Ecology History Research Articles

Hierarchies of ecologic changes and their roles in the Phanerozoic taxonomic and ecologic diversification history of the Class Bivalvia

Hierarchies of ecologic changes and their roles in the Phanerozoic taxonomic and ecologic diversification history of the Class Bivalvia

Phylogenomics reveals the slow-burning fuse of diatom evolution

Evolution is often uneven in its pace and outcomes, with long periods of stasis interrupted by abrupt increases in morphological and ecological disparity. With thousands of gene histories, phylogenomics can uncover the genomic signatures of these broad macroevolutionary trends. Diatoms are a species-rich lineage of microeukaryotes that contribute greatly to the global cycling of carbon, oxygen, and silica, which they use to build elaborately structured cell walls. We combined fossil information with newly sequenced transcriptomes from 181 diverse diatom species to reconstruct the pattern, timing, and genomic context of major evolutionary transitions. Diatoms originated 270 Mya, and after >100 My of relative stasis in morphology and ecology, a radiation near the Jurassic-Cretaceous boundary led to the diversity of habitats and cell wall architectures characteristic of modern diatoms. This transition was marked by a genome duplication and high levels of gene tree discordance. However, short generation times increase the probability of coalescence between speciation events, minimizing the impacts of incomplete lineage sorting and implicating sequence saturation and gene tree error as the main sources of discordance. Nevertheless, a rigorous tree-based approach to ortholog selection resulted in strongly supported relationships, including some that were uncertain previously. Three pulses of accelerated speciation were detected, two of which were associated with the evolution of novel traits and ecological transitions. The first 100 My of diatom evolution was a slow-burning fuse that led to a burst of innovations in ecology, morphology, and life history that are hallmarks of contemporary diatom assemblages.

Mycoheterotrophic continuum in rhizoctonia associations: Genetic divergence and carbon acquisition variation among Odontochilus orchids.

Mycoheterotrophy is a nutritional strategy in which plants obtain carbon and essential nutrients from fungal partners. Comparative studies of closely related taxa differing in mycoheterotrophic dependency offer important insights into the evolutionary transitions underlying this lifestyle. We integrated stable isotope (δ¹³C and δ15N) analyses, MIG-seq-based phylogenetics, and fungal metabarcoding to investigate the physiological ecology and evolutionary history of three Odontochilus taxa: the large-leaved O. fissus, the small-leaved O. nakaianus (including albino, chlorophyll-deficient variants), and the very small-leaved O. aff. fissus. Morphologically, O. aff. fissus differs from O. fissus in having reduced, often reddish scale leaves and coralloid rhizomes, which are traits commonly observed in fully mycoheterotrophic orchids or mixotrophic orchids with high heterotrophy. Albino individuals and protocorms of O. nakaianus exhibited isotope signatures characteristic of full mycoheterotrophy, whereas normal individuals of O. fissus, O. nakaianus, and O. aff. fissus displayed isotopic patterns indicative of partial mycoheterotrophy, with fungal dependence likely inversely correlated with leaf size. Metabarcoding revealed that all taxa consistently associated with Ceratobasidiaceae OTUs, suggesting that similar rhizoctonia fungi support varying degrees of mycoheterotrophy. MIG-seq analysis confirmed that O. aff. fissus, O. fissus, and O. nakaianus form distinct genetic clusters, while albino O. nakaianus individuals were genetically indistinguishable from their green counterparts. These findings provide evidence of both genetic and nutritional divergence between O. fissus and O. aff. fissus. The results expand our understanding of the mycoheterotrophic continuum in Odontochilus species associated with rhizoctonia fungi.

Unravelling the Effects of Ecology and Evolutionary History in the Phenotypic Convergence of Fishes.

Understanding the ecological drivers and limitations of adaptive convergence is a fundamental challenge. Here, we explore how adaptive convergence of planktivorous fishes has been influenced by multiple ecological factors, evolutionary history, and chance. Using ecomorphological data for over 1600 marine species, we integrate pattern-based metrics of convergence with evolutionary model fitting to test whether phenotypic similarities among specialist planktivores exceed expectations under null models and whether ecology, evolutionary history, or their combined effects best explain trait evolution. We find that planktivores are significantly more similar in phenotype than expected. Traits with functional relevance for prey detection and capture, such as eye diameter and lower jaw length, are strongly convergent, while general body size and shape are constrained by deep divisions between clades where the effects of evolutionary history are most pronounced. Since not all traits undergo strong selection toward a convergent ecomorph, their evolutionary trajectories have not entirely overcome ancestral differences in the multivariate trait space, resulting in a specific form of convergence termed conservatism. We show how adaptive responses to feeding ecology intertwine with other ecological pressures (i.e., light environment) and historical contingency to shape fish phenotype evolution over deep time, offering key insights into the generality of phenotypic evolution.

Variation in adult sex ratios in tetrapods is linked to sex chromosomes through mortality differences between males and females.

Sex chromosomes can determine male and female phenotypes, and the resulting sex differences may have significant impacts on ecology and life history. One manifestation of this link is that ZW/ZZ sex-determination systems are associated with more male-skewed adult sex ratio (ASR, proportion of males in the adult population) than XX/XY systems across tetrapods (amphibians, reptiles, birds, and mammals). Here, we investigate four demographic processes: male and female offspring production, sex differences in juvenile and adult mortalities and in timing of maturation that can contribute to ASR variation between XX/XY and ZW/ZZ systems, using phylogenetic analyses of a large dataset collected from tetrapod species in the wild. We show that sex differences in adult mortality reliably predict ASR that is also more male-biased in XX/XY species than in ZW/ZZ species. Sex differences in juvenile mortality and in maturation time also contribute to ASR skews, but do not differ consistently between XX/XY and ZW/ZZ systems. Phylogenetic path analyses confirm an influence of sex-determination system on ASR through sex-biased adult mortalities. Together these results infer that sex chromosomes can impact, via demographic pathways, frequency-dependent selection emerging from the relative number of males and females. We call for follow-up studies to uncover the potentially complex web of associations between sex determination, population dynamics, and social behavior.

The ecological niche and population history shape mosquito population genetics on a group of three Caribbean islands

BackgroundWhile studies on mosquito population genetics have primarily focused on medically relevant species, fewer have examined the genetic population structure of mosquitoes from a diverse range of species within a single geographical area. The limited comparison between native and non-native species, as well as ecologically divergent species from the same region, hampers our ability to generalise previously described patterns in mosquito population genetics. This study uses the mosquito fauna of the Caribbean islands of Aruba, Curaçao and Bonaire as a case study to explore population genetic variation among both native and non-native mosquito species, as well as among native species occupying different ecological niches. We examine how genetic patterns relate to their population history and species-specific ecologies.MethodsMitochondrial COII sequences were obtained from 258 mosquito specimens belonging to six species, occurring on all three islands. Sequences were used in haplotype network analysis to assess the genetic variation between mosquito populations of each of the six ecologically diverse species, which vary in both their population history and ecological niche.ResultsBoth the genetic diversity and population genetic structure were found to differ strongly between sets of species, leading to a subdivision into three species groups: (1) non-native species with low genetic diversity across all three investigated islands, (2) locally native species with high genetic diversity and closely related haplotypes occurring on different islands and (3) locally native species with high genetic diversity and locally restricted haplotypes.ConclusionsOur results show that the population genetics of non-native and native species strongly differ, likely as a result of population history. Furthermore, the results suggest that mosquito species sharing the same area may display distinct population genetic structure, likely related to differences in their ecology and dispersal capacity. We suggest that addressing a broader range of species within a single area will benefit future research on mosquito population genetics to place observed patterns into a broader historical, ecological and evolutionary context.Graphical

Exploring Socio-Ecological Change at Multiple Temporal Scales in the Bas-Ogooué Ramsar Site, Gabon

Environmental and climatic changes interact within specific socio-ecological contexts shaped by historical human-landscape interactions. This study explores the interconnection between long- and short-term drivers of environmental change and current landscape uses in the Gabon’s Bas-Ogooué Ramsar site. Working in five villages, we combined georeferenced data of human settlements (n = 166) with individual and group interviews and household surveys (n = 108 informants), to map landscape dynamics over time. We found that the current landscape reflects four periods of human mobility shaped by shifts in land governance and resource management practices. Documenting 30 reported local indicators of environmental change and their respective perceived drivers, we analyzed their interwoven and cascading effects on the social-ecological system. Recent impacts of conservation policies, combined with environmental changes, challenge local livelihoods and the balance of the social-ecological system. These insights advance African historical ecology and emphasize the need for inclusive, context-sensitive strategies to achieve sustainable conservation.

PhyBaSE: A Bayesian structural equation model approach to causal inference in phylogenetic comparative analyses

Abstract One of the main limitations of phylogenetic comparative analyses is that associations between traits can only be interpreted as correlations. Here, we present a novel Bayesian structural equation model (PhyBaSE) which allows us to disentangle direct from indirect relationships among variables to propose potential causal hypotheses while accounting for phylogenetic non‐independence. Compared with the existing maximum‐likelihood based approach, PhyBaSE models are more flexible, allowing the inclusion of trait and phylogenetic uncertainty, as well as non‐continuous variables. To facilitate the application of the method, we provide worked examples, data and code. We exemplify the method both with simulated as well as empirical data. Our analyses with simulated data indicate that PhyBaSE models have higher power than classic Phylogenetic Path Analysis to discriminate between competing models. As an example of PhyBaSE using empirical data, we revisit different hypotheses proposed to explain the relationship between relative brain size and group size in Bovids. Our results challenge the previously supported social brain hypothesis and provide support for an allometric effect of body size on social group size and an effect of brain size on life span, as predicted by the cognitive buffer hypothesis. The flexibility of PhyBaSE models will allow researchers to explore more complex hypotheses on the evolution of behavioural, ecological and life history traits at a macroevolutionary level and how these are linked to anthropogenic drivers of biodiversity loss and extinction, taking full advantage of the increasing number of publicly available species‐specific datasets.

Reconstructing the Past: Bridging Deep History and Modernity for a Resilient Planet

This paper presents the critical roles of exploring deep-time human ecological histories to inform modern climate resilience and sustainability efforts. Building on existing data from paleoanthropological contexts across East Africa, this ongoing study seeks to demonstrate how our knowledge of long-term patterns of human ecological flexibility, innovation, and survival under intense and recurrent environmental changes offers insights for navigating modern climate crises. This paper advocates for the integration of Indigenous ecological knowledge with scientific enquiries.

From Historical Archives to Algorithms: Reconstructing Biodiversity Patterns in 19th Century Bavaria

Historical archives hold untapped potential for understanding long-term biodiversity change. This study introduces computational approaches to historical ecology, combining archival research, text analysis, and spatial mapping to reconstruct past biodiversity patterns. Using the 1845 Bavarian Animal Observation Dataset (AOD1845), a comprehensive survey of vertebrate species across 119 districts, we transform 5400 prose records into structured ecological data. Our analyses reveal how species distributions, habitat associations, and human–wildlife interactions were shaped by land use and environmental pressures in pre-industrial Bavaria. Beyond documenting ecological baselines, the study captures early perceptions of habitat loss and species decline. We emphasise the critical role of historical expertise in interpreting archival sources and avoiding anachronisms when integrating historical data with modern biodiversity frameworks. By bridging the humanities and environmental sciences, this work shows how digitised archives and computational methods can open new frontiers for conservation science, restoration ecology, and Anthropocene studies. The findings advocate for the systematic mobilisation of historical datasets to better understand biodiversity change over time.

Гуманитаризация экологии: история и методология

The article is devoted to the analysis of the humanitarization of ecology. The topic is relevant because it opens up new prospects for the development of environmental science. The novelty of the topic is due to the fact that many areas of humanitarian ecology are just beginning to be developed. The work is based on the analysis of materials on the history of ecology, human ecology, the works of classical ecologists, as well as works on the philosophy of science. The analysis of the stages of ecology development is carried out, their methodological features are highlighted, the role of evolutionary theory, theory of adaptation, and the concept of the biosphere is revealed. It is shown how modern ecology has become a “human-sized” science from a biological science. Through the transitional stage of human ecology, humanitarian ecologies were formed – the ecology of culture, language, and the digital environment. With their “ancestor”, bioecology, these sciences are united by an environmental approach. The environment is understood by the author as significant and meaningful for a living organism (umwelt). It is concluded that the principles of consistency and interaction are the most important unifying principles for biological and humanitarian ecologies. The use of humanitarian methods of understanding and experiencing instead of the natural science method of explanation opens up new perspectives in the field of environmental education and combating environmental problems.

Biparental Care in a Southeast Asian Passerine, the Scarlet-Backed Flowerpecker (Dicaeum cruentatum).

We opportunistically observed a nest pair of scarlet-backed flowerpeckers (Dicaeum cruentatum) for 5 days during the fledging period in late February 2020 within the Sakaerat Biosphere Reserve, Nakhon Ratchasima, Thailand. We observed both parents feeding the fledgling, with either parent returning within 3-20 min of leaving to forage. Over 5 days, both parents fed the fledgling green mistletoe fruits (Dendrophthoe pentandra [L.] Miq., family Loranthaceae). Between feeding periods, the fledgling remained mostly stationary on its perch. Our observations are similar to those reported for other species in the flowerpecker family (Dicaeidae), suggesting that biparental care is relatively common across the flowerpecker family, though there remains a paucity of direct observations and reporting. By making direct observations and subsequent discussions, we can better understand the ecology and natural history of Dicaeidae species, ultimately aiding in their conservation.

Anthropogenic Landscape Alteration, but Not Urbanization, Influences Non-Adaptive Evolution in Common Milkweed (Asclepias syriaca L.).

Urbanization can alter mating and dispersal, with consequences for non-adaptive evolution in populations. Potential outcomes vary widely due to the heterogeneity of urban landscapes and the diverse life history strategies of taxa. Furthermore, it is unclear how plants, which are significantly understudied in this context, are impacted. To better understand how urbanization influences non-adaptive evolution in a native plant of conservation importance, we analyzed patterns of neutral genetic variation in common milkweed (Asclepias syriaca). From 256 individuals sampled across 122 locations throughout the Greater Toronto Area, Canada, we created two datasets of 2,835 and 972 single nucleotide polymorphisms through genotype-by-sequencing. Genetic diversity and effective population size N e were mostly consistent between urban and rural habitats. Genetic differentiation between urban and rural habitats was low, and samples originated from a single genetic population. Demographic analysis indicated that N e decreased by > 99% within the past 800 years, with the rate of loss accelerating over time. These findings suggest that this A. syriaca population was little affected by the transition from rural to urban habitat; rather, anthropogenic activity prior to urbanization, such as precontact Indigenous inhabitation and colonial settlement, had observable effects on population demography. This study demonstrates how anthropogenic factors can modify the degree to which urbanization impacts evolution and emphasizes the importance of contextualizing results with demographic, ecological, and cultural histories.

Integrating marine historical ecology into management of Alaska’s Pacific cod fishery for climate readiness

Abstract The Pacific cod (Gadus macrocephalus) fishery was closed in 2020 after a rapid decline in biomass caused by the marine heat waves of 2014–2019. Pacific cod are exceptionally thermally sensitive and management of this fishery is now challenged by increasingly unpredictable climate conditions. Fisheries monitoring is critical for climate readiness, but short-term monitoring data may be inadequate for recognizing and anticipating change under rapid climate changes. We propose an interdisciplinary, marine historical ecology framework that looks to long-term records (local and traditional knowledge, history, archaeology, and paleoclimatology) to capture a long range of ecological variability and provide historical context for management. In order to connect to contemporary fisheries management, this framework must be built on a common vocabulary and an understanding of the key metrics used in fisheries stock assessments. Here, we propose metrics derived from Pacific cod stock assessment and synthesize information relevant to understanding the effects of past warming periods on cod populations across the Gulf of Alaska and Bering Sea. This case study provides a framework for thinking about how to use these historical records in the context of fisheries management under rapidly changing climate conditions.

Comparative phylogeography of four lizard taxa within an oceanic island.

Comparative phylogeography of four lizard taxa within an oceanic island.

Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone

The deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic diversity and metabolic novelty, and the metabolic capabilities and ecological roles of these communities remain largely unknown. We observed a widespread and relatively abundant bacterial phylum (CSP1-3) in deep soils and evaluated its phylogeny, ecology, metabolism, and evolutionary history. Genome analysis indicated that members of CSP1-3 were actively replicating in situ and were widely involved in the carbon, nitrogen, and sulfur cycles. We identified potential adaptive traits of CSP1-3 members for the oligotrophic deep soil environments, including a mixotrophic lifestyle, flexible energy metabolisms, and conservation pathways. The ancestor of CSP1-3 likely originated in an aquatic environment, subsequently colonizing topsoil and, later, deep soil environments, with major CSP1-3 clades adapted to each of these distinct niches. The transition into the terrestrial environment was associated with genome expansion, including the horizontal acquisition of a range of genes for carbohydrate and energy metabolism and, in one lineage, high-affinity terminal oxidases to support a microaerophilic lifestyle. Our results highlight the ecology and genome evolution of microbes in the deep Critical Zone.

The Bay of Porto Paone: the first "tiny underwater nature reserve" in the Gulf of Naples (1960-1966).

From 1960 to 1966, the Bay of Porto Paone, a volcanic crater located on the islet of Nisida, was home to the first "tiny underwater nature reserve" of the Gulf of Naples. The concession of the stretch of water was requested by the Stazione Zoologica di Napoli (in 1982 renamed Stazione Zoologica Anton Dohrn), a marine biological institution traditionally devoted to laboratory studies of fundamental biological phenomena, which at the time aimed at strengthening its international visibility as a place for field ecological research. The first part of the paper contextualizes this local event in the broader international trend towards the development of ecological sciences and the rising call for field sites as essential infrastructures for ecological research. The second part reconstructs the legal, administrative and scientific practices that made it possible the establishment of an "underwater reserve" in the Bay of Porto Paone and describes the main research projects carried out there. The last part of the paper goes one step beyond historiography and addresses issues related to the importance of historical narratives on past place-based research projects for contemporary studies in historical ecology.

Ecological and developmental history impacts the equitable distribution of services

The ecological and developmental history of the Chicago, Illinois, region has affected the current distribution of forests therein. These same factors, along with systemic and long‐lasting racial segregation, have shaped the distribution of the urban populations that benefit from the ecosystem services provided by urban forests. This study demonstrates that forest patch history is related to forest attributes like tree species composition, tree density, canopy height, and structural heterogeneity—all of which are important predictors of a forest's ability to provide ecosystem services. However, this effect of forest history was only seen in forest cores, as forest edges were similar regardless of patch history. We also found that forests in minoritized communities tended to be less able to support high levels of ecosystem services. This research indicates that, when improving green equity, it is important to consider the variable capacity of forests to provide ecosystem services.

The roles of natural history during ecological research

It is commonly posited that natural history is an essentially descriptive activity focused on local case studies, lacking an explicit link with theory. Still, some authors suggest that patient observation of natural history must be valued as ‘an essential first step in the scientific method’. We think that there is a strong connection between ecology and natural history, and thus delve into such relationship to propose that a) natural history observations are necessary for science problematization (i.e., for the detection of meaningful ecological research problems) and, in some specific contexts, for generating low-level or pattern hypotheses. Notwithstanding, these natural history observations themselves play a secondary role in inspiring explanatory, mechanismic or theoretical hypotheses, and b) a fundamental role of natural history during ecological research is to provide key assumptions (i.e., initial conditions) used to define the experimental design and collect the appropriate data, as well as to deduce hypotheses and predictions. This latter function fruitfully articulates natural history with ecological theory.

Interweaving Personal and Ecological Histories: Eco-Feminism, Environmental Concerns, and the Impact of Political Upheavals in Anuradha Roy’s All the Lives We Never Lived

Interweaving Personal and Ecological Histories: Eco-Feminism, Environmental Concerns, and the Impact of Political Upheavals in Anuradha Roy’s All the Lives We Never Lived