California Academy of Sciences
  • San Francisco, United States
Recent publications
Graphical abstract Highlights d Coevolutionary interactions arise from community assembly events, not host tracking d Structural colors in model and mimetic systems use different nano-level mechanisms d We resolved the phylogeny of Doliops using a design of more than 30,000 UCE loci
Cryptantha whippleae D.A.York & M.G.Simpson (Boraginaceae) is described as new. This species is currently known to occur in serpentine barrens in the Shasta-Trinity National Forest of Siskiyou County, California, with one outlier population in possible serpentine of Lake County, California. The new species is most similar to Cryptantha grandiflora and to C. milobakeri, these three likely each others’ closest relatives. All three have a relatively large corolla limb width and similar smooth, lance-ovate to ovate, marginally rounded, acuminate and abaxially transversely flattened nutlets. Cryptantha whippleae differs from C. grandiflora in having a short, as opposed to a tall, stem height; bifurcate as opposed to trifurcate primary axis cymules; and typically 2–3 nutlets per fruit, as opposed to usually one nutlet per fruit. Cryptantha whippleae differs from C. milobakeri also in having a short, versus tall, stem height; appressed-strigose and spreading-hispid stem vestiture, as opposed to strigose only or strigose and hirsute; calyx trichomes with two distinct vestiture types, these marginally appressed hirsute and medially hispid, as opposed to calyx trichomes of one type, dense, appressed to ascending, whitish sericeous; and 2–3 nutlets per fruit, as opposed to one nutlet per fruit. Cryptantha whippleae is relatively rare and joins seven other Cryptantha species that are found on serpentine, either obligately or facultatively. Current molecular phylogenetic studies support the mostly convergent evolution of serpentine adaptation in Cryptantha, but additional studies are needed.
The origin of most reef biodiversity of the southwestern Atlantic Ocean dates back to the Eocene, when the center of diversity of modern reef organisms was in the Tethys Sea, a vast extent of tropical shallow marine habitats situated between the Atlantic and Indian oceans. Following the closure of the Tethys Sea, the Atlantic reef biodiversity became increasingly isolated from the world’s centers of biodiversity (i.e. tropical Indo-Pacific). Moderate rates of origination and extinction shaped endemic lineages and a lower diversity of species compared with the Indo-Pacific. Within the Atlantic, the Brazilian Province is characterized by high endemism and by the presence of a secondary center of biodiversity, driven by a combination of isolation, distinct ecological conditions, and the overlap of tropical and subtropical species. Many evolutionary processes shape the current distribution of species along the coast and in offshore areas such as seamounts and oceanic islands. The taxonomic and functional structure of reef fishes and benthic organisms in the Brazilian Province are related to both historical events and environmental factors, and changes considerably along its latitudinal extent. Today, increased and disordered human development, associated with inadequate conservation measures, is quickly threatening millions of years of eco-evolutionary processes responsible for the origin of this unique biodiversity.
Background We observed a discrepancy between dengue NS1 antigen test and molecular diagnostics, with the emergence of (DENV) serotype 3 in Sri Lanka and sought to understand the cause for the rise in cases and high failure rates of molecular diagnostics. Methods Whole genomic sequencing was carried out in 22 DENV-3 samples. Phylogenetic and molecular clock analysis were done for genotype assignment and to understand the rate of evolution. Mutation analysis was done to understand the reasons for PCR non-detection. Results We identified two DENV-3 genotypes (I and III) co-circulating. DENV-3 genotype III strains shared a common ancestor with a sequence from India collected in 2022, while DENV-3 genotype I, was found to share a common ancestor with DENV-3 sequences from China. DENV-3 genotype III was detected by the modified CDC DENV-3 primers whereas, genotype I evaded detection due to key mutations at forward and reverse primer binding sites. We identified point mutations, C744T and A756G of the forward primer binding sites and in position G795A of the reverse primer binding sites which were not identified in DENV-3 genotype III. Furthermore, our Sri Lankan DENV-3 strains demonstrated a high root to tip ratio, compared to the previous DENV-3 sequences, indicating a high mutation rate during the points of sampling (year 2017 to 2023). Conclusion The co-circulation of multiple genotypes associated with an increase in cases highlights the importance of continuous surveillance of DENVs to identify mutations resulting in non-detection by diagnostics and differences in virulence.
The outcomes of speciation across organismal dimensions (e.g., ecological, genetic, phenotypic) are often assessed using phylogeographic methods. At one extreme, reproductively isolated lineages represent easily delimitable species differing in many or all dimensions, and at the other, geographically distinct genetic segments introgress across broad environmental gradients with limited phenotypic disparity. In the ambiguous gray zone of speciation, where lineages are genetically delimitable but still interacting ecologically, it is expected that these lineages represent species in the context of ontology and the evolutionary species concept when they are maintained over time with geographically well‐defined hybrid zones, particularly at the intersection of distinct environments. As a result, genetic structure is correlated with environmental differences and not space alone, and a subset of genes fail to introgress across these zones as underlying genomic differences accumulate. We present a set of tests that synthesize species delimitation with the speciation process. We can thereby assess historical demographics and diversification processes while understanding how lineages are maintained through space and time by exploring spatial and genome clines, genotype‐environment interactions, and genome scans for selected loci. Employing these tests in eight lineage‐pairs of snakes in North America, we show that six pairs represent 12 “good” species and that two pairs represent local adaptation and regional population structure. The distinct species pairs all have the signature of divergence before or near the mid‐Pleistocene, often with low migration, stable hybrid zones of varying size, and a subset of loci showing selection on alleles at the hybrid zone corresponding to transitions between distinct ecoregions. Locally adapted populations are younger, exhibit higher migration, and less ecological differentiation. Our results demonstrate that interacting lineages can be delimited using phylogeographic and population genetic methods that properly integrate spatial, temporal, and environmental data.
Nudibranch molluscs Coryphella are widely distributed and species-rich gastropod group lacking fossil record and displaying a complex distribution across both Southern and Northern hemispheres. In this paper we provide a detailed review of the morphology, ecology, and distribution of Coryphella, estimation of divergence times between species, an ancestral area reconstruction, and a population analysis of widely distributed trans-Arctic species Coryphella verrucosa to investigate the evolution, phylogeographic patterns and reconstruct possible historical routes of oceanic dispersal. The inclusion of a larger sample size and five molecular markers has revealed a complex evolutionary history of Coryphella, shaped by transgression, vicariance, and dietary shifts, and overall driven by the pervasive effect of glacial cycles. We also revealed the presence of additional cryptic diversity, which suggests that further sampling may produce additional species in this group of nudibranchs. Tree calibration indicates the genus Coryphella originates in the middle Miocene in the Pacific Ocean and the early divergence within this group also occurred in the Pacific, specifically in different regions of the North Pacific. The ancestral area reconstruction inferred five independent instances of transgression from the Pacific Ocean to the Atlantic via different migration routes, including the Panamanian seaway and the Bering Strait. Among them, we identified three cases of successful transition to the Arctic waters from the North Pacific via the Bering Strait, associated with interglacial conditions of middle Pleistocene. Consequently, Pleistocene glacial cycles likely prompted pulses of boreal faunal elements to disperse southwards followed by range disjunction and temporary isolation of distant populations and resulting in allopatric speciation. Evidence from the population structure of contemporary trans-Arctic species suggests an occurrence of independent recolonization pathways of Arctic waters from both southernly and northernly refugia after the Last Glacial Maximum.
The males of the family Formicidae of the Malagasy region, including the islands of the southwest Indian Ocean (Madagascar, Mauritius, Reunion, Comoros, and Seychelles) are reviewed. A male-based synopsis of each subfamily and genera are provided. A richly illustrated male-based key to the eight subfamilies and 72 genera for which males are known are provided. The key is specific to the ant genera and species of the Malagasy region. Terminologies for morphology and wing cells are also reviewed. The keys are a product of three decades of collecting across the region. Despite efforts to collect males for all genera, males from five genera (Brachyponera, Chrysapace, Dicroaspis, Linepithema, Ochetellus) were included in the keys based on males from species collected outside the region, and males from one genus (Parvaponera) are unknown globally and not included in the key.
Barnacles of the genus Conopea are obligate epibionts of gorgonians and antipatharians. The species Conopea saotomensis Carrison-Stone et al. 2013, previously only known from the islands of São Tomé and Príncipe and the coast of Gabon, is reported from the Bijagós archipelago, Guinea-Bissau, based on morphological examination and DNA barcoding of specimens. The new record extends the known range of the species about 3000 km to the northwest.
Phylogenomic data are revolutionizing the field of insect phylogenetics. One of the most tenable and cost-effective methods of generating phylogenomic data is target enrichment, which has resulted in novel phylogenetic hypotheses and revealed new insights into insect evolution. Orthoptera is the most diverse insect order within polyneoptera and includes many evolutionarily and ecologically interesting species. Still, the order as a whole has lagged behind other major insect orders in terms of transitioning to phylogenomics. In this study, we developed an Orthoptera-specific target enrichment (OR-TE) probe set from 80 transcriptomes across Orthoptera. The probe set targets 1828 loci from genes exhibiting a wide range of evolutionary rates. The utility of this new probe set was validated by generating phylogenomic data from 36 orthopteran species that had not previously been subjected to phylogenomic studies. The OR-TE probe set captured an average of 1037 loci across the tested taxa, resolving relationships across broad phylogenetic scales. Our detailed documentation of the probe design and bioinformatics process is intended to facilitate the widespread adoption of this tool.
Despite the increasing burden of dengue, the regional emergence of the virus in Kenya has not been examined. This study investigates the genetic structure and regional spread of dengue virus-2 in Kenya. Viral RNA from acutely ill patients in Kenya was enriched and sequenced. Six new dengue-2 genomes were combined with 349 publicly available genomes and phylogenies used to infer gene flow between Kenya and other countries. Analyses indicate two dengue-2 Cosmopolitan genotype lineages circulating in Kenya, linked to recent outbreaks in coastal Kenya and Burkina Faso. Lineages circulating in Western, Southern, and Eastern Africa exhibiting similar evolutionary features are also reported. Phylogeography suggests importation of dengue-2 into Kenya from East and Southeast Asia and bidirectional geneflow. Additional lineages circulating in Africa are also imported from East and Southeast Asia. These findings underscore how intermittent importations from East and Southeast Asia drive dengue-2 circulation in Kenya and Africa more broadly.
Insects are increasingly promoted as a sustainable protein alternative for human consumption. Yet consumers have shown varied levels of acceptance, especially in countries without a tradition of eating insects. Even in countries where people traditionally eat insects, farmed insects might be considered novel foods if they are not the same species locals traditionally consume. In this work, we measured acceptance of a farmed cricket ( Gryllus madagascariensis ) as food at eight primary schools in the central highlands of Madagascar, a country with a long tradition of eating insects but not this species. We evaluated the role of education as a strategy to increase acceptance of insects as food. We also assessed whether education interventions affect children’s willingness to try cricket-based products, comparing three five-minute education interventions : historical overview of entomophagy in Madagascar, nutritional benefits of consuming insects, and preparation of cricket-based meals. Out of the 483 children, 73% had consumed insects in the past. The percentage of children willing to eat novel farmed crickets in school meals jumped from 16% before the education sessions to 87% after the education sessions. Education based on preparation of cricket-based meals was the most effective, as 86% of the reluctant children changed their minds. Finally, we found strong evidence that males were more willing to try insects than females before and after education. Our results are in line with past studies, and underscore the importance of education in promoting insect consumption. The drastic increase in the proportion of children willing to try insects suggests that barriers to consuming farmed insects are low in countries with a tradition of insect consumption and can be overcome through education. Our study supports the acceptability of novel farmed insects as an alternative protein solution to combat malnutrition in children in developing countries like Madagascar.
Mesophotic coral ecosystems are characterised by the presence of photosynthetic scleractinian corals despite the decreasing amounts of light available with depth. To better understand physiological strategies across a broad depth gradient, we studied the biological trait responses of Pocillopora cf. verrucosa from 6 to 60 m depth and Pachyseris “speciosa” spp. from 20 to 90 m depth at four islands of French Polynesia. Specifically, we characterised associated Symbiodiniaceae communities, photophysiological traits (Symbiodiniaceae density and chlorophyll concentrations), micro-morphology and trophic plasticity (autotrophy vs heterotrophy inferred from stable isotopes). Our results showed that both taxa can live at mesophotic depths without significant genetic structuring in their generic Symbiodiniaceae communities, mainly composed of Cladocopium and Durusdinium. Yet, the prevalence of Symbiodiniaceae ITS2 profiles revealed location-based variations that sometimes interact with depth and highlight putative shallow- or depth-tolerant taxa. For both taxa, symbiont density and chlorophyll pigment concentrations increased with increasing depth. We also found a change in their skeletal micro-morphology with an increase in the inter-corallite distance for Pocillopora cf. verrucosa and a decrease in the height of septa for Pachyseris “speciosa” spp. with depth. Finally, we found no isotopic evidence of switching to a more heterotrophic diet as their primary energy source, although host–tissue δ¹³C ratios became more negative with depth in both corals. Overall, our findings show similarity (across the two species) and species-specific strategies (biological trait patterns with increasing depth) underlying the capacity of symbiotic scleractinian corals to live in low-light environments.
Harriotta avia sp. nov., a new species of long-nose chimaera (Holocephali: Chimaeriformes: Rhinochimaeridae), is described from specimens collected off New Zealand in the Southwest Pacific Ocean. The species is distinguished from its congeners by a combination of the following characters: elongated, narrow and depressed snout up to 56% BDL; long, slender trunk; beak-like vomerine tooth plate; large eye, length 8–12% BDL and height 5–7% BDL; long dorsal spine reaching slightly beyond apex of the dorsal fin; and slender rod-like pelvic claspers. The skin is deciduous, and uniform chocolate brown when intact. Harriotta avia sp. nov. is also distinguished from other Harriotta species based on DNA sequence divergence of the NADH2 gene. Harriotta avia sp. nov. is reported from the New Zealand-Australian region. Conclusions here show that Harriotta raleighana, a presumed globally distributed species, likely comprises several species and the genus Harriotta warrants a revision with specimens representing all ocean basins.
Vermillion Snapper ( Rhomboplites aurorubens , Lutjanidae) inhabits deep waters (20-300 m) from North America through Brazil, sustaining significant commercial and recreational fisheries. Despite its economic importance, knowledge of its biology is limited. Classified as Vulnerable on the Red List due to overfishing, populations have declined by over 30% in recent generations. We assembled and annotated the first chromosome-scale genome of this species by combining PacBio long reads, Illumina short reads, and Hi-C data. The resulting assembly is 987.5 Mbp, with a scaffold N50 size of 41.3 Mbp, and 135 contigs clustered and ordered onto 24 chromosomes with 34,496 predicted genes. The high-quality assembly and annotation contained 98% complete and single-copy BUSCO genes. This is the most complete, chromosome-level genome assembly of an Atlantic snapper to date. The Vermillion Snapper genome assembly and its supporting data are valuable tools for ecological and comparative genomics studies of snappers and other valuable commercial species within the family.
The processes that influence community assembly, such as competition for resources and environmental filtering, are often scale dependent and vary across ecotones. Trait‐based ecology provides a useful framework for testing which ecological processes most strongly influence local community composition, especially across environmental gradients where species diversity varies. Where environmental filtering dominates, species distributions are expected to be defined by strong turnover along environmental gradients, with more similar species occupying more similar habitats. Where interspecific competition dominates, species are expected to diverge in relative abundance and resource utilization at sites, so species can co‐occur. Here, we integrate measurements of functional traits, microhabitat usage, isotopic composition (δ¹⁵N and δ¹³C), and abundance to test the importance of environmental filtering and resource/habitat partitioning in shaping a montane ground beetle species assemblage (Carabidae: Nebriini: Nebria) in the isolated, volcanic peaks of the northern Cascades Range, USA. Across species of Nebria, body size, pronotal shape, temperature preference, and isotopic enrichment varied across habitats ([gravel, rocks 10 cm–50 cm in diameter], large rocks [>50 cm in diameter], vegetation‐covered rocks, and alpine [snowfields and talus]), and habitat/microhabitat features were reliable predictors of species presence. Resource consumption among mid‐elevation species on Mt. Rainier—the peak with the greatest species diversity—is highly overlapping. Species turnover and nestedness varied significantly across habitat gradients and peaks throughout this region and varied nearly significantly across sites. Across habitat types and sites, more similar species are more likely to coexist. These results suggest that environmental filtering is the primary process structuring this species assemblage, although we find detailed evidence for microhabitat niche partitioning among species of Nebria at the site scale.
Understanding why some individuals age faster than others is essential to evolutionary biology and geroscience, but measuring variation in biological age is difficult. One solution may lie in measuring gut microbiome composition because microbiota change with many age-related factors (e.g., immunity and behavior). Here we create a microbiome-based age predictor using 13,563 gut microbial profiles from 479 wild baboons collected over 14 years. The resulting “microbiome clock” predicts host chronological age. Deviations from the clock’s predictions are linked to demographic and socio-environmental factors that predict baboon health and survival: animals who appear old-for-age tend to be male, sampled in the dry season (for females), and high social status (both sexes). However, an individual’s “microbiome age” does not predict the attainment of developmental milestones or lifespan. Hence, the microbiome clock accurately reflects age and some social and environmental conditions, but not the pace of development or mortality risk.
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205 members
Gopinathan Menon
  • Ornithology & Mammology
Robert Drewes
  • Department of Herpetology
John Philip Dumbacher
  • Institute for Biodiversity Science and Sustainability
Matthew R Lewin
  • Center for Exploration and Travel Health
Iria Fernandez-Silva
  • Department of Ichthyology
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