Andrew M. Simons’s research while affiliated with Bethel University and other places

Hydrodynamic forces and their absence appear to exert differential selection pressure on aquatic biodiversity in lake and stream habitats, creating a tight fit between organismal phenotypes and their environments. Ecophenotypic variants may be the result of genetic differentiation or phenotypic plasticity, where a genotype can produce multiple phenotypes dependent on the environment. Freshwater mussels possess a wide degree of morphological variation that frequently covaries with the environment, making them a good system to understand the mechanisms of ecophenotypic variation across hydrological conditions. We designed a two‐year experiment where individuals from the same Pyganodon grandis maternal brood (half and full siblings) were reared at a controlled site and four natural sites involving one lake and three streams. At the end of the experiment, shell shape was quantified for recaptured ( N = 70), wild ( N = 206), and zoo‐reared ( N = 305) mussels. The maternal individual and 46 recaptured mussels were sequenced for genomic single nucleotide polymorphisms to test for multiple paternity and its effect on offspring morphology. Analysis of covariance found significant differences in shell shape between rearing sites, particularly between stream and lake habitats, but no shape differences were detected across the three stream sites. At two of the four sites, the shell shape of recaptured individuals was not significantly different than that of wild populations. Genomic sequencing and parentage analysis identified 11–27 different fathers among recaptured individuals. Yet no genetic differences were present between stream and lake habitats, and there was no paternal effect on shell shape. Taken together, phenotypic plasticity, over genetic differentiation, is identified as the primary mechanism of ecophenotypic variation. Plasticity is likely ubiquitous across freshwater mussels and may be a key adaptation given their high variance in habitat use. Multiple paternity may also play a role in the evolution of phenotypic plasticity, allowing more males from greater distances opportunities for fertilization, thus increasing genetic connectivity. Lastly, phenotypic plasticity and multiple paternity are convenient properties for freshwater mussel conservation and propagation. Multiple fathers increase the genetic variation of propagated broods, while plasticity may provide resilience to the release of stocked individuals across environmental heterogeneity.

The isolated river drainages of eastern North America serve as a natural laboratory to investigate the roles of allopatry and secondary contact in the evolutionary trajectories of recently diverged lineages. Drainage divides facilitate allopatric speciation, but due to their sensitivity to climatic and geomorphological changes, neighboring rivers frequently coalesce, creating recurrent opportunities of isolation and contact throughout the history of aquatic lineages. The freshwater mussel Quadrula quadrula is widely distributed across isolated rivers of eastern North America and possesses high phenotypic and molecular variation across its range. We integrate sequence data from three genomes, including female‐ and male‐inherited mitochondrial markers and thousands of nuclear encoded SNPs with morphology and geography to illuminate the group's divergence history. Across contemporary isolated rivers, we found continuums of molecular and morphological variation, following a pattern of isolation by distance. In contact zones, hybridization was frequent with no apparent fitness consequences, as advanced hybrids were common. Accordingly, we recognize Q. quadrula as a single cohesive species with subspecific variation ( Q. quadrula rumphiana ). Demographic modeling and divergence dating supported a divergence history characterized by allopatric vicariance followed by secondary contact, likely driven by river rearrangements and Pleistocene glacial cycles. Despite clinal range‐wide variation and hybridization in contact zones, the process‐based species delimitation tool delimitR , which considers demographic scenarios like secondary contact, supported the delimitation of the maximum number of species tested. As such, when interpreting species delimitation results, we suggest careful consideration of spatial sampling and subsequent geographic patterns of biological variation, particularly for wide‐ranging taxa.

In the published publication [...]

Migration independently evolved numerous times in animals, with a myriad of ecological and evolutionary implications. In fishes, perhaps the most extreme form of migration is diadromy, the migration between marine and freshwater environments. Key and longstanding questions are: how many times has diadromy evolved in fishes, how frequently do diadromous clades give rise to non-diadromous species, and does diadromy influence lineage diversification rates? Many diadromous fishes have large geographic ranges with constituent populations that use isolated freshwater habitats. This may limit gene flow among some populations, increasing the likelihood of speciation in diadromous lineages relative to non-diadromous lineages. Alternatively, diadromy may reduce lineage diversification rates if migration is associated with enhanced dispersal capacity that facilitates gene flow within and between populations. Clupeiformes (herrings, sardines, shads and anchovies) is a model clade for testing hypotheses about the evolution of diadromy because it includes an exceptionally high proportion of diadromous species and several independent evolutionary origins of diadromy. However, relationships among major clupeiform lineages remain unresolved and existing phylogenies sparsely sampled diadromous species, limiting the resolution of phylogenetically-informed statistical analyses. We assembled a phylogenomic dataset and used multi-species coalescent and concatenation-based approaches to generate the most comprehensive, highly-resolved clupeiform phylogeny to date, clarifying associations among several major clades and identifying recalcitrant relationships needing further examination. We determined that variation in rates of sequence evolution (heterotachy) and base-composition (non-stationarity) had little impact on our results. Using this phylogeny, we characterized evolutionary patterns of diadromy and tested for differences in lineage diversification rates between diadromous, marine, and freshwater lineages. We identified thirteen transitions to diadromy, all during the Cenozoic Era (ten origins of anadromy, two origins of catadromy, and one origin of amphidromy), and seven losses of diadromy. Two diadromous lineages rapidly generated non-diadromous species, demonstrating that diadromy is not an evolutionary dead-end. We discovered considerably faster transition rates out of diadromy than to diadromy. The largest lineage diversification rate increase in Clupeiformes was associated with a transition to diadromy, but we uncovered little statistical support for categorically faster lineage diversification rates in diadromous versus non-diadromous fishes. We propose that diadromy may increase the potential for accelerated lineage diversification, particularly in species that migrate long distances. However, this potential may only be realized in certain biogeographic contexts, such as when diadromy allows access to ecosystems in which there is limited competition from incumbent species.

Hydrodynamic forces and their absence appears to exert differential selection pressure between lake and stream populations, creating a tight fit between organismal phenotypes and their environments. Ecophenotypic variants may be the result from isolated genetic evolution or phenotypic plasticity, where a widespread genotype can produce multiple phenotypes dependent on the environment. Freshwater mussels possess a wide degree of morphological variation that frequently covaries with the environment, making them a good system to understand the mechanisms of ecophenotypic variation across hydrological conditions. We designed a two-year experiment where individuals from the same Pyganodon grandis maternal brood (half-full siblings) were reared at a controlled site and four natural sites involving one lake and three streams. At the end of the experiment, shell shape was quantified for recaptured (N=70), wild (N=206), and zoo-reared (N=305) mussels. Analysis of covariance found significant differences in shell shape between rearing sites, particularly between stream and lake habitats, but no shape differences were detected across the three stream sites. At two of the four sites, shell shape of recaptured individuals matched the morphology of wild populations. Genomic sequencing and parentage analysis identified 27 different fathers among recaptured individuals. Yet, no genetic differences were present between stream and lake habitats and there was no effect of parentage on shell shape. Taken together, phenotypic plasticity, over genetic differentiation, is identified as the primary mechanism of shell shape ecophenotypy. Plasticity may be a key adaptation for freshwater mussels and possibly provide a buffer against their imperilment in degraded habitats. 1. Summary statement Streamlined and obese freshwater mussel shell shapes in stream-lake environments are developed from the same maternal brood and may reflect adaptations to the presence and absence of streamflow.

Frequent and strong morphological convergence suggests that determinism tends to supersede historical contingencies in evolutionary radiations. For many lineages living within the water column of rivers and streams, hydrodynamic forces drive widespread morphological convergence. Living below the sediment-water interface may release organisms from these hydrodynamic pressures, permitting a broad array of morphologies, and thus less convergence. However, we show here that the semi-infaunal freshwater mussels have environmentally determined convergence in shell morphology. Using 3D morphometric data from 715 individuals among 164 Nearctic species, we find that species occurring in rivers with high flow rates have evolved traits that resist dislodgement from their burrowed position in the streambed: thicker shells for their body size, with the thickest sector of the shell being the most deeply buried. Species occurring in low flow environments have evolved thinner and more uniformly thickened shells, corresponding to an alternative adaptation to dislodgement: increased burrowing efficiency. Within species, individuals also show increased shell thickness for their body size at higher flow rates, suggesting that ecophenotypy may, in part, be an important mechanism for establishing populations in new environments and thus evolutionary divergence in this highly imperiledinvertebrate group.

Aim The latitudinal diversity gradient of increasing species richness from poles to equator is one of the most striking and pervasive spatial patterns of biodiversity. Climate appears to have been key to the formation of the latitudinal diversity gradient, but the processes through which climate shaped species richness remain unclear. We tested predictions of the time for speciation, carrying capacity and diversification rate latitudinal diversity gradient hypotheses in a trans‐marine/freshwater clade of fishes. Location Global in marine and freshwater environments. Taxon Clupeiformes (anchovies, herrings, sardines and relatives). Methods We tested predictions of latitudinal diversity gradient hypotheses using a molecular phylogeny, species distribution data and phylogenetic comparative approaches. To test the time for speciation hypothesis, we conducted ancestral state reconstructions to infer the ages of temperate, subtropical and tropical lineages and frequency of evolutionary transitions between climates. We tested the carry capacity hypothesis by characterizing changes in net diversification rates through time. To test the diversification rate hypothesis, we qualitatively compared the diversification rates of temperate, subtropical and tropical lineages and conducted statistical tests for associations between latitude and diversification rates. Results We identified four transitions to temperate climates and two transitions out of temperate climates. We found no differences in diversification rates among temperate and tropical clupeiforms. Net diversification rates remained positive in crown Clupeiformes since their origin ~150 Ma in both tropical and temperate lineages. Climate niche characters exhibited strong phylogenetic signal. All temperate clupeiform lineages arose <50 Ma, after the Early Eocene Climatic Optimum. Main conclusions Our results support the time for speciation hypothesis, which proposes that climate niche conservatism and fluctuations in the extent of temperate climates limited the time for species to accumulate in temperate climates, resulting in the latitudinal diversity gradient. We found no support for the carrying capacity or diversification rate hypotheses.

We used a multi-locus phylogenetic approach (i.e., combining both mitochondrial and nuclear DNA fragments) to address some long-standing taxonomic inconsistencies within the diverse fish clade of Combtooth Blennies (Blenniidae—unranked clade Almadablennius). The obtained phylogenetic trees revealed some major inconsistencies in the current taxonomy of Parablennini, such as the paraphyletic status of the Salaria and Parablennius genera, casting some doubt regarding their actual phylogenetic relationship. Furthermore, a scarce-to-absent genetic differentiation was observed among the three species belonging to the genus Chasmodes. This study provides an updated taxonomy and phylogeny of the former genus Salaria, ascribing some species to the new genus Salariopsis gen. nov., and emphasizes the need for a revision of the genus Parablennius

Modes of teleost tooth replacement and attachment have historically been described using discrete classification systems that categorize major patterns across taxa. While useful, these discrete classification schemes understate teleost tooth diversity. The “unattached” dentition of salariin combtooth blennies (Blenniiformes: Blenniidae: Salariini) is frequently overlooked due to its perceived complexity, so we examined the Pacific Leaping Blenny, Alticus arnoldorum, to describe this complex morphology. Using a range of methods including histology, SEM, microCT scanning, and clearing and staining, we establish a descriptive model of tooth replacement for A. arnoldorum. We then use our descriptive model of tooth replacement to propose a hypothesis of tooth function in salariin blennies. Our results show that A. arnoldorum exhibits grouped, extraosseous replacement of feeding teeth upon a discontinuous, permanent dental lamina. We also find that tooth replacement occurs within lip tissue that is laterally displaced from the distal margins of the jaw bones, a process previously undocumented in teleost fish. Feeding teeth attach to the dentigerous bone via a primary attachment mode consisting of a continuous collagen band at the posterior base of the teeth, and a secondary attachment mode consisting of epithelial cells. Alticus arnoldorum presents novel modes of tooth replacement and attachment that challenge historical classification modes of teleost dentition. Our descriptive tooth replacement model also provides a reliable framework to propose hypotheses of tooth function that can be applied in future comparative studies on salariin blennies and other long‐toothed teleosts to further elucidate the functional role of long‐toothed fishes in aquatic ecosystems.