Biology subjects

Guralnick, R. P.

Publications and source records attributed to Guralnick, R. P..

33 records · Page 2Linked to original sources

bioRxiv2023

Spatial phylogenetics of Fagales: Investigating the history of temperate forests

AimQuantifying the phylogenetic diversity of temperate trees is essential for understanding what processes are implicated in shaping the modern distribution of temperate broadleaf forest and other major forest biomes. Here we focus on Fagales, an iconic member of forests worldwide, to uncover global diversity and endemism patterns and investigate potential drivers responsible for the spatial distribution of fagalean forest communities. LocationGlobal. TaxonFagales. MethodsWe combined phylogenetic data covering 60.2% of living species, fine-scale distribution models covering 90% of species, and nodulation data covering all species to investigate the distribution of species richness at fine spatial scales and compare this to relative phylogenetic diversity (RPD) and phylogenetic endemism. Further, we quantify phylogenetic betadiversity and bioregionalization of Fagales and determine hotspots of Fagales species engaging in root nodule symbiosis (RNS) with nitrogen-fixing actinomycetes. ResultsWe find the highest richness in temperate east Asia, eastern North America, and equatorial montane regions of Asia and Central America. By contrast, RPD is highest at higher latitudes, where RNS also predominates. We found a strong spatial structuring of regionalizations of Fagales floras as defined by phylogeny and traits related to RNS, reflecting distinct Northern and Southern Hemisphere floras (with the exception of a unique Afro-Boreal region) and highly distinct tropical montane communities. Main conclusionsSpecies richness and phylogenetic regionalization accord well with traditional biogeographic concepts for temperate forests, but RPD does not. This may reflect ecological filtering specific to Fagales, as RNS strategies are almost universal in the highest RPD regions. Our results highlight the importance of global-scale, clade-specific spatial phylogenetics and its utility for understanding the history behind temperate forest diversity.

evolutionary biology↗

bioRxiv2023

Fagalean phylogeny in a nutshell: Chronicling the diversification history of Fagales

Reconstructing the biogeographical history and timing of the diversification of temperate forests is essential for understanding their history and resolving uncertainties about how flowering plants emerged from their deep tropical origins to dominate in todays freezing terrestrial environments. The angiosperm order Fagales, comprising iconic components of temperate forests worldwide with an extensive fossil record, are an excellent plant system in which to apply a fossil-aware paradigm, such as the fossilized birth-death (FBD) process, for investigating the macroevolution of temperate forest biomes. Here, we improve upon previous efforts to resolve phylogeny and incorporate fossils in Fagales using low-copy nuclear loci and an expanded morphological matrix to reevaluate the Fagales fossil record and: (1) infer the phylogenetic relationships and the time of origin of the clade using the FBD model as implemented in RevBayes, (2) provide a framework for evaluating the climatic and biogeographic history of Fagales, and (3) investigate how the inclusion of fossils via the FBD method influences ancestral reconstruction and diversification estimation. The phylogenetic relationships we recovered are conventional except for the position of Nothofagaceae, while our inferred ages support older timelines than previously proposed, with a mid-Cretaceous date for the most recent common ancestor (MRCA) of the order. Biogeographical analysis shows an origin of Fagales consistent with an ancestral circumboreal temperate distribution corroborated by ancestral niche reconstructions. While distributions today largely reflect the general conservatism of temperate forests, we identified two episodes of high diversification, one at the mid-Cretaceous origin of the clade and the other continuing from the Miocene to the present. Removing fossil taxa from the tree reveals a different story, shifting the origin of extant families from North America to East Asia, reflecting refugial distributions in this biodiversity "museum" and implying a general bias towards low extinction areas in biogeographic reconstruction. Likewise, without fossil data, diversification estimates were higher and unable to detect an early diversification burst. Based on our analyses, we close with recommendations regarding the interpretation of estimates of diversification and ancestral state reconstruction using phylogenetic trees with only extant species as tips.

plant biology↗

bioRxiv2022

Testing the evolutionary drivers of nitrogen-fixing symbioses in challenging soil environments

O_LIWhile the importance of root nodular symbioses (RNS) in plants has long been recognized, the ecological and evolutionary factors maintaining RNS remain obscure. RNS is associated with environmental stressors such as aridity and nitrogen-poor soils; the ability to tolerate harsh environments may provide ecological opportunities for diversification, yet, nodulators are also diverse outside these environments. C_LIO_LIWe test several environmental determinants of increased survival and enhanced diversification of RNS species, using an explicitly phylogenetic approach for the first time. We assembled the largest phylogeny of the nitrogen-fixing clade to date and a comprehensive set of abiotic niche estimates and nodulation data. We used comparative phylogenetic tools to test environmental and diversification associations. C_LIO_LIWe found that RNS is associated with warm, arid, and nitrogen-poor habitats. However, RNS was gained long before lineages entered these habitats. RNS is associated with accelerated diversification, but diversification rates are heterogeneous among nodulators, and non-legume nodulators do not show elevated diversification. C_LIO_LIOur findings undermine the interpretation that RNS directly drove the invasion of challenging habitats, and do not support a direct relationship between soil or climate and the diversity of nodulators. Still, RNS may have been an important exaptation allowing further niche evolution. C_LI

plant biology↗

bioRxiv2022

Identifying climatic drivers of hybridization in Heuchereae (Saxifragaceae)

Applications of molecular phylogenetic approaches have uncovered evidence of hybridization across numerous clades of life, yet the environmental factors responsible for driving opportunities for hybridization remain obscure. Verbal models implicating geographic range shifts that brought species together during the Pleistocene have often been invoked, but quantitative tests using paleoclimatic data are needed to validate these models. Here, we produce a phylogeny for Heuchereae, a clade of 15 genera and 83 species in Saxifragaceae, with complete sampling of recognized species, using 277 nuclear loci and nearly complete chloroplast genomes. We then employ an improved framework with a coalescent simulation approach to test and ultimately confirm previous hybridization hypotheses and identify one new intergeneric hybridization event. Focusing on the North American distribution of Heuchereae, we introduce and implement a newly developed approach to reconstruct potential past distributions for ancestral lineages across all species in the clade and across a paleoclimatic record extending from the late Pliocene. Time calibration based on both nuclear and chloroplast trees recovers a mid- to late-Pleistocene date for most inferred hybridization events, a timeframe concomitant with repeated geographic range restriction into overlapping refugia. Our results indicate an important role for past episodes of climate change, and the contrasting responses of species with differing ecological strategies, in generating novel patterns of range contact among plant communities and therefore new opportunities for hybridization.

evolutionary biology↗

bioRxiv2022

Two shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants

Root nodule symbiosis (RNS) allows plants to access atmospheric nitrogen converted into usable forms through a mutualistic relationship with soil bacteria. RNS is a complex trait requiring coordination from both the plant host and the bacterial symbiont, and pinpointing the evolutionary origins of root nodules is critical for understanding the genetic basis of RNS. This endeavor is complicated by data limitations and the intermittent presence of RNS in a single clade of ca. 30,000 species of flowering plants, i.e., the nitrogen-fixing clade (NFC). We developed the most extensive de novo phylogeny for all major lineages of the NFC and an enhanced root nodule trait database to reconstruct the evolution of RNS. Through identification of the evolutionary pathway to RNS gain, we show that shifts among heterogeneous evolutionary rates can explain how a complex trait such as RNS can arise many times across a large phylogeny. Our analysis identifies a two-step process in which an ancestral precursor state gave rise to a more labile state from which RNS was quickly gained at specific points in the NFC. Our rigorous reconstruction of ancestral states illustrates how a two-step pathway could have led to multiple independent gains and losses of RNS, contrary to recent hypotheses invoking just a single gain and numerous losses. RNS may be an example of multi-level convergent evolution, thus requiring a broader phylogenetic and genetic scope for genome-phenome mapping to elucidate mechanisms enabling fully functional RNS.

evolutionary biology↗

bioRxiv2022

Computer vision for assessing species color pattern variation from web-based community science images

Openly available community science digital vouchers provide a wealth of data to study phenotypic change across space and time. However, extracting phenotypic data from these resources requires significant human effort. Here, we demonstrate a workflow and computer vision model for automatically categorizing species color pattern from community science images. Our work is focused on documenting the striped/unstriped color polymorphism in the Eastern Red-backed Salamander (Plethodon cinereus). We used an ensemble convolutional neural network model to analyze this polymorphism in 20,318 iNaturalist images. Our model was highly accurate ([~]98%) despite image heterogeneity. We used the resulting annotations to document extensive niche overlap between morphs, but wider niche breadth for striped morphs at the range-wide scale. Our work showcases key design principles for using machine learning with heterogeneous community science image data to address questions at an unprecedented scale.

bioinformatics↗

bioRxiv2020

Spatial phylogenetics of butterflies in relation to environmental drivers and angiosperm diversity across North America

Broad-scale quantitative assessments of biodiversity and the factors shaping it remain particularly poorly explored in insects. Here, we undertook a spatial phylogenetic analysis of North American butterflies via assembly of a time-calibrated phylogeny of the region coupled with a unique, complete range assessment for ~75% of the known species. We utilized a suite of phylodiversity metrics and associated environmental data to test whether climate stability and temperature gradients have shaped North American butterfly phylogenetic diversity and endemism. We also undertook the first direct, quantitative comparisons of spatial phylogenetic patterns between butterflies and flowering plants in North America. We expected concordance between butterflies and angiosperms based on both shared historical environmental drivers and presumed strong butterfly-host plant specializations. We instead found that biodiversity patterns in butterflies are strikingly different from flowering plants in some regions of the continent. In particular, the warm desert regions of the southwestern United States and Mexico showed surprisingly high butterfly phylogenetic diversity and endemism, in contrast to much lower values for angiosperms. Butterflies did not show patterns of phylogenetic clustering as found in flowering plants, suggesting differences in habitat conservation between the two groups. Finally, we found weak relationships and spatially structured biases in relative branching timing between angiosperms and butterflies. These results suggest that shared biogeographic histories and trophic associations do not necessarily assure similar diversity outcomes. The work has applied value in conservation planning, documenting warm deserts as an important North American butterfly biodiversity hotspot.

ecology↗

bioRxiv2019

Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plant Saniculiphyllum guangxiense (Saxifragaceae)

BackgroundPlastid gene loss and pseudogenization has been widely documented in parasitic and mycoheterotrophic plants, which have relaxed selective constraints on photosynthetic function. More enigmatic are sporadic reports of degradation and loss of important photosynthesis genes in lineages thought to be fully photosynthetic. Here we report the complete plastid genome of Saniculiphyllum guangxiense, a critically endangered and phylogenetically isolated plant lineage, along with genomic evidence of reduced chloroplast function. We also report 22 additional plastid genomes representing the diversity of its containing clade Saxifragales, characterizing gene content and placing variation in a broader phylogenetic context. ResultsWe find that the plastid genome of Saniculiphyllum has experienced pseudogenization of five genes of the NDH complex (ndhA, ndhB, ndhD, ndhF, and ndhK), previously reported in flowering plants with an aquatic habit, as well as the more surprising pseudogenization of two genes more central to photosynthesis (ccsA and cemA), contrasting with strong phylogenetic conservatism of plastid gene content in all other sampled Saxifragales. These genes participate in photooxidative protection, cytochrome synthesis, and carbon uptake. Nuclear paralogs exist for all seven plastid pseudogenes, yet these are also unlikely to be functional. ConclusionsSaniculiphyllum appears to represent the greatest degree of plastid gene loss observed to date in any fully photosynthetic lineage, yet plastid genome length, structure, and substitution rate are within the variation previously reported for photosynthetic plants. These results highlight the increasingly appreciated dynamism of plastid genomes, otherwise highly conserved across a billion years of green plant evolution, in plants with highly specialized life history traits.

evolutionary biology↗

bioRxiv2019

Opportunistically collected photographs can be used to estimate large-scale phenological trends

PremiseResearch on large-scale patterns of phenology have utilized multiple sources of data to analyze the timing of events such as flowering, fruiting, and leaf out. In-situ observations from standardized surveys are ideal, but remain spatially sparse. Herbarium records and phenology-focused citizen science programs provide a source of historic data and spatial replication, but the sample sizes for any one season are still relatively low. A novel and rapidly growing source of broad-scale phenology data are photographs from the iNaturalist platform, but methods utilizing these data must generalize to a range of different species with varying season lengths and occurring across heterogenous areas. They must also be robust to different sample sizes and potential biases toward well travelled areas such as roads and towns.\n\nMethods/ResultsWe developed a spatially explicit model, the Weibull Grid, to estimate flowering onset across large-scales, and utilized a simulation framework to test the approach using different phenology and sampling scenarios. We found that the model is ideal when the underlying phenology is non-linear across space. We then use the Weibull Grid model to estimate flowering onset of two species using iNaturalist photographs, and compare those estimates with independent observations of greenup from the Phenocam network. The Weibull Grid model estimate consistently aligned with Phenocam greenup across four years and broad latitudes.\n\nConclusioniNaturalist observations can considerably increase the amount of phenology observations and also provide needed spatial coverage. We showed here they can accurately describe large-scale trends as long as phenological and sampling processes are considered.

ecology↗

bioRxiv2019

Methods for broad-scale plant phenology assessments using citizen scientists’ photographs

Broad-scale plant flowering phenology data has predominantly come from geographically and taxonomically restricted monitoring networks. However, platforms such as iNaturalist, where citizen scientists upload photographs and curate identifications, provide a promising new source of data. Here we develop a general set of best practices for scoring iNaturalist digital records supporting downstream re-use in phenology studies. We focus on a case study group, Yucca, because it has showy flowers and is well documented on iNaturalist. Additionally, drivers of Yucca phenology are not well-understood despite need for Yucca to synchronize flowering with obligate moth pollinators. Finally, evidence of anomalous flowering events have been recently reported, but the extent of those events is unknown. We use best-practices approach to annotate nearly 9,000 Yucca iNaturalist records, and compare the spatiotemporal coverage of this dataset with other broad-scale monitoring resources. Our findings demonstrate that iNaturalist provides unique phenology information, including delineation of extents of unusual flowering events. We also determine if unusual early flowering events impact later, typical flowering periods. Finally, we adapt a plant phenology global knowledge-store to integrate iNaturalist annotation results, supporting broadest reuse. Our approach has application to other plant groups, leveraging rapidly increasing data resources from iNaturalist to study phenology.

ecology↗

bioRxiv2019

Estimating rates and patterns of diversification with incomplete sampling: A case study in the rosids

Premise of the StudyRecent advances in generating large-scale phylogenies enable broad-scale estimation of species diversification rates. These now-common approaches typically (1) are characterized by incomplete coverage without explicit sampling methodologies, and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. Here we use an empirical example to examine effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionists based on those results.\n\nMethodsWe used a supermatrix for rosids, a large clade of angiosperms, and its well-sampled subclade Cucurbitaceae, as empirical case studies. We compared results using this large phylogeny with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA, BAMM) and semiparametric (DR).\n\nKey ResultsWe find the impact of sampling on diversification estimates is idiosyncratic and often strong. As compared to full empirical sampling, representative and random sampling schemes either depress or exaggerate speciation rates depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa.\n\nConclusionsWe (1) urge caution in use of summary backbone trees containing only higher-level taxa, (2) caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees, and (3) stress the importance of explicit sampling methodologies in macroevolutionary studies.

evolutionary biology↗

bioRxiv2019

Exploring the phylogeny of rosids with a five-locus supermatrix from GenBank

Current advances in sequencing technology have greatly increased the availability of sequence data from public genetic databases. With data from GenBank, we assemble and phylogenetically investigate a 19,740-taxon, five-locus supermatrix (i.e., atpB, rbcL, matK, matR, and ITS) for rosids, a large clade containing over 90,000 species, or approximately a quarter of all angiosperms (assuming an estimate of 400,000 angiosperm species). The topology and divergence times of the five-locus tree generally agree with previous estimates of rosid phylogeny, and we recover greater resolution and support in several areas along the rosid backbone, but with a few significant differences (e.g., the placement of the COM clade, as well as Myrtales, Vitales, and Zygophyllales). Our five-locus phylogeny is the most comprehensive DNA data set yet compiled for the rosid clade. Yet, even with 19,740 species, current sampling represents only 16-22% of all rosids, and we also find evidence of strong phylogenetic bias in the accumulation of GenBank data, highlighting continued challenges for species coverage. These limitations also exist in other major angiosperm clades (e.g., asterids, monocots) as well as other large, understudied branches of the Tree of Life, highlighting the need for broader molecular sampling. Nevertheless, the phylogeny presented here improves upon sampling by more than two-fold and will be an important resource for macroevolutionary studies of this pivotal clade.

evolutionary biology↗

bioRxiv2019

Tracking trends in monarch abundances over the 20th century is currently impossible using museum records: a response to Boyle et al. (2019)

The onslaught of opportunistic data offers new opportunities to examine biodiversity patterns at large scales. However, the techniques for tracking abundance trends with such data are new and require careful consideration to ensure that variations in sampling effort do not lead to biased estimates. The analysis by Boyle et al. (2019) showing a mid-century increase in monarch abundance followed by a decrease starting in the 1960s used an inappropriate correction with respect to three dimensions of sampling effort: taxonomy, place, and time. When the data presentenced by Boyle et al. (2019) are corrected to account for biases in the collection process, the results of their analyses do not hold. The paucity of data that remain after accounting for spatial and temporal biases suggests that analyses of monarch trends back to the beginning of the 20th are currently not possible. Continued digitization of museum records is needed to provide a firm data basis to estimate population trends.

ecology↗

bioRxiv2018

For comparing phylogenetic diversity among communities, go ahead and use synthesis phylogenies

Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis-based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose-built phylogenies and their corresponding synthesis-based trees (two from Phylomatic and one from the Open Tree of Life [OTL]). We simulated 1,000 communities and 12,000 continuous traits along each purpose-built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagels {lambda} and Blombergs K). Synthesis-based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose-built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearmans{rho} > 0.8 in most cases). Mean pairwise distance (both alpha and beta) is the index that is most robust to the differences in tree construction that we tested. Measures of phylogenetic diversity based on the OTL showed the highest correlation with measures based on the purpose-built phylogenies. Trait phylogenetic signal estimated with synthesis-based phylogenies, especially from the OTL, were also highly correlated with estimates of Blombergs K or close to Pagels {lambda} from purpose-built phylogenies when traits were simulated under Brownian Motion. For commonly employed community phylogenetic analyses, our results justify taking advantage of recently developed and continuously improving synthesis trees, especially the Open Tree of Life.

ecology↗

bioRxiv2017

Geographic range dynamics drove ancient hybridization in a lineage of angiosperms

Factors explaining global distribution patterns have been central to biology since the 19th century, yet failure to combine dispersal-based biogeography with shifts in habitat suitability remains a present-day setback in understanding geographic distributions present and past, and time-extended trajectories of lineages. The lack of methods in a suitable integrative framework stands as a conspicuous shortcoming for reconstructing these dynamics. Here we showcase novel methods to overcome these methodological gaps, broadening the prospects for phyloclimatic modeling. We focus on a clade in the angiosperm genus Heuchera endemic to southern California that experienced ancient introgression from circumboreally distributed species of Mitella, testing hypotheses regarding biotic contact in the past between ancestral species lacking a fossil record. We obtain strong support for a past contact zone in northwestern North America, resolving this paradox of hybridization between ancestors of taxa currently separated by [~]1300 km.

evolutionary biology↗