiveness of Ulex europaeus L.

by Hisashi Kato-Noguchi and Midori Kato

Diversity 2025, 17(11), 805; https://doi.org/10.3390/d17110805 - 20 Nov 2025

Abstract

Ulex europaeus L. has been introduced into many countries as an ornamental and hedgerow plant, and it often escapes its intended location, establishing dense, feral thickets. These thickets threaten the structure and function of native flora and fauna in areas where the plant [...] Read more.

Ulex europaeus L. has been introduced into many countries as an ornamental and hedgerow plant, and it often escapes its intended location, establishing dense, feral thickets. These thickets threaten the structure and function of native flora and fauna in areas where the plant has been introduced. Because of its invasive nature, U. europaeus is considered one of the world’s 100 worst alien invasive species. It exhibits rapid growth, and high biomass accumulation with a high nitrogen fixation ability. Its flowering phenology depends on local conditions and population. It produces a large number of viable seeds and establishes extensive seed banks. These seeds remain viable for a long time due to physical dormancy. Ulex europaeus produces elaiosomes on the seed surface that are likely used solely for seed dispersal by ants. Ulex europaeus has a high level of genetic diversity due to its allohexaploid chromosome sets. This allows the plant to adapt to different habitats and tolerate various climate conditions. It can survive in areas with limited sunlight beneath tall plant canopies. Its shade tolerance surpasses that of other shrub species. Ulex europaeus produces several compounds, including quinolizidine alkaloids, monoterpenes, flavonoids, and cinnamic acid derivatives. These compounds play a role in defensive responses to biotic stressors, including pathogen infections, herbivorous insects, and neighboring plants competing for resources. These life history traits and defensive abilities may contribute to the expansion of U. europaeus populations into new habitats, enabling the plant to thrive as an invasive species. This is the first study to examine the invasiveness of U. europaeus in terms of its growth, reproduction, ability to adapt to different conditions, and defensive responses to biotic stressors. Full article

(This article belongs to the Special Issue Emerging Alien Species and Their Invasion Processes—2nd Edition)

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22 pages, 4332 KB

Open AccessArticle

β-Glucosidases: In Silico Analysis of Physicochemical Properties and Domain Architecture Diversity Revealed by Metagenomic Technology

by Thi Quy Nguyen, Thi Huyen Do, Ngoc Giang Le, Hong Duong Nguyen, Trong Khoa Dao, Nho Thai Dinh and Nam Hai Truong

Diversity 2025, 17(11), 804; https://doi.org/10.3390/d17110804 - 20 Nov 2025

Abstract

β-Glucosidases, ubiquitous enzymes with significant contribution to several industries were previously identified as diverse in bacterial metagenomes from Vietnamese native goat rumens, wood humus from Cuc Phuong national forest, and termite gut. In this study, we systematically analyzed their sequence diversity, domain architectures, [...] Read more.

β-Glucosidases, ubiquitous enzymes with significant contribution to several industries were previously identified as diverse in bacterial metagenomes from Vietnamese native goat rumens, wood humus from Cuc Phuong national forest, and termite gut. In this study, we systematically analyzed their sequence diversity, domain architectures, domain arrangements, physicochemical properties, and producers associated with their structures, conserving catalytic domains. A total of 833 β-glucosidase sequences were categorized into three families: GH1, GH16, and GH3, forming 30 distinct domain architectures with variable isoelectric points, alkaline scores, and melting temperatures across ecological niches. GH1 enzymes exhibited the lowest architectural diversity, whereas GH16 enzymes were frequently associated with carbohydrate-binding module 4 (CBM4) and CBM12 domains. Over 90% of GH3 enzymes contained fibronectin type III (FN3) and accessory domains such as PA14, CBM6, Big_2, or ExoP, with some harboring secondary catalytic domains. Most goat rumen β-glucosidases originated from cellulosome-producing bacteria. A recombinant β-glucosidase GH3-31 expressed in E. coli exhibited optimal activity at 40 °C (lower than the predicted Tm of 49.8 °C), pH5.5 (near the predicted pI of 5.61), Km of 1.37 mM ± 0.08 mM, and Vmax of 43.17 ± 0.6 U/mg. Its activity was enhanced by Tween 20, Tween 80, Triton X-100, and CTAB. These findings provide a comprehensive resource for β-glucosidase engineering and application-oriented screening. Full article

(This article belongs to the Section Microbial Diversity and Culture Collections)

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17 pages, 2512 KB

Open AccessArticle

Glyphosate-Induced Shifts in Edaphic Microbiota: A Comparative Study of Bacterial and Fungal Responses in Historical Milpa Soils

by María Alejandra Ocaña-Ek, Anell del Carmen García-Romero, Oscar Omar Álvarez-Rivera, Magnolia del Carmen Tzec-Gamboa, Héctor Estrada-Medina and Miriam M. Ferrer

Diversity 2025, 17(11), 803; https://doi.org/10.3390/d17110803 - 20 Nov 2025

Abstract

Glyphosate is the most widely used herbicide worldwide and in Mexico; however, its effects on soil microbiota in traditional agroecosystems remain unclear. We evaluated bacterial, archaeal, and fungal responses to commercial glyphosate in three representative karst soils of the Yucatán Peninsula (black Leptosol, [...] Read more.

Glyphosate is the most widely used herbicide worldwide and in Mexico; however, its effects on soil microbiota in traditional agroecosystems remain unclear. We evaluated bacterial, archaeal, and fungal responses to commercial glyphosate in three representative karst soils of the Yucatán Peninsula (black Leptosol, red Leptosol, and red Cambisol) historically associated with the Mayan milpa system. The high-throughput sequencing of the 16S rRNA V4 and ITS1 regions was used to assess diversity patterns and differential abundance. Glyphosate application did not significantly alter alpha or beta diversity; however, fifteen taxa classified at the genus level exhibited shifts in relative abundance. Most bacterial taxa were depauperated in treated soils, whereas others, such as Arthrobacter, were enriched after application, indicating the presence of tolerant or resistant bacteria that may play a role in glyphosate degradation. Cordyceps, an entomopathogenic fungus, was depleted, indicating potential for natural pest control. The similarity of the core microbiota between samples with and without glyphosate application indicates that these communities are resilient. Overall, under short-term exposure, glyphosate induced compositional shifts in specific taxa without major effects on community structure but with potential implications for soil functionality and resilience in the Mayan milpa. Full article

(This article belongs to the Special Issue Microbial Diversity in Changing Ecosystems: From Environmental Adaptation Mechanisms to Applications)

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24 pages, 8096 KB

Open AccessArticle

Diversity and Selection of Superior Algarrobos (Neltuma pallida) Phenotypes in the Natural Dry Forests of Peru for Sustainable Conservation and Genetic Improvement

by Sebastian Casas-Niño, Juan Rodrigo Baselly-Villanueva, Evelin Judith Salazar-Hinostroza, Sheyla Yanett Chumbimune-Vivanco, William Nauray, Nery Tirabante-Terrones, Max Ramirez Rojas and Flavio Lozano-Isla

Diversity 2025, 17(11), 802; https://doi.org/10.3390/d17110802 - 20 Nov 2025

Abstract

Neltuma pallida (algarrobo) is a keystone species of the Peruvian dry forest whose persistence is threatened by overexploitation and habitat degradation, making its conservation and genetic improvement a national priority. This study aimed to identify outstanding phenotypes of N. pallida through phenotypic characterization [...] Read more.

Neltuma pallida (algarrobo) is a keystone species of the Peruvian dry forest whose persistence is threatened by overexploitation and habitat degradation, making its conservation and genetic improvement a national priority. This study aimed to identify outstanding phenotypes of N. pallida through phenotypic characterization in the regions of Piura and Tumbes in northern Peru. A stratified random sampling design was applied, establishing forest plots in 13 localities and evaluating 631 adult individuals. Dendrometric and phenotypic traits were recorded together with physiographic, climatic, and edaphic variables obtained from soil analyses and geographic information systems. Phenotypic differentiation among populations was assessed using the index

P_{S T}

, which quantifies between- and within-population variance components. High morphological variability was detected across populations, with significant differences in tree height, diameter, and fruit production, largely explained by environmental heterogeneity, particularly soil fertility and organic matter. The

P_{S T}

values, ranging from 0.83 to 0.98, revealed strong phenotypic divergence among populations, suggesting adaptive differentiation rather than neutral variation. Eight superior individuals were identified as potential candidates for inclusion in a germplasm bank to support breeding and restoration programs. This study provides a scientific basis for the sustainable management and conservation of N. pallida in the arid ecosystems. Full article

(This article belongs to the Section Biodiversity Conservation)

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16 pages, 1809 KB

Open AccessArticle

Urban Foraging and Plant Toxicological Risks for Rose-Ringed Parakeets (Psittacula krameri) in Athens

by Mathis A. B. Christodoulopoulos, Efthimia Cotou, Nektarios Politakis, Nikolaos Tsekouras, Vasileios V. Paraskeuas, Yannis Kotzamanis, Georgios Christodoulopoulos and Athanasios C. Pappas

Diversity 2025, 17(11), 801; https://doi.org/10.3390/d17110801 - 18 Nov 2025

Abstract

The Rose-ringed Parakeet (Psittacula krameri) is an invasive parrot increasingly established in European cities, including Athens, Greece, yet its diet and exposure to plant toxins in Mediterranean ecosystems remain poorly documented. We examined seasonal foraging patterns in Athens and assessed the [...] Read more.

The Rose-ringed Parakeet (Psittacula krameri) is an invasive parrot increasingly established in European cities, including Athens, Greece, yet its diet and exposure to plant toxins in Mediterranean ecosystems remain poorly documented. We examined seasonal foraging patterns in Athens and assessed the toxicity of key food items using a brine shrimp lethality assay. Field observations recorded 601 feeding events across 10 plant species. Four foods—cypress seeds (Cupressus sempervirens), chinaberries (Melia azedarach), Canary Island dates (Phoenix canariensis), and olives (Olea europaea)—accounted for 82.9% of feeding events. Dietary diversity was highest in winter and summer, while foraging density remained relatively stable, peaking in autumn. Toxicity assessment of aqueous plant extracts with Brine Shrimp (Artemia franciscana) Lethality Test (BSLT) identified chinaberries as the most toxic, indicating potential dietary risks. These findings indicate that P. krameri exhibits flexible, opportunistic foraging and can tolerate plant compounds that are harmful to other vertebrates, suggesting that toxicity does not seem to limit its diet. Seasonal dietary shifts and ecological plasticity likely support its urban invasion success, highlighting the importance of understanding diet composition and potential exposure to plant toxins in urban parakeet populations. Full article

(This article belongs to the Topic Mediterranean Biodiversity, 2nd Edition)

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25 pages, 6508 KB

Open AccessArticle

Environmental DNA Reveals Fish Diversity Reestablishment of China’s Lake Ecosystem Driven by Extreme Drought and Human Intervention

by Yingchun Xing, Kai Li, Wanru Gao, Yucheng Wang, Ting Jiang, Rui Xi, Huiqin Li and Yahui Zhao

Diversity 2025, 17(11), 800; https://doi.org/10.3390/d17110800 - 17 Nov 2025

Abstract

Extreme droughts caused by current climate changes affect the diversity, composition and function of fish communities in lake ecosystems. Poyang Lake is the largest freshwater lake in China, and it is home to many important avian, fish and aquatic mammals. In 2022, Poyang [...] Read more.

Extreme droughts caused by current climate changes affect the diversity, composition and function of fish communities in lake ecosystems. Poyang Lake is the largest freshwater lake in China, and it is home to many important avian, fish and aquatic mammals. In 2022, Poyang Lake experienced one of the most severe droughts in recorded history. Understanding how fish communities responded to this event can offer key knowledge in developing strategies for coping with future climatic extremes, particularly given that the local government has been actively posting several middle- to long-term policies on managing the fish diversity of Poyang Lake, including fishery resource supplements and the well-known “ten-year fishing ban”. To understand how the fish diversity of Poyang Lake has been altered by climate change and human interventions, here, we analyzed the α- and β-taxonomic diversity (TD) and functional diversity (FD) of fish species using environmental DNA (eDNA), and we compared the fish diversity and community changes before and after the 2022 drought. In total, 77 native fish species and 4 invasive species were detected. The species richness and Shannon–Wiener index decreased significantly, and Simpson’s index had no significant difference post-drought. Rao’s Quadratic Entropy (Rao’sQE) index increased significantly, and the Functional Evenness (FEve) index decreased significantly. The differences in α- and β-TD and FD in the north part and south part of Poyang Lake also reflect the impact of drought. When calculating biodiversity contribution rates of the different species, we found that small-sized species were dominant pre-drought, while medium- and large-sized species were predominant post-drought. These patterns indicate that the fish community of Poyang Lake is undergoing a reestablishing process after the extreme drought. This fish community reestablishment post-drought does not correspond to the natural process of community recovery; instead, it is the result of human intervention while being affected by drought brought about by climate change. Full article

(This article belongs to the Special Issue Applications on Environmental DNA in Aquatic Ecology and Biodiversity)

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19 pages, 2148 KB

Open AccessArticle

Benthic Producers, Methane Carbon, and Diazotrophic Nitrogen as Sources of Nutrients in the Food Web of a Subarctic Lake

by Nadezhda A. Berezina, Yulia I. Gubelit and Alexey A. Maximov

Diversity 2025, 17(11), 799; https://doi.org/10.3390/d17110799 - 17 Nov 2025

Abstract

The majority of research on food webs has focused on temperate lakes, and little is known about the food web of lakes in polar regions. Subarctic lakes are particularly sensitive to climate change, which affects their stability. Therefore, the trophic structure of the [...] Read more.

The majority of research on food webs has focused on temperate lakes, and little is known about the food web of lakes in polar regions. Subarctic lakes are particularly sensitive to climate change, which affects their stability. Therefore, the trophic structure of the food web in such lakes was considered as the object of this study. We studied a clear-water oligotrophic lake located in the subarctic region of Eurasia, specifically in northern Karelia and the White Sea coast of Russia. The study examined both open water periods (summer–autumn) and ice-covered periods (winter–spring) in this lake. Stable isotope analysis of carbon (¹³C/¹²C ratio or δ¹³C value) and nitrogen (¹⁵N/¹⁴N, δ¹⁵N) in producers and consumers was applied and revealed significant seasonal variations in the structure of the food web. The results indicate the presence of both pelagic and littoral/benthic food web compartments, with a notable contribution of autochthonous carbon derived from benthic sources. Omnivorous fish (perch, Perca fluviatilis; vendace, Coregonus albula; nine-spined sticklebacks, Pungitius pungitius) and some benthic invertebrates (mayfly, Ephemera vulgata; bivalves, Sphaerium corneum) had intermediate δ¹³C values, integrating these compartments by obtaining resources from both. Planktonic invertebrates had significantly depleted ¹³C, with the lowest δ¹³C value reaching −41.7‰, indicating an important contribution of methane-derived carbon. The study also revealed close trophic relationships between lake invertebrates and cyanobacteria, namely with planktonic Dolichospermum lemmermannii and benthic Phormidium sp. Seasonal changes in δ¹⁵N values and in trophic position have been observed among predacious omnivorous fish and crustaceans (amphipods, Gammaracanthus loricatus, and copepods, Cyclops scutifer), which are capable of a generalist feeding strategy depending on food availability. Using the example of this lake, it can be concluded that polar lake ecosystems are characterized by different seasonal intakes of allochthonous organic carbon from wetland catchment (humic compounds) and nitrogen because of nitrogen fixation in the air by cyanoprocaryotes. Alternative energy sources, such as carbon derived from methane, can also contribute to the energy balance of lake ecosystems. This study contributes to our understanding of energy flow and connectivity between producers and consumers in high-latitude lakes. Full article

(This article belongs to the Special Issue 15th Anniversary of Diversity—Biodiversity, Conservation and Ecology of Animals, Plants and Microorganisms)

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14 pages, 1502 KB

Open AccessArticle

Effects of Temperature and Precipitation at Large Spatial Scales on Genetic Diversity, Genetic Structure, and Potential Distribution of Agropyron michnoi

by Zhuo Zhang, Ruyan Song, Tingting Yang and Chan Zhou

Diversity 2025, 17(11), 798; https://doi.org/10.3390/d17110798 - 16 Nov 2025

Abstract

The genetic diversity and the genetic structure of widely distributed species are meaningful to explore plant adaptation mechanisms to the environment. This study investigated the effects of climatic factors on the genetic diversity and structure of Agropyron michnoi, and modeled its large-scale [...] Read more.

The genetic diversity and the genetic structure of widely distributed species are meaningful to explore plant adaptation mechanisms to the environment. This study investigated the effects of climatic factors on the genetic diversity and structure of Agropyron michnoi, and modeled its large-scale potential distribution shifts. A. michnoi was studied under different temperature and precipitation gradients on grassland of Inner Mongolia and North China using rbcL and trnL-F sequences. The results showed that the genetic diversity of A. michnoi was low and significantly influenced by precipitation. AMOVA results showed that genetic variation in A. michnoi occurred mainly within the population, accounting for 70.57%. Both Mantel test and partial Mantel test support a significant IBE pattern. STRUCTURE and UPGMA analyses divided the populations into two clusters. Population 10 was closely related to one cluster. The haplotype network shows only one cluster H1, and all other haplotypes have evolved from H1, which is likely the ancestral haplotype. A. michnoi, as a widely distributed species. Originating from a primitive haplotype. Large scale precipitation caused genetic differentiation into two genetic branches. The MaxEnt model predicts that A. michnoi’s distribution has expanded since the Last Glacial Maximum and will shift to higher elevations in the future due to climate change. Full article

(This article belongs to the Section Plant Diversity)

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22 pages, 1953 KB

Open AccessReview

Ecological Restoration in Laurentian Great Lakes Wetlands: A Literature Review

by Dominique Rumball, Scott M. Reid and Nicholas E. Mandrak

Diversity 2025, 17(11), 797; https://doi.org/10.3390/d17110797 - 16 Nov 2025

Abstract

The Laurentian Great Lakes basin, the largest surface freshwater ecosystem in the world, is heavily impacted by anthropogenic stressors including wetland degradation and loss. Ecological restoration has been identified as a tool to conserve and manage Great Lakes wetlands where studies undergo planning, [...] Read more.

The Laurentian Great Lakes basin, the largest surface freshwater ecosystem in the world, is heavily impacted by anthropogenic stressors including wetland degradation and loss. Ecological restoration has been identified as a tool to conserve and manage Great Lakes wetlands where studies undergo planning, action, and evaluation stages. A review of 57 studies (1967–2023) on Great Lakes coastal and inland wetlands was conducted to determine when and where ecological restoration is occurring, what approaches are being taken, and how effective they are. Restoration occurred most in coastal wetlands located in the United States of America and Lake Erie. The most implemented monitoring designs were control-impact and before-after-control-impact designs. A common ecological objective of restoration was altering species composition for invasive species management. Studies targeting changes in biological communities integrated ecological theory well within the three stages of restoration. Variable restoration effectiveness was detected, where a mix of ecological objectives were targeted and monitored through many study designs. Future restoration efforts would benefit from greater financial and monitoring investments (especially during the planning stage), continued integration of ecological theory, development of lake-specific benchmarks to assess restoration success, and a collaborative approach that includes practitioner knowledge and Traditional Ecological Knowledge. Full article

(This article belongs to the Special Issue Ecological Restoration, Functioning and Conservation of Coastal Wetlands)

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23 pages, 5702 KB

Open AccessArticle

All Is Not Quiet on the Western Front: High Host–Parasite (Echinodermata and Caenogastropoda) Diversity Revealed at an Australian Marine Transition Zone

by Henry Carrick and Lisa Kirkendale

Diversity 2025, 17(11), 796; https://doi.org/10.3390/d17110796 - 14 Nov 2025

Abstract

While substantial eulimid diversity has been revealed in the Indo-West Pacific marine diversity hotspot, many neighbouring areas are still unexplored, including in Western Australia. The Houtman Abrolhos are a unique chain of islands in a well-characterised marine transition zone where tropical and temperate [...] Read more.

While substantial eulimid diversity has been revealed in the Indo-West Pacific marine diversity hotspot, many neighbouring areas are still unexplored, including in Western Australia. The Houtman Abrolhos are a unique chain of islands in a well-characterised marine transition zone where tropical and temperate waters meet along the mid-west coast. During a biodiversity survey of the islands in 2025, sixty-two eulimids from 15 stations were collected, a family of marine gastropods never-before documented from this region. Here we incorporate newly collected and legacy material from the Western Australian Museum to illustrate 23 new eulimid morphospecies records for the Houtman Abrolhos. Sixteen hosts, representing all five classes of Echinodermata, were identified. Most eulimids were attached externally to their hosts, though Stilifer utinomii and two unidentified species of Melanella were found embedded in Disasterina longispina and Actinopyga mauritiana, respectively. Apicalia angulata, Peasistilifer nitidula and Stilifer utinomii are newly recorded for Western Australia, and Thyca ectoconcha and Vitreobalcis tripneusticola are new Australian records. The biogeographic affinities of these symbionts, like other marine life surveyed in the Houtman Abrolhos islands, are overwhelmingly tropical in nature, representing in many instances the southernmost records of otherwise widespread Indo-West Pacific species. Full article

(This article belongs to the Section Marine Diversity)

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12 pages, 2323 KB

Open AccessArticle

A New Species of Encotyllabe Diesing, 1850 (Monopisthocotylea: Capsalidae), from the Pharyngeal Plates of Sciaena deliciosa (Tschudi, 1846) (Eupercaria: Sciaenidae) in Peru, with Notes on the Nomenclatural Status of E. callaoensis Tantaleán, 1974

by Andrés Huerta, Carlos Villena, Moises Ramos, Joanna Rojas, Kelly Milla, Aarón Mondragón-Martínez, Luis Ñacari, Celso Luis Cruces and Jhon Darly Chero

Diversity 2025, 17(11), 795; https://doi.org/10.3390/d17110795 - 14 Nov 2025

Abstract

A new species of Encotyllabe Diesing, 1850 (Monopisthocotylea: Capsalidae), Encotyllabe tantaliani n. sp., is described from the pharyngeal plates of the Lorna drum, Sciaena deliciosa (Tschudi, 1846) (Eupercaria: Sciaenidae), collected from two localities along the Peruvian coast. This new species was originally proposed [...] Read more.

A new species of Encotyllabe Diesing, 1850 (Monopisthocotylea: Capsalidae), Encotyllabe tantaliani n. sp., is described from the pharyngeal plates of the Lorna drum, Sciaena deliciosa (Tschudi, 1846) (Eupercaria: Sciaenidae), collected from two localities along the Peruvian coast. This new species was originally proposed as E. callaoensis Tantaleán, 1974, in an unpublished doctoral thesis, and is herein recognized as a nomen nudum under the International Code of Zoological Nomenclature (ICZN). Encotyllabe tantaliani n. sp. is distinguished from all known congeners by the following combination of morphological features: (1) an anteriorly tapering body proper, (2) slightly lobed testes markedly larger than the ovary, (3) vitelline follicles beginning at the level of the male copulatory organ (MCO) and absent from the regions of the reproductive organs, (4) a genital pore positioned posterolateral to the pharynx, and (5) an oblong-shaped MCO. Phylogenetic analysis based on cox1 sequence places E. tantaliani n. sp. in a clade with Encotyllabe percussa Morales-Ávila, Jufaili & Ogawa, 2024, a parasite of Lethrinus nebulosus (Forsskål, 1775) (Eupercaria: Lethrinidae) from the Arabian Gulf. Pairwise genetic distances support the distinctiveness of the new species from its closest congeners. Encotyllabe tantaliani n. sp. represents the first species of the genus described from a host belonging to the Sciaenidae host. Full article

(This article belongs to the Special Issue Diversity and Phylogenetics of Parasites in Aquatic Animals)

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20 pages, 7877 KB

Open AccessArticle

Draft Genome Assembly of Parnassius epaphus Provides New Insights into Transposable Elements That Drive Genome Expansion in Alpine Parnassius butterflies

by Wantao Rong, Nan Wei, Jing Song, Guole Qin and Delong Guan

Diversity 2025, 17(11), 794; https://doi.org/10.3390/d17110794 - 13 Nov 2025

Abstract

The expansion of genomes is a major evolutionary force, yet its role in facilitating adaptation to extreme environments remains enigmatic. Here, we investigate alpine Parnassius butterflies, a rare genus characterized by exceptionally large genomes, to unravel the interplay between genome architecture and [...] Read more.

The expansion of genomes is a major evolutionary force, yet its role in facilitating adaptation to extreme environments remains enigmatic. Here, we investigate alpine Parnassius butterflies, a rare genus characterized by exceptionally large genomes, to unravel the interplay between genome architecture and high-altitude colonization. We present a new, 1.46 Gb draft genome assembly for Parnassius epaphus and perform a comparative analysis across six species. Our findings reveal a massive 3- to 5-fold genome expansion driven predominantly by Long Interspersed Nuclear Elements (LINEs). Counterintuitively, we discover that larger genomes possess a proportionally smaller fraction of young, active transposable elements (TEs), challenging the prevailing paradigm that recent TE proliferation is the primary driver of genome size. Instead, our temporal analysis demonstrates that this expansion is a legacy of two ancient TE waves (~8 and ~14 Mya), which remarkably coincide with major uplift phases of the Tibetan Plateau. We propose a model where the selective retention of these ancient TEs, mechanistically linked to major geological upheavals, provided the crucial genomic plasticity for colonizing Earth’s most extreme terrestrial habitats. This study re-frames TEs not merely as genomic parasites but as pivotal architects of adaptive genome evolution in response to profound environmental change. Full article

(This article belongs to the Special Issue Conservation of Endangered Animal Biodiversity from Genetic and Genomic Perspectives)

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32 pages, 2795 KB

Open AccessReview

How Will Environmental Conditions Affect Species Distribution and Survival in the Coming Decades—A Review

by Pavel Kindlmann, Spyros Tsiftsis, Lucie Buchbauerová, Iva Traxmandlová and Zuzana Štípková

Diversity 2025, 17(11), 793; https://doi.org/10.3390/d17110793 - 13 Nov 2025

Abstract

Species are disappearing worldwide and the expectation is that this will increase in the future. This review summarizes information on the reasons for the global reduction in biodiversity and what might happen in the future. The literature indicates that the most important factors [...] Read more.

Species are disappearing worldwide and the expectation is that this will increase in the future. This review summarizes information on the reasons for the global reduction in biodiversity and what might happen in the future. The literature indicates that the most important factors responsible for this are changes in climate and land use. As changes in land use result in the destruction of natural habitats, they are thought to be the prime driver in the future. Climate change is, however, also often cited as a major driving force. To reduce the effect of climate change on the decline in biodiversity, it is important to know, how climate change affects the abundance and distribution of species. A particular emphasis should be placed not only on conserving specific species but also the environment and communities they live in. In addition, there are many other factors that might play a role, e.g., overexploitation, eutrophication and the introduction and spread of invasive non-native species. Full article

(This article belongs to the Section Biodiversity Conservation)

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19 pages, 1362 KB

Open AccessReview

Diversity and Environmental Challenges in the Ecuadorian Amazon: Integrating Agriculture and Conservation in the Face of Deforestation

by Roy Vera-Velez and Raúl Ramos-Veintimilla

Diversity 2025, 17(11), 792; https://doi.org/10.3390/d17110792 - 12 Nov 2025

Abstract

The biosphere is undergoing critical transformations due to deforestation, agricultural expansion, and logging, which have led to biodiversity loss, degradation of ecosystem services, and climate change. In tropical forests such as the Ecuadorian Amazon, these pressures are especially severe because reductions in forest [...] Read more.

The biosphere is undergoing critical transformations due to deforestation, agricultural expansion, and logging, which have led to biodiversity loss, degradation of ecosystem services, and climate change. In tropical forests such as the Ecuadorian Amazon, these pressures are especially severe because reductions in forest cover compromise key ecological processes. The purpose of this article is to analyze the relationship between shifting agriculture, food security, and conservation in the Ecuadorian Amazon, with emphasis on the agroforestry system known as the chakra practiced by Kichwa communities. This model integrates crops such as cacao, maize, and cassava with native trees, without chemical inputs, and constitutes a practice that is both culturally significant and environmentally sustainable. Whereas conventional shifting agriculture tends to reduce soil fertility and the forest’s regenerative capacity, chakras maintain important levels of floristic diversity, favor the conservation of endemic species, and provide ecosystem services such as carbon sequestration and nutrient regulation. In this sense, chakras represent a resilient yet context-dependent agroforestry alternative that connects food security and sovereignty, biological conservation, income, Indigenous identity, and climate-change mitigation, although their long-term sustainability remains influenced by market forces, land-use pressure, and policy support in tropical contexts. Full article

(This article belongs to the Special Issue Biodiversity, Community Structure and Ecology of Terrestrial Ecosystems Under Global Change)

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18 pages, 5762 KB

Open AccessArticle

Impact of the 2023–2024 ENSO Event of the North Pacific Coral Reefs of Costa Rica

by Juan José Alvarado, Fabio Quesada-Perez, María J. Solano, Maricruz Calvo-Fong and Sebastián Mena

Diversity 2025, 17(11), 791; https://doi.org/10.3390/d17110791 - 12 Nov 2025

Abstract

Coral reefs are increasingly impacted by marine heatwaves and global warming, with the 2023–2024 El Niño–Southern Oscillation (ENSO) event causing unprecedented thermal stress across the Eastern Tropical Pacific. This study assessed the effects of this event on coral reefs in the Gulf of [...] Read more.

Coral reefs are increasingly impacted by marine heatwaves and global warming, with the 2023–2024 El Niño–Southern Oscillation (ENSO) event causing unprecedented thermal stress across the Eastern Tropical Pacific. This study assessed the effects of this event on coral reefs in the Gulf of Papagayo, Costa Rica. Sea surface temperatures exceeded the bleaching threshold for seven months, reaching a record 10.2 Degree Heating Weeks—twice the levels recorded during the 1997–1998 ENSO. Benthic and fish community surveys revealed severe coral mortality, particularly in Pocillopora-dominated reefs, with some sites losing over 90% of live coral cover. Resilience varied across sites, likely influenced by factors such as local water circulation, coral genetic diversity, symbiont type, and heterotrophic capacity. Reefs with higher genetic diversity and thermally tolerant Durusdinium symbionts showed partial recovery. Seasonal upwelling appeared to buffer thermal stress in some areas, potentially acting as a natural climate refuge. Bleaching also impacted reef fish communities, with a notable decline in invertebrate-feeding species on degraded reefs. These findings highlight the interplay between prolonged thermal stress, coral biology, and local oceanographic processes in shaping reef resilience. Identifying and protecting such climate refugia will be critical for coral conservation under future climate change scenarios. Full article

(This article belongs to the Special Issue Eco-Physiology of Shallow Benthic Communities)

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12 pages, 4272 KB

Open AccessArticle

The Relationship Between Abundance and Actual Spatial Distribution of Terrestrial Isopods (Oniscidea)

by Martin Martinka and Ivan Hadrián Tuf

Diversity 2025, 17(11), 790; https://doi.org/10.3390/d17110790 - 11 Nov 2025

Abstract

(1) Studying the spatial distribution of wingless arthropods restricted to the Earth’s surface presents numerous challenges. In this study, we focused on the spatial distribution of terrestrial isopods (Oniscidea) within a managed forest ecosystem, examining relationships among abundance, variance, occupancy, and clumpiness (i.e., [...] Read more.

(1) Studying the spatial distribution of wingless arthropods restricted to the Earth’s surface presents numerous challenges. In this study, we focused on the spatial distribution of terrestrial isopods (Oniscidea) within a managed forest ecosystem, examining relationships among abundance, variance, occupancy, and clumpiness (i.e., aggregation) to highlight their significant roles in the observed phenomena. (2) Terrestrial isopods were collected using pitfall traps along a gradient spanning deforested and forested areas. For analysis, we employed summary statistics to describe the community using 18 different coefficients. Abundance–variance and abundance–occupancy models, together with Taylor’s power law and ordination symbol plots were performed. (3) Nearly 1000 individuals representing 8 species were identified and analyzed. All species exhibited a clumped distribution; however, Ligidium hypnorum displayed the highest degree of clumpiness, which resulted in notably low frequency and constancy despite its high overall abundance. Shrubs were the habitat with the highest rate of aggregation. Most species concentrated their individuals in just up to 5 of the 75 pitfall traps, with the remaining traps typically containing fewer or no individuals. (4) Species that are highly abundant on a local scale can be surprisingly limited in their spatial distribution, making their assumed dominance questionable and causing them to deviate from established trends. Awareness of species-specific traits and attention to such details can progressively improve the interpretation of observed ecological patterns. Full article

(This article belongs to the Section Animal Diversity)

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