Ecological causes of speciation and species richness in the mammal tree of life, bioRxiv, 2019-01-05
ABSTRACTBiodiversity is distributed unevenly from the poles to the equator, and among branches of the tree of life, yet how those patterns are related is unclear. We investigated global speciation-rate variation across crown Mammalia using a novel time-scaled phylogeny (N=5,911 species, ~70% with DNA), finding that trait- and latitude-associated speciation has caused uneven species richness among groups. We identify 24 branch-specific shifts in net diversification rates linked to ecological traits. Using time-slices to define clades, we show that speciation rates are a stronger predictor of clade richness than age. Mammals that are low dispersal or diurnal diversify the fastest, indicating roles for geographic and ecological speciation, respectively. Speciation is slower in tropical than extra-tropical lineages, consistent with evidence that longer tropical species durations underpin the latitudinal diversity gradient. These findings juxtapose modes of lineage diversification that are alternatively turnover-based, and thus non-adaptive, or persistence-based as associated with resource adaptations.
biorxiv evolutionary-biology 200-500-users 2019Ecological causes of uneven diversification and richness in the mammal tree of life, bioRxiv, 2019-01-05
AbstractThe uneven distribution of species in the tree of life is rooted in unequal speciation and extinction among groups. Yet the causes of differential diversification are little known despite their relevance for sustaining biodiversity into the future. Here we investigate rates of species diversification across extant Mammalia, a compelling system that includes our own closest relatives. We develop a new phylogeny of nearly all ∼6000 species using a 31-gene supermatrix and fossil node- and tip-dating approaches to establish a robust evolutionary timescale for mammals. Our findings link the causes of uneven modern species richness with ecologically-driven variation in rates of speciation andor extinction, including 24 detected shifts in net diversification. Speciation rates are a stronger predictor of among-clade richness than clade age, countering claims of clock-like speciation in large phylogenies. Surprisingly, speciation rate heterogeneity in recent radiations shows limited association with latitude, despite the well-known increase in species richness toward the equator. Instead, we find a deeper-time association where clades of high-latitude species have the highest speciation rates, suggesting that species durations are shorter (turnover is higher) outside than inside the tropics. At shallower timescales (i.e., young clades), diurnality and low vagility are both linked to greater speciation rates and extant richness. We suggest that high turnover among small-ranged allopatric species has erased the signal of vagility in older clades, while diurnality has adaptively promoted lineage persistence. These findings highlight the underappreciated joint roles of ephemeral (turnover-based) and adaptive (persistence-based) processes of diversification, which manifest in recent and more ancient evolutionary radiations of mammals to explain modern diversity.Author SummaryThe over 6000 living species in the mammalian tree of life are distributed unevenly among branches so that similarly aged groups sometimes differ many fold in species richness (e.g., ∼2500 rodent species versus 8 pangolins). Why differential bursts of species diversification occur, and how long they persist, has implications for sustaining biodiversity. Here we develop a robust evolutionary timescale for most extant species, recovering signatures of rate-variable diversification linked to ecological factors. Mammals with low dispersal or that are day-active show the fastest recent speciation rates, consistent with mechanisms of allopatric isolation and ecological opportunity, respectively. Speciation is surprisingly faster in extra-tropical than tropical lineages, suggesting that longer species durations for tropical lineages underpin the latitudinal diversity gradient in mammal.
biorxiv evolutionary-biology 200-500-users 2019Recording of sonic attacks on U.S. diplomats in Cuba spectrally matches the echoing call of a Caribbean cricket, bioRxiv, 2019-01-04
Beginning in late 2016, diplomats posted to the United States embassy in Cuba began to experience unexplained health problems including ear pain, tinnitus, vertigo, and cognitive difficulties which reportedly began after they heard strange noises in their homes or hotel rooms. In response, the U.S. government dramatically reduced the number of diplomats posted at the U.S. embassy in Havana. U.S. officials initially believed a sonic attack might be responsible for their ailments. The sound linked to these attacks, which has been described as a high-pitched beam of sound, was recorded by U.S. personnel in Cuba and released by the Associated Press (AP). Because these recordings are the only available non-medical evidence of the sonic attacks, much attention has focused on identifying health problems and the origin of the acoustic signal. As shown here, the calling song of the Indies short-tailed cricket (Anurogryllus celerinictus) matches, in nuanced detail, the AP recording in duration, pulse repetition rate, power spectrum, pulse rate stability, and oscillations per pulse. The AP recording also exhibits frequency decay in individual pulses, a distinct acoustic signature of cricket sound production. While the temporal pulse structure in the recording is unlike any natural insect source, when the cricket call is played on a loudspeaker and recorded indoors, the interaction of reflected sound pulses yields a sound virtually indistinguishable from the AP sample. This provides strong evidence that an echoing cricket call, rather than a sonic attack or other technological device, is responsible for the sound in the released recording. Although the causes of the health problems reported by embassy personnel are beyond the scope of this paper, our findings highlight the need for more rigorous research into the source of these ailments, including the potential psychogenic effects, as well as possible physiological explanations unrelated to sonic attacks.
biorxiv biophysics 200-500-users 2019Enjoy The Violence Is appreciation for extreme music the result of cognitive control over the threat response system?, bioRxiv, 2019-01-03
Traditional neurobiological theories of musical emotions explain well why extreme music such as punk, hardcore or metal, whose vocal and instrumental characteristics share much similarity with acoustic threat signals, should evoke unpleasant feelings for a large proportion of listeners. Why it doesn't for metal music fans, however, remains a theoretical challenge metal fans may differ from non-fans in how they process acoustic threat signals at the sub-cortical level, showing deactivated or reconditioned responses that differ from controls. Alternatively, it is also possible that appreciation for metal depends on the inhibition by cortical circuits of a normal low-order response to auditory threat. In a series of three experiments, we show here that, at a sensory level, metal fans actually react equally negatively, equally fast and even more accurately to cues of auditory threat in vocal and instrumental contexts than non-fans. Conversely, cognitive load somewhat appears to reduce fans' appreciation of metal to the level reported by non-fans. Taken together, these results are not compatible with the idea that extreme music lovers do so because of a different low-level response to threat, but rather, highlight a critical contribution of higher-order cognition to the aesthetic experience. These results are discussed in the light of recent higher-order theories of emotional consciousness, which we argue should be generalized to the emotional experience of music across musical genres.
biorxiv neuroscience 200-500-users 2019Highly Heritable and Functionally Relevant Breed Differences in Dog Behavior, bioRxiv, 2019-01-02
AbstractVariation across dog breeds presents a unique opportunity for investigating the evolution and biological basis of complex behavioral traits. We integrated behavioral data from more than 17,000 dogs from 101 breeds with breed-averaged genotypic data (N = 5,697 dogs) from over 100,000 loci in the dog genome. Across 14 traits, we found that breed differences in behavior are highly heritable, and that clustering of breeds based on behavior accurately recapitulates genetic relationships. We identify 131 single nucleotide polymorphisms associated with breed differences in behavior, which are found in genes that are highly expressed in the brain and enriched for neurobiological functions and developmental processes. Our results provide insight into the heritability and genetic architecture of complex behavioral traits, and suggest that dogs provide a powerful model for these questions.
biorxiv animal-behavior-and-cognition 200-500-users 2019Whole-genome sequencing of rare disease patients in a national healthcare system, bioRxiv, 2019-01-02
Most patients with hereditary rare diseases do not receive a molecular diagnosis and the aetiological variants and mediating genes for half such disorders remain to be discovered. We implemented whole-genome sequencing (WGS) in a national healthcare system to streamline diagnosis and to discover unknown aetiological variants, in the coding and non-coding regions of the genome. In a pilot study for the 100,000 Genomes Project, we generated WGS data for 13,037 participants, of whom 9,802 had a rare disease, and provided a genetic diagnosis to 1,040 of the 7,065 patients with detailed phenotypic data. We identified 99 Mendelian associations between genes and rare diseases, of which at least 80 are confirmed aetiological. Using WGS of UK Biobank, we showed that rare alleles can explain the presence of some individuals in the tails of a quantitative red blood cell (RBC) trait 1. Finally, we reported novel non-coding variants which cause disease through the disruption of transcription of ARPC1B, GATA1, LRBA and MPL. Our study demonstrates a synergy by using WGS for diagnosis and aetiological discovery in routine healthcare.
biorxiv genomics 200-500-users 2019