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Snake venom can vary both among and within species. While some groups of New World pitvipers—such as rattlesnakes—have been well studied, very little is known about the venom of montane pitvipers (Cerrophidion) found across the Mesoamerican highlands. Compared to most well-studied rattlesnakes, which are widely distributed, the isolated montane populations of Cerrophidion may facilitate unique evolutionary trajectories and venom differentiation. Here, we describe the venom gland transcriptomes for populations of C. petlalcalensis, C. tzotzilorum, and C. godmani from Mexico, and a single individual of C. sasai from Costa Rica. We explore gene expression variation in Cerrophidion and sequence evolution of toxins within C. godmani specifically. Cerrophidion venom gland transcriptomes are composed primarily of snake venom metalloproteinases, phospholipase A 2 s (PLA 2 s), and snake venom serine proteases. Cerrophidion petlalcalensis shows little intraspecific variation; however, C. godmani and C. tzotzilorum differ significantly between geographically isolated populations. Interestingly, intraspecific variation was mostly attributed to expression variation as we did not detect signals of selection within C. godmani toxins. Additionally, we found PLA 2 -like myotoxins in all species except C. petlalcalensis, and crotoxin-like PLA 2 s in the southern population of C. godmani. Our results demonstrate significant intraspecific venom variation within C. godmani and C. tzotzilorum. The toxins of C. godmani show little evidence of directional selection where variation in toxin sequence is consistent with evolution under a model of mutation–drift equilibrium. Cerrophidion godmani individuals from the southern population may exhibit neurotoxic venom activity given the presence of crotoxin-like PLA 2 s; however, further research is required to confirm this hypothesis. [ABSTRACT FROM AUTHOR]

Sea level variability along the US West Coast is analyzed using multi-year time series records from tide gauges and a high-resolution regional ocean model, the base of the West Coast Ocean Forecast System (WCOFS). One of the metrics utilized is the frequency of occurrences when model prediction is within 0.15 m from the observed sea level, F. A target level of F = 90% is set by an operational agency. A combination of the tidal sea level from a shallow water inverse model, inverted barometer (IB) term computed using surface air pressure from a mesoscale atmospheric model, and low-pass filtered sea level from WCOFS representing the effect of coastal ocean dynamics (DYN) provides the most straightforward approach to reaching levels F>80%. The IB and DYN components each add between 5 and 15% to F. Given the importance of the DYN term bringing F closer to the operational requirement and its role as an indicator of the coastal ocean processes on scales from days to interannual, additional verification of the WCOFS subtidal sea level is provided in terms of the model-data correlation, standard deviation of the band-pass filtered (2-60 days) time series, the annual cycle amplitude, and alongshore sea level coherence in the range of 5-120-day periods. Model-data correlation in sea level increases from south to north along the US coast. The rms amplitude of model sea level variability in the 2-60-day band and its annual amplitude are weaker than observed north of 42 N, in the Pacific Northwest (PNW) coast region. The alongshore coherence amplitude and phase patterns are similar in the model and observations. Availability of the multi-year model solution allows computation and analysis of spatial maps of the coherence amplitude. For a reference location in the Southern California Bight, relatively short-period sea level motions (near 10 days) are incoherent with those north of the Santa Barbara Channel (in part, due to coastal trapped wave scattering and/or dissipation). At a range of periods around 60 days, the coastal sea level in Southern California is coherent with the sea surface height (SSH) variability over the shelf break in Oregon, Washington, and British Columbia, more than with the coastal SSH at the same latitudes. [ABSTRACT FROM AUTHOR]

• Coastal modeling lacks scientific rigor due to proliferation of many gray areas. • We propose three guiding principles for the modeling community. • We debunk commonly held myths that make the coastal modeling lack rigor. • We describe end-to-end defensible modeling centered on digital elevation models. • Focusing on process-based assessment simplifies the calibration process. Despite tremendous progress in algorithm development, computational efficiency and transition into operations over the past two decades, coastal modeling still lacks scientific rigor due to proliferation of many 'gray' areas related to various modeling choices made by modelers. In this paper, we propose some guiding principles for the modeling community to improve performance, and we also debunk commonly held myths that make the coastal modeling lack rigor. Using our own experience in developing seamless cross-scale unstructured-grid based models for the past two decades, we describe in unprecedented detail the end-to-end modeling process (i.e., from digital elevation models (DEMs) to mesh generation to post analysis), and demonstrate that defensible modeling is within reach for any end user by following three guiding principles: (1) Bathymetry is a first order forcing in coastal domains and thus should be respected in all aspects of modeling; (2) Oceanographic processes are driven across multiple spatial scales and so models should enable appropriate resolution as needed; and (3) Model assessment should focus on physical processes. Through qualitative and quantitative model assessments, we demonstrate the fundamental role played by bathymetry/topography as embedded in DEMs in making the results defensible, which is unfortunately glossed over in many modeling studies. Focusing on process-based assessment simplifies the calibration process. A major conclusion of this work is that model developers and operators should maximize the scientific rigor for in silico oceanography by avoiding some common pitfalls that rely on error compensation at the expense of representation of physical system processes. We present some best practice procedures for defensive and trustworthy numerical modeling. [ABSTRACT FROM AUTHOR]

Species‐level taxonomy derives from empirical sources (data and techniques) that assess the existence of spatiotemporal evolutionary lineages via various species "concepts." These concepts determine if observed lineages are independent given a particular methodology and ontology, which relates the metaphysical species concept to what "kind" of thing a species is in reality. Often, species concepts fail to link epistemology back to ontology. This lack of coherence is in part responsible for the persistence of the subspecies rank, which in modern usage often functions as a placeholder between the evolutionary events of divergence or collapse of incipient species. Thus, prospective events like lineages merging or diverging require information from unknowable future information. This is also conditioned on evidence that the lineage already has a detectably distinct evolutionary history. Ranking these lineages as subspecies can seem attractive given that many lineages do not exhibit intrinsic reproductive isolation. We argue that using subspecies is indefensible on philosophical and empirical grounds. Ontologically, the rank of subspecies is either identical to that of species or undefined in the context of evolutionary lineages representing spatiotemporally defined individuals. Some species concepts more inclined to consider subspecies, like the Biological Species Concept, are disconnected from evolutionary ontology and do not consider genealogy. Even if ontology is ignored, methods addressing reproductive isolation are often indirect and fail to capture the range of scenarios linking gene flow to species identity over space and time. The use of subspecies and reliance on reproductive isolation as a basis for an operational species concept can also conflict with ethical issues governing the protection of species. We provide a way forward for recognizing and naming species that links theoretical and operational species concepts regardless of the magnitude of reproductive isolation. [ABSTRACT FROM AUTHOR]

Accurate representation of tides is a pre-requisite for simulating many complex coastal processes. This study examines several most important factors for rigorous validation of nearshore tides: bottom friction, quality of DEM (Digital Elevation Model) information, horizontal resolution of model mesh, and 3D baroclinic effects. The results demonstrate that a rigorous model validation against tide gauge observation requires (1) good-quality DEM information be available; (2) locally very high mesh resolution (which has not been used in previous models) be used to capture the small-scale bathymetric/geometric features near the tide gauges; and (3) 3D effects be included. On the other hand, attempts to compensate errors by tuning other parameters such as bottom friction might produce erroneous results away from the validation sites, as tides undergo complex nonlinear transformations in the nearshore regime. Consequently, a most skilled tidal simulation should use a 3D model with locally very high resolution to faithfully represent DEMs of good quality (not just high resolution). Our results also highlight the central role played by the bathymetry on coastal processes. [ABSTRACT FROM AUTHOR]

Non‐native (invasive) species offer a unique opportunity to study the geographical distribution and range limits of species, wherein the evolutionary change driven by interspecific interactions between native and non‐native closely related species is a key component. The red‐eared slider turtle, Trachemys scripta elegans (TSE), has been introduced and successfully established worldwide. It can coexist with its native congeners T. cataspila, T. venusta and T. taylori in Mexico. We performed comprehensive fieldwork, executed a battery of genetic analyses and applied a novel species distribution modelling approach to evaluate their historical lineage relationships and contemporary population genetic patterns. Our findings support the historical common ancestry between native TSE and non‐native (TSEalien), while also highlighting the genetic differentiation of the exotic lineage. Genetic patterns are associated with their range size/endemism gradient; the microendemic T. taylori showed significant reduced genetic diversity and high differentiation, whereas TSEalien showed the highest diversity and signals of population size expansion. Counter to our expectations, lower naturally occurring distribution overlap and little admixture patterns were found between TSE and its congeners, exhibiting reduced gene flow and clear genetic separation across neighbouring species despite having zones of contact. We demonstrate that these native Trachemys species have distinct climatic niche suitability, probably preventing establishment of and displacement by the TSEalien. Moreover, we found major niche overlap between TSEalien and native species worldwide, supporting our prediction that sites with closer ecological optima to the invasive species have higher establishment risk than those that are closer to the niche‐centre of the native species. [ABSTRACT FROM AUTHOR]

Abstract: Challenges posed by the Columbia River estuary–plume–shelf system have led to the development of ELCIRC, a model designed for the effective simulation of 3D baroclinic circulation across river-to-ocean scales. ELCIRC uses a finite-volume/finite-difference Eulerian–Lagrangian algorithm to solve the shallow water equations, written to realistically address a wide range of physical processes and of atmospheric, ocean and river forcings. The numerical algorithm is volume conservative, stable and computationally efficient, and it naturally incorporates wetting and drying of tidal flats. ELCIRC has been subject to systematic benchmarking, and applied to the description of the Columbia River circulation. This paper motivates and describes the formulation, presents and critically analyzes the results of selected benchmarks, and introduces ELCIRC as an open-source code available for community use and enhancement. A companion paper describes the application of ELCIRC to the Columbia River. [Copyright &y& Elsevier]

The article discusses the corrected taxonomic history of the North American ratsnakes (Pantherophis obsoletus Complex). It mentions that differential isolation across the genomes of geographic lineages is possible, with some chromosomal regions showing low levels of introgression and others showing considerable admixture. It states that differential level of migration among loci is expected under a process of speciation with ecological adaptation via natural selection.

Inferring the history of divergence between species in a framework that permits the presence of gene flow has been crucial for characterizing the "gray zone" of speciation, which is the period of time where lineages have diverged but have not yet achieved strict reproductive isolation. However, estimates of both divergence times and rates of gene flow often ignore spatial information, for example when considering the location and width of hybrid zones with respect to changes in the environment between lineages. Using population genomic data from the North American ratsnake complex (Pantherophis obsoletus), we connected phylogeographic estimates of lineage structure, migration, historical demography, and timing of divergence with hybrid zone dynamics. We examined the spatial context of diversification by linking migration and timing of divergence to the location and widths of hybrid zones. Artificial neural network approaches were applied to understand how landscape features and past climate have influenced population genetic structure among these lineages. We found that rates of migration between lineages were associated with the overall width of hybrid zones. Timing of divergence was not related to migration rate or hybrid zone width across species pairs but may be related to the number of alleles weakly introgressing through hybrid zones. This research underscores how incomplete reproductive isolation can be better understood by considering differential allelic introgression and the effects of historical and contemporary landscape features on the formation of lineages as well as overall genomic estimates of migration rates through time. [ABSTRACT FROM AUTHOR]

Compound flooding is usually induced by the concurrence of coastal storm surge and heavy precipitation induced river flooding, with the former involving oceanic processes and the latter involving hydrological processes. The simulation of these two types of processes is traditionally handled by two different types of models separately, i.e., hydrological models (e.g., NOAA's National Water Model (NWM)) and hydrodynamic models. This dichotomy leaves gaps in simulating the interrelated processes in a holistic fashion. In this paper, we present a creek-to-ocean 3D baroclinic model based on SCHISM (Semi-implicit Cross-scale Hydroscience Integrated System Model) that aims to unite traditional hydrologic and hydrodynamic models in a single modeling platform to simulate compound floods, by taking full advantage of the model polymorphism (i.e., a single model grid can seamlessly morph between full 3D, 2DV, 2DH, and quasi-1D modes). Using Hurricane Irene's impact on Delaware Bay as an example, a seamless 2D-3D model grid is implemented to include the entire US East Coast and Gulf of Mexico with a highly resolved Delaware Bay (down to 20-m resolution). The streamflow from NWM is injected into SCHISM grid at the intersections of NWM's segments and SCHISM's land boundary, and the pluvial and fluvial processes are directly handled by SCHISM. We demonstrate the model's accuracy, stability, and robustness with focus on the compound flooding events. The relative role of different physical processes in such events is examined by a series of sensitivity tests. Our results confirm the occurrence of backwater process into far upstream rivers and creeks and thus demonstrate the need for a dynamic two-way coupling between the hydrodynamic and hydrological models. [ABSTRACT FROM AUTHOR]

Bathymetric changes within estuarine and coastal waters can alter the hydrodynamic evolution of sea level and currents, which in turn can influence the ecosystem by altering material property distributions. Here we apply the Tampa Bay Coastal Ocean Model (TBCOM), with an unstructured, high-resolution grid to investigate the hydrodynamic response to bathymetric changes at the periphery of the Tampa Bay mouth over a relatively small area when compared to the whole model domain. Two separate numerical experiments are conducted with the same forcing, one using the original bathymetry and the other employing a revised synthetic bathymetry. The simulated sea level, amplitude and phase of the M2 tide, and associated currents are compared for the two experiments. Significant changes in water level (up to+/-10 cm) and current velocities (up to 20 cm/s) are found in the shallow peripheral area with the two different bathymetric data sets. These bathymetric influences are not limited to the locations where the bathymetric changes occur; they also extend to remote areas of the bay. Since Tampa Bay bathymetry varies with storm-induced sediment redistributions and human actives such as shipping channel dredging and beach nourishment, these findings emphasize the need for accurate and updated bathymetry for coastal ocean modeling and applications. • The Hydrodynamic response to bathymetric changes is investigated for Tampa Bay. • Numerical experiments are conducted using original and synthetic bathymetry. • Local changes in tides and currents are found due to bathymetric changes. • These local changes can propagate throughout the bay. • Accurate bathymetry is essential for coastal ocean modeling applications. [ABSTRACT FROM AUTHOR]

A major challenge in compound flooding simulation is representing small rivers in the model mesh. A parallel Python-based tool is developed to support the construction of unstructured grids (UGs) at continental scales. The tool is driven by Digital Elevation Model (DEM), ensuring accurate representation of geomorphic features in the resulting mesh. Its first component (pyDEM) extends an existing tool to detect river thalwegs from DEMs. The second component (RiverMapper) uses the thalwegs to generate river 'arcs', which can be directly ingested into meshing tools (e.g., the Surface-water Modeling System). The novelty lies in the explicit 2D representation of rivers in both along- and cross-channel directions, making it ideal for accurate, efficient, and high-resolution continental-scale research. The tool is employed to create a UG for a 3D creek-to-ocean model encompassing the US East and Gulf Coasts, and it greatly improves the flow exchange between the watershed and the coastal zone. • A Python-based tool is developed to explicitly specify the 2D river representation. • Locally very high resolution is enabled for river channels in unstructured grids. • The new mesh generation method improves compound flooding simulation results. [ABSTRACT FROM AUTHOR]

Investigates the two-dimensional (2-D) effects associated with titanium silicidation on small and nonuniform structures. Function of salicide or self-aligned silicide; Application of titanium silicidation; Titanium silicidation process.

Coastal hazard is rarely driven by only one source, as exemplified by the compound flooding from Hurricane Harvey in Galveston Bay in 2017. A 3D creek-to-ocean model is developed to explicitly resolve, without grid nesting, the marine (combination of atmospheric forcing and tides), fluvial and pluvial extremes for this extreme event. We first thoroughly assess the model skills using all available observations in the Galveston Bay region, including High Water Marks (HWMs) and field estimates of maximum inundation extent in the watershed. Subject to uncertainties in the river flows, atmospheric forcing, initial condition of salinity and temperature, and digital elevation model of bathymetry-topography, the model is shown to generally exhibit good skills for predicting inundation and compound surges, with a hit rate for inundation extent of 0.92, average mean-absolute-errors of 0.65 m for HWMs, 1.7 psu for salinity, and 1.4 °C for temperature. We then apply the model to quantify the individual contributions from the three major forcings (ocean, river and precipitation). Comparison of results (in the form of 'compound ratio') from the simulations with three factors being applied individually with those from the baseline simulation with all factors included in a single model reveals the nonlinear compounding effects in most of the areas in Galveston Bay, and indicates that the compound flooding problems are best simulated using a single model that integrates across all factors because the interactions among processes are very complex and highly nonlinear; in other words, summing up the results from individual forcings would lead to large errors. For example, the hydrodynamic model results forced by river inflows at boundary and oceanic and atmospheric forcings, without explicitly accounting for the direct precipitation in the coastal watersheds, would severely underestimate the resultant flow and surge by up to 90%. 'Regions of dominance' are also identified for each forcing factor from the sensitivity results. These concepts are applicable to other compound flooding studies as well. • Extreme flooding during Hurricane Harvey studied using a 3D creek-to-ocean model. • Predicted surges critically depend on river flows, DEMs and atmospheric forcing. • Simply summing up results from individual forcings would lead to large errors. • Compound flooding is best simulated using same model that integrates all factors. [ABSTRACT FROM AUTHOR]

We present a creek-to-ocean 3D baroclinic model based on unstructured grids that aims to unite traditional hydrologic and ocean models in a single modeling platform, by taking full advantage of the polymorphism (i.e. a single model grid can seamlessly morph between full 3D, 2DV, 2DH and quasi-1D configurations). Using Hurricane Irene (2011)'s impact on the Delaware Bay as an example, a seamless 2D–3D model grid is implemented to include the entire US East Coast and Gulf of Mexico with a highly resolved Delaware Bay (down to 20-m resolution). The model is forced by flows from a hydrological model (National Water Model) at the landward boundary. We demonstrate the model's accuracy, stability and robustness with the simulation of the storm surge and subsequent river flooding events and compound surges. Through a series of sensitivity tests, we illustrate the importance of including in the simulation the baroclinic effects, as provided by the large-scale Gulf Stream, in order to correctly capture the adjustment process following the main surge and the subsequent compound flooding events. The baroclinicity can explain up to 14% of the elevation error during the adjustment phase after the storm. • Simulation of compound flooding by a creek-to-ocean 3D baroclinic model. • Coupling with a continental-scale hydrologic model at 10 m above mean sea level. • Pluvial processes in a significant portion of the watershed are directly simulated. • Baroclinicity is shown to be important in the adjustment phase after the storm. [ABSTRACT FROM AUTHOR]

Phylogenomics allows us to uncover the historical signal of evolutionary processes through time and estimate phylogenetic networks accounting for these signals. Insight from genome-wide data further allows us to pinpoint the contributions to phylogenetic signal from hybridization, introgression, and ancestral polymorphism across the genome. Here we focus on how these processes have contributed to phylogenetic discordance among rattlesnakes (genera Crotalus and Sistrurus), a group for which there are numerous conflicting phylogenetic hypotheses based on a diverse array of molecular datasets and analytical methods. We address the instability of the rattlesnake phylogeny using genomic data generated from transcriptomes sampled from nearly all known species. These genomic data, analyzed with coalescent and network-based approaches, reveal numerous instances of rapid speciation where individual gene trees conflict with the species tree. Moreover, the evolutionary history of rattlesnakes is dominated by incomplete speciation and frequent hybridization, both of which have likely influenced past interpretations of phylogeny. We present a new framework in which the evolutionary relationships of this group can only be understood in light of genome-wide data and network-based analytical methods. Our data suggest that network radiations, like seen within the rattlesnakes, can only be understood in a phylogenomic context, necessitating similar approaches in our attempts to understand evolutionary history in other rapidly radiating species., (© The Author(s) 2024. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Although several phylogeographic studies of Asian snakes have been conducted, most have focused on pitvipers, with non-venomous snakes, such as colubrids or natricids, remaining poorly studied. The Chinese keelback water snake ( Trimerodytes percarinatus Boulenger) is a widespread, semiaquatic, non-venomous species occurring in China and southeastern Asia. Based on mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data, we explored the population genetic structure, genetic diversity, and evolutionary history of this species. MtDNA-based phylogenetic analysis showed that T. percarinatus was composed of five highly supported and geographically structured lineages. SNP-based phylogenetic analysis, principal component analysis, and population structure analysis consistently revealed four distinct, geographically non-overlapping lineages, which was different from the mtDNA-based analysis in topology. Estimation of divergence dates and ancestral area of origin suggest that T. percarinatus originated ~12.68 million years ago (95% highest posterior density: 10.36-15.96 Mya) in a region covering southwestern China and Vietnam. Intraspecific divergence may have been triggered by the Qinghai-Xizang Plateau uplift. Population demographics and ecological niche modeling indicated that the effective population size fluctuated during 0.5 Mya and 0.002 Mya. Based on the data collected here, we also comment on the intraspecific taxonomy of T. percarinatus and question the validity of the subspecies T. p. suriki ., Competing Interests: The authors declare no competing interests., (© 2024 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

We present partial genome sequences of 50 salamander species (Urodela) from 10 genera and 4 families. These span nearly the entire range of genome sizes in salamanders, from ~14-130GB, the latter of which is among the largest of all animal genomes. Only three salamander genomes were available to this point, from Ambystomatidae (one species) and Salamandridae (two species from two genera), to which we have added Amphiumidae (one species), Plethodontidae (45 species from 6 genera), Proteidae (one species), and Sirenidae (three species from two genera). These span ~140 million years of evolutionary divergence, leaving only Cryptobranchidae, Hynobiidae, and Rhyacotritonidae as salamander families without genome assemblies. These data should facilitate additional future work on speciation and genome evolution, both within Urodela and across Animalia.

The number of reference genomes of snakes lags behind several other vertebrate groups (e.g. birds and mammals). However, in the last two years, a concerted effort by researchers from around the world has produced new genomes of snakes representing members from several new families. Here, we present a high-quality, annotated genome of the central ratsnake (Pantherophis alleghaniensis), a member of the most diverse snake lineage, Colubroidea. Pantherophis alleghaniensis is found in the central part of the Nearctic, east of the Mississippi River. This genome was sequenced using 10X Chromium synthetic long reads and polished using Illumina short reads. The final genome assembly had an N50 of 21.82 Mb and an L50 of 22 scaffolds with a maximum scaffold length of 82.078 Mb. The genome is composed of 49.24% repeat elements dominated by long interspersed elements. We annotated this genome using transcriptome assemblies from 14 tissue types and recovered 28,368 predicted proteins. Finally, we estimated admixture proportions between two species of ratsnakes and discovered that this specimen is an admixed individual containing genomes from the western (Pantherophis obsoletus) and central ratsnakes (P. alleghaniensis). We discuss the importance of considering interspecific admixture in downstream approaches for inferring demography and phylogeny., Competing Interests: Conflicts of interest The author(s) declare no conflict of interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.)

Comparisons of intraspecific genetic diversity across species can reveal the roles of geography, ecology, and life history in shaping biodiversity. The wide availability of mitochondrial DNA (mtDNA) sequences in open-access databases makes this marker practical for conducting analyses across several species in a common framework, but patterns may not be representative of overall species diversity. Here, we gather new and existing mtDNA sequences and genome-wide nuclear data (genotyping-by-sequencing; GBS) for 30 North American squamate species sampled in the Southeastern and Southwestern United States. We estimated mtDNA nucleotide diversity for 2 mtDNA genes, COI (22 species alignments; average 16 sequences) and cytb (22 species; average 58 sequences), as well as nuclear heterozygosity and nucleotide diversity from GBS data for 118 individuals (30 species; 4 individuals and 6,820 to 44,309 loci per species). We showed that nuclear genomic diversity estimates were highly consistent across individuals for some species, while other species showed large differences depending on the locality sampled. Range size was positively correlated with both cytb diversity (phylogenetically independent contrasts: R2 = 0.31, P = 0.007) and GBS diversity (R2 = 0.21; P = 0.006), while other predictors differed across the top models for each dataset. Mitochondrial and nuclear diversity estimates were not correlated within species, although sampling differences in the data available made these datasets difficult to compare. Further study of mtDNA and nuclear diversity sampled across species' ranges is needed to evaluate the roles of geography and life history in structuring diversity across a variety of taxonomic groups., (© The American Genetic Association. 2023.)

Secondary sympatry amongst sister lineages is strongly associated with genetic and ecological divergence. This pattern suggests that for closely related species to coexist in secondary sympatry, they must accumulate differences in traits that mediate ecological and/or reproductive isolation. Here, we characterized inter- and intraspecific divergence in three giant tree frog species whose distributions stretch across West and Central Africa. Using genome-wide single-nucleotide polymorphism data, we demonstrated that species-level divergence coincides temporally and geographically with a period of large-scale forest fragmentation during the late Pliocene. Our environmental niche models further supported a dynamic history of climatic suitability and stability, and indicated that all three species occupy distinct environmental niches. We found modest morphological differentiation amongst the species with significant divergence in tympanum diameter and male advertisement call. In addition, we confirmed that two species occur in secondary sympatry in Central Africa but found no evidence of hybridization. These patterns support the hypothesis that cycles of genetic exchange and isolation across West and Central Africa have contributed to globally significant biodiversity. Furthermore, divergence in both ecology and reproductive traits appear to have played important roles in maintaining distinct lineages. At the intraspecific level, we found that climatic refugia, precipitation gradients, marine incursions, and potentially riverine barriers generated phylogeographic structure throughout the Pleistocene and into the Holocene. Further studies examining phenotypic divergence and secondary contact amongst these geographically structured populations may demonstrate how smaller scale and more recent biogeographic barriers contribute to regional diversification., (© 2021 John Wiley & Sons Ltd.)

Despite the medical significance to humans and important ecological roles filled by vipers, few high-quality genomic resources exist for these snakes outside of a few genera of pitvipers. Here we sequence, assemble, and annotate the genome of Fea's Viper (Azemiops feae). This taxon is distributed in East Asia and belongs to a monotypic subfamily, sister to the pitvipers. The newly sequenced genome resulted in a 1.56 Gb assembly, a contig N50 of 1.59 Mb, with 97.6% of the genome assembly in contigs >50 Kb, and a BUSCO completeness of 92.4%. We found that A. feae venom is primarily composed of phospholipase A2 (PLA2) proteins expressed by genes that likely arose from lineage-specific PLA2 gene duplications. Additionally, we show that renin, an enzyme associated with blood pressure regulation in mammals and known from the venoms of two viper species including A. feae, is expressed in the venom gland at comparative levels to known toxins and is present in the venom proteome. The cooption of this gene as a toxin may be more widespread in viperids than currently known. To investigate the historical population demographics of A. feae, we performed coalescent-based analyses and determined that the effective population size has remained stable over the last 100 kyr. This suggests Quaternary glacial cycles likely had minimal influence on the demographic history of A. feae. This newly assembled genome will be an important resource for studying the genomic basis of phenotypic evolution and understanding the diversification of venom toxin gene families., (© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Gene flow and reticulation are increasingly recognized as important processes in the diversification of many taxonomic groups. With the increasing ease of collecting genomic data and the development of multispecies coalescent network approaches, such reticulations can be accounted for when inferring phylogeny and diversification. Caribbean Anolis lizards are a classic example of an adaptive radiation in which species have independently radiated on the islands of the Greater Antilles into the same ecomorph classes. Within the Jamaican radiation at least one species, Anolis opalinus, has been documented to be polyphyletic in its mitochondrial DNA, which could be the result of an ancient reticulation event or incomplete lineage sorting (ILS). Here, we generate mtDNA and genotyping-by-sequencing (GBS) data and implement gene tree, species tree, and multispecies coalescent network methods to infer the diversification of this group. Our mtDNA gene tree recovers the same relationships previously inferred for this group, which is strikingly different from the species tree inferred from our GBS data. Posterior predictive simulations suggest that our genomic data violate commonly adopted assumptions of the multispecies coalescent model (MSCM), so we use network approaches to infer phylogenetic relationships. The inferred network topology contains a reticulation event but does not explain the mtDNA polyphyly observed in this group; however, coalescent simulations suggest that the observed mtDNA topology is likely the result of past introgression. How common a signature of gene flow and reticulation is across the radiation of Anolis is unknown; however, the reticulation events that we demonstrate here may have allowed for adaptive evolution, as has been suggested in other, more recent, adaptive radiations. [Adaptive radiation; hybridization; introgression; multispecies network coalescent; posterior predictive simulation.]., (© The Authors 2021. Published by Oxford University Press on behalf of the Society of Systematic Biologists. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Hybridization and introgression are important, but often overlooked processes when inferring phylogenies. When these processes are not accounted for and a strictly diverging phylogenetic model is applied to groups with a history of hybridization, phylogenetic inference and parameter estimation can be inaccurate. Recent developments in phylogenetic network approaches coupled with the increasing availability of genomic data allow inferences of reticulate evolutionary histories across the tree of life. The western rattlesnake species group (C. viridis species complex, C. mitchellii species complex, C. scutulutas, and C. tigris) is an iconic snake lineage that is widespread across western North America. This group is composed of several species complexes with unclear species limits, likely the result of ongoing gene flow among nascent lineages. Here I generate reduced representation genomic data and test for a history of reticulation within this group. I demonstrate that all species have undergone hybridization with at least one other lineage, suggesting introgression is widespread in this group. Topologies differ between phylogenies estimated under the multispecies coalescent and multispecies network coalescent methods, indicating that gene flow has obscured phylogenetic relationships within this group. These past introgression events are predominantly restricted to species that co-occur geographically. However, within species that have a history of introgression, this signature is detected regardless of specimen sampling across geography. Overall, my results suggest the accumulation of reproductive isolating barriers occurs slowly in rattlesnakes which likely leads to the difficulty in delimiting species, furthermore, the results of this study have implications for trait evolution in this group., (Copyright © 2021 Elsevier Inc. All rights reserved.)