Contradictory phylogenetic signals in the laurasiatheria anomaly zone

G.M.H. was funded by a UCD Ad Astra Fellowship. C.L. was funded by a UCD Ad Astra studentship. L.R. was funded by an SFI Centre for Research Training in Genomics Data Science grant (18/CRT/6214). L.M.D. was supported in part by NSF awards 1838273 and 2032063. E.C.T. and T.L. were funded by an SFI Frontiers for the Future Programme grant (19/FFP/6790).Relationships among laurasiatherian clades represent one of the most highly disputed topics in mammalian phylogeny. In this study, we attempt to disentangle laurasiatherian interordinal relationships using two independent genome-level approaches: (1) quantifying retrotransposon presence/absence patterns, and (2) comparisons of exon datasets at the levels of nucleotides and amino acids. The two approaches revealed contradictory phylogenetic signals, possibly due to a high level of ancestral incomplete lineage sorting. The positions of Eulipotyphla and Chiroptera as the first and second earliest divergences were consistent across the approaches. However, the phylogenetic relationships of Perissodactyla, Cetartiodactyla, and Ferae, were contradictory. While retrotransposon insertion analyses suggest a clade with Cetartiodactyla and Ferae, the exon dataset favoured Cetartiodactyla and Perissodactyla. Future analyses of hitherto unsampled laurasiatherian lineages and synergistic analyses of retrotransposon insertions, exon and conserved intron/intergenic sequences might unravel the conflicting patterns of relationships in this major mammalian clade.Publisher PDFPeer reviewe

SINE-Based Phylogenomics Reveal Extensive Introgression and Incomplete Lineage Sorting in Myotis

Using presence/absence data from over 10,000 Ves SINE insertions, we reconstructed a phylogeny for 11 Myotis species. With nearly one-third of individual Ves gene trees discordant with the overall species tree, phylogenetic conflict appears to be rampant in this genus. From the observed conflict, we infer that ILS is likely a major contributor to the discordance. Much of the discordance can be attributed to the hypothesized split between the Old World and New World Myotis clades and with the first radiation of Myotis within the New World. Quartet asymmetry tests reveal signs of introgression between Old and New World taxa that may have persisted until approximately 8 MYA. Our introgression tests also revealed evidence of both historic and more recent, perhaps even contemporary, gene flow among Myotis species of the New World. Our findings suggest that hybridization likely played an important role in the evolutionary history of Myotis and may still be happening in areas of sympatry. Despite limitations arising from extreme discordance, our SINE-based phylogeny better resolved deeper relationships (particularly the positioning of M. brandtii) and was able to identify potential introgression pathways among the Myotis species sampled

SINE-Based Phylogenomics Reveal Extensive Introgression and Incomplete Lineage Sorting in <i>Myotis</i>

Using presence/absence data from over 10,000 Ves SINE insertions, we reconstructed a phylogeny for 11 Myotis species. With nearly one-third of individual Ves gene trees discordant with the overall species tree, phylogenetic conflict appears to be rampant in this genus. From the observed conflict, we infer that ILS is likely a major contributor to the discordance. Much of the discordance can be attributed to the hypothesized split between the Old World and New World Myotis clades and with the first radiation of Myotis within the New World. Quartet asymmetry tests reveal signs of introgression between Old and New World taxa that may have persisted until approximately 8 MYA. Our introgression tests also revealed evidence of both historic and more recent, perhaps even contemporary, gene flow among Myotis species of the New World. Our findings suggest that hybridization likely played an important role in the evolutionary history of Myotis and may still be happening in areas of sympatry. Despite limitations arising from extreme discordance, our SINE-based phylogeny better resolved deeper relationships (particularly the positioning of M. brandtii) and was able to identify potential introgression pathways among the Myotis species sampled

Increasing evidence that bats actively forage at wind turbines

Although the ultimate causes of high bat fatalities at wind farms are not well understood, several lines of evidence suggest that bats are attracted to wind turbines. One hypothesis is that bats would be attracted to turbines as a foraging resource if the insects that bats prey upon are commonly present on and around the turbine towers. To investigate the role that foraging activity may play in bat fatalities, we conducted a series of surveys at a wind farm in the southern Great Plains of the US from 2011–2016. From acoustic monitoring we recorded foraging activity, including feeding buzzes indicative of prey capture, in the immediate vicinity of turbine towers from all six bat species known to be present at this site. From insect surveys we found Lepidoptera, Coleoptera, and Orthoptera in consistently high proportions over several years suggesting that food resources for bats were consistently available at wind turbines. We used DNA barcoding techniques to assess bat diet composition of (1) stomach contents from 47 eastern red bat (Lasiurus borealis) and 24 hoary bat (Lasiurus cinereus) carcasses collected in fatality searches, and (2) fecal pellets from 23 eastern red bats that were found on turbine towers, transformers, and tower doors. We found that the majority of the eastern red bat and hoary bat stomachs, the two bat species most commonly found in fatality searches at this site, were full or partially full, indicating that the bats were likely killed while foraging. Although Lepidoptera and Orthoptera dominated the diets of these two bat species, both consumed a range of prey items with individual bats having from one to six insect species in their stomachs at the time of death. The prey items identified from eastern red bat fecal pellets showed similar results. A comparison of the turbine insect community to the diet analysis results revealed that the most abundant insects at wind turbines, including terrestrial insects such as crickets and several important crop pests, were also commonly eaten by eastern red and hoary bats. Collectively, these findings suggest that bats are actively foraging around wind turbines and that measures to minimize bat fatalities should be broadly implemented at wind facilities

Data for: Mercury bioaccumulation in bats reflects dietary connectivity to aquatic food webs

Individual data for bat species, sex, sampling site, and hair THg (mg/kg) from Belize

Chiropterans Are a Hotspot for Horizontal Transfer of DNA Transposons in Mammalia.

Horizontal transfer of transposable elements (TEs) is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of TEs at what appears to be a high rate compared with other mammals. We investigated the occurrence of horizontally transferred (HT) DNA transposons involving bats. We found over 200 putative HT elements within bats; 16 transposons were shared across distantly related mammalian clades, and 2 other elements were shared with a fish and two lizard species. Our results indicate that bats are a hotspot for horizontal transfer of DNA transposons. These events broadly coincide with the diversification of several bat clades, supporting the hypothesis that DNA transposon invasions have contributed to genetic diversification of bats

Chiropterans are a hotspot for horizontal transfer of DNA transposons in mammalia

This project was supported by the National Science Foundation (grant numbers DEB 1838283 and IOS 2032006 to D.M.-S. and Dav.R. and DEB 1838273 and DGE 1633299 to L.D.), National Institutes of Health (grant numbers R01HG002939 and U24HG010136 to J.S., R.H., A.F.A.S., and Je.R.), NHGRI (grant number R01HG008742 to Z.C.), Irish Research Council (grant number IRCLA/ 2017/58 to E.T.), Science Foundation Ireland (grant number 19/FFP/6790 to E.T.), Max Planck Research Group awarded by the Max Planck Gesellschaft to S.V., Human Frontiers Science Program (grant number RGP0058/2016 to S.V.), UK Research and Innovation (grant number MR/T021985/1 to S.V.), and the Swedish Research Council Distinguished Professor Award to K.L.-T.Horizontal transfer of transposable elements (TEs) is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of TEs at what appears to be a high rate compared with other mammals. We investigated the occurrence of horizontally transferred (HT) DNA transposons involving bats. We found over 200 putative HT elements within bats; 16 transposons were shared across distantly related mammalian clades, and 2 other elements were shared with a fish and two lizard species. Our results indicate that bats are a hotspot for horizontal transfer of DNA transposons. These events broadly coincide with the diversification of several bat clades, supporting the hypothesis that DNA transposon invasions have contributed to genetic diversification of bats.Publisher PDFPeer reviewe

Leveraging base-pair mammalian constraint to understand genetic variation and human disease

Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease