Diatomite deposits of the lacustrine Truckee Formation near Hazen, Northern Nevada, are of Miocene age (ca. 10.3 million years old) and consist of varved deposits within commercial mines. These exposed deposits have been primary source of paleontological samples of stickleback fish fossils (Gasterosteous doryssus) spanning 100,000 years. These samples have revealed stasis, rapid morphological and genetic evolution, and local extinction of G. doryssus against a background of changing diatom communities. Here, we draw on geological, limnological, anthropogenic, and bibliographical data to illustrate the geographic and paleontological context of the Hazen diatomite deposits. We include a stratigraphic section describing lithology and stickleback specimen frequency at a 1 mm resolution. This paper should help researchers identify patterns in fossil site distribution and better understand the geological processes that have shaped the area, spurring new sampling and future research.

Darwin attributed the absence of species transitions in the fossil record to his hypothesis that speciation occurs within isolated habitat patches too geographically restricted to be captured by fossil sequences. Mayr's peripatric speciation model added that such speciation would be rapid, further explaining missing evidence of diversification. Indeed, Eldredge and Gould's original punctuated equilibrium model combined Darwin's conjecture, Mayr's model and 124 years of unsuccessfully sampling the fossil record for transitions. Observing such divergence, however, could illustrate the tempo and mode of evolution during early speciation. Here, we investigate peripatric divergence in a Miocene stickleback fish, Gasterosteus doryssus. This lineage appeared and, over approximately 8000 generations, evolved significant reduction of 12 of 16 traits related to armour, swimming and diet, relative to its ancestral population. This was greater morphological divergence than we observed between reproductively isolated, benthic-limnetic ecotypes of extant Gasterosteus aculeatus . Therefore, we infer that reproductive isolation was evolving . However, local extinction of G. doryssus lineages shows how young, isolated, speciating populations often disappear, supporting Darwin's explanation for missing evidence and revealing a mechanism behind morphological stasis. Extinction may also account for limited sustained divergence within the stickleback species complex and help reconcile speciation rate variation observed across time scales.

Adaptation to replicated environmental conditions can be remarkably predictable, suggesting parallel evolution may be a common feature of adaptive radiation. An open question, however, is how phenotypic variation itself evolves during repeated adaptation. Here, we use a dataset of morphological measurements from 35 populations of threespine stickleback, consisting of 16 parapatric lake- stream pairs and three marine populations, to understand how phenotypic variation has evolved during transitions from marine to freshwater environments, and during subsequent diversification across the lake-stream boundary. We find statistical support for divergent phenotypic covariance ( P ) across populations, with most diversification of P occurring across freshwater populations. Despite a close correspondence between within-population phenotypic variation and among population divergence, we find that variation in P is unrelated to total variation in population means across the set of populations. Within lake-stream pairs, however, we find that theoretical predictions for microevolutionary change can explain over 30% of the total divergence in P matrices across the habitat boundary. Together, our results indicate that variance evolution occurs primarily in dimensions of trait space with low phenotypic integration, driven by divergence into disparate lake and stream environments, illustrating how conserved and divergent features of multivariate variation can underlie adaptive radiation.

Island ecosystems have significant conservation value owing to their higher endemic biotas. Moreover, studies of regional communities that compare differences in species composition (species dissimilarity) among islands and the mainland suggest that community assembly on islands is different from that on the mainland. However, the uniqueness of island biotic assembly has been little studied at the global scale, nor have phylogenetic information or alien species been considered in these patterns. We evaluate taxonomic and phylogenetic change from one community to the next, focusing on differences in species composition between mainland-mainland (M-M) pairs compared to differences between mainland-island pairs (M-I) and between island-island pairs (I-I), using herpetofauna on islands and adjacent mainland areas worldwide. Our analyses detect greater taxonomic and phylogenetic dissimilarity for M-I and I-I comparisons than predicted by M-M model, indicating different island herpetofauna assembly patterns compared with mainland counterparts across the world. However, this higher M-I dissimilarity has been significantly decreased after considering alien species. Our results provide global evidence on the importance of island biodiversity conservation from the aspect of both the taxonomic and phylogenetic uniqueness of island biotic assembly.

Acute exposure to ionizing radiation has well-documented, immediate negative consequences for individuals. However, the evolutionary consequences for populations exposed to ionizing radiation is unclear. For example, a meta-analysis of taxa exposed to Chernobyl fallout found some evidence for elevated mutation rates in animal and plant taxa; however, in people, de novo mutation rates in offspring of parents exposed to radiation during and after the Chernobyl accident were no higher than controls. Furthermore, whether irradiation and increased mutation rates drive adaptation to radiation also has mixed support. Ambiguity in both cases likely arises from the difficulty of studying mutation rates and adaptation after rare nuclear events whose ionizing radiation is distributed heterogeneously in time and space. Here, we report an attempt to better address this difficulty with a “resurrection ecology” study of Daphnia spp . in Utah lakes that experienced nuclear fallout from US Department of Energy weapons testing in the 1950s and 1960s. The idea was to recover dormant Daphnia eggs from sediment cores that spanned the nuclear testing era in the American West. We predicted that survival and fecundity of eggs hatched in the lab would show fitness declines correlated with ionizing radiation fallout and a potential recovery once nuclear testing stopped. We successfully obtained multiple cores from three lakes that dated back to the 1800s. We isolated >4700 dormant eggs from those cores, spanning the nuclear era, but were only able to hatch a single egg in the lab. Thus, we could not conduct life history experiments to test our prediction. The purpose of this manuscript, therefore, is to describe the study and make our radioisotope core dating and sedimentation data available to other paleolimnological researchers. We also report a side study of stable isotope change through time measured from dormant eggs and the sediment.

Phytoliths are opal silica particles formed within plant tissues. Diatoms are aquatic, single-celled photosynthetic algae with silica skeletons. Phytolith and diatom morphotypes vary depending on local environmental and climatic conditions and because their silicate structures preserve well, the study of phytolith and diatom morphotypes can be used to better understand paleoclimatic and paleoenvironmental dynamics and changes. This article presents original data from an 820cm-deep stratigraphy excavated at the Hazen diatomite deposits, a high-elevation desert paleolake in the Fernley District, Northern Nevada, USA. The site has been studied for an assemblage of fossilized threespine stickleback, Gasterosteus doryssus, that reveal adaptive evolution. For this study, a total of 157 samples were extracted at 20 cm intervals covering approximately 24,500 years. After extraction, the samples were mounted on slides and viewed under 400-1000x light microscopy, enabling classification of 14 phytolith and 45 diatom morphotypes. Our data support paleoenvironmental reconstructions of the Hazen Miocene paleolake.

Recent studies have shown that the repeated evolution of similar phenotypes in response to similar ecological conditions (here "parallel evolution") often occurs through mutations in the same genes. However, many previous studies have focused on known candidate genes in a limited number of systems. Thus, the question of how often parallel phenotypic evolution is due to parallel genetic changes remains open. Here, we used quantitative trait locus (QTL) mapping in F2 intercrosses between lake and stream threespine stickleback (Gasterosteus aculeatus) from four independent watersheds on Vancouver Island, Canada to determine whether the same QTL underlie divergence in the same phenotypes across, between, and within watersheds. We find few parallel QTL, even in independent crosses from the same watershed or for phenotypes that have diverged in parallel. These findings suggest that different mutations can lead to similar phenotypes. The low genetic repeatability observed in these lake-stream systems contrasts with the higher genetic repeatability observed in other stickleback systems. We speculate that differences in evolutionary history, gene flow, and/or the strength and direction of selection might explain these differences in genetic parallelism and emphasize that more work is needed to move beyond documenting genetic parallelism to identifying the underlying causes.

An evolutionary debate contrasts the importance of genetic convergence versus genetic redundancy. In genetic convergence, the same adaptive trait evolves because of similar genetic changes. In genetic redundancy, the adaptive trait evolves using different genetic combinations, and populations might not share the same genetic changes. Here we address this debate by examining single nucleotide polymorphisms (SNPs) associated with the rapid evolution of character displacement in Anolis carolinensis populations inhabiting replicate islands with and without a competitor species (1Spp and 2Spp islands, respectively). We identify 215-outliers SNPs that have improbably large FST values, low nucleotide variation, greater linkage than expected and that are enriched for genes underlying animal movement. The pattern of SNP divergence between 1Spp and 2Spp populations supports both genetic convergence and genetic redundancy for character displacement. In support of genetic convergence: all 215-outliers SNPs are shared among at least three of the five 2Spp island populations, and 23% of outlier SNPS are shared among all five 2Spp island populations. In contrast, in support of genetic redundancy: many outlier SNPs only have meaningful allele frequency differences between 1Spp and 2Spp islands on a few 2Spp islands. That is, on at least one of the 2Spp islands, 77% of outlier SNPs have allele frequencies more similar to those on 1Spp islands than to those on 2Spp islands. Focusing on genetic convergence is scientifically rigorous because it relies on replication. Yet, this focus distracts from the possibility that there are multiple, redundant genetic solutions that enhance the rate and stability of adaptive change.

Species competing for resources also commonly share predators. While competition often drives divergence between species, the effects of shared predation are less understood. Theoretically, competing prey species could either diverge or evolve in the same direction under shared predation depending on the strength and symmetry of their interactions. We took an empirical approach to this question, comparing antipredator and trophic phenotypes between sympatric and allopatric populations of threespine stickleback and prickly sculpin fish that all live in the presence of a trout predator. We found divergence in antipredator traits between the species: in sympatry, antipredator adaptations were relatively increased in stickleback but decreased in sculpin. Shifts in feeding morphology, diet and habitat use were also divergent but driven primarily by stickleback evolution. Our results suggest that asymmetric ecological character displacement indirectly made stickleback more and sculpin less vulnerable to shared predation, driving divergence of antipredator traits between sympatric species.

Allometric scaling describes the relationship of trait size to body size within and among taxa. The slope of the population-level regression of trait size against body size (i.e. static allometry) is typically invariant among closely related populations and species. Such invariance is commonly interpreted to reflect a combination of developmental and selective constraints that delimit a phenotypic space into which evolution could proceed most easily. Thus, understanding how allometric relationships do eventually evolve is important to understanding phenotypic diversification. In a lineage of fossil Threespine Stickleback (Gasterosteus doryssus), we investigated the evolvability of static allometric slopes for nine traits (five armour and four non-armour) that evolved significant trait differences across 10 samples over 8500 years. The armour traits showed weak static allometric relationships and a mismatch between those slopes and observed evolution. This suggests that observed evolution in these traits was not constrained by relationships with body size, perhaps because prior, repeated adaptation to freshwater habitats by Threespine Stickleback had generated strong selection to break constraint. In contrast, for non-armour traits, we found stronger allometric relationships. Those allometric slopes did evolve on short time scales. However, those changes were small and fluctuating and the slopes remained strong predictors of the evolutionary trajectory of trait means over time (i.e. evolutionary allometry), supporting the hypothesis of allometry as constraint.

Small vertebrates can be stained and cleared using a trypsin enzyme, Alcian blue, and Alizarin red stains. The process is completed over several weeks and the final product allows clear viewing of internal structures including bone and cartilage. Cleared and stained vertebrate specimen can be used for educational or scientific purposes. Final products are stored in pure glycerin for an indefinite amount of time and can be viewed over a light box when needed.

Small vertebrates can be stained and cleared using a trypsin enzyme, Alcian blue, and Alizarin red stains. The process is completed over several weeks and the final product allows clear viewing of internal structures including bone and cartilage. Cleared and stained vertebrate specimen can be used for educational or scientific purposes. Final products are stored in pure glycerin for an indefinite amount of time and can be viewed over a light box when needed.

Oxygen depletion in estuaries and coastal waters is often associated with reduced biodiversity, coastal dead zones, and the loss of important ecosystem services. However, some species can benefit from low oxygen conditions due to the indirect effects these conditions have on trophic relationships. In Narragansett Bay, Rhode Island, U.S.A., northern quahogs (Mercenaria mercenaria) reach their highest densities in the areas of the Bay most prone to oxygen depletion. One line of evidence suggests that suboxic events (hypoxia and anoxia) can aid quahogs by excluding predators. Here, we analyze data from long-term surveys of water quality and quahog abundances to test whether a hypoxia-induced predation refuge is strong enough to explain quahog population dynamics in Narragansett Bay. We found that quahog cohorts were larger when they had been exposed to low oxygen conditions as juveniles, consistent with the predation refuge hypothesis. However, cohort size was also strongly associated with location and year settled, suggesting that a predation refuge is but one of a suite of factors influencing M. mercenaria populations.

Abstract Loss and reduction in paired appendages are common in vertebrate evolution. How often does such convergent evolution depend on similar developmental and genetic pathways? For example, many populations of the threespine stickleback and ninespine stickleback (Gasterosteidae) have independently evolved pelvic reduction, usually based on independent mutations that caused reduced Pitx1 expression. Reduced Pitx1 expression has also been implicated in pelvic reduction in manatees. Thus, hindlimb reduction stemming from reduced Pitx1 expression has arisen independently in groups that diverged tens to hundreds of millions of years ago, suggesting a potential for repeated use of Pitx1 across vertebrates. Notably, hindlimb reduction based on the reduction in Pitx1 expression produces left‐larger directional asymmetry in the vestiges. We used this phenotypic signature as a genetic proxy, testing for hindlimb directional asymmetry in six genera of squamate reptiles that independently evolved hindlimb reduction and for which genetic and developmental tools are not yet developed: Agamodon anguliceps, Bachia intermedia, Chalcides sepsoides, Indotyphlops braminus, Ophisaurus attenuatuas and O. ventralis, and Teius teyou. Significant asymmetry occurred in one taxon, Chalcides sepsoides, whose left‐side pelvis and femur vestiges were 18% and 64% larger than right‐side vestiges, respectively, suggesting modification in Pitx1 expression in that species. However, there was either right‐larger asymmetry or no directional asymmetry in the other five taxa, suggesting multiple developmental genetic pathways to hindlimb reduction in squamates and the vertebrates more generally.

Appendages have been reduced or lost hundreds of times independently during vertebrate evolution. This suggests that selection routinely favors appendage reduction. How often are the same developmental and genetic pathways used during loss by independent lineages? We reviewed the developmental and evolutionary literatures of appendage reduction in 12 genera spanning fish, reptiles, birds, and mammals. We found that appendage reduction and loss resulted from modified gene expression in each case but one. However, the genes for which expression was modified were rarely shared. Our findings suggest that adaptive loss of complex traits might proceed relatively easily through changes in gene expression along multiple developmental pathways.

Photo 1. Glugea infection on a stickleback from Theimer Lake, Vancouver Island, Canada. Photo credit: Daniel Bolnick. Photo 2. Ergasilus infection on gills from a stickleback from Campbell River Marsh, Vancouver Island. Photo credit: Daniel Bolnick. Photo 3. Field researchers collecting stickleback on Roberts Lake, Vancouver Island. Photo credit: Daniel Bolnick. Photo 4. Blackspot (trematode) infection on a stickleback. Photo credit: Daniel Bolnick. Photo 5. Schistocephalus solidus cestodes dissected from an infected stickleback from Gosling Lake, Vancouver Island. Photo credit: Daniel Bolnick. These photographs illustrate the article “Scale-dependent effects of host patch traits on species composition in a stickleback parasite metacommunity” by Daniel I. Bolnick, Emlyn J. Resetarits, Kimberly Ballare, Yoel E. Stuart, William E. Stutz published in Ecology. https://doi.org/10.1002/ecy.3181.