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16 Oct 2019
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What do ossification sequences tell us about the origin of extant amphibians?

The origins of Lissamphibia

Recommended by based on reviews by Jennifer Olori and 2 anonymous reviewers

Among living vertebrates, there is broad consensus that living tetrapods consist of amphibians and amniotes. Crown clade Lissamphibia contains frogs (Anura), salamanders (Urodela) and caecilians (Gymnophiona); Amniota contains Sauropsida (reptiles including birds) and Synapsida (mammals). Within Lissamphibia, most studies place frogs and salamanders in a clade together to the exclusion of caecilians (see Pyron & Wiens 2011). Among fossils, there are a number of amphibian and amphibian-like taxa generally placed in Temnospondyli and Lepospondyli. In contrast to the tree of living tetrapods, affinities of these fossils to some or all of the three extant lissamphibian groups have proven to be much harder to resolve. For example, temnospondyls might be stem tetrapods and lissamphibians a derived group of lepospondyls; alternatively, temnospondyls might be closer to the clade of frogs and salamanders, and lepospondyls to caecilians (compare Laurin et al. 2019: fig. 1d vs. 1f). Here, in order to assess which of these and other mutually exclusive topologies is optimal, Laurin et al. (2019) extract phylogenetic information from developmental sequences, in particular ossification. Several major differences in ossification are known to distinguish vertebrate clades. For example, due to their short intrauterine development and need to climb from the reproductive tract into the pouch, marsupial mammals famously accelerate ossification of their facial skeleton and forelimb; in contrast to placentals, newborn marsupials can climb, smell & suck before they have much in the way of lungs, kidneys, or hindlimbs (Smith 2001). Divergences among living and fossil amphibian groups are likely pre-Triassic (San Mauro 2010; Pyron 2011), much older than a Jurassic split between marsupials and placentals (Tarver et al. 2016), and the quality of the fossil record generally decreases with ever-older divergences. Nonetheless, there are a number of well-preserved examples of "amphibian"-grade tetrapods representing distinct ontogenetic stages (Schoch 2003, 2004; Schoch and Witzmann 2009; Olori 2013; Werneburg 2018; among others), all amenable to analysis of ossification sequences. Putting together a phylogenetic dataset based on ossification sequences is not trivial; sequences are not static features apparent on individual specimens. Rather, one needs multiple specimens representing discrete developmental stages for each taxon to be compared, meaning that sequences are usually available for only a few characters. Laurin et al. (2019) have nonetheless put together the most exhaustive matrix of tetrapod sequences so far, with taxon coverage ranging from 62 genera for appendicular characters to 107 for one of their cranial datasets, each sampling between 4-8 characters (Laurin et al. 2019: table 1). The small number of characters means that simply applying an optimality criterion (such as parsimony) is unlikely to resolve most nodes; treespace is too flat to be able to offer optimal peaks up which a search algorithm might climb. However, Laurin et al. (2019) were able to test each of the main competing hypotheses, defined a priori as a branching topology, given their ossification sequence dataset and a likelihood optimality criterion. Their most consistent result comes from their cranial ossification sequences and supports their "LH", or lepospondyl hypothesis (Laurin et al. 2019: fig. 1d). That is, relative to extinct, "amphibian"-grade taxa, Lissamphibia is monophyletic and nested within lepospondyls. Compared to mammals and birds (including dinosaurs), crown amphibian branches of the Tree of Life are exceptionally old. Each lissamphibian clade likely had diverged during Permian times (Marjanovic & Laurin 2008) and the crown group itself may even date to the Carboniferous (Pyron 2011). In contrast to mammoths and moas, no ancient DNA or collagen sequences are going to be available from >300 million-year-old fossils like the lepospondyl *Hyloplesion* (Olori 2013), although recently published methods for incorporating genomic signal from extant taxa (Beck & Baillie 2018; Asher et al. 2019) into studies of fossils could also be applied to these ancient divergences among amphibian-grade tetrapods. Ossification sequences represent another important, additional source of data with which to test the conclusion of Laurin et al. (2019) that monophyletic Lissamphibians shared a common ancestor with lepospondyls, among other hypotheses. **References** Asher, R. J., Smith, M. R., Rankin, A., & Emry, R. J. (2019). Congruence, fossils and the evolutionary tree of rodents and lagomorphs. Royal Society Open Science, 6(7), 190387. doi: [ 10.1098/rsos.190387 ]( 10.1098/rsos.190387 ) Beck, R. M. D., & Baillie, C. (2018). Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny. Proceedings of the Royal Society B: Biological Sciences, 285(1893), 20181632. doi: [ 10.1098/rspb.2018.1632]( 10.1098/rspb.2018.1632) Laurin, M., Lapauze, O., & Marjanović, D. (2019). What do ossification sequences tell us about the origin of extant amphibians? BioRxiv, 352609, ver. 4 peer-reviewed by PCI Paleo. doi: [ 10.1101/352609]( 10.1101/352609) Marjanović, D., & Laurin, M. (2008). Assessing confidence intervals for stratigraphic ranges of higher taxa: the case of Lissamphibia. Acta Palaeontologica Polonica, 53(3), 413–432. doi: [ 10.4202/app.2008.0305]( 10.4202/app.2008.0305) Olori, J. C. (2013). Ontogenetic sequence reconstruction and sequence polymorphism in extinct taxa: an example using early tetrapods (Tetrapoda: Lepospondyli). Paleobiology, 39(3), 400–428. doi: [ 10.1666/12031]( 10.1666/12031) Pyron, R. A. (2011). Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Systematic Biology, 60(4), 466–481. doi: [ 10.1093/sysbio/syr047]( 10.1093/sysbio/syr047) Pyron, R. A., & Wiens, J. J. (2011). A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians. Molecular Phylogenetics and Evolution, 61(2), 543–583. doi: [ 10.1016/j.ympev.2011.06.012]( 10.1016/j.ympev.2011.06.012) San Mauro, D. (2010). A multilocus timescale for the origin of extant amphibians. Molecular Phylogenetics and Evolution, 56(2), 554–561. doi: [ 10.1016/j.ympev.2010.04.019]( 10.1016/j.ympev.2010.04.019) Schoch, R. R. (2003). Early larval ontogeny of the Permo-Carboniferous temnospondyl *Sclerocephalus*. Palaeontology, 46(5), 1055–1072. doi: [ 10.1111/1475-4983.00333]( 10.1111/1475-4983.00333) Schoch, R. R. (2004). Skeleton formation in the Branchiosauridae: a case study in comparing ontogenetic trajectories. Journal of Vertebrate Paleontology, 24(2), 309–319. doi: [ 10.1671/1950]( 10.1671/1950) Schoch, R. R., & Witzmann, F. (2009). Osteology and relationships of the temnospondyl genus *Sclerocephalus*. Zoological Journal of the Linnean Society, 157(1), 135–168. doi: [ 10.1111/j.1096-3642.2009.00535.x]( 10.1111/j.1096-3642.2009.00535.x) Smith, K. K. (2001). Heterochrony revisited: the evolution of developmental sequences. Biological Journal of the Linnean Society, 73(2), 169–186. doi: [ 10.1111/j.1095-8312.2001.tb01355.x]( 10.1111/j.1095-8312.2001.tb01355.x) Tarver, J. E., dos Reis, M., Mirarab, S., Moran, R. J., Parker, S., O’Reilly, J. E., & Pisani, D. (2016). The interrelationships of placental mammals and the limits of phylogenetic inference. Genome Biology and Evolution, 8(2), 330–344. doi: [ 10.1093/gbe/evv261]( 10.1093/gbe/evv261) Werneburg, R. (2018). Earliest “nursery ground” of temnospondyl amphibians in the Permian. Semana, 32, 3–42.

What do ossification sequences tell us about the origin of extant amphibians?Michel Laurin, Océane Lapauze, David Marjanović<p>The origin of extant amphibians has been studied using several sources of data and methods, including phylogenetic analyses of morphological data, molecular dating, stratigraphic data, and integration of ossification sequence data, but a consen...Evo-Devo, Phylogenetics, Systematics, Vertebrate paleontologyRobert Asher2018-06-22 08:21:31 View
22 Sep 2018
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Palaeobiological inferences based on long bone epiphyseal and diaphyseal structure - the forelimb of xenarthrans (Mammalia)

Inferences on the lifestyle of fossil xenarthrans based on limb long bone inner structure

Recommended by based on reviews by Andrew Pitsillides and 1 anonymous reviewer

Bone inner structure bears a strong functional signal and can be used in paleontology to make inferences about the ecology of fossil forms. The increasing use of microtomography enables to analyze both cortical and trabecular features in three dimensions, and thus in long bones to investigate the diaphyseal and epiphyseal structures. Moreover, this can now be done through quantitative, and not only qualitative analyses. Studies focusing on the diaphyseal inner structure (cortical bone and sometimes also spongious bone) of long bones are rather numerous, but essentially based on 2D sections. It is only recently that analyses of the whole diaphyseal structure have been investigated. Studies on the trabecular architecture are much rarer.

Amson & Nyakatura (2018) propose a comparative quantitative analysis combining parameters of the epiphyseal trabecular architecture and of the diaphyseal structure, using phylogenetically informed discriminant analyses, and with the aim of inferring the lifestyle of extinct taxa. The group of interest is xenarthrans, one of the four major extant clades of placental mammals. Xenarthrans exhibit different lifestyles, from fully terrestrial to arboreal, and show various degrees of fossoriality. The authors analyzed forelimb long bones of some fossil sloths and made comparisons with several species of extant xenarthrans. The aim was notably to discuss the degree of arboreality and fossoriality of these fossil forms.

This study is among the first ones to conjointly analyze both diaphyseal and trabecular parameters to characterize lifestyles, and the first one outside of primates. No fossil form could undoubtedly be assigned to one lifestyle exhibited by extant xenarthrans, though some previous ecological hypotheses could be corroborated. This study also raised some technical challenges, linked to the sample and to the parameters studied, and thus constitutes a great step, from which to go further.


Amson, E., & Nyakatura, J. A. (2018). Palaeobiological inferences based on long bone epiphyseal and diaphyseal structure - the forelimb of xenarthrans (Mammalia). bioRxiv, 318121, ver. 5 peer-reviewed and recommended by PCI Paleo. doi: 10.1101/318121

Palaeobiological inferences based on long bone epiphyseal and diaphyseal structure - the forelimb of xenarthrans (Mammalia)Eli Amson & John A. Nyakatura<p>Trabecular architecture (i.e., the main orientation of the bone trabeculae, their number, mean thickness, spacing, etc.) has been shown experimentally to adapt with great accuracy and sensitivity to the loadings applied to the bone during life....Biomechanics & Functional morphology, Comparative anatomy, Evolutionary biology, Histology, Methods, Morphological evolution, Paleobiology, Vertebrate paleontologyAlexandra Houssaye2018-05-14 08:35:20 View