Models of speciation‐with‐gene‐flow have shown that the reduction in recombination between alternative chromosome arrangements can facilitate the fixation of locally adaptive genes in the face of gene flow and contribute to speciation. However, it has proven frustratingly difficult to show empirically that inversions have reduced gene flow and arose during or shortly after the onset of species divergence rather than represent ancestral polymorphisms. Here, we present an analysis of whole genome data from a pair of cactophilic fruit flies, Drosophila mojavensis and D. arizonae, which are reproductively isolated in the wild and differ by several large inversions on three chromosomes. We found an increase in divergence at rearranged compared to colinear chromosomes. Using the density of divergent sites in short sequence blocks we fit a series of explicit models of species divergence in which gene flow is restricted to an initial period after divergence and may differ between colinear and rearranged parts of the genome. These analyses show that D. mojavensis and D. arizonae have experienced postdivergence gene flow that ceased around 270 KY ago and was significantly reduced in chromosomes with fixed inversions. Moreover, we show that these inversions most likely originated around the time of species divergence which is compatible with theoretical models that posit a role of inversions in speciation with gene flow.

Online enhancements: appendixes, zip file. Dryad data: http://dx.doi.org/10.5061/dryad.3sk15. abstract:The incorporation of ecological processes into models of trait evolution is important for understanding past drivers of evolutionary change. Species interactions have long been thought to be key drivers of trait evolution. However, models for comparative data that account for interactions between species are lacking. One of the challenges is that such models are intractable and difficult to express analytically. Here we present phylogenetic models of trait evolution that include interspecific competition among chosen species. Competition is modeled as a tendency of sympatric species to evolve toward difference from one another, producing trait overdispersion and high phylogenetic signal. The model predicts elevated trait variance across species and a slowdown in evolutionary rate both across the clade and within each branch. The model also predicts a reduction in correlation between otherwise correlated traits. We use an approximate Bayesian computation approach to estimate model parameters. We find reasonable power to detect competition in sufficiently large (201 species) trees compared with Brownian trait evolution and with OrnsteinUhlenbeck and early burst models. We apply the model to examine the evolution of bill morphology of Darwin's finches and find evidence that competition affects the evolution of bill length.

The disparity in species’ traits arises through variation in the tempo and mode of evolution over time and between lineages. Understanding these patterns is a core goal in evolutionary biology. Here we present the comprehensively updated r package MOTMOT: Models Of Trait Macroevolution On Trees that contains methods to fit and test models of continuous trait evolution on phylogenies of extant and extinct species. MOTMOT provides functions to investigate a range of evolutionary hypotheses, including flexible approaches to investigate heterogeneous rates and modes of evolution, models of trait change under interspecific competition and patterns of trait change across significant evolutionary transitions such as mass extinctions. We introduce and test novel algorithms of heterogeneous tempo and mode of evolution that allow for phylogeny‐wide shifts in evolution at specific times on a tree. We use these new MOTMOT functions to highlight an exceptionally high rate of mammalian body mass evolution for 10 million years following the Cretaceous–Palaeogene mass extinction. These methods provide biologists and palaeontologists with the tools to analyse continuous trait data on phylogenies, including large trees of up to thousands of species.

The incorporation of ecological processes into models of trait evolution is important for understanding past drivers of evolutionary change. Species interactions have long been thought to be key drivers of trait evolution. However, models for comparative data that account for interactions between species are lacking. One of the challenges is that such models are intractable and difficult to express analytically. Here we present phylogenetic models of trait evolution that includes interspecific competition amongst species.Competition is modelled as a tendency of sympatric species to evolve towards distinct niches, producing trait overdispersion and high phylogenetic signal. The model predicts elevated trait variance across species and a slowdown in evolutionary rate both across the clade and within each branch. The model also predicts a reduction in correlation between otherwise correlated traits. We used an Approximate Bayesian Computation (ABC) approach to estimate model parameters. We tested the power of the model to detect deviations from Brownian trait evolution using simulations, finding reasonable power to detect competition in sufficiently large (20+ species) trees. We applied the model to examine the evolution of bill morphology of Darwin's finches, and found evidence that competition affects the evolution of bill length.peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/033647 doi: bioRxiv preprint first posted online Dec. 4, 2015; 3 Introduction 1 There is an increasing drive to combine evolutionary and ecological perspectives in order to 2 fully capture the long-term dynamics of ecological communities (Johnson & Stinchcombe 3 2007, Cavender- Bares et al. 2009, Schoener 2011, Pennell and Harmon 2013 2014, Price et al. 2014, Pigot and Etienne 2015). This has led to insights into the roles of 5 ecological processes such as competitive exclusion and character displacement in shaping 6 distributions of traits (Webb et al. 2002, Kraft et al. 2007, Emerson and Gillespie 2008 Vamosi et al. 2009). However linking such patterns in data to underlying processes is 10Evidence that competition has shaped trait evolution has been generated using two 11 main approaches. This first is the observation of character displacement, i.e. a tendency for 12 species with overlapping ranges to exhibit increased phenotypic differences where they (De Mazencourt et al. 2008). Phylogenetic comparative models of adaptive 25 radiations have slowing evolutionary rates, implicitly assuming that competition for finite 26 peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/033647 doi: bioRxiv preprint first posted online Dec. 4, 2015; 4 niche space is an underpinning mechanism (e.g. the 'early burst' model, Harmon 2010a). One approach could be to explicitly model the evo...

Dupl~caUon 9p syndrome 1s a cl~mcally well described syndrome characterized b, growth retardauoq developmental delay, skeletal malformatrons and cran~ofac~al anomal~es We report a farmly starung w t h a male ~nfant born by c-secuon at 39 weeks geslatlon to a 38 yo G6 P 4-0-14 The pregnancy was remarkable for an abnormal MSAFP placmg the pregnancy at a 1 17 nsk for Down Syndrome The parem refused amruocentesls after recelvlng genetlc counselmg At 35 weeks gestauon a fetal ultrasound demonstrated rmld polyhydrarmnos borderline hydrocephalus and a urulateral nght pyelecmls along wth a proxlmal hydroureter The pauent had an unremarkable dellvery at an outs~de mUMlon w t h Apgars of 9 and L O Birth welglit was 4790g (>95%) Ten hours post del~verv the patlent began to develop slgruf~canr lymphedema of the nght lower extrermty wluch IS what brought hun to our attention On presentallon the pallent appeared WIII b~temporal narrowng, short palpebral fissures, and small deep set eyes The n g h~ extreuuty showed s~grukicant edema lnvolvlng the foot eaendlng to the dstal purtlon of the h g h An x-ray of the extrermty shoaed no fracture A cat scan of the head demonstrated a s e cerebral volume loss with a sl~ghtlv prominent left ventncle when compared to the nght A small left subdural hygroma was also noted A cardac echocardogram and a renal ultrasound were both normal Cytogenet~c study on penpheral blood lymphocytes revealed add~honal matenal on 9p A FISH pant for chromosome 9 mdcated that the extra matenal was d u p b m o n of 9 The G-band~ng panem suggested dupllcauon of 9p13p22 Penpheral blood was obtained From both parents and an ~dentlcal kary0t)pe \%as found m the mother T l~e mother was noted to have sinular p l i e n o~p~c features to tl~e proban4 namely short palpebral fissures and small deep set e\es The mother reported havlng a leanung d s a b~l~n as a cluld completing onl\ a 9' grade educauon Furlher fanul) luston showed tlie lnotllcr to Iia\e tluee other chlldren aU wltll anollier partner ages I I 16 and 19 years of age All 3 half s~bllngs to the proband are reponed as slow These slbllngs are currently belng worked up q