Settling a family feud: a high‐level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes

American Journal of Botany, Journal Year: 2021, Volume and Issue: 108(7), P. 1143 - 1165

Published: July 1, 2021

Comprising five families that vastly differ in species richness-ranging from Gelsemiaceae with 13 to the Rubiaceae 13,775 species-members of Gentianales are often among most species-rich and abundant plants tropical forests. Despite considerable phylogenetic work within particular genera, several alternative topologies for family-level relationships have been presented previous studies.Here we present a phylogenomic analysis based on nuclear genes targeted by Angiosperms353 probe set approximately 150 species, representing all 85% formally recognized tribes. We were able retrieve partial plastomes off-target reads taxa infer trees comparison nuclear-derived trees.We recovered high support over 80% nodes. The plastid data largely agreement, except some weakly moderately supported relationships. discuss implications our results order's classification, highlighting points increased previously uncertain is sister clade comprising (Gentianaceae + Gelsemiaceae) (Apocynaceae Loganiaceae).The higher-level confidently resolved. In contrast recent studies, division into two subfamilies: Cinchonoideae Rubioideae. do not recognize Coptosapelteae Luculieae any subfamily but treat them as incertae sedis. Our framework paves way further phylogenetics, biogeography, morphological evolution, macroecology this important group flowering plants.

Language: Английский

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Dissecting Incongruence between Concatenation- and Quartet-Based Approaches in Phylogenomic Data

Systematic Biology, Journal Year: 2021, Volume and Issue: 70(5), P. 997 - 1014

Published: Feb. 18, 2021

Topological conflict or incongruence is widespread in phylogenomic data. Concatenation- and coalescent-based approaches often result incongruent topologies, but the causes of this can be difficult to characterize. We examined stemming from between likelihood-based signal (quantified by difference gene-wise log-likelihood score $\Delta $GLS) quartet-based topological quartet $GQS) for every gene three studies animals, fungi, plants, which were chosen because their concatenation-based IQ-TREE (T1) ASTRAL (T2) phylogenies are known produce eight conflicting internal branches (bipartitions). By comparing types phylogenetic all genes these data matrices, we found that 30-36% each matrix inconsistent, is, has a higher T1 versus T2 (i.e., $GLS $>$0) whereas its topology lower than $GQS $<$0) vice versa. Comparison inconsistent consistent using variety metrics (e.g., evolutionary rate, tree topology, distribution branch lengths, hidden paralogy, discordance) showed more likely recover neither nor have levels discordance genes. Simulation analyses demonstrate removal sets with low incomplete lineage sorting (ILS) medium estimation error (GTEE) reduced increased accuracy. In contrast, high ILS GTEE eliminated extensively incongruence, resulting congruent species not always topologically identical true trees.[Conflict; tree; signal; phylogenetics; phylogenomics; Tree Life.].

Language: Английский

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Integrative taxonomy and geographic sampling underlie successful species delimitation

Ornithology, Journal Year: 2021, Volume and Issue: 138(2)

Published: April 6, 2021

Abstract Species delimitation requires a broad assessment of population-level variation using multiple lines evidence, process known as integrative taxonomy. More specifically, studies species limits must address underlying questions what the distribution populations, how traits vary in association with different environments, and whether observed trait differences may lead to speciation through reproductive isolation. While genomic data have revolutionized delimiting species, such should be analyzed along phenotypic, behavioral, ecological that shape individuals across geographic environmental space. The integration promotes taxonomic stability major guiding principle for delimitation. Equally important, however, is thorough sampling adequately represent variation—both allopatry putative contact zones. We discuss importance both these factors context concepts present examples from birds illustrate criteria In addition, we review decade proposals species-level revisions considered by American Ornithological Society’s North Classification Committee, summarize basis decisions on split or lump species. Finally, recommendations challenges (specifically permits, time, funding) studies. This an exciting time studying birds: many remain, methodological advances increased access enable new approaches age-old problems avian

Language: Английский

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Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica

American Journal of Botany, Journal Year: 2021, Volume and Issue: 108(7), P. 1289 - 1306

Published: June 26, 2021

PREMISE Recent, rapid radiations present a challenge for phylogenetic reconstruction. Fast successive speciation events typically lead to low sequence divergence and poorly resolved relationships with standard markers. Target capture of many independent nuclear loci has the potential improve resolution radiations. METHODS Here we applied target 353 protein‐coding genes (Angiosperms353 bait kit) Veronica sect. Hebe (common name hebe) determine its utility improving section originated 5–10 million years ago in New Zealand, forming monophyletic radiation ca 130 extant species. RESULTS We obtained approximately 150 kbp exons an additional 200 flanking noncoding sequences each 77 hebe two outgroup When comparing coding, noncoding, combined data sets, found that latter provided best overall resolution. While some deep nodes remained unresolved, our phylogeny broad often improved support subclades identified by both morphology markers previous studies. Gene‐tree discordance was nonetheless widespread, indicating methods are needed disentangle fully history radiation. CONCLUSIONS Phylogenomic sets increase signal deliver new insights into complex evolutionary as compared traditional Improving resolve remaining among from is now important facilitate further study

Language: Английский

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Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

eLife, Journal Year: 2022, Volume and Issue: 11

Published: March 22, 2022

Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence their crown group is documented by few specimens unclear affinities, rendering early history uncertain. The origin sand dollars, one its most distinctive clades, also due to an unstable phylogenetic context. We employ 18 novel genomes and transcriptomes build phylogenomic dataset with near-complete sampling major lineages. With it, we revise phylogeny divergence times echinoids, place within broader context echinoderm evolution. introduce concept chronospace - multidimensional representation node ages use it explore methodological decisions involved in time calibrating phylogenies. find choice clock model have strongest impact on times, while site-heterogeneous models alternative prior distributions show minimal effects. loci has intermediate impact, affecting mostly deep Paleozoic nodes, for which clock-like genes recover dates more congruent evidence. Our results reveal that echinoids originated Permian diversified rapidly Triassic, despite relative lack evidence this diversification. clarify relationships between dollars close relatives confidently date origins Cretaceous, implying ghost ranges spanning approximately 50 million years, discrepancy rich record.

Language: Английский

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Phylotranscriptomic insights into a Mesoproterozoic–Neoproterozoic origin and early radiation of green seaweeds (Ulvophyceae)

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: March 22, 2022

Abstract The Ulvophyceae, a major group of green algae, is particular evolutionary interest because its remarkable morphological and ecological diversity. Its phylogenetic relationships diversification timeline, however, are still not fully resolved. In this study, using an extensive nuclear gene dataset, we apply coalescent- concatenation-based approaches to reconstruct the phylogeny Ulvophyceae explore sources conflict in previous phylogenomic studies. recovered as paraphyletic group, with Bryopsidales being sister Chlorophyceae, remaining taxa forming clade (Ulvophyceae sensu stricto ). Molecular clock analyses different calibration strategies emphasize large impact fossil calibrations, indicate Meso-Neoproterozoic origin ( ), earlier than estimates. results imply that ulvophyceans may have had profound influence on oceanic redox structures global biogeochemical cycles at Mesoproterozoic-Neoproterozoic transition.

Language: Английский

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Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles

Animals, Journal Year: 2023, Volume and Issue: 13(3), P. 471 - 471

Published: Jan. 29, 2023

Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles—lizards and snakes—recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity phenotypic genomic traits, resources in non-avian have accumulated more slowly than they mammals birds, remaining amniotes. Here we review remarkable natural history reptiles, focus on physical characteristics, sequence compositional patterns that key axes variation across We argue high evolutionary can fuel new generation whole-genome phylogenomic analyses. A survey phylogenetic investigations shows capture-based approaches are commonly used, studies markers known ultraconserved elements (UCEs) especially well represented. However, many other types exist increasingly being mined from genome assemblies silico, including some greater information potential UCEs for certain investigations. discuss importance high-quality methods bioinformatically extracting range marker sets assemblies. Finally, encourage herpetologists working genomics, genetics, biology, fields to work collectively towards building squamates, rival those already place birds. Overall, development this cross-amniote tree life will contribute illuminate interesting dimensions biodiversity broader

Language: Английский

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Incomplete lineage sorting and long-branch attraction confound phylogenomic inference of Pancrustacea

Frontiers in Ecology and Evolution, Journal Year: 2024, Volume and Issue: 12

Published: Jan. 30, 2024

Introduction The phylogenetic relationships within Pancrustacea (including Crustacea and Hexapoda) remain elusive despite analyses using various molecular data sets analytical approaches over the past decade. relationship between major lineages of Allotriocarida, which includes Hexapoda, most species-rich animal taxon, is particularly recalcitrant. Methods To investigate resolve root ambiguity in Pancrustacea, we re-evaluated evolutionary pancrustacean clades a phylogenetically informed orthology approach assessed effect systematic errors, with focus on long branch attraction (LBA) incomplete lineage sorting (ILS). A set comprising 1086 orthologs from 106 species representing all extant classes pancrustaceans was assembled used gene tree construction after filtering processes. Results discussion Regardless criteria analyses, resulting trees consistently supported (1) sister Remipedia Hexapoda (hence rejecting monophyly Xenocarida, i.e. + Cephalocarida), (2) refuted Multicrustacea, as Copepoda either to or nested Allotriocarida. Examination reveals that grouping Multicrustacea Xenocarida previous studies may represent LBA artefacts. Phylogenetic signal suggest low resolution an incidence strong conflicting signals at deep splits. Further indicate partial contribution (ILS) contradictory allotriocaridan phylogeny, leading limited support for any potential Branchiopoda, Cephalocarida Copepoda. This study suggests need further examination other sources discordance, such introgression estimation error fully understand history Pancrustacea.

Language: Английский

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Target capture and genome skimming for plant diversity studies

Applications in Plant Sciences, Journal Year: 2023, Volume and Issue: 11(4)

Published: July 1, 2023

Recent technological advances in long-read high-throughput sequencing and assembly methods have facilitated the generation of annotated chromosome-scale whole-genome sequence data for evolutionary studies; however, generating such can still be difficult many plant species. For example, obtaining high-molecular-weight DNA is typically impossible samples historical herbarium collections, which often degraded DNA. The need to fast-freeze newly collected living conserve high-quality complicated when plants are only found remote areas. Therefore, short-read reduced-genome representations, as target capture genome skimming, remain important studies. Here, we review pros cons each technique non-model taxa. We provide guidance related logistics, budget, genomic resources previously available clade, nature study. Furthermore, assess bioinformatic analyses, detailing best practices pitfalls, suggest pathways combine generated with legacy data. Finally, explore possible downstream analyses allowed by type using technique. a practical guide help researchers make best-informed choice regarding reduced representation studies cases where remains impractical.

Language: Английский

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Partitioned Gene-Tree Analyses and Gene-Based Topology Testing Help Resolve Incongruence in a Phylogenomic Study of Host-Specialist Bees (Apidae: Eucerinae)

Molecular Biology and Evolution, Journal Year: 2020, Volume and Issue: 38(3), P. 1090 - 1100

Published: Nov. 11, 2020

Incongruence among phylogenetic results has become a common occurrence in analyses of genome-scale data sets. originates from uncertainty underlying evolutionary processes (e.g., incomplete lineage sorting) and difficulties determining the best analytical approaches for each situation. To overcome these difficulties, more studies are needed that identify incongruences demonstrate practical ways to confidently resolve them. Here, we present phylogenomic study based on analysis 197 taxa 2,526 ultraconserved element (UCE) loci. We investigate relationships Eucerinae, diverse subfamily apid bees (relatives honey bumble bees) with >1,200 species. sampled representatives all tribes within group >80% genera, including two mysterious South American Chilimalopsis Teratognatha. Initial UCE revealed conflicting hypotheses tribes. incongruence, tested concatenation species tree used variety additional strategies locus filtering, partitioned gene-trees searches, gene-based topological tests. show within-locus partitioning improves gene subsequent species-tree estimation, this approach, resolves incongruence observed our set. After exploring proposed strategy eucerine bees, validated its efficacy hard problems by implementing it published set Adephaga (Insecta: Coleoptera). Our provide robust hypothesis Eucerinae resolving other

Language: Английский

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