John Gatesy

Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales

Whales in the suborder Mysticeti are filter feeders that use baleen to sift zooplankton and small fish from ocean waters. Adult mysticetes lack teeth, although tooth buds are present in foetal stages. Cladistic analyses suggest that functional teeth were lost in the common ancestor of crown-group Mysticeti. DNA sequences for the tooth-specific genes, ameloblastin (AMBN), enamelin (ENAM) and amelogenin (AMEL), have frameshift mutations and/or stop codons in this taxon, but none of these molecular cavities are shared by all extant mysticetes. Here, we provide the first evidence for pseudogenization of a tooth gene, enamelysin (MMP20), in the common ancestor of living baleen whales. Specifically, pseudogenization resulted from the insertion of a CHR-2 SINE retroposon in exon 2 of MMP20. Genomic and palaeontological data now provide congruent support for the loss of enamel-capped teeth on the common ancestral branch of crown-group mysticetes. The new data for MMP20 also document a polymorphic stop codon in exon 2 of the pygmy sperm whale (Kogia breviceps), which has enamel-less teeth. These results, in conjunction with the evidence for pseudogenization of MMP20 in Hoffmanns two-toed sloth (Choloepus hoffmanni), another enamel-less species, support the hypothesis that the only unique, non-overlapping function of the MMP20 gene is in enamel formation.

A Critique of Matrix Representation with Parsimony Supertrees

Strict and semi-strict supertree construction methods can be used to summarize groups that are consistent with all source phylogenies. Other procedures, such as Matrix Representation with Parsimony (MRP), arbitrate conflicts among incompatible source trees, and can provide more topological resolution than strict and semi-strict methods. MRP has been used to construct most of the large supertrees that have been published to date. We review some of the inherent problems with MRP and other supertree methods, point out specific difficulties in previously published Mrp-supertree analyses, question some of the possible advantages of supertrees, and suggest that supermatrix analyses of character data should provide the primary framework for comparative biology in the 21st century.

Inactivation of the olfactory marker protein (OMP) gene in river dolphins and other odontocete cetaceans

Various toothed whales (Odontoceti) are unique among mammals in lacking olfactory bulbs as adults and are thought to be anosmic (lacking the olfactory sense). At the molecular level, toothed whales have high percentages of pseudogenic olfactory receptor genes, but species that have been investigated to date retain an intact copy of the olfactory marker protein gene (OMP), which is highly expressed in olfactory receptor neurons and may regulate the temporal resolution of olfactory responses. One hypothesis for the retention of intact OMP in diverse odontocete lineages is that this gene is pleiotropic with additional functions that are unrelated to olfaction. Recent expression studies provide some support for this hypothesis. Here, we report OMP sequences for representatives of all extant cetacean families and provide the first molecular evidence for inactivation of this gene in vertebrates. Specifically, OMP exhibits independent inactivating mutations in six different odontocete lineages: four river dolphin genera (Platanista, Lipotes, Pontoporia, Inia), sperm whale (Physeter), and harbor porpoise (Phocoena). These results suggest that the only essential role of OMP that is maintained by natural selection is in olfaction, although a non-olfactory role for OMP cannot be ruled out for lineages that retain an intact copy of this gene. Available genome sequences from cetaceans and close outgroups provide evidence of inactivating mutations in two additional genes (CNGA2, CNGA4), which imply further pseudogenization events in the olfactory cascade of odontocetes. Selection analyses demonstrate that evolutionary constraints on all three genes (OMP, CNGA2, CNGA4) have been greatly reduced in Odontoceti, but retain a signature of purifying selection on the stem Cetacea branch and in Mysticeti (baleen whales). This pattern is compatible with the echolocation-priority hypothesis for the evolution of OMP, which posits that negative selection was maintained in the common ancestor of Cetacea and was not relaxed significantly until the evolution of echolocation in Odontoceti.

On the importance of homology in the age of phylogenomics

Homology is perhaps the most central concept of phylogenetic biology. Molecular systematists have traditionally paid due attention to the homology statements that are implied by their alignments of orthologous sequences, but some authors have suggested that manual gene-by-gene curation is not sustainable in the phylogenomics era. Here, we show that there are multiple ways to efficiently screen for and detect homology errors in phylogenomic data sets. Application of these screening approaches to two phylogenomic data sets, one for birds and another for mammals, shows that these data are replete with homology errors including alignments of different exons to each other, alignments of exons to introns, and alignments of paralogues to each other. The extent of these homology errors weakens the conclusions of studies based on these data sets. Despite advances in automated phylogenomic pipelines, we contend that much of the long, difficult, and sometimes tedious work of systematics is still required to guard against pervasive homology errors. This conclusion is underscored by recent studies that show that just a few outlier genes can impact phylogenetic results at short, tightly spaced internodes that are deep in the Tree of Life. The view that widespread DNA sequence alignment errors are not a major concern for rigorous systematic research is not tenable. If a primary goal of phylogenomics is to resolve the most challenging phylogenetic problems with the abundant data that are now available, researchers must employ effective procedures to screen for and correct homology errors prior to performing downstream phylogenetic analyses.

Phylogenomic red flags: Homology errors and zombie lineages in the evolutionary diversification of placental mammals

Phylogenomic studies can settle long-standing debates but should be scrutinized when well-established clades are contradicted and divergence dates are highly incompatible with the fossil record. Liu et al. (1) construct a species tree for Mammalia based on 4,388 protein-coding genes from 90 taxa to derive a novel model for the placental radiation, but their coalescence time tree shows multiple “red flags” that suggest underlying problems. Three well-validated clades (2⇓⇓–5), Odontoceti (toothed whales), Lemuriformes (lemurs, aye-aye), and Afrosoricida (tenrecs, golden moles) are robustly contradicted (100% bootstrap) in their preferred STAR species tree (1). Odontoceti has been corroborated repeatedly over the past 20 y (2⇓–4), and 12 homoplasy-free transposons diagnose the clade (5), so it is remarkable that … nn[↵][1]2To whom correspondence may be addressed. Email: jgatesy{at}amnh.org or springer{at}ucr.edu.nn [1]: #xref-corresp-1-1

Evolution of the MC5R gene in placental mammals with evidence for its inactivation in multiple lineages that lack sebaceous glands

MC5R is one of five melanocortin receptor genes found in placental mammals. MC5R plays an important role in energy homeostasis and is also expressed in the terminal differentiation of sebaceous glands. Among placental mammals there are multiple lineages that either lack or have degenerative sebaceous glands including Cetacea (whales, dolphins, and porpoises), Hippopotamidae (hippopotamuses), Sirenia (manatees and dugongs), Proboscidea (elephants), Rhinocerotidae (rhinos), and Heterocephalus glaber (naked mole rat). Given the loss or diminution of sebaceous glands in these taxa, we procured MC5R sequences from publicly available genomes and transcriptomes, supplemented by a newly generated sequence for Choeropsis liberiensis (pygmy hippopotamus), to determine if this gene remains intact or is inactivated in association with loss/reduction of sebaceous glands. Our data set includes complete MC5R sequences for 114 placental mammal species including two individuals of Mammuthus primigenius (woolly mammoth) from Oimyakon and Wrangel Island. Complete loss or inactivation of the MC5R gene occurs in multiple placental lineages that have lost sebaceous glands (Cetacea, West Indian manatee, African elephant, white rhinoceros) or are characterized by unusual skin (pangolins, aardvarks). Both M. primigenius individuals share inactivating mutations with the African elephant even though sebaceous glands have been reported in the former. MC5R remains intact in hippopotamuses and the naked mole rat, although slightly elevated dN/dS ratios in these lineages allow for the possibility that the accumulation of inactivating mutations in MC5R may lag behind the relaxation of purifying selection. For Cetacea and Hippopotamidae, the absence of shared inactivating mutations in two different skin genes (MC5R, PSORS1C2) is consistent with the hypothesis that semi-aquatic lifestyles were acquired independently in these clades following divergence from a common ancestor.

Pinniped Diphyly and Bat Triphyly: More Homology Errors Drive Conflicts in the Mammalian Tree

Homology is perhaps the most central concept of phylogenetic biology. At difficult to resolve polytomies that are deep in the Tree of Life, a few homology errors in phylogenomic data can drive spurious phylogenetic results. Feijoo and Parada (2017) assembled three phylogenomic data sets for mammals and reported methodological discrepancies and unexpected results that contradict the monophyly of well-established clades in Pinnipedia and Yangochiroptera. Examination of Feijoo and Paradas (2017) data sets reveals extensive homology errors (paralogous sequences, alignments of different exons to each other) and cross-contamination of sequences from different species. These problems predictably result in distorted estimates of gene trees, species trees, bootstrap support, and branch lengths. Correction of these errors resulted in robust support for conventional relationships in Pinnipedia and Yangochiroptera. Phylogenomic data sets are not immune to the problems of homology errors in sequence alignments. Rather, sequence alignments underlie all inferences in molecular phylogenetics and evolution and should be spot-checked for obvious errors via manual inspection of alignments and gene trees.

Microstructure and mechanical properties of different keratinous horns

Animal horns play an important role during intraspecific combat. This work investigates the microstructure and mechanical properties of horns from four representative ruminant species: the bighorn sheep (Ovis canadensis), domestic sheep (Ovis aries), mountain goat (Oreamnos americanus) and pronghorn (Antilocapra americana), aiming to understand the relation between evolved microstructures and mechanical properties. Microstructural similarity is found where disc-shaped keratin cells attach edge-to-edge along the growth direction of the horn core (longitudinal direction) forming a lamella; multiple lamellae are layered face to face along the impact direction (radial direction, perpendicular to horn core growth direction), forming a wavy pattern surrounding a common feature, the tubules. Differences among species include the number and shape of the tubules, the orientation of aligned lamellae and the shape of keratin cells. Water absorption tests reveal that the pronghorn horn has the largest water-absorbing ability due to the presence of nanopores in the keratin cells. The loading direction (compressive and tensile) and level of hydration vary among the horns from different species. The differences in mechanical properties among species may relate to their different fighting behaviours: high stiffness and strength in mountain goat to support the forces during stabbing; high tensile strength in pronghorn for interlocked pulling; impact energy absorption properties in domestic and bighorn sheep to protect the skull during butting. These design rules based on evolutionary modifications among species can be applied in synthetic materials to meet different mechanical requirements.

On the Illogic of Coalescence Simulations for Distinguishing the Causes of Conflict among Gene Trees

Mark S. Springer1*and John Gatesy2* 1Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, California 92521, USA 2Division of Vertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA *Corresponding authors: Mark S. Springer, Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, California 92521, USA, Tel: 951-827-6458; E-mail: springer@ucr.edu; John Gatesy, John Gatesy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA, Tel: 212-313-7529; E-mail: jgatesy@amnh.org