Loss Of Diversity Research Articles

The effect of habitat health and environmental change on cultural diversity and richness in animals.

There is increasing evidence that habitat decline via fragmentation or species loss can lead to loss of cultural diversity, complexity or richness in non-human animals. For example, a reduction in local bird species richness leads lyrebirds to sing fewer complex songs, while great apes living in fragmented landscapes have smaller cultural repertoires. However, the link between animal culture and local ecology remains understudied, and the potentially complex interactions between ongoing ecological change and animal culture are poorly understood. Here, we review the current state of knowledge on how ecology influences animal culture, focusing on vocal communication and foraging behaviour. We identify key factors affecting cultural patterning, including direct effects (e.g. environmental variability) and indirect effects (e.g. connectivity). We then review the emerging evidence for the effects of environmental change on culture, identifying three major threatening processes: habitat fragmentation, habitat degradation and urbanization. Finally, we develop a predictive framework for the effect of these threatening processes on animal culture and highlight how the loss of cultural diversity and complexity can lead to fitness costs with conservation implications.This article is part of the theme issue 'Animal culture: conservation in a changing world'.

Long read genome unravels MHC I genomic architecture, evolution, and diversity loss in Gubernatrix cristata

Long read genome unravels MHC I genomic architecture, evolution, and diversity loss in Gubernatrix cristata

The Evolutionary History of the Extinct Baltic Sea Harp Seal Population

ABSTRACTThe now‐extinct harp seal population that inhabited the Baltic Sea from the Mesolithic to the Iron Age is an enigma. It occurred outside the species' contemporary Arctic range, likely deviated from typical harp seal migratory behaviour, and experienced body size reductions and dramatic population fluctuations leading up to its extinction. Here we use ancient DNA analyses to shed more light on the evolutionary history of the Baltic Sea harp seal population, including its origin, timing of colonisation, diversity and factors contributing to its demise. We generated 49 ancient Baltic and eight ancient Arctic harp seal mitogenomes, which we analysed together with 53 contemporary Arctic harp seal mitogenomes. We detected limited phylogeographic resolution among ancient and contemporary populations, which we interpret as a late Pleistocene range expansion from a common refugial population with subsequent gene flow. Ancient Baltic harp seals were significantly genetically differentiated from contemporary harp seal populations and retained their own genetic composition throughout time. The genetic diversity of Baltic harp seals decreased over time, yet was comparable to that of contemporary populations. This suggests that Baltic harp seals formed a distinct breeding population, which may occasionally have received immigrants from the Arctic but was itself confined in the Baltic Sea until the end. We hypothesise that loss of genetic diversity and the ultimate extinction of the Baltic harp seal population was a consequence of population fluctuations caused by climatic change, reduced salinity and biological productivity, and periodic intense human harvest.

A shortcut to sample coverage standardization in metabarcoding data provides new insights into land-use effects on insect diversity.

Identifying key drivers of insect diversity decline in the Anthropocene remains a major challenge in biodiversity research. Metabarcoding has rapidly gained popularity for species identification, yet the lack of abundance data complicates accurate diversity metrics like sample coverage-standardized species richness. Additionally, the vast number of taxa lacks a unified phylogeny or trait database. We introduce a new workflow for metabarcoding insect data that constructs a phylogenetic tree for most insect families, standardizes sample coverage and assesses both taxonomic and phylogenetic diversity along the Hill series. Applying this workflow to Central Europe, we analysed insect diversity from 400 families across a land-use gradient. Our results show that land-use intensity significantly affects sample coverage, highlighting the necessity of biodiversity standardization. Taxonomic diversity declined by 27-44% and phylogenetic diversity by 13-29% across 39 000 operational taxonomic units, with diversity decreasing from forests to agricultural areas. When focusing on rare species communities exhibited greater phylogenetic diversity loss than taxonomic diversity, whereas dominant species experienced smaller phylogenetic losses but more pronounced declines in taxonomic diversity. Our findings underscore the detrimental effects of agriculture on insect taxa and reveal a dramatic loss of phylogenetic diversity among rare species with potential consequences for ecosystem stability.

Sex differences in the association between long-term ambient particulate air pollution and the intestinal microbiome composition of children.

Sex differences in the association between long-term ambient particulate air pollution and the intestinal microbiome composition of children.

Litter biomass was the main factor driving plant diversity following grazing exclusion in shrub - Grassland ecotone of eastern Qilian Mountains.

Litter biomass was the main factor driving plant diversity following grazing exclusion in shrub - Grassland ecotone of eastern Qilian Mountains.

Biodiversity loss disrupts seasonal carbon dynamics in a species-rich temperate grassland.

Biodiversity loss poses a significant threat to ecosystem functioning. However, much of the empirical evidence for these effects is based on artificial experiments that often fail to simulate the structure of natural communities. Hence, it is still unclear whether natural diversity losses would significantly affect the functioning of "real-world" ecosystems. As subordinate and rare species constitute most of the diversity in natural communities and are often more vulnerable to local extinction, we evaluated their contribution to ecosystem functioning in a naturally species-rich grassland. We focused on two mechanisms by which they can support ecosystem functions: redundancy and complementarity. We conducted two long-term field experiments (>6 years) simulating contrasting biodiversity loss scenarios through the manual removal of plant species and measured the consequences of species loss on various ecosystem functions related to carbon dynamics. The latter were examined seasonally to explore diversity effects outside the typical peak of vegetation. We found that dominant removal led to substantial reductions in aboveground phytomass and litter production and altered the annual carbon fixation capacity of the vegetation, highlighting the pivotal role of dominant species in driving ecosystem functioning. Despite high species diversity, other species could not fully compensate for the loss of a single dominant even after more than 25 years, challenging assumptions about redundancy. Complementarity effects were not detected at the peak of vegetation but were evident in early spring and autumn when subordinate and rare species enhanced ecosystem functions. Surprisingly, belowground phytomass, soil organic carbon content, and litter decomposition were unaffected by species removal, suggesting complex interactions in belowground processes. These findings underscore the importance of dominant species in maintaining ecosystem functioning and emphasize the need for nuanced approaches to studying biodiversity loss in real-world communities. Comprehensive seasonal measurements are essential for accurately discerning the effects of biodiversity on ecosystem dynamics and informing effective conservation strategies that maintain ecosystem functioning.

Conservation genetics of Mahogany Gliders and their complex evolutionary relationship with Squirrel Gliders

Abstract Squirrel Gliders (Petaurus norfolcensis) are widely distributed throughout the woodlands of eastern Australia, while the similar but larger Mahogany Glider (Petaurus gracilis) inhabits the coastal woodlands of the Wet Tropics in northeastern Queensland. The Mahogany Glider is an Endangered species due to habitat loss and fragmentation. This study used single nucleotide polymorphism markers (SNPs) from field and museum-derived samples to investigate genetic relationships within the Squirrel/Mahogany Glider complex and conduct a conservation genetics assessment for the Mahogany Glider. Analyses of genetic structure, phylogenomics, and outlier loci identified four genetic groups: Mahogany Glider and three distinct groups in Squirrel Gliders (North Queensland, Cape Cleveland, and mid-eastern/south-eastern Queensland). We found genetic admixture between these groups, but whether the admixture is historic or current remains unclear. Squirrel Gliders from North Queensland were genetically more similar to Mahogany Gliders in some analyses than to the other two Squirrel Glider groups. Morphological analysis confirmed that Mahogany Gliders are distinguishable from other gliders primarily by their larger body size but did not provide clear differences for the other three genetic groups. We hypothesize that the four genetic groups represent four subspecies of Squirrel Glider, of which the Mahogany Glider is one. This hypothesis can be tested with further field sampling of genetics and morphology, particularly in identified areas of potential contact. When assessing Mahogany Gliders alone, we found a clear north–south split in genetic structuring, with the southern cluster being more structured than the northern cluster. Genetic diversity within Mahogany Gliders was generally comparable to that of Squirrel Gliders, but some sampling localities indicated loss of genetic diversity and low effective population size. Regardless of whether Mahogany Gliders are classified as a species or subspecies, their Endangered status underscores the need for targeted conservation efforts. The genetic findings offer practical pathways for on-ground management to enhance population recovery and connectivity.

Obesity in the context of the «old friends» hypothesis

Currently, there is an unprecedented increase in the prevalence of obesity worldwide. The «old friends» hypothesis states that a decrease in exposure to micro- and macroorganisms with which humanity has co-evolved is one of the causes of the increase in obesity prevalence and associated diseases. Objective. To analyze the causes and pathophysiological mechanisms of metabolic disorders related to the loss of species diversity in the human body’s ecosystem. Materials and methods. An unsystematic search was conducted in the PubMed and eLibrary databases using the keywords «Old friends hypothesis+obesity/metabolic diseases», «Hygienic hypothesis obesity/metabolic diseases», and «Old friends hypothesis+obesity/metabolic diseases». Results. Since its inception, humanity has formed a symbiosis with many micro- and macroorganisms living outside and inside the human body. Advances in civilization, such as caesarean section delivery, wide use of antibiotics, deworming, and changes in the food environment, have destabilized this symbiotic process, which may contribute to the increased prevalence of obesity and associated diseases. Conclusion. Natural childbirth, prolonged breastfeeding, and rational antibiotic therapy play an important role in the formation of health. Drugs based on excretory and secretory products of helminths can be a promising method in the treatment of obesity and associated diseases.

Mitochondrial sequencing to guide the management of endangered turtles in Colombia

Introduction: Turtles are extensively harvested to supply the demand for food, pets, and products. Conservation strategies often involve the release of seized individuals and ex-situ breeding programs. However, several traded species have particular genetic characteristics, and the origins of captive individuals are often unknown. Despite their potential to aid in the recovery of populations, these strategies have faced criticism due to the risk of outbreeding depression and genetic diversity loss. Objective: To explore the use of mitochondrial sequencing to estimate the origin of captive individuals from three of Colombia's most traded turtle species: Chelonoidis carbonarius, Trachemys venustacallirostris, and Rhinoclemmys melanosterna. Methods: Firstly, we constructed genetic reference databases using 350 sequences from previous phylogeographic studies and new ones from individuals with known origins. Secondly, through phylogenetic and population genetics analyses we delimited phylogeographic groups. Thirdly, we compared the sequences of 157 turtles of unknown origins, successfully assigning them to their species and the most likely areas of origin. Results: We identified genetic structure in wild populations, heterogeneity of origins in captive individuals, and complex trade networks involving harvesting from multiple distant poaching areas and transportation to central regions. Conclusions: This study shows the efficacy of mitochondrial molecular markers in determining the possible region of origin for confiscated turtle individuals affected by illegal trade and emphasizes the importance of intra-specific conservation efforts to safeguard Colombian wildlife’s genetic identity and diversity.

Evolutionary Origin and Genetic Diversity of the Pannonian Ecotype of Apis mellifera carnica Colonies in Hungary Based on Mitochondrial DNA and Microsatellite Markers

Honey bees are crucial to both the ecosystem and the economy. However, they are subject to different influences that can lead to a loss of genetic diversity. In this study, we used mitochondrial DNA information and nuclear microsatellite markers to compare worker individuals that strictly meet the morphological breed standard of the Pannonian bee in Hungary to those with morphological disorders (yellow color of the abdomen). Additionally, this study involves Carniolan colonies from two European countries and other bee subspecies as a reference group that might have crossed into the Pannonian bee. As for the mitochondrial DNA, the combined assessment of COI and 16S genes identified six haplotypes. Based on the tRNAleu-cox2 intergenic region (E2/H2), our samples belonged to the C evolutionary lineage. According to the microsatellite data, the level of inbreeding was low in all groups investigated, and only the genotypes of the Pannonian bee showed significant deviation from the Hardy–Weinberg equilibrium state. Cluster analysis and the Discriminant Analysis of Principal Components showed that bees that failed the morphological breed identification had started to diverge genetically from those meeting the breed standards, becoming more similar to the Carniolan bee. Our findings suggest that the genetic status of the Pannonian bees investigated in this study is satisfactory. However, in order to maintain an adequate level of diversity, periodic genetic monitoring of the colonies is necessary.

Can genomic analysis actually estimate past population size?

Can genomic analysis actually estimate past population size?

Integrating in situ strategies and molecular genetics for the conservation of the endangered Azorean endemic plant Lotus azoricus

In this paper, we integrate in situ conservation strategies with population genetic analyses to improve future prospects for preserving the endangered species Lotus azoricus P.W.Ball (Fabaceae), currently found on three islands of the Azores: Santa Maria, Pico, and São Jorge. The two largest populations are in Ponta do Castelo (Santa Maria) and Calheta de Nesquim (Pico). Project LIFE VIDALIA recently implemented a comprehensive conservation plan, which included seed propagation, population reinforcement for four populations on Pico and São Jorge, and control of invasive plant species and rats. To assess genetic diversity and population structure, we analysed L. azoricus populations using retrotransposons. An increase in population size was observed at Calheta de Nesquim following the implementation of these actions, despite the negative impact of Hurricane Lorenzo in 2019. Genetic analysis revealed some admixture, with translocated plants used in reinforcements on Pico showing a distinct founder effect and differing genetic patterns compared to original individuals. Overall genetic differentiation was low, however Saint Lourenço population (Santa Maria) presented significant genetic differentiation. Gene flow between populations was high, likely due to natural or human-mediated seed dispersal. The highest genetic diversity was found at Calheta de Nesquim, likely influenced by gene flow and population growth. Some populations are prioritised for conservation based on high allelic richness and unique genetic markers. To prevent potential loss of genetic diversity, translocation between genetically distinct populations should be avoided. Collaboration between conservation stakeholders and researchers is essential for creating holistic conservation plans, and prior knowledge of population genetics will enable more effective planning.

Sex-specific systemic metabolic predictors of resistance to calorie restriction-induced weight loss in obese Diversity Outbred mice.

Calorie restriction (CR) is a well-established weight loss strategy, albeit with variation in response. Using genetically heterogeneous mice, we sought to identify metabolic predictors of resistance to CR-induced weight loss. Diversity Outbred mice (150 males, 150 females) were fed a high-fat diet for 12 weeks to generate diet-induced obesity (DIO), then underwent CR for 8 weeks. Body weight and composition, blood glucose, and plasma levels of 9 metabolic hormones were assessed at baseline, following DIO, and following CR. In response to each dietary intervention, the mice displayed substantial heterogeneity across all outcomes, often with sexual dimorphism. Among the metabolic markers, leptin changed the most in response to each dietary intervention. Logistic regression found that resistance to CR-induced weight loss in obese mice was associated with lower glucose levels in males, and with lower levels of insulin, resistin, homeostatic model assessment for insulin resistance (HOMA-IR), and plasminogen activator inhibitor-1, and higher levels of ghrelin in females. Moreover, lower leptin levels predicted resistance to CR-induced weight loss in obese mice, regardless of sex. These preclinical findings provide proof-of-principle that the genetic and phenotypic heterogeneity of DO mice can be leveraged to identify mechanistic predictors that may enhance the personalization of weight loss interventions.

Gut Microbiota and Parasite Dynamics in an Amazonian Community Undergoing Urbanization in Colombia.

Changes in the diversity and composition of gut microbiota in urban populations have been linked to the rise of non-communicable chronic diseases, such as autoimmune conditions, diabetes, and cancer. As developing countries undergo a demographic shift towards increased urbanization, accompanied by changes in diet, housing, and medication use, there is a concerning loss of microbial diversity. Therefore, it is essential to investigate microbiota changes in overlooked populations, such as indigenous communities in the Colombian Amazon basin. A better understanding of local and generalizable changes in gut microbial composition through urbanization may facilitate the development of targeted programs aimed at promoting lifestyle and diet changes, to prevent diseases that healthcare systems may be ill-equipped to effectively address.

Phylogeography of the marine benthic alga Gracilaria salicornia (Gracilariales, Rhodophyta) in Southeast Asia

Abstract Recent and future coastal habitat degradation and climate change can result in the loss of genetic diversity, especially in Southeast Asia. Despite its economic importance for the agar industry, the phylogeography of the intertidal red alga Gracilaria salicornia from Vietnam remains unexplored. Here we used 399 mitochondrial COI sequences, including 55 newly generated from Vietnam, to decipher the phylogeographic pattern of G. salicornia. The COI phylogeny and haplotype network revealed the presence of three haplogroups in G. salicornia. Haplogroup I, comprising 18 haplotypes, predominantly inhabited the west of the South China Sea, while haplogroup II, consisting of eight haplotypes from Japan and the Philippines, likely reflecting the influence of the Kuroshio Current. A single haplotype from the Philippines was placed in haplogroup III. G. salicornia exhibited high genetic diversity, with neutrality test, mismatch distribution, and Bayesian skyline plot suggesting a sudden demographic or range expansion during the mid-Pleistocene. The divergence of haplogroups I and II, occupying the eastern and western sides of the South China Sea, likely resulted from sea currents and glacial sea-level changes. Our study on historical phylogeography offers valuable insights that will encourage further research into the population history of tropical red algae in Southeast Asia, a region for its remarkable marine biodiversity.

Critical Care Nutrition from a Metabolic Point of View: A Narrative Review.

Background: Critical illness induces profound metabolic alterations, characterized by a hypermetabolic state, insulin resistance, protein catabolism, and gut barrier dysfunction, which contribute to increased morbidity and mortality. Emerging evidence highlights the role of the gut microbiome and its metabolites in modulating systemic inflammation and immune responses during critical illness. This narrative review explores the metabolic evolution of critically ill patients, the impact of gut dysbiosis on disease progression, and the potential role of nutrition in modulating metabolism and improving patient outcomes. Methods: A comprehensive literature search was conducted across PubMed and Google Scholar for articles published up to February 2025. Search terms included "critical illness", "metabolism", "gut microbiota", "nutrition", and related keywords. Articles published in English addressing metabolic alterations, microbiome changes, and nutritional strategies in critically ill patients were included. After screening for eligibility, relevant articles were synthesized to outline current knowledge and identify gaps. Results: Metabolic changes in critical illness progress through distinct phases, from catabolism-driven hypermetabolism to gradual recovery. Gut dysbiosis, characterized by a loss of microbial diversity and increased gut permeability, contributes to systemic inflammation and organ dysfunction. Nutritional strategies, including enteral nutrition, probiotics, prebiotics, and metabolomics-driven interventions, may help restore microbial balance, preserve gut barrier integrity, and modulate immune and metabolic responses. Future nutrition therapy should focus on metabolic modulation rather than solely addressing nutrient deficits. Conclusions: Advances in gut microbiome research and metabolomics offer new avenues for personalized nutrition strategies tailored to the metabolic demands of critically ill patients. Integrating these approaches may improve clinical and functional recovery while mitigating the long-term consequences of critical illness.

Towards Loss-Resilient Image Coding for Unstable Satellite Networks

Geostationary Earth Orbit (GEO) satellite communication demonstrates significant advantages in emergency short burst data services. However, unstable satellite networks, particularly those with frequent packet loss, present a severe challenge to accurate image transmission. To address it, we propose a loss-resilient image coding approach that leverages end-to-end optimization in learned image compression (LIC). Our method builds on the channel-wise progressive coding framework, incorporating Spatial-Channel Rearrangement (SCR) on the encoder side and Mask Conditional Aggregation (MCA) on the decoder side to improve reconstruction quality with unpredictable errors. By integrating the Gilbert-Elliot model into the training process, we enhance the model's ability to generalize in real-world network conditions. Extensive evaluations show that our approach outperforms traditional and deep learning-based methods in terms of compression performance and stability under diverse packet loss, offering robust and efficient progressive transmission even in challenging environments.

TimeCHEAT: A Channel Harmony Strategy for Irregularly Sampled Multivariate Time Series Analysis

Irregularly sampled multivariate time series (ISMTS) are prevalent in reality. Due to their non-uniform intervals between successive observations and varying sampling rates among series, the channel-independent (CI) strategy, which has been demonstrated more desirable for complete multivariate time series forecasting in recent studies, has failed. This failure can be further attributed to the sampling sparsity, which provides insufficient information for effective CI learning, thereby reducing its capacity. When we resort to the channel-dependent (CD) strategy, even higher capacity cannot mitigate the potential loss of diversity in learning similar embedding patterns across different channels. We find that existing work considers CI and CD strategies to be mutually exclusive, primarily because they apply these strategies to the global channel. However, we hold the view that channel strategies do not necessarily have to be used globally. Instead, by appropriately applying them locally and globally, we can create an opportunity to take full advantage of both strategies. This leads us to introduce the Channel Harmony ISMTS Transformer (TimeCHEAT), which utilizes the CD strategy locally and the CI strategy globally. Specifically, we segment the ISMTS into sub-series level patches. Locally, the CD strategy aggregates information within each patch for time embedding learning, maximizing the use of relevant observations while reducing long-range irrelevant interference. Here, we enhance generality by transforming embedding learning into an edge weight prediction task using bipartite graphs, eliminating the need for special prior knowledge. Globally, the CI strategy is applied across patches, allowing the Transformer to learn individualized attention patterns for each channel. Experimental results indicate our proposed TimeCHEAT demonstrates competitive state-of-the-art performance across three mainstream tasks including classification, forecasting and interpolation.

Eutrophication drives functional and beta diversity loss in epiphytic cyanobacteria

Abstract The structure of epiphytic cyanobacteria and patterns of β- and functional diversity are crucial for understanding how aquatic environments respond to disturbances. This study evaluated how epiphytic cyanobacteria’s biomass, adaptive strategy groups, and β- and functional diversity components respond to increasing eutrophication and environmental homogenization in three tropical reservoirs. Hypereutrophic conditions supported greater biomass of competitive species (C-strategists), while stress-tolerant (S-strategists) were more abundant in oligo-mesotrophic waters. In contrast, ruderal species (R-strategists) were most abundant in the eutrophic system and influenced by rainfall. Total β-diversity and turnover were significantly lower in eutrophic and hypereutrophic systems, correlating with greater environmental homogenization. The oligo-mesotrophic reservoir presented a higher local contribution to β-diversity, highlighting the presence of unique species. Communities in the hypereutrophic system were subsets of species from richer communities, exhibiting higher nestedness. Eutrophication also negatively impacted functional diversity, with eutrophic and hypereutrophic environments showing lower functional evenness, divergence, dispersion, and dissimilarity, and higher functional redundancy due to the loss of unique functions. These results emphasize the detrimental impact of eutrophication on β- and functional diversity of epiphytic cyanobacterial communities, underscoring the need for eutrophication control measures in tropical reservoirs.