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The disjunct distribution of relict earthworm genera clarifies the early historical biogeography of the Lumbricidae (Crassiclitellata, Annelida)

The historical biogeography of the Lumbricidae, the main Palearctic earthworm family, may be linked to the paleogeography of their putative ancestral range in Iberia-Southeastern France-Corsica-Sardinia. Although molecular phylogenetics has recently been used to analyze most endemic genera in this area, the genus Kritodrilus has not yet been studied. The generotype Kritodrilus calarensis and other closely related species inhabit Southeastern France. However, other species from the Iberian Peninsula (e.g. Kr. osellai ) have been assigned to Kritodrilus , the same for the Vindobonic (Hungarian-Austrian-Czech-Slovakian) Dendrobaena mrazeki . In order to unravel the paleobiogeographic, evolutionary and taxonomic significance of Kritodrilus, the aforementioned species (and three potential relatives) were sequenced for seven molecular markers. Molecular phylogenetic inference recovered a clade of French Kritodrilus (including Et. setusmontanus ) closely related to the Northwestern Iberian Galiciandrilus and Compostelandrilus , the latter being a sister clade to the Vindobonic species (described as a new genus). Time-calibrated phylogenetic inference estimated that these three clades diverged around 55Ma. Ecological Niche Models for these clades were mainly influenced by the same environmental variables, but showed non-overlapping highly suitable areas (except for Kritodrilus ). Ancestral area reconstruction inferred the origin of the Lumbricidae in Corsica-Sardinia and the Iberian Peninsula, with eventual expansion eastwards towards France, Central Europe and the Carpato-Balkanic area. For Kritodrilus and its relatives, this expansion may have been contemporaneous with the Paleocene-Eocene Thermal Maximum. Later climatic changes may explain the strikingly disjunct ranges. This work highlights the evolutionary and biogeographic significance of these isolated earthworm lineages and the importance of their preservation.


Phylogenetic analyses and time-calibrated phylogenetic inference
Sequences were aligned with MAFFT v.7 (Katoh & Standley 2013) with default settings and concatenated with BioEdit (Hall 1999), resulting in a matrix of 4,183 bp (Suppl. Information Alignment S1). The best fitting evolutionary model for each partition was selected with jModelTest v. 2.1. 3 (Darriba et al., 2012) by applying the Akaike information criterion (AIC; Akaike, 1973) and the Bayesian information criterion (BIC;Schwarz, 1978). tRNAs were analyzed as a separate partition from 16S. GTR + I + G was selected as best-fitting evolutionary model for COI, 28S and ND1, GTR + G was selected for 12S, and HKY+I+G was selected for 16S, tRNAs and COII.
Bayesian Inference of the phylogeny was estimated with MrBayes v.3.2.6 (Ronquist et al., Gateway V. 3.3 (Miller et al. 2010). The analysis was performed with default parameters, and each of the two independent runs was set to 50 million generations sampling every 5,000th generation (10,000 trees). Twenty-percent of the trees were discarded as burn-in, with remaining trees combined and summarized on a 50% majority-rule consensus tree. Maximum Likelihood phylogenetic inference was performed using RAxML-NG (Kozlov et al. 2019) in the CIPRES Science Gateway V. 3.3 platform, from 10 random starting trees and 1,000 rapid bootstrap replicates.

2012) as implemented in CIPRES Science
To generate a suitable starting tree for the time-calibrated phylogenetic inference, the Maximum Likelihood tree was converted into an ultrametric tree by non-parametric rate smoothing (NPRS) using the chronopl function in the R package ape v5.2. The maximum and minimum ages of the clades were the same as those used in the downstream BEAST analysis.
The final ultrametric tree was generated with BEAST v. 1. 10 (Suchard et al., 2018) using the NPRS tree as the starting tree. Each partition was trimmed with GBlocks (Castresana, 2000) under the less stringent parameters, with the best-fitting evolutionary model (shown above) as the evolutionary model for each.
The following calibration points were implemented as uniform priors: -87-170 mya for the Criodrilidae + Lumbricidae + Hormogastridae clade -82-147 mya for the Lumbricidae+Hormogastridae clade These age intervals correspond to the 95% HPD (highest posterior density) intervals obtained by Marchán et al. (2017). A Yule diversification model and an uncorrelated lognormal relaxed clock were specified.
Three parallel runs were performed, each including 50 million generations, sampling every 5,000th generation. Tree and log files were combined in Logcombiner v.1. 10 (Suchard et al., 2018) by resampling at a lower frequency (15,000) and the results were visualized in Tracer v. 1.7.1 (Rambaut et al., 2018). The final tree was generated by TreeAnnotator v.1. 10 (Suchard et al., 2018) with a burn-in of 2000 generations.

Ancestral area reconstruction
Ancestral area reconstruction was performed in RASP 4 (Yu et al. 2020), and the most suitable model was chosen using BioGeoBEARS (DEC+j) and allowing a maximum of 3 areas for each node. The areas considered were coded as follows: A-Iberian Peninsula, B-France, C-Tyrrhenian (Corsica, Sardinia and Italian Penninsula), D-Central Europe (including Alpine Italy), E-Carphato-Balkanic, F-Easten Eurasia, G-North America. Species ranges were mainly obtained from DriloBase Taxo (http://taxo.drilobase.org/); for cosmopolitan/peregrine species, the original range was included when available in the literature, if not they were removed from the analysis. Species ranges are shown in Table 2 and Appendix 1.

Ecological Niche Modelling
Presence data (Table S1)  Human disturbance (ANTHRO) was incorporated through the 'Human footprint' data setrepresenting the human influence on land surface (Sanderson et al. 2002).
Ecological niche models were obtained using the R package 'SSDM' (Schmitt et al. 2017).

Phylogenetic analysis and time-calibrated phylogenetic inference
Bayesian phylogenetic inference (Figure 1)  Thus, Kritodrilus in the most inclusive sense appears to be polyphyletic, with some representatives placed within loosely-related clades and a well-delimited and strongly supported clade including the generotype (K. calarensis) as well as a species originally assigned to a different genus (Et. setusmontanus).    (Fig. 2) and its internal clades. The biogeographical scenario reconstructed by our analysis does not exactly correspond with that expected from such a West-East colonization route, as the earlierbranching ancestral area (Carpato-Balkanic) is located further than the Central European area.
However, this could be explained by a more crownward phylogenetic position of the Carpato-Balkanic clade (comprising Cernosvitovia, Serbiona, Karpatodinariona and related taxa) or the extinction/failure to sample of Central European taxa.
The same paleogeographic event is also compatible with the inferred historical biogeography of clade E: from an ancestral area located in the Iberian Peninsula, it would have expanded to Southeastern France (Kritodrilus) and to Central Europe (Vindoboscolex), with the Northwestern Iberian Galiciandrilus and Compostelandrilus as remnants of the original range.
However, the 1700 km disjunction between the current ranges of Vindoboscolex and its Iberian relatives is difficult to understand. One possible explanation can be found in the large global climatic changes during the Tertiary. There is a significant overlap between the estimated times of divergence between these clades (including Kritodrilus) and the climatic event known as the Paleocene-Eocene Thermal Maximum (at around 55.5 Ma -Bowen et al. 2015). Superimposed on a general trend of long-term global warming, this episode resulted in increased temperatures of up to 8º C. The resulting climatic conditions were very different from those found from the Eocene to the present day. It is possible that, under these conditions, suitable habitat for the ancestors of the disjunct clades was distributed continuously across their ranges, unlike at present (Fig. 3). Under a progressively cooler, drier climate, the ecological niche of these taxa would have diverged and become more restricted, explaining their current isolation.
Intermediate species would probably have become extinct, contributing to the biogeographical gap.
It is worth noting that most cladogenetic events within other lumbricid genera (for example

List of supporting information
Supporting information alignment S1. Alignment of the molecular markers COI (1-606), COII   Figure S1. Bayesian inference of the phylogenetic relationships of the studied Lumbricidae representatives based on the concatenated sequence of molecular markers COI, COII,16S,tRNAs,28S,12S,ND1.