The conservation status of most plant species is currently unknown, despite the fundamental role of plants in ecosystem health. To facilitate the costly process of conservation assessment, we ...developed a predictive protocol using a machine-learning approach to predict conservation status of over 150,000 land plant species. Our study uses open-source geographic, environmental, and morphological trait data, making this the largest assessment of conservation risk to date and the only global assessment for plants. Our results indicate that a large number of unassessed species are likely at risk and identify several geographic regions with the highest need of conservation efforts, many of which are not currently recognized as regions of global concern. By providing conservation-relevant predictions at multiple spatial and taxonomic scales, predictive frameworks such as the one developed here fill a pressing need for biodiversity science.
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Premise of the Study
Polyploidy or whole‐genome duplication (WGD) pervades the evolutionary history of angiosperms. Despite extensive progress in our understanding of WGD, the role of these events in ...promoting diversification is still not well understood. We seek to clarify the possible association between WGD and diversification rates in flowering plants.
Methods
Using a previously published phylogeny spanning all land plants (31,749 tips) and WGD events inferred from analyses of the 1000 Plants (1KP) transcriptome data, we analyzed the association of WGDs and diversification rates following numerous WGD events across the angiosperms. We used a stepwise AIC approach (MEDUSA), a Bayesian mixture model approach (BAMM), and state‐dependent diversification analyses (MuSSE) to investigate patterns of diversification. Sister‐clade comparisons were used to investigate species richness after WGDs.
Key Results
Based on the density of 1KP taxon sampling, 106 WGDs were unambiguously placed on the angiosperm phylogeny. We identified 334–530 shifts in diversification rates. We found that 61 WGD events were tightly linked to changes in diversification rates, and state‐dependent diversification analyses indicated higher speciation rates for subsequent rounds of WGD. Additionally, 70 of 99 WGD events showed an increase in species richness compared to the sister clade.
Conclusions
Forty‐six of the 106 WGDs analyzed appear to be closely associated with upshifts in the rate of diversification in angiosperms. Shifts in diversification do not appear more likely than random within a four‐node lag phase following a WGD; however, younger WGD events are more likely to be followed by an upshift in diversification than older WGD events.
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Hybridization, incomplete lineage sorting, and phylogenetic error produce similar incongruence patterns, representing a great challenge for phylogenetic reconstruction. Here, we use sequence capture ...data and multiple species tree and species network approaches to resolve the backbone phylogeny of the Neotropical genus Lachemilla, while distinguishing among sources of incongruence.
We used 396 nuclear loci and nearly complete plastome sequences from 27 species to clarify the relationships among the major groups of Lachemilla, and explored multiple sources of conflict between gene trees and species trees inferred with a plurality of approaches.
All phylogenetic methods recovered the four major groups previously proposed for Lachemilla, but species tree methods recovered different topologies for relationships between these four clades. Species network analyses revealed that one major clade, Orbiculate, is likely of ancient hybrid origin, representing one of the main sources of incongruence among the species trees. Additionally, we found evidence for a potential whole genome duplication event shared by Lachemilla and allied genera.
Lachemilla shows clear evidence of ancient and recent hybridization throughout the evolutionary history of the group. Also, we show the necessity to use phylogenetic network approaches that can simultaneously accommodate incomplete lineage sorting and gene flow when studying groups that show patterns of reticulation.
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Advances in high-throughput sequencing (HTS) have allowed researchers to obtain large amounts of biological sequence information at speeds and costs unimaginable only a decade ago. Phylogenetics, and ...the study of evolution in general, is quickly migrating towards using HTS to generate larger and more complex molecular datasets. In this paper, we present a method that utilizes microfluidic PCR and HTS to generate large amounts of sequence data suitable for phylogenetic analyses. The approach uses the Fluidigm Access Array System (Fluidigm, San Francisco, CA, USA) and two sets of PCR primers to simultaneously amplify 48 target regions across 48 samples, incorporating sample-specific barcodes and HTS adapters (2,304 unique amplicons per Access Array). The final product is a pooled set of amplicons ready to be sequenced, and thus, there is no need to construct separate, costly genomic libraries for each sample. Further, we present a bioinformatics pipeline to process the raw HTS reads to either generate consensus sequences (with or without ambiguities) for every locus in every sample or--more importantly--recover the separate alleles from heterozygous target regions in each sample. This is important because it adds allelic information that is well suited for coalescent-based phylogenetic analyses that are becoming very common in conservation and evolutionary biology. To test our approach and bioinformatics pipeline, we sequenced 576 samples across 96 target regions belonging to the South American clade of the genus Bartsia L. in the plant family Orobanchaceae. After sequencing cleanup and alignment, the experiment resulted in ~25,300 bp across 486 samples for a set of 48 primer pairs targeting the plastome, and ~13,500 bp for 363 samples for a set of primers targeting regions in the nuclear genome. Finally, we constructed a combined concatenated matrix from all 96 primer combinations, resulting in a combined aligned length of ~40,500 bp for 349 samples.
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Our growing understanding of the plant tree of life provides a novel opportunity to uncover the major drivers of angiosperm diversity.
Using a time-calibrated phylogeny, we characterized hot and cold ...spots of lineage diversification across the angiosperm tree of life by modeling evolutionary diversification using stepwise AIC (MEDUSA). We also tested the whole-genome duplication (WGD) radiation lag-time model, which postulates that increases in diversification tend to lag behind established WGD events.
Diversification rates have been incredibly heterogeneous throughout the evolutionary history of angiosperms and reveal a pattern of ‘nested radiations’ – increases in net diversification nested within other radiations. This pattern in turn generates a negative relationship between clade age and diversity across both families and orders. We suggest that stochastically changing diversification rates across the phylogeny explain these patterns. Finally, we demonstrate significant statistical support for the WGD radiation lag-time model.
Across angiosperms, nested shifts in diversification led to an overall increasing rate of net diversification and declining relative extinction rates through time. These diversification shifts are only rarely perfectly associated with WGD events, but commonly follow them after a lag period.
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When designing phylogeographic investigations researchers can choose to collect many different types of molecular markers, including mitochondrial genes or genomes, SNPs from reduced representation ...protocols, large sequence capture data sets, and even whole genomes. Given that the statistical power and accuracy of various analyses are expected to differ depending on both the type of marker and the amount of data collected, an exploration of the variance across methodological results as a function of marker type should provide valuable information to researchers. Here we collect mitochondrial Cytochrome b sequences, whole mitochondrial genomes, single nucleotide polymorphisms (SNP)s isolated using a genotype by sequencing (GBS) protocol, sequences from ultraconserved elements, and low-coverage nuclear genomes from the North American water vole (Microtus richardsoni). We estimate genetic distances, population genetic structure, and historical demography using data from each of these datasets and compare the results across markers. As anticipated, the results exhibit differences across marker types, particularly in terms of the resolution offered by different analyses. A cost-benefit analysis indicates that SNPs collected using a GBS protocol are the most cost-effective molecular marker, with inferences that mirror those collected from the whole genome data at a fraction of the cost per sample.
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Early flowering plants are thought to have been woody species restricted to warm habitats. This lineage has since radiated into almost every climate, with manifold growth forms. As angiosperms spread ...and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf phenology (evergreen or deciduous), diameter of hydraulic conduits (that is, xylem vessels and tracheids) and climate occupancies (exposure to freezing). To model the evolution of species' traits and climate occupancies, we combined these data with an unparalleled dated molecular phylogeny (32,223 species) for land plants. Here we show that woody clades successfully moved into freezing-prone environments by either possessing transport networks of small safe conduits and/or shutting down hydraulic function by dropping leaves during freezing. Herbaceous species largely avoided freezing periods by senescing cheaply constructed aboveground tissue. Growth habit has long been considered labile, but we find that growth habit was less labile than climate occupancy. Additionally, freezing environments were largely filled by lineages that had already become herbs or, when remaining woody, already had small conduits (that is, the trait evolved before the climate occupancy). By contrast, most deciduous woody lineages had an evolutionary shift to seasonally shedding their leaves only after exposure to freezing (that is, the climate occupancy evolved before the trait). For angiosperms to inhabit novel cold environments they had to gain new structural and functional trait solutions; our results suggest that many of these solutions were probably acquired before their foray into the cold.
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New powerful biogeographic methods have focused attention on long-standing hypotheses regarding the influence of the break-up of Gondwana on the biogeography of Southern Hemisphere plant groups. ...Studies to date have often concluded that these groups are too young to have been influenced by these ancient continental movements. Here we examine a much larger and older angiosperm clade, the Campanulidae, and infer its biogeographic history by combining Bayesian divergence time information with a likelihood-based biogeographic model focused on the Gondwanan landmasses.
Our analyses imply that campanulids likely originated in the middle Albian (~105 Ma), and that a substantial portion of the early evolutionary history of campanulids took place in the Southern Hemisphere, despite their greater species richness in the Northern Hemisphere today. We also discovered several disjunctions that show biogeographic and temporal correspondence with the break-up of Gondwana.
While it is possible to discern traces of the break-up of Gondwana in clades that are old enough, it will generally be difficult to be confident in continental movement as the prime cause of geographic disjunctions. This follows from the need for the geographic disjunction, the inferred biogeographic scenario, and the dating of the lineage splitting events to be consistent with the causal hypothesis.
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The Mind of a Mouse Abbott, Larry F.; Bock, Davi D.; Callaway, Edward M. ...
Cell,
09/2020, Volume:
182, Issue:
6
Journal Article
Peer reviewed
Open access
Large scientific projects in genomics and astronomy are influential not because they answer any single question but because they enable investigation of continuously arising new questions from the ...same data-rich sources. Advances in automated mapping of the brain’s synaptic connections (connectomics) suggest that the complicated circuits underlying brain function are ripe for analysis. We discuss benefits of mapping a mouse brain at the level of synapses.
Large scientific projects in genomics and astronomy are influential not because they answer any single question but because they enable investigation of continuously arising new questions from the same data-rich sources. Advances in automated mapping of the brain’s synaptic connections (connectomics) suggest that the complicated circuits underlying brain function are ripe for analysis. We discuss benefits of mapping a mouse brain at the level of synapses.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Pleistocene glacial cycles drastically changed the distributions of taxa endemic to temperate rainforests in the Pacific Northwest, with many experiencing reduced habitat suitability during glacial ...periods. In this study, we investigate whether glacial cycles promoted intraspecific divergence and whether subsequent range changes led to secondary contact and gene flow. For seven invertebrate species endemic to the PNW, we estimated species distribution models (SDMs) and projected them onto current and historical climate conditions to assess how habitat suitability changed during glacial cycles. Using single nucleotide polymorphism (SNP) data from these species, we assessed population genetic structure and used a machine‐learning approach to compare models with and without gene flow between populations upon secondary contact after the last glacial maximum (LGM). Finally, we estimated divergence times and rates of gene flow between populations. SDMs suggest that there was less suitable habitat in the North Cascades and Northern Rocky Mountains during glacial compared to interglacial periods, resulting in reduced habitat suitability and increased habitat fragmentation during the LGM. Our genomic data identify population structure in all taxa, and support gene flow upon secondary contact in five of the seven taxa. Parameter estimates suggest that population divergences date to the later Pleistocene for most populations. Our results support a role of refugial dynamics in driving intraspecific divergence in the Cascades Range. In these invertebrates, population structure often does not correspond to current biogeographic or environmental barriers. Rather, population structure may reflect refugial lineages that have since expanded their ranges, often leading to secondary contact between once isolated lineages.
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