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Abstract The outcomes of speciation across organismal dimensions (e.g., ecological, genetic, phenotypic) are often assessed using phylogeographic methods. At one extreme, reproductively isolated lineages represent easily delimitable species differing in many or all dimensions, and at the other, geographically distinct genetic segments introgress across broad environmental gradients with limited phenotypic disparity. In the ambiguous gray zone of speciation, where lineages are genetically delimitable but still interacting ecologically, it is expected that these lineages represent species in the context of ontology and the evolutionary species concept when they are maintained over time with geographically well‐defined hybrid zones, particularly at the intersection of distinct environments. As a result, genetic structure is correlated with environmental differences and not space alone, and a subset of genes fail to introgress across these zones as underlying genomic differences accumulate. We present a set of tests that synthesize species delimitation with the speciation process. We can thereby assess historical demographics and diversification processes while understanding how lineages are maintained through space and time by exploring spatial and genome clines, genotype‐environment interactions, and genome scans for selected loci. Employing these tests in eight lineage‐pairs of snakes in North America, we show that six pairs represent 12 “good” species and that two pairs represent local adaptation and regional population structure. The distinct species pairs all have the signature of divergence before or near the mid‐Pleistocene, often with low migration, stable hybrid zones of varying size, and a subset of loci showing selection on alleles at the hybrid zone corresponding to transitions between distinct ecoregions. Locally adapted populations are younger, exhibit higher migration, and less ecological differentiation. Our results demonstrate that interacting lineages can be delimited using phylogeographic and population genetic methods that properly integrate spatial, temporal, and environmental data. 

Abstract Rivers are prominent landscape features, acting as key promoters of diversification among freshwater organisms. Albeit generally considered potential barriers to species movement, they may also facilitate gene flow and structure populations of semiaquatic species (Riverine Thruway Hypothesis, RTH). We evaluated the role of rivers on the processes responsible for current genetic variation in the semiaquatic frog Pseudis bolbodactyla, testing whether each hydrographic basin harbours distinct genetic lineages. We sequenced three markers on 166 samples from 13 localities along the Paraná (PR), Araguaia–Tocantins (AT), and São Francisco (SF) River basins in Brazil. We recovered three populations geographically matching each hydrographic basin. Our results indicate migration among basins, with the best model selected using approximate Bayesian computation, including migration between AT and SF and ancient gene flow from PR to the AT–SF ancestor. Our findings are likely related to the orogenic events in Central Brazil dating to the Late Miocene (5 Mya), when hydrographic basins and the geomorphological features of the Brazilian Shield were formed. This suggests that P. bolbodactyla probably represents a species complex, with each lineage occurring in a distinct hydrographic basin, matching the predictions of the RTH. 

Saw-scaled vipers (genus Echis) are small (up to 58 cm snout-to-vent length), venomous, eastern hemisphere snakes of the subfamily Viperinae. They are distributed across northern Africa, the Arabian Peninsula, and southwestern Asia. This group has been separated into four species complexes and twelve proposed species, however the true diversity within these groups is unclear even given numerous studies on this genus. This is partly due to uneven geographic sampling of specimens and tissue samples, overlapping distributions, and historically difficult to access species’ ranges making this genus difficult to research. Furthermore, previous studies have not used objective species delimitation approaches with either molecular or morphological data. Using recently collected tissue samples, we generate cytochrome b sequences for 24 specimens and combine these with sequences available on GenBank in order to create a time-calibrated phylogeny and estimate species level diversity using single locus species delimitation methods. We couple this with morphological analysis of specimens from the California Academy of Sciences and UC Berkeley Museum of Vertebrate Zoology collections, in order to determine if these genetically delimited species are morphologically diverged. These data can further aid in identifying specimens to species in this genus, as was demonstrated by classifying individuals to species within the Academy’s collection. 

Abstract 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. 

Abstract 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. 

Two sessions were organized during the 2018 Fall AGU Meeting entitled, (1) Coastal Response to Extreme Events: Fidelity of Model Predictions of Surge, Inundation, and Morphodynamics and (2) Improved Observational and Modeling Skills to Understand the Hurricane and Winter Storm Induced Surge and Meteotsunami. The focus of these sessions was on examining the impact of natural disasters on estuarine and coastal regions worldwide, including the islands and mainland in the northwestern Atlantic and the northwestern Pacific. The key research interests are the investigations on the regional dynamics of storm surges, coastal inundations, waves, tides, currents, sea surface temperatures, storm inundations and coastal morphology using both numerical models and observations during tropical and extratropical cyclones. This Special Issue (SI) ‘Estuarine and coastal natural hazards’ in Estuarine Coastal and Shelf Science is an outcome of the talks presented at these two sessions. Five themes are considered (effects of storms of wave dynamics; tide and storm surge simulations; wave-current interaction during typhoons; wave effects on storm surges and hydrodynamics; hydrodynamic and morphodynamic responses to typhoons), arguably reflecting areas of greatest interest to researchers and policy makers. This synopsis of the articles published in the SI allows us to obtain a better understanding of the dynamics of natural hazards (e.g., storm surges, extreme waves, and storm induced inundation) from various physical aspects. The discussion in the SI explores future dimensions to comprehend numerical models with fully coupled windwave- current-morphology interactions at high spatial resolutions in the nearshore and surf zone during extreme wind events. In addition, it would be worthwhile to design numerical models incorporating climate change projections (sea level rise and global warming temperatures) for storm surges and coastal inundations to allow more precisely informed coastal zone management plans. 

Abstract 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 The mechanisms and geographic distribution of global tidal dissipation in barotropic tidal models are examined using a high resolution unstructured mesh finite element model. Mesh resolution varies between 2 and 25 km and is especially focused on inner shelves and steep bathymetric gradients. Tidal response sensitivities to bathymetric changes are examined to put into context response sensitivities to frictional processes. We confirm that the Ronne Ice Shelf dramatically affects Atlantic tides but also find that bathymetry in the Hudson Bay system is a critical control. We follow a sequential frictional parameter optimization process and use TPXO9 data‐assimilated tidal elevations as a reference solution. From simulated velocities and depths, dissipation within the global model is estimated and allows us to pinpoint dissipation at high resolution. Boundary layer dissipation is extremely focused with 1.4% of the ocean accounting for 90% of the total. Internal tide friction is much more distributed with 16.7% of the ocean accounting for 90% of the total. Often highly regional dissipation can impact basin‐scale and even ocean wide tides. Optimized boundary layer friction parameters correlate very well with the physical characteristics of the locality with high friction factors associated with energetic tidal regions, deep ocean island chains, and ice covered areas. Global complex M₂tide errors are 1.94 cm in deep waters. Total global boundary layer and internal tide dissipation are estimated, respectively, at 1.83 and 1.49 TW. This continues the trend in the literature toward attributing more dissipation to internal tides.