Estimation of phylogenetic divergence times in Panagrolaimidae and other nematodes using relaxed molecular clocks calibrated with insect and crustacean fossils

Abstract

This study presents the use of relaxed molecular clock methods to infer the dates of divergence between Panagrolaimus species. Autocorrelated relaxed tree methods, combined with well characterised fossil calibration dates, yield estimates of nematode divergence dates in accordance with the palaeontological age of fossil ascarid eggs and with the previously estimated date of 18 Ma (range 11.6 to 29.9 Ma) for the divergence of the Caenorhabditis lineage. Our data indicate that Panagrolaimus davidi from Antarctica separated ca 21.98 Ma from its currently known, most closely related strain. Thus, P. davidi may have existed in Antarctica prior to the Last Glacial Maximum, although this seems unlikely as it shares physiological and life history traits with closely related nematodes from temperate climates. These traits may have facilitated colonisation of Antarctica by P. davidi after the quaternary glaciation, analogous to the colonisation of Surtsey Island, Iceland, by P. superbus after its volcanic formation. This study demonstrates that autocorrelated relaxed tree methods combined with well characterised fossil calibration dates may be used as a method to estimate the divergence dates within nematodes in order to gain insight into their evolutionary history.

The genome of a subterrestrial nematode reveals adaptations to heat

“…3a). The divergence of suborders Rhabditina ( C. elegans , D. pachys , D. coronatus ) and Tylenchina ( P. redivivus and H. mephisto ) has been estimated at 22 million years ago using molecular clock methods 52 . A. suum is a member of Spirurina and separated from the Rhabditina 80 million years ago 53 , and the putative HGT event must predate these divergences.…”

“…As the founding genome sequence of the Halicephalobus genus, H. mephisto illuminates previously unexplored territory. H. mephisto separated from Caenorhabditis at least 22 million years ago 52,64 , and likely over 100 million years ago 65 , though calibrating the nematode molecular clock is difficult because of their poor fossil record 64 . Our data suggest that nematodes access the deep subsurface from surface waters facilitated by seismic activity 66 .…”

The genome of a subterrestrial nematode reveals an evolutionary strategy for adaptation to heat

“…As the founding genome sequence of the Halicephalobus genus, H. mephisto is a rich repository of novel biology. H. mephisto separated from Caenorhabditis at least 22 million years ago 52,64 , and likely over 100 million years ago 65 , though calibrating the nematode molecular clock is difficult because of their poor fossil record 64 . Our data suggest that nematodes access the deep subsurface from surface waters facilitated by seismic activity 66 .…”

“…Given that we found five nematode species host orthologs of the AIG1-like domain in their genomes ( Figure 3A) the HGT event must have been in a Chromadorean ancestor lineage, not in contemporary D. pachys, though H. mephisto has undergone a spectacular expansion of this gene family that is not present in the other lineages, most of which have only a few copies ( Figure 3A). The divergence of suborders Rhabditina (C. elegans, D. pachys, D. coronatus) and Tylenchina (P. redivivus and H. mephisto) has been estimated at 22 million years ago using molecular clock methods 52 . A. suum is a member of Spirurina and separated from the Rhabditina 80 million years ago 53 , and the putative HGT event 10 must predate these divergences.…”

A tale of three kingdoms: members of the Phylum Nematoda independently acquired the detoxifying enzyme cyanase through horizontal gene transfer from plants and bacteria

“…Trichinella and Trichuris are members of the order Trichinellida, and Soboliphyme belongs to the order Dioctophymatida. If acquired from a single HGT event, this would have occurred before the split, which is estimated to have transpired 400–470 MYA (McGill et al ., 2017). In like manner, HGT of the plant-derived spider mite cyanase genes has been projected to have occurred before or shortly after the formation of the Acariformes which was >435 MYA (Dabert et al ., 2010).…”