Near-complete phylogeny of extant Crocodylia (Reptilia) using mitogenome-based data

Abstract

<jats:title>Abstract</jats:title> <jats:p>Species of the order Crocodylia are mostly large, predatory and semi-aquatic reptiles. Crocodylia, the closest living relatives of birds, first appeared in the Late Cretaceous period. In the present study, the complete mitochondrial (mt) genomes of 19 Crocodylia species, including two species (Melanosuchus niger and Caiman yacare) that have not been previously sequenced for mitogenomes, were processed through Illumina sequencing to offer genetic resources and compare with the mitogenomes of Crocodylia species reported previously. In addition, a high-resolution phylogenetic tree of nearly all current recognized species of Crocodylia is constructed based on mitogenomic data. Phylogenetic analyses support monophyly of three families: Alligatoridae (four genera: Alligator, Caiman, Melanosuchus and Paleosuchus), Crocodylidae (three genera: Crocodylus, Mecistops and Osteolaemus) and Gavialidae (two genera: Gavialis and Tomistoma). The tree topology is generally similar to previous studies. Molecular dating suggests that the first split within Crocodylia date back to the Upper Cretaceous (approx. 86.75 Mya). The estimated time to the most recent common ancestor (TMRCA) of Alligatoridae is 53.33 Mya and that of Crocodylidae and Gavialidae is 50.13 Mya, which might be closely linked to climate changes during the Late Palaeocene and Early Eocene. Additionally, this study proves that the diversification rate within Crocodylia began to increase from the Late Eocene (about 36 Mya) and two diversification peak periods of Crocodylia (0–10 Mya and 10–20 Mya) are disclosed, which is roughly consistent with the estimated crocodylian species richness through time. Combining all these clues, we can suggest that climate fluctuation may have played a decisive role in the speciation of Crocodylia.</jats:p>

Australia’s prehistoric ‘swamp king’: revision of the Plio-Pleistocene crocodylian genusPallimnarchusde Vis, 1886

“…The vast majority of published phylogenetic analyses based exclusively on morphological data have recovered Gavialidae in a basal position within Crocodylia, while Alligatoroidea and Crocodyloidea (including Tomistominae) are usually found forming a separate clade (=Brevirostres; Norell, 1989;Brochu, 1999Brochu, , 2003Salisbury et al, 2006;Salas-Gismondi et al, 2016;Jouve, 2016). In contrast, results from molecular data are in opposition to those derived from morphological datasets alone by suggesting that Gavialis Oppel, 1811 and Tomistoma Müller, 1846 are actually closely related (Densmore, 1983;Densmore & Owen, 1989;Hass et al, 1992;Gatesy et al, 2003;McAliley et al, 2006;Willis et al, 2007;Oaks, 2011;Pan et al, 2020). In recent years, several studies that performed analyses combining morphological and molecular data have managed to recover topologies that are in Q u i n k a n a t i m a r a Figure 34 Reduced 50% majority-rule consensus topology from the first phylogenetic analysis, run without using the Implied Weighting method.…”

Redescription and phylogenetic affinities of the caimanine Eocaiman cavernensis (Crocodylia, Alligatoroidea) from the Eocene of Argentina

“…Other studies obtained divergence times for Crocodylia using only molecular data, including Oaks (2011) and the recently published work of Pan et al . (2020). These two studies found the most recent common ancestor of all living caimanines to be much younger (Eocene and Oligocene–Miocene, respectively) than our estimates for Caimaninae, even for crown caimanines (70.95–62.55 Ma; median = 66.34 Ma).…”

“…in the case of Pan et al . 2020) or the omission of some recently discovered taxa in node‐dating analyses (i.e. in the case of Oaks 2011).…”

Complex macroevolutionary dynamics underly the evolution of the crocodyliform skull

“…Although using fossilized birth–death tip dating in this way is common practice for time-calibrating trees containing extinct taxa and has previously been used to date Crocodylomorpha phylogenies [ 4 ], we recovered divergence dates among extant taxa that are much more recent than estimates based on molecular evidence [ 51 ]. To be able to evaluate the effects of different dating approaches, we created a fourth phylogenetic hypothesis by modifying topology (C) to have divergence dates among extant taxa matching the mean node dates from a recent mitogenome-based phylogeny [ 51 ].…”