Predicting the Impact of Describing New Species on Phylogenetic Patterns

Abstract Although our inventory of Earth’s biodiversity remains incomplete, we still require analyses using the Tree of Life to understand evolutionary and ecological patterns. Because incomplete sampling may bias our inferences, we must evaluate how future additions of newly discovered species might impact analyses performed today. We describe an approach that uses taxonomic history and phylogenetic trees to characterize the impact of past species discoveries on phylogenetic knowledge using patterns of branch-length variation, tree shape, and phylogenetic diversity. This provides a framework for assessing the relative completeness of taxonomic knowledge of lineages within a phylogeny. To demonstrate this approach, we use recent large phylogenies for amphibians, reptiles, flowering plants, and invertebrates. Well-known clades exhibit a decline in the mean and range of branch lengths that are added each year as new species are described. With increased taxonomic knowledge over time, deep lineages of well-known clades become known such that most recently described new species are added close to the tips of the tree, reflecting changing tree shape over the course of taxonomic history. The same analyses reveal other clades to be candidates for future discoveries that could dramatically impact our phylogenetic knowledge. Our work reveals that species are often added non-randomly to the phylogeny over multiyear time-scales in a predictable pattern of taxonomic maturation. Our results suggest that we can make informed predictions about how new species will be added across the phylogeny of a given clade, thus providing a framework for accommodating unsampled undescribed species in evolutionary analyses.

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Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not

mBio ◽

10.1128/mbio.02158-14 ◽

2014 ◽

Vol 5 (6) ◽

Cited By ~ 63

Author(s):

Jessica Hedge ◽

Daniel J. Wilson

Keyword(s):

Phylogenetic Tree ◽

Phylogenetic Analyses ◽

Phylogenetic Reconstruction ◽

Branch Length ◽

Great Accuracy ◽

Population History ◽

Genome Sequences ◽

Whole Genomes ◽

Branch Lengths ◽

The Impact

ABSTRACT Phylogenetic inference in bacterial genomics is fundamental to understanding problems such as population history, antimicrobial resistance, and transmission dynamics. The field has been plagued by an apparent state of contradiction since the distorting effects of recombination on phylogeny were discovered more than a decade ago. Researchers persist with detailed phylogenetic analyses while simultaneously acknowledging that recombination seriously misleads inference of population dynamics and selection. Here we resolve this paradox by showing that phylogenetic tree topologies based on whole genomes robustly reconstruct the clonal frame topology but that branch lengths are badly skewed. Surprisingly, removing recombining sites can exacerbate branch length distortion caused by recombination. IMPORTANCE Phylogenetic tree reconstruction is a popular approach for understanding the relatedness of bacteria in a population from differences in their genome sequences. However, bacteria frequently exchange regions of their genomes by a process called homologous recombination, which violates a fundamental assumption of phylogenetic methods. Since many researchers continue to use phylogenetics for recombining bacteria, it is important to understand how recombination affects the conclusions drawn from these analyses. We find that whole-genome sequences afford great accuracy in reconstructing evolutionary relationships despite concerns surrounding the presence of recombination, but the branch lengths of the phylogenetic tree are indeed badly distorted. Surprisingly, methods to reduce the impact of recombination on branch lengths can exacerbate the problem.

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Efficient inference, potential, and limitations of site-specific substitution models

10.1101/2020.01.18.911255 ◽

2020 ◽

Cited By ~ 2

Author(s):

Vadim Puller ◽

Pavel Sagulenko ◽

Richard A. Neher

Keyword(s):

Phylogenetic Trees ◽

Simulated Data ◽

Branch Length ◽

Large Data ◽

Joint Estimation ◽

Rate Variation ◽

Evolutionary Patterns ◽

Site Specific ◽

Branch Lengths ◽

Substitution Models

AbstractNatural selection imposes a complex filter on which variants persist in a population resulting in evolutionary patterns that vary greatly along the genome. Some sites evolve close to neutrally, while others are highly conserved, allow only specific states or only change in concert with other sites. Most commonly used evolutionary models, however, ignore much of this complexity and at best account for variation in the rate at which different sites change. Here, we present an efficient algorithm to estimate more complex models that allow for site-specific preferences and explore the accuracy at which such models can be estimated from simulated data. We find that an iterative approximate maximum likelihood scheme uses information in the data efficiently and accurately estimates site-specific preferences from large data sets with moderately diverged sequences. Ignoring site-specific preferences during estimation of branch length of phylogenetic trees – an assumption of most phylogeny software – results in substantial underestimation comparable to the error incurred when ignoring rate variation. However, the joint estimation of branch lengths, site-specific rates, and site-specific preferences can suffer from identifiability problems and is typically unable to recover the correct branch lengths. Site-specific preferences estimated from large HIV pol alignments show qualitative concordance with intra-host estimates of fitness costs. Analysis of site-specific HIV substitution models suggests near saturation of divergence after a few hundred years. Such saturation can explain the inability to infer deep divergence times of HIV and SIVs using molecular clock approaches and time-dependent rate estimates.

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A review of the taxonomic history and biodiversity of the genus Urodeta (Lepidoptera: Elachistidae: Elachistinae), with description of new species

Zootaxa ◽

10.11646/zootaxa.3488.1.2 ◽

2012 ◽

Vol 3488 (1) ◽

pp. 41 ◽

Cited By ~ 1

Author(s):

JURATE DE PRINS ◽

VIRGINIJUS SRUOGA

Keyword(s):

South Africa ◽

New Species ◽

Species Diversity ◽

Taxonomic History ◽

History Of ◽

Annotated Catalogue ◽

Three New Species ◽

The Impact

The taxonomic history of the genus Urodeta Stainton 1869 (Lepidoptera: Elachistidae: Elachistinae) is presented. Three new species: Urodeta acinacella Sruoga et De Prins, sp. nov., U. quadrifida Sruoga et De Prins, sp. nov. and U. trilobata Sruoga et De Prins, sp. nov., from South Africa are described. The new species are diagnosed and illustrated with photographs of the adults and genitalia. A global, annotated catalogue of the Urodeta species diversity is presented. The impact of formerly published taxonomic decisions on the position of Urodeta within Gelechioidea is discussed.

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Linking Branch Lengths Across Loci Provides the Best Fit for Phylogenetic Inference

10.1101/467449 ◽

2018 ◽

Cited By ~ 2

Author(s):

David A. Duchêne ◽

K. Jun Tong ◽

Charles S. P. Foster ◽

Sebastián Duchêne ◽

Robert Lanfear ◽

...

Keyword(s):

Gene Tree ◽

Branch Length ◽

Phylogenetic Inference ◽

Data Sets ◽

Length Variation ◽

Gene Trees ◽

Data Set ◽

Branch Lengths ◽

Future Work ◽

Best Fit

AbstractEvolution leaves heterogeneous patterns of nucleotide variation across the genome, with different loci subject to varying degrees of mutation, selection, and drift. Appropriately modelling this heterogeneity is important for reliable phylogenetic inference. One modelling approach in statistical phylogenetics is to apply independent models of molecular evolution to different groups of sites, where the groups are usually defined by locus, codon position, or combinations of the two. The potential impacts of partitioning data for the assignment of substitution models are well appreciated. Meanwhile, the treatment of branch lengths has received far less attention. In this study, we examined the effects of linking and unlinking branch-length parameters across loci. By analysing a range of empirical data sets, we find that the best-fitting model for phylogenetic inference is consistently one in which branch lengths are proportionally linked: gene trees have the same pattern of branch-length variation, but with varying absolute tree lengths. This model provided a substantially better fit than those that either assumed identical branch lengths across gene trees or that allowed each gene tree to have its own distinct set of branch lengths. Using simulations, we show that the fit of the three different models of branch lengths varies with the length of the sequence alignment and with the number of taxa in the data set. Our findings suggest that a model with proportionally linked branch lengths across loci is likely to provide the best fit under the conditions that are most commonly seen in practice. In future work, improvements in fit might be afforded by models with levels of complexity intermediate to proportional and free branch lengths. The results of our study have implications for model selection, computational efficiency, and experimental design in phylogenomics.

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New species and findings of Pagastia Oliver (Diptera: Chironomidae: Diamesinae) from Central Asia, with DNA barcoding of known species of the genus

Zootaxa ◽

10.11646/zootaxa.4951.3.8 ◽

2021 ◽

Vol 4951 (3) ◽

pp. 559-570

Author(s):

EUGENYI A. MAKARCHENKO ◽

ALEXANDER A. SEMENCHENKO ◽

DMITRY M. PALATOV

Keyword(s):

New Species ◽

Central Asia ◽

Cytochrome Oxidase ◽

Phylogenetic Trees ◽

Morphological Characters ◽

Molecular Data ◽

Adult Males ◽

Cytochrome Oxidase Subunit ◽

Oxidase Subunit ◽

Coi Sequences

Chironomids of the genus Pagastia Oliver (Diamesinae, Diamesini) from the mountains of Central Asia are revised using both morphological characters and molecular data. Illustrated descriptions of the adult male Pagastia (P.) caelestomontana sp. nov. from Kirgizstan and Tajikistan, P. (P.) hanseni sp. nov. from Tajikistan, and record of a finding apparently a new species P. (P.) aff. lanceolata (Tokunaga) from Tajikistan as well as an updated a key to the determination of the adult males of all known species of Pagastia are provided. A phylogenetic framework is reconstructed based on two mitochondrial genes cytochrome oxidase subunit I (COI) sequences of 34 samples belonging to 7 species of the genus Pagastia and cytochrome oxidase subunit II (COII) available for most samples. Phylogenetic trees of some known species of the genus Pagastia were reconstructed using the combined dataset and Bayesian inference (BI) and Maximum Likelihood (ML) methods. The interspecific K2P distances between seven Pagastia species including P. (P.) caelestomontana sp. nov., P. (P.) hanseni sp. nov. and undescribed P. (P.) aff. lanceolata (Tokunaga) are 6.3–13.2 which corresponding to species level.

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Spatangoid echinoids from the Eocene of Jamaica

Journal of Paleontology ◽

10.1017/s0022336000032777 ◽

2000 ◽

Vol 74 (4) ◽

pp. 654-661 ◽

Cited By ~ 1

Author(s):

Stephen K. Donovan ◽

Deborah-Ann C. Rowe

Keyword(s):

New Species ◽

First Record ◽

Trace Fossils ◽

Upper Eocene ◽

Area Effects ◽

Low Diversity ◽

First Time ◽

Incomplete Sampling

Paleocene spatangoids are unknown from the Antilles, apart from evidence from trace fossils. The peak of spatangoid diversity was the Eocene. Jamaican Oligo-Miocene spatangoids have a relatively low diversity compared with that of the Antillean region. Plio-Pleistocene spatangoids are poorly known from the Antilles (four genera), in contrast to the Oligo-Miocene (16 genera) and Holocene (17 genera). The depauperate Paleocene and Plio-Pleistocene spatangoid faunas are probably in part artifacts of incomplete sampling, facies-related absences, outcrop area effects and the relative brevity of these stratigraphic intervals.To the large echinoid fauna of the Swanswick Formation (Middle-Upper Eocene) of Jamaica is added the schizasterid Aguayoaster schickleri new species. This is the first record of this genus outside Cuba; it is distinctly more elongate than all other known specimens of this genus. The schizasterid Caribbaster loveni (Cotteau, 1875) is recorded from the Swanswick Formation for the first time, the youngest occurrence of this genus in Jamaica. The coeval Claremont Formation has not previously yielded spatangoid echinoids; the brissid Eupatagus cf. antillarum (Cotteau) from a new locality is the first spatangoid known from a lagoonal unit of the White Limestone Group.

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Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2015.0225 ◽

2016 ◽

Vol 371 (1691) ◽

pp. 20150225 ◽

Cited By ~ 36

Author(s):

Daniele Silvestro ◽

Alexander Zizka ◽

Christine D. Bacon ◽

Borja Cascales-Miñana ◽

Nicolas Salamin ◽

...

Keyword(s):

North America ◽

Fossil Record ◽

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Historical Biogeography ◽

Extinction Rates ◽

Climatic Cooling ◽

Fossil Data ◽

Incomplete Sampling ◽

Des Model

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.

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Mitochondrial DNAs provide insight into trypanosome phylogeny and molecular evolution

10.21203/rs.3.rs-27858/v1 ◽

2020 ◽

Author(s):

Christopher Kay ◽

Tom A Williams ◽

Wendy Gibson

Keyword(s):

Molecular Evolution ◽

Trypanosoma Brucei ◽

Rna Editing ◽

Phylogenetic Trees ◽

Nucleotide Composition ◽

Sub Saharan Africa ◽

African Trypanosomes ◽

Animal Pathogens ◽

Recent Emergence ◽

The Impact

Abstract Background: Trypanosomes are single-celled eukaryotic parasites characterised by the unique biology of their mitochondrial DNA (mtDNA). African livestock trypanosomes impose a major burden on agriculture across sub-Saharan Africa, but are poorly understood compared to those that cause sleeping sickness and Chagas disease in humans. Here we explore the potential of trypanosome mtDNA to study the evolutionary history of trypanosomes and the molecular evolution of their mtDNAs.Results: We used long-read sequencing to completely assemble mtDNAs from four previously uncharacterized African trypanosomes, and leveraged these assemblies to scaffold and assemble a further 103 trypanosome mtDNAs from published short-read data. While synteny was largely conserved, there were repeated, independent losses of Complex I genes. Comparison of edited and non-edited genes revealed the impact of RNA editing on nucleotide composition, with non-edited genes approaching the limits of GC loss. African tsetse-transmitted trypanosomes showed high levels of RNA editing compared to other trypanosomes. Whole mtDNA coding regions were used to construct time-resolved phylogenetic trees, revealing deep divergence events among isolates of the pathogens Trypanosoma brucei and T. congolense .Conclusions: Our mtDNA data represents a new resource for experimental and evolutionary analyses of trypanosome phylogeny, molecular evolution and function. Molecular clock analyses yielded a timescale for trypanosome evolution congruent with major biogeographical events in Africa and revealed the recent emergence of Trypanosoma brucei gambiense and T. equiperdum , major human and animal pathogens.

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New names, species and synonyms in a changing Velloziaceae world

Phytotaxa ◽

10.11646/phytotaxa.309.1.3 ◽

2017 ◽

Vol 309 (1) ◽

pp. 35

Author(s):

RENATO MELLO-SILVA

Keyword(s):

New Species ◽

Distinct Species ◽

New Name ◽

New Synonyms ◽

Taxonomic History ◽

A New Species

Vellozia leptopetala corresponds to V. epidendroides, a much older name, and its taxonomic history encompass also V. epidendroides var. divaricata and V. epidendroides var. major, which are quite distinct species. For solving this situation, new synonyms of V. epidendroides, a new name, V. ornithophila, and a new status for both varieties of V. epidendroides are here presented. Vellozia virgata corresponds to V. sellowii, also a much older name. For solving this situation, the sinking of V. virgata into V. sellowii, and a new species, V. linearis, based on the isotypes of V. virgata, are presented. Vellozia asperula var. filifolia showed to be a very distinct species from V. asperula. For mending this situation, a new status for V. asperula var. filifolia is proposed.

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The green puzzle Stichococcus (Trebouxiophyceae, Chlorophyta): New generic and species concept among this widely distributed genus

Phytotaxa ◽

10.11646/phytotaxa.441.2.2 ◽

2020 ◽

Vol 441 (2) ◽

pp. 113-142 ◽

Cited By ~ 1

Author(s):

THOMAS PRÖSCHOLD ◽

TATYANA DARIENKO

Keyword(s):

New Species ◽

Species Delimitation ◽

Species Concept ◽

Phylogenetic Analyses ◽

Complex Life Cycle ◽

New Genera ◽

Rdna Sequences ◽

Taxonomic History ◽

Culture Independent ◽

Science Community

Phylogenetic analyses have revealed that the traditional order Prasiolales, which contains filamentous and pseudoparenchymatous genera Prasiola and Rosenvingiella with complex life cycle, also contains taxa of more simple morphology such as coccoids like Pseudochlorella and Edaphochlorella or rod-like organisms like Stichococcus and Pseudostichococcus (called Prasiola clade of the Trebouxiophyceae). Recent studies have shown a high biodiversity among these organisms and questioned the traditional generic and species concept. We studied 34 strains assigned as Stichococcus, Pseudostichococcus, Diplosphaera and Desmocococcus. Phylogenetic analyses using a multigene approach revealed that these strains belong to eight independent lineages within the Prasiola clade of the Trebouxiophyceae. For testing if these lineages represent genera, we studied the secondary structures of SSU and ITS rDNA sequences to find genetic synapomorphies. The secondary structure of the V9 region of SSU is diagnostic to support the proposal for separation of eight genera. The complex taxonomic history was summarized and revised. The ITS-2/CBC approach was used for species delimitation. Considering all these results, we revised the genera Stichococcus, Pseudostichococcus, Diplosphaera and Desmococcus and proposed four new genera and four new species for the science community. The usage of the V9 region and the ITS-2 barcodes discovered potential new species among the Stichococcus-like organisms in culture-independent studies.

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