Increased Taxon Sampling Research Articles

Molecular phylogenetics of the superfamily Stromboidea (Caenogastropoda): New insights from increased taxon sampling

AbstractThe superfamily Stromboidea is a clade of morphologically distinctive gastropods which include the iconic Strombidae, or ‘true conchs’. In this study, we present the most taxonomically extensive phylogeny of the superfamily to date, using fossil calibrations to produce a chronogram and extant geographical distributions to reconstruct ancestral ranges. From these results, we confirm the monophyly of all stromboidean families; however, six genera are not monophyletic using current generic assignments (Strombidae: Lentigo, Canarium, Dolomena, Doxander; Xenophoridae: Onustus, Xenophora). Within Strombidae, analyses resolve an Indo‐West Pacific (IWP) clade sister to an East Pacific/Atlantic clade, together sister to a second, larger IWP clade. Our results also indicate two pulses of strombid diversification within the Miocene, and a Tethyan/IWP origin for Strombidae—both supported by the fossil record. However, conflicts between divergence time estimates and the fossil record warrant further exploration. Species delimitation analyses using the COI barcoding gene support several taxonomic changes. We synonymise Euprotomus aurora with Euprotomus bulla, Strombus alatus with Strombus pugilis, Dolomena abbotti with Dolomena labiosa, and Dolomena operosa with Dolomena vittata. We identified cryptic species complexes within Terebellum terebellum, Lambis lambis, “Canarium” wilsonorum, Dolomena turturella and Maculastrombus mutabilis. We reinstate Rimellopsis laurenti as a species (previously synonymised with R. powisii) and recognise Harpago chiragra rugosus and Lambis truncata sowerbyi valid at the rank of species. Finally, we establish several new combinations to render Lentigo, Dolomena, and Canarium monophyletic: Lentigo thersites, Dolomena robusta, Dolomena epidromis, Dolomena turturella, Dolomena taeniata, Dolomena vanikorensis, D. vittata, “Canarium” wilsonorum, Hawaiistrombus scalariformis, Maculastrombus mutabilis, Maculastrombus microurceus.

Modeling compositional heterogeneity resolves deep phylogeny of flowering plants

Angiosperms experienced one of the most remarkable radiations of land plants and are now the dominant autotrophs in terrestrial ecosystems. Recent phylogenomic studies based on large-scale data from plastid, mitochondrial, or nuclear transcriptomes/genomes and increased taxon sampling have provided unprecedent resolution into the phylogeny of flowering plants. However, owing to ancient rapid radiations, the interrelationships among the five lineages of Mesangiospermae, the vast majority of angiosperms, remain contentious. Here we show that, although plastid and mitochondrial genomes lack sufficient phylogenetic signal for resolving deeper phylogeny, the relationships among five mesangiosperm lineages can be confidently resolved under better-fitting models using genome-scale data. According to our Bayesian cross-validation and model test in a maximum likelihood framework, site-heterogeneous models (e.g., CAT-GTR + G4, LG + C20 + F + G) outperform site-homogeneous or partition models often used in previous studies. Under site-heterogeneous models, the approximately unbiased test favored our preferred tree recovered from various datasets: Ceratophyllales (coontails) are robustly recovered as sister to monocots, and they together are sister to the clade comprising magnoliids, Chloranthales, and eudicots. Our phylogenomic analyses resolve the last enigma of the deeper phylogeny of angiosperms and emphasize the efficacy of modeling compositional heterogeneity in resolving rapid radiations of plants.

Organellar phylogenomics at the epidendroid orchid base, with a focus on the mycoheterotrophic Wullschlaegelia.

Heterotrophic plants have long been a challenge for systematists, exemplified by the base of the orchid subfamily Epidendroideae, which contains numerous mycoheterotrophic species. Here we address the utility of organellar genomes in resolving relationships at the epidendroid base, specifically employing models of heterotachy, or lineage-specific rate variation over time. We further conduct comparative analyses of plastid genome evolution in heterotrophs and structural variation in matK. We present the first complete plastid genomes (plastomes) of Wullschlaegelia, the sole genus of the tribe Wullschlaegelieae, revealing a highly reduced genome of 37 kilobases, which retains a fraction of the genes present in related autotrophs. Plastid phylogenomic analyses recovered a strongly supported clade composed exclusively of mycoheterotrophic species with long branches. We further analyzed mitochondrial gene sets, which recovered similar relationships to those in other studies using nuclear data, but the placement of Wullschlaegelia remains uncertain. We conducted comparative plastome analyses among Wullschlaegelia and other heterotrophic orchids, revealing a suite of correlated substitutional and structural changes relative to autotrophic species. Lastly, we investigated evolutionary and structural variation in matK, which is retained in Wullschlaegelia and a few other 'late stage' heterotrophs and found evidence for structural conservation despite rapid substitution rates in both Wullschlaegelia and the leafless Gastrodia. Our analyses reveal the limits of what the plastid genome can tell us on orchid relationships in this part of the tree, even when applying parameter-rich heterotachy models. Our study underscores the need for increased taxon sampling across all three genomes at the epidendroid base, and illustrates the need for further research on addressing heterotachy in phylogenomic analyses.

Phylogenomic data exploration with increased sampling provides new insights into the higher-level relationships of butterflies and moths (Lepidoptera)

A robust and stable phylogenetic framework is a fundamental goal of evolutionary biology. As the third largest insect order in the world following Coleoptera and Diptera, Lepidoptera (butterflies and moths) play a central role in almost every terrestrial ecosystem as indicators of environmental change and serve as important models for biologists exploring questions related to ecology and evolutionary biology. However, for such a charismatic insect group, the higher-level phylogenetic relationships among its superfamilies are still poorly resolved. Compared to earlier phylogenomic studies, we increased taxon sampling among Lepidoptera (37 superfamilies and 68 families containing 263 taxa) and acquired a series of large amino-acid datasets from 69,680 to 400,330 for phylogenomic reconstructions. Using these datasets, we explored the effect of different taxon sampling with significant increases in the number of included genes on tree topology by considering a series of systematic errors using maximum-likelihood (ML) and Bayesian inference (BI) methods. Moreover, we also tested the effectiveness in topology robustness among the three ML-based models. The results showed that taxon sampling is an important determinant in tree robustness of accurate lepidopteran phylogenetic estimation. Long-branch attraction (LBA) caused by site-wise heterogeneity is a significant source of bias giving rise to unstable positions of ditrysian groups in phylogenomic reconstruction. Phylogenetic inference showed the most comprehensive framework to reveal the relationships among lepidopteran superfamilies, and presented some newly relationships with strong supports (Papilionoidea was sister to Gelechioidea and Immoidea was sister to Galacticoidea, respectively), but limited by taxon sampling, the relationships within the species-rich and relatively rapid radiation Ditrysia and especially Apoditrysia remain poorly resolved, which need to increase taxon sampling for further phylogenomic reconstruction. The present study demonstrates that taxon sampling is an important determinant for an accurate lepidopteran tree of life and provides some essential insights for future lepidopteran phylogenomic studies.

Robustness of Felsenstein's Versus Transfer Bootstrap Supports With Respect to Taxon Sampling.

The bootstrap method is based on resampling sequence alignments and re-estimating trees. Felsenstein's bootstrap proportions (FBP) are the most common approach to assess the reliability and robustness of sequence-based phylogenies. However, when increasing taxon sampling (i.e., the number of sequences) to hundreds or thousands of taxa, FBP tend to return low support for deep branches. The transfer bootstrap expectation (TBE) has been recently suggested as an alternative to FBP. TBE is measured using a continuous transfer index in [0,1] for each bootstrap tree, instead of the binary {0,1} index used in FBP to measure the presence/absence of the branch of interest. TBE has been shown to yield higher and more informative supports while inducing a very low number of falsely supported branches. Nonetheless, it has been argued that TBE must be used with care due to sampling issues, especially in datasets with a high number of closely related taxa. In this study, we conduct multiple experiments by varying taxon sampling and comparing FBP and TBE support values on different phylogenetic depths, using empirical datasets. Our results show that the main critique of TBE stands in extreme cases with shallow branches and highly unbalanced sampling among clades, but that TBE is still robust in most cases, while FBP is inescapably negatively impacted by high taxon sampling. We suggest guidelines and good practices in TBE (and FBP) computing and interpretation.

A transcriptome-based phylogeny for Polynoidae (Annelida: Aphroditiformia)

Polynoidae is the most diverse radiation of Aphroditiformia and one of the most successful groups of all Annelida in terms of diversity and habitats colonized. With such an unmatched diversity, phylogenetic investigations have struggled to understand their evolutionary relationships. Previous phylogenetic analyses have slowly increased taxon sampling and employed methodologies, but despite their diversity and biological importance, large genomic sampling is limited. To investigate the internal relationships within Polynoidae, we conducted the first phylogenomic analyses of the group based on 12 transcriptomes collected from species inhabiting a broad array of habitats, including shallow and deep waters, as well as hydrothermal vents, anchialine caves and the midwater. Our phylogenomic analyses of Polynoidae recovered congruent tree topologies representing the clades Polynoinae, Macellicephalinae and Lepidonotopodinae. Members of Polynoinae and Macellicephalinae clustered in well-supported and independent clades. In contrast, Lepidonotopodinae taxa were always recovered nested within Macellicephalinae. Though our sampling only covers a small proportion of the species known for Polynoidae, our results provide a robust phylogenomic framework to build from, emphasizing previously hypothesized relationships between Macellicephalinae and Lepidonotopodinae taxa, while providing new insights on the origin of enigmatic cave and pelagic lineages.

A molecular phylogeny of Noctuini (Lepidoptera: Noctuidae: Noctuinae)

Abstract The tribe Noctuini is comprised over 520 species; many are economically important species that impact human agriculture. Despite their diversity and relevance, relationships of Noctuini have been difficult to resolve. There have been extensive morphological revisions of some of these taxa (e.g., Agrotis Ochsenheimer, Euxoa Hübner); however, there are no studies that focus exclusively on the phylogenetic relationships of the Noctuini. Currently, Noctuini are separated into 2 subtribes, Agrotina and Noctuina. In this study, we tested previous classification schemes with 2 analyses. The total evidence analysis utilized 3 loci for 3 outgroup taxa and 54 noctuine species. Using museum specimens, we collected data from cytochrome oxidase I (COI), Dopa Decarboxylase (DDC), and Elongation factor 1-α (EF1-α) to generate a dataset of 1,378 base pairs (bp) for a total evidence approach. We also used previously published COI sequences for 626 species, resulting in a matrix of 690 bp, termed “the barcode analysis.” We used both Maximum Likelihood and Bayesian approaches for the total evidence analysis, and ML for the barcode analysis. In both sets of results, we found equivocal support for monophyletic Agrotina and Noctuina. We found strong support for smaller, well-described genera (e.g., Spaelotis), but poor support for large genera such as Euxoa, Feltia Walker, and Agrotis. It is likely that a combination of limited taxon/gene sampling, limited gene choice, and the rapid evolution of these species resulted in a lack of phylogenetic resolution in the total evidence topologies. Based on these results, we recommend increased taxon sampling and inclusion of loci that target these rapidly evolving lineages to achieve a better understanding of the phylogeny of Noctuini and its genera.

Killer Knots: Molecular Evolution of Inhibitor Cystine Knot Toxins in Wandering Spiders (Araneae: Ctenidae).

Venom expressed by the nearly 50,000 species of spiders on Earth largely remains an untapped reservoir of a diverse array of biomolecules with potential for pharmacological and agricultural applications. A large fraction of the noxious components of spider venoms are a functionally diverse family of structurally related polypeptides with an inhibitor cystine knot (ICK) motif. The cysteine-rich nature of these toxins makes structural elucidation difficult, and most studies have focused on venom components from the small handful of medically relevant spider species such as the highly aggressive Brazilian wandering spider Phoneutria nigriventer. To alleviate difficulties associated with the study of ICK toxins in spiders, we devised a comprehensive approach to explore the evolutionary patterns that have shaped ICK functional diversification using venom gland transcriptomes and proteomes from phylogenetically distinct lineages of wandering spiders and their close relatives. We identified 626 unique ICK toxins belonging to seven topological elaborations. Phylogenetic tests of episodic diversification revealed distinct regions between cysteine residues that demonstrated differential evidence of positive or negative selection, which may have structural implications towards the specificity and efficacy of these toxins. Increased taxon sampling and whole genome sequencing will provide invaluable insights to further understand the evolutionary processes that have given rise to this diverse class of toxins.

A Sister-Group Comparison of Branching and Pedicellariae in Brittlestars (Echinodermata: Ophiuroidea).

Branching of arms and presence of pedicellariae are characters among ophiuroids found only in the order Euryalida (snakestars and basketstars). Family Asteronychidae has neither character; family Euryalidae has 2 small clades with branched arms; and family Gorgonocephalidae has all species with pedicellariae and 3 or 4 clades with branched arms. Despite the rare occurrence of these characters in the Ophiuroidea, they might be key adaptations within the Euryalida that have led to relatively high diversification. Sister-group comparison of the distribution of these 2 characters among taxa indicates that neither character alone explains diversity patterns within the order. In particular, branching restricted to the tips of arms seems not strongly adaptive, probably for the lack of integration of basal forks with the disc. On the other hand, 2 clades of gorgonocephalids with basal branching exceed their snakestar sister groups in numbers of species, indicating an advantage of branching within the family. Unfortunately, the analysis cannot benefit from statistics, for at least 5 independent comparisons are required for a one-tailed sign test. Because branching and pedicellariae are probably not independent variables, future sister-group comparisons should be done only within the Gorgonocephalidae once clade structure is better clarified with increased taxon sampling (10 currently missing genera) and resolution of intra-generic inconsistencies in the most recent cladograms available. Branching might confer upon gorgonocephalid basketstars a more efficient use of pedicellariae for upstream capture of zooplankton over their snakestar relatives as well as over the Euryalidae, which retain ancestral downstream capture by mucus-laden podia.

An Evolutionary Framework of Acanthaceae Based on Transcriptomes and Genome Skims

Abstract— Acanthaceae is a family of tropical flowering plants with approximately 4900 species. Despite remarkable variation in morphological traits, research on patterns of character evolution has been limited by uncertain relationships among some of the major lineages. We sampled 16 taxa from these major lineages to estimate a phylogenomic framework using a combination of five newly sequenced shotgun genome skims plus seven new and four publicly available transcriptomes. We used OrthoFinder2 to infer a species tree with strong branch support. Except for the placement of Crabbea, our results corroborate the most recent chloroplast and nrITS sequence-based topology. Of 587 single copy loci, 10 were recovered for all 16 species; a RAxML tree estimated from these 10 loci resulted in the same topology as other datasets assembled in this study, with the exception of relationships among three sampled species of Barleria; however, branch support was lower compared to the tree reconstructed using more data. ABBA-BABA tests were conducted to investigate patterns of introgression involving Crabbea; few nucleotides supported alternative topologies. SplitsTree networks of the 587 loci and 6136 orthogroup trees revealed conflict among the branches leading to Andrographideae, Whitfieldieae, and Neuracanthus. A principal components analysis in treespace found no distinct clusters of trees. Our results based on combined genome skim and transcriptome sequences strongly corroborate the previously published chloroplast and nr-ITS-based phylogeny of Acanthaceae with increased resolution among Barlerieae, Andrographideae, Whitfieldieae, and Neuracanthus. This advance in our knowledge of Acanthaceae relationships will allow us to investigate character evolution and other phenomena within this diverse group of plants in studies with increased taxon sampling.

Re‐assessing the phylogenetic status and evolutionary relationship of Forest Owlet (Athene blewitti (Hume 1873)) using genomic data

Phylogenetic relationships are often challenging to resolve in recent/younger lineages when only a few loci are used. Ultra‐conserved elements (UCEs) are highly conserved regions across taxa that help resolve shallow and deep divergences. We utilized UCEs harvested from whole genomes to assess the phylogenetic position and taxonomic affiliation of an endangered endemic owlet in the family Strigidae, the Forest Owlet Athene blewitti. The taxonomic placement of this species has been revised multiple times. A multigene study attempted to address the question but showed a discrepancy across datasets in its placement of species within the genus Athene. We assembled a dataset of 5018 nuclear UCE loci with increased taxon sampling. Forest Owlet was found to be an early split from the Athene clade but sister to other Athene, consistently across three approaches – maximum likelihood, Bayesian and the multispecies coalescence. Divergence dating using fossil calibrations suggests that the Athene lineage split from its ancestor about 7.6 mya, and Forest Owlet diverged about 5.2 mya. This estimate is consistent with previous multigene approaches and confirms the role of climate‐aridification across the Indian peninsula in species diversification. Despite osteological differences from other Athene, we suggest placement of the Forest Owlet as a member of the Athene to emphasize its evolutionary relationship.

RE-EVALUATION OF SYMPOVENTURIACEAE.

Abstract Sympoventuriaceae (Venturiales, Dothideomycetes) comprises genera including saprophytes, endophytes, plant pathogens, as well as important animal or human opportunistic pathogens with diverse ecologies and wide geographical distributions. Although the taxonomy of Sympoventuriaceae has been well studied, generic boundaries within the family remain poorly resolved due to the lack of type materials and molecular data. To address this issue and establish a more stable and reliable classification system in Sympoventuriaceae, we performed multi-locus phylogenetic analyses using sequence data of seven genes (SSU, ITS, LSU, act1, tub2, tef1 and rpb2) with increased taxon sampling and morphological analysis. The molecular data combined with detailed morphological studies of 143 taxa resolved 22 genera within the family, including one new genus, eight new species, five new combinations and one new name. Finally, we further investigated the evolutionary history of Sympoventuriaceae by reconstructing patterns of lifestyle diversification, indicating the ancestral state to be saprophytic, with transitions to endophytic, animal or human opportunistic and plant pathogens. Citation: Wei TP, Zhang H, Zeng XY, et al. 2022. Re-evaluation of Sympoventuriaceae. Persoonia 48: 219-260. https://doi.org/10.3767/persoonia.2022.48.07.. Effectively published online: 17 June 2022 [Received: 2 February 2022; Accepted: 27 April 2022].

Re-evaluation of Sympoventuriaceae

Sympoventuriaceae ( Venturiales, Dothideomycetes) comprises genera including saprophytes, endophytes, plant pathogens, as well as important animal or human opportunistic pathogens with diverse ecologies and wide geographical distributions. Although the taxonomy of Sympoventuriaceae has been well studied, generic boundaries within the family remain poorly resolved due to the lack of type materials and molecular data. To address this issue and establish a more stable and reliable classification system in Sympoventuriaceae, we performed multilocus phylogenetic analyses using sequence data of seven genes (SSU, ITS, LSU, act1, tub2, tef1 and rpb2) with increased taxon sampling and morphological analysis. The molecular data combined with detailed morphological studies of 143 taxa resolved 22 genera within the family, including one new genus, eight new species, five new combinations and one new name. Finally, we further investigated the evolutionary history of Sympoventuriaceae by reconstructing patterns of lifestyle diversification, indicating the ancestral state to be saprophytic, with transitions to endophytic, animal or human opportunistic and plant pathogens.

Phylogeny of Strombidae (Gastropoda) Based on Mitochondrial Genomes

The marine gastropod Strombidae is widely distributed in tropical and subtropical regions all over the world and possesses high morphological diversity. In order to better understand how morphological characteristics evolved within Strombidae, a robust phylogenetic framework is needed. In the present study, the complete mitochondrial genomes ofLentigo lentiginosus,Euprotomus aratrum, andCanarium labiatumwere sequenced. The three newly sequenced mt genomes contained 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and several non-coding regions, indicating a similar pattern with respect to genome size, gene order, and nucleotide composition compared with those of other strombids reported before. Two different datasets derived from mitochondrial genes were constructed to resolve the internal phylogenetic relationships of Stromboidea and Strombidae. Within Stromboidea, the sister group formed by Clade I [Rostellariidae + (Seraphsidae + Strombidae)] and Clade II [Xenophoridae + (Struthiolariidae + Aporrhaidae)] were fully recovered and supported by morphological synapomorphies as previously suggested. The phylogenetic positions ofL. lentiginosus,E. aratrum, andC. labiatumwere confirmed within Strombidae, and several morphological similarities were observed corresponding to the present phylogeny. A correlation between strombids speciation events and paleoclimate change was presumed. Our results indicate that complete mt genomes would be a promising tool to reconstruct a robust phylogeny of Strombidae with an increased taxon sampling in the future.

Detecting and Removing Sample Contamination in Phylogenomic Data: An Example and its Implications for Cicadidae Phylogeny (Insecta: Hemiptera).

Contamination of a genetic sample with DNA from one or more nontarget species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and next-generation sequencing studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on the detection of bimodal distributions of patristic distances across gene trees. When contamination occurs between samples within a data set, a comparison between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. This new method does not rely on a priori knowledge of taxon relatedness nor does it determine the causes(s) of the contamination. Exclusion of putatively contaminated loci from a data set generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination. While the anchored hybrid enrichment markers used here, which target hemipteroid taxa, proved effective in resolving deep and shallow level Cicadidae relationships in aggregate, individual markers contained inadequate phylogenetic signal, in part probably due to short length. The cleaned data set, consisting of 429 loci, from 90 genera representing 44 of 56 current Cicadidae tribes, supported three of the four sampled Cicadidae subfamilies in concatenated-matrix maximum likelihood (ML) and multispecies coalescent-based species tree analyses, with the fourth subfamily weakly supported in the ML trees. No well-supported patterns from previous family-level Sanger sequencing studies of Cicadidae phylogeny were contradicted. One taxon (Aragualna plenalinea) did not fall with its current subfamily in the genetic tree, and this genus and its tribe Aragualnini is reclassified to Tibicininae following morphological re-examination. Only subtle differences were observed in trees after the removal of loci for which divergent base frequencies were detected. Greater success may be achieved by increased taxon sampling and developing a probe set targeting a more recent common ancestor and longer loci. Searches for contamination are an essential step in phylogenomic analyses of all kinds and our pipeline is an effective solution. [Auchenorrhyncha; base-composition bias; Cicadidae; Cicadoidea; Hemiptera; phylogenetic conflict.].

Huntsman spider phylogeny informs evolution of life history, egg sacs, and morphology

Huntsman spiders (Araneae: Sparassidae) are among the most speciose spider families, with a near-worldwide distribution, diverse habitats, equally diverse life histories, and five prolonged subsocial species. Previous molecular phylogenies have focused on individual subfamilies or clades. Here, we provide a phylogenetic inference with broadened sampling from 37 genera and eight of the eleven sparassid subfamilies. We increased taxon sampling by including species not previously sequenced and most available data on GenBank of two mitochondrial (COI, 16S rRNA) and two nuclear (H3, 28S rRNA) genes for a total of 262 ingroup taxa and nine outgroup taxa. Divergence dates were estimated using outgroup fossil taxa suggesting the sparassids evolved ∼ 100 mya (stem age), while the clade containing all subfamilies except Sparianthinae evolved ∼ 90 mya (stem age). Using a stochastic map approach with 40 species, this is the first sparassid phylogeny to incorporate extensive biology and life history data. Correlations of life history traits with solitary, subsocial, and prolonged subsocial behavior are examined using the D-test. Sparassid sociality is associated with life history traits that allow developing spiders to remain in their natal retreat longer (e.g., larger permanent retreats, plastered egg sacs, and ontogenetically delayed foraging), but is unrelated to body size or lifespan. Detailed morphological scoring of the endemic Australian subfamily Deleninae contextualizes existing molecular data, including in the Isopeda-Holconia-Isopedella complex. This study supports the monophyly of many major lineages, including for the first time, the Sparianthinae, but indicates multiple clades (Sparassinae and Eusparassinae) are paraphyletic and need further revision.

Exploring mitogenome evolution in Branchiopoda (Crustacea) lineages reveals gene order rearrangements in Cladocera

The class Branchiopoda, whose origin dates back to Cambrian, includes ~ 1200 species which mainly occupy freshwater habitats. The phylogeny and systematics of the class have been debated for long time, until recent phylogenomic analyses allowed to better clarify the relationships among major clades. Based on these data, the clade Anostraca (fairy and brine shrimps) is sister to all other branchiopods, and the Notostraca (tadpole shrimps) results as sister group to Diplostraca, which includes Laevicaudata + Spinicaudata (clam shrimps) and Cladoceromorpha (water fleas + Cyclestherida). In the present analysis, thanks to an increased taxon sampling, a complex picture emerges. Most of the analyzed mitogenomes show the Pancrustacea gene order while in several other taxa they are found rearranged. These rearrangements, though, occur unevenly among taxa, most of them being found in Cladocera, and their taxonomic distribution does not agree with the phylogeny. Our data also seems to suggest the possibility of potentially homoplastic, alternative gene order within Daphniidae.

Providing a phylogenetic framework for trait-based analyses in brown algae: Phylogenomic tree inferred from 32 nuclear protein-coding sequences

In the study of the evolution of biological complexity, a reliable phylogenetic framework is needed. Many attempts have been made to resolve phylogenetic relationships between higher groups (i.e., interordinal) of brown algae (Phaeophyceae) based on molecular evidence, but most of these relationships remain unclear. Analyses based on small multi-gene data (including chloroplast, mitochondrial and nuclear sequences) have yielded inconclusive and sometimes contradictory results. To address this problem, we have analyzed 32 nuclear protein-coding sequences in 39 Phaeophycean species belonging to eight orders. The resulting nuclear-based phylogenomic trees provide virtually full support for the phylogenetic relationships within the studied taxa, with few exceptions. The relationships largely confirm phylogenetic trees based on nuclear, chloroplast and mitochondrial sequences, except for the placement of the Sphacelariales with weak bootstrap support. Our study indicates that nuclear protein-coding sequences provide significant support to conclusively resolve phylogenetic relationships among Phaeophyceae, and may be a powerful approach to fully resolve interordinal relationships with increased taxon sampling.

Evolution of a novel cell type in Dictyostelia required gene duplication of a cudA-like transcription factor

SummaryThe evolution of novel cell types has been proposed to result from duplication of gene regulatory networks, but proven examples are rare. In addition to stalk cells and spores that make up the fruiting bodies of three major groups of Dictyostelia, those in group 4 additionally evolved basal disc and cup cells that respectively anchor the stalk to the substratum and the spore mass to the stalk. We noted a putative group-4-specific duplication of a cudA-like transcription factor (TF) in a comparative analysis of group-representative genomes. Using increased taxon sampling, we here confirmed that this TF, cdl1, duplicated into cdl1a and cdl1b in the common ancestor to group 4. cdl1a, but not cdl1b, showed signatures of positive selection, indicative of functional innovation. Deletion of cdl1a in Dictyostelium discoideum resulted in fruiting bodies with sagging spore heads that lacked the supporting cup cells and expression of cup-specific genes. Deletion of cdl1b resulted in thinner fruiting body stalks, while a cdl1b−cdl1a− double knockout showed more severe stalk defects, suggesting an ancestral role of cdl1 in stalk formation. This was confirmed in a closely related non-group 4 species, Polysphondylium violaceum, where cdl1 knockout caused defective stalk formation. These data indicate that the group-specific duplication of cdl1 and subsequent diversification of cdl1a played a pivotal role in the evolution of a novel somatic cell type in group 4 Dictyostelia.

Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements

BackgroundDivergence time estimation is fundamental to understanding many aspects of the evolution of organisms, such as character evolution, diversification, and biogeography. With the development of sequence technology, improved analytical methods, and knowledge of fossils for calibration, it is possible to obtain robust molecular dating results. However, while phylogenomic datasets show great promise in phylogenetic estimation, the best ways to leverage the large amounts of data for divergence time estimation has not been well explored. A potential solution is to focus on a subset of data for divergence time estimation, which can significantly reduce the computational burdens and avoid problems with data heterogeneity that may bias results.ResultsIn this study, we obtained thousands of ultraconserved elements (UCEs) from 130 extant galliform taxa, including representatives of all genera, to determine the divergence times throughout galliform history. We tested the effects of different “gene shopping” schemes on divergence time estimation using a carefully, and previously validated, set of fossils. Our results found commonly used clock-like schemes may not be suitable for UCE dating (or other data types) where some loci have little information. We suggest use of partitioning (e.g., PartitionFinder) and selection of tree-like partitions may be good strategies to select a subset of data for divergence time estimation from UCEs. Our galliform time tree is largely consistent with other molecular clock studies of mitochondrial and nuclear loci. With our increased taxon sampling, a well-resolved topology, carefully vetted fossil calibrations, and suitable molecular dating methods, we obtained a high quality galliform time tree.ConclusionsWe provide a robust galliform backbone time tree that can be combined with more fossil records to further facilitate our understanding of the evolution of Galliformes and can be used as a resource for comparative and biogeographic studies in this group.