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Botta-Dukát, Zoltán. "Devil in the details: how can we avoid potential pitfalls of CATS regression when our data do not follow a Poisson distribution?" PeerJ 10 (January 14, 2022): e12763. http://dx.doi.org/10.7717/peerj.12763.
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Background Community assembly by trait selection (CATS) allows for the detection of environmental filtering and estimation of the relative role of local and regional (meta-community-level) effects on community composition from trait and abundance data without using environmental data. It has been shown that Poisson regression of abundances against trait data results in the same parameter estimates. Abundance data do not necessarily follow a Poisson distribution, and in these cases, other generalized linear models should be fitted to obtain unbiased parameter estimates. Aims This paper discusses how the original algorithm for calculating the relative role of local and regional effects has to be modified if Poisson model is not appropriate. Results It can be shown that the use of the logarithm of regional relative abundances as an offset is appropriate only if a log-link function is applied. Otherwise, the link function should be applied to the product of local total abundance and regional relative abundances. Since this product may be outside the domain of the link function, the use of log-link is recommended, even if it is not the canonical link. An algorithm is also suggested for calculating the offset when data are zero-inflated. The relative role of local and regional effects is measured by Kullback-Leibler R2. The formula for this measure presented by Shipley (2014) is valid only if the abundances follow a Poisson distribution. Otherwise, slightly different formulas have to be applied. Beyond theoretical considerations, the proposed refinements are illustrated by numerical examples. CATS regression could be a useful tool for community ecologists, but it has to be slightly modified when abundance data do not follow a Poisson distribution. This paper gives detailed instructions on the necessary refinement.
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Alroy, John. "The shape of terrestrial abundance distributions." Science Advances 1, no. 8 (September 2015): e1500082. http://dx.doi.org/10.1126/sciadv.1500082.
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Ecologists widely accept that the distribution of abundances in most communities is fairly flat but heavily dominated by a few species. The reason for this is that species abundances are thought to follow certain theoretical distributions that predict such a pattern. However, previous studies have focused on either a few theoretical distributions or a few empirical distributions. I illustrate abundance patterns in 1055 samples of trees, bats, small terrestrial mammals, birds, lizards, frogs, ants, dung beetles, butterflies, and odonates. Five existing theoretical distributions make inaccurate predictions about the frequencies of the most common species and of the average species, and most of them fit the overall patterns poorly, according to the maximum likelihood–related Kullback-Leibler divergence statistic. Instead, the data support a low-dominance distribution here called the “double geometric.” Depending on the value of its two governing parameters, it may resemble either the geometric series distribution or the lognormal series distribution. However, unlike any other model, it assumes both that richness is finite and that species compete unequally for resources in a two-dimensional niche landscape, which implies that niche breadths are variable and that trait distributions are neither arrayed along a single dimension nor randomly associated. The hypothesis that niche space is multidimensional helps to explain how numerous species can coexist despite interacting strongly.
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Chaves, Cleber Juliano Neves, Júlio César Dyonisio, and Davi Rodrigo Rossatto. "Host trait combinations drive abundance and canopy distribution of atmospheric bromeliad assemblages." AoB Plants 8 (2016): plw010. http://dx.doi.org/10.1093/aobpla/plw010.
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Garlow, Steven J., Ericka Boone, Wei Li, Michael J. Owens, and Charles B. Nemeroff. "Genetic Analysis of the Hypothalamic Corticotropin-Releasing Factor System." Endocrinology 146, no. 5 (May 1, 2005): 2362–68. http://dx.doi.org/10.1210/en.2004-1450.
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Abstract The goal of this study was to use BxD recombinant inbred mice to search for genes that control the hypothalamic corticotrophin-releasing factor (CRF) system. The specific phenotype that was measured was abundance of transcripts that encode CRF, CRF receptor (Crf-R1), CRF binding protein, and arginine vasopressin (AVP) in total hypothalamic RNA. The strain distribution patterns for the transcript abundances for each target were continuously distributed, consistent with these being quantitative traits. Marker regression and interval mapping revealed associations with quantitative trait loci (QTL) for CRF transcript abundance on chromosome 1 (at 89.2 cM), chromosome 12 (between 54–58 cM), and chromosome 13 (between 26–30 cM); for Crf-R1 transcript abundance on chromosome 7 (at 1.5 cM), chromosome 12 (at 37 cM), and chromosome X (at 30 cM); for CRF binding protein transcript abundance on chromosome 7 (at 48.5 cM), chromosome 8 (at 65 cM), and chromosome 12 (at 19 cM); and for AVP transcript abundance on chromosome 7 (at 1 cM), chromosome 12 (at 13 cM), and chromosome 13 (at 45 cM). The transcript abundance QTL were not linked to their respective structural genes. Interval mapping on chromosome 7 reveals substantial overlap between QTL that control AVP and Crf-R1 transcript abundance and on chromosome 12 for QTL that control CRF and Crf-R1, which may indicate loci that coordinate regulation of the CRF system. There are QTL for all four targets on chromosome 12. There are a number of neurodevelopmental genes in very close proximity to the transcript abundance QTL that are potential candidate genes.
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Doan-Nhu, Hai, Tam-Vinh Nguyen, Hoang Do-Huu, Joseph P. Montoya, and Lam Nguyen-Ngoc. "Copepods key traits in diverse habitats of tropical waters." Journal of Plankton Research 44, no. 1 (January 2022): 158–74. http://dx.doi.org/10.1093/plankt/fbab088.
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Abstract Copepods are the dominant marine zooplankton and perform important functions in the marine food web. However, copepod traits have not been studied in many waters. We studied the copepod community under influence of the Mekong River and the Southern Vietnamese coastal upwelling, based on their functional traits, during the southwest monsoon period in 2016. Fourteen trait categories of four key functional traits (trophic-groups, feeding-types, reproductive-strategies and diel migration) of copepod data were analyzed to investigate how environmental gradients impact on their distribution and abundance among the four defined habitats: Mekong River (MKW), upwelling (UpW), nearshore (OnSW) and offshore waters (OSW). There were seven functional groups identified in the study waters based on multiple correspondence analysis of distribution, abundance and traits of 139 copepod species. Herbivorous, current-feeding and sac-spawning copepods were dominant in all habitats with the highest abundance in OSW. Specifically, herbivorous species dominated in MKW and UpW, whereas omnivorous species dominated in OnSW and OSW. Sac-spawners dominated in all habitats, but decreased from MKW and UpW to OnSW and lowest in OSW. Cruise feeders were 2-fold higher than ambush feeders in the UpW, but the opposite was observed in the other habitats. The results suggest that impacts of Mekong River and coastal upwelling led to distinctive copepod assemblages with specific functional traits.
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Wehner, Katja, Matthias Brandt, Andrea Hilpert, Nadja K. Simons, and Nico Blüthgen. "Little evidence for land-use filters on intraspecific trait variation in three arthropod groups." Web Ecology 23, no. 1 (March 27, 2023): 35–49. http://dx.doi.org/10.5194/we-23-35-2023.
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Abstract. Declines in species richness and abundance of insects over the last decades are often driven by anthropogenic land use and can have severe consequences for ecosystem functioning. Many studies investigated the effects of land-use intensification on the distribution of phenotypic traits across species at the community level, often with mixed results. However, biotic and abiotic environmental filters and potential selection act on individuals within each species, i.e., at the species' population level, and thus drive the extent of intraspecific phenotypic variation. Here, we compare the morphological trait variation within selected species of dung beetles, bees and grasshoppers and link this variation to land-use intensity in forests and grasslands. Selected traits included absolute body size measures and relative leg, wing or eye size, or shape and are often interpreted as “functional traits” in the context of specific ecological responses or effects. We predicted that trait variability among individuals of arthropod species is reduced in intensively used ecosystems (with pronounced environmental filtering) compared to low-intensity ones, particularly for arthropod species that were more abundant in intensively used sites (“land-use winners” compared to “losers”). In general, only few effects of land-use intensity on trait variation were found showing a decreasing variation with increasing land-use intensity in forests but an increasing variation in grasslands. Although many studies confirmed strong land-use impacts on species composition, diversity and trait distribution, including evidence from the same land-use gradients, we were not able to confirm consistent effects at the intraspecific level. However, the choice of which traits are included in analyses and the linkage between phenotypic variation and genetic variability can strongly influence the conclusions drawn on ecological processes. Therefore, we suggest extending the use of intraspecific trait variation on other, more specific response or effect traits and a broader range of species in future studies.
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Roberts, Wade R., Adam M. Siepielski, and Andrew J. Alverson. "Diatom abundance in the polar oceans is predicted by genome size." PLOS Biology 22, no. 8 (August 8, 2024): e3002733. http://dx.doi.org/10.1371/journal.pbio.3002733.
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A principal goal in ecology is to identify the determinants of species abundances in nature. Body size has emerged as a fundamental and repeatable predictor of abundance, with smaller organisms occurring in greater numbers than larger ones. A biogeographic component, known as Bergmann’s rule, describes the preponderance, across taxonomic groups, of larger-bodied organisms in colder areas. Although undeniably important, the extent to which body size is the key trait underlying these patterns is unclear. We explored these questions in diatoms, unicellular algae of global importance for their roles in carbon fixation and energy flow through marine food webs. Using a phylogenomic dataset from a single lineage with worldwide distribution, we found that body size (cell volume) was strongly correlated with genome size, which varied by 50-fold across species and was driven by differences in the amount of repetitive DNA. However, directional models identified temperature and genome size, not cell size, as having the greatest influence on maximum population growth rate. A global metabarcoding dataset further identified genome size as a strong predictor of species abundance in the ocean, but only in colder regions at high and low latitudes where diatoms with large genomes dominated, a pattern consistent with Bergmann’s rule. Although species abundances are shaped by myriad interacting abiotic and biotic factors, genome size alone was a remarkably strong predictor of abundance. Taken together, these results highlight the cascading cellular and ecological consequences of macroevolutionary changes in an emergent trait, genome size, one of the most fundamental and irreducible properties of an organism.
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Easson, Cole G., Kenan O. Matterson, Christopher J. Freeman, Stephanie K. Archer, and Robert W. Thacker. "Variation in species diversity and functional traits of sponge communities near human populations in Bocas del Toro, Panama." PeerJ 3 (November 5, 2015): e1385. http://dx.doi.org/10.7717/peerj.1385.
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Recent studies have renewed interest in sponge ecology by emphasizing the functional importance of sponges in a broad array of ecosystem services. Many critically important habitats occupied by sponges face chronic stressors that might lead to alterations in their diversity, relatedness, and functional attributes. We addressed whether proximity to human activity might be a significant factor in structuring sponge community composition, as well as potential functional roles, by monitoring sponge diversity and abundance at two structurally similar sites that vary in distance to areas of high coastal development in Bocas Del Toro, Panama. We surveyed sponge communities at each site using belt transects and differences between two sites were compared using the following variables: (1) sponge species richness, Shannon diversity, and inverse Simpson’s diversity; (2) phylogenetic diversity; (3) taxonomic and phylogenetic beta diversity; (4) trait diversity and dissimilarity; and (5) phylogenetic and trait patterns in community structure. We observed significantly higher sponge diversity at Punta Caracol, the site most distant from human development (∼5 km). Although phylogenetic diversity was lower at Saigon Bay, the site adjacent to a large village including many houses, businesses, and an airport, the sites did not exhibit significantly different patterns of phylogenetic relatedness in species composition. However, each site had a distinct taxonomic and phylogenetic composition (beta diversity). In addition, the sponge community at Saigon included a higher relative abundance of sponges with high microbial abundance and high chlorophyllaconcentration, whereas the community at Punta Caracol had a more even distribution of these traits, yielding a significant difference in functional trait diversity between sites. These results suggest that lower diversity and potentially altered community function might be associated with proximity to human populations. This study highlights the importance of evaluating functional traits and phylogenetic diversity in addition to common diversity metrics when assessing potential environmental impacts on benthic communities.
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Schulze, Torsten, Ulrich Baade, Hendrik Dörner, Reiner Eckmann, Susanne S. Haertel-Borer, Franz Hölker, and Thomas Mehner. "Response of the residential piscivorous fish community to introduction of a new predator type in a mesotrophic lake." Canadian Journal of Fisheries and Aquatic Sciences 63, no. 10 (October 1, 2006): 2202–12. http://dx.doi.org/10.1139/f06-099.
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Although the effects of introduced predators on prey populations in aquatic ecosystems have been studied frequently, less is known about the interactions between predators. We performed a whole-lake experiment by stocking a non-native top predator (pikeperch (Sander lucioperca)) to two residential piscivores (Eurasian perch (Perca fluviatilis) and northern pike (Esox lucius)). By analyzing spatial distribution, diet composition, growth, and consumption rates of the piscivores before and after pikeperch introduction, we tested how both density-dependent and trait-mediated responses affected interactions between the three predators. Total piscivore biomass increased 1.5 times and annual consumption by the piscivores increased 1.7 times after stocking, attributable to the stocked pikeperch and increased northern pike abundances. Abundance, distribution, and consumption data indicated that northern pike was hardly affected by pikeperch stocking and even increased its biomass, whereas piscivorous perch shifted its habitat use towards the littoral lake areas in response to competition with pikeperch. Furthermore, all piscivores increasingly fed on small perch. The forced habitat shift of piscivorous perch in combination with increased predation on small perch led to a decreased abundance of large perch, attributable to the compensatory effects of intraguild predation and cannibalism.
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Olán-González, Manuel, Patricia Briones-Fourzán, Enrique Lozano-Álvarez, Gilberto Acosta-González, and Lorenzo Alvarez-Filip. "Similar functional composition of fish assemblages despite contrasting levels of habitat degradation on shallow Caribbean coral reefs." PLOS ONE 18, no. 12 (December 27, 2023): e0295238. http://dx.doi.org/10.1371/journal.pone.0295238.
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Functional trait-based approaches provide an opportunity to assess how changes in habitat affect the structure of associated communities. Global analyses have found a similarity in the composition of reef fish functional traits despite differences in species richness, environmental regimes, and habitat components. These large-scale patterns raised the question of whether this same stability can be observed at smaller spatial scales. Here, we compared the fish trait composition and their functional diversity in two Caribbean shallow coral reefs with contrasting levels of habitat degradation: Limones (>30% cover), constituted mainly by colonies of Acropora palmata and Bonanza, a reef with extensive areas of dead Acropora structures, dominated by algae. To characterize the functional structure of fishes on each reef, we calculated the community-weighted mean trait values (CWM), functional richness, functional evenness, functional dispersion, and functional originality. Despite the differences in habitat quality, reefs exhibited a similar proportion and common structure on fish functional traits. Functional richness and functional evenness differed significantly, but functional dispersion and functional originality did not show differences between reefs. The greater niche complexity driven by the high availability of microhabitats provided by A. palmata may explain the higher functional richness in Limones, whereas the reef degradation in Bonanza may contribute to a higher functional evenness because of a similar distribution of abundance per fish trait combinations. Our results suggest that widespread degradation on Caribbean reefs has limited the type, variety, and range of traits, which could lead to a functional homogenization of fish communities even at local scales.
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O'Meara, Brian C., Stacey D. Smith, W. Scott Armbruster, Lawrence D. Harder, Christopher R. Hardy, Lena C. Hileman, Larry Hufford, et al. "Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity." Proceedings of the Royal Society B: Biological Sciences 283, no. 1830 (May 11, 2016): 20152304. http://dx.doi.org/10.1098/rspb.2015.2304.
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Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction) and non-equilibrium dynamics on the evolutionary history of angiosperms, a clade well known for the abundance of some trait combinations and the rarity of others. Our analysis reveals that three character states (corolla present, bilateral symmetry, reduced stamen number) act synergistically as a key innovation, doubling diversification rates for lineages in which this combination occurs. However, this combination is currently less common than predicted at equilibrium because the individual characters evolve infrequently. Simulations suggest that angiosperms will remain far from the equilibrium frequencies of character states well into the future. Such non-equilibrium dynamics may be common when major innovations evolve rarely, allowing lineages with ancestral forms to persist, and even outnumber those with diversification-enhancing states, for tens of millions of years.
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Millington, Rebecca, Peter M. Cox, Jonathan R. Moore, and Gabriel Yvon-Durocher. "Modelling ecosystem adaptation and dangerous rates of global warming." Emerging Topics in Life Sciences 3, no. 2 (April 25, 2019): 221–31. http://dx.doi.org/10.1042/etls20180113.
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Abstract We are in a period of relatively rapid climate change. This poses challenges for individual species and threatens the ecosystem services that humanity relies upon. Temperature is a key stressor. In a warming climate, individual organisms may be able to shift their thermal optima through phenotypic plasticity. However, such plasticity is unlikely to be sufficient over the coming centuries. Resilience to warming will also depend on how fast the distribution of traits that define a species can adapt through other methods, in particular through redistribution of the abundance of variants within the population and through genetic evolution. In this paper, we use a simple theoretical ‘trait diffusion’ model to explore how the resilience of a given species to climate change depends on the initial trait diversity (biodiversity), the trait diffusion rate (mutation rate), and the lifetime of the organism. We estimate theoretical dangerous rates of continuous global warming that would exceed the ability of a species to adapt through trait diffusion, and therefore lead to a collapse in the overall productivity of the species. As the rate of adaptation through intraspecies competition and genetic evolution decreases with species lifetime, we find critical rates of change that also depend fundamentally on lifetime. Dangerous rates of warming vary from 1°C per lifetime (at low trait diffusion rate) to 8°C per lifetime (at high trait diffusion rate). We conclude that rapid climate change is liable to favour short-lived organisms (e.g. microbes) rather than longer-lived organisms (e.g. trees).
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López-Aguirre, Camilo, and Jairo Pérez-Torres. "Asimetría cráneo-mandibular de Artibeus lituratus (Chiroptera, Phyllostomidae) en Colombia." Universitas Scientiarum 20, no. 1 (October 10, 2014): 141. http://dx.doi.org/10.11144/javeriana.sc20-1.acal.
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Analyzing asymmetry in species associated with disturbed environments enables the evaluation of the morphological plasticity of generalistic species and the different evolutionary responses of sexes or populations to environmental or genetic stress. This report is a study of the cranial and mandibular asymmetry of Colombian Artibeus lituratus. This species has a wide distribution and high abundance, but its morphological plasticity remains uncertain. We characterized its presence, fluctuating asymmetry, directional asymmetry and antisymmetry by measuring 11 craneometric traits in 146 adults from different localities. Fluctuating asymmetry was present in all traits; directional asymmetry and antisymmetry in three; and no measurement error in any trait. Females showed more fluctuating asymmetry in the splachnocranium and males in the neurocranium. Traits with functional importance while biting had lower levels of asymmetry and higher similarity. Traits with antisymmetry did not show association while traits with directional asymmetry showed mandibular association. We discuss the relation between the presence of cranial and mandibular asymmetry, with the functional similarity of different traits.
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Armenteros, Maickel, and Alexei Ruiz-Abierno. "Body size distribution of free-living marine nematodes from a Caribbean coral reef." Nematology 17, no. 10 (2015): 1153–64. http://dx.doi.org/10.1163/15685411-00002930.
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Body size is a fundamental property of organisms but its distribution is almost unknown for marine nematodes. We measured the length and width of 7446 nematodes of 186 species to describe their morphological landscape and the relationship between abundance and body size. The body shape has a bimodal distribution with two morphotypes, suggesting adaptations to lifestyle. In fine sediments (seagrass bed), slender nematodes dominated, whereas sandy sediments had mostly stout nematodes but also slender forms. Seaweed turf from hard bottom substrates may favour mostly slender nematodes, whereas dead coral harbours both morphotypes, probably as a result of high heterogeneity of the substrate. The size spectra of abundance vs mass class shows a negative exponential relationship, suggesting that the energetic equivalence hypothesis holds for nematodes. The shape and position of the size spectra depended on the type of habitat. Body size is an important organismal trait that offers valuable information for disentangling ecological patterns in Nematoda.
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Chanam, Joyshree, Srinivasan Kasinathan, Gautam K. Pramanik, Amaraja Jagdeesh, Kanchan A. Joshi, and Renee M. Borges. "Context dependency of rewards and services in an Indian ant–plant interaction: southern sites favour the mutualism between plants and ants." Journal of Tropical Ecology 30, no. 3 (April 22, 2014): 219–29. http://dx.doi.org/10.1017/s026646741400011x.
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Abstract:Protection-based ant–plant mutualisms may vary in strength due to differences in ant rewards, abundance of protective ants and herbivory pressure. We investigated geographical and temporal variation in host plant traits and herbivory pressure at five sites spanning the distribution range of the myrmecophyteHumboldtia brunonis(Fabaceae) in the Indian Western Ghats. Southern sites had, on average, 2.4 times greater abundance of domatia-bearing individuals, 1.6 times greater extrafloral nectary numbers per leaf, 1.2 times larger extrafloral nectary sizes, 2.2 times greater extrafloral nectar (EFN) volumes and a two-fold increase in total amino acid and total sugar concentrations in EFN compared with northern sites. A strong protection-based mutualism with ants occurred at only one southern site where herbivory was highest, suggesting that investments in attracting ants correlate with anti-herbivore benefits gained from the presence of protective ants. Our results confirm a temporally stable north–south gradient in myrmecophytic traits in this ant-plant as several of these traits were re-sampled after a 5-y interval. However, the chemical composition of EFN varied at both spatial and short-term temporal scales suggesting that only repeated measurements of rewards such as EFN can reveal the real spectrum of trait variation in an ant–plant mutualistic system.
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Bell, James R., Mark S. Taylor, Chris R. Shortall, Sue J. Welham, and Richard Harrington. "The trait and host plant ecology of aphids and their distribution and abundance in the United Kingdom." Global Ecology and Biogeography 21, no. 4 (June 14, 2011): 405–15. http://dx.doi.org/10.1111/j.1466-8238.2011.00685.x.
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Owusu, Kwabena, Micaela Kulesz, and Agostino Merico. "Extraction Behaviour and Income Inequalities Resulting from a Common Pool Resource Exploitation." Sustainability 11, no. 2 (January 21, 2019): 536. http://dx.doi.org/10.3390/su11020536.
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Using an experimental approach, we investigate income distribution among heterogeneous subjects exploiting a Common Pool Resource (CPR). The CPR experiments are conducted in continuous time and under different treatments, including combinations of communication and monitoring. While many studies have focused on how real-life income inequality affects cooperation and resource use among groups, here we examine the relationship between individuals’ cooperative traits, harvest inequalities, and institutional arrangements. We found that: (1) When combined with monitoring, communication decreases harvest inequality—that is, harvest is more equally distributed among individuals in all treatments; and (2) the cooperative trait of individuals significantly predicts harvest inequality. The relative proportion of non-cooperators and cooperators (i.e., the cooperative dependency ratio) drives the within-session harvest distribution—as the cooperative dependency ration increases, the income distribution becomes increasingly unequal, leading to a downward spiral of resource overexploitation and scarcity. Finally, our results suggest that harvest and income inequalities are contingent to resource abundance, because under this regime, non-cooperators exert the greatest amount effort—thus leading to resource scarcity and income inequalities.
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Ying, Rui, Fanny M. Monteiro, Jamie D. Wilson, and Daniela N. Schmidt. "ForamEcoGEnIE 2.0: incorporating symbiosis and spine traits into a trait-based global planktic foraminiferal model." Geoscientific Model Development 16, no. 3 (February 2, 2023): 813–32. http://dx.doi.org/10.5194/gmd-16-813-2023.
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Abstract. Planktic foraminifera are major marine calcifiers in the modern ocean, regulating the marine inorganic carbon pump, and generating marine fossil archives of past climate change. The foraminifera contain ecogroups with and without spines and algal symbionts, creating functional trait diversity which expands their ecological niches. Here, we incorporate symbiosis and spine traits into the symbiont-barren non-spinose foraminifer functional type in EcoGEnIE to represent all the extant foraminifera species. We calibrated the modelled new traits using Latin hypercube sampling (LHS) and identified the optimal model parameters from an ensemble of 1200 runs compared with global observations from core-top sediment samples, sediment traps, and plankton nets. The model successfully describes the global distribution and seasonal abundance variation of the four major foraminiferal functional groups. The model reproduces the dominance of the symbiont-obligate group in subtropical gyres and of the symbiont-barren types in the productive subpolar oceans. Global annual mean biomass and foraminifer-derived carbon export rate are correctly predicted compared to data, with biomass ranging from 0.001 to 0.010 mmol C m−3 and organic carbon export 0.002–0.031 mmol C m−2 d−1. The model captures the seasonal peak time of biomass and organic carbon export but struggles to reproduce the amplitude of both in productive areas. The sparseness and uneven distribution of observations and the model's limitation in upwelling regions likely contribute to this discrepancy. Our model overcomes the lack of major groups in the previous ForamEcoGEnIE 1.0 version and offers the potential to explore foraminiferal ecology dynamics and its impact on biogeochemistry in modern, future, and paleogeographic environments.
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Cheng, Bixuan, Chao Yu, Heling Fu, Lijun Zhou, Le Luo, Huitang Pan, and Qixiang Zhang. "Evaluation of the morphological diversity of tea roses (Rosa x odorata) based on phenotypic traits." Plant Genetic Resources: Characterization and Utilization 18, no. 3 (June 2020): 149–58. http://dx.doi.org/10.1017/s1479262120000179.
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AbstractRosa x odorata (sect. Chinenses, Rosaceae) is an important species distributed only in Yunnan Province, China. There is an abundance of wild variation within the species. Using 22 germplasm resources collected from the wild, as well as R. chinensis var. spontanea, R. chinensis ‘Old Blush’ and R. lucidissima, this study involved morphological variation analysis, inter-trait correlation analysis, principal component analysis and clustering analysis based on 16 morphological traits. This study identified a high degree of morphological diversity in R. x odorata germplasm resources and the variation coefficients had a distribution range from 18.00 to 184.04%. The flower colour had the highest degree of variation, while leaflet length/width had the lowest degree of variation. Inter-trait correlation analysis revealed that there was an extremely significant positive correlation between leaflet length and leaflet width. There was also a significant positive correlation between the number of petals and duration of blooming, and the L* and a* values of flower colour were significantly negatively correlated. Principal component analysis screened five principal components with the highest cumulative contribution rate (81.679%) to population variance. Among the 16 morphological traits, style length, sepal width, flower diameter, flower colour, leaflet length and leaflet width were important indices that influenced the morphology of R. x odorata. This study offers guidance for the further development and utilization of R. x odorata germplasm resources.
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Liu, Fei, Fangze Zi, Xinyue Wang, Honghui Zeng, Bin Huo, Chengxin Wang, Jianmin Ge, Shengao Chen, and Baoqiang Wang. "Assessing the Impact of Anthropic Pressures on Aquatic Macroinvertebrates: A Functional Trait Approach in the Irtysh River Watershed." Biology 12, no. 10 (October 8, 2023): 1315. http://dx.doi.org/10.3390/biology12101315.
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Little is known about how changes in the biodiversity and functional traits of macroinvertebrates in rivers respond to the responses of anthropic pressures and their driving factors. Macroinvertebrates were sampled at 17 sites in the Irtysh River Basin and classified macroinvertebrates into 10 traits and 38 categories between May and August 2022. Then, we performed R-mode linked to Q-mode (RLQ) analysis and calculated functional richness, evenness, divergence, and Rao’s quadratic entropy (RaoQ) for each site and community-weighted means for each trait category. Our results indicated that there were pronounced alterations in species variability in the urban region. Functional divergence indicated fierce competition among species and considerable niche overlap in the urban region. Functional evenness indicated that species abundance distribution and interspecific functional distance were not uniform in the urban region. Functional richness indicated that the urban region was the strongest region in terms of niche occupation, resource utilization, and buffering capacity for environmental fluctuations. Rao’s quadratic entropy showed that the trait difference of macroinvertebrates was the largest in all regions, which was caused by the gradient environmental difference. Research has revealed that urbanization significantly influences the evolutionary trajectory of macroinvertebrate fauna, culminating in an upsurge in pollution-tolerant species and a convergence of functional traits. We recommend strengthening the control of urban and industrial pollution and wise planning and management of land and water resources to mitigate the impact of anthropogenic destruction on habitat fragmentation in the Irtysh River Basin.
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VARGAS, RENZO R., FRANCISCO E. FONTÚRBEL, ELISA BONACORSO, and JAVIER A. SIMONETTI. "Variation in reproductive life-history traits of birds in fragmented habitats: a review and meta-analysis." Bird Conservation International 22, no. 4 (December 16, 2011): 462–67. http://dx.doi.org/10.1017/s0959270911000475.
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SummaryThe effects of habitat fragmentation on the distribution and abundance of birds is a well-researched topic but there is little information published in terms of how habitat fragmentation affects reproductive life history traits. We reviewed the available literature on this subject and found that only 8% of the 1,433 studies dealing with birds in fragmented habitat studied life history traits and only 1.3% provided appropriate data to perform statistics. We found no effect of fragmentation on clutch and brood size patterns. Those patterns did not change when corrected by phylogeny. However, there is a significant heterogeneity among species responses, thus data on large-bodied, ground-nesting, and precocial birds suggest an increasing response in brood size in fragmented habitats. Finally, our review shows that despite birds being the most studied vertebrate group, crucial information such as the effects of habitat fragmentation on life history traits is still scarce and insufficient, especially on species of conservation concern. Indeed, only one out of 15 species reviewed here was threatened. Studies on reproductive, behavioural and life history trait variation are urgently needed in order to advance conservation actions.
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Panzera, Francisco, Ángeles Cuadrado, Pablo Mora, Teresa Palomeque, Pedro Lorite, and Sebastián Pita. "Differential Spreading of Microsatellites in Holocentric Chromosomes of Chagas Disease Vectors: Genomic and Evolutionary Implications." Insects 14, no. 9 (September 19, 2023): 772. http://dx.doi.org/10.3390/insects14090772.
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This study focused on analyzing the distribution of microsatellites in holocentric chromosomes of the Triatominae subfamily, insect vectors of Chagas disease. We employed a non-denaturing FISH technique to determine the chromosomal distribution of sixteen microsatellites across twenty-five triatomine species, involving five genera from the two principal tribes: Triatomini and Rhodniini. Three main hybridization patterns were identified: strong signals in specific chromosomal regions, dispersed signals dependent on microsatellite abundance and the absence of signals in certain chromosomal regions or entire chromosomes. Significant variations in hybridization patterns were observed between Rhodniini and Triatomini species. Rhodniini species displayed weak and scattered hybridization signals, indicating a low abundance of microsatellites in their genomes. In contrast, Triatomini species exhibited diverse and abundant hybridization patterns, suggesting that microsatellites are a significant repetitive component in their genomes. One particularly interesting finding was the high abundance of GATA repeats, and to a lesser extent AG repeats, in the Y chromosome of all analyzed Triatomini species. In contrast, the Y chromosome of Rhodniini species did not show enrichment in GATA and AG repeats. This suggests that the richness of GATA repeats on the Y chromosome likely represents an ancestral trait specific to the Triatomini tribe. Furthermore, this information can be used to elucidate the evolutionary relationships between Triatomini and other groups of reduviids, contributing to the understanding of the subfamily’s origin. Overall, this study provides a comprehensive understanding of the composition and distribution of microsatellites within Triatominae genomes, shedding light on their significance in the evolutionary processes of these species.
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Cherniavskih, V. I., and T. N. Glubscheva. "About Some Features of the Ability of Flowering Specials Crocus reticulatus in Various Elements of the Mesorelief of Beams in the Southern of the Middle Russian Hill." Field Biologist Journal 2, no. 2 (June 30, 2020): 147–63. http://dx.doi.org/10.18413/2658-3453-2020-2-2-147-163.
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The article presents the results of a three-year study of two populations of Crocus reticulatus, in the conditions of the beams of the Veidelevsky district of the Belgorod region. We studied the abundance of flowering individuals (potentially reproductive abundance) of C. reticulatus in two model populations and their distribution in different elements of the beam mesorelief along the gradient: the upper part of the slope – the base of the slope – the bottom of the beam. Comprehensive stationary monitoring studies were carried out in 2018-2020. in key areas in accordance with the program and methodology of biogeocenotic studies by the method of randomized repetition with the allocation of organized factors: Factor A – «habitat» and Factor B – «gradient of the slope». The results of the variance analysis of the one-factor complex in some years showed that the influence of the «gradient of the slope» factor on the productive trait «the abundance of flowering individuals» in key plot N 1 ranged from 98.4 % in 2020 to 99.6 % in 2018, in the key plot N 2 - from 98.5 % in 2019 to 99.5 % in 2020. On average, over 3 years of research in key area No. 1, an abundance of 336.2 ind./100 m2 was observed at Cv = 179.6 % in the gradient of the slope. An abundance of 237.4 ind./100 m2 at Cv = 101.1 % along the gradient of the slope was noted at key area N 2. The maximum number of flowering individuals was noted in the narrow ecotone part of the transition of the slope to the bottom of the beam (transects I): in plot N 1 – 1,890 ind./100 m2, and in plot No 2 – 856.7 ind./100 m2. An analysis of the share of the influence of organized factors by the method of variance analysis of two-factor complexes on average for 2018-2019 showed that the factor B, “gradient of the slope”, h2x = 79.5 %, exerted the greatest influence on the resultant trait “abundance of flowering individuals”. The factor “habitat of the population” and the interaction of factors had a significantly smaller effect on the number of individuals – 1.2 and 17.0 %, respectively. It is concluded that the study of the potentially reproductive abundance of C. reticulatus in natural conditions can contribute to the process of creating narrow-local artificial populations with a number of specific features, including those useful from an economic point of view for introduction into culture and breeding.
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Shen, Xiaomeng, Lei Liu, Thu Tran, Qiang Ning, Manfei Li, Liangliang Huang, Ran Zhao, et al. "KRN5b regulates maize kernel row number through mediating phosphoinositol signalling." Plant Biotechnology Journal 22, no. 12 (September 20, 2024): 3427–41. http://dx.doi.org/10.1111/pbi.14463.
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SummaryKernel row number (KRN) is a major yield related trait for maize (Zea mays L.) and is also a major goal of breeders, as it can increase the number of kernels per plant. Thus, identifying new genetic factors involving in KRN formation may accelerate improving yield‐related traits genetically. We herein describe a new kernel number‐related gene (KRN5b) identified from KRN QTL qKRN5b and encoding an inositol polyphosphate 5‐phosphatase (5PTase). KRN5b has phosphatase activity towards PI(4,5)P2, PI(3,4,5)P3, and Ins(1,4,5)P3 in vitro. Knocking out KRN5b caused accumulation of PI(4,5)P2 and Ins(1,4,5)P3, resulting in disordered kernel rows and a decrease in the number of kernels and tassel branches. The introgression of the allele with higher expression abundance into different inbred lines could increase the ear weight of the inbred lines and the corresponding hybrids by 10.1%–12.2% via increasing KRN, with no adverse effects on other agronomic traits. Further analyses showed that KRN5b regulates inflorescence development through affecting the synthesis and distribution of hormones. Together, KRN5b contributes to spikelet pair meristem development through inositol phosphate and phosphatidylinositols, making it a selecting target for yield improvement.
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Krasnov, Boris R., Georgy I. Shenbrot, Elizabeth M. Warburton, Luther van der Mescht, Elena N. Surkova, Sergei G. Medvedev, Nadezhda Pechnikova, Natalia Ermolova, Boris K. Kotti, and Irina S. Khokhlova. "Species and site contributions toβ-diversity in fleas parasitic on the Palearctic small mammals: ecology, geography and host species composition matter the most." Parasitology 146, no. 5 (November 15, 2018): 653–61. http://dx.doi.org/10.1017/s0031182018001944.
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AbstractTheβ-diversity of fleas parasitic on small mammals in 45 regions of the Palearctic was partitioned into species [species contributions toβ-diversity (SCBD)] and site ( = assemblage) contributions [local contributions toβ-diversity (LCBD)]. We asked what are the factors affecting SCBD and LCBD and tested whether (a) variation in ecological, morphological, life history and geographic traits of fleas can predict SCBD and (b) variation in flea and host community metrics, off-host environmental factors, host species composition of flea assemblages can predict LCBD. We used spatial variables to describe geographic distribution of flea assemblages with various LCBD values. SCBD significantly increased with an increase in abundance and a decrease in phylogenetic host specificity of a flea as well as with size and latitude of its geographic range, but was not associated with any morphological/life history trait. LCBD of flea assemblages did not depend on either flea or host species richness or environmental predictors, but was significantly affected by compositional uniqueness ( = LCBD) of regional host assemblages and variables describing their species composition. In addition, variation in LCBD was also explained by broad-to-moderate-scale spatial variables. We conclude that SCBD of fleas could be predictedviatheir ecological and geographic traits, whereas LCBD of their assemblages could be predictedviahost composition.
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ANTIT, M., A. DAOULATLI, J. URRA, J. L. RUEDA, S. GOFAS, and C. SALAS. "Seasonality and trophic diversity in molluscan assemblages from the Bay of Tunis (southern Mediterranean Sea)." Mediterranean Marine Science 17, no. 3 (September 26, 2016): 692. http://dx.doi.org/10.12681/mms.1712.
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Soft bottom molluscan assemblages from the Bay of Tunis have been studied in order to analyse their seasonality and trophic diversity in relation to environmental variables. A total of 147 species of molluscs was identified, with gastropods displaying the highest species richness and bivalves the highest abundances, and including five non-indigenous species such as the dominant ectoparasite Polycerella emertoni. Carnivorous and scavenger gastropods were among the most frequent species, reflecting a diverse benthic community. Seasonal changes were significant, being more acute at 3-4 m than at 10-15 m depth, and were driven mainly by seawater temperature and percentage of organic matter in the sediment. The high affluence of tourists in summer was coincident with high decreases in species richness and abundance of molluscs, together with a strong siltation of the sediment. Nevertheless, most trophic groups remained and the trophic diversity was relatively high. Significant relationships were found between the index of trophic diversity and Shannon-Wiener diversity and evenness indices, suggesting that the identity of the species with its particular trophic trait, together with the good distribution of the individuals among the species (density) would be the drivers for the maintenance of the molluscan food web under environmental stress. The abundance of P. emertoni altered the trophic structure of the molluscan assemblage, with the ectoparasite trophic group reaching an unusual punctual higher dominance. Soft bottom molluscan assemblages of the Bay of Tunis should be taken into account in monitoring programs for anthropogenic impacts and non-indigenous species trends throughout the Mediterranean basin.
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Marazzi, Luca, Anson W. Mackay, Richard Mazebedi, and Vivienne J. Jones. "Assemblage Patterns of Microalgae along the Upstream to Downstream Gradient of the Okavango Delta: Abundance, Taxonomic Diversity, and Functional Diversity." Water 15, no. 15 (July 26, 2023): 2692. http://dx.doi.org/10.3390/w15152692.
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This study addresses the gap in understanding the diversity, species, and functional trait distribution of different algal groups that occur in the Okavango Delta (a near-pristine subtropical wetland in northwestern Botswana) across hydrological and habitat gradients. We systematically characterize the delta’s algal flora, addressing the gap left by previous research that was limited to single algal groups (e.g., diatoms) and/or only looking at upstream areas in the Okavango River basin. We analyzed 130 algal samples from 49 upstream and downstream sites with higher and lower flooding frequency, respectively, across a river-to-floodplain habitat gradient. Chlorophyta and Bacillariophyta dominated both abundance and taxon richness (>80%) of the total 494 taxa found from 49,158 algal units counted (cells, colonies, coenobia, and filaments). Smaller algae were more abundant in downstream floodplains than in upstream channels and lagoons. Motile and siliceous algae were much more abundant than non-motile, nitrogen fixing, and phagotrophic algae. The frequency of these traits was associated more with flooding frequency than habitat type. The highest algal richness and diversity were found downstream, where shallow floodplain ecosystems with seasonally fluctuating water depths offer greater habitat heterogeneity, and macronutrients are resuspended. The increasing threats from upstream water abstraction plans, fracking, and climate change require enhanced protection and monitoring of the Okavango Delta’s natural annual flood-pulse to maintain the high species and functional diversity of this unique wetland’s microalgae.
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Vrbanec, Lara, Vanja Matijević, and Anja Guenther. "Enhanced problem-solving ability as an adaptation to urban environments in house mice." Proceedings of the Royal Society B: Biological Sciences 288, no. 1945 (February 17, 2021): 20202504. http://dx.doi.org/10.1098/rspb.2020.2504.
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Humans have a large impact on the distribution and abundance of animal species worldwide. The ecological effects of human-altered environments are being increasingly recognized and understood, but their effects on evolution are largely unknown. Enhanced cognitive abilities and the ability to innovate have been suggested as crucial traits for thriving in human-altered habitats. We tested if house mice ( Mus musculus ) subspecies have evolved enhanced innovative problem-solving abilities throughout their commensal lives with humans. The time that subspecies lived commensally with humans ranges between approximately 3000 years to more than 11 000 years, thus providing an excellent example of human–animal coexistence. In addition, we tested whether differences in problem-solving were mediated by differences in object and place exploration, motivation, persistence or inhibitory control. We found that populations of subspecies living commensally the longest excelled in problem-solving across seven food-extraction tasks over subspecies living commensally short or intermediate times. These differences were not mediated by exploration, motivation, persistence or inhibitory control suggesting that subspecies have evolved better cognitive abilities when living commensally in urban environments. This suggests that the ability to problem-solve may be an important trait promoting prosperity in human-altered environments.
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Bladon, Andrew J., Paul F. Donald, Nigel J. Collar, Jarso Denge, Galgalo Dadacha, Mengistu Wondafrash, and Rhys E. Green. "Climatic change and extinction risk of two globally threatened Ethiopian endemic bird species." PLOS ONE 16, no. 5 (May 19, 2021): e0249633. http://dx.doi.org/10.1371/journal.pone.0249633.
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Climate change is having profound effects on the distributions of species globally. Trait-based assessments predict that specialist and range-restricted species are among those most likely to be at risk of extinction from such changes. Understanding individual species’ responses to climate change is therefore critical for informing conservation planning. We use an established Species Distribution Modelling (SDM) protocol to describe the curious range-restriction of the globally threatened White-tailed Swallow (Hirundo megaensis) to a small area in southern Ethiopia. We find that, across a range of modelling approaches, the distribution of this species is well described by two climatic variables, maximum temperature and dry season precipitation. These same two variables have been previously found to limit the distribution of the unrelated but closely sympatric Ethiopian Bush-crow (Zavattariornis stresemanni). We project the future climatic suitability for both species under a range of climate scenarios and modelling approaches. Both species are at severe risk of extinction within the next half century, as the climate in 68–84% (for the swallow) and 90–100% (for the bush-crow) of their current ranges is predicted to become unsuitable. Intensive conservation measures, such as assisted migration and captive-breeding, may be the only options available to safeguard these two species. Their projected disappearance in the wild offers an opportunity to test the reliability of SDMs for predicting the fate of wild species. Monitoring future changes in the distribution and abundance of the bush-crow is particularly tractable because its nests are conspicuous and visible over large distances.
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Sherow, Brie A., Emma L. Johnston, and Graeme F. Clark. "Piers are hotspots for benthic marine debris in an urbanised estuary." PLOS ONE 17, no. 12 (December 28, 2022): e0274512. http://dx.doi.org/10.1371/journal.pone.0274512.
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Records of anthropogenic marine debris and the threats it poses are increasing worldwide, yet we know relatively little about the distribution of benthic debris. The seafloor is the final destination for a large proportion of debris due to the degradation and sinking of items. A more detailed understanding of debris distributions in hotspots such as urbanised estuaries can help decision makers target management and remediation activities. We selected sites frequented by fishers and boaters in Sydney Harbour, an urbanised estuary, to investigate the impacts of recreational activities on debris abundance. The aim of this study was to examine variation in macro debris (>5mm in diameter) type and abundance at two habitat types (piers and non-piers). We chose five locations at various distances from the estuary mouth. In each location SCUBA teams performed fixed transects at two sites, one under a pier and one over nearby soft-sediment habitat. Debris was recovered by the divers and brought to the surface for classification and disposal. Surveys were repeated multiple times at each location between November 2019 and February 2020, recording a total of 2803 debris items over 36 survey events. Overall, piers had more than ten times the debris abundance of soft-sediment sites, and much higher proportion of debris types related to recreational fishing. Over half of the debris items in this study were plastic (65%), and approximately 70% of the total debris was classified as related to recreational fishing. This trait was most prominent in debris at sites closest to the estuary mouth, likely reflecting increased fishing activity in this area. This study indicates that policy makers and community groups in urbanised estuaries should focus monitoring, reduction, and remediation efforts near artificial structures such as piers, and that public awareness campaigns should target the behaviour of recreational users of these structures.
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Smith, Joshua G., Joseph Tomoleoni, Michelle Staedler, Sophia Lyon, Jessica Fujii, and M. Tim Tinker. "Behavioral responses across a mosaic of ecosystem states restructure a sea otter–urchin trophic cascade." Proceedings of the National Academy of Sciences 118, no. 11 (March 8, 2021): e2012493118. http://dx.doi.org/10.1073/pnas.2012493118.
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Consumer and predator foraging behavior can impart profound trait-mediated constraints on community regulation that scale up to influence the structure and stability of ecosystems. Here, we demonstrate how the behavioral response of an apex predator to changes in prey behavior and condition can dramatically alter the role and relative contribution of top-down forcing, depending on the spatial organization of ecosystem states. In 2014, a rapid and dramatic decline in the abundance of a mesopredator (Pycnopodia helianthoides) and primary producer (Macrocystis pyrifera) coincided with a fundamental change in purple sea urchin (Strongylocentrotus purpuratus) foraging behavior and condition, resulting in a spatial mosaic of kelp forests interspersed with patches of sea urchin barrens. We show that this mosaic of adjacent alternative ecosystem states led to an increase in the number of sea otters (Enhydra lutris nereis) specializing on urchin prey, a population-level increase in urchin consumption, and an increase in sea otter survivorship. We further show that the spatial distribution of sea otter foraging efforts for urchin prey was not directly linked to high prey density but rather was predicted by the distribution of energetically profitable prey. Therefore, we infer that spatially explicit sea otter foraging enhances the resistance of remnant forests to overgrazing but does not directly contribute to the resilience (recovery) of forests. These results highlight the role of consumer and predator trait-mediated responses to resource mosaics that are common throughout natural ecosystems and enhance understanding of reciprocal feedbacks between top-down and bottom-up forcing on the regional stability of ecosystems.
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Plue, J., J. L. Dupouey, K. Verheyen, and M. Hermy. "Forest seed banks along an intensity gradient of ancient agriculture." Seed Science Research 19, no. 2 (June 2009): 103–14. http://dx.doi.org/10.1017/s0960258509306662.
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AbstractRecently, forest seed banks were proven to not only reflect former (decades-old) but also ancient (centuries-old) land use. Yet, as land-use intensity determines the magnitude of seed-bank changes in recent forests, this study aims to identify whether an ancient land-use gradient would also be reflected in the seed bank. On a forested 1600-year-old archaeological site, five different land-use intensities were mapped and sampled. Apart from seed density, species richness and composition, functional seed-bank types, defined by nine seed-bank-related plant traits, were related to the land-use intensity gradient. The land-use gradient from gardens to undisturbed sites was still clearly reflected in the soil seed bank. Six emergent functional seed-bank types, characterized by specific plant traits, changed significantly in abundance, parallel to the land-use gradient. In particular, dispersal agent (and related traits) proved an important explanatory trait of present (functional) seed-bank patterns. Poor dispersers (large and heavy seeds) were not found in the intensively used areas, contrary to animal-dispersed species. Wind-dispersers may have been inhibited in the extension of their distribution by recruitment bottlenecks (low seed production) and/or competitive exclusion. Additionally, the agricultural land-use probably introduced ruderal species into the seed bank of the most intensively used areas, yielding a simultaneous increase in vegetation–seed-bank dissimilarity with land-use intensity, eliminating present vegetation as a driver behind the differences over the seed-bank gradient. We conclude by arguing how coppice-with-standards management possibly maintained the seed-bank gradient.
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Gruber, Andreas, Gerhard Wieser, Marion Fink, and Walter Oberhuber. "Impact of Environmental Conditions on Wood Anatomical Traits of Green Alder (Alnus alnobetula) at the Alpine Treeline." Forests 15, no. 1 (December 21, 2023): 24. http://dx.doi.org/10.3390/f15010024.
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Due to land use change, green alder (Alnus alnobetula), formerly restricted to moist slopes, is now expanding to drier sun-exposed sites at the alpine treeline. The highly productive shrub is forming closed thickets, establishing nitrogen-saturated species in poor shrublands. To evaluate wood anatomical adaptations to changing environmental conditions, we analyzed vessel characteristics (mean vessel area, MVA; vessel density, VD; and theoretic conductive area, TCA) and axial parenchyma abundance, as well as their distribution in the annual ring at a moist north-facing and a dry south-facing site at the alpine treeline on Mt. Patscherkofel (Central European Alps, Austria). Results revealed that lower soil water availability and enhanced evaporative demand did not affect MVA while VD and TCA were significantly reduced at the dry south-facing site. This suggests that in green alder, vessel size is a static trait whereas vessel number isresponds plastic. Limited water availability also triggered a significant increase in axial parenchyma, confirming the important role of xylem parenchyma in water relations. Harsh environmental conditions at the distributional limit of green alder may have affected xylogenesis, leading to a near semi-ring-porous distribution of vessels and an accumulation of parenchyma in the late growing season. We conclude that in a warmer and drier climate, growth limitation and physiological stress may set limits to the distribution of Alnus alnobetula at drought-prone sites in the alpine treeline ecotone.
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Tchkonia, Tamara, Nino Giorgadze, Tamar Pirtskhalava, Yourka Tchoukalova, Iordanes Karagiannides, R. Armour Forse, Matthew DePonte, et al. "Fat depot origin affects adipogenesis in primary cultured and cloned human preadipocytes." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 282, no. 5 (May 1, 2002): R1286—R1296. http://dx.doi.org/10.1152/ajpregu.00653.2001.
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Fat distribution varies among individuals with similar body fat content. Innate differences in adipose cell characteristics may contribute because lipid accumulation and lipogenic enzyme activities vary among preadipocytes cultured from different fat depots. We determined expression of the adipogenic transcription factors peroxisome proliferator activated receptor-γ (PPAR-γ) and CCAAT/enhancer binding protein-α (C/EBP-α) and their targets in abdominal subcutaneous, mesenteric, and omental preadipocytes cultured in parallel from obese subjects. Subcutaneous preadipocytes, which had the highest lipid accumulation, glycerol-3-phosphate dehydrogenase (G3PD) activity, and adipocyte fatty acid binding protein (aP2) abundance, had highest PPAR-γ and C/EBP-α expression. Levels were intermediate in mesenteric and lowest in omental preadipocytes. Overexpression of C/EBP-α in transfected omental preadipocytes enhanced differentiation. The proportion of differentiated cells in colonies derived from single subcutaneous preadipocytes was higher than in mesenteric or omental clones. Only cells that acquired lipid inclusions exhibited C/EBP-α upregulation, irrespective of depot origin. Thus regional variation in adipogenesis depends on differences at the level of transcription factor expression and is a trait conferred on daughter cells.
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Serrat, Alba, and Marta Muñoz. "Can the Life History Trait Divergence of Two Extremes of a Cold-Water Genus Distribution Offer Evidence for Their Vulnerability to Sea Warming?" Fishes 7, no. 4 (June 21, 2022): 143. http://dx.doi.org/10.3390/fishes7040143.
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Cold- and deep-water species such as Molva species show low resilience to anthropogenic pressures, and they become particularly vulnerable at the warm edges of their distribution. In this study, the poorly documented Mediterranean ling (Molva macrophthalma) population from the northwestern Mediterranean Sea was analysed. This area is considered a cul-de-sac in a sea-warming hotspot, where M. macrophthalma shows a low population health status and is experiencing a climate-related reduction in abundance. Several life-history traits (length at maturity, reproductive cycle, fecundity style, oocyte recruitment pattern, and breeding strategy) are here described for the first time to evaluate the reproductive performance (oocyte diameter and production) in relation to the fish condition status (the HSI and relative condition index). Additionally, the results are compared with those of a population of a similar species, the blue ling (Molva dypterygia), inhabiting the cool edge of its distribution, hypothesised to have a higher condition status. Our results indicate that M. macrophthalma is a capital breeder with restricted secondary growth recruitment and group-synchronous oocyte development. In relative terms, the stressed southern M. macrophthalma exhibited a worse condition, a lower investment in reproduction, a smaller size at maturity, larger but fewer primary growth oocytes, and a smaller size-standardized production of secondary growth oocytes than the northern M. dypterygia. Significant differences in the secondary growth oocyte recruitment were also found. These findings reinforce the environment’s role in shaping the reproductive potential and condition status. Altogether, this study suggests high sensitivity to anthropogenic pressures for both species, and, especially for Mediterranean ling, it shows the importance of introducing monitoring and conservation measures to ensure the sustainability of its populations.
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Brunialti, Giorgio, Paolo Giordani, Sonia Ravera, and Luisa Frati. "The Reproductive Strategy as an Important Trait for the Distribution of Lower-Trunk Epiphytic Lichens in Old-Growth vs. Non-Old Growth Forests." Forests 12, no. 1 (December 28, 2020): 27. http://dx.doi.org/10.3390/f12010027.
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(1) Research Highlights: The work studied the beta diversity patterns of epiphytic lichens as a function of their reproductive strategies in old-growth and non-old growth forests from the Mediterranean area. (2) Background and Objectives: The reproductive strategies of lichens can drive the dispersal and distribution of species assemblages in forest ecosystems. To further investigate this issue, we analyzed data on epiphytic lichen diversity collected from old-growth and non-old growth forest sites (36 plots) located in Cilento National Park (South Italy). Our working hypothesis was that the dispersal abilities due to the different reproductive strategies drove species beta diversity depending on forest age and continuity. We expected a high turnover for sexually reproducing species and high nestedness for vegetative ones. We also considered the relationship between forest continuity and beta diversity in terms of species rarity. (3) Materials and Methods: we used the Bray–Curtis index of dissimilarity to partition lichen diversity into two components of beta diversity for different subsets (type of forest, reproductive strategy, and species rarity). (4) Results: The two forest types shared most of the common species and did not show significant differences in alpha and gamma diversity. The turnover of specific abundance was the main component of beta diversity, and was significantly greater for sexually reproducing species as compared to vegetative ones. These latter species had also the least turnover and greater nestedness in old-growth forests. Rare species showed higher turnover than common ones. (5) Conclusions: Our results suggest that sexually reproducing lichen species always have high turnover, while vegetative species tend to form nested assemblages, especially in old-growth forests. The rarity level contributes to the species turnover in lichen communities. Contrary to what one might expect, the differences between old-growth and non-old growth forests are not strong.
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Nowicka, Malgorzata, and Mark D. Robinson. "DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics." F1000Research 5 (June 13, 2016): 1356. http://dx.doi.org/10.12688/f1000research.8900.1.
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There are many instances in genomics data analyses where measurements are made on a multivariate response. For example, alternative splicing can lead to multiple expressed isoforms from the same primary transcript. There are situations where the total abundance of gene expression does not change (e.g. between normal and disease state), but differences in the relative ratio of expressed isoforms may have significant phenotypic consequences or lead to prognostic capabilities. Similarly, knowledge of single nucleotide polymorphisms (SNPs) that affect splicing, so-called splicing quantitative trait loci (sQTL), will help to characterize the effects of genetic variation on gene expression. RNA sequencing (RNA-seq) has provided an attractive toolbox to carefully unravel alternative splicing outcomes and recently, fast and accurate methods for transcript quantification have become available. We propose a statistical framework based on the Dirichlet-multinomial distribution that can discover changes in isoform usage between conditions and SNPs that affect splicing outcome using these quantifications. The Dirichlet-multinomial model naturally accounts for the differential gene expression without losing information about overall gene abundance and by joint modeling of isoform expression, it has the capability to account for their correlated nature. The main challenge in this approach is to get robust estimates of model parameters with limited numbers of replicates. We approach this by sharing information and show that our method improves on existing approaches in terms of standard statistical performance metrics. The framework is applicable to other multivariate scenarios, such as Poly-A-seq or where beta-binomial models have been applied (e.g., differential DNA methylation). Our method is available as a Bioconductor R package called DRIMSeq.
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Lu, Li-Li, Bo-Han Jiao, Feng Qin, Gan Xie, Kai-Qing Lu, Jin-Feng Li, Bin Sun, et al. "Artemisia pollen dataset for exploring the potential ecological indicators in deep time." Earth System Science Data 14, no. 9 (September 2, 2022): 3961–95. http://dx.doi.org/10.5194/essd-14-3961-2022.
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Abstract. Artemisia, along with Chenopodiaceae, is the dominant component growing in the desert and dry grassland of the Northern Hemisphere. Artemisia pollen with its high productivity, wide distribution, and easy identification is usually regarded as an eco-indicator for assessing aridity and distinguishing grassland from desert vegetation in terms of the pollen relative abundance ratio of Chenopodiaceae/Artemisia (C/A). Nevertheless, divergent opinions on the degree of aridity evaluated by Artemisia pollen have been circulating in the palynological community for a long time. To solve the confusion, we first selected 36 species from nine clades and three outgroups of Artemisia based on the phylogenetic framework, which attempts to cover the maximum range of pollen morphological variation. Then, sampling, experiments, photography, and measurements were taken using standard methods. Here, we present pollen datasets containing 4018 original pollen photographs, 9360 pollen morphological trait measurements, information on 30 858 source plant occurrences, and corresponding environmental factors. Hierarchical cluster analysis on pollen morphological traits was carried out to subdivide Artemisia pollen into three types. When plotting the three pollen types of Artemisia onto the global terrestrial biomes, different pollen types of Artemisia were found to have different habitat ranges. These findings change the traditional concept of Artemisia being restricted to arid and semi-arid environments. The data framework that we designed is open and expandable for new pollen data of Artemisia worldwide. In the future, linking pollen morphology with habitat via these pollen datasets will create additional knowledge that will increase the resolution of the ecological environment in the geological past. The Artemisia pollen datasets are freely available at Zenodo (https://doi.org/10.5281/zenodo.6900308; Lu et al., 2022).
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Long, Richard A., and Farooq Azam. "Antagonistic Interactions among Marine Pelagic Bacteria." Applied and Environmental Microbiology 67, no. 11 (November 1, 2001): 4975–83. http://dx.doi.org/10.1128/aem.67.11.4975-4983.2001.
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ABSTRACT Recent studies suggest that bacterial abundance and species diversity in the ocean's water column are variable at the millimeter scale, apparently in response to the small-scale heterogeneity in the distribution of organic matter. We hypothesized that bacterium-bacterium antagonistic interactions may contribute to variations in community structure at the microscale. We examined each of the 86 isolates for their inhibition of growth of the remaining 85 isolates by the Burkholder agar diffusion assay. More than one-half of the isolates expressed antagonistic activity, and this trait was more common with particle-associated bacteria than with free-living bacteria. This was exemplified by members of the α subclass of the class Proteobacteria (α-proteobacteria), in which production of antagonistic molecules was dominated by attached bacteria. We found that γ-proteobacteria (members of the ordersAlteromonadales and Vibrionales) are the most prolific producers of inhibitory materials and also the most resilient to them, while members of the Bacteriodetes were the organisms that were least productive and most sensitive to antagonistic interactions. Widespread interspecies growth inhibition is consistent with the role of this phenomenon in structuring bacterial communities at the microscale. Furthermore, our results suggest that bacteria from pelagic marine particles may be an underutilized source of novel antibiotics.
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Šabić, Azra, and Nejc Jogan. "One year spread and insight into ecology of invasive Impatiens glandulifera in Ljubljansko barje area (Central Slovenia)." Acta Biologica Slovenica 65, no. 1 (July 1, 2022): 48–69. http://dx.doi.org/10.14720/abs.65.1.16030.
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Impatiens glandulifera Royle (Himalayan balsam) is an annual plant, native to humid parts of the Himalayas. Brought to Europe in the XIX century, it has since successfully naturalized and spread throughout the continent, becoming one of the best-known invasive plants. Even though it has been thoroughly studied by many authors, some aspects of its biology and ecology remain unclear and debatable, such as its spreading dynamics, negative impacts in invaded ecosystems and ecological adaptability regarding moisture, nutrients, and light. This 2019 field study from the Ljubljana Marsh (Slovenia) has proved that Himalayan balsam successfully develops under mesophilic conditions, where it easily compensates moderate deviations from its ecological optimum. The species thrives in riparian zones, out-competing native vegetation, trait shown as potentially the biggest negative impact of chosen species in this context. This study additionally gave us a different insight into - usually highly emphasized - dynamics of species’ spreading. Spreading was not either dependent on hydrochory or as drastic as mentioned in literary sources, giving it a secondary role in species’ invasiveness on the chosen area. Lastly, we proposed rough estimates of eradication expenses for given area, based on our field results of species’ abundance and distribution on chosen area.
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Bouzid, M., F. He, G. Schmitz, R. E. Häusler, A. P. M. Weber, T. Mettler-Altmann, and J. De Meaux. "Arabidopsis species deploy distinct strategies to cope with drought stress." Annals of Botany 124, no. 1 (January 19, 2019): 27–40. http://dx.doi.org/10.1093/aob/mcy237.
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Abstract Background and Aims Water limitation is an important determinant of the distribution, abundance and diversity of plant species. Yet, little is known about how the response to limiting water supply changes among closely related plant species with distinct ecological preferences. Comparison of the model annual species Arabidopsis thaliana with its close perennial relatives A. lyrata and A. halleri, can help disentangle the molecular and physiological changes contributing to tolerance and avoidance mechanisms, because these species must maintain tolerance and avoidance mechanisms to increase long-term survival, but they are exposed to different levels of water stress and competition in their natural habitat. Methods A dry-down experiment was conducted to mimic a period of missing precipitation. The covariation of a progressive decrease in soil water content (SWC) with various physiological and morphological plant traits across a set of representative genotypes in A. thaliana, A. lyrata and A. halleri was quantified. Transcriptome changes to soil dry-down were further monitored. Key Results The analysis of trait covariation demonstrates that the three species differ in the strategies they deploy to respond to drought stress. Arabidopsis thaliana showed a drought avoidance reaction but failed to survive wilting. Arabidopsis lyrata efficiently combined avoidance and tolerance mechanisms. In contrast, A. halleri showed some degree of tolerance to wilting but it did not seem to protect itself from the stress imposed by drought. Transcriptome data collected just before plant wilting and after recovery corroborated the phenotypic analysis, with A. lyrata and A. halleri showing a stronger activation of recovery- and stress-related genes, respectively. Conclusions The response of the three Arabidopsis species to soil dry-down reveals that they have evolved distinct strategies to face drought stress. These strategic differences are in agreement with the distinct ecological priorities of the stress-tolerant A. lyrata, the competitive A. halleri and the ruderal A. thaliana.
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Gogina, Mayya, Judith Rahel Renz, Stefan Forster, and Michael L. Zettler. "Benthic Macrofauna Community Bioirrigation Potential (BIPc): Regional Map and Utility Validation for the South-Western Baltic Sea." Biology 11, no. 7 (July 20, 2022): 1085. http://dx.doi.org/10.3390/biology11071085.
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Benthic community bioirrigation potential (BIPc), an index developed to quantify the anticipated capacity of macrofauna to influence the solute exchange at the sediment–water interface, was calculated for the south-western Baltic Sea. This index can be regarded as an effect trait that is useful for predicting ecosystem processes impacted by animal burrow ventilation. The special feature, and presumably an advantage, of BIPc, compared to alternative recently developed benthic macrofauna-based bioirrigation indices, lies in its ability to distinguish the taxa-specific score values between diffusion- and advection-dominated sediment systems. The usefulness of the BIPc index was compared against the estimates of the well-established community bioturbation potential index (BPc). The BIPc index displayed a moderately but significantly stronger correlation with estimates of irrigation rates derived from tracer experiments. Using a random forest machine learning approach and a number of available relevant environmental predictor layers, we have modelled and mapped the spatial differences in this ecosystem functioning expression. The key species contributing to bioirrigation potential in the study area were identified. The interannual variation in BIPc was assessed on a small exemplary dataset. The scores required to calculate the index, that were assigned to 120 taxa dominating abundance and biomass in the region, are provided for reuse. The utility, temporal variability and uncertainty of the distribution estimate are discussed.
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Messier, Julie, Antoine Becker‐Scarpitta, Yuanzhi Li, Cyrille Violle, and Mark Vellend. "Root and biomass allocation traits predict changes in plant species and communities over four decades of global change." Ecology, September 9, 2024. http://dx.doi.org/10.1002/ecy.4389.
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AbstractGlobal change is affecting the distribution and population dynamics of plant species across the planet, leading to trends such as shifts in distribution toward the poles and to higher elevations. Yet, we poorly understand why individual species respond differently to warming and other environmental changes, or how the trait composition of communities responds. Here we ask two questions regarding plant species and community changes over 42 years of global change in a temperate montane forest in Québec, Canada: (1) How did the trait composition, alpha diversity, and beta diversity of understory vascular plant communities change between 1970 and 2010, a period over which the region experienced 1.5°C of warming and changes in nitrogen deposition? (2) Can traits predict shifts in species elevation and abundance over this time period? For 46 understory vascular species, we locally measured six aboveground traits, and for 36 of those (not including shrubs), we also measured five belowground traits. Collectively, they capture leading dimensions of phenotypic variation that are associated with climatic and resource niches. At the community level, the trait composition of high‐elevation plots shifted, primarily for two root traits: specific root length decreased and rooting depth increased. The mean trait values of high‐elevation plots shifted over time toward values initially associated with low‐elevation plots. These changes led to trait homogenization across elevations. The community‐level shifts in traits mirrored the taxonomic shifts reported elsewhere for this site. At the species level, two of the three traits predicting changes in species elevation and abundance were belowground traits (low mycorrhizal fraction and shallow rooting). These findings highlight the importance of root traits, which, along with leaf mass fraction, were associated with shifts in distribution and abundance over four decades. Community‐level trait changes were largely similar across the elevational and temporal gradients. In contrast, traits typically associated with lower elevations at the community level did not predict differences among species in their shift in abundance or distribution, indicating a decoupling between species‐ and community‐level responses. Overall, changes were consistent with some influence of both climate warming and increased nitrogen availability.
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Green, Stephanie J., Cole B. Brookson, Natasha A. Hardy, and Larry B. Crowder. "Trait-based approaches to global change ecology: moving from description to prediction." Proceedings of the Royal Society B: Biological Sciences 289, no. 1971 (March 16, 2022). http://dx.doi.org/10.1098/rspb.2022.0071.
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Trait-based approaches are increasingly recognized as a tool for understanding ecosystem re-assembly and function under intensifying global change. Here we synthesize trait-based research globally ( n = 865 studies) to examine the contexts in which traits may be used for global change prediction. We find that exponential growth in the field over the last decade remains dominated by descriptive studies of terrestrial plant morphology, highlighting significant opportunities to expand trait-based thinking across systems and taxa. Very few studies (less than 3%) focus on predicting ecological effects of global change, mostly in the past 5 years and via singular traits that mediate abiotic limits on species distribution. Beyond organism size (the most examined trait), we identify over 2500 other morphological, physiological, behavioural and life-history traits known to mediate environmental filters of species' range and abundance as candidates for future predictive global change work. Though uncommon, spatially explicit process models—which mechanistically link traits to changes in organism distributions and abundance—are among the most promising frameworks for holistic global change prediction at scales relevant for conservation decision-making. Further progress towards trait-based forecasting requires addressing persistent barriers including (1) matching scales of multivariate trait and environment data to focal processes disrupted by global change, and (2) propagating variation in trait and environmental parameters throughout process model functions using simulation.
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Bouchard, Elise, Eric B. Searle, Pierre Drapeau, Jingjing Liang, Javier G. P. Gamarra, Meinrad Abegg, Giorgio Alberti, et al. "Global patterns and environmental drivers of forest functional composition." Global Ecology and Biogeography, December 26, 2023. http://dx.doi.org/10.1111/geb.13790.
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AbstractAimTo determine the relationships between the functional trait composition of forest communities and environmental gradients across scales and biomes and the role of species relative abundances in these relationships.LocationGlobal.Time periodRecent.Major taxa studiedTrees.MethodsWe integrated species abundance records from worldwide forest inventories and associated functional traits (wood density, specific leaf area and seed mass) to obtain a data set of 99,953 to 149,285 plots (depending on the trait) spanning all forested continents. We computed community‐weighted and unweighted means of trait values for each plot and related them to three broad environmental gradients and their interactions (energy availability, precipitation and soil properties) at two scales (global and biomes).ResultsOur models explained up to 60% of the variance in trait distribution. At global scale, the energy gradient had the strongest influence on traits. However, within‐biome models revealed different relationships among biomes. Notably, the functional composition of tropical forests was more influenced by precipitation and soil properties than energy availability, whereas temperate forests showed the opposite pattern. Depending on the trait studied, response to gradients was more variable and proportionally weaker in boreal forests. Community unweighted means were better predicted than weighted means for almost all models.Main conclusionsWorldwide, trees require a large amount of energy (following latitude) to produce dense wood and seeds, while leaves with large surface to weight ratios are concentrated in temperate forests. However, patterns of functional composition within‐biome differ from global patterns due to biome specificities such as the presence of conifers or unique combinations of climatic and soil properties. We recommend assessing the sensitivity of tree functional traits to environmental changes in their geographic context. Furthermore, at a given site, the distribution of tree functional traits appears to be driven more by species presence than species abundance.
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García Criado, Mariana, Isla H. Myers-Smith, Anne D. Bjorkman, Signe Normand, Anne Blach-Overgaard, Haydn J. D. Thomas, Anu Eskelinen, et al. "Plant traits poorly predict winner and loser shrub species in a warming tundra biome." Nature Communications 14, no. 1 (June 28, 2023). http://dx.doi.org/10.1038/s41467-023-39573-4.
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AbstractClimate change is leading to species redistributions. In the tundra biome, shrubs are generally expanding, but not all tundra shrub species will benefit from warming. Winner and loser species, and the characteristics that may determine success or failure, have not yet been fully identified. Here, we investigate whether past abundance changes, current range sizes and projected range shifts derived from species distribution models are related to plant trait values and intraspecific trait variation. We combined 17,921 trait records with observed past and modelled future distributions from 62 tundra shrub species across three continents. We found that species with greater variation in seed mass and specific leaf area had larger projected range shifts, and projected winner species had greater seed mass values. However, trait values and variation were not consistently related to current and projected ranges, nor to past abundance change. Overall, our findings indicate that abundance change and range shifts will not lead to directional modifications in shrub trait composition, since winner and loser species share relatively similar trait spaces.
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Lazzari, J., C. F. Sato, and D. A. Driscoll. "Traits influence reptile responses to fire in a fragmented agricultural landscape." Landscape Ecology, July 19, 2022. http://dx.doi.org/10.1007/s10980-022-01417-9.
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Abstract Context Habitat loss and fragmentation can interact with other threats, including altered fire regimes, and responses to these effects can be mediated by functional traits. Objectives To determine how richness and abundance of reptile trait groups respond to habitat fragmentation, patch isolation and fire. Methods We surveyed reptiles in 30 sites over 3 years. Sites in remnant patches in farmland were adjacent to a conservation park with either recently burnt or long-unburnt habitat. The remnant patches were stratified by distance from the reserve. Sites were spatially paired, and we experimentally burnt one of each pair in farmland. Trait groups included size, reproduction, habitat position, diet, and activity period. Results None of the trait groups benefited from experimental burns, while the burns reduced abundance of viviparous, small, and above-ground species. Species richness was lower in isolated sites than in sites close to the conservation park, while generalist trait groups appeared unaffected by patch isolation. Large-sized reptiles had higher abundance in remnants. There was not more rapid colonisation of burnt sites near recently burnt conservation park. Instead, low initial abundance may have been caused by fire in combination with drought, with high rainfall during the study allowing recovery and spill-over into adjacent remnants. Conclusions Landscape structure appears to interact with natural fires, restoration burns and longer-term climatic trends to influence the abundance and distribution of reptiles. Traits mediate responses, enabling us to formulate a set of testable mechanistic hypotheses, which illustrates a pathway to generalisation and prediction.
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Schatke, Mona, Lena Ulber, Talie Musavi, Jana Wäldchen, and Christoph von Redwitz. "From unwanted to wanted: Blending functional weed traits into weed distribution maps." Weed Research, September 30, 2024. http://dx.doi.org/10.1111/wre.12664.
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AbstractSite‐specific weed management (SSWM) is increasingly employed to reduce herbicide inputs. Incorporating functional traits of weed species allows for the selection of SSWM methods that effectively reduce the abundance of weeds with a high competitive potential (disservice) while preserving weeds that provide beneficial ecosystem services (service). In this study, we aim to assess relevant weed functional traits and translate this information into a spatial trait distribution map for weed (dis‐)service provision. The distribution of weed abundance in a field was recorded using a spatial grid. Data on functional traits for the recorded weed species were extracted from published datasets and combined into the two variables, service and disservice. Individual traits (service/disservice) were weighted for each pixel of the weed distribution map based on the number of individual plants per species. Principal component analysis was employed to generate independent variables to describe the potential for service and disservice provision. As a result, two (dis‐)service trait‐based distribution maps were generated: one highlights field areas that provide enhanced ecological services, while the other displays areas with a high disservice potential. The results show that around 61% of the area in the field had a high service potential. The area with a high disservice was slightly higher than the half of the area with a high service, while about 32% of the field has both high service and disservice potential in the same area. This study presents a spatially explicit approach to incorporate information on weed functional traits into SSWM approaches targeted at reducing weed competition while at the same time enhancing weed functional diversity.
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Nemani, Shreya, Benjamin Misiuk, David Cote, Evan Edinger, Julia Mackin-McLaughlin, Adam Templeton, and Katleen Robert. "Incorporating functional traits with habitat maps: patterns of diversity in coastal benthic assemblages." Frontiers in Marine Science 11 (October 3, 2024). http://dx.doi.org/10.3389/fmars.2024.1141737.
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Benthic species assemblages are groups of species that co-occur on the seafloor. Linking assemblages to physical environmental features allows for understanding and predicting their spatial distribution. Species identity and abundance are commonly quantified using a taxonomic approach to assess benthic diversity, yet functional traits that describe the behavior, life history, and morphology of a species may be equally or more important. Here, we investigate the biodiversity of five benthic species assemblages in relation to their habitat and environmental conditions in an Ecologically and Biologically Significant Area (EBSA) along Canada’s east coast, using both a taxonomic approach and biological traits analysis. Random Forest regression was applied to map spatial patterns of functional and taxonomic diversity metrics, including richness, Shannon index, and Rao’s quadratic entropy. We evaluate discrepancies between related taxonomic and trait measures, and the community-weighted mean of trait data was calculated to characterize each assemblage. Taxonomic and functional richness – representing the number of species and the species community volume in the trait space, respectively – showed similar spatial patterns. However, when considering diversity, which also accounts for the relative abundance and differences among species or traits, these patterns diverged. Taxonomically different assemblages exhibited similar trait compositions for two assemblages, indicating potential trait equivalencies, while one assemblage exhibited traits potentially indicating sensitivity to human activity. The taxonomic and functional metrics of richness and diversity were low close to the coast, which could be indicative of disturbance. Consideration of functional metrics can support spatial planning and prioritization for management and conservation efforts by assessing the sensitivity of traits to different stressors.
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Xu, Liang, Sander Van Doorn, Hanno Hildenbrandt, and Rampal S. Etienne. "Inferring the Effect of Species Interactions on Trait Evolution." Systematic Biology, September 22, 2020. http://dx.doi.org/10.1093/sysbio/syaa072.
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Abstract Models of trait evolution form an important part of macroevolutionary biology. The Brownian motion model and Ornstein–Uhlenbeck models have become classic (null) models of character evolution, in which species evolve independently. Recently, models incorporating species interactions have been developed, particularly involving competition where abiotic factors pull species toward an optimal trait value and competitive interactions drive the trait values apart. However, these models assume a fitness function rather than derive it from population dynamics and they do not consider dynamics of the trait variance. Here, we develop a general coherent trait evolution framework where the fitness function is based on a model of population dynamics, and therefore it can, in principle, accommodate any type of species interaction. We illustrate our framework with a model of abundance-dependent competitive interactions against a macroevolutionary background encoded in a phylogenetic tree. We develop an inference tool based on Approximate Bayesian Computation and test it on simulated data (of traits at the tips). We find that inference performs well when the diversity predicted by the parameters equals the number of species in the phylogeny. We then fit the model to empirical data of baleen whale body lengths, using three different summary statistics, and compare it to a model without population dynamics and a model where competition depends on the total metabolic rate of the competitors. We show that the unweighted model performs best for the least informative summary statistic, while the model with competition weighted by the total metabolic rate fits the data slightly better than the other two models for the two more informative summary statistics. Regardless of the summary statistic used, the three models substantially differ in their predictions of the abundance distribution. Therefore, data on abundance distributions will allow us to better distinguish the models from one another, and infer the nature of species interactions. Thus, our framework provides a conceptual approach to reveal species interactions underlying trait evolution and identifies the data needed to do so in practice. [Approximate Bayesian computation; competition; phylogeny; population dynamics; simulations; species interaction; trait evolution.]