Phylogenetic Models Research Articles

Parallel evolution of semicircular canal form and sensitivity in subterranean mammals.

The vertebrate vestibular system is crucial for balance and navigation, and the evolution of its form and function in relation to species' lifestyle and mode of locomotion has been the focus of considerable recent study. Most research, however, has concentrated on aboveground mammals, with much less published on subterranean fauna. Here, we explored variation in anatomy and sensitivity of the semicircular canals among 91 mammal species, including both subterranean and non-subterranean representatives. Quantitative phylogenetically informed analyses showed significant widening of the canals relative to radius of curvature in subterranean species. A relative canal width above 0.166 indicates with 95% certainty that a species is subterranean. Fluid-structure interaction modelling predicted that canal widening leads to a substantial increase in canal sensitivity; a reasonably good estimation of the absolute sensitivity is possible based on the absolute internal canal width alone. In addition, phylogenetic comparative modelling and functional landscape exploration revealed repeated independent evolution of increased relative canal width and anterior canal sensitivity associated with the transition to a subterranean lifestyle, providing evidence of parallel adaptation. Our results suggest that living in dark, subterranean tunnels requires good balance and/or navigation skills which may be facilitated by more sensitive semicircular canals.

Seasonal variation significantly influenced the stochasticity of community assembly of amphibian symbiotic bacteria.

Seasonal variation has been shown to influence symbiotic bacterial community composition and structure in amphibians. It is still unknown how the symbiotic bacterial community assembly changes during different seasons, especially for amphibians who are particularly sensitive to environmental change. We found significant differences in the composition and diversity (alpha and beta diversity) of amphibian skin and gut bacteria. Co-occurrences network analysis showed that seasonal variation reduced the microbial network complexity of amphibians from summer to autumn. The normalized stochastic ratio (NST) and phylogenetic bin-based null model analysis (iCAMP) models showed that the same result that stochastic processes was the major factor regulating the symbiotic bacterial community assembly mechanisms of amphibians. From summer to autumn, the symbiotic bacterial community assembly mechanisms declined in the contribution of stochastic processes, while increasing in the contribution of deterministic processes. Dispersal limitation was the dominant microbial assembly mechanism, followed by homogeneous selection, and then heterogeneous selection in the symbiotic bacterial community communities of amphibians between summer and autumn. Furthermore, higher niche width of the symbiotic bacterial community of amphibians was found in summer than autumn. Overall, these results demonstrated that seasonal variation influenced amphibian symbiotic bacterial community between summer and autumn.

Do closely related species interact with similar partners? Testing for phylogenetic signal in bipartite interaction networks

Whether interactions between species are conserved on evolutionary time-scales has spurred the development of both correlative and process-based approaches for testing phylogenetic signal in interspecific interactions: do closely related species interact with similar partners? Here we use simulations to test the statistical performances of the two approaches that are the most widely used in the field: Mantel tests and the Phylogenetic Bipartite Linear Model (PBLM). Mantel tests investigate the correlation between phylogenetic distances and dissimilarities in sets of interacting partners, while PBLM is a process-based approach that relies on strong assumptions about how interactions evolve. We find that PBLM often detects a phylogenetic signal when it should not. Simple Mantel tests instead have infrequent false positives and moderate statistical power; however, they often artifactually detect that closely related species interact with dissimilar partners. Partial Mantel tests, which are used to partial out the phylogenetic signal in the number of partners, actually fail at correcting for this confounding effect, and we instead recommend evaluating the significance of Mantel tests with network permutations constraining the number of partners. We also explore the ability of simple Mantel tests to analyze clade- specific phylogenetic signals. We provide general guidelines and an application on an interaction network between orchids and mycorrhizal fungi.

Correlated evolution between colour conspicuousness and drum speed in woodpeckers.

Sexual selection drives the evolution of many spectacular animal displays that we see in nature. Yet, how selection combines and elaborates different signal traits remains unclear. Here, we investigate this issue by testing for correlated evolution between head plumage colour and drumming behaviour in woodpeckers. These signals function in the context of mate choice and male–male competition, and they may appear to a receiver as a single multimodal display. We test for such correlations in males of 132 species using phylogenetic linear models, while considering the effect of habitat. We find that the plumage chromatic contrast is positively correlated with the speed of the drum, supporting the idea that species evolving more conspicuous plumage on their head also evolve faster drum displays. By contrast, we do not find evidence of correlated evolution between drum speed and head colour diversity, size of the head's red patch, or extent of the plumage achromatic contrast. Drum length was not correlated with any of the plumage coloration metrics. Lastly, we find no evidence that habitat acts as a strong selective force driving the evolution of head coloration or drumming elaboration. Coevolution between different signal modalities is therefore complex, and probably depends on the display components in question.

SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework.

Genomic epidemiology is now widely used for viral outbreak investigations. Still, this methodology faces many challenges. First, few methods account for intra-host viral diversity. Second, maximum parsimony principle continues to be employed for phylogenetic inference of transmission histories, even though maximum likelihood or Bayesian models are usually more consistent. Third, many methods utilize case-specific data, such as sampling times or infection exposure intervals. This impedes study of persistent infections in vulnerable groups, where such information has a limited use. Finally, most methods implicitly assume that transmission events are independent, although common source outbreaks violate this assumption. We propose a maximum likelihood framework, SOPHIE, based on the integration of phylogenetic and random graph models. It infers transmission networks from viral phylogenies and expected properties of inter-host social networks modeled as random graphs with given expected degree distributions. SOPHIE is scalable, accounts for intra-host diversity, and accurately infers transmissions without case-specificepidemiological data.

Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes

Abstract The availability of population genomic data through new sequencing technologies gives unprecedented opportunities for estimating important evolutionary forces such as genetic drift, selection and mutation biases across organisms. Yet, analytical methods that can handle polymorphisms jointly with sequence divergence across species are rare and not easily accessible to empiricists. We implemented polymorphism‐aware phylogenetic models (PoMos), an alternative approach for species tree estimation, in the Bayesian phylogenetic software RevBayes. PoMos naturally account for incomplete lineage sorting, which is known to cause difficulties for phylogenetic inference in species radiations, and scale well with genome‐wide data. Simultaneously, PoMos can estimate mutation and selection biases. We have applied our methods to resolve the complex phylogenetic relationships of a young radiation of Chorthippus grasshoppers, based on coding sequences. In addition to establishing a well‐supported species tree, we found a mutation bias favouring AT alleles and selection bias promoting the fixation of GC alleles, the latter consistent with GC‐biased gene conversion. The selection bias is two orders of magnitude lower than genetic drift, validating the critical role of nearly neutral evolutionary processes in species radiation. PoMos offer a wide range of models to reconstruct phylogenies and can be easily combined with existing models in RevBayes—for example, relaxed clock and divergence time estimation—offering new insights into the evolutionary processes underlying molecular evolution and, ultimately, species diversification.

Ecological and evolutionary dynamics of multi-strain RNA viruses.

Potential interactions among co-circulating viral strains in host populations are often overlooked in the study of virus transmission. However, these interactions probably shape transmission dynamics by influencing host immune responses or altering the relative fitness among co-circulating strains. In this Review, we describe multi-strain dynamics from ecological and evolutionary perspectives, outline scales in which multi-strain dynamics occur and summarize important immunological, phylogenetic and mathematical modelling approaches used to quantify interactions among strains. We also discuss how host-pathogen interactions influence the co-circulation of pathogens. Finally, we highlight outstanding questions and knowledge gaps in the current theory and study of ecological and evolutionary dynamics of multi-strain viruses.

Environmental similarity is more important than distance in the community structuring processes of ammonia-oxidizing archaea in agricultural soils

Archaeal ammonia oxidizers (AOA) are important in converting ammonia into nitrates in soils. While many aspects of their community structure have been studied, the relative importance of stochastic versus deterministic processes has been poorly understood. We compared AOA communities across the North China Plain, targeting the amoA gene. A phylogenetic null modelling approach was used to calculate beta-nearest taxon index (beta-NTI) to quantify the influence of stochastic and deterministic processes. We found that spatial distance between samples predicted the perceived processes involved in community structuring, with stochastic processes dominating at more local scales. At greater distances, stochasticity became weaker. However, differences in soil pH – which were also the strongest determinant of AOA community – were a much stronger predictor of the community structuring, leaving distance effects redundant as an explanation of community structuring processes. AOA communities differing by less than 1 pH unit differ mainly stochastically in terms of OTU composition. At larger pH differences, deterministic processes based on heterogeneous selection between clades become increasingly dominant. It appears that AOA community composition is largely determined by environment. The exception is amongst very similar pH environments, whether spatially near or far, in which stochastic effects dominate in causing differences in community composition.

Sexual selection, feather wear, and time constraints on the pre-basic molt explain the acquisition of the pre-alternate molt in European passerines.

Avian feathers need to be replaced periodically to fulfill their functions, with natural, social, and sexual selection presumably driving the evolution of molting strategies. In temperate birds, a common pattern is to molt feathers immediately after the breeding season, the pre‐basic molt. However, some species undergo another molt in winter‐spring, the pre‐alternate molt. Using a sample of 188 European passerine species, Bayesian phylogenetic mixed models, and correlated evolution analyses, we tested whether the occurrence of the pre‐alternate molt was positively associated with proxies for sexual selection (sexual selection hypothesis) and nonsexual social selection (social selection hypothesis), and with factors related to feather wear (feather wear hypothesis) and time constraints on the pre‐basic molt (time constraints hypothesis). We found that the pre‐alternate molt was more frequent in migratory and less gregarious species inhabiting open/xeric habitats and feeding on the wing, and marginally more frequent in species with strong sexual selection and those showing a winter territorial behavior. Moreover, an increase in migratory behavior and sexual selection intensity preceded the acquisition of the pre‐alternate molt. These results provide support for the feather wear hypothesis, partial support for the sexual selection and time constraints hypotheses, and no support for the social selection hypothesis.

Characterisation of a soil MINPP phytase with remarkable long-term stability and activity from Acinetobacter sp.

Phylogenetic analysis, homology modelling and biochemical methods have been employed to characterize a phytase from a Gram-negative soil bacterium. Acinetobacter sp. AC1-2 phytase belongs to clade 2 of the histidine (acid) phytases, to the Multiple Inositol Polyphosphate Phosphatase (MINPP) subclass. The enzyme was extraordinarily stable in solution both at room temperature and 4°C, retaining near 100% activity over 755 days. It showed a broad pH activity profile from 2-8.5 with maxima at 3, 4.5-5 and 6. The enzyme showed Michaelis-Menten kinetics and substrate inhibition (Vmax, Km, and Ki, 228 U/mg, 0.65 mM and 2.23 mM, respectively). Homology modelling using the crystal structure of a homologous MINPP from a human gut commensal bacterium indicated the presence of a potentially stabilising polypeptide loop (a U-loop) straddling the active site. By employ of the enantiospecificity of Arabidopsis inositol tris/tetrakisphosphate kinase 1 for inositol pentakisphosphates, we show AC1-2 MINPP to possess D6-phytase activity, which allowed modelling of active site specificity pockets for InsP6 substrate. While phytase gene transcription was unaltered in rich media, it was repressed in minimal media with phytic acid and orthophosphate as phosphate sources. The results of this study reveal AC1-2 MINPP to possess desirable attributes relevant to biotechnological use.

Total evidence time-scaled phylogenetic and biogeographic models for the evolution of sea cows (Sirenia, Afrotheria).

Molecular phylogenetic studies that have included sirenians from the genera Trichechus, Dugong, and Hydrodamalis have resolved their interrelationships but have yielded divergence age estimates that are problematically discordant. The ages of these lineage splits have profound implications for how to interpret the sirenian fossil record—including clade membership, biogeographic patterns, and correlations with Earth history events. In an effort to address these issues, here we present a total evidence phylogenetic analysis of Sirenia that includes living and fossil species and applies Bayesian tip-dating methods to estimate their interrelationships and divergence times. In addition to extant sirenians, our dataset includes 56 fossil species from 106 dated localities and numerous afrotherian outgroup taxa. Genetic, morphological, temporal, and biogeographic data are assessed simultaneously to bring all available evidence to bear on sirenian phylogeny. The resulting time-tree is then used for Bayesian geocoordinates reconstruction analysis, which models ancestral geographic areas at splits throughout the phylogeny, thereby allowing us to infer the direction and timing of dispersals. Our results suggest that Pan-Sirenia arose in North Africa during the latest Paleocene and that the Eocene evolution of stem sirenians was primarily situated in the Tethyan realm. In the late Eocene, some lineages moved into more northern European latitudes, an area that became the source region for a key trans-Atlantic dispersal towards the Caribbean and northern-adjacent west Atlantic. This event led to the phylogenetic and biogeographic founding of crown Sirenia with the Dugongidae-Trichechidae split occurring at the Eocene-Oligocene boundary (~33.9 Ma), temporally coincident with the onset of dropping global sea levels and temperatures. This region became the nexus of sirenian diversification and supported taxonomically-rich dugongid communities until the earliest Pliocene. The Dugonginae-Hydrodamalinae split occurred near Florida during the early Miocene (~21.2 Ma) and was followed by a west-bound dispersal that gave rise to the Pacific hydrodamalines. The late middle Miocene (~12.2 Ma) split of Dugong from all other dugongines also occurred near Florida and our analyses suggest that the Indo-Pacific distribution of modern dugongs is the result of a trans-Pacific dispersal. From at least the early Miocene, trichechid evolution was based entirely in South America, presumably within the Pebas Wetlands System. We infer that the eventual establishment of Amazon drainage into the South Atlantic allowed the dispersal of Trichechus out of South America no earlier than the mid-Pliocene. Our analyses provide a new temporal and biogeographic framework for understanding major events in sirenian evolution and their possible relationships to oceanographic and climatic changes. These hypotheses can be further tested with the recovery and integration of new fossil evidence.

A class of identifiable phylogenetic birth–death models

In a striking result, Louca and Pennell [S. Louca, M. W. Pennell, Nature 580, 502-505 (2020)] recently proved that a large class of phylogenetic birth-death models is statistically unidentifiable from lineage-through-time (LTT) data: Any pair of sufficiently smooth birth and death rate functions is "congruent" to an infinite collection of other rate functions, all of which have the same likelihood for any LTT vector of any dimension. As Louca and Pennell argue, this fact has distressing implications for the thousands of studies that have utilized birth-death models to study evolution. In this paper, we qualify their finding by proving that an alternative and widely used class of birth-death models is indeed identifiable. Specifically, we show that piecewise constant birth-death models can, in principle, be consistently estimated and distinguished from one another, given a sufficiently large extant timetree and some knowledge of the present-day population. Subject to mild regularity conditions, we further show that any unidentifiable birth-death model class can be arbitrarily closely approximated by a class of identifiable models. The sampling requirements needed for our results to hold are explicit and are expected to be satisfied in many contexts such as the phylodynamic analysis of a global pandemic.

Predicting Long Pendant Edges in Model Phylogenies, with Applications to Biodiversity and Tree Inference.

In the simplest phylogenetic diversification model (the pure-birth Yule process), lineages split independently at a constant rate $\lambda$ for time $t$. The length of a randomly chosen edge (either interior or pendant) in the resulting tree has an expected value that rapidly converges to $\frac{1}{2\lambda}$ as $t$ grows and thus is essentially independent of $t$. However, the behavior of the length $L$ of the longest pendant edge reveals remarkably different behavior: $L$ converges to $t/2$ as the expected number of leaves grows. Extending this model to allow an extinction rate $\mu$ (where $\mu<\lambda$), we also establish a similar result for birth-death trees, except that $t/2$ is replaced by $t/2 \cdot (1-\mu/\lambda)$. This "complete" tree may contain subtrees that have died out before time $t$; for the "reduced tree" that just involves the leaves present at time $t$ and their direct ancestors, the longest pendant edge length $L$ again converges to $t/2$. Thus, there is likely to be at least one extant species whose associated pendant branch attaches to the tree approximately half-way back in time to the origin of the entire clade. We also briefly consider the length of the shortest edges. Our results are relevant to phylogenetic diversity indices in biodiversity conservation, and to quantifying the length of aligned sequences required to correctly infer a tree. We compare our theoretical results with simulations and with the branch lengths from a recent phylogenetic tree of all mammals. [Birth-death process; phylogenetic diversification models; phylogenetic diversity.].

The Emergence, Diversification, and Transmission of Subgroup J Avian Leukosis Virus Reveals that the Live Chicken Trade Plays a Critical Role in the Adaption and Endemicity of Viruses to the Yellow-Chickens.

The geographical spread and inter-host transmission of the subgroup J avian leukosis virus (ALV-J) may be the most important issues for epidemiology. An integrated analysis, including phylogenetic trees, homology modeling, evolutionary dynamics, selection analysis and viral transmission, based on the gp85 gene sequences of the 665 worldwide ALV-J isolates during 1988-2020, was performed. A new Clade 3 has been emerging and was evolved from the dominating Clade 1.3 of the Chinese Yellow-chicken, and the loss of a α-helix or β-sheet of the gp85 protein monomer was found by the homology modeling. The rapid evolution found in Clades 1.3 and 3 may be closely associated with the adaption and endemicity of viruses to the Yellow-chickens. The early U.S. strains from Clade 1.1 acted as an important source for the global spread of ALV-J and the earliest introduction into China was closely associated with the imported chicken breeders in the 1990s. The dominant outward migrations of Clades 1.1 and 1.2, respectively, from the Chinese northern White-chickens and layers to the Chinese southern Yellow-chickens, and the dominating migration of Clade 1.3 from the Chinese southern Yellow-chickens to other regions and hosts, indicated that the long-distance movement of these viruses between regions in China was associated with the live chicken trade. Furthermore, Yellow-chickens have been facing the risk of infections of the emerging Clades 2 and 3. Our findings provide new insights for the epidemiology and help to understand the critical factors involved in ALV-J dissemination. IMPORTANCE Although the general epidemiology of ALV-J is well studied, the ongoing evolutionary and transmission dynamics of the virus remain poorly investigated. The phylogenetic differences and relationship of the clades and subclades were characterized, and the epidemics and factors driving the geographical spread and inter-host transmission of different ALV-J clades were explored for the first time. The results indicated that the earliest ALV-J (Clade 1.1) from the United States, acted as the source for global spreads, and Clades 1.2, 1.3 and 3 were all subsequently evolved. Also the epidemiological investigation showed that the early imported breeders and the inter-region movements of live chickens facilitated the ALV-J dispersal throughout China and highlighted the needs to implement more effective containment measures.

Geographic isolation drives speciation in Nearctic aphids

Across herbivorous insect clades, species richness and host-use diversity tend to positively covary. This could be because host-use divergence drives speciation, or because it raises the ecological limits on species richness. To evaluate these hypotheses, we performed phylogenetic path model analyses of the species diversity of Nearctic aphids. Here, we show that variation in the species richness of aphid clades is caused mainly by host-use divergence, whereas variation in speciation rates is caused more by divergence in non-host-related niche variables. Aphid speciation is affected by both the evolution of host and non-host-related niche components, but the former is largely caused by the latter. Thus, our analyses suggest that host-use divergence can both raise the ecological limits on species richness and drive speciation, although in the latter case, host-use divergence tends to be a step along the causal path leading from non-host-related niche evolution to speciation.

The evolution of carotenoid-based plumage colours in passerine birds.

Many birds use carotenoids to colour their plumage yellow to red. Because birds cannot synthesise carotenoids, they need to obtain these pigments from food, although some species metabolise dietary carotenoids (which are often yellow) into derived carotenoids (often red). Here, we study the occurrence of yellow and red carotenoid-based plumage colours in the passerines, the largest bird radiation and quantify the effects of potential ecological and life-history drivers on their evolution. We scored the presence/absence of yellow and red carotenoid-based plumage in nearly 6,000 species and use Bayesian phylogenetic mixed models to assess the effects of carotenoid-availability in diet, primary productivity, body size, habitat and sexual selection. We also test the widespread assumption that red carotenoid-based colours are more likely to be the result of metabolization. Finally, we analyse the pattern of evolutionary transitions between yellow and red carotenoid-based plumage colours to determine whether, as predicted, the evolution of yellow carotenoid-based colours precedes red. We show that, as expected, both colours are more likely to evolve in smaller species and in species with carotenoid-rich diets. Yellow carotenoid-based plumage colours, but not red, are more prevalent in species that inhabit environments with higher primary productivity and closed vegetation. In general, females were more likely to have yellow and males more likely to have red carotenoid-based plumage colours, closely matching the effects of sexual selection. Our analyses also confirm that red carotenoid-based colours are more likely to be metabolised than yellow carotenoid-based colours. Evolutionary gains and losses of yellow and red carotenoid-based plumage colours indicate that red colours evolved more readily in species that already deposited yellow carotenoids, while the reverse was rarely the case. Our study provides evidence for a general, directional evolutionary trend from yellow to red carotenoid-based colours, which are more likely to be the result of metabolization. This may render them potentially better indicators of quality, and thus favoured by sexual selection.

Principled, practical, flexible, fast: a new approach to phylogenetic factor analysis.

Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic comparative methods seek to disentangle these relationships across the evolutionary history of a group of organisms. Unfortunately, most existing methods fail to accommodate high-dimensional data with dozens or even thousands of observations per taxon. Phylogenetic factor analysis offers a solution to the challenge of dimensionality. However, scientists seeking to employ this modeling framework confront numerous modeling and implementation decisions, the details of which pose computational and replicability challenges.We develop new inference techniques that increase both the computational efficiency and modeling flexibility of phylogenetic factor analysis. To facilitate adoption of these new methods, we present a practical analysis plan that guides researchers through the web of complex modeling decisions. We codify this analysis plan in an automated pipeline that distills the potentially overwhelming array of decisions into a small handful of (typically binary) choices.We demonstrate the utility of these methods and analysis plan in four real-world problems of varying scales. Specifically, we study floral phenotype and pollination in columbines, domestication in industrial yeast, life history in mammals, and brain morphology in New World monkeys.General and impactful community employment of these methods requires a data scientific analysis plan that balances flexibility, speed and ease of use, while minimizing model and algorithm tuning. Even in the presence of non-trivial phylogenetic model constraints, we show that one may analytically address latent factor uncertainty in a way that (a) aids model flexibility, (b) accelerates computation (by as much as 500-fold) and (c) decreases required tuning. These efforts coalesce to create an accessible Bayesian approach to high-dimensional phylogenetic comparative methods on large trees.

Soil pH Determines the Spatial Distribution, Assembly Processes, and Co-existence Networks of Microeukaryotic Community in Wheat Fields of the North China Plain.

Soil microeukaryotes play a pivotal role in soil nutrient cycling and crop growth in agroecosystems. However, knowledge of microeukaryotic community distribution patterns, assembly processes, and co-existence networks is greatly limited. Here, microbial eukaryotes in bulk and rhizosphere soils of the North China Plain were investigated. The results showed that soil pH was the driving factor for the microeukaryotic community composition in the bulk and rhizosphere soils. The soil microeukaryotic community could significantly differ between alkaline and acidic soils. The results indicated that the soil pH had a stronger effect than niche differences on community composition. Partial Mantel tests showed that soil pH and spatial distance had similar effects on the microeukaryotic community composition in the bulk soil. However, in the rhizosphere soil, spatial distance had a stronger effect than soil pH. Infer Community Assembly Mechanisms by Phylogenetic bin-based null model (iCAMP) analysis revealed that drift was the most important process driving microeukaryotic community assembly, with an average relative importance of 37.4–71.1%. Dispersal limitation displayed slightly greater importance in alkaline rhizosphere than in alkaline bulk soils. Meanwhile, the opposite trend was observed in acidic soils. In addition, the contribution of each assembly process to each iCAMP lineage “bin” varied according to the acidic or alkaline conditions of the soil and the niche environment. High proportions of positive links were found within the four ecological networks. Alkaline soil networks, especially the alkaline bulk soil network, showed greater complexity than the acidic soil networks. Natural connectivity analysis revealed that the rhizosphere community had a greater stability than the bulk soil community in alkaline soil. This study provides a foundation for understanding the potential roles of microbial eukaryotes in agricultural soil ecosystem functioning.

Riparian buffers provide refugia during secondary forest succession

AbstractAimSecondary forests regenerating from human disturbance are increasingly becoming a predominant forest type in many regions, and they play a significant role in forest community dynamics. Understanding the factors that underlie the variation in species responses during secondary succession is important for understanding community assembly and biodiversity monitoring and management. Because species vary in ecology and behaviour, responses to ecosystem change should vary among species. Here, we show that habitat type (riparian, upland), phylogeny, and species traits mediate anuran and lizard probability of occurrence and species richness in pasture and secondary forest.LocationSarapiquí and Osa Peninsula, Costa Rica.MethodsWe used phylogenetic occupancy models to estimate assemblage‐level and species‐specific responses to forest succession in 30 chronosequence sites that include pasture, secondary forest regenerating from pasture, and mature forest sites.ResultsFor the majority of species, we found increasing probability of occurrence in upland habitats as forest regenerated from pasture to secondary forest and similar probability of occurrence in riparian habitats across pasture, secondary forest, and mature forest sites. Species' responses to forest stage were phylogenetically correlated, and the trend was especially strong for anuran response to pasture sites. Anurans with lentic larval habitat had a positive occupancy response to pasture upland habitat, and anurans with lotic larval habitat had a variable response to different forest stages compared to mature forest.Main ConclusionsOur study, which focuses on sites that are minimally isolated from mature forest reference sites, indicated that anuran and lizard occupancy rapidly recovered to a level similar to mature forest in a relatively short time span (approximately 20 years). Riparian habitats are key ecosystem features in our system and provide refugia for organisms in early successional stages. Maintenance of vegetation along streams shows that we can mitigate forest conversion by maintaining riparian buffers.

High salt stress increases archaeal abundance and network connectivity in saline agricultural soils

Archaea are present in most ecosystems and are known to play a pivotal role in many ecological and biogeochemical processes. However, archaeal biogeographic patterns and driving processes in saline agricultural ecosystems remain poorly understood. To address this, we conducted a regional-scale survey of archaeal communities in saline agricultural soils throughout northwest China. While archaeal abundance was positively correlated with soil organic matter and total nitrogen levels, archaeal diversity was positively associated with salinity and ammonium-nitrogen (NH4+-N) levels. Dominant phyla belonged to Thaumarchaeota (45.52%) and Euryarchaeota (37.32%), however, the environmental factors affected these two phyla in opposing ways. Archaeal spatial distribution patterns and environmental preferences were also assessed and significant distance-decay relationships for dissimilarity in archaeal community structures were identified. Soil physicochemical properties, particularly salinity and organic matter, were strong determinants of archaeal community variation. Sixty percent of the variation could be explained by edaphic factors (34.5%) and spatial parameters (25.7%). Archaeal co-occurrence patterns were explored and more intra- than inter-kingdom associations were observed. The network topological features revealed that archaeal networks under the highest soil salinity level (>20 g kg−1) were more complex and had greater associations than those under a medium salinity level (5–20 g kg−1). Phylogenetic null modeling of community assembly suggested that archaea may transition from stochasticity in medium salinity soils to determinism in higher salinity soils. Overall, these findings offer new insight into the distribution patterns and drivers of archaeal community assembly in saline soils.