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At least 19 recordsLinked to original sources
PubMed2025

Climatic data sources and limitations of ecological niche models impact the estimations of historical ranges and niche overlaps in distantly related Korean salamanders.

BACKGROUND: Ecological niche models (ENMs) and analyses of niche overlap/divergence have become popular methods in ecology and evolutionary biology. These analyses rely on environmental data available from several databases. However, the influence of data sources on these analyses is rarely tested. Here, we test the impact of climatic data choice on the prediction of current and Plio-Pleistocene suitable habitats for two distantly related, but broadly sympatric, salamanders endemic to the Korean Peninsula. We ran MaxEnt separately on WorldClim and CHELSA climate data. We then hindcasted ENMs to five time periods of the Plio-Pleistocene, bracketing the estimated intraspecific divergence times for these species. We then quantified the differences in predictions between WorldClim- and CHELSA-based models. Also, given the sympatry and similar habitat requirements of the two species, we tested for niche overlaps using niche identity and background tests and tested the sensitivity of the results to climatic data choice. RESULTS: The ENMs successfully predicted contemporary suitable habitats for the two species. However, the predictions were highly sensitive to climatic data choice as well as variable combinations. The hindcasted ENMs produced contrasting predictions depending on the choice of climatic dataset and failed to predict suitable habitats for some Pleistocene time periods regardless of the climatic data choice. The niche analyses were also sensitive to climatic data choice, with results suggesting either niche overlaps or divergence depending on the climatic dataset used for the analyses. CONCLUSIONS: Our study highlights the influence of climatic data choice on the outcomes of ENMs and niche analyses. Our results also underscore the limitations of macroclimate-based ENMs, especially when the species is likely buffered from macroclimatic changes by microhabitat. We argue for the need for additional ecological, ecophysiological, and population genomic studies to better understand the range formation of these enigmatic species.

Animals↗
PubMed1994

Evidence for a single-niche model of positive selection.

Thymocyte maturation depends on interactions with thymic stromal elements expressing major histocompatibility complex (MHC) molecules. Mutant mouse strains lacking MHC class I (beta 2-microglobulin-null) or class II (A beta-null) expression fail to generate normal CD8 or CD4 T-cell populations and provide model systems for reconstitution experiments. We have constructed in vitro chimeras between normal and MHC-deficient thymi to evaluate the efficiency of positive selection. Unexpectedly, the generation of mature single-positive thymocytes was proportional to the fraction of wild-type (i.e., MHC-expressing) stroma over a wide range of chimerism. Similar results were obtained for the development of T-cell receptor-transgenic thymocytes in graded chimeras expressing selecting and nonselecting MHC alleles. These findings are best explained by hypothesizing that positive selection involves a rate-limiting step at which each thymocyte can interact with only one stromal cell niche.

Animals↗
PubMed2026

The evolutionary origins of the parthenogenetic lizard Aspidoscelis tesselatus.

Most vertebrate species reproduce sexually. The whiptail lizards (Aspidoscelis) are a notable exception; at least 11 of the 45 recognized species are parthenogenetic. Here, we focus on one such species (Aspidoscelis tesselatus) as a case study to understand how parthenogenetic species originate and evolve. Using genome-wide sequence data and ecological niche modelling, we find that A. tesselatus likely arose from a single hybrid speciation event between A. scalaris and A. marmoratus less than 500,000 years ago. The geographic ranges of A. tesselatus and its parental species overlap currently, and niche modelling shows this zone of sympatry was even broader during the period when A. tesselatus likely formed. We additionally show evidence that A. tesselatus has a dynamic genome post-formation, with de novo mutations, introgression, and double-strand break associated events all contributing to variation within the species. These results show that asexual lineages can continue to be shaped by ongoing genomic and ecological dynamics, illuminating the processes that influence transitions in reproductive mode.

asexuality↗
PubMed2025

Conservation genomics of a threatened subtropical Rhododendron species highlights the distinct conservation actions required in marginal and admixed populations.

With the impact of climate change and anthropogenic activities, the underlying threats facing populations with different evolutionary histories and distributions, and the associated conservation strategies necessary to ensure their survival, may vary within a species. This is particularly true for marginal populations and/or those showing admixture. Here, we re-sequence genomes of 102 individuals from 21 locations for Rhododendron vialii, a threatened species distributed in the subtropical forests of southwestern China that has suffered from habitat fragmentation due to deforestation. Population structure results revealed that R. vialii can be divided into five genetic lineages using neutral single-nucleotide polymorphisms (SNPs), whereas selected SNPs divide the species into six lineages. This is due to the Guigu (GG) population, which is identified as admixed using neutral SNPs, but is assigned to a distinct genetic cluster using non-neutral loci. R. vialii has experienced multiple genetic bottlenecks, and different demographic histories have been suggested among populations. Ecological niche modeling combined with genomic offset analysis suggests that the marginal population (Northeast, NE) harboring the highest genetic diversity is likely to have the highest risk of maladaptation in the future. The marginal population therefore needs urgent ex situ conservation in areas where the influence of future climate change is predicted to be well buffered. Alternatively, the GG population may have the potential for local adaptation, and will need in situ conservation. The Puer population, which carries the heaviest genetic load, needs genetic rescue. Our findings highlight how population genomics, genomic offset analysis, and ecological niche modeling can be integrated to inform targeted conservation.

Rhododendron↗
PubMed2026

Have we entered a 'post-model' era in plant biology?

Models such as arabidopsis (Arabidopsis thaliana) have underpinned genomic and physiological research in plant science. Advances in genome sequencing, pangenomics, and genome editing have prompted claims of a 'post-model' era, with model-crops and crops such as rice and bread wheat combining agricultural relevance with experimental tractability. We argue that the 'simplicity-to-complexity' approach remains valid, although model systems have evolved. Arabidopsis remains indispensable for interpreting multi-omics data, testing developmental hypotheses, and generating mechanistic insights difficult to obtain in crops. Linking these strengths to model-crops adds translational value by bridging discovery and breeding, while niche models such as Brachypodium distachyon and legumes address grass cell wall biology and nitrogen fixation. Future progress depends on diverse species with complementary strengths across fundamental and applied plant biology.

arabidopsis↗
PubMed1990

Some evolutionary properties of parental investment per offspring in a heterogeneous environment.

The possibility of protected polymorphisms and of monomorphic evolutionarily stable strategies for parental investment per offspring in a heterogeneous environment is theoretically analysed. A high density two-niche model of the classical soft selection kind is used, although it incorporates the possibility of rare strategies invading an empty niche the contribution of which is not constant. Protected polymorphisms can be found whether or not both strategies included produce surviving offspring in both niches. However, a monomorphic evolutionarily stable strategy exists unless offspring of the optimal size in one of the niches cannot survive in the other. The robustness of the model is graphically illustrated under a variety of circumstances, and some evolutionary consequences are briefly discussed.

Animals↗
PubMed1999

Conservatism of ecological niches in evolutionary time

Theory predicts low niche differentiation between species over evolutionary time scales, but little empirical evidence is available. Reciprocal geographic predictions based on ecological niche models of sister taxon pairs of birds, mammals, and butterflies in southern Mexico indicate niche conservatism over several million years of independent evolution (between putative sister taxon pairs) but little conservatism at the level of families. Niche conservatism over such time scales indicates that speciation takes place in geographic, not ecological, dimensions and that ecological differences evolve later.

Journal Article↗
PubMed1998

'Prehab program' can slow down functional decline in geriatric patients.

The following model was one of four recommended by Nurses Improving Care to the Hospitalized Elderly (NICHE), a national initiative designed to help hospitals prepare for the nation's burgeoning aging population. For more information on other NICHE models, see the January issue of Patient-Focused Care and Satisfaction.

Aged↗
PubMed2026

Genetically diverse populations hold the keys to climatic adaptation in the Western barn owl (Tyto alba).

Although local adaptation influences species distributions, its role in driving evolutionary resilience under climate change remains unclear. Current predictive models focus on genetic adaptation to present climates, providing limited insight into future adaptive capacity. We hypothesise that historical responses to climatic shifts can reveal candidate loci for local adaptation in the future. Combining ecological niche modelling and genomic analyses, we investigate spatiotemporal patterns and mechanisms of local adaptation of the Western Palearctic barn owl (Tyto alba). Ecological modelling reveals that barn owls now occupy a broader climatic niche than during the Last Glacial Maximum. Genomic analyses indicate ongoing adaptation, with regions under selection linked to environmental factors across all populations. We find that local adaptation drives evolutionary changes across populations, enabling colonisation of new habitats and shaping responses to climate change in resident populations. We show that standing genetic diversity plays a crucial role in adaptation to past, present, and future environmental shifts.

Animals↗
PubMed2000

Simple rules yield complex food webs.

Several of the most ambitious theories in ecology describe food webs that document the structure of strong and weak trophic links that is responsible for ecological dynamics among diverse assemblages of species. Early mechanism-based theory asserted that food webs have little omnivory and several properties that are independent of species richness. This theory was overturned by empirical studies that found food webs to be much more complex, but these studies did not provide mechanistic explanations for the complexity. Here we show that a remarkably simple model fills this scientific void by successfully predicting key structural properties of the most complex and comprehensive food webs in the primary literature. These properties include the fractions of species at top, intermediate and basal trophic levels, the means and variabilities of generality, vulnerability and food-chain length, and the degrees of cannibalism, omnivory, looping and trophic similarity. Using only two empirical parameters, species number and connectance, our 'niche model' extends the existing 'cascade model and improves its fit ten-fold by constraining species to consume a contiguous sequence of prey in a one-dimensional trophic niche.

Ecology↗
PubMed1989

Chronic CEI alters effect of low Na+ diet in normal and coarcted pups. I. BP, renin, and GFR.

To assess the renin-angiotensin (RA) dependence of evolving neonatally induced coarctation hypertension (NICH) in inbred pups, we randomized sex-matched littermates to a high dose of converting-enzyme inhibitor (CEI:MK-421) or placebo from the time of neonatal aortic banding (coarcted) vs. no banding (control). In phase 1 studies, pups were examined serially on normal diet (Bagby and Fuchs, Hypertension In press.): chronic CEI lowered systolic blood pressure (BP) equally in coarcted and controls and failed to prevent systolic BP excess in coarcted dogs. In phase 2 studies, the same pups were exposed to a low sodium (LS) diet at 4 mo of age, a time when the untreated NICH model exhibits increased forelimb systolic BP. Measurements of systolic BP, RA components, renal function, and extracellular volume (ECV) were made before and serially during 12 days on the LS diet. Responses of coarcted and control pups to the LS diet were similar, with or without CEI, providing no evidence for exaggerated angiotensin II (ANG II) dependence in evolving NICH. Independently of coarctation status, chronic CEI significantly modified RA and renal functional responses to the LS diet: a greater renin rise but abnormal renin substrate fall, thus no rise in ANG I or ANG I generation rate; a greater rise in creatinine and a trend toward a greater fall in glomerular filtration rate (GFR). Despite these findings compatible with sustained ANG II deficit, chronic CEI unexpectedly failed to impair maintenance of systolic BP during a superimposed LS diet.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2000

Museum specimen data predict crop damage by tropical rodents.

Museum collections constitute a massive store of information on biological diversity. We used museum specimen data to generate ecological niche models that provide predictions of geographic distributions of native rodent pest species and agricultural census data that summarize the geographic distribution of nine crops in the state of Veracruz, Mexico, as well as crop losses between planting and harvest. Herein, we show that crop damage is related significantly to the predicted presence of rodent species for seven of nine crops. Museum collections may thus provide important baseline information for designing land-use and agricultural pest-management programs.

Animals↗
PubMed2001

Investigating stem cells in human colon by using methylation patterns.

The stem cells that maintain human colon crypts are poorly characterized. To better determine stem cell numbers and how they divide, epigenetic patterns were used as cell fate markers. Methylation exhibits somatic inheritance and random changes that potentially record lifelong stem cell division histories as binary strings or tags in adjacent CpG sites. Methylation tag contents of individual crypts were sampled with bisulfite sequencing at three presumably neutral loci. Methylation increased with aging but varied between crypts and was mosaic within single crypts. Some crypts appeared to be quasi-clonal as they contained more unique tags than expected if crypts were maintained by single immortal stem cells. The complex epigenetic patterns were more consistent with a crypt niche model wherein multiple stem cells were present and replaced through periodic symmetric divisions. Methylation tags provide evidence that normal human crypts are long-lived, accumulate random methylation errors, and contain multiple stem cells that go through "bottlenecks" during life.

Adolescent↗
PubMed2000

Extraordinary multilocus genetic organization in mole crickets, Gryllotalpidae.

Allozymic diversity at 21 loci was analyzed in 470 individuals of three species of mole cricket superspecies, Gryllotalpa gryllotalpa (two new chromosomal species, G. tali and G. marismortui) and G. africana in Israel, which are distributed along a southward transect of increasing aridity. Two outstanding findings emerged in G. tali and G. marismortui: (1) genetic polymorphism was high but heterozygosity very low, indicating significant deviations from Hardy-Weinberg expectations; and (2) significant linkage disequilibria at an unprecedented level for outbreeders and remarkable intersite differences. The results may characterize subterranean gryllotalpids worldwide because a single sample of Neocurtilla hexadactyla from Tefé, Amazonia, shows the same features. Significant variation of heterozygote paucity among loci, combined with the biology of the species, rejects the simple explanation of inbreeding or any other single explanatory model. Likewise, direct selection against heterozygotes or specific multilocus associations can explain, but is not necessary nor likely to explain, the observed results in mole crickets. To explain these results, we developed a multiple-factor mathematical model combining niche viability selection, niche choice, and positive assortative mating. This model involves a special case of Wahlund effect and inbreeding. Simulations based on this model showed that a combination of these three mechanisms may produce the observed distribution of alleles, via selection on a few loci, to affect the entire genome organization.

Animals↗
PubMed1992

Variation in O-antigens, niche-specific selection and bacterial populations.

Bacterial populations usually consist of distinct clones, often apparently adapted to specific niches. A formal model is developed whereby niche-specific selection maintains the polymorphisms involved in clonal adaptation. Infrequent transfer of non-adaptive alleles to a clone is balanced by the selection for the resident adaptive allele. The model can account for the extensive polymorphism in surface antigens observed in bacteria, and also for the existence of sympatric clones of pathogenic species which differ in host range and/or mode of pathogenesis. Niche-specific selection combined with low levels of genetic transfer can also account for the high level of neutral variation in bacteria, and indirectly for their ability to respond rapidly to environmental changes.

Adaptation, Physiological↗
PubMed2026

Genomic-Environmental Integration Predicts Climate Vulnerability and Adaptive Potential of Tibetan Plateau Herpetofauna.

The herpetofauna of the Tibetan Plateau, home to Earth's highest-elevation ectothermic vertebrates, face escalating threats from rapid climate change. However, conventional conservation strategies often overlook intraspecific genetic variation and adaptive potential, limiting their predictive accuracy and effectiveness. Here, we integrate whole-genome resequencing data with environmental modeling to assess climate vulnerability in two endemic species: Nanorana parkeri (Tibetan frog) and Thermophis baileyi (hot-spring snake). Results suggest that the western populations of the two species exhibit higher genomic offsets under future climate, while some eastern populations of the Tibetan frog face a decrease in niche suitability, and the hot-spring snake will experience varying degrees of loss of suitable habitats. Furthermore, heterozygosity, genetic diversity, and genetic load demonstrate significant correlations with genomic offsets, suggesting that low genetic diversity and high genetic load may weaken the potential to adapt to environmental changes. Based on a genome-niche index that combines genomic offsets with niche suitability change, we identified evolutionary rescue populations that are potentially tolerant to climate change. Our findings underscore the importance of integrating genomic and environmental data to forecast the adaptive potential and enable effective conservation management of high-altitude herpetofauna under rapid climate change.

Animals↗