A multi-species co-occurrence index to avoid type II errors in null model testing

Community structure is determined by the interplay among different processes, including biotic interactions, abiotic filtering, and dispersal. Their effects can be detected by comparing observed patterns of co-occurrence between different species (e.g. C-score and the natural metric) to patterns generated by null models based on permutations of species-by-site matrices under constraints on row or column sums. These comparisons enable us to detect significant signals of species association or dissociation, from which the type of biotic interactions between species (e.g. facilitative or antagonistic) can be inferred. Commonly used patterns are based on the levels of co-occurrence between randomly paired species. The level of co-occurrence for three or more species is rarely considered, ignoring the potential existence of functional guilds or motifs composed of multiple species within the community. Null model tests that do not consider multi-species co-occurrence could therefore generate false negatives (Type II error) in detecting non-random forces at play that would only be apparent for such guilds. Here, we propose a multi-species co-occurrence index (hereafter, joint occupancy) that measures the number of sites jointly occupied by multiple species simultaneously, of which the pairwise metric of co-occurrence is a special case. Using this joint occupancy index along with standard permutation algorithms for null model testing, we illustrate nine archetypes of multi-species co-occurrence and explore how frequent they are in the seminal database of 289 species-by-site community matrices published by Atmar and Patterson in 1995. We show that null model testing using pairwise co-occurrence metrics could indeed lead to severe Type II errors in one specific archetype, accounting for 2.4% of the tested community matrices.

The effect of forest land allocation on understory plant species associations

Species association is a reciprocal relationship among species within a community and can estimate the community composition. This research aimed to obtain information regarding the level of dominance and plant species association in each forest land allocation. Data analysis tested in this study constituted an analysis of the importance value index and association analysis performed on the main constituent species with INP > 10% using a 2x2 Contingency Table. The research revealed that species association in understorey plants in plantation forests contained one pair with real associations, five with unreal associations, six with positive associations, and none with negative associations. Meanwhile, there were no real associations in protected forest areas, ten pairs with unreal associations, four pairs with positive associations, and six pairs with negative ones. There were two pairs with real associations in natural forests outside the company’s concessions, 13 species with unreal associations, four pairs with positive associations, and 11 pairs with negative associations.

Diversity of Predators Associated with the Mealybug Complex in Cassava Growing Districts of Tamil Nadu, India

An extensive survey was carried to study the diversity of predators associated with the mealybug complex in the cassava growing districts viz., Salem, Namakkal, Erode, Tiruppur and Coimbatore of Tamil Nadu, India from January to September, 2021. The survey revealed the dominance of Phenacoccus manihoti Matile-Ferrero 1977 (Hemiptera: Pseudococcidae) than other mealybug species in all the surveyed districts. The incidence of P. manihoti ranged from 12 to 90 per cent while Paracoccus marginatus Williams and Granara de Willink 1992 (Hemiptera: Pseudococcidae) incidence was found to be between 8 and 54 per cent. The incidence of Ferrisia virgata Cockerell 1893 (Hemiptera: Pseudococcidae) was found to be very low (8-16%) compared to other mealybug species. Association of total predators with P. manihoti were found to be maximum (30.87%) followed by the total predators with P. marginatus (6.49%) whereas 0.53 per cent of total predators associated with F. virgata. The fourteen different predators viz., Cryptolaemus montrouzieri Mulsant 1853 (Coleoptera: Coccinellidae), Menocheilus sexmaculatus Fabricius 1781 (Coleoptera: Coccinellidae), Anegleis cardoni Weise 1892 (Coleoptera: Coccinellidae), Hyperaspis maindroni Sicard 1929 (Coleoptera: Coccinellidae), Brumoides suturalis Fabricius 1798 (Coleoptera: Coccinellidae), Scymnus spp. (Coleoptera: Coccinellidae), Chrysoperla spp. (Neuroptera: Chrysopidae), Mallada spp. (Neuroptera: Chrysopidae), Spalgis epeus Westwood 1851 (Lepidoptera: Lycaenidae), Geocoris spp. (Hemiptera: Geocoridae), Cardiastethus spp. (Hemiptera: Anthocoridae), Diadiplosis spp. (Diptera: Cecidomyiidae), Oxyopes spp. (Araneae: Oxyopidae) and Argiope spp. (Araneae: Araneidae) were found to associated with the mealybug species viz.,P. manihoti, P. marginatus and F. virgata. Among the predators of the mealybug complex, the most relative abundant species were H. maindroni (11.74%) associated with P. manihoti and C. montrouzieri (6.49%) associated with P. marginatus followed by S. epeus (0.67%) associated with F. virgata. The diversity of predators assessed through Simpson’s Index of Diversity, Shannon-Wiener, Pielou’s Evenness and Margalef indices revealed highest species diversity, species richness and species evenness in Namakkal district.

Vegetation community and species association of Castanopsis spp. at its habitat in the remnant forest of Cibodas Botanical Garden, Indonesia

Nurdiana DR, Buot IE Jr. 2021. Vegetation community and species association of Castanopsis spp. at its habitat in the remnant forest of Cibodas Botanical Garden, Indonesia. Biodiversitas 22: 4799-4807. Castanopsis is one of the genera of Fagaceae with a large distribution in Indonesia. The genus can be found easily in Java, Sumatera and Kalimantan. Several studies have found an association between Castanopsis and environmental factors dealing with the diversity, dispersal and propagation. So far, there has been no agreement on how Castanopsis interacts with other species within the same genus in nature, especially in the remnant forest under a fragmented state. The objectives of the study were to determine the vegetation associated with Castanopsis and whether each species of the genus Castanopsis co-occur within the remnant forest? A total of 60 plots have been studied in 3 different sites of the remnant forest. The nested sampling method was used to identify the trees, saplings and seedlings. Sixty-seven total species of trees, 140 species of saplings and 121 species of seedlings in Cibodas Botanical Garden remnant forest were recorded. The diversity index for tree, sapling and seedling were 3.5, 3.9 and 4.1, respectively, while evenness index for tree, sapling and seedling were 0.81, 0.8 and 0.85 respectively. The interspecific association of the genus Castanopsis was restricted to C. javanica x C. tungurrut. They are associated positively at sapling stage with Jaccard index of 0.2. However, at tree stage, there was no association out of the pair, C. javanica x C. tungurrut. Competition within genus Castanopsis occurred in the same habitat, though at a lesser degree which needs to be studied further. Dominance of many pioneer species (Oreocnide integrifolia (Gaudich.) Miq., Ostodes paniculata Blume, Cestrum aurantiacum Lindl. and others) at tree stage had been evident. This implies that the Cibodas remnant forest is still in the process of succession towards a more stable climax state.

Announcing Big-Bee: An initiative to promote understanding of bees through image and trait digitization

While bees are critical to sustaining a large proportion of global food production, as well as pollinating both wild and cultivated plants, they are decreasing in both numbers and diversity. Our understanding of the factors driving these declines is limited, in part, because we lack sufficient data on the distribution of bee species to predict changes in their geographic range under climate change scenarios. Additionally lacking is adequate data on the behavioral and anatomical traits that may make bees either vulnerable or resilient to human-induced environmental changes, such as habitat loss and climate change. Fortunately, a wealth of associated attributes can be extracted from the specimens deposited in natural history collections for over 100 years. Extending Anthophila Research Through Image and Trait Digitization (Big-Bee) is a newly funded US National Science Foundation Advancing Digitization of Biodiversity Collections project. Over the course of three years, we will create over one million high-resolution 2D and 3D images of bee specimens (Fig. 1), representing over 5,000 worldwide bee species, including most of the major pollinating species. We will also develop tools to measure bee traits from images and generate comprehensive bee trait and image datasets to measure changes through time. The Big-Bee network of participating institutions includes 13 US institutions (Fig. 2) and partnerships with US government agencies. We will develop novel mechanisms for sharing image datasets and datasets of bee traits that will be available through an open, Symbiota-Light (Gilbert et al. 2020) data portal called the Bee Library. In addition, biotic interaction and species association data will be shared via Global Biotic Interactions (Poelen et al. 2014). The Big-Bee project will engage the public in research through community science via crowdsourcing trait measurements and data transcription from images using Notes from Nature (Hill et al. 2012). Training and professional development for natural history collection staff, researchers, and university students in data science will be provided through the creation and implementation of workshops focusing on bee traits and species identification. We are also planning a short, artistic college radio segment called "the Buzz" to get people excited about bees, biodiversity, and the wonders of our natural world.

Renewed Public Health Threat from Emerging Lyssaviruses

Pathogen discovery contributes to our knowledge of bat-borne viruses and is linked to the heightened interest globally in bats as recognised reservoirs of zoonotic agents. The transmission of lyssaviruses from bats-to-humans, domestic animals, or other wildlife species is uncommon, but interest in these pathogens remains due to their ability to cause an acute, progressive, invariably fatal encephalitis in humans. Consequently, the detection and characterisation of bat lyssaviruses continues to expand our knowledge of their phylogroup definition, viral diversity, host species association, geographical distribution, evolution, mechanisms for perpetuation, and the potential routes of transmission. Although the opportunity for lyssavirus cross-species transmission seems rare, adaptation in a new host and the possibility of onward transmission to humans requires continued investigation. Considering the limited efficacy of available rabies biologicals it is important to further our understanding of protective immunity to minimize the threat from these pathogens to public health. Hence, in addition to increased surveillance, the development of a niche pan-lyssavirus vaccine or therapeutic biologics for post-exposure prophylaxis for use against genetically divergent lyssaviruses should be an international priority as these emerging lyssaviruses remain a concern for global public health.

Snakes on an African plain: the radiation of Crotaphopeltis and Philothamnus into open habitat (Serpentes: Colubridae)

Background The African continent is comprised of several different biomes, although savanna is the most prevalent. The current heterogeneous landscape was formed through long-term vegetation shifts as a result of the global cooling trend since the Oligocene epoch. The overwhelming trend was a shift from primarily forest, to primarily savanna. As such, faunal groups that emerged during the Paleogene/Neogene period and have species distributed in both forest and savanna habitat should show a genetic signature of the possible evolutionary impact of these biome developments. Crotaphopeltis and Philothamnus (Colubridae) are excellent taxa to investigate the evolutionary impact of these biome developments on widespread African colubrid snakes, and whether timing and patterns of radiation are synchronous with biome reorganisation. Methods A phylogenetic framework was used to investigate timing of lineage diversification. Phylogenetic analysis included both genera as well as other Colubridae to construct a temporal framework in order to estimate radiation times for Crotaphopeltis and Philothamnus. Lineage diversification was estimated in Bayesian Evolutionary Analysis Sampling Trees (BEAST), using two mitochondrial markers (cyt–b, ND4), one nuclear marker (c–mos), and incorporating one fossil and two biogeographical calibration points. Vegetation layers were used to classify and confirm species association with broad biome types (‘closed’ = forest, ‘open’ = savanna/other), and the ancestral habitat state for each genus was estimated. Results Philothamnus showed an ancestral state of closed habitat, but the ancestral habitat type for Crotaphopeltis was equivocal. Both genera showed similar timing of lineage diversification diverging from their sister genera during the Oligocene/Miocene transition (ca. 25 Mya), with subsequent species radiation in the Mid-Miocene. Philothamnus appeared to have undergone allopatric speciation during Mid-Miocene forest fragmentation. Habitat generalist and open habitat specialist species emerged as savanna became more prevalent, while at least two forest associated lineages within Crotaphopeltis moved into Afromontane forest habitat secondarily and independently. Discussion With similar diversification times, but contrasting ancestral habitat reconstructions, we show that these genera have responded very differently to the same broad biome shifts. Differences in biogeographical patterns for the two African colubrid genera is likely an effect of distinct life-history traits, such as the arboreous habits of Philothamnus compared to the terrestrial lifestyle of Crotaphopeltis.

Cross-species Association Between Telomere Length and Glucocorticoid Exposure

Context Chronic exposure to glucocorticoids (GCs) or stress increases the risk of medical disorders, including cardiovascular and neuropsychiatric disorders. GCs contribute to an accelerated aging, while the link between chronic GCs exposure and disease onset is well established, the underpinning mechanisms are not clear. Objective we explored the potential nexus between GCs or stress exposure and telomere length. Design, Setting, and Participants rats exposed to three weeks of chronic stress; an iatrogenic mouse model of Cushing’s syndrome (CS); a mouse neuronal cell line; 33 patients with CS and 75 healthy human people were studied. Results 1.Telomere length is associated with exposure to stress in rats: 54.5% (P=0.036) reduction in telomere length in the stressed animals. Genomic DNA extracted from the dentate gyrus of stressed and unstressed rats showed 43.2% reduction in telomere length (P=0.006). 2. Mice were exposed to corticosterone (CORT), this treatment produced a 61.4% reduction in telomere length in the blood gDNA (P=5.75x 10-5). 3. We observed a 40.8% reduction in the telomere length in patients with active CS compared to healthy controls (P=0.006). There was a 17.8% reduction in telomere length in cured CS patients, no different from controls (P=0.08). For both cured and active CS, telomere length correlated significantly with the duration of hypercortisolism (R2=0.22, P=0.007). 4. There was a 27.6% reduction in telomere length between low vs. high tertiles in bedtime cortisol levels (P=0.019). Conclusions Our findings demonstrate that exposure to stress and/or glucocorticoids is associated with shortened telomeres, and that shortening may be partially reversible.

The affinity of mangrove species using Association and Cluster Index in North Coast of Jakarta and Segara Anakan of Cilacap, Indonesia

Hilmi E, Sari LK, Cahyo TN, Muslih, Mahdiana A, Samudra SR. 2021. The affinity of mangrove species using Association and Cluster Index in North Coast of Jakarta and Segara Anakan of Cilacap, Indonesia. Biodiversitas 22: 2907-2920. The affinity of mangrove species using association and cluster index describe relationship among mangrove species. The species association and clustering explain the degree of utilization of resources and space by mangrove species. The association and cluster also describe specific species adaptation in mangrove ecosystems. This paper was aimed to analyze species affinity using association and clustering index of mangrove species. The association index used Chi-square equation and the clustered index used Euclidian distance analysis. The results showed that (i) mangrove density in Segara Anakan (166-4000 trees ha-1) > North Jakarta (220-1100 trees ha-1). (ii) Nypa fruticans, Avicennia marina, Rhizophora stylosa and Rhizophora apiculata dominated in Segara Anakan of Cilacap, and Rhizophora stylosa and Avicennia marina dominated in North Jakarta (iii) The association index had 12 pairs of negative species association and 17 pairs of positive species association, but most of mangrove vegetations had no association. (iv) mangrove ecosystem in Segara Anakan and North Jakarta had four clusters with Euclidean distance (ED score) 484 to describe cluster between Bruguiera parviflora-Bruguiera sexangula until 76430847 to describe cluster among Bruguiera gymnorrhiza, Bruguiera parviflora, Ceriops decandra, Exoecaria agallocha, Nypa fruticans, Ceriops tagal, Rhizophora stylosa, and Sonneratia caseolaris