Community similarity and species overlap between habitats provide insight into the deep reef refuge hypothesis

The deep reef refuge hypothesis (DRRH) postulates that mesophotic coral ecosystems (MCEs) may provide a refuge for shallow coral reefs (SCRs). Understanding this process is an important conservation tool given increasing threats to coral reefs. To establish a better framework to analyze the DRRH, we analyzed stony coral communities in American Sāmoa across MCEs and SCRs to describe the community similarity and species overlap to test the foundational assumption of the DRRH. We suggest a different approach to determine species as depth specialists or generalists that changes the conceptual role of MCEs and emphasizes their importance in conservation planning regardless of their role as a refuge or not. This further encourages a reconsideration of a broader framework for the DRRH. We found 12 species of corals exclusively on MCEs and 183 exclusively on SCRs with another 63 species overlapping between depth zones. Of these, 19 appear to have the greatest potential to serve as reseeding species. Two additional species are listed under the U.S. Endangered Species Act, Acropora speciosa and Fimbriaphyllia paradivisa categorized as an occasional deep specialist and a deep exclusive species, respectively. Based on the community distinctiveness and minimal species overlap of SCR and MCE communities, we propose a broader framework by evaluating species overlap across coral reef habitats. This provides an opportunity to consider the opposite of the DRRH where SCRs support MCEs.

Landscape Anthropization Affects Mosquito Diversity in a Deciduous Forest in Southeastern Mexico

Mosquitoes (Diptera: Culicidae) are considered the group of insects that most impacts human health. Land use change, conversion of conserved sites into agricultural environments, urbanization, defaunation, and introduction of domestic animals can affect mosquito diversity positively or negatively, increasing the risk of transmission of zoonotic diseases. Here, we describe the diversity of adult mosquitoes in two environments (deciduous forest and anthropized zone) over 2 yr (2014–2016), using eight CDC traps at each site in three climatic seasons (rainy, cold, and dry). We captured 795 individuals belonging to 22 species. We constructed rank-abundance curves to determine spatial and temporal changes in the mosquito communities. We measured alpha diversity using the Shannon index (H′), Shannon exponential (eH) and Simpson dominance (Ds), and beta diversity using Jaccard’s coefficient of similarity (Ij). The most abundant species were Culex quinquefasciatus (40.5%), Culex coronator (18.3%), and Anopheles pseudopunctipennis (12.4%). The highest mosquito diversity was in the deciduous forest during the rainy season. Beta diversity analysis showed that species overlap varied among climatic seasons, with the sites sharing 65% species during the rainy season, but only 33% of species during the dry season. We found differences in the diversity of mosquitoes at the two sites, and the mosquito assemblage of the anthropized zone was significantly different from that of the deciduous forest.

Quantifying Late Pennsylvanian Multivariate Morphological Change in the Fusulinid Genus Triticites from the Central and Southwestern United States

ABSTRACT Fusulinid Foraminifera are important for biostratigraphic correlation of strata in the Upper Paleozoic of the central and southwestern United States due to their high abundance and diversity in shallow marine carbonates. These correlations rely on consistent species-level identifications as well as geographically consistent morphological variation within species. However, many taxonomically important characters are described qualitatively, which can lead to conflicting identifications among taxonomists and cause biostratigraphic disagreements. Quantitative morphometric comparisons among species can increase the consistency of identifications among workers and capture temporal and geographic morphological gradients. Here, we used 14 linear measurements to describe the morphology of 18 biostratigraphically important species within the genus Triticites. Canonical variates analysis (CVA) showed that whereas specimens of a given species occupy similar areas of morphospace, species overlap considerably and, thus, these linear measurements poorly differentiate among species. However, species morphology covaried with geological age and multivariate analyses focused on age differences reveal an increase in the size of the initial chamber (proloculus) and a relative decrease in test expansion along the long axes over time. These morphological changes are consistent with an adaptation to shallow water conditions following the fall in relative sea-level across the Virgilian-Newwellian/Bursumian transition. Given the consistency of the morphological shift among North American basins, these morphological changes may be more useful for the recognition of the Virgilian-Newwellian/Bursumian transition than species-level biozones because they do not depend on consistent species identification.

Metabarcoding Malaise traps and soil eDNA reveals seasonal and local arthropod diversity shifts

Forest habitats host enormous diversity, but little is known about the seasonal turnover of arthropod species between the above- and below ground forest layers. In this study, we used metabarcoding approaches to uncover arthropod diversity in different forest types and seasons. Our study shows that metabarcoding soil eDNA and Malaise trap bulk samples can provide valuable insights into the phenology and life cycles of arthropods. We found major differences in arthropod species diversity between soil samples and Malaise traps, with only 11.8% species overlap. Higher diversity levels were found in Malaise traps in summer whereas soil samples showed a diversity peak in winter, highlighting the seasonal habitat preferences and life strategies of arthropods. We conclude that collecting time series of bulk arthropod samples and eDNA in the same locations provides a more complete picture of local arthropod diversity and turnover rates and may provide valuable information on climate induced phenological shifts for long-term monitoring.

Infrared light sensors permit rapid recording of wingbeat frequency and bioacoustic species identification of mosquitoes

Recognition and classification of mosquitoes is a critical component of vector-borne disease management. Vector surveillance, based on wingbeat frequency and other parameters, is becoming increasingly important in the development of automated identification systems, but inconsistent data quality and results frequently emerge from different techniques and data processing methods which have not been standardized on wingbeat collection of numerous species. We developed a simple method to detect and record mosquito wingbeat by multi-dimensional optical sensors and collected 21,825 wingbeat files from 29 North American mosquito species. In pairwise comparisons, wingbeat frequency of twenty six species overlapped with at least one other species. No significant differences were observed in wingbeat frequencies between and within individuals of Culex quinquefasciatus over time. This work demonstrates the potential utility of quantifying mosquito wingbeat frequency by infrared light sensors as a component of an automated mosquito identification system. Due to species overlap, wingbeat frequency will need to integrate with other parameters to accurately delineate species in support of efficient mosquito surveillance, an important component of disease intervention.

Orthology clusters from gene trees with Possvm

Possvm (Phylogenetic Ortholog Sorting with Species oVerlap and MCL) is a tool that automates the process of classifying clusters of orthologous genes from precomputed phylogenetic trees. It identifies orthology relationships between genes using the species overlap algorithm to infer taxonomic information from the gene tree topology, and then uses the Markov Clustering Algorithm (MCL) to identify orthology clusters and provide annotated gene family classifications. Our benchmarking shows that this approach, when provided with accurate phylogenies, is able to identify manually curated orthogroups with high precision and recall. Overall, Possvm automates the routine process of gene tree inspection and annotation in a highly interpretable manner, and provides reusable outputs that can be used to obtain phylogeny-informed gene annotations and inform comparative genomics and gene family evolution analyses.

Isotopic niche provides an insight into the ecology of a symbiont during its geographic expansion

The study of the recent colonization of a symbiont and its interaction with host communities in new locations is an opportunity to understand how they interact. The use of isotopic ratios in trophic ecology can provide measurements of a species’ isotopic niche, as well as knowledge about how the isotopic niches between symbiont and host species overlap. Stable isotope measurements were used to assess the sources of carbon assimilated by the host species (the bivalves Mytilus galloprovincialis and Scrobicularia plana) and their associated symbiont pea crab Afropinnotheres monodi, which occurs within these bivalves’ mantle cavities. The mixing model estimates suggest that all of them assimilate carbon from similar sources, particularly from pseudofaeces and particulate organic matter in this symbiotic system based on filter feeding. The symbiotic species occupy comparable trophic levels and its association seems to be commensal or parasitic depending on the duration of such association. The pea crab A. monodi reflects a sex-specific diet, where males are more generalist than the soft females because the latter’s habitat is restricted to the host bivalve. The high isotopic overlap between soft females and M. galloprovincialis may reflect a good commensal relationship with the host.

Potential impacts of marine urbanization on benthic macrofaunal diversity

Urbanization and associated human activities have caused numerous changes to natural environments, including the loss of natural habitats and replacement with artificial structures. How these changes impact coastal marine biodiversity and ecosystem functioning is not well known. In this study, we examined the potential impacts of habitat changes by comparing species commonality and community structure (i.e., species richness, abundance, and functional composition) among artificial (a breakwater wall) and natural habitats (eelgrass bed, intertidal flat, and subtidal bottom) within a semi-enclosed coastal sea impacted by marine urbanization. We found considerable species overlap (i.e., high species sharing) among the eelgrass bed, intertidal flat, and subtidal bottom habitats. By contrast, the breakwater wall was a distinctive habitat with little overlap in species and functional groups with the other habitats, and was therefore a poor substitute for natural habitats. Our study suggests that marine urbanization degrades redundancy and inhibits the maintenance of biodiversity in coastal marine zones.

Protist communities along freshwater–marine transition zones in Hudson Bay (Canada)

One of the most striking ecological divides on Earth is between marine and nearby freshwater environments, as relatively few taxa can move between the two. Microbial eukaryotes contribute to biogeochemical and energy cycling in both fresh and marine waters, with little species overlap between the two ecosystems. Arctic and sub-Arctic marine systems are relatively fresh compared to tropical and temperate systems, but details of microbial eukaryote communities along river-to-sea transitions are poorly known. To bridge this knowledge gap, we investigated three river-to-sea transitions (Nelson, Churchill, and Great Whale Rivers) in sub-Arctic Hudson Bay through 18S rRNA amplicon sequencing to identify microbial eukaryotes along the salinity and biogeochemical gradients. Salinity acted as the principal dispersal barrier preventing freshwater microorganisms from colonizing marine coastal waters, with microbial eukaryote communities of the three rivers clustering together. Just offshore, communities clustered by coastal regions associated with nutrient concentrations. Analysis of indicator species revealed that communities in the nitrate-depleted coastal water off the Churchill and Great Whale Rivers were dominated by heterotrophic taxa and small photosynthetic protists. In contrast, the Nelson offshore community was characterized by a high proportion of the diatom Rhizosolenia. A distinct community of heterotrophic protists was identified in the three estuarine transition zones, suggesting specialized estuarine communities. Such specialization was most marked in the Nelson River system that was sampled more intensely and showed estuarine circulation. The autochthonous community was composed of the bacterial grazers Katablepharis, Mataza, and Cryothecomonas, as well as brackish species of the diatoms Skeletonema and Thalassiosira. These findings suggest that flow regulation on the Nelson River that modifies estuarine circulation would affect estuarine community composition and distribution in the transition zone.

Asymmetric interspecific competition drives shifts in signalling traits in fan-throated lizards

Interspecific competition can occur when species are unable to distinguish between conspecific and heterospecific mates or competitors when they occur in sympatry. Selection in response to interspecific competition can lead to shifts in signalling traits—a process called agonistic character displacement. In two fan-throated lizard species— Sitana laticeps and Sarada darwini —females are morphologically indistinguishable and male agonistic signalling behaviour is similar. Consequently, in areas where these species overlap, males engage in interspecific aggressive interactions. To test whether interspecific male aggression between Si. laticeps and Sa. darwini results in agonistic character displacement, we quantified species recognition and signalling behaviour using staged encounter assays with both conspecifics and heterospecifics across sympatric and allopatric populations of both species. We found an asymmetric pattern, wherein males of Si. laticeps but not Sa. darwini showed differences in competitor recognition and agonistic signalling traits (morphology and behaviour) in sympatry compared with allopatry. This asymmetric shift in traits is probably due to differences in competitive abilities between species and can minimize competitive interactions in zones of sympatry. Overall, our results support agonistic character displacement, and highlight the role of asymmetric interspecific competition in driving shifts in social signals.