Early divergence dates of demosponges based on mitogenomics and evaluated fossil calibrations

Ma, Jinshuang; Yang, Qun

doi:10.1016/j.palwor.2015.03.004

Cited by 18 publications

(10 citation statements)

References 52 publications

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“…As the origin time of the FBD process should be greater than the maximum value of the root age with a log-normal distribution [25], we obtained different divergence times for Heteroscleromorpha/Keratosa in both analyses with the root age affecting the divergence time (see Table 1, Figure 1, node R). Previous ages estimated for crown-group Demospongiae, using different software, clock-model settings, and taxon sets, varied between 657-872 Ma [30,47,50,60], which is in the range of both of our analyses (see Table 1, Figure 1 and Suppl. Figure 4, node R).…”

Section: Implications For Divergence Time Estimates For Heterosclerommentioning

confidence: 74%

“…The fossilized birth-death model [25,45] as implemented in BEAST v.2.4.3 [46] was used with the following settings for both analyses: An uncorrelated relaxed molecular clock model was chosen using default settings. No partitioning was applied on the data matrix as it had no influence on the divergence time estimation in [47] (see Table 4 and Figure 3 in [47]). For the molecular sequence data, a Gamma Site model with the JTT amino acid substitution model [48] was specified.…”

Section: Fbd Model Settingsmentioning

confidence: 99%

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Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

Schuster¹,

Vargas²,

Knapp

et al. 2017

Preprint

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Approximately 80% of all recent sponge species belong to the class Demospongiae. Yet, despite their diversity and importance, accurate divergence times are still unknown for most demosponge clades. The estimation of demosponge divergence time is key to answering fundamental questions like e.g. the origin of Demospongiae, their diversification and historical biogeography. Molecular sequence data alone is not informative on an absolute time scale, and therefore needs to be "calibrated" with additional data such as fossils. Here, we apply the fossilized birth-death model (FBD), which has the advantage, compared to strict node dating with the oldest fossil occurrences, that it allows for the inclusion of young and old fossils in the analysis of divergence time. We use desma-bearing sponges, a diverse group of demosponges that form rigid skeletons and have a rich and continuous fossil record dating back to the Cambrian (⇠500 Ma), aiming to date the demosponge radiation and constrain the timing of key evolutionary events, like the transition from marine to freshwater habitats. To do so, we assembled mitochondrial genomes of six desma-bearing demosponges from size-selected reducedrepresentation genomic libraries and apply a fossilized birth-death model including 30 fossils and 33 complete demosponge mitochondrial genomes to infer a dated phylogeny of Demospongiae. Our study supports a Neoproterozoic origin of Demospongiae. Novel age estimates for the split of freshwater and marine sponges dating back to the Carboniferous and the previously assumed Recent (⇠18 Ma) diversification of freshwater sponges is supported. Moreover, we provide detailed age estimates for a possible diversification of Tetractinellidae (⇠315 Ma), the Astrophorina (⇠240 Ma), the Spirophorina (⇠120 Ma) and the family Corallistidae (⇠188 Ma) all of which are considered as key groups for dating the Demospongiae, due to their extraordinary rich and continuous fossil history.

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Section: Implications For Divergence Time Estimates For Heterosclerommentioning

confidence: 74%

Section: Fbd Model Settingsmentioning

confidence: 99%

Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

Schuster¹,

Vargas²,

Knapp

et al. 2017

Preprint

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“…Recent molecular phylogenetic studies support the common sense view that sponges (Porifera) are the sister group to all other animals [63,64]. Relaxed molecular clocks put the origin of crown-group demosponges 872-657 Ma (across studies) [65] consistent with biomarkers ∼660-640 Ma [58][59][60], but put silicification and spicule production later at 648-616 Ma [66]. Hence, the gap to the first widely accepted fossil sponges in the early Cambrian ∼535 Ma [67][68][69] could be partly due to poor preservation potential.…”

Section: Sessile Animals and Benthic Matsmentioning

confidence: 89%

The effects of marine eukaryote evolution on phosphorus, carbon and oxygen cycling across the Proterozoic–Phanerozoic transition

Lenton

Daines

2018

Emerging Topics in Life Sciences

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A ‘Neoproterozoic oxygenation event’ is widely invoked as a causal factor in animal evolution, and often attributed to abiotic causes such as post-glacial pulses of phosphorus weathering. However, recent evidence suggests a series of transient ocean oxygenation events ∼660–520 Ma, which do not fit the simple model of a monotonic rise in atmospheric oxygen (pO2). Hence, we consider mechanisms by which the evolution of marine eukaryotes, coupled with biogeochemical and ecological feedbacks, potentially between alternate stable states, could have caused changes in ocean carbon cycling and redox state, phosphorus cycling and atmospheric pO2. We argue that the late Tonian ocean ∼750 Ma was dominated by rapid microbial cycling of dissolved organic matter (DOM) with elevated nutrient (P) levels due to inefficient removal of organic matter to sediments. We suggest the abrupt onset of the eukaryotic algal biomarker record ∼660–640 Ma was linked to an escalation of protozoan predation, which created a ‘biological pump’ of sinking particulate organic matter (POM). The resultant transfer of organic carbon (Corg) and phosphorus to sediments was strengthened by subsequent eukaryotic innovations, including the advent of sessile benthic animals and mobile burrowing animals. Thus, each phase of eukaryote evolution tended to lower P levels and oxygenate the ocean on ∼104 year timescales, but by decreasing Corg/P burial ratios, tended to lower atmospheric pO2 and deoxygenate the ocean again on ∼106 year timescales. This can help explain the transient nature and ∼106 year duration of oceanic oxygenation events through the Cryogenian–Ediacaran–Cambrian.

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“…In addition to resolving phylogenetic relationships among major lineages (orders) of heteroscromorphs, we provide molecular clock estimates for the divergences among them. While several molecular clock studies using demosponge mt-genome data have been recently conducted (Ma and Yang, 2016;Schuster et al, 2018b) they used much smaller datasets of mitogenomic sequences. Paradoxically, Schuster et al (2018) study was also based on a clearly erroneous phylogenetic tree of demosponge relationships with marine haplosclerids placed deep within the G4 clade (compare to Lavrov et al, 2008;Simion et al, 2017), which made most of their time estimates a priori misleading.…”

Section: Timing Molecular Phylogenymentioning

confidence: 99%

“…mtDNA sequences are well suited for phylogenetic analysis in Demospongiae as they contain a large amount of data, have a relatively low rate of nucleotide substitutions, and are homogeneous in nucleotide composition (Lavrov and Lang, 2005a;Lavrov et al, 2008;Ma and Yang, 2016;Schuster et al, 2017). Furthermore, in addition to sequence data, mitochondrial gene arrangements can be used to support or refute phylogenetic relationships (Boore and Brown, 1998;Lavrov and Lang, 2005a).…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic relationships of heteroscleromorph demosponges and the affinity of the genusMyceliospongia(Demospongiaeincertae sedis)

Lavrov

Maldonado

Pérez

et al. 2019

Preprint

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Class Demospongiae -the largest in the phylum Porifera (Sponges)encompasses 7,581 accepted species across the three recognized subclasses: Keratosa, Verongimorpha, and Heteroscleromorpha. The latter subclass contains the majority of demosponge species and was previously subdivided into subclasses Heteroscleromorpha sensu stricto and Haploscleromorpha. The current classification of demosponges is the result of nearly three decades of molecular studies that culminated in a formal proposal of a revised taxonomy (Morrow and Cardenas, 2015). However, because most of the molecular work utilized partial sequences of nuclear rRNA genes, this classification scheme needs to be tested by additional molecular markers. Here we used sequences and gene order data from complete or nearly complete mitochondrial genomes of 117 demosponges (including 60 new sequences determined for this study and 6 assembled from public sources) and three additional partial mt-genomes to test the phylogenetic relationships within demosponges in general and Heteroscleromorpha sensu stricto in particular. We also investigated the phylogenetic position of Myceliospongia araneosa -a highly unusual demosponge without spicules and spongin fibers, currently classified as Demospongiae incertae sedis.Our results support the sub-class relationship within demosponges and reveal four main clades in Heteroscleromorpha sensu stricto: Clade 1 composed of Spongillida, Sphaerocladina, and Scopalinida; Clade 2 composed of Axinellida, Biemnida, Bubarida; Clade 3 composed of Tetractinellida and "Rhizomorina" lithistids; and Clade 4 composed of Agelasida, Polymastida, Clionaida, Suberitida, Poecilosclerida, and Tethyida. The four clades appear to be natural lineages that unite previously defined taxonomic orders. Therefore, if those clades are to be systematically interpreted, they will have the rank of superorders (hence S1-S4). We inferred the following relationships among the newly defined clades: (S1(S2(S3+S4))). Analysis of molecular data from Myceliospongia araneosa -first from this species/genus -placed it in S3 as a sister group to Microscleroderma sp. and Leiodermatium sp.("Rhizomorina"). Molecular clock analysis indicated that the origin of the Heteroscleromorpha sensu stricto as well as the basal split in this group between S1 and the rest of the superorder go back to Cambrian, while the divergences among the three other superorders occurred in Ordovician (with the 95% standard variation from Late Cambrian to Early Silurian). Furthermore most of the proposed orders within Heteroscleromorpha appear to have middle Paleozoic origin, while crown groups within order date mostly to Paleozoic to Mesozoic transition. We propose that these molecular clock estimates can be used to readjust ranks for some of the higher taxa within Heteroscleromorpha.In addition to phylogenetic information, we found several unusual mtgenomic features among the sampled species, broadening our understanding of mitochondrial genome evolution in this group and animals in general. In particu...

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Early divergence dates of demosponges based on mitogenomics and evaluated fossil calibrations

Cited by 18 publications

References 52 publications

Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

The effects of marine eukaryote evolution on phosphorus, carbon and oxygen cycling across the Proterozoic–Phanerozoic transition

Phylogenetic relationships of heteroscleromorph demosponges and the affinity of the genusMyceliospongia(Demospongiaeincertae sedis)

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