Understanding what shapes variation in organisms’ capacity to utilize novel resources is essential to predicting how species will respond to environmental change. For herbivores, exposure to toxic phytochemicals in novel plants may limit persistence in new habitats. We investigated the behavioral, physiological, genetic, and microbial consequences of diet switching in two closely related species of rodent herbivores that each consume differentially toxic plants in their native habitat, and that maintain different dietary strategies (i.e., relative dietary specialist versus relative generalist). In reciprocal laboratory feeding trials, we exposed wild-caught woodrats (genus Neotoma) to toxins characteristic of either familiar or novel plant secondary compounds. We measured changes in food and water intake, locomotor activity, gut microbial composition, and gene expression across the digestive tract following feeding trials. The dietary generalist responded minimally, but the specialist responded strongly when exposed to the novel diet. This response included behavioral and genetic components including increased water intake, reduction in locomotor activity, increased differential expression of detoxification genes, and a greater shift in gut microbial composition. The dietary specialist exhibited a strong response to diet switching that corresponded with ecologically relevant shifts in behavior and physiology that would have negative fitness consequences. Although the dietary specialist had a strong genetic and microbial response to novel plant secondary compounds, this response would likely be insufficient to overcome the immediate challenge of exposure to novel dietary toxins in the wild. Our results underscore the link between feeding strategy and the capacity to shift to novel dietary resources in response to environmental change.

Understanding lineage divergence is crucial for uncovering cryptic biodiversity. Adaptive divergence, geographic isolation and life-history traits drive speciation in heterogeneous environments. The gentoo penguin complex (Pygoscelis spp.), historically treated as a single species, provides an ideal system to examine divergence across its full distribution. Here, we show the existence of four divergent evolutionary lineages (northern, southern, southeastern, and eastern), supported by phylogenomic and lineage-specific selective pressures, despite ancestral gene flow. South Georgia and Macquarie individuals whose status has been debated, were included. Genomic scans reveal lineage-specific signals of positive selection in genes related to thermoregulation, oxygen transport, metabolism, and skeletal development, consistent with ecological and morphological differentiation across the Antarctic Polar Front. Future niche projections indicate severe habitat losses for three lineages, whereas the southern gentoo may expand its range. We propose a taxonomic revision recognizing four distinct gentoo penguin species, including Pygoscelis kerguelensis sp. nov., with important conservation implications.

Trachemys nebulosa is a freshwater turtle found on the Baja California Peninsula (BCP) and mainland northwestern Mexico. Two subspecies are recognized: Trachemys nebulosa nebulosa from the BCP and Trachemys nebulosa hiltoni from the mainland. Previous genetic studies found small differences between these taxa, but limited sampling left questions about their distinctiveness and origins. Most authors who have studied this species have invoked human-mediated transport to explain its distribution. To test this hypothesis, we combined previously published genetic data with expanded sampling. Mainland and peninsular populations did not share mitochondrial or nuclear sequences, and data from both genomes separated them into distinct groups. These results support retaining T. n. hiltoni and T. n. nebulosa as separate taxa and favor a natural dispersal from the BCP to the mainland, followed by isolation of mainland populations. Because T. n. hiltoni has a limited distribution and is harvested for food, recognizing it as a distinct lineage has conservation implications. Additional sampling, particularly from the Cape Region of the BCP, will help further test historical connections between mainland and peninsular populations.

BackgroundStaphylococcus aureus is a gram-positive bacterium commonly found in the nares and oropharynx of one in three individuals and has the potential to cause significant health problems. With antibiotic-resistant strains causing 11,000 deaths yearly and ~2% of the population nasally colonized with methicillin-resistant S. aureus, a search for predictive markers and associative relationships between carriage have been long-sought goals. Within our study, we leveraged monozygotic twin participants in concert with multi-site microbiome analyses to characterize the impacts of S. aureus on composition.ResultsWe recruited 147 monozygotic twin pairs and characterized three sites, i.e., the nares, oropharynx, and hand microbiomes, using 16S rRNA v3-v4 sequencing in addition to S. aureus carriage status. The prevalence of S. aureus was highest in the oropharynx followed by nares and hand with concordance between twin pairs highest in the nares, followed by oropharynx. The detection of S. aureus was statistically correlated with differences in microbiome composition across sites, as indicated by beta diversity and DESeq2 analyses. Microbiome composition was most similar in twins’ nares that were S. aureus culture-positive concordant, whereas twins that were culture-negative concordant had the most similarity in the oropharynx. Of significance, Moraxella nonliquefacians and Capnocytophaga were inversely associated with S. aureus in the nares and oropharynx, respectively.ConclusionsThis improved understanding of S. aureus colonization in nares, oropharynx, and hand microbiomes in monozygotic twin pairs is a further step towards unraveling the degree to which the microbiome is influenced by host genetics and S. aureus carriage.

Abstract Background Staphylococcus aureus is a gram-positive bacterium commonly found in the nares and oropharynx of one in three individuals and has the potential to cause significant health problems. With antibiotic resistant strains causing 11,000 deaths yearly and ~ 2% of the population nasally colonized with MRSA, a search for predictive markers and causal relationships between carriage have been long-sought goals. Within our study, we leveraged monozygotic twin participants in concert with spatial microbiome analyses to characterize impacts of S. aureus on composition. Results: We recruited 147 monozygotic twin pairs and characterized three sites: nares, oropharynx, and hand microbiomes using 16S rRNA v3-v4 sequencing in addition to S. aureus carriage status. Prevalence of S. aureus was highest in the oropharynx followed by nares and hand with concordance between twin pairs highest in the nares, followed by oropharynx. All microbiome sites were significantly modified by the presence of S. aureus as illustrated by beta diversity and DESeq2 analyses. Microbiome composition was most similar in twins’ nares that were S. aureus culture positive concordant, whereas twins that were culture negative concordant had the most similarity in the Oropharynx. Of significance, Moraxella nonliquefacians and Capnocytophaga were inversely associated with S. aureus in the nares and oropharynx, respectively. Based on Maaslin2 analyses, we identify that S. aureus prevalence significantly affected pathways associated with Biosynthesis of Secondary Metabolites, Infectious Diseases, Amino Acid Metabolism, Cellular Processes and Signaling, and Immune System Diseases only in the nares microbiome. Conclusions: This improved understanding of S. aureus colonization on nares, oropharynx, and hand microbiomes in monozygotic twin pairs is a further step towards unraveling the degree to which the microbiome are influenced by host genetics and S. aureus carriage.

The microbiome is critical to an organism's phenotype, and its composition is shaped by, and a driver of, eco-evolutionary interactions. We investigated how host ancestry, habitat and diet shape gut microbial composition in a mammalian hybrid zone between Neotoma lepida and N. bryanti that occurs across an ecotone between distinct vegetation communities. We found that habitat is the primary determinant of diet, while host genotype is the primary determinant of the gut microbiome-a finding further supported by intermediate microbiome composition in first-generation hybrids. Despite these distinct primary drivers, microbial richness was correlated with diet richness, and individuals that maintained higher dietary richness had greater gut microbial community stability. Both relationships were stronger in the relative dietary generalist of the two parental species. Our findings show that host ancestry interacts with dietary habits to shape the microbiome, ultimately resulting in the phenotypic plasticity that host-microbial interactions allow.

Background Seahorses, seadragons, pygmy pipehorses, and pipefishes (Syngnathidae, Syngnathiformes) are among the most recognizable groups of fishes because of their derived morphology, unusual life history, and worldwide distribution. Despite previous phylogenetic studies and recent new species descriptions of syngnathids, the evolutionary relationships among several major groups within this family remain unresolved. Results Here, we provide a reconstruction of syngnathid phylogeny based on genome-wide sampling of 1314 ultraconserved elements (UCEs) and expanded taxon sampling to assess the current taxonomy and as a basis for macroevolutionary insights. We sequenced a total of 244 new specimens across 117 species and combined with published UCE data for a total of 183 species of Syngnathidae, about 62% of the described species diversity, to compile the most data-rich phylogeny to date. We estimated divergence times using 14 syngnathiform fossils, including nine fossils with newly proposed phylogenetic affinities, to better characterize current and historical biogeographical patterns, and to reconstruct diversification through time. We present a phylogenetic hypothesis that is well-supported and provides several notable insights into syngnathid evolution. We found nine non-monophyletic genera, evidence for seven cryptic species, five potentially invalid synonyms, and identified a novel sister group to the seahorses, the Indo-Pacific pipefishes Halicampus macrorhynchus and H. punctatus . In addition, the morphologically distinct southwest Pacific seahorse Hippocampus jugumus was recovered as the sister to all other non-pygmy seahorses. As found in many other groups, a high proportion of syngnathid lineages appear to have originated in the Central Indo-Pacific and subsequently dispersed to adjoining regions. Conversely, we also found an unusually high subsequent return of lineages from southern Australasia to the Central Indo-Pacific. Diversification rates rose abruptly during the Middle Miocene Climate Transition and peaked after the closure of the Tethys Sea. Conclusions Our results reveal a previously underappreciated diversity of syngnathid lineages. The observed biogeographic patterns suggest a significant role of the southern Australasian region as a source and sink of lineages. Shifts in diversification rates imply possible links to declining global temperatures, the separation of the Atlantic and Pacific faunas, and the environmental changes associated with these events.

The land snail genus Helminthoglypta is broadly distributed from northern Baja California Norte, Mexico, through California, to southern Oregon, USA. Its taxonomy has been largely based on characters of the shell and reproductive system, with previous molecular studies limited to arid and desert taxa. Here we investigate the molecular relationships among Helminthoglypta taxa occurring in the forests of northern California and southern Oregon using fragments of the mitochondrial gene cyto-chrome c oxidase subunit I (COI) and the mitochondrial large ribosomal subunit (16S). Most of the taxa identified on morphological criteria appear as monophyletic clades in our analyses. Exceptions include the mixing of H. hertleini and H. cypreophila in a single clade, the possible differentiation of H. talmadgei into 2 clades, and the presence of an undescribed species in southern Oregon. Because Helminthoglypta species likely reflect the health of the forest ecosystems in which they occur, accurate species identifications are essential for meaningful results from survey and monitoring programs; our preliminary findings suggest that further studies are needed to fully resolve Helminthoglypta diversity in this region.

The phylogeny of the carabid beetle supertribe Nebriitae is inferred from analyses of DNA sequence data from eight gene fragments including one nuclear ribosomal gene (28S), four nuclear-protein coding genes (CAD, topoisomerase 1, PEPCK, andwingless), and three mitochondrial gene fragments (16S + tRNA-Leu + ND1, COI (“barcode” region) and COI (“Pat/Jer” region)). Our taxon sample included 264 exemplars representing 241 species and subspecies (25% of the known nebriite fauna), 39 of 41 currently accepted genera and subgenera (all exceptNotiokasisandArchileistobrius), and eight outgroup taxa. Separate maximum likelihood (ML) analyses of individual genes, combined ML analyses of nuclear, nuclear protein-coding, and mitochondrial genes, and combined ML and Bayesian analyses of the eight-gene-fragment matrix resulted in a well-resolved phylogeny of the supertribe, with most nodes in the tree strongly supported. Within Nebriitae, 167 internal nodes of the tree (out of the maximum possible 255) are supported by maximum-likelihood bootstrap values of 90% or more. The tribes Notiophilini, Opisthiini, Pelophilini, and Nebriini are well supported as monophyletic but relationships among these are not well resolved.Nippononebriais a distinct genus more closely related toLeistusthanNebria.Archastes,Oreonebria,Spelaeonebria, andEurynebria, previously treated as distinct genera by some authors, are all nested within a monophyletic genusNebria.WithinNebria, four major clades are recognized: (1) theOreonebriaSeries, including eight subgenera arrayed in two subgeneric complexes (theEonebriaandOreonebriaComplexes); (2) the Nebriola Series, including only subgenus Nebriola; (3) theNebriaSeries, including ten subgenera arrayed in two subgeneric complexes, theBoreonebriaandNebriaComplexes, with the latter further subdivided into three subgeneric subcomplexes (theNebria,Epinebriola, andEunebriaSubcomplexes)); and (4) theCatonebriaSeries, including seven subgenera arrayed in two subgeneric complexes (theReductonebriaandCatonebriaComplexes). A strong concordance of biogeography with the inferred phylogeny is noted and some evident vicariance patterns are highlighted. A revised classification, mainly within the Nebriini, is proposed to reflect the inferred phylogeny. Three genus-group taxa (Nippononebria,VancouveriaandArchastes) are given revised status and seven are recognized as new synonymies (NebrioritesJeannel, 1941 andMarggiaHuber, 2014 =OreonebriaDaniel, 1903;PseudonebriolaLedoux & Roux, 1989 =BoreonebriaJeannel, 1937;PatrobonebriaBänninger, 1923,ParanebriaJeannel, 1937 andBarbonebriolaHuber & Schmidt, 2017 =EpinebriolaDaniel & Daniel, 1904; andAsionebriaShilenkov, 1982 =PsilonebriaAndrewes, 1923). Six new subgenera are proposed and described for newly recognized clades: Parepinebriola Kavanaugh subgen. nov. (type species:Nebria delicataHuber & Schmidt, 2017), Insulanebria Kavanaugh subgen. nov. (type species:Nebria carbonariaEschscholtz, 1829), Erwinebria Kavanaugh subgen. nov. (type speciesNebria sahlbergiiFischer von Waldheim, 1828),NivalonebriaKavanaughsubgen. nov.(type species:Nebria paradisiDarlington, 1931),NeaptenonebriaKavanaughsubgen. nov.(type species:Nebria ovipennisLeConte, 1878), andPalaptenonebriaKavanaughsubgen. nov.(type species:Nebria mellyiGebler, 1847). Future efforts to better understand relationships within the supertribe should aim to expand the taxon sampling of DNA sequence data, particularly within subgeneraLeistusandEvanoleistus of genusLeistusand theNebriaComplex of genusNebria.

Abstract A population of Vaccinium from San Bruno Mountain in San Mateo County, California has been confused with V. cespitosum Michx. (V. sect. Myrtillus), a species documented from the mountain, since its initial collection in 1961. These plants resemble V. cespitosum and other species in V. sect. Myrtillus in several characters, but differ most notably in their evergreen habit and well developed calyx lobes. The latter characters are shared by V. ovatum Pursh (V. sect. Pyxothamnus), the only other species of Vaccinium known from San Bruno Mountain, suggesting that the population is a hybrid between V. cespitosum and V. ovatum. We used data from gross morphology, leaf anatomy, and DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) and plastid matK and ndhF regions to test the hybrid status of this population. Hybrid status is supported by: 1) a plastid sequence profile identical to that of V. cespitosum from San Bruno Mountain and different from the profiles of all other Vaccinium samples in the study, 2) an ITS profile that differs from V. cespitosum from the mountain by only two polymorphic sites, and 3) the possession of gross morphological and anatomical characters that are either shared with one putative parent or the other, or are intermediate between them. Although ITS variation was non-additive and closely matched one of the putative parents, uniparental inheritance has been observed in other hybrids. Two novel gross morphological characters were also observed in the hybrid. The study documents a case of likely intersectional hybridization within Vaccinium, only rarely observed under natural conditions. Vaccinium cespitosum may have been outcompeted by the hybrid to the point of its extirpation from San Bruno Mountain. The population is here newly described as the nothospecies Vaccinium ×brunoense P.W.Fritsch, occurring in an area of only ca. 200 m2 with the number of individuals remaining uncertain because of clonal growth.

Penguins are the only extant family of flightless diving birds. They currently comprise at least 18 species, distributed from polar to tropical environments in the Southern Hemisphere. The history of their diversification and adaptation to these diverse environments remains controversial. We used 22 new genomes from 18 penguin species to reconstruct the order, timing, and location of their diversification, to track changes in their thermal niches through time, and to test for associated adaptation across the genome. Our results indicate that the penguin crown-group originated during the Miocene in New Zealand and Australia, not in Antarctica as previously thought, and that Aptenodytes is the sister group to all other extant penguin species. We show that lineage diversification in penguins was largely driven by changing climatic conditions and by the opening of the Drake Passage and associated intensification of the Antarctic Circumpolar Current (ACC). Penguin species have introgressed throughout much of their evolutionary history, following the direction of the ACC, which might have promoted dispersal and admixture. Changes in thermal niches were accompanied by adaptations in genes that govern thermoregulation and oxygen metabolism. Estimates of ancestral effective population sizes (N-e) confirm that penguins are sensitive to climate shifts, as represented by three different demographic trajectories in deeper time, the most common (in 11 of 18 penguin species) being an increased N-e between 40 and 70 kya, followed by a precipitous decline during the Last Glacial Maximum. The latter effect is most likely a consequence of the overall decline in marine productivity following the last glaciation.

Abstract Hybrid zones are natural laboratories for investigating the dynamics of gene flow, reproductive isolation, and speciation. A predominant marine hybrid (or suture) zone encompasses Christmas Island (CHR) and Cocos (Keeling) Islands (CKE), where 15 different instances of interbreeding between closely related species from Indian and Pacific Oceans have been documented. Here, we report a case of hybridization between genetically differentiated Pacific and Indian Ocean lineages of the three‐spot dascyllus, Dascyllus trimaculatus (Rüppell, 1829). Field observations indicate there are subtle color differences between Pacific and Indian Ocean lineages. Most importantly, population densities of color morphs and genetic analyses (mitochondrial DNA and SNPs obtained via RADSeq) suggest that the pattern of hybridization within the suture zone is not homogeneous. At CHR, both color morphs were present, mitochondrial haplotypes of both lineages were observed, and SNP analyses revealed both pure and hybrid genotypes. Meanwhile, in CKE, the Indian Ocean color morphs were prevalent, only Indian Ocean mitochondrial haplotypes were observed, and SNP analysis showed hybrid individuals with a large proportion (~80%) of their genotypes assigning to the Indian Ocean lineage. We conclude that CHR populations are currently receiving an influx of individuals from both ocean basins, with a greater influence from the Pacific Ocean. In contrast, geographically isolated CKE populations appear to be self‐recruiting and with more influx of individuals from the Indian Ocean. Our research highlights how patterns of hybridization can be different at scales of hundreds of kilometers, due to geographic isolation and the history of interbreeding between lineages.

Studying how isolation can impact population divergence and adaptation in co-distributed species can bring us closer to understanding how landscapes affect biodiversity. The Sargo, Anisotremus davidsonii (Haemulidae), and the Longjaw mudsucker, Gillichthys mirabilis (Gobiidae), offer a notable framework to study such mechanisms as their Pacific populations cross phylogeographic breaks at Point Conception, California, United States, and Punta Eugenia, Mexico, and are separated to those in the Sea of Cortez by the Baja California peninsula. Here, thousands of loci are genotyped from 48 Sargos and 73 mudsuckers using RADseq to characterize overall genomic divergence, and search for common patterns of putatively neutral and non-neutral structure based on outlier loci among populations with hypothesized different levels of isolation. We further search for parallels between population divergence and the total proportion of outliers, outlier FST distribution, and the proportion of outliers matching coding regions in GenBank. Statistically significant differentiation is seen across Point Conception in mudsucker (FST = 0.15), Punta Eugenia in Sargo (FST = 0.02), and on either side of the Baja California peninsula in both species (FST = 0.11 and 0.23, in Sargo and mudsucker, respectively). Each species shows structure using neutral and non-neutral loci. Finally, higher population divergence yields a more even distribution of outliers along their differentiation range but does not always translate into higher outlier proportions or higher rates in which outliers are matched to coding regions. If repeated in similar systems, observed genomic patterns might reveal speciation signatures in diverse networks of population isolation.

Among vertebrates, turtles have many unique characteristics providing biologists with opportunities to study novel evolutionary innovations and processes. We present here a high-quality, partially phased, and chromosome-level Red-Eared Slider (Trachemys scripta elegans, TSE) genome as a reference for future research on turtle and tetrapod evolution. This TSE assembly is 2.269Gb in length, has one of the highest scaffold N50 and N90 values of any published turtle genome to date (N50 = 129.68Mb and N90 = 19Mb), and has a total of 28,415 annotated genes. We introduce synteny analyses using BUSCO single-copy orthologs, which reveal two chromosome fusion events accounting for differences in chromosome counts between emydids and other cryptodire turtles and reveal many fission/fusion events for birds, crocodiles, and snakes relative to TSE. This annotated chromosome-level genome will provide an important reference genome for future studies on turtle, vertebrate, and chromosome evolution.

The most ubiquitous, abundant, and invasive turtle on Earth, Trachemys scripta elegans (TSE, "red-eared slider"), is one of four taxa in a clade that is native to the USA and adjacent Mexico (three subspecies of Trachemys scripta plus Trachemys gaigeae). The present range-wide study of this clade is based on 173 known-locality mtDNA sequences combined with ddRAD libraries for 43 samples emphasizing the western part of the range of TSE, its contact with that of T. gaigeae, and anthropogenic hybrids between TSE and T. s. scripta. The data presented here are the first to sample the TSE x T. s. scripta intergrade zone or TSEx T. s. scripta crosses from introduced turtles. In the western part of its range (New Mexico and Texas), most samples of TSE from the Pecos River have mtDNA haplotypes matching T. gaigeae. Structure analysis of SNPs from the ddRAD show evidence of genetic admixture between T. gaigeae and TSE in all included samples from the Rio Grande and Pecos River. These populations also exhibit T. gaigeae-like head stripes, i.e., a postorbital marking that does not reach the eye. The genetic and morphological data are thereby reconciled, as both suggest that these TSE are intergrades. We recommend that these populations continue to be considered TSE, despite the admixture with T. gaigeae. In the Eastern United States, some samples of the morphologically intermediate subspecies T. s. troostii are not genetically distinct from TSE and some samples share morphological characters and genetic affinities with T. s. scripta. Based on these observations we conclude that the taxon T. s. troostii represents intergrades between TSE and T. s. scripta and should not be considered a valid taxon. Near the already established part of the intergrade zone between TSE and T. s. scripta, TSE mtDNA haplotypes have naturally introgressed into typical-looking samples of T. s. scripta in Georgia. Hybrids between introduced TSE and T. s. scripta are also confirmed deeper within the natural range of T. s. scripta in South Carolina and Virginia. Given the examples of feral hybrids deep within its range shown here and elsewhere, the threat of genetic pollution of T. s. scripta by feral TSE is established.