Multiple Taxa Research Articles

A SEROLOGIC SURVEY OF FRANCISELLA TULARENSIS EXPOSURE IN WILDLIFE ON THE ARCTIC COASTAL PLAIN OF ALASKA, USA.

Tularemia is an infectious zoonotic disease caused by one of several subspecies of Francisella tularensis bacteria. Infections by F. tularensis are common throughout the northern hemisphere and have been detected in more than 250 wildlife species. In Alaska, US, where the pathogen was first identified in 1938, studies have identified F. tularensis antibodies in a diverse suite of taxa, including insects, birds, and mammals. However, few such investigations have been conducted recently and knowledge about the current distribution and disease ecology of F. tularensis is limited, particularly in Arctic Alaska, an area undergoing rapid environmental changes from climate warming. To help address these information gaps and provide insights about patterns of exposure among wildlife, we assessed the seroprevalence of F. tularensis antibodies in mammals and tundra-nesting geese from the Arctic Coastal Plain of Alaska, 2014-17. With a commercially available slide agglutination test, we detected antibodies in 14.7% of all individuals sampled (n=722), with titers ranging from 1:20 to 1:320. We detected significant differences in seroprevalence between family groups, with Canidae (foxes, Vulpes spp.) and Sciuridae (Arctic ground squirrel, Spermophilus parryii) having the highest seroprevalence at 21.5% and 33.3%, respectively. Mean seroprevalence for Ursidae (polar bears, Ursus maritimus) was 13.3%, whereas Cervidae (caribou, Rangifer tarandus) had comparatively low seroprevalence at 6.5%. Antibodies were detected in all Anatidae species sampled, with Black Brant (Branta bernicla nigricans) having the highest seroprevalence at 13.6%. The detection of F. tularensis antibodies across multiple taxa from the Arctic Coastal Plain and its nearshore marine region provides evidence of exposure to this pathogen throughout the region and highlights the need for renewed surveillance in Alaska.

Whole-Genome Sequence, Assembly and Annotation of an Invasive Plant, Lonicera maackii (Amur Honeysuckle)

The invasive species Lonicera maackii (Amur Honeysuckle) is an increasing problem sweeping from the eastern United States toward the west, impacting normal forest development and animal survival across multiple taxa. Little is known about the genomics of this species, although a related invasive, Lonicera japonica, has been sequenced. Understanding the genomic foundation of the Lonicera maackii species could help us understand the biochemistry and life history that are the underpinnings of invasive success, as well as potential vulnerabilities and strengths which could guide research and development to control its spread. Here we present a draft, but high-quality, short-read whole-genome sequence, assembly, and annotation of Lonicera maackii, demonstrating that inexpensive and rapid short-read technologies can be successfully used in invasive species research. Despite being a short-read assembly, the genome length (7.93 × 108) and completeness (estimated as 90.2-92.1% by BUSCO and Merqury) are close to the previously published chromosome-level sequencing of L. japonica. No bias, by means of a Gene Ontology analysis, was identified among missing BUSCOs. A duplication of the 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase gene in both Lonicera species is identified, and the potential impact on controlling these invasive species is discussed. Future prospects for a diversity analysis of invasive species is also discussed.

Evidence of virulence and antibiotic resistance genes from the microbiome mapping in minimally processed vegetables producing facilities

Daily consumption of fresh vegetables is highly recommended by international health organizations, because of their high content of nutrients. However, fresh vegetables might harbour several pathogenic microorganisms or contribute to spread antibiotic resistance, thus representing a hazard for consumers. In addition, little is known about the transmission routes of the residential microbiome from the food handling environment to vegetables. Therefore, we collected environmental and food samples from three manufactures producing fresh vegetables to estimate the relevance of the built environment microbiome on that of the finished products. Our results show that food contact surfaces sampled after routine cleaning and disinfection procedures host a highly diverse microbiome, including pathogens such as the enterotoxigenic Bacillus cereus sensu stricto. In addition, we provide evidence of the presence of a wide range of antibiotic resistance and virulence genes on food contact surfaces associated with multiple taxa, thus supporting the hypothesis that selection of resistant and pathogenic taxa might occur on sanitized surfaces. This study also highlights the potential of microbiome mapping routinely applied in food industries monitoring programs to ensure food safety.

Predictors of sequence capture in a large-scale anchored phylogenomics project

Next-generation sequencing (NGS) technologies have revolutionized phylogenomics by decreasing the cost and time required to generate sequence data from multiple markers or whole genomes. Further, the fragmented DNA of biological specimens collected decades ago can be sequenced with NGS, reducing the need for collecting fresh specimens. Sequence capture, also known as anchored hybrid enrichment, is a method to produce reduced representation libraries for NGS sequencing. The technique uses single-stranded oligonucleotide probes that hybridize with pre-selected regions of the genome that are sequenced via NGS, culminating in a dataset of numerous orthologous loci from multiple taxa. Phylogenetic analyses using these sequences have the potential to resolve deep and shallow phylogenetic relationships. Identifying the factors that affect sequence capture success could save time, money, and valuable specimens that might be destructively sampled despite low likelihood of sequencing success. We investigated the impacts of specimen age, preservation method, and DNA concentration on sequence capture (number of captured sequences and sequence quality) while accounting for taxonomy and extracted tissue type in a large-scale butterfly phylogenomics project. This project used two probe sets to extract 391 loci or a subset of 13 loci from over 6,000 butterfly specimens. We found that sequence capture is a resilient method capable of amplifying loci in samples of varying age (0–111 years), preservation method (alcohol, papered, pinned), and DNA concentration (0.020 ng/μl - 316 ng/ul). Regression analyses demonstrate that sequence capture is positively correlated with DNA concentration. However, sequence capture and DNA concentration are negatively correlated with sample age and preservation method. Our findings suggest that sequence capture projects should prioritize the use of alcohol-preserved samples younger than 20 years old when available. In the absence of such specimens, dried samples of any age can yield sequence data, albeit with returns that diminish with increasing age.

Taxonomic dependency of beta diversity for bacteria, archaea, and fungi in a semi-arid lake

Microbial beta diversity has been recently studied along the water depth in aquatic ecosystems, however its turnover and nestedness components remain elusive especially for multiple taxonomic groups. Based on the beta diversity partitioning developed by Baselga and Local Contributions to Beta Diversity (LCBD) partitioning by Legendre, we examined the water-depth variations in beta diversity components of bacteria, archaea and fungi in surface sediments of Hulun Lake, a semi-arid lake in northern China, and further explored the relative importance of environmental drivers underlying their patterns. We found that the relative abundances of Proteobacteria, Chloroflexi, Euryarchaeota, and Rozellomycota increased toward deep water, while Acidobacteria, Parvarchaeota, and Chytridiomycota decreased. For bacteria and archaea, there were significant (p < 0.05) decreasing water-depth patterns for LCBD and LCBDRepl (i.e., species replacement), while increasing patterns for total beta diversity and turnover, implying that total beta diversity and LCBD were dominated by species turnover or LCBDRepl. Further, bacteria showed a strong correlation with archaea regarding LCBD, total beta diversity and turnover. Such parallel patterns among bacteria and archaea were underpinned by similar ecological processes like environmental selection. Total beta diversity and turnover were largely affected by sediment total nitrogen, while LCBD and LCBDRepl were mainly constrained by water NO2 --N and NO3 --N. For fungal community variation, no significant patterns were observed, which may be due to different drivers like water nitrogen or phosphorus. Taken together, our findings provide compelling evidences for disentangling the underlying mechanisms of community variation in multiple aquatic microbial taxonomic groups.

An application of zooms to identify archaeological avian fauna from Teotihuacan, Mexico

The remains of aquatic birds often represent the best surviving evidence for prehispanic lake exploitation in highland Central Mexico, an important center of urban development with vast lacustrine resources. Yet unlike the sustained focus on turkey husbandry in Mesoamerican research, the economic importance of ducks and other lacustrine birds has received little attention. The diversity of birds in Central Mexico presents challenges to species identification from skeletal remains. To overcome these challenges, we present a new application of ZooMS, a collagen-based identification technique, to identify archaeological avian fauna from Teotihuacan. We develop the first database of avian biomarkers to include specimens across multiple taxonomic groups and apply ZooMS on 295 bone fragments to identify fragmentary and unidentified avian remains from the Tlajinga district of Teotihuacan. Our results indicate that ZooMS has good potential to identify avian fauna to below family level and that the residents of Tlajinga exploited a range of aquatic birds.

Twenty-four months of bacterial colonialization and infection rates in patients with transcutaneous osseointegrated prosthetic systems after lower limb amputation-A prospective analysis.

Transcutaneous osseointegrated prosthesis systems (TOPS) are alternative rehabilitation methods to socket prosthetics, after limb amputation. TOPS compromise a two-step surgery: starting with the implantation of the stem which is then followed by the creation of the transcutaneous stoma through which the exoprosthesis can be connected. Immediately after surgery, this opening is permanently exposed to pathogens. This study aimed to investigate the dynamics of bacterial colonization of the stoma to analyze whether obligate bacterial colonization leads to a risk of periprosthetic infections after TOPS treatment. This prospective study analyzed data from 66 patients (aged 26-75 years) after TOPS treatment between 2017 and 2019. Microbiological swabs from the stoma were analyzed on the first postoperative day and 3, 6, 12, and 24 months after stoma creation. Infection rates, laboratory values (CRP, leukocyte count, hemoglobin), and body temperature were recorded at these points in time. Statistical analysis was performed using SPSS 28. The results show the formation of a stable environment dominated by Gram-positive bacteria in the stoma of TOPS patients over 24 months. Staphylococcus aureus, Staphylococcus spp., and Streptococcus spp. were the most common species found. With regard to the cohort up to the 3 months follow-up, 7.9% (five patients) developed infections surrounding the TOPS procedure. In relation to the whole cohort with loss to follow-up of 80.3% at the 24 months follow-up the infection rates increased up to 38.3%. The soft tissue inside and around the transcutaneous stoma is colonialized by multiple taxa and changes over time. A stable Gram-positive dominated bacterial taxa could be a protective factor for ascending periprosthetic infections and could possibly explain the relatively low infection rate in this study as well as in literature.

Precipitation drives species accumulation whereas temperature drives species decline in Himalayan vertebrates

AbstractAimMany studies have explored taxon‐specific richness patterns with elevation, but few have concurrently evaluated different mechanisms to explain elevational patterns across multiple taxa. We used a novel, cross‐taxa approach to study species richness patterns combined with a framework that tests drivers of species accumulation versus decline along the elevational gradient in the Himalayas.LocationThe Himalayas.TaxonMammals, birds and amphibians.MethodsWe used geographical and elevational data of 314 mammals, 842 breeding birds and 147 amphibians to investigate species richness patterns across elevational and geographical spaces. We divided the elevational species richness gradient into segments of species accumulation versus species decline by piecewise linear regressions. We used path analysis to disentangle the direct and indirect effects of the predictors on species richness for the overall pattern and its divided segments. We test the asymmetry of main drivers between the accumulation and decline segments of richness by iteration procedure.ResultsSpecies richness for most taxa tracks an elevational hump‐shaped distribution. The dominant driver of the overall pattern varied by taxa and in context to subregion. Across taxa, precipitation best predicts the accumulation of species richness, whereas temperature best predicts the decline in species richness. Moreover, temperature and precipitation can affect species richness indirectly through productivity, showcasing a large interactional effect of climate and productivity on species richness.Main conclusionsResource allocation of the ecosystem and requirements of the species differ between the lower and upper elevation segments but remain consistent across the overall gradient. The resources essential for promoting diversity and mediating stochastic processes are directly tied to precipitation at the process of species accumulation and temperature at the process of species richness decline. Our findings support the existing theory in climate change science that reduced precipitation combined with increasing temperature may cause species extinction in the species‐rich lowlands.

Multi-trial analysis of HIV-1 envelope gp41-reactive antibodies among global recipients of candidate HIV-1 vaccines.

Many participants in HIV-1 vaccine trials, who have not previously been exposed to or vaccinated against HIV-1, display serum immunoglobulin antibodies that bind the gp41 region of HIV-1 envelope prior to vaccination. Previous studies have hypothesized that these pre-existing antibodies may be cross-reactive and may skew future vaccine responses. In 12 large studies conducted by the HIV Vaccine Trial Network (HVTN) (n=1470 individuals), we find wide variation among participants in the pre-vaccine levels of gp41-reactive antibodies as measured by the binding antibody multiplex assay (BAMA). In the absence of exposure to the gp41 immunogen, anti-gp41 IgG levels were temporally stable over 26-52 weeks in repeated measures of placebo recipients. The analysis revealed that the geometric mean of pre-vaccine anti-gp41 IgG response was greater among participants in South Africa compared with participants in the United States. With gene-level metagenomic sequencing of pre-vaccination fecal samples collected from participants in one trial (HVTN 106), we detected positive associations between pre-vaccine anti-gp41 IgG and abundance of genes from multiple taxa in the Eubacteriales order. The genes most strongly associated with higher baseline anti-gp41 IgG mapped to a clade containing Blautia wexlerae and closely related strains. In trials with vaccine products containing the full or partial portion of gp41 immunogen alongside a gp120 immunogen, we did not find evidence that individuals with higher baseline anti-gp41 IgG had different levels of anti-gp120 IgG after vaccination compared to individuals with lower pre-vaccine anti-gp41 levels (pooled estimate of standardized mean difference -0.01 with a 95% CI [-0.37; 0.34]).

Brazilian marine phylogeography: A literature synthesis and analysis of barriers.

In the last 30 years a plethora of phylogeography studies have been published targeting Brazilian marine species. To date, several historical and extant physical and ecological processes have been identified as drivers of allopatric, sympatric and parapatric population genetic differentiation detected along the Brazilian coast. Examples of extant physical barriers include the split of the South Equatorial Current into the Brazil and North Brazil boundary currents, the mouth of major rivers (e.g., Amazon, São Francisco and Doce rivers) and coastal upwellings. Examples of historical barriers include the Vitória-Trindade seamount chain promoting genetic differentiation during periods of glacial maxima and lower sea levels. Examples of ecological speciation include adaptations to different substrata, resource use and reproductive biology. We used published data to build data sets and generalized additive models to identify patterns of spatial phylogeographical concordance across multiple taxa and markers. Our results identify Cape São Roque as the most dominant extant barrier to gene flow along the Brazilian coast, followed by the Vitória-Trindade seamount chain and Cape Santa Marta. Cape Santa Marta is the northern winter limit of the Rio da Plata plume and is intermittently influenced by the Malvinas Current. This study provides a novel explicit quantitative approach to comparative phylogeography that recognizes four Brazilian phylogeographical regions delimited by processes associated with barriers to gene flow.

Sunlight and lifestyle: linking prenatal light conditions and personality development in a wild bird

Even though personality is a major determinant of individual survival, the development of animal personality traits is still poorly understood. Beyond an individual's genetic background, personality may be shaped by the conditions experienced during embryonic development. Light is a salient and variable ecological factor that can affect organismal physiology, establish brain asymmetries and ultimately modulate postnatal phenotypes across multiple taxa. Exposure to light is known to vary among avian embryos due to changes in parental incubatory constancy, but whether differences in the prenatal light environment can influence offspring personality development has rarely been explored. Here, we investigated whether the prenatal light environment shapes a key dimension of animal personality, the shy–bold axis, in hatchlings of a semiprecocial seabird, the yellow-legged gull, Larus michahellis . In gulls, the prenatal light environment may be especially important for last-laid eggs, as parental attendance during late incubation is more variable for last-laid than for senior eggs. We manipulated the levels of embryonic exposure to light (within the natural range previously documented in the wild) during the last stages of egg incubation and assessed differences in boldness in newly hatched junior chicks. We then used structural equation modelling to explore whether the effect of prenatal light exposure on the shy–bold axis is linked to the establishment of brain asymmetries (lateralization) and/or changes in plasma corticosterone levels. Prenatal light exposure promoted bolder phenotypes in gull chicks, which may improve their individual performance when competing for parental resources. Prenatal light also promoted the lateralization of the begging behaviour in newly hatched chicks, which was negatively associated with boldness. Finally, light induced changes in glucocorticoid levels, but these changes did not impact chicks' personality. Our findings unambiguously confirm that the prenatal light environment strongly affects the development of shy–bold phenotypes in gull hatchlings through a complex multipath mechanism. • Can the prenatal environment shape animal personality? • Last-hatched gull eggs are highly exposed to sunlight during late incubation. • We explored whether prenatal exposure to light shapes boldness in hatchlings. • Prenatal light promoted bold phenotypes and brain lateralization in gull chicks. • These adjustments might improve chick performance under competitive disadvantage.

Getting the GIST: Testing an integrative data structure for linking taxonomy, biodiversity and conservation

Assessing and addressing biodiversity needs are of critical and time-sensitive importance, with the post-2020 Global Biodiversity Framework’s Global Taxonomy Initiative underscoring the need to build capacity in how we conceptualize biodiversity (Abrahamse et al. 2021). Species—as biological units—and their names are the backbone for the data integration and synthesis needed for biodiversity research and conservation decision-making (Grace et al. 2021). In integrating name sources for a single taxonomic group, barriers frequently limit linking species names across regional and global authoritative sources. In response to such challenges, we present a case study testing a Globally Integrated Structure of Taxonomy (GIST) to ensure the integration of taxonomy in biodiversity and conservation sciences. This framework characterizes the components enabling transparent association of species names through synonymy (alternate names or spellings), authorship, specimens, versions and timestamps, and taxonomic relationships in space and time. Taxonomy provides a critical link between biodiversity data types and databases. Efforts towards global taxonomic integration are confounded by insufficient connectivity between taxonomic assemblages, with implications for research, monitoring, and conservation practice (Christie et al. 2021, Jetz et al. 2019, McClure et al. 2020). In attempting to match multiple taxonomic groups across databases, we highlight current progress and remaining challenges to produce and use a GIST. We evaluate the standardized, comprehensive taxonomies of mammals, birds, reptiles, amphibians, dragonflies and damselflies, butterflies, ants, plants, and crabs produced for the Map of Life project (Jetz et al. 2012), identifying which missing components impede their utility. We show that for terrestrial mammals, GIST standards are almost fulfilled, but for invertebrate taxa, such as butterflies, GIST standards are unmet, resulting in broken taxonomic links between aggregators of genetic, spatial, functional, and physical data. We find that even the comprehensive taxonomies we examine do not harmonize well with taxonomies of global genetics, phylogenetics, macroecology, and conservation databases. This is because current taxonomic data infrastructures on biodiversity respositories lack the necessary structural components, searchability, and name source transparency to fully integrate taxonomies, as different independently advancing data sources lack standard metadata practices and operable interfaces. The GIST components enable data linkage and provide clear sourcing and metadata, enabling taxonomic data accessibility, reuse, and interoperability. This structure can act as a step toward open and FAIR (Findable, Accessible, Interoperable, and Reusable) data practice as it relates to taxon names (Wilkinson et al. 2016). Without transparent, integrated, accessible, and updated taxonomic information, macroecological inferences and conservation decisions for even charismatic groups are impeded.

Metabarcoding data reveal vertical multitaxa variation in topsoil communities during the colonization of deglaciated forelands.

Ice-free areas are expanding worldwide due to dramatic glacier shrinkage and are undergoing rapid colonization by multiple lifeforms, thus representing key environments to study ecosystem development. It has been proposed that the colonization dynamics of deglaciated terrains is different between surface and deep soils but that the heterogeneity between communities inhabiting surface and deep soils decreases through time. Nevertheless, tests of this hypothesis remain scarce, and it is unclear whether patterns are consistent among different taxonomic groups. Here, we used environmental DNA metabarcoding to test whether community diversity and composition of six groups (Eukaryota, Bacteria, Mycota, Collembola, Insecta, and Oligochaeta) differ between the surface (0-5 cm) and deeper (7.5-20cm) soil at different stages of development and across five Alpine glaciers. Taxonomic diversity increased with time since glacier retreat and with soil evolution. The pattern was consistent across groups and soil depths. For Eukaryota and Mycota, alpha-diversity was highest at the surface. Time since glacier retreat explained more variation of community composition than depth. Beta-diversity between surface and deep layers decreased with time since glacier retreat, supporting the hypothesis that the first 20cm of soil tends to homogenize through time. Several molecular operational taxonomic units of bacteria and fungi were significant indicators of specific depths and/or soil development stages, confirming the strong functional variation of microbial communities through time and depth. The complexity of community patterns highlights the importance of integrating information from multiple taxonomic groups to unravel community variation in response to ongoing global changes.

Sex- and age-specific migratory strategies of blue whales in the northeast Pacific Ocean

Migration is a complex behavior that has evolved in multiple taxonomic groups as a means of accessing productive foraging grounds and environmentally stable areas suitable for reproduction. For migratory whales that forage throughout the year because of their high energetic demands, changes in the abundance of prey in different areas along their migratory route(s) can have serious implications for individual fitness and population viability. Thus, identifying the regions these species use to forage and breed while evaluating their migratory plasticity at the individual level can provide key information for their management and conservation. Serial stable isotope analysis of whale baleen, a continuously growing but metabolically inert tissue, has proven useful in generating individual migratory and foraging records over several years prior to death. We measured carbon (δ13C) and nitrogen (δ15N) isotope values along the length of baleen plates collected from thirteen blue whales of different sex and age classes, representing the largest collection analyzed to date in the northeast Pacific Ocean. Adult females exhibited relatively stable seasonal movements between temperate latitude foraging grounds and subtropical breeding grounds, although two skipped migration one year and subsequently moved to the same subtropical breeding ground near the Costa Rica Dome, potentially to give birth. Adult males exhibited two movement strategies with most remaining at temperate latitudes for 3-4 years before death, while two migrated to subtropical breeding grounds. In contrast, movement patterns in juveniles were erratic. These results are potentially driven by the energetic requirements during pregnancy and nursing in adult females, intra-specific competition among adult males, and inexperience in locating prey in juveniles. We also describe baleenδ15N patterns in recently weaned whales (&amp;lt;16.5m) that reflect switching from the consumption of milk to solid food (krill). In addition, baleenδ13C data suggest that weaned whales continue to use stored nutrients (blubber) acquired during the nursing period long after they are weaned. These results broaden our understanding of habitat selection in this species, highlight the importance of nursing for the critical period after weaning, and indicate that the Costa Rica Dome is an important calving region for this endangered population.

Reproductive and developmental toxicity of perfluorooctane sulfonate (PFOS) in the white-footed mouse (Peromyscus leucopus)

Concerns about per- and polyfluoroalkyl substances (PFAS) stem from their ubiquitous presence in the environment, bioaccumulation, resistance to degradation, and toxicity. Previously, toxicity data relevant to ecological risk assessment has largely been aquatic, terrestrial invertebrates, or avian in origin. In this study, repeated oral exposures of perfluorooctane sulfonate (PFOS) were administered to white-footed mice (Peromyscus leucopus) to evaluate effects on reproduction and development. Prenatal exposure to high doses of PFOS caused neonatal mortality, though growth and development were unaffected by low doses. Additionally, parental (P) generation animals exhibited increased liver:body weight, increased hepatocyte cytoplasmic vacuolization, and decreased serum thyroxine (T4) levels. Total litter loss was selected as the protective critical effect in this study resulting in a benchmark dose low (BMDL) of 0.12 mg/kg-d PFOS. Importantly, PFOS exposure has been linked to reduced adult recruitment in myriad species and at similar thresholds to this study. Similarities in critical/toxicologic effects across taxa may add confidence in risk assessments at sites with multiple taxa or environments.

Taxonomic uncertainty and the challenge of estimating global species richness

Taxonomic uncertainty and the challenge of estimating global species richness

A general theory for temperature dependence in biology

At present, there is no simple, first principles-based, and general model for quantitatively describing the full range of observed biological temperature responses. Here we derive a general theory for temperature dependence in biology based on Eyring-Evans-Polanyi's theory for chemical reaction rates. Assuming only that the conformational entropy of molecules changes with temperature, we derive a theory for the temperature dependence of enzyme reaction rates which takes the form of an exponential function modified by a power law and that describes the characteristic asymmetric curved temperature response. Based on a few additional principles, our model can be used to predict the temperature response above the enzyme level, thus spanning quantum to classical scales. Our theory provides an analytical description for the shape of temperature response curves and demonstrates its generality by showing the convergence of all temperature dependence responses onto universal relationships-a universal data collapse-under appropriate normalization and by identifying a general optimal temperature, around 25 ∘C, characterizing all temperature response curves. The model provides a good fit to empirical data for a wide variety of biological rates, times, and steady-state quantities, from molecular to ecological scales and across multiple taxonomic groups (from viruses to mammals). This theory provides a simple framework to understand and predict the impact of temperature on biological quantities based on the first principles of thermodynamics, bridging quantum to classical scales.

Long-term hydrographic changes in the Gulf of California and ecological impacts: A crack in the World’s Aquarium?

Although the Gulf of California is widely recognized as a region of high productivity and biodiversity, recent oceanographic and ecological changes have had a significant impact on its overall health. We review the relevant history of the economically important fishery based on large Humboldt (jumbo flying) squid (Dosidicus gigas) (>50 cm mantle-length and 10 kg body weight) that existed in the Guaymas Basin from the 1990′s until 2009, when a strong El Niño was accompanied by precocious spawning of squid at extremely small size (<30 cm mantle length and 0.1 kg). This short-lived phenotype is characteristic of the equatorial part of the species range and cannot be profitably fished. This phenomenon also occurred in conjunction with the strong 1997–1998 El Niño. Although rapid recovery of squid size and landings occurred after the 1997–1998 event, recovery after 2009–2010 El Niño was still incomplete when another strong El Niño occurred in 2015–2016. This last event has led to fixation of the small size-at-maturity phenotype in the Gulf of California — an effective poleward migration of the tropical phenotype. We also document years between El Niño 2009–2010 and 2015–2016 as being characterized by significant subsurface warming, leading to decreased productivity and restricted nighttime foraging opportunities for squid in the upper water column. These climatic trends have likely altered trophic webs throughout the Gulf of California, impacting many other taxa, including small pelagic fishes that are ecologically vital and commercially harvested in large quantities, as well as a suite of larger teleost fishes that are targeted by sport fishers. From these disparate data sources, collected and collated in coordination with regional resource users and environmental monitoring programs, an overall pattern emerges of long-term decline across multiple taxa. We also present evidence of a significant abatement of subsurface warming after 2015 and consider when – or if – the Gulf of California will return to a ‘normal’ state like that prior to 2010. Despite the potential for shifting to a cooler oceanic regime, the small phenotype for jumbo squid has persisted until present (2022), and the overall trajectory of ecological recovery is unclear. Integrated analyses of additional oceanographic and biological time-series, fisheries records, and other data will be necessary to identify critical processes and trajectories occurring in the Gulf of California.

The effect of natural disturbances on forest biodiversity: an ecological synthesis.

Disturbances alter biodiversity via their specific characteristics, including severity and extent in the landscape, which act at different temporal and spatial scales. Biodiversity response to disturbance also depends on the community characteristics and habitat requirements of species. Untangling the mechanistic interplay of these factors has guided disturbance ecology for decades, generating mixed scientific evidence of biodiversity responses to disturbance. Understanding the impact of natural disturbances on biodiversity is increasingly important due to human-induced changes in natural disturbance regimes. In many areas, major natural forest disturbances, such as wildfires, windstorms, and insect outbreaks, are becoming more frequent, intense, severe, and widespread due to climate change and land-use change. Conversely, the suppression of natural disturbances threatens disturbance-dependent biota. Using a meta-analytic approach, we analysed a global data set (with most sampling concentrated in temperate and boreal secondary forests) of species assemblages of 26 taxonomic groups, including plants, animals, and fungi collected from forests affected by wildfires, windstorms, and insect outbreaks. The overall effect of natural disturbances on α-diversity did not differ significantly from zero, but some taxonomic groups responded positively to disturbance, while others tended to respond negatively. Disturbance was beneficial for taxonomic groups preferring conditions associated with open canopies (e.g. hymenopterans and hoverflies), whereas ground-dwelling groups and/or groups typically associated with shady conditions (e.g. epigeic lichens and mycorrhizal fungi) were more likely to be negatively impacted by disturbance. Across all taxonomic groups, the highest α-diversity in disturbed forest patches occurred under moderate disturbance severity, i.e. with approximately 55% of trees killed by disturbance. We further extended our meta-analysis by applying a unified diversity concept based on Hill numbers to estimate α-diversity changes in different taxonomic groups across a gradient of disturbance severity measured at the stand scale and incorporating other disturbance features. We found that disturbance severity negatively affected diversity for Hill number q= 0 but not for q= 1 and q= 2, indicating that diversity-disturbance relationships are shaped by species relative abundances. Our synthesis of α-diversity was extended by a synthesis of disturbance-induced change in species assemblages, and revealed that disturbance changes the β-diversity of multiple taxonomic groups, including some groups that were not affected at the α-diversity level (birds and woody plants). Finally, we used mixed rarefaction/extrapolation to estimate biodiversity change as a function of the proportion of forests that were disturbed, i.e. the disturbance extent measured at the landscape scale. The comparison of intact and naturally disturbed forests revealed that both types of forests provide habitat for unique species assemblages, whereas species diversity in the mixture of disturbed and undisturbed forests peaked at intermediate values of disturbance extent in the simulated landscape. Hence, the relationship between α-diversity and disturbance severity in disturbed forest stands was strikingly similar to the relationship between species richness and disturbance extent in a landscape consisting of both disturbed and undisturbed forest habitats. This result suggests that both moderate disturbance severity and moderate disturbance extent support the highest levels of biodiversity in contemporary forest landscapes.

Structure and evolution of neuronal wiring receptors and ligands.

One of the fundamental properties of a neuronal circuit is the map of its connections. The cellular and developmental processes that allow for the growth of axons and dendrites, selection of synaptic targets, and formation of functional synapses use neuronal surface receptors and their interactions with other surface receptors, secreted ligands, and matrix molecules. Spatiotemporal regulation of the expression of these receptors and cues allows for specificity in the developmental pathways that wire stereotyped circuits. The families of molecules controlling axon guidance and synapse formation are generally conserved across animals, with some important exceptions, which have consequences for neuronal connectivity. Here, we summarize the distribution of such molecules across multiple taxa, with a focus on model organisms, evolutionary processes that led to the multitude of such molecules, and functional consequences for the diversification or loss of these receptors.