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The impact of preserved museum specimens is transforming and increasing by three-dimensional (3D) imaging that creates high-fidelity online digital specimens. Through examples from the openVertebrate (oVert) Thematic Collections Network, we describe how we created a digitization community dedicated to the shared vision of making 3D data of specimens available and the impact of these data on a broad audience of scientists, students, teachers, artists, and more. High-fidelity digital 3D models allow people from multiple communities to simultaneously access and use scientific specimens. Based on our multiyear, multi-institution project, we identify significant technological and social hurdles that remain for fully realizing the potential impact of digital 3D specimens.

 

Many subspecies were described to capture phenotypic variation in wide-ranging taxa, with some later being found to correspond to divergent genetic lineages. We investigate whether currently recognized subspecies correspond to distinctive and coherent evolutionary lineages in the widespread Australian lizard Ctenotus pantherinus based on morphological, mitochondrial and genome-wide nuclear variation. We find weak and inconsistent correspondence between morphological patterns and the presumed subspecies ranges, with character polymorphism within regions and broad morphological overlap across regions. Phylogenetic analyses suggest paraphyly of populations assignable to each subspecies, mitonuclear discordance and little congruence between subspecies ranges and the distribution of inferred clades. Genotypic clustering supports admixture across regions. These results undermine the presumed phenotypic and genotypic coherence and distinctiveness of C. pantherinus subspecies. Based on our findings, we comment on the operational and conceptual shortcomings of morphologically defined subspecies and discuss practical challenges in applying the general notion of subspecies as incompletely separated population lineages. We conclude by highlighting a historical asymmetry that has implications for ecology, evolution and conservation: subspecies proposed in the past are difficult to falsify even in the face of new data that challenge their coherence and distinctiveness, whereas modern researchers appear hesitant to propose new subspecies.

 

Australia harbors the most diverse lizard assemblages on Earth, yet the biodiversity of its vast arid zone remains incompletely characterized. Recent sampling of remote regions has revealed new species with unique phenotypes and unclear evolutionary affinities. Here, we describe a new species of scincid lizard that appears to be widely distributed across the Great Victoria Desert and adjacent regions. The new species was previously overlooked among specimens of the wide-ranging desert taxon Ctenotus schomburgkii but is distinguished from it by coloration and scalation characters. Phylogenetic analyses based on mitochondrial and genome-wide nuclear loci confirmed that the new species is highly divergent from C. schomburgkii, with which it appears to be sympatric across much of its range. In addition to the new species, our survey of genetic variation within C. schomburgkii as currently recognized revealed three additional lineages that approach one another in southern and northwestern Australia, and which may also represent distinct species. These results suggest that our knowledge of the extraordinary biodiversity of arid Australia remains incomplete, with implications for the conservation and management of this unique fauna. The targeted collection of voucher specimens in undersampled regions, coupled with population genetic screening of lineage diversity, will be crucial for characterizing species boundaries and understanding the composition of Australia’s vertebrate communities. 

Understanding phenotypic disparity across the tree of life requires identifying where and when evolutionary rates change on phylogeny. A primary methodological challenge in macroevolution is therefore to develop methods for accurate inference of among-lineage variation in rates of phenotypic evolution. Here, we describe a method for inferring among-lineage evolutionary rate heterogeneity in both continuous and discrete traits. The method assumes that the present-day distribution of a trait is shaped by a variable-rate process arising from a mixture of constant-rate processes and uses a single-pass tree traversal algorithm to estimate branch-specific evolutionary rates. By employing dynamic programming optimization techniques and approximate maximum likelihood estimators where appropriate, our method permits rapid exploration of the tempo and mode of phenotypic evolution. Simulations indicate that the method reconstructs rates of trait evolution with high accuracy. Application of the method to data sets on squamate reptile reproduction and turtle body size recovers patterns of rate heterogeneity identified by previous studies but with computational costs reduced by many orders of magnitude. Our results expand the set of tools available for detecting macroevolutionary rate heterogeneity and point to the utility of fast, approximate methods for studying large-scale biodiversity dynamics. [Brownian motion; continuous characters; discrete characters; macroevolution; Markov process; rate heterogeneity.]

 

Genomic‐scale datasets, sophisticated analytical techniques, and conceptual advances have disproportionately failed to resolve species boundaries in some groups relative to others. To understand the processes that underlie taxonomic intractability, we dissect the speciation history of an Australian lizard clade that arguably represents a “worst‐case” scenario for species delimitation within vertebrates: theCtenotus inornatusspecies group, a clade beset with decoupled genetic and phenotypic breaks, uncertain geographic ranges, and parallelism in purportedly diagnostic morphological characters. We sampled hundreds of localities to generate a genomic perspective on population divergence, structure, and admixture. Our results revealed rampant paraphyly of nominate taxa in the group, with lineages that are either morphologically cryptic or polytypic. Isolation‐by‐distance patterns reflect spatially continuous differentiation among certain pairs of putative species, yet genetic and geographic distances are decoupled in other pairs. Comparisons of mitochondrial and nuclear gene trees, tests of nuclear introgression, and historical demographic modelling identified gene flow between divergent candidate species. Levels of admixture are decoupled from phylogenetic relatedness; gene flow is often higher between sympatric species than between parapatric populations of the same species. Such idiosyncratic patterns of introgression contribute to species boundaries that are fuzzy while also varying in fuzziness. Our results suggest that “taxonomic disaster zones” like theC. inornatusspecies group result from spatial variation in the porosity of species boundaries and the resulting patterns of genetic and phenotypic variation. This study raises questions about the origin and persistence of hybridizing species and highlights the unique insights provided by taxa that have long eluded straightforward taxonomic categorization.

 

Rates of species formation vary widely across the tree of life and contribute to massive disparities in species richness among clades. This variation can emerge from differences in metapopulation-level processes that affect the rates at which lineages diverge, persist, and evolve reproductive barriers and ecological differentiation. For example, populations that evolve reproductive barriers quickly should form new species at faster rates than populations that acquire reproductive barriers more slowly. This expectation implicitly links microevolutionary processes (the evolution of populations) and macroevolutionary patterns (the profound disparity in speciation rate across taxa). Here, leveraging extensive field sampling from the Neotropical Cerrado biome in a biogeographically controlled natural experiment, we test the role of an important microevolutionary process—the propensity for population isolation—as a control on speciation rate in lizards and snakes. By quantifying population genomic structure across a set of codistributed taxa with extensive and phylogenetically independent variation in speciation rate, we show that broad-scale patterns of species formation are decoupled from demographic and genetic processes that promote the formation of population isolates. Population isolation is likely a critical stage of speciation for many taxa, but our results suggest that interspecific variability in the propensity for isolation has little influence on speciation rates. These results suggest that other stages of speciation—including the rate at which reproductive barriers evolve and the extent to which newly formed populations persist—are likely to play a larger role than population isolation in controlling speciation rate variation in squamates. 

For many species, both local abundance and regional occupancy are highest near the centre of their geographic distributions. One hypothesis for this pattern is that niche suitability declines with increasing distance from a species geographic centre, such that populations near range margins are characterized by reduced density and increased patchiness. In these smaller edge populations, genetic drift is more powerful, leading to the loss of genetic diversity. This simple verbal model has been formalized as the central‐marginal hypothesis, which predicts that core populations should have greater genetic diversity than edge populations. Here, we tested the central‐marginal hypothesis using a genomic data set of 25 species‐level taxa of Australian scincid lizards in the generaCtenotusandLerista. A majority of taxa in our data set showed range‐wide patterns of genetic variation consistent with central‐marginal hypothesis, and eight of 25 taxa showed significantly greater genetic diversity in the centre of their range. We then explored biological, historical, and methodological factors that might predict which taxa support the central‐marginal hypothesis. We found that taxa with the strongest evidence for range expansion were the least likely to follow predictions of the central‐marginal hypothesis. The majority of these taxa had range expansions that originated at the range edge, which led to a gradient of decreasing genetic diversity from the range edge to the core, contrary to the central‐marginal hypothesis.

 

Abstract Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger data sets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species of squamates that span higher-level diversity within the clade, which we augmented with publicly available sequences for an additional 17 taxa. Using a locus-by-locus approach, we evaluated support for alternative topologies at 17 contentious nodes in the phylogeny. We identified shared properties of conflicting loci, finding that rate and compositional heterogeneity drives discordance between gene trees and species tree and that conflicting loci rarely overlap across contentious nodes. Finally, by comparing our tests of nodal conflict to previous phylogenomic studies, we confidently resolve 9 of the 17 problematic nodes. We suggest this locus-by-locus and node-by-node approach can build consensus on which topological resolutions remain uncertain in phylogenomic studies of other contentious groups. [Anchored hybrid enrichment (AHE); gene tree conflict; molecular evolution; phylogenomic concordance; target capture; ultraconserved elements (UCE).]