• A molecular phylogeny of the Pacific clade of Cyrtandra (Gesneriaceae) reveals a Fijian origin, recent diversification, and the importance of founder events

      Johnson, Melissa A.; Clark, John R.; Wagner, Warren L.; McDade, Lucinda A. (2017)
      Cyrtandra (Gesneriaceae) is among the largest genera of flowering plants in the remote oceanic islands of the Pacific, with an estimated 175 species distributed across an area that extends from the Solomon Islands, east to the Marquesas Islands, and north to the Hawaiian Islands. The vast majority of species are single-island endemics that inhabit upland rainforests....
    • Comparative genomics reveals insights into avian genome evolution and adaptation

      Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; et al. (2014)
      Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades....
    • Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species

      Hale, Vanessa L; Tan, Chia L.; Niu, Kefeng; Yang, Yeqin; Knight, Rob; Zhang, Qikun; Cui, Duoying; Amato, Katherine R (2018)
      Both diet and host phylogeny shape the gut microbial community, and separating out the effects of these variables can be challenging. In this study, high-throughput sequencing was used to evaluate the impact of diet and phylogeny on the gut microbiota of nine colobine monkey species (N = 64 individuals)....
    • Ecological specialization and morphological diversification in Greater Antillean boas

      Reynolds, R. Graham; Collar David C.; Pasachnik, Stesha A.; Niemiller Matthew L.; Puente-Rolón, Alberto R.; Revell, Liam J. (2016)
      Colonization of islands can dramatically influence the evolutionary trajectories of organisms, with both deterministic and stochastic processes driving adaptation and diversification. Some island colonists evolve extremely large or small body sizes, presumably in response to unique ecological circumstances present on islands. One example of this phenomenon, the Greater Antillean boas, includes both small (<90 cm) and large (4 m) species occurring on the Greater Antilles and Bahamas, with some islands supporting pairs or trios of body‐size divergent species. These boas have been shown to comprise a monophyletic radiation arising from a Miocene dispersal event to the Greater Antilles, though it is not known whether co‐occurrence of small and large species is a result of dispersal or in situ evolution. Here, we provide the first comprehensive species phylogeny for this clade combined with morphometric and ecological data to show that small body size evolved repeatedly on separate islands in association with specialization in substrate use. Our results further suggest that microhabitat specialization is linked to increased rates of head shape diversification among specialists. Our findings show that ecological specialization following island colonization promotes morphological diversity through deterministic body size evolution and cranial morphological diversification that is contingent on island‐ and species‐specific factors.
    • Incorporating indels as phylogenetic characters: Impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora)

      Luan, P.T.; Ryder, Oliver A.; Davis, H.; Zhang, Y.P.; Yu, L. (2013)
      Insertion and deletion events (indels) provide a suite of markers with enormous potential for molecular phylogenetics. Using many more indel characters than those in previous studies, we here for the first time address the impact of indel inclusion on the phylogenetic inferences of Arctoidea (Mammalia: Carnivora)….
    • Molecular phylogeny and chromosomal evolution of Alcelaphini (Antilopinae)

      Steiner, Cynthia C.; Charter, Suellen J.; Houck, Marlys L.; Ryder, Oliver A. (2014)
      Robertsonian (Rb) translocations, in particular centric fusions, are thought to play a primary role in evolution and speciation of the Bovidae family....This work studies chromosome variation in 72 captive individuals of 6 species of Alcelaphini (Antilopinae): The hartebeest (genus Alcelaphus), hirola (Beatragus), black and blue wildebeests (Connochaetes), and the topi and bontebok (Damaliscus)….
    • The birds of Genome10K

      OBrien, Stephen J.; Haussler, David; Ryder, Oliver A. (2014)
      Everyone loves the birds of the world. From their haunting songs and majesty of flight to dazzling plumage and mating rituals, bird watchers – both amateurs and professionals - have marveled for centuries at their considerable adaptations. Now, we are offered a special treat with the publication of a series of papers in dedicated issues of Science, Genome Biology and GigaScience (which also included pre-publication data release). These present the successful beginnings of an international interdisciplinary venture, the Avian Phylogenomics Project that lets us view, through a genomics lens, modern bird species and the evolutionary events that produced them.
    • Whole-genome analyses resolve early branches in the tree of life of modern birds

      Jarvis, Erich D.; Mirarab, Siavash; Aberer, Andre J.; Li, Bo; Houde, Peter; Li, Cai; Ho, Simon Y. W.; Faircloth, Brant C.; Nabholz, Benoit; Howard, Jason T.; et al. (2014)
      To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships.....