To explain the frequency and distribution of heteromorphic sex chromosomes in the lizard genus Anolis we compared the relative roles of sex chromosome conservation vs. turnover of sex determining mechanisms. We used model based comparative methods to reconstruct karyotype evolution and the presence of heteromorphic sex chromosomes onto a newly generated Anolis phylogeny. We found that heteromorphic sex chromosomes evolved multiple times in the genus. Fluorescent in situ hybridization (FISH) of repetitive DNA showed variable...
Genome-scale data offer the opportunity to clarify phylogenetic relationships that are difficult to resolve with few loci, but they can also identify genomic regions with evolutionary history distinct from that of the species history. We collected whole-genome sequence data from 29 taxa in the legume genus Medicago, then aligned these sequences to the M. truncatula reference genome to confidently identify 87,596 variable homologous sites. We used this data set to estimate phylogenetic relationships among Medicago...
Data from: An empirical comparison of a character-based and a coalescent-based approach to species delimitation in a young avian complexBailey D. McKay, Mays Jr., Herman L., Yuchun Wu, Hui Li, Cheng-Te Yao, Isao Nishiumi, Fasheng Zou & Herman L. Mays
The process of discovering species is a fundamental responsibility of systematics. Recently, there has been a growing interest in coalescent-based methods of species delimitation aimed at objectively identifying species early in the divergence process. However, few empirical studies have compared these new methods with character-based approaches for discovering species. In this study, we applied both a character-based and a coalescent-based approaches to delimit species in a closely related avian complex, the light-vented/Taiwan bulbul (Pycnonotus sinensis/Pycnonotus...
Data from: Candidate genes and genetic architecture of symbiotic and agronomic traits revealed by whole-genome, sequence-based association genetics in Medicago truncatulaJohn Stanton-Geddes, Timothy Paape, Brendan Epstein, Roman Briskine, Jeremy Yoder, Joann Mudge, Arvind K. Bharti, Andrew D. Farmer, Peng Zhou, Roxanne Denny, Gregory D. May, Stephanie Erlandson, Mohammed Yakub, Masayuki Sugawara, Michael J. Sadowsky, Nevin D. Young & Peter Tiffin
Genome-wide association study (GWAS) has revolutionized the search for the genetic basis of complex traits. To date, GWAS have generally relied on relatively sparse sampling of nucleotide diversity, which is likely to bias results by preferentially sampling high-frequency SNPs not in complete linkage disequilibrium (LD) with causative SNPs. To avoid these limitations we conducted GWAS with >6 million SNPs identified by sequencing the genomes of 226 accessions of the model legume Medicago truncatula. We used...
Data from: Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatulaTimothy Paape, Thomas Bataillon, Peng Zhou, Tom J. Y. Kono, Roman Briskine, Nevin D. Young, Peter Tiffin & Tom J. Y. Kono
Sequence data for >20 000 annotated genes from 56 accessions of Medicago truncatula were used to identify potential targets of positive selection, the determinants of evolutionary rate variation and the relative importance of positive and purifying selection in shaping nucleotide diversity. Based upon patterns of intraspecific diversity and interspecific divergence, c. 50–75% of nonsynonymous polymorphisms are subject to strong purifying selection and 1% of the sampled genes harbour a signature of positive selection. Combining polymorphism...
Data from: Going to extremes: contrasting rates of diversification in a recent radiation of New World passerine birdsFrederick Keith Barker, Kevin J. Burns, John Klicka, Scott M. Lanyon, Irby J. Lovette, Frederick Keith Barker, Kevin J. Burns, John Klicka, Scott M. Lanyon, Irby J. Lovette & F. Keith Barker
Recent analyses suggest that a few major shifts in diversification rate may be enough to explain most of the disparity in diversity among vertebrate lineages. At least one significant increase in diversification rate appears to have occurred within the birds; however, several nested lineages within birds have been identified as hyperdiverse by different studies. A clade containing the finches and relatives (within the avian order Passeriformes), including a large radiation endemic to the New World...
Data from: The distribution of fruit and seed toxicity during development for eleven Neotropical trees and vines in Central PanamaNoelle G. Beckman
Secondary compounds in fruit mediate interactions with natural enemies and seed dispersers, influencing plant survival and species distributions. The functions of secondary metabolites in plant defenses have been well-studied in green tissues, but not in reproductive structures of plants. In this study, the distribution of toxicity within plants was quantified and its influence on seed survival was determined in Central Panama. To investigate patterns of allocation to chemical defenses and shifts in allocation with fruit...
Data from: Range dynamics, rather than convergent selection, explain the mosaic distribution of red-winged blackbird phenotypesMatthew J. Dufort, F. Keith Barker & F. Keith Barker
Geographic distributions of genetic and phenotypic characters can illuminate historical evolutionary processes. In particular, mosaic distributions of phenotypically similar populations can arise from parallel evolution or from irregular patterns of dispersal and colonization by divergent forms. Two phenotypically divergent forms of the red-winged blackbird (Agelaius phoeniceus) show a mosaic phenotypic distribution, with a “bicolored” form occurring disjunctly in California and Mexico. We analyzed the relationships among these bicolored populations and neighboring typical populations, using ~600...
Data from: Effects of gene flow on phenotype matching between two varieties of Joshua tree (Yucca brevifolia; Agavaceae) and their pollinatorsJeremy B. Yoder, Christopher I. Smith, Daniel J. Rowley, Ramona Flatz, William Godsoe, Christopher Drummond, Olle Pellmyr, W. Godsoe, D. J. Rowley, C. Drummond, O. Pellmyr, C. I. Smith, R. Flatz & J. B. Yoder
In animal-pollinated plants, local adaptation to pollinator behaviour or morphology can restrict gene flow among plant populations; but gene flow may also prevent divergent adaptation. Here, we examine possible effects of gene flow on plant-pollinator trait matching in two varieties of Joshua tree (Agavaceae: Yucca brevifolia). The two varieties differ in strikingly in floral morphology, which matches differences in the morphology of their pollinators. However, this co-divergence is not present at a smaller scale: within...
It is thought that behaviourally flexible species will be able to cope with novel and rapidly changing environments associated with human activity. However, it is unclear whether such environments are selecting for increases in behavioural plasticity, and whether some species show more pronounced evolutionary changes in plasticity. To test whether anthropogenic environments are selecting for increased behavioural plasticity within species, we measured variation in relative cranial capacity over time and space in 10 species of...
Data from: Tempo and mode of multicellular adaptation in experimentally evolved Saccharomyces cerevisiaeWilliam C. Ratcliff, Jennifer T. Pentz & Michael Travisano
Multicellular complexity is a central topic in biology, but the evolutionary processes underlying its origin are difficult to study and remain poorly understood. Here we use experimental evolution to investigate the tempo and mode of multicellular adaptation during a de novo evolutionary transition to multicellularity. Multicelled “snowflake” yeast evolved from a unicellular ancestor after 7 days of selection for faster settling through liquid media. Over the next 220 days, snowflake yeast evolved to settle 44%...
Estimates of range-wide abundance, harvest, and harvest rate are fundamental for sound inferences about the role of exploitation in the dynamics of free-ranging wildlife populations, but reliability of existing survey methods for abundance estimation is rarely assessed using alternative approaches. North American mallard populations have been surveyed each spring since 1955 using internationally coordinated aerial surveys, but population size can also be estimated with Lincoln's method using banding and harvest data. We estimated late summer...
Data from: The early diversification history of didelphid marsupials: a window into South America’s “Splendid Isolation”Sharon A. Jansa, F. Keith Barker & Robert S. Voss
The geological record of South American mammals is spatially biased because productive fossil sites are concentrated at high latitudes. As a result, the history of mammalian diversification in Amazonia and other tropical biomes is largely unknown. Here we report diversification analyses based on a time-calibrated molecular phylogeny of opossums (Didelphidae), a species-rich clade of mostly tropical marsupials descended from a Late Oligocene common ancestor. Optimizations of habitat and geography on this phylogeny suggest that (1)...
Data from: Cryptic speciation reversal in the Etheostoma zonale (Teleostei: Percidae) species group, with an examination of the effect of recombination and introgression on species tree inferenceDominik Halas & Andrew M. Simons
Mitochondrial and nuclear introgression among closely related taxa can greatly complicate the process of determining their phylogenetic relationships. In the Central Highlands of North America, many fish taxa have undergone introgression; in this study, we demonstrate the existence of an unusual introgression event in the Etheostoma zonale species group. We used one mitochondrial and seven nuclear loci to determine the relationships of the taxa within the E. zonale group, and their degree of differentiation. We...
Data from: Diffuse symbioses: roles of plant–plant, plant–microbe and microbe–microbe interactions in structuring the soil microbiomeMatthew G. Bakker, Daniel C. Schlatter, Lindsey Otto-Hanson & Linda L. Kinkel
A conceptual model emphasizing direct host–microbe interactions has dominated work on host-associated microbiomes. To understand plant–microbiome associations, however, broader influences on microbiome composition and functioning must be incorporated, such as those arising from plant–plant and microbe–microbe interactions. We sampled soil microbiomes associated with target plant species (Andropogon gerardii, Schizachyrium scoparium, Lespedeza capitata, Lupinus perennis) grown in communities varying in plant richness (1-, 4-, 8- or 16-species). We assessed Streptomyces antagonistic activity and analysed bacterial and...
University of Minnesota15
Colorado State University2
University of Kansas1
Cincinnati Museum Center1
University of Nevada Reno1
National Center for Genome Resources1
University of Rochester1
University of Zurich1
University of Idaho1
American Museum of Natural History1
University of Canterbury1