An Exceptionally Preserved Specimen From the Green River Formation Elucidates Complex Phenotypic Evolution in Gruiformes and Charadriiformes

Abstract

The stem lineage relationships and early phenotypic evolution of Charadriiformes (shorebirds) and Gruiformes (rails, cranes, and allies) remain unresolved. It is still debated whether these clades are sister-taxa. New phylogenetic analyses incorporating Paleogene fossils have the potential to reveal the evolutionary connections of these two speciose and evolutionarily critical neoavian subclades. Although Gruiformes have a rich Paleogene fossil record, most of these fossils have not been robustly placed. The Paleogene fossil record of Charadriiformes is scarce and largely consists of fragmentary single elements. Only one proposed Eocene charadriiform-like taxon, Scandiavis mikkelseni of Denmark, is represented by a partial skeleton. Here, we describe a new species from the early Eocene Green River Formation of North America comprising a partial skeleton and feather remains. Because the skeleton lacks the pectoral girdle and forelimbs as in S. mikkelseni, only features of the skull, axial skeleton, and hind limb are available to resolve the phylogenetic placement of this taxon. These anatomical subregions initially showed features seen in Charadriiformes and Gruiformes. To assess placement of this taxon, we use a matrix consisting of 693 morphological characters and 60 taxa, including S. mikkelseni and the oldest known charadriiform taxa represented by single elements. These more fragmentary records comprise two distal humeri from the earliest Eocene Naranbulag Formation of Mongolia and the early Eocene Nanjemoy Formation of Virginia. Our phylogenetic analyses recover the new taxon and S. mikkelseni alternatively as a charadriiform or as a stem-gruiform; placement is contingent upon enforced relationships for major neoavian subclades recovered by recent molecular-based phylogenies. Specifically, when constraint trees based on results that do not recover Charadriiformes and Gruiformes as sister-taxa are used, the new taxon and S. mikkelseni are recovered within stem Gruiformes. Both Paleogene fossil humeri are consistently recovered within crown Charadriiformes. If placement of these humeri or the new taxon as charadriiforms are correct, this may indicate that recent divergence time analyses have underestimated the crown age of another major crown avian subclade; however, more complete sampling of these taxa is necessary, especially of more complete specimens with pectoral elements.

Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes)

“…Under all three topological constraints, IGM 100/1435 emerged as a crown-group charadriiform and specifically as a total-group member of the Chionoidea (average PP = 0.909; Supplementary Information, Fig. S10), a position also supported by some of the original, partially constrained parsimony analyses (Musser and Clarke, 2020). For the purposes of calibration design, we took the conservative approach of associating the specimen with the least inclusive clade to which it could be assigned with a PP ≥ 0.95, a condition satisfied only by the entire charadriiform crown group (Table 2).…”

“…Here, we chose a gruiform species as the outgroup, as the Gruiformes were found to be the sister group of shorebirds in two recent genomescale analyses (Jarvis et al, 2014;Kuhl et al, 2020). This hypothesis is also supported by phylogenetic analyses of phenotypic data from extant taxa (McKitrick, 1991;Livezey and Zusi, 2007) and a high degree of morphological similarity between the early members of both clades (Musser and Clarke, 2020). To maximize data coverage for this outgroup, we specifically selected the Gray-crowned Crane (Balearica regulorum), a taxon for which both the complete nuclear genome (Zhang et al, 2014) and the complete mitochondrial genome (Krajewski et al, 2010) are available.…”

“…We paid particular attention to the choice of the root calibration, since multiple fossils have been put forward as the earliest known shorebird remains (Mayr, 2000(Mayr, , 2016Smith, 2015;Hood et al, 2019). In particular, a recent phylogenetic analysis suggested a crown-charadriiform affinity for at least two fossils dating to the early Eocene (Musser and Clarke, 2020). However, the resulting trees either exhibited a lack of resolution within Charadriiformes or contradicted well-established molecular results, rendering the placement of the fossils within the crown inconclusive.…”

“…To assess the confidence in the phylogenetic position of the early Eocene fossils, we re-analyzed the morphological character matrix of Musser and Clarke (2020) under three sets of "soft" topological constraints which fixed the relationships among most of the extant taxa but allowed the 8 included fossils to attach anywhere in the tree. The constraints enforced interfamilial relationships within all orders represented by more than two taxa (Anseriformes, Charadriiformes, Gruiformes) in addition to all applicable supraordinal relationships from three recent avian phylogenomic trees (Prum et al, 2015;Reddy et al, 2017;Kimball et al, 2019).…”

“…The constraints enforced interfamilial relationships within all orders represented by more than two taxa (Anseriformes, Charadriiformes, Gruiformes) in addition to all applicable supraordinal relationships from three recent avian phylogenomic trees (Prum et al, 2015;Reddy et al, 2017;Kimball et al, 2019). Note that in the analyses of Musser and Clarke (2020), the interfamilial relationships within Charadriiformes were left unconstrained, and the supraordinal relationships were only selectively enforced. All three analyses were performed us- (Inoue et al, 2009), Soft-bounded uniform = uniform distribution U (t L , t U ) with a power-decay left tail (0, t L ) and an exponential-decay right tail (t U , ∞) (Yang and Rannala, 2005).…”