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opencc-zeroFeb 2024View details →

Data from: Phylogenomics of American pika (Ochotona princeps) lineage diversification

Quaternary climate oscillations have profoundly influenced current species distributions. For many montane species, these fluctuations were a prominent driver in species range shifts, often resulting in intraspecific diversification, as has been the case for American pikas (Ochotona princeps). Range shifts and population declines in this thermally-sensitive lagomorph have been linked to historical and contemporary environmental changes across its western North American range, with previous research reconstructing five mitochondrial DNA lineages. Here, we paired genome-wide data (25,244 SNPs) with range-wide sampling to re-examine the number and distribution of intra-specific lineages, and investigate patterns of within- and among-lineage divergence and diversity. Our results provide genomic evidence of O. princeps monophyly, reconstructing six distinct lineages that underwent multiple rounds of divergence (0.809-2.81mya), including a new Central Rocky Mountain lineage. We further found evidence for population differentiation across multiple spatial scales, and reconstructed levels of standing variation comparable to those found in other small mammals. Overall, our findings demonstrate the influence of past glacial cycles on O. princeps lineage diversification, suggest that current subspecific taxonomy may need to be revisited, and provide an important framework for investigations of American pika adaptive potential in the face of anthropogenic climate change.

opencc-zeroMar 2024View details →

Skull evolution and lineage diversification in endemic Malagasy carnivorans

Madagascar is one of the world's foremost biodiversity hotspots with more than 90% of its species endemic to the island. Malagasy carnivorans are one of only four extant terrestrial mammalian clades endemic to Madagascar. Although there are only eight extant species, these carnivorans exhibit remarkable phenotypic and ecological diversity that is often hypothesized to have diversified through an adaptive radiation. Here, we investigated the evolution of skull diversity in Malagasy carnivorans and tested if they exhibited characteristics of convergence and an adaptive radiation. We found that their skull disparity exceeds that of any other feliform family, as their skulls vary widely and strikingly capture a large amount of the morphological variation found across all feliforms. We also found evidence of shared adaptive zones in cranial shape between euplerid subclades and felids, herpestids, and viverrids. Lastly, contrary to predictions of adaptive radiation, we found that Malagasy carnivorans do not exhibit rapid lineage diversification and only marginally faster rates of mandibular shape evolution, and to a lesser extent cranial shape evolution, compared to other feliforms. These results reveal that exceptional diversification rates are not necessary to generate the striking phenotypic diversity that evolved in carnivorans after their dispersal to and isolation in Madagascar.

opencc-by-4.0Mar 2024View details →

figure 5 Lineage through time plot within G. subgutturosa with cytb. The 95 in Unraveling goitered gazelle (Gazella subgutturosa) diversification: insights from phylogeography and species distribution modeling

figure 5 Lineage through time plot within G. subgutturosa with cytb. The 95% highest posterior density interval is shown in blue.

opencc-by-4.0Jul 2022View details →

Fig. 3 in Diversification rates in Tardigrada indicate a decreasing tempo of lineage splitting regardless of reproductive mode

Fig. 3 The negative relation between values of γ statistics and the number of entities based on which they were calculated. Circles indicate Tardigrada; triangles indicate Rotifera; black indicates asexual reproduction; white indicates sexual reproduction

opencc-by-4.0Jul 2022View details →

Fig. 2 in Diversification rates in Tardigrada indicate a decreasing tempo of lineage splitting regardless of reproductive mode

Fig. 2 Bayesian phylogenetic reconstructions for three distinct evolutionary lineages of Tardigrada with respective lineage-through-time plots. The trees were calculated based on the reduced datasets with singular sequence representing a given species/entity delimited in this study with multiple DNA taxonomy approaches (see the "Mate-

Figure 4 in Diversification and species limits in scale-backed antbirds (Willisornis: Thamnophilidae), an Amazonian endemic lineage

Figure 4. Graphs of BAPS clusters and geographic distribution of individuals analysed when considering A, mitochondrial (K = 8); B, BF5 (K = 3); C, MUSK (K = 6) datasets. Samples were plotted on the map in the pie chart format representing the percentage of admixture recovered by the bar graphs.

Figure 2 in Diversification and species limits in scale-backed antbirds (Willisornis: Thamnophilidae), an Amazonian endemic lineage

Figure 2. Multilocus coalescent species tree of Willisornis lineages identified in previous molecular analyses (Fig. 1). Nodes contain posterior probabilities of clades (above line) and associated confidence intervals (95% HPD) for splitting times (blue bars). Numbers on the timescale below represent millions of years. The colours are the same as used for the recovered groups in Figure 1.

Figure 6 in Diversification and species limits in scale-backed antbirds (Willisornis: Thamnophilidae), an Amazonian endemic lineage

Figure 6. Ancestral range estimates for the genus Willisornis obtained with BioGeoBEARS. The model selected was DIVALIKE (see text for details). Node pie charts represent the likelihoods of ancestral area states. Colours represent major Amazonian geological provinces selected as areas for the analysis, with those differing from the ones in the map corresponding to combinations of areas: GUI, Guiana Shield; BAC, Amazonian foreland basins; BRA, Brazilian Shield; GUIBAC, Guiana Shield + Amazonian foreland basins; GUIBRA, Guiana Shield + Brazilian Shield; and BACBRA, Amazonian foreland basins + Brazilian Shield. Numbers on the timescale below represent millions of years.

Figure 3. A in Diversification and species limits in scale-backed antbirds (Willisornis: Thamnophilidae), an Amazonian endemic lineage

Figure 3. A, BP&P posterior probabilities for different prior settings corresponding to the degree of significant coalescence between reciprocally monophyletic Willisornis lineages. Θ corresponds to the population size parameter and τ to the divergence time priors at the root of the species tree. ε, α and m are different values of fine-tune parameters. B, overlapping coalescent trees for each scenario generated by BP&P.

Figure 5 in Diversification and species limits in scale-backed antbirds (Willisornis: Thamnophilidae), an Amazonian endemic lineage

Figure 5. Clusters of BAPS for Willisornis poecilinotus gutturalis and W. p. griseiventris A in western Amazonia. Each graph corresponds to analyses made with A, mitochondrial; B, BF5; C, MUSK datasets. The coloured bars represent the proportion of genetic similarity to each population for each specimen included in the analysis while the maps on the right show the geographic distribution of the samples used. Specimen CAM021 is highlighted by a red rectangle and arrow.

publicMar 2024View details →

Data from: Phylogenomics of American pika (Ochotona princeps) lineage diversification

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publicMar 2024View details →

Skull evolution and lineage diversification in endemic Malagasy carnivorans

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opencc-zeroOct 2019View details →

Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus)

Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus) Species endemic to alpine environments can evolve via steep ecological selection gradients between lowland and upland environments. Additionally, many alpine environments have faced repeated glacial episodes over the past two million years, fracturing these endemics into isolated populations. In this "glacial pulse" model of alpine diversification, cycles of allopatry and ecologically divergent glacial refugia play a role in generating biodiversity, including novel admixed ("fused") lineages. We tested for patterns of glacial pulse lineage diversification in the Yosemite toad (Anaxyrus [Bufo] canorus), an alpine endemic tied to glacially influenced meadow environments. Using double-digest RADseq on populations densely sampled from a portion of the species range, we identified nine distinct lineages with divergence times ranging from 18–724 ka, coinciding with multiple Sierra Nevada glacial events. Three lineages have admixed origins, and demographic models suggest these fused lineages have persisted throughout past glacial cycles. Directionality indices supported the hypothesis that some lineages recolonized Yosemite from east of the ice sheet, whereas other lineages remained in western refugia. Finally, refugial niche reconstructions suggest that low- and high-elevation lineages have convergently adapted to similar climatic niches. Our results suggest glacial cycles and refugia may be important crucibles of adaptive diversity across deep evolutionary time. Gene pool boundaries for the Yosemite toad (Anaxyrus canorus) reveal asymmetrical migration within meadow neighborhoods The Yosemite toad (Anaxyrus [Bufo] canorus) is a federally threatened species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. The species is one of the first amphibians to undergo a large demographic collapse that was well documented, and is reputed to remain in low abundance throughout its range. Recent phylogeographic work has demonstrated that Pleistocene toad lineages diverged and then admixed to differing extents across an elevational gradient. Although lineage divisions may have significant effects on evolutionary trajectories over large spatial and temporal scales, present-day population dynamics must be delineated in order to manage and conserve the species effectively. In this study, we used a double-digest RADseq dataset to address three primary questions: (1) Are single meadows or neighborhoods of nearby meadows most correlated with population boundaries? (2) Does asymmetrical migration occur among neighborhoods of nearby meadows? (3) What topographic or hydrological variables predict such asymmetrical migration in these meadow neighborhoods? Hierarchical STRUCTURE and AMOVA analyses suggested that populations are typically circumscribed by a single meadow, although 84% of meadows exist in neighborhoods of at least two meadows connected by low levels of migration, and over half (53%) of neighborhoods examined display strong asymmetrical migration. Meadow neighborhoods often contain one or more large and flat "hub" meadows that experience net immigration, surrounded by smaller and topographically rugged "satellite" meadows with net emigration. Hubs tend to contain more genetic diversity and could be prioritized for conservation and habitat management and as potential sources for reestablishment efforts. Landscape genetics of a sub-alpine toad: Climate change predicted to induce upward range shifts via asymmetrical migration corridors Climate change is expected to have a major hydrological impact on the core breeding habitat and migration corridors of many amphibians in the 21st century. The Yosemite toad (Anaxyrus canorus) is a species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. Despite living entirely on federal lands, it has recently faced severe extirpations, yet our understanding of climatic influences on population connectivity is limited. In this study, we used a previously published double-digest RADseq dataset along with numerous remotely sensed habitat features in a landscape genetics framework to answer two primary questions in Yosemite National Park: (1) Which fine-scale climate, topographic, soil, and vegetation features most facilitate meadow connectivity? (2) How is climate change predicted to influence both the magnitude and net asymmetry of genetic migration? We developed an approach for simultaneously modeling multiple toad migration paths, akin to circuit theory, except raw environmental features can be separately considered. Our workflow identified the most likely migration corridors between meadows and used the unique cubist machine learning approach to fit and forecast environmental models of connectivity. We identified the permuted modeling importance of numerous snowpack-related features, such as runoff and groundwater recharge. Our results highlight the importance of considering phylogeographic structure, and asymmetrical migration in landscape genetics. We predict an upward elevational shift for this already high elevation species, as measured by the net vector of anticipated genetic movement, and a north-eastward shift in species distribution via the network of genetic migration corridors across the park. ** Note: Multiple articles are associated with this dataset

opencc-zeroDec 2016View details →

Data from: Diversification of trait combinations in coevolving plants and insect lineages

Closely related species often have similar traits and sometimes interact with the same species. A crucial problem in evolutionary ecology is therefore to understand how coevolving species diverge when they interact with a set of closely related species from another lineage rather than with a single species. We evaluated geographic differences in the floral morphology of all woodland star plant species (Lithophragma, Saxifragaceae) that are pollinated by Greya (Prodoxidae) moths. Flowers of each woodland star species differed depending on whether plants interact locally with one, two, or no pollinating moth species. Plants of one species grown in six different environments showed few differences in floral traits, suggesting that the geographic differences are not due significantly to trait plasticity. Greya moth populations also showed significant geographic divergence in morphology, depending on the local host and on whether the moth species co-occurred locally. Divergence in the plants and the moths involved shifts in combinations of partially correlated traits, rather than any one trait. The results indicate that the geographic mosaic of coevolution can be amplified as coevolving lineages diversify into separate species and come together in different combinations in different ecosystems.

opencc-zeroDec 2015View details →

Data from: Ecological and geographic dimensions of diversification in Piper subgenus Ottonia: a lineage of neotropical rainforest shrubs

The Neotropics are home to incomparable plant diversity. To evaluate the potential roles of geography and ecology on speciation in Neotropical plants we selected a small, tractable lineage of shrubby angiosperms, Piper subgenus Ottonia. We reconstructed a molecular phylogeny and provided insights into the species divergence times based on fossil calibration of the molecular clock. We support the monophyly of Piper subg. Ottonia and the two main lineages: Amazonian and Atlantic Forest, the latter containing the non-Atlantic species pair P. darienense‐P. piscatorum. We also propose the origin of Piper subg. Ottonia in the early Eocene and suggest that the diversification of Piper subg. Ottonia was influenced by geo-historical events such as the Paleocene-Eocene Thermal Maximum (PETM) and the uplift of the Andes in the Miocene, as is the case for other angiosperms. Furthermore, we combined our phylogeny with geographic and environmental data in order to evaluate geographical and ecological contexts for speciation. We indicate that neither climatic/edaphic divergence nor geographic isolation appears to be needed to explain speciation in this lineage.

opencc-zeroJan 2024View details →

Supplemental Data for: Lineage diversification and rampant hybridization among subspecies explain taxonomic confusion in the endemic Hawaiian fern Polypodium pellucidum

Premise: Polypodium pellucidum, a fern endemic to the Hawaiian Islands, encompasses a broad spectrum of morphological and ecological variation, suggesting a complex history involving divergence and hybridization. In contrast to angiosperm systems, spore dispersal in ferns presents a unique opportunity to study how highly dispersible organisms diversify in the dynamic landscape of the archipelago. Key Results: We infer P. pellucidum is monophyletic, dispersing to the Hawaiian archipelago 11.53 to 7.77 Mya, with diversification into extant clades 5.66 to 4.73 Mya. We identify four non-hybrid clades with unique morphologies, ecological niches, and distributions. Additionally, we elucidate several intraspecific hybrid combinations and evidence for undiscovered or extinct 'ghost' lineages contributing to extant hybrids populations. Conclusions: We provide a roadmap for revising the taxonomy of P. pellucidum to account for cryptic lineages and intraspecific hybrids. Geologic succession of the Hawaiian Islands through cycles of volcanism, vegetative succession, and erosion has determined the available habitats and distribution of ecologically specific divergent clades within P. pellucidum, with intraspecific hybrids arising as a result of ecological and or geological transitions, often persisting after the local extinction of their progenitors. This research contributes to our understanding of the evolution of Hawaii's diverse fern flora and allows for better conservation efforts that are often complicated by the presence of cryptic taxa and hybridization.

opencc-zeroJun 2022View details →

Dataset from: Incomplete lineage sorting and reticulate evolution mask species relationships in Brunelliaceae, an Andean family with rapid, recent diversification

Premise: To date, phylogenetic relationships within the monogeneric Brunelliaceae have been based on morphological evidence, which does not provide sufficient phylogenetic resolution. Here we use target-enriched nuclear data to improve our understanding of phylogenetic relationships in the family. Methods: We used the Angiosperms353 toolkit for targeted recovery of exonic regions and supercontigs (exons + introns) from low copy nuclear genes from 53 of 70 species in Brunellia, and several outgroup taxa. We removed loci that indicated biased relationships and applied concatenated and coalescent methods to infer Brunellia phylogeny. We identified conflicts among gene trees that may reflect hybridization or incomplete lineage-sorting events and assessed their impact on the phylogeny. Finally, we performed ancestral-state reconstructions of morphological traits and assessed the homology of character states used to define sections and subsections in Brunellia. Results: Brunellia comprises two major clades and several subclades. Most of these clades/subclades do not correspond to previous infrageneric taxa. There is high topological incongruence among the subclades across analyses. Conclusions: Phylogenetic reconstructions point to rapid species diversification in Brunelliaceae, reflected in very short branches between successive species splits. The removal of putatively biased loci slightly improves phylogenetic support for individual clades. Reticulate evolution due to hybridization and/or incomplete lineage sorting likely both contribute to gene-tree discordance. Morphological characters used to define taxa in current classification schemes are homoplastic in the ancestral character state reconstructions. While target enrichment data allows us to broaden our understanding of diversification in Brunellia, the relationships among subclades remain incompletely understood.