Numbers and odds: TCR repertoire size and its age changes impacting on T cell functions.

A vast array of αß T cell receptors (TCRs) is generated during T cell development in the thymus through V(D)J recombination, which involves the rearrangement of multiple V, D, and J genes and the pairing of α and ß chains. These diverse TCRs provide protection to the human body against a multitude of foreign pathogens and internal cancer cells. The entirety of TCRs present in an individual's T cells is referred to as the TCR repertoire. Despite an estimated 4 × 1011 T cells in the adult human body, the lower bound estimate for the TCR repertoire is 3.8 × 108. While the number of circulating T cells may slightly decrease with age, the changes in the diversity of the TCR repertoire is more apparent. Here, I review recent advancements in TCR repertoire studies, the methods used to measure it, how richness and diversity change as humans age, and some of the known consequences associated with these changes.

Biodiversity and productivity in eastern US forests.

Despite experimental and observational studies demonstrating that biodiversity enhances primary productivity, the best metric for predicting productivity at broad geographic extents-functional trait diversity, phylogenetic diversity, or species richness-remains unknown. Using >1.8 million tree measurements from across eastern US forests, we quantified relationships among functional trait diversity, phylogenetic diversity, species richness, and productivity. Surprisingly, functional trait and phylogenetic diversity explained little variation in productivity that could not be explained by tree species richness. This result was consistent across the entire eastern United States, within ecoprovinces, and within data subsets that controlled for biomass or stand age. Metrics of functional trait and phylogenetic diversity that were independent of species richness were negatively correlated with productivity. This last result suggests that processes that determine species sorting and packing are likely important for the relationships between productivity and biodiversity. This result also demonstrates the potential confusion that can arise when interdependencies among different diversity metrics are ignored. Our findings show the value of species richness as a predictive tool and highlight gaps in knowledge about linkages between functional diversity and ecosystem functioning.

Historical redlining is associated with disparities in wildlife biodiversity in four California cities.

Legacy effects describe the persistent, long-term impacts on an ecosystem following the removal of an abiotic or biotic feature. Redlining, a policy that codified racial segregation and disinvestment in minoritized neighborhoods, has produced legacy effects with profound impacts on urban ecosystem structure and health. These legacies have detrimentally impacted public health outcomes, socioeconomic stability, and environmental health. However, the collateral impacts of redlining on wildlife communities are uncertain. Here, we investigated whether faunal biodiversity was associated with redlining. We used home-owner loan corporation (HOLC) maps [grades A (i.e., "best" and "greenlined"), B, C, and D (i.e., "hazardous" and "redlined")] across four cities in California and contributory science data (iNaturalist) to estimate alpha and beta diversity across six clades (mammals, birds, insects, arachnids, reptiles, and amphibians) as a function of HOLC grade. We found that in greenlined neighborhoods, unique species were detected with less sampling effort, with redlined neighborhoods needing over 8,000 observations to detect the same number of unique species. Historically redlined neighborhoods had lower native and nonnative species richness compared to greenlined neighborhoods across each city, with disparities remaining at the clade level. Further, community composition (i.e., beta diversity) consistently differed among HOLC grades for all cities, including large differences in species assemblage observed between green and redlined neighborhoods. Our work spotlights the lasting effects of social injustices on the community ecology of cities, emphasizing that urban conservation and management efforts must incorporate an antiracist, justice-informed lens to improve biodiversity in urban environments.

Three decades of increasing fish biodiversity across the northeast Atlantic and the Arctic Ocean.

Observed range shifts of numerous species support predictions of climate change models that species will shift their distribution northward into the Arctic and sub-Arctic seas due to ocean warming. However, how this is affecting overall species richness is unclear. Here we analyze 20,670 scientific research trawls from the North Sea to the Arctic Ocean collected from 1994 to 2020, including 193 fish species. We found that demersal fish species richness at the local scale has doubled in some Arctic regions, including the Barents Sea, and increased at a lower rate at adjacent regions in the last three decades, followed by an increase in species richness and turnover at a regional scale. These changes in biodiversity correlated with an increase in sea bottom temperature. Within the study area, Arctic species' probability of occurrence generally declined over time. However, the increase in species from southern latitudes, together with an increase in some Arctic species, ultimately led to an enrichment of the Arctic and sub-Arctic marine fauna due to increasing water temperature consistent with climate change.

Tree diversity enhances predation by birds but not by arthropods across climate gradients.

Tree diversity can promote both predator abundance and diversity. However, whether this translates into increased predation and top-down control of herbivores across predator taxonomic groups and contrasting environmental conditions remains unresolved. We used a global network of tree diversity experiments (TreeDivNet) spread across three continents and three biomes to test the effects of tree species richness on predation across varying climatic conditions of temperature and precipitation. We recorded bird and arthropod predation attempts on plasticine caterpillars in monocultures and tree species mixtures. Both tree species richness and temperature increased predation by birds but not by arthropods. Furthermore, the effects of tree species richness on predation were consistent across the studied climatic gradient. Our findings provide evidence that tree diversity strengthens top-down control of insect herbivores by birds, underscoring the need to implement conservation strategies that safeguard tree diversity to sustain ecosystem services provided by natural enemies in forests.

Nitrogen availability and plant functional composition modify biodiversity-multifunctionality relationships.

Biodiversity typically increases multiple ecosystem functions simultaneously (multifunctionality) but variation in the strength and direction of biodiversity effects between studies suggests context dependency. To determine how different factors modulate the diversity effect on multifunctionality, we established a large grassland experiment manipulating plant species richness, resource addition, functional composition (exploitative vs. conservative species), functional diversity and enemy abundance. We measured ten above- and belowground functions and calculated ecosystem multifunctionality. Species richness and functional diversity both increased multifunctionality, but their effects were context dependent. Richness increased multifunctionality when communities were assembled with fast-growing species. This was because slow species were more redundant in their functional effects, whereas different fast species promoted different functions. Functional diversity also increased multifunctionality but this effect was dampened by nitrogen enrichment and enemy presence. Our study suggests that a shift towards fast-growing communities will not only alter ecosystem functioning but also the strength of biodiversity-functioning relationships.

The Evolution of Local Co-occurrence in Birds in Relation to Latitude, Degree of Sympatry, and Range Symmetry.

AbstractRecent speciation rates and the degree of range-wide sympatry are usually higher farther from the equator. Is there also a higher degree of secondary syntopy (coexistence in local assemblages in sympatry) at higher latitudes and, subsequently, an increase in local species richness? We studied the evolution of syntopy in passerine birds using worldwide species distribution data. We chose recently diverged species pairs from subclades not older than 5 or 7 million years, range-wide degree of sympatry not lower than 5% or 25%, and three definitions of the breeding season. We related their syntopy to latitude, the degree of sympatry (breeding range overlap), range symmetry, and the age of split. Syntopy was positively related to latitude, but it did not differ between tropical and temperate regions, instead increasing from the Southern to the Northern Hemisphere. Syntopy was also higher in species pairs with a higher degree of sympatry and more symmetric ranges, but it did not predict local species richness. Following speciation, species in the Northern Hemisphere presumably achieve positive local co-occurrence faster than elsewhere, which could facilitate their higher speciation rates. However, this does not seem to be linked to local species richness, which is probably governed by other processes.

Radiating diversification and niche conservatism jointly shape the inverse latitudinal diversity gradient of Potentilla L. (Rosaceae).

BACKGROUND: The latitudinal diversity gradient (LDG), characterized by an increase in species richness from the poles to the equator, is one of the most pervasive biological patterns. However, inverse LDGs, in which species richness peaks in extratropical regions, are also found in some lineages and their causes remain unclear. Here, we test the roles of evolutionary time, diversification rates, and niche conservatism in explaining the inverse LDG of Potentilla (ca. 500 species). We compiled the global distributions of ~ 90% of Potentilla species, and reconstructed a robust phylogenetic framework based on whole-plastome sequences. Next, we analyzed the divergence time, ancestral area, diversification rate, and ancestral niche to investigate the macroevolutionary history of Potentilla. RESULTS: The genus originated in the Qinghai-Tibet Plateau during the late Eocene and gradually spread to other regions of the Northern Hemisphere posterior to the late Miocene. Rapid cooling after the late Pliocene promoted the radiating diversification of Potentilla. The polyploidization, as well as some cold-adaptive morphological innovations, enhanced the adaptation of Potentilla species to the cold environment. Ancestral niche reconstruction suggests that Potentilla likely originated in a relatively cool environment. The species richness peaks at approximately 45 °N, a region characterized by high diversification rates, and the environmental conditions are similar to the ancestral climate niche. Evolutionary time was not significantly correlated with species richness in the latitudinal gradient. CONCLUSIONS: Our results suggest that the elevated diversification rates in middle latitude regions and the conservatism in thermal niches jointly determined the inverse LDG in Potentilla. This study highlights the importance of integrating evolutionary and ecological approaches to explain the diversity pattern of biological groups on a global scale.

The causes of species richness patterns among clades.

Two major types of species richness patterns are spatial (e.g. the latitudinal diversity gradient) and clade-based (e.g. the dominance of angiosperms among plants). Studies have debated whether clade-based richness patterns are explained primarily by larger clades having faster rates of species accumulation (speciation minus extinction over time; diversification-rate hypothesis) or by simply being older (clade-age hypothesis). However, these studies typically compared named clades of the same taxonomic rank, such as phyla and families. This study design is potentially biased against the clade-age hypothesis, since clades of the same rank may be more similar in age than randomly selected clades. Here, we analyse the causes of clade-based richness patterns across the tree of life using a large-scale, time-calibrated, species-level phylogeny and random sampling of clades. We find that within major groups of organisms (animals, plants, fungi, bacteria, archaeans), richness patterns are most strongly related to clade age. Nevertheless, weaker relationships with diversification rates are present in animals and plants. These overall results contrast with similar large-scale analyses across life based on named clades, which showed little effect of clade age on richness. More broadly, these results help support the overall importance of time for explaining diverse types of species richness patterns.

Mechanisms of biodiversity loss under nitrogen enrichment: unveiling a shift from light competition to cation toxicity.

The primary mechanisms contributing to nitrogen (N) addition induced grassland biodiversity loss, namely light competition and soil cation toxicity, are often examined separately in various studies. However, their relative significance in governing biodiversity loss along N addition gradient remains unclear. We conducted a 4-yr field experiment with five N addition rates (0, 2, 10, 20, and 50 g N m-2 yr-1) and performed a meta-analysis using global data from 239 observations in N-fertilized grassland ecosystems. Results from our field experiment and meta-analysis indicate that both light competition and soil cation (e.g. Mn2+ and Al3+) toxicity contribute to plant diversity loss under N enrichment. The relative importance of these mechanisms varied with N enrichment intensity. Light competition played a more significant role in influencing species richness under low N addition (≤ 10 g m-2 yr-1), while cation toxicity became increasingly dominant in reducing biodiversity under high N addition (>10 g m-2 yr-1). Therefore, a transition from light competition to cation toxicity occurs with increasing N availability. These findings imply that the biodiversity loss along the N gradient is regulated by distinct mechanisms, necessitating the adoption of differential management strategies to mitigate diversity loss under varying intensities of N enrichment.

Mycorrhizal type and tree diversity affect foliar elemental pools and stoichiometry.

Species-specific differences in nutrient acquisition strategies allow for complementary use of resources among plants in mixtures, which may be further shaped by mycorrhizal associations. However, empirical evidence of this potential role of mycorrhizae is scarce, particularly for tree communities. We investigated the impact of tree species richness and mycorrhizal types, arbuscular mycorrhizal fungi (AM) and ectomycorrhizal fungi (EM), on above- and belowground carbon (C), nitrogen (N), and phosphorus (P) dynamics. Soil and soil microbial biomass elemental dynamics showed weak responses to tree species richness and none to mycorrhizal type. However, foliar elemental concentrations, stoichiometry, and pools were significantly affected by both treatments. Tree species richness increased foliar C and P pools but not N pools. Additive partitioning analyses showed that net biodiversity effects of foliar C, N, P pools in EM tree communities were driven by selection effects, but in mixtures of both mycorrhizal types by complementarity effects. Furthermore, increased tree species richness reduced soil nitrate availability, over 2 yr. Our results indicate that positive effects of tree diversity on aboveground nutrient storage are mediated by complementary mycorrhizal strategies and highlight the importance of using mixtures composed of tree species with different types of mycorrhizae to achieve more multifunctional afforestation.

Leaf isotopes reveal tree diversity effects on the functional responses to the pan-European 2018 summer drought.

Recent droughts have strongly impacted forest ecosystems and are projected to increase in frequency, intensity, and duration in the future together with continued warming. While evidence suggests that tree diversity can regulate drought impacts in natural forests, few studies examine whether mixed tree plantations are more resistant to the impacts of severe droughts. Using natural variations in leaf carbon (C) and nitrogen (N) isotopic ratios, that is δ13C and δ15N, as proxies for drought response, we analyzed the effects of tree species richness on the functional responses of tree plantations to the pan-European 2018 summer drought in seven European tree diversity experiments. We found that leaf δ13C decreased with increasing tree species richness, indicating less drought stress. This effect was not related to drought intensity, nor desiccation tolerance of the tree species. Leaf δ15N increased with drought intensity, indicating a shift toward more open N cycling as water availability diminishes. Additionally, drought intensity was observed to alter the influence of tree species richness on leaf δ15N from weakly negative under low drought intensity to weakly positive under high drought intensity. Overall, our findings suggest that dual leaf isotope analysis helps understand the interaction between drought, nutrients, and species richness.

Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales.

The macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change. We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes. Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high in situ diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than the other regions. The relatively common lineage dispersals out of temperate hotspots highlight strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae. The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid in situ diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high in situ diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales.

The role of Pleistocene dispersal in shaping species richness of sky island wintergreens from the Himalaya-Hengduan Mountains.

In addition to topography and climate, biogeographic dispersal has been considered to influence plant diversity in the Himalaya-Hengduan Mountains (HHM), yet, the mode and tempo of sky island dispersal and its influence on species richness has been little explored. Through phylogenetic analysis of Gaultheria ser. Trichophyllae, a sky island alpine clade within the HHM, we test the hypothesis that dispersal has affected current local species richness. We inferred the dynamics of biogeographic dispersal with correlation tests on direction, distance, occurrence time, and regional species richness. We found that G. ser. Trichophyllae originated at the end of the Miocene and mostly dispersed toward higher longitudes (eastward). In particular, shorter intra-regional eastward dispersals and longer inter-regional westward dispersals were most frequently observed. We detected a prevalence of eastward intra-region dispersals in both glacial periods and interglacials. These dispersals may have been facilitated by the reorganization of paleo-drainages and monsoon intensification through time. We suggest that the timing of dispersal corresponding to glacial periods and the prevalence of intra-region dispersal, rather than dispersal frequency, most influenced the pattern of species richness of G. ser. Trichophyllae. This study facilitates a more comprehensive understanding of biodiversity in the sky islands within the HHM.

How many species will Earth lose to climate change?

Climate change may be an important threat to global biodiversity, potentially leading to the extinction of numerous species. But how many? There have been various attempts to answer this question, sometimes yielding strikingly different estimates. Here, we review these estimates, assess their disagreements and methodology, and explore how we might reach better estimates. Large-scale studies have estimated the extinction of ~1% of sampled species up to ~70%, even when using the same approach (species distribution models; SDMs). Nevertheless, worst-case estimates often converge near 20%-30% species loss, and many differences shrink when using similar assumptions. We perform a new review of recent SDM studies, which show ~17% loss of species to climate change under worst-case scenarios. However, this review shows that many SDM studies are biased by excluding the most vulnerable species (those known from few localities), which may lead to underestimating global species loss. Conversely, our analyses of recent climate change responses show that a fundamental assumption of SDM studies, that species' climatic niches do not change over time, may be frequently violated. For example, we find mean rates of positive thermal niche change across species of ~0.02°C/year. Yet, these rates may still be slower than projected climate change by ~3-4 fold. Finally, we explore how global extinction levels can be estimated by combining group-specific estimates of species loss with recent group-specific projections of global species richness (including cryptic insect species). These preliminary estimates tentatively forecast climate-related extinction of 14%-32% of macroscopic species in the next ~50 years, potentially including 3-6 million (or more) animal and plant species, even under intermediate climate change scenarios.

Human activity and climate change accelerate the extinction risk to non-human primates in China.

Human activity and climate change affect biodiversity and cause species range shifts, contractions, and expansions. Globally, human activities and climate change have emerged as persistent threats to biodiversity, leading to approximately 68% of the ~522 primate species being threatened with extinction. Here, we used habitat suitability models and integrated data on human population density, gross domestic product (GDP), road construction, the normalized difference vegetation index (NDVI), the location of protected areas (PAs), and climate change to predict potential changes in the distributional range and richness of 26 China's primate species. Our results indicate that both PAs and NDVI have a positive impact on primate distributions. With increasing anthropogenic pressure, species' ranges were restricted to areas of high vegetation cover and in PAs surrounded by buffer zones of 2.7-4.5 km and a core area of PAs at least 0.1-0.5 km from the closest edge of the PA. Areas with a GDP below the Chinese national average of 100,000 yuan were found to be ecologically vulnerable, and this had a negative impact on primate distributions. Changes in temperature and precipitation were also significant contributors to a reduction in the range of primate species. Under the expected influence of climate change over the next 30-50 years, we found that highly suitable habitat for primates will continue to decrease and species will be restricted to smaller and more peripheral parts of their current range. Areas of high primate diversity are expected to lose from 3 to 7 species. We recommend that immediate action be taken, including expanding China's National Park Program, the Ecological Conservation Redline Program, and the Natural Forest Protection Program, along with a stronger national policy promoting alternative/sustainable livelihoods for people in the local communities adjacent to primate ranges, to offset the detrimental effects of anthropogenic activities and climate change on primate survivorship.

Microclimate modulation: An overlooked mechanism influencing the impact of plant diversity on ecosystem functioning.

Changes in climate and biodiversity are widely recognized as primary global change drivers of ecosystem structure and functioning, also affecting ecosystem services provided to human populations. Increasing plant diversity not only enhances ecosystem functioning and stability but also mitigates climate change effects and buffers extreme weather conditions, yet the underlying mechanisms remain largely unclear. Recent studies have shown that plant diversity can mitigate climate change (e.g. reduce temperature fluctuations or drought through microclimatic effects) in different compartments of the focal ecosystem, which as such may contribute to the effect of plant diversity on ecosystem properties and functioning. However, these potential plant diversity-induced microclimate effects are not sufficiently understood. Here, we explored the consequences of climate modulation through microclimate modification by plant diversity for ecosystem functioning as a potential mechanism contributing to the widely documented biodiversity-ecosystem functioning (BEF) relationships, using a combination of theoretical and simulation approaches. We focused on a diverse set of response variables at various levels of integration ranging from ecosystem-level carbon exchange to soil enzyme activity, including population dynamics and the activity of specific organisms. Here, we demonstrated that a vegetation layer composed of many plant species has the potential to influence ecosystem functioning and stability through the modification of microclimatic conditions, thus mitigating the negative impacts of climate extremes on ecosystem functioning. Integrating microclimatic processes (e.g. temperature, humidity and light modulation) as a mechanism contributing to the BEF relationships is a promising avenue to improve our understanding of the effects of climate change on ecosystem functioning and to better predict future ecosystem structure, functioning and services. In addition, microclimate management and monitoring should be seen as a potential tool by practitioners to adapt ecosystems to climate change.

Indigenous Peoples' Lands are critical for safeguarding vertebrate diversity across the tropics.

Indigenous Peoples are long-term custodians of their lands, but only recently are their contributions to conservation starting to be recognized in biodiversity policy and practice. Tropical forest loss and degradation are lower in Indigenous lands than unprotected areas, yet the role of Indigenous Peoples' Lands (IPL) in biodiversity conservation has not been properly assessed from regional to global scales. Using species distribution ranges of 11,872 tropical forest-dependent vertebrates to create area of habitat maps, we identified the overlap of these species ranges with IPL and then compared values inside and outside of IPL for species richness, extinction vulnerability, and range-size rarity. Of assessed vertebrates, at least 76.8% had range overlaps with IPL, on average overlapping ~25% of their ranges; at least 120 species were found only within IPL. Species richness within IPL was highest in South America, while IPL in Southeast Asia had highest extinction vulnerability, and IPL in Dominica and New Caledonia were important for range-size rarity. Most countries in the Americas had higher species richness within IPL than outside, whereas most countries in Asia had lower extinction vulnerability scores inside IPL and more countries in Africa and Asia had slightly higher range-size rarity in IPL. Our findings suggest that IPL provide critical support for tropical forest-dependent vertebrates, highlighting the need for greater inclusion of Indigenous Peoples in conservation target-setting and program implementation, and stronger upholding of Indigenous Peoples' rights in conservation policy.

Positive effects of tree species diversity on productivity switch to negative after severe drought mortality in a temperate forest experiment.

The synthesis of a large body of evidence from field experiments suggests more diverse plant communities are more productive as well as more resistant to the effects of climatic extremes like drought. However, this view is strongly based on data from grasslands due to the limited empirical evidence from tree diversity experiments. Here we report on the relationship between tree diversity and productivity over 10 years in a field experiment established in 2005 that was then affected by the 2018 mega-drought in central Europe. Across a number of years, tree species diversity and productivity were significantly positively related; however, the slope switched to negative in the year of the drought. Net diversity effects increased through time, with complementarity effects making greater contributions to the net diversity effect than selection effects. Complementarity effects were clearly positive in three- and five-species mixtures before the drought (2012-2016) but were found to decrease in the year of the drought. Selection effects were clearly positive in 2016 and remained positive in the drought year 2018 in two-, three-, and five-species mixtures. The survival of Norway spruce (Picea abies) plummeted in response to the drought, and a negative relationship between species diversity and spruce survival was found. Taken together, our findings suggest that tree diversity per se may not buffer communities against the impacts of extreme drought and that tree species composition and the drought tolerance of tree species (i.e., species identity) will be important determinants of community productivity as the prevalence of drought increases.

Foliar phenols and flavonoids level in pteridophytes: an insight to culturable fungal endophyte colonisation.

There are many available reports of secondary metabolites as bioactive molecules from culturable endophytes, nevertheless, there are scarce research pertaining to the levels of metabolites in plants with respect to the incidence and colonisation of fungal endophytes in the same foliar tissues. Therefore, the study was focussed to examine whether fungal endophyte colonisation and the accumulation of secondary metabolites, such as flavonoids and phenols, in the plants are related in any way. For this reason, the study aims to analyse phenols and flavonoids from the fronds of eleven pteridophytes along with the culture-dependent isolation of fungal endophytes from the host plants subsequently assigning them to morphological category and their quantitative analysis and further resolving its identities through molecular affiliation. The results revealed that nine morpho-categories of fungal endophytes were allotted based on culture attributes, hyphal patterns and reproductive structural characters. Highest numbers of species were isolated from Adiantum capillus-veneris and least was recorded from Pteris vittata and Dicranopteris linearis. Maximum phenol content was analysed from the fronds of P. vittata and lowest was recorded in A. capillus-veneris. Highest flavonoid content was measured in D. linearis and lowest was detected in Christella dentata. Significant negative correlation was observed between phenol content of ferns and species richness of fungi. Moreover, significant positive correlation was observed with the relative abundance of Chaetomium globosum and flavonoid content of ferns and negative significant relation was found between relative abundance of Pseudopestalotiopsis chinensis and phenol content of pteridophytes. The occurrence and the quantitative aspects of endophytes in ferns and their secondary metabolites are discussed.