Interrogating Genomic Data in the Phylogenetic Placement of Treeshrews Reveals Potential Sources of Conflict

The position of some taxa on the Tree of Life remains controversial despite the increase in genomic data used to infer phylogenies. While analyzing large datasets alleviates stochastic errors, it does not prevent systematic errors in inference, caused by both biological (e.g., incomplete lineage sorting, hybridization) and methodological (e.g., incorrect modeling, erroneous orthology assessments) factors. In our study, we systematically investigated factors that could result in these controversies, using the treeshrew (Scandentia, Mammalia) as a study case. Recent studies have narrowed the phylogenetic position of treeshrews to three competing hypotheses: sister to primates and flying lemurs (Primatomorpha), sister to rodents and lagomorphs (Glires), or sister to a clade comprising all of these. We sampled 50 mammal species including three treeshrews, a selection of taxa from the potential sister groups, and outgroups. Using a large diverse set of loci, we assessed support for the alternative phylogenetic position of treeshrews. A plurality of loci support treeshrews as sister to rodents and lagomorphs; however, only a few loci exhibit strong support for any hypothesis. Surprisingly, we found that a subset of loci that strongly support the monophyly of Primates, support treeshrews as sister to primates and flying lemurs. The overall small magnitude of differences in phylogenetic signal among the alternative hypotheses suggests that these three groups diversified nearly simultaneously. However, with our large dataset and approach to examining support, we provide evidence for the hypothesis of treeshrews as sister to rodents and lagomorphs, while demonstrating why support for alternate hypotheses has been seen in prior work. We also suggest that locus selection can unwittingly bias results.

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Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

Systematic Biology ◽

10.1093/sysbio/syaa034 ◽

2020 ◽

Vol 70 (1) ◽

pp. 49-66 ◽

Cited By ~ 4

Author(s):

Paul M Hime ◽

Alan R Lemmon ◽

Emily C Moriarty Lemmon ◽

Elizabeth Prendini ◽

Jeremy M Brown ◽

...

Keyword(s):

Tree Species ◽

Incomplete Lineage Sorting ◽

Phylogenetic Signal ◽

Gene Tree ◽

Strong Support ◽

Species Tree ◽

Tree Of Life ◽

Lineage Sorting ◽

Sister Relationship ◽

Gene Tree Discordance

Abstract Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree–species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree–species tree discordance; genomics; information theory.]

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Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents

Systematic Biology ◽

10.1093/sysbio/syz044 ◽

2019 ◽

Vol 69 (3) ◽

pp. 431-444 ◽

Cited By ~ 5

Author(s):

Emily J Roycroft ◽

Adnan Moussalli ◽

Kevin C Rowe

Keyword(s):

Sequence Data ◽

Incomplete Lineage Sorting ◽

Phylogenetic Signal ◽

Strong Support ◽

Bootstrap Support ◽

Data Sets ◽

Lineage Sorting ◽

Nucleotide Sequence Data ◽

Branch Support ◽

Partitioning Strategy

Abstract The estimation of robust and accurate measures of branch support has proven challenging in the era of phylogenomics. In data sets of potentially millions of sites, bootstrap support for bifurcating relationships around very short internal branches can be inappropriately inflated. Such overestimation of branch support may be particularly problematic in rapid radiations, where phylogenetic signal is low and incomplete lineage sorting severe. Here, we explore this issue by comparing various branch support estimates under both concatenated and coalescent frameworks, in the recent radiation Australo-Papuan murine rodents (Muridae: Hydromyini). Using nucleotide sequence data from 1245 independent loci and several phylogenomic inference methods, we unequivocally resolve the majority of genus-level relationships within Hydromyini. However, at four nodes we recover inconsistency in branch support estimates both within and among concatenated and coalescent approaches. In most cases, concatenated likelihood approaches using standard fast bootstrap algorithms did not detect any uncertainty at these four nodes, regardless of partitioning strategy. However, we found this could be overcome with two-stage resampling, that is, across genes and sites within genes (using -bsam GENESITE in IQ-TREE). In addition, low confidence at recalcitrant nodes was recovered using UFBoot2, a recent revision to the bootstrap protocol in IQ-TREE, but this depended on partitioning strategy. Summary coalescent approaches also failed to detect uncertainty under some circumstances. For each of four recalcitrant nodes, an equivalent (or close to equivalent) number of genes were in strong support ($>$ 75% bootstrap) of both the primary and at least one alternative topological hypothesis, suggesting notable phylogenetic conflict among loci not detected using some standard branch support metrics. Recent debate has focused on the appropriateness of concatenated versus multigenealogical approaches to resolving species relationships, but less so on accurately estimating uncertainty in large data sets. Our results demonstrate the importance of employing multiple approaches when assessing confidence and highlight the need for greater attention to the development of robust measures of uncertainty in the era of phylogenomics.

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Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data

10.1101/2020.07.27.224022 ◽

2020 ◽

Author(s):

Sungsik Kong ◽

Laura S. Kubatko

Keyword(s):

Statistical Power ◽

Evolutionary Dynamics ◽

Mean Squared Error ◽

Incomplete Lineage Sorting ◽

Introgressive Hybridization ◽

Genomic Data ◽

Lineage Sorting ◽

Comparative Performance ◽

Pattern Frequency ◽

Hybrid Detection

AbstractInterspecific hybridization is an important evolutionary phenomenon that generates genetic variability in a population and fosters species diversity in nature. The availability of large genome scale datasets has revolutionized hybridization studies to shift from the examination of the presence or absence of hybrids in nature to the investigation of the genomic constitution of hybrids and their genome-specific evolutionary dynamics. Although a handful of methods have been proposed in an attempt to identify hybrids, accurate detection of hybridization from genomic data remains a challenging task. The available methods can be classified broadly as site pattern frequency based and population genetic clustering approaches, though the performance of the two classes of methods under different hybridization scenarios has not been extensively examined. Here, we use simulated data to comparatively evaluate the performance of four tools that are commonly used to infer hybridization events: the site pattern frequency based methods HyDe and the D-statistic (i.e., the ABBA-BABA test), and the population clustering approaches structure and ADMIXTURE. We consider single hybridization scenarios that vary in the time of hybridization and the amount of incomplete lineage sorting (ILS) for different proportions of parental contributions (γ); introgressive hybridization; multiple hybridization scenarios; and a mixture of ancestral and recent hybridization scenarios. We focus on the statistical power to detect hybridization, the false discovery rate (FDR) for the D-statistic and HyDe, and the accuracy of the estimates of γ as measured by the mean squared error for HyDe, structure, and ADMIXTURE. Both HyDe and the D-statistic demonstrate a high level of detection power in all scenarios except those with high ILS, although the D-statistic often has an unacceptably high FDR. The estimates of γ in HyDe are impressively robust and accurate whereas structure and ADMIXTURE sometimes fail to identify hybrids, particularly when the proportional parental contributions are asymmetric (i.e., when γ is close to 0). Moreover, the posterior distribution estimated using structure exhibits multimodality in many scenarios, making interpretation difficult. Our results provide guidance in selecting appropriate methods for identifying hybrid populations from genomic data.

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Phylogenetic relationships based on nuclear and plastid DNA sequences reveal recent diversification and discordant patterns of morphological evolution of the Chilean genera of Gilliesieae (Amaryllidaceae: Allioideae)

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boaa035 ◽

2020 ◽

Vol 194 (1) ◽

pp. 84-99

Author(s):

Inelia Escobar ◽

Eduardo Ruiz-Ponce ◽

Paula J Rudall ◽

Michael F Fay ◽

Oscar Toro-Núñez ◽

...

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Incomplete Lineage Sorting ◽

Morphological Evolution ◽

Strong Support ◽

Plastid Dna ◽

Lineage Sorting ◽

Generic Level ◽

Molecular Analyses ◽

Floral Diversity

Abstract Gilliesieae are a South American tribe of Amaryllidaceae characterized by high floral diversity. Given different taxonomic interpretations and proposals for generic and specific relationships, a representative phylogenetic analysis is required to clarify the systematics of this group. The present study provides a framework for understanding phylogenetic relationships and contributing to the development of an appropriate taxonomic treatment of Gilliesieae. Molecular analyses, based on nuclear (ITS) and plastid DNA sequences (trnL-F and rbcL), resolve with strong support the monophyly of the tribe and the differentiation of two major clades. Clade I comprises the genera Gilliesia, Gethyum and Solaria and Clade II includes Miersia and Speea. These well-supported clades are mostly congruent with vegetative and karyotype characters rather than, e.g., floral symmetry. At the generic level, all molecular analyses reveal the paraphyly of Gilliesia and Miersia. Gethyum was found to be paraphyletic, resulting in the confirmation of Ancrumia as a distinct genus. Several instances of incongruent phylogenetic signals were found among data sets. The calibrated tree suggests a recent diversification of the tribe (Pliocene–Pleistocene), a contemporary process of speciation in which instances of hybridization and incomplete lineage sorting could explain patterns of paraphyly and incongruence of floral morphology.

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Phylogeny, biogeography and foliar manganese accumulation of Gossia (Myrtaceae)

Australian Systematic Botany ◽

10.1071/sb18018 ◽

2018 ◽

Cited By ~ 1

Author(s):

Todd McLay ◽

Gareth D. Holmes ◽

Paul I. Forster ◽

Susan E. Hoebee ◽

Denise R. Fernando

Keyword(s):

Sequence Data ◽

Incomplete Lineage Sorting ◽

Phylogenetic Position ◽

Strongly Correlated ◽

Lineage Sorting ◽

Dna Sequence Data ◽

Australian Species ◽

Wide Range ◽

Single Clade ◽

The Relationship

The rainforest genus Gossia N.Snow & Guymer (Myrtaceae) occurs in Australia, Melanesia and Malesia, and is capable of hyperaccumulating the heavy metal manganese (Mn). Here, we used nuclear ribosomal and plastid spacer DNA-sequence data to reconstruct the phylogeny of 19 Australian species of Gossia and eight New Caledonian taxa. Our results indicated that the relationship between Gossia and Austromyrtus (Nied.) Burret is not fully resolved, and most Australian species were supported as monophyletic. Non-monophyly might be related to incomplete lineage sorting or inaccurate taxonomic classification. Bark type appears to be a morphological synapomorphy separating two groups of species, with more recently derived lineages having smooth and mottled ‘python’ bark. New Caledonian species were well resolved in a single clade, but were not the first diverging Gossia lineage, calling into doubt the results of a recent study that found Zealandia as the ancestral area of tribe Myrteae. Within Australia, the evolution of multiple clades has probably been driven by well-known biogeographic barriers. Some species with more widespread distributions have been able to cross these barriers by having a wide range of soil-substrate tolerances. Novel Mn-hyperaccumulating species were identified, and, although Mn hyperaccumulation was not strongly correlated with phylogenetic position, there appeared to be some difference in accumulation levels among clades. Our study is the first detailed phylogenetic investigation of Gossia and will serve as a reference for future studies seeking to understand the origin and extent of hyperaccumulation within the Myrteae and Myrtaceae more broadly.

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Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow-mouth frogs

Evolution ◽

10.1111/evo.13133 ◽

2016 ◽

Vol 71 (2) ◽

pp. 475-488 ◽

Cited By ~ 18

Author(s):

Alana M. Alexander ◽

Yong-Chao Su ◽

Carl H. Oliveros ◽

Karen V. Olson ◽

Scott L. Travers ◽

...

Keyword(s):

Adaptive Radiation ◽

Phylogenetic Relationships ◽

Incomplete Lineage Sorting ◽

Genomic Data ◽

Lineage Sorting

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C4 photosynthetic evolution : sub-types, diversity, and function within the grass tribe Paniceae

10.32469/10355/64234 ◽

2017 ◽

Author(s):

◽

Jacob Daniel Washburn

Keyword(s):

Incomplete Lineage Sorting ◽

Strong Support ◽

Cell Types ◽

Bioenergy Crops ◽

Comparative Genomic ◽

Lineage Sorting ◽

Dna And Rna ◽

Genomic Studies ◽

Rna Expression Profiling ◽

And Function

Most plants convert sunlight into chemical energy using a process known as C[subscript 3] photosynthesis. However, some of the world's most successful plants instead use the C[subscript 4] photosynthetic pathway which allows them to more efficiently use water, nitrogen, and solar energy. In the past 30 million years, C4 photosynthesis has convergently evolved from C3 over 60 times and new lineages are in the process of evolving even today. Because of this complex evolutionary history, C[subscript 4] is not "one" uniform photosynthetic type, but a diverse collection of photosynthetic sub-types that are classically grouped according to their use of three different biochemical pathways. The grass tribe Paniceae is especially interesting in this aspect because it contains all three of these biochemical subtypes as well as important food and bioenergy crops. To better understand the evolution of C[subscript 4] photosynthesis, DNA and RNA sequencing were undertaken for various species from within the Paniceae and used for phylogenetic and comparative genomic studies. Cell type specific RNA expression profiling for the two major C4 cell types was also completed for representative species of each C[subscript 4] sub-type. Streamlined bioinformatics pipelines for both chloroplast and nuclear phylogenetics were developed for processing the data. These analyses resulted in: 1) The first "genome scale" phylogenetic tree of the grass tribe Paniceae, 2) The clearest evidence to date of the evolutionary relationships between the three classically defined C[subscript 4] sub-types, 3) The most convincing results to date that the chloroplast and nuclear phylogenies of the Paniceae are incongruent, 4) Evidence that this chloroplast nuclear incongruence is likely due to introgression and/or incomplete lineage sorting, and 5) Strong support for sub-type mixing as well as the existence of a PCK sub-type.

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A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario

10.21203/rs.3.rs-133136/v1 ◽

2020 ◽

Author(s):

Montrai Spikes ◽

Rodet Rodríguez-Silva ◽

Kerri-Ann Bennett ◽

Stefan Bräger ◽

James Josaphat ◽

...

Keyword(s):

Incomplete Lineage Sorting ◽

Strong Support ◽

Greater Antilles ◽

Lineage Sorting ◽

Complete Sequences ◽

History Of ◽

Adaptive Radiations ◽

The Caribbean ◽

High Level

Abstract The Caribbean is one of the most important biodiversity hotspots on the planet due to the high level of species diversity and endemism in plants and animals. As elsewhere, adaptive radiations in the Caribbean lead to many speciation events within a limited period and hence are particularly prominent biodiversity generators. The general prediction from Island Biogeography that relates species richness to island size is valid for livebearing fishes in general in the Greater Antilles, where larger islands have higher numbers of species mainly due to in situ speciation. A prime example of this speciation process can be seen in the genus Limia, endemic to the Greater Antilles. Within Hispaniola, nine species have been described from a single isolated site, Lake Miragoâne, pointing towards extraordinary sympatric speciation in Limia. Few studies have examined the evolutionary history of the fishes found in Lake Miragoâne. Here, we address the gaps in present knowledge by providing a preliminary phylogeny of Limia and testing whether the species found in Lake Miragoâne may originated from an in situ radiation. We targeted the mitochondrial cytochrome b gene, a well-established marker for lower-level taxonomic relationships for which we obtained almost complete sequences for 13 species. The general topology of the phylogenies we produced are in concordance with other published phylogenies of Limia. There is also strong support that the species found in Lake Miragoâne in Haiti are indeed monophyletic (BS=97; PP=1.0), confirming the hypothesis of a recent local radiation. Within Lake Miragoâne, speciation is likely extremely recent, leading to incomplete lineage sorting in the mtDNA. Future studies are needed using multiple unlinked genetic markers to disentangle the relationships within the Lake Miragoâne clade.

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A robust phylogenomic timetree for biotechnologically and medically important fungi in the genera Aspergillus and Penicillium

10.1101/370429 ◽

2018 ◽

Cited By ~ 2

Author(s):

Jacob L. Steenwyk ◽

Xing-Xing Shen ◽

Abigail L. Lind ◽

Gustavo H. Goldman ◽

Antonis Rokas

Keyword(s):

Amino Acid ◽

Molecular Clock ◽

Plant Pathogens ◽

Incomplete Lineage Sorting ◽

Phylogenetic Signal ◽

Data Matrix ◽

Comparative Genomic ◽

Lineage Sorting ◽

Full Data ◽

Gene Data

AbstractAbbreviations:NT, nucleotide; AA, amino acid; CI, credible interval; RCV, relative composition variability; IC, internode certainty; GSF, gene support frequencies; GLS, gene-wise log-likelihood scores; DVMC, degree of violation of a molecular clockThe filamentous fungal family Aspergillaceae contains > 1,000 known species, mostly in the genera Aspergillus and Penicillium. Several species are used in the food, biotechnology, and drug industries (e.g., Aspergillus oryzae, Penicillium camemberti), while others are dangerous human and plant pathogens (e.g., Aspergillus fumigatus, Penicillium digitatum). To infer a robust phylogeny and pinpoint poorly resolved branches and their likely underlying contributors, we used 81 genomes spanning the diversity of Aspergillus and Penicillium to construct a 1,668-gene data matrix. Phylogenies of the nucleotide and amino acid versions of this full data matrix as well as of five additional 834-gene data matrices constructed by subsampling the top 50% of genes according to different criteria associated with strong phylogenetic signal were generated using three different maximum likelihood schemes (i.e., gene-partitioned, unpartitioned, and coalescence). Examination of the topological agreement among these 36 phylogenies and measures of internode certainty identified 12 / 78 (15.4%) bipartitions that were incongruent and pinpoint the likely underlying contributing factors (incomplete lineage sorting, hybridization or introgression, and reconstruction artifacts associated with poor taxon sampling). Relaxed molecular clock analyses suggest that Aspergillaceae likely originated in the lower Cretaceous and the Aspergillus and Penicillium genera in the upper Cretaceous. Our results shed light on the ongoing debate on Aspergillus systematics and taxonomy and provide a robust evolutionary and temporal framework for comparative genomic analyses in Aspergillaceae. More broadly, our approach provides a general template for phylogenomic identification of resolved and contentious branches in densely genome-sequenced lineages across the tree of life.

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The convoluted evolutionary history of the capped-golden langur lineage (Cercopithecidae: Colobinae) – concatenation versus coalescent analyses

10.1101/508929 ◽

2018 ◽

Cited By ~ 2

Author(s):

Kunal Arekar ◽

Abhijna Parigi ◽

K. Praveen Karanth

Keyword(s):

Evolutionary History ◽

Incomplete Lineage Sorting ◽

Phylogenetic Position ◽

Lineage Sorting ◽

Nuclear Markers ◽

Mitochondrial Markers ◽

Multispecies Coalescent ◽

Nuclear Species ◽

History Of ◽

Golden Langur

AbstractEvolutionary studies have traditionally relied on concatenation based methods to reconstruct relationships from multiple markers. However, due to limitations of concatenation analyses, recent studies have proposed coalescent based methods to address evolutionary questions. Results from these methods tend to diverge from each other under situations where there is incomplete lineage sorting or hybridization. Here we used concatenation as well as multispecies coalescent (MSC) methods to understand the evolutionary origin of capped and golden langur (CG) lineage. Previous molecular studies have retrieved conflicting phylogenies, with mitochondrial tree grouping CG lineage with a largely Indian genus Semnopithecus, while nuclear markers support their affinities with a Southeast Asian genus, Trachypithecus. However, as pointed by others, the use of nuclear copies of mitochondrial DNA in the above studies might have generated the discordance. Because of this discordance, the phylogenetic position of CG lineage has been much debated in recent times. In this study, we have used nine nuclear and eight mitochondrial markers. Concatenated nuclear as well as the mitochondrial dataset recovered congruent relationships where CG lineage was sister to Trachypithecus. However nuclear species tree estimated using different MSC methods were incongruent with the above result, suggesting presence of incomplete lineage sorting (ILS)/hybridisation. Furthermore, CG lineage is morphologically intermediate between Semnopithecus and Trachypithecus. Based on this evidence, we argue that CG lineage evolved through hybridisation between Semnopithecus and Trachypithecus. Finally, we reason that both concatenation as well as coalescent methods should be used in conjunction for better understanding of various evolutionary hypotheses.

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