Diversity Patterns Research Articles

Understanding the Influence of Host Radiation on Symbiont Speciation through Parasites of Species Flocks.

(Adaptive) radiations have attracted evolutionary biologists for a long time as ideal model systems to study patterns and processes of often rapid speciation. However, whereas a wealth of (sometimes already genome-scale) data is available for host radiations, very few studies target the patterns of diversification in their symbionts, even though they would be excellent models to study symbiont speciation. Our review summarizes what little is known about general patterns of symbiont diversification in often iconic adaptive host radiations and to what extent these patterns are dependent on the evolutionary trajectories of their hosts. We identify research gaps that need to be addressed in the future and discuss the potential of approaches not yet typically used in these study systems, such as epidemiological disease modeling and new omics technologies, for significantly advancing our understanding of these complex eco-evolutionary relationships.

Molecular phylogeny and spatio‐temporal diversification of the Millettioid/Phaseoloid clade (Fabaceae: Papilionoideae)

AbstractThe Millettioid/Phaseoloid (or the Millettioid) clade is a major lineage of the subfamily Papilionoideae (Fabaceae) that is poorly understood in terms of its diversification and biogeographic history. To fill this gap, we generated a time‐calibrated phylogeny for 749 species representing c. 80% of the genera of this clade using nrDNA ITS, plastid matK, and plastome sequence (including 38 newly sequenced plastomes). Using this phylogenetic framework, we explored the clade's temporal diversification and reconstructed its ancestral areas and dispersal events. Our phylogenetic analyses support the monophyly of the Millettioid/Phaseoloid clade and four of its tribal lineages (Abreae, Desmodieae, Indigofereae, and Psoraleeae), while two tribal lineages sensu lato millettioids and phaseoloids are polyphyletic. The fossil‐calibrated dating analysis showed a nearly simultaneous divergence between the stem node (c. 62 Ma) and the crown node (c. 61 Ma) of the Millettioid/Phaseoloid clade in the Paleocene. The biogeographic analysis suggested that the clade originated in Africa and dispersed to Asia, Europe, Australia, and the Americas at different periods in the Cenozoic. We found evidence for shifts in diversification rates across the phylogeny of the Millettioid/Phaseoloid clade throughout the Cenozoic, with a rapid increase in net diversification rates since c. 10 Ma. Possible explanations for the present‐day species richness and distribution of the Millettioid/Phaseoloid clade include boreotropical migration, frequent intra‐ and intercontinental long‐distance dispersals throughout the Cenozoic, and elevated speciation rates following the Mid‐Miocene Climatic Optimum. Together, these results provide novel insights into major diversification patterns of the Millettioid/Phaseoloid clade, setting the stage for future evolutionary research on this important legume clade.

A roadmap of phylogenomic methods for studying polyploid plant genera.

Phylogenetic inference of polyploid species is the first step towards understanding their patterns of diversification. In this paper, we review the challenges and limitations of inferring species relationships of polyploid plants using traditional phylogenetic sequencing approaches, as well as the mischaracterization of the species tree from single or multiple gene trees. We provide a roadmap to infer interspecific relationships among polyploid lineages by comparing and evaluating the application of current phylogenetic, phylogenomic, transcriptomic, and whole-genome approaches using different sequencing platforms. For polyploid species tree reconstruction, we assess the following criteria: (1) the amount of prior information or tools required to capture the genetic region(s) of interest; (2) the probability of recovering homeologs for polyploid species; and (3) the time efficiency of downstream data analysis. Moreover, we discuss bioinformatic pipelines that can reconstruct networks of polyploid species relationships. In summary, although current phylogenomic approaches have improved our understanding of reticulate species relationships in polyploid-rich genera, the difficulties of recovering reliable orthologous genes and sorting all homeologous copies for allopolyploids remain a challenge. In the future, assembled long-read sequencing data will assist the recovery and identification of multiple gene copies, which can be particularly useful for reconstructing the multiple independent origins of polyploids.

Impacts of Quaternary Climatic Changes on the Diversification of Riverine Cichlids in the Lower Congo River.

Climatic and geomorphological changes during the Quaternary period impacted global patterns of speciation and diversification across a wide range of taxa, but few studies have examined these effects on African riverine fish. The lower Congo River is an excellent natural laboratory for understanding complex speciation and population diversification processes, as it is hydrologically extremely dynamic and recognized as a continental hotspot of diversity harboring many narrowly endemic species. A previous study using genome-wide SNP data highlighted the importance of dynamic hydrological regimes to the diversification and speciation in lower Congo River cichlids. However, historical climate and hydrological changes (e.g., reduced river discharge during extended dry periods) have likely also influenced ichthyofaunal diversification processes in this system. The lower Congo River offers a unique opportunity to study climate-driven changes in river discharge, given the massive volume of water from the entire Congo basin flowing through this short stretch of the river. Here, we, for the first time, investigate the impacts of paleoclimatic factors on ichthyofaunal diversification in this system by inferring divergence times and modeling patterns of gene flow in four endemic lamprologine cichlids, including the blind cichlid, Lamprologus lethops. Our results suggest that Quaternary climate changes associated with river discharge fluctuations may have impacted the diversification of species along the system and the emergence of cryptophthalmic phenotype in some endemic species. Our study, using reduced representation sequencing (2RADseq), indicates that the lower Congo River lamprologines emerged during the Early-Middle Pleistocene transition, characterized as one of the earth's major climatic transformation periods. Modeling results suggest that gene flow across populations and between species was not constant but occurred in temporally constrained pulses. We show that these results correlate with glacial-interglacial fluctuations. The current hyper-diverse fish assemblages of the lower Congo River riverscape likely reflect the synergistic effects of multiple drivers fueling complex evolutionary processes through time.

Bears into the Niche-Space: Phylogeography and Phyloclimatic Model of the Family Ursidae

Assessing niche evolution remains an open question and an actively developing area of study. The family Ursidae consists of eight extant species for which, despite being the most studied family of carnivores, little is known about the influence of climate on their evolutionary history and diversification. We evaluated their evolutionary patterns based on a combined phylogeography and niche modeling approach. We used complete mitogenomes, estimated divergence times, generated ecological niche models and applied a phyloclimatic model to determine the species evolutionary and diversification patterns associated with their respective environmental niches. We inferred the family evolutionary path along the environmental conditions of maximum temperature and minimum precipitation, from around 20 million years ago to the present. Our findings show that the phyloclimatic niches of the bear species occupy most of the environmental space available on the planet, except for the most extreme warm conditions, in accordance with the wide geographic distribution of Ursidae. Moreover, some species exhibit broader environmental niches than others, and in some cases, they explore precipitation axes more extensively than temperature axes or vice versa, suggesting that not all species are equally adaptable to these variables. We were able to elucidate potential patterns of niche conservatism and evolution, as well as niche overlapping, suggesting interspecific competitive exclusion between some of the bear species. We present valuable insights into the ecological and evolutionary processes driving the diversification and distribution of the Ursidae. Our approach also provides essential information for guiding effective conservation strategies, particularly in terms of distribution limits in the face of climate change.

Patterns of morphological diversification are influenced by dietary evolution in a highly species-rich lizard radiation

The diversification of lineages is facilitated or constrained by the simultaneous evolution of multiple components of the phenotype that interact with each other during the course of speciation. When evolutionary radiations are adaptive, lineages proliferate via the emergence of multiple phenotypic optima that underlie diversification of species across multiple ecological niches. When radiations are non-adaptive, lineage proliferation unfolds constrained by similar (or nearly identical) correlations among traits that keep phenotypic and ecological diversity across newly emerging species within a single optimum. Nature offers very few opportunities where both types of diversification occur between closely related and highly diverse lineages. The Liolaemidae family of South American lizards offers unique such opportunities given two speciose lineages that have rapidly proliferated via adaptive (Liolaemus) and non-adaptive (Phymaturus) radiations. We analyze body shape in lizards in association with type of diet (herbivory, omnivory or carnivory). In these lizards, diet types have been suggested to be linked to body size. Our results confirm this hypothesis, with three body size optima tightly linked to all three diet types when radiation is both adaptive and non-adaptive. Diet reconstruction along their evolutionary history showed that the common ancestor of Liolaemidae was likely omnivorous, which is matched by ancestral reconstruction of body size. Phylogenetic PCA revealed that herbivorous species generally have more differentiated body shape than insectivores and omnivores. Herbivorous species have evolved larger heads, shorter hindlimbs and a small difference between forelimb and hindlimb length. In contrast, omnivores and insectivores have smaller heads and longer hindlimbs. Collectively, trophic niche plays an important role in defining body shape and size across species within lineages, and the patterns of trait–ecology correlations remain consistent when lineages have diversified via adaptive and non-adaptive radiation.

Genetically- and environmentally-dependent processes drive interspecific and intraspecific divergence in the Chinese relict endemic genus Dipteronia

China is a hotspot of relict plant species that were once widespread throughout the Northern Hemisphere. Recent research has demonstrated that the occurrence of long-term stable refugia in the mountainous regions of central and south-western China allowed their persistence through the late Neogene climate fluctuations. One of these relict lineages is Dipteronia, an oligotypic tree genus with a fossil record extending to the Paleocene. Here, we investigated the genetic variability, demographic dynamics and diversification patterns of the two currently recognized Dipteronia species (Dipteroniasinensis and D.dyeriana). Molecular data were obtained from 45 populations of Dipteronia by genotyping three cpDNA regions, two single copy nuclear genes and 15 simple sequence repeat loci. The genetic study was combined with niche comparison analyses on the environmental space, ecological niche modeling, and landscape connectivity analysis. We found that the two Dipteronia species have highly diverged both in genetic and ecological terms. Despite the incipient speciation processes that can be observed in D. sinensis, the occurrence of long-term stable refugia and, particularly, a dispersal corridor along Daba Shan-west Qinling, likely ensured its genetic and ecological integrity to date. Our study will not only help us to understand how populations of Dipteronia species responded to the tectonic and climatic changes of the Cenozoic, but also provide insight into how Arcto-Tertiary relict plants in East Asia survived, evolved, and diversified.

Dense infraspecific sampling reveals cryptic differentiation in the enigmatic hemiparasitic love vine Cassytha filiformis (Lauraceae)

AbstractSpecies delimitation remains a challenge worldwide, especially in highly diverse tropical and subtropical regions. Here, we use an integrative approach that combines morphology, phylogenomics, and species distribution modeling (SDM) to clarify the cryptic differentiation within the enigmatic hemiparasitic love vine Cassytha filiformis (Lauraceae) in China and adjacent regions. We generated complete plastid genomes and nuclear ribosomal sequences for diverse samples from across the species range and compared results with previously published plastid data, recovering two well‐supported monophyletic clades. Further, the analysis revealed significant differences in two morphological characters and SDM, indicating distinct environmental factors influencing their distributions. Fossil‐calibrated analyses to estimate the origins and diversification patterns for the cryptic species gave divergence age estimates corresponding to the Oligo‐Miocene; a period of new ecological opportunities associated with the prevailing East Asian monsoon. Multivariate analyses support the conclusion that southern China and adjacent regions have a different, previously unknown, cryptic lineage of C. filiformis. Our study highlights the importance of using multivariate approach to characterize plant species, as well as the significant role that past climatic changes have played in driving speciation in parasitic plants in tropical and subtropical zones.

Phylogenomics of Tetraopes longhorn beetles unravels their evolutionary history and biogeographic origins

Tetraopes longhorn beetles are known for their resistance to milkweed plant toxins and their coevolutionary dynamics with milkweed plants (Asclepias). This association is considered a textbook example of coevolution, in which each species of Tetraopes is specialized to feed on one or a few species of Asclepias. A major challenge to investigating coevolutionary hypotheses and conducting molecular ecology studies lies in the limited understanding of the evolutionary history and biogeographical patterns of Tetraopes. By integrating genomic, morphological, paleontological, and geographical data, we present a robust phylogeny of Tetraopes and their relatives, using three inference methods with varying subsets of data, encompassing 2–12 thousand UCE loci. We elucidate the diversification patterns of Tetraopes species across major biogeographical regions and their colonization of the American continent. Our findings suggest that the genus originated in Central America approximately 21 million years ago during the Miocene and diversified from the Mid-Miocene to the Pleistocene. These events coincided with intense geological activity in Central America. Additionally, independent colonization events in North America occurred from the Late Miocene to the early Pleistocene, potentially contributing to the early diversification of the group. Our data suggest that a common ancestor of Tetraopini migrated into North America, likely facilitated by North Atlantic land bridges, while closely related tribes diverged in Asia and Europe during the Paleocene. Establishing a robust and densely sampled phylogeny of Tetraopes beetles provides a foundation for investigating micro- and macroevolutionary phenomena, including clinal variation, coevolution, and detoxification mechanisms in this ecologically important group.

Seed bank and aboveground vegetation of Atlantic Forest re‐growing on mining tailings in Mariana: Highlighting diversity patterns of functional groups

AbstractNatural regeneration after mining activities depends largely on the soil seed bank (SSB) and aboveground vegetation (AGV) richness and composition. We evaluated the species diversity pattern of the SSB and AGV on soil and technosol across second‐growth Atlantic Forests (SGFs) after mining tailings deposition in Mariana, southeastern Brazil. Two second‐growth Atlantic seasonal semideciduous forests of different stand ages were selected: a 3‐year‐old stand of SGF re‐growing on tailings (SGF tailings) and a 30‐year‐old stand of native reference forest not affected by tailings (SGF nontailings). Overall, the results showed significant differences in forest attributes (species richness and composition) in the SSB and AGV between the two forest patches evaluated (SGF tailings and SGF nontailings). Moreover, both nonzoochoric and zoochoric dispersed species of AGV showed significant differences between second‐growth forests, with higher variability of community‐weighted mean in SGF tailings. The result shows smaller differences in species richness between forest types for both SBB (ranging 85 and 90 species) and AGV (~55 species). Despite the time difference between the secondary forest and the absence of zoochoric species in the tailings seed bank, the AGV that are re‐growing on mining tailings presented a high proportion of zoochoric species. This pattern of species richness and community composition variability observed in the technosol seed bank, and AGV that are re‐growing after the deposition of mining tailings are important recovery indicators for plant communities affected.

Conserved patterns of sequence diversification provide insight into the evolution of two-component systems in Enterobacteriaceae.

Two-component regulatory systems (TCSs) are a major mechanism used by bacteria to sense and respond to their environments. Many of the same TCSs are used by biologically diverse organisms with different regulatory needs, suggesting that the functions of TCS must evolve. To explore this topic, we analysed the amino acid sequence divergence patterns of a large set of broadly conserved TCS across different branches of Enterobacteriaceae, a family of Gram-negative bacteria that includes biomedically important genera such as Salmonella, Escherichia, Klebsiella and others. Our analysis revealed trends in how TCS sequences change across different proteins or functional domains of the TCS, and across different lineages. Based on these trends, we identified individual TCS that exhibit atypical evolutionary patterns. We observed that the relative extent to which the sequence of a given TCS varies across different lineages is generally well conserved, unveiling a hierarchy of TCS sequence conservation with EnvZ/OmpR as the most conserved TCS. We provide evidence that, for the most divergent of the TCS analysed, PmrA/PmrB, different alleles were horizontally acquired by different branches of this family, and that different PmrA/PmrB sequence variants have highly divergent signal-sensing domains. Collectively, this study sheds light on how TCS evolve, and serves as a compendium for how the sequences of the TCS in this family have diverged over the course of evolution.

Assessing genetic diversity and geographical differentiation in a global collection of wild soybean (Glycine soja Sieb. et Zucc.) and assigning a mini-core collection.

Wild soybean (Glycine soja), the ancestor of the cultivated soybean (G. max), is a crucial resource for capturing the genetic diversity of soybean species. In this study, we used a set of 78 genome-wide microsatellite markers to analyse the genetic diversity and geographic differentiation patterns in a global collection of 2,050 G. soja accessions and a mini-core collection of G. max stored in two public seed banks. We observed a notable reduction in the genetic diversity of G. max compared with G. soja and identified a close phylogenetic relationship between G. max and a G. soja subpopulation located in central China. Furthermore, we revealed substantial genetic divergence between northern and southern subpopulations, accompanied by diminished genetic diversity in the northern subpopulations. Two clusters were discovered among the accessions from north-eastern China-one genetically close to those from South Korea and Southern Japan, and another close to those from Amur Oblast, Russia. Finally, 192 accessions were assigned to a mini-core collection of G. soja, retaining 73.8% of the alleles detected in the entire collection. This mini-core collection is accessible to those who need it, facilitating efficient evaluation and utilization of G. soja genetic resources in soybean breeding initiatives.

Species Diversity and Conservation of Typhlocybinae (Heteroptera: Cicadellidae) in China

Abstract Species diversity is undergoing rapid reductions globally. Identifying the causes underlying species diversity patterns and biodiversity hotspots is critical for developing conservation strategies. In this study, the 4,594 occurrence records of 854 Typhlocybinae (Heteroptera: Cicadellidae) species in China were used to investigate the factors affecting species richness and endemism patterns as well as identify species diversity hotspots to establish their conservation status. Generalized linear models and hierarchical partitioning were used to assess the effects of 6 environmental factors on species richness and endemism. Species diversity hotspots were obtained by integrating the 10 grids with highest levels of species richness and endemism; the conservation status of these hotspots was assessed via gap analysis. We found that species richness and endemism distribution of Typhlocybinae in China were heterogeneous, mainly concentrated in southern and central areas. The results also showed that plants were the most important environmental factors affecting species richness and endemism patterns, followed by niche conservatism. The 10 hotspots were identified; however, they were not fully protected by the existing nature reserves. This study highlights the importance of plants and niche conservatism in shaping species richness and endemism patterns of Typhlocybinae. Moreover, establishment of new nature reserves in hotspot areas with a conservation gap is required.

Biodiversity patterns of macrofauna associated with Halodule wrightii (Ascherson) in meadows of north-eastern Brazil

Context Seagrass meadows are highly productive habitats with a vast species diversity that perform multiple ecosystem services. The fauna associated with these environments is responsible for many of the ecosystem services. Therefore, the fauna composition and functional characteristics should be considered in studies addressing seagrass meadows. Aims This study aimed to evaluate the differences in the taxonomic and functional compositions of the macrofauna associated with Halodule wrightii (Ascherson) meadows subject to different settings of habitat characteristics in the shallow coastal regions of the north-eastern coast of Brazil. Methods We used the Hill diversity series to estimate taxonomic diversity, whereas functional diversity was estimated through biological-trait analyses. Key results Distinct patterns of taxonomic and functional diversities were observed among meadows. However, the composition of functional traits diverged more. Lower taxonomic and functional diversity were observed in the Suape meadows, with values mainly related to the low organic matter content. Catuama meadows presented opposite results, associated with higher organic matter and plant density. Conclusions The meadow heterogeneity can influence the associated macrofauna and its functional characteristics. Implications These results are highly relevant for predicting the consequences of changes in seagrass meadows and how this affects the functioning of these ecosystems.

Global patterns and determinants of multiple facets of plant diversity

AbstractAimCombining different biodiversity dimensions can reveal new diversity patterns disclosing the relative roles of historical, environmental and anthropogenic factors in shaping global seed plant diversity.LocationGlobal.Time periodPresent.Major taxa studiedVascular plants.MethodsWe collated a database encompassing taxonomic (249,000 species), functional and phylogenetic information (34,694 species) of seed plants across different regions of the world. Species richness in each region was weighted accounting for their phylogenetic and functional distinctiveness, obtaining a new metric—μ‐diversity—which was modelled to disentangle the relative roles of historical factors such as climate variability since the Last Glacial Maximum (LGM), environmental features (e.g. actual evapotranspiration—AET) and anthropogenic factors (past and current).ResultsHigher μ‐diversity was observed in Papuasia, South East Asia, Australia and Central America, whereas the lowest values were primarily located in the Northern Hemisphere. Climate variability and AET were the most important determinants of μ‐diversity and individual diversity facets, whereas the importance of past human impacts (i.e. the onset of pastoralism) equated or exceeded those of the present ones.Main conclusionsOur integrative approach proved more sensitive in describing species diversity patterns. Few areas on Earth host high and unique proportions of multiple diversity facets and individual diversity facets contribute differently to μ‐diversity across continents. Historical climate stability and water‐energy dynamics strongly affect species diversity, but we also observed that past land‐use legacy may have influenced current plant diversity, which is under intense anthropogenic pressure, especially in Asia as well as in Central and South America.

Eco-evolutionary evidence for the global diversity pattern of Cycas (Cycadaceae).

The evolution of the latitudinal diversity gradient (LDG), characterized by a peak in diversity toward the tropics, has captured significant attention in evolutionary biology and ecology. However, the inverse LDG (i-LDG) mechanism, wherein species richness increases toward the poles, remains inadequately explored. Cycads are among one of the oldest lineages of extant seed plants and have undergone extensive diversification in the tropics. Intriguingly, the extant cycad abundance exhibits an i-LDG pattern, and the underlying causes for this phenomenon remain largely elusive. Here, using 1,843 nuclear genes from a nearly complete sampling, we conducted comprehensive phylogenomic analyses to establish a robust species-level phylogeny for Cycas, the largest genus within cycads. We then reconstructed the spatial-temporal dynamics and integrated global environmental data to evaluate the roles of species ages, diversification rates, contemporary environment, and conservatism to ancestral niches in shaping the i-LDG pattern. We found Cycas experienced decreased diversification rates, coupled with the cooling temperature since its origin in the Eocene from continental Asia. Different regions have distinctively contributed to the formation of i-LDG for Cycas, with the northern hemisphere acting as evolutionary museums and the southern hemisphere serving as cradles. Moreover, water-related climate variables, specifically precipitation seasonality and potential evapotranspiration, were identified as paramount factors constraining Cycas species richness in the rainforest biome near the equator. Notably, the adherence to ancestral monsoonal climates emerges as a critical factor in sustaining the diversity pattern. This study underscores the imperative of integrating both evolutionary and ecological approaches to comprehensively unravel the mechanisms underpinning global biodiversity patterns.

Relatedness and regional economic complexity: Good news for some, bad news for others

PurposeThis article aims to evaluate the entry and exit of companies from local productive structures, with a specific focus on the sectoral complexity of these activities and the complexity of these portfolios. The study focuses on empirically demonstrating the thesis that related economic diversification exacerbates the development gap between more and less complex regions.Design/methodology/approachThe article uses indicators formulated by the economic complexity approach. They allow a relevant descriptive analysis of the economic diversification process in Brazilian micro-regions and provide the foundation for the econometric tests conducted. Through three distinct estimation strategies (OLS, logit, probit), the influence of complexity and relatedness on the entry and exit events of firms from local portfolios is tested.FindingsIn all estimated models, the stronger relationship between an activity and a portfolio significantly increases its probability of entering the productive structure and, at the same time, acts as a significant factor in preventing its exit. Furthermore, the results reveal that the complexity of a sector reduces the probability of its specialization in less complex regions while increasing it in more complex regions. On the other hand, sectoral complexity significantly increases the probability of a sector leaving less complex local structures but has no significant effect in highly complex regions.Research limitations/implicationsDue to the data used, the indicators are calculated considering only formal job numbers. Additionally, the tests do not detect the influence of spatial issues. These limitations should be addressed by future research.Practical implicationsThe article characterizes a prevailing process of uneven development among Brazilian regions and brings relevant implications, primarily for policymakers. Specifically, for less complex regions, policies should focus on creating opportunities to improve their diversification capabilities in complex sectors that are not too distant from their portfolios.Originality/valueThe article makes an original contribution by proposing an evaluation of regional diversification in Brazil with a focus on complexity, introducing a more detailed differentiation of regions based on their complexity levels and examining the impact of sectoral complexity on diversification patterns within each group.

Spatiotemporal distribution patterns of soil ciliate communities in the middle reaches of the Yarlung Zangbo River

Introduction: Soil ciliates, as protozoa, play a crucial role in biogeochemical cycling and the soil food web, yet they are highly sensitive to environmental fluctuations in soil conditions. The diversity and biogeographic characteristics of soil ciliates in the Tibetan Plateau remain poorly understood. As part of a regional survey focused on soil ciliate diversity, we investigated the composition and spatiotemporal variations of soil ciliate communities along the Yarlung Zangbo River, a representative soil habitat in the Tibetan Plateau.Methods: A total of 290 soil samples were collected from four habitat types of grassland, shrubland, forestland and wetland in the middle reaches of the Yarlung Zangbo River during the wet and dry seasons, and 138 species of ciliates were identified.Results: Soil ciliate diversity exhibited greater variation across habitat types than seasons. Moreover, soil ciliate diversity was higher during the wet season compared to the dry season, with the wetland habitat showing the highest diversity and the grassland habitat displaying the lowest. We observed spatiotemporal heterogeneity in the composition of soil ciliate communities across different seasons and habitat types. Notably, Litostomatea, Karyorelictea, and Prostomatea predominated in ciliate communities during the wet season and in grassland habitat. Phyllopharyngers dominated during dry seasons and in forested regions, while Spirotrichea species were prevalent in wetland and forested areas. The co-occurrence network analysis showed that soil ciliate community was more complex in wet season than in dry season, and the stability of soil ciliate community in wet season was higher than that in dry season. The stability of soil ciliate community in wetland was higher than that in forestland, shrubland and grassland, and the anti-interference ability was stronger. Soil temperature (ST), Total nitrogen (TN), Soil organic matter (SOM) and Soil water content (SWC) are important factors affecting the structure of soil ciliate community. By influencing the metabolic rate and nutrient acquisition of soil ciliates, the distribution pattern of soil ciliate community diversity in the middle reaches of Yarlung Zangbo River is shaped.Discussion: In summary, this study revealed the distribution pattern of soil ciliate community diversity in the Yarlung Zangbo River Basin, and the key factors affecting the spatial and temporal differences and stability of the community, enhancing our understanding of how ciliates adapt to environmental conditions in soil habitats across the Tibetan Plateau.

Integration of genomic and ecological methods inform management of an undescribed, yet highly exploited, sardine species.

Assessing genetic diversity within species is key for conservation strategies in the context of human-induced biotic changes. This is important in marine systems, where many species remain undescribed while being overfished, and conflicts between resource-users and conservation agencies are common. Combining niche modelling with population genomics can contribute to resolving those conflicts by identifying management units and understanding how past climatic cycles resulted in current patterns of genetic diversity. We addressed these issues on an undescribed but already overexploited species of sardine of the genus Harengula. We find that the species distribution is determined by salinity and depth, with a continuous distribution along the Brazilian mainland and two disconnected oceanic archipelagos. Genomic data indicate that such biogeographic barriers are associated with two divergent intraspecific lineages. Changes in habitat availability during the last glacial cycle led to different demographic histories among stocks. One coastal population experienced a 3.6-fold expansion, whereas an island-associated population contracted 3-fold, relative to the size of the ancestral population. Our results indicate that the island population should be managed separately from the coastal population, and that a Marine Protected Area covering part of the island population distribution can support the viability of this lineage.

Integrative phylogenetic, phylogeographic and morphological characterisation of the Unio crassus species complex reveals cryptic diversity with important conservation implications

The global decline of freshwater mussels and their crucial ecological services highlight the need to understand their phylogeny, phylogeography and patterns of genetic diversity to guide conservation efforts. Such knowledge is urgently needed for Unio crassus, a highly imperilled species originally widespread throughout Europe and southwest Asia. Recent studies have resurrected several species from synonymy based on mitochondrial data, revealing U. crassus to be a complex of cryptic species. To address long-standing taxonomic uncertainties hindering effective conservation, we integrate morphometric, phylogenetic, and phylogeographic analyses to examine species diversity within the U. crassus complex across its entire range. Phylogenetic analyses were performed using cytochrome c oxidase subunit I (815 specimens from 182 populations) and, for selected specimens, whole mitogenome sequences and Anchored Hybrid Enrichment (AHE) data on ∼ 600 nuclear loci. Mito-nuclear discordance was detected, consistent with mitochondrial DNA gene flow between some species during the Pliocene and Pleistocene. Fossil-calibrated phylogenies based on AHE data support a Mediterranean origin for the U. crassus complex in the Early Miocene. The results of our integrative approach support 12 species in the group: the previously recognised Unio bruguierianus, Unio carneus, Unio crassus, Unio damascensis, Unio ionicus, Unio sesirmensis, and Unio tumidiformis, and the reinstatement of five nominal taxa: Unio desectusstat. rev., Unio gontieriistat. rev., Unio mardinensisstat. rev., Unio nanusstat. rev., and Unio vicariusstat. rev. Morphometric analyses of shell contours reveal important morphospace overlaps among these species, highlighting cryptic, but geographically structured, diversity. The distribution, taxonomy, phylogeography, and conservation of each species are succinctly described.