Browsing by Subject "Phylogeny"

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    Anatomy, Systematics, and Evolution of Catarrhines from the Late Oligocene and Early Miocene of Eastern Africa
    (2019-10) Jansma, Rutger
    The early Miocene catarrhines are key taxa for elucidating the evolutionary history of the Hominoidea and Cercopithecoidea because they are temporally and morphologically intermediate between more primitive Oligocene faunas and modern primate communities. However, insight into the adaptive processes that led to the living catarrhine clades is obscured because of confusion over both taxonomic diversity and systematic affinities within key early Miocene groups. The research presented in this dissertation takes advantage of the increase in new, more complete fossils and taxa to overcome these limitations. The small catarrhines and nyanzapithecines are revised following a comprehensive review, resulting in the description of two new genera (Gen. nov. A and Gen. nov. B), a new species of Dendropithecus, and transfer of Nyanzapithecus harrisoni to Turkanapithecus. This revision provides evidence for increased geographic and ecological differentiation among sympatric small catarrhines, nyanzapithecines, and large-bodied hominoids during the early Miocene. A new phylogenetic analysis using maximum parsimony includes 64 taxa and 243 characters, and recovered a well-resolved consensus tree (MPTs = 18, 901 steps long) that supports monophyly of Cercopithecoidea and Hominoidea. Within Hominoidea, the Pliopithecidae, Dendropithecidae, and Proconsulidae are identified as successively more derived monophyletic clades. A monophyletic Oreopithecidae clade containing Oreopithecus and the nyanzapithecines is also well supported within Hominoidea. However, the positions of Pliopithecidae and Oreopithecidae are strongly influenced by the morphology preserved within single species in these clades. This demonstrates both the importance of comprehensive taxonomic sampling and the impact of missing data on phylogenetic results. The analysis also reveals that suspensory adaptations documented in living apes appeared independently in four hominoid clades (Pliopithecidae, Oreopithecidae, Hylobatidae, and Hominidae). This result is realized through the large taxon sampling in the analysis and demonstrate that the homoplastic character states in these taxa are expressed differently among clades. Finally, a general perspective on catarrhine evolution emphasizes that the appearance of the ancestral hominin cannot be properly interpreted without making reference to the entire Miocene ape radiation.
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    Phylogeny of the microcaddisflies with a revision of the genus Leucotrichia Mosely (Trichoptera: Hydroptilidae)
    (2014-04) Thomson, Robin Elizabeth
    Hydroptilidae Stephens, 1836 is the most diverse family [6 subfamilies, 76 genera (including 3 fossil genera), and over 2,100 species] belonging to the order Trichoptera. The family is cosmopolitan, occurring in all faunal regions of the world. A summary of the general morphology, biology, and taxonomic history and an overview of historically recognized taxa of Hydroptilidae are provided. Monophyly of Hydroptilidae and each of the 6 subfamilies was tested using 90 ingroup taxa, mitochondrial DNA (COI), and ribosomal RNA (D1-3). Maximum likelihood and Bayesian analysis methods were used to estimate phylogeny. Monophyly was recovered for Hydroptilidae, but not Ptilocolepidae. Monophyly was also recovered for the subfamilies Leucotrichiinae, Neotrichiinae, Ochrotrichiinae, and Stactobiinae. Monophyly for the subfamilies Hydroptilinae and Orthotrichiinae was not recovered. The genera Alisotrichia and Cerasmatrichia were recovered as a clade separate from all other subfamilies, as was the genus Byrsopteryx. The genus Dibusa, formerly incertae sedis, was recovered as sister to all other hydroptilids genera, excluding Palaeagapetus and Ptilocolepus. The genus Orphninotrichia, also formerly incertae sedis, was recovered within one clade of Hydroptilinae genera. Several taxonomic changes were necessary for classification to reflect phylogeny. Accordingly, I propose that the ptilocolepid genera Palaeagapaetus and Ptilocolepus be returned to Hydroptilidae as 2 genera separate from any subfamily. I also propose that the status of Alisotrichia, Byrsopteryx, and Cerasmatrichia be changed to incertae sedis within Hydroptilidae and that Dibusa and Orphninotrichia be removed from incertae sedis. A species-level revision of Leucotrichia was also completed, including a generic diagnosis, illustrations, a key, and descriptions of males. A total of 43 species were treated, 13 described as new: Leucotrichia angelinae, new species (Venezuela), L. denticulata, new species (Mexico), L. dianeae, new species (Costa Rica), L. fulminea, new species (Ecuador), L. hispida, new species (Costa Rica), L. kateae, new species (Venezuela), L. pectinata, new species (Ecuador), L. procera, new species (Brazil), L. repanda, new species (Venezuela), L. rhomba, new species (Costa Rica), L. riostoumae, new species (Ecuador), L. sidneyi, new species (Venezuela), and L. tapantia, new species (Costa Rica). Descriptions and new records for hydroptilid species found in Brazil and Venezuela were also provided. Illustrations and descriptions of males were given for all new species. A total of 10 new species were described: Acostatrichia digitata, new species (Venezuela), Betrichia alibrachia, new species (Brazil), Hydroptila cressae, new species (Venezuela), Leucotrichia bicornuta, new species (Brazil), Metrichia bostrychion, new species (Venezuela), Ochrotrichia spira, new species (Venezuela), Oxyethira bettyae, new species (Venezuela), Oxyethira quiramae, new species (Venezuela), Oxyethira redunca, new species (Venezuela), and Rhyacopsyche shorti, new species (Venezuela). New records were provided for 2 species: Neotrichia feolai Santos and Nessimian, 2009 (Venezuela) and Oxyethira picita Harris and Davenport, 1999 (Venezuela).
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    Systematics Of Cernotina Ross And Cyrnellus Banks (Insecta: Trichoptera: Polycentropodidae)
    (2020-07) Camargos, Lucas
    The family Polycentropodidae occurs worldwide, and is represented in the Americas by Cernotina Ross 1938, Cyrnellus Banks 1913, Nyctiophylax Brauer 1865, Polycentropus Banks 1907 and Polyplectropus Ulmer 1905. Cernotina and Cyrnellus are exclusive to the New World, reaching their highest diversity in the Neotropics, with 75 and 12 described species respectively. Despite this diversity, none of the two have had revisionary work done, and the taxonomic information is scattered in many different papers by many authors across the 20th and early 21st Century. In Chapter 1, I ran the first phylogenetic analyses on the diverse genus Cernotina, using morphological characters of the male adult, especially the genitalia. To analyze the character matrix, I used Maximum Parsimony and Bayesian inference. In Maximum Parsimony, I used equally-weighted analyses with two different search strategies, one simple run and another with multiple rounds saving suboptimal trees to filter for a better set of most parsimonious trees, and an implied-weights analysis, using a posteriori character weigthing to achieve better resolution. In the Bayesian inference, I used Mk model + lognormal distribution, commonly used in morphological data. The results suggest the monophyly of Cernotina, adds phylogenetic evidence for synonymization of Ce. perpendicularis with Ce. lanceolata, and Ce. hastilis with Ce. nigridentata, and group certain species with morphological and geographic congruence, such as Ce. acalyptra + Ce. cystophora + Ce. encrypta, and Ce. lutea + Ce. cadeti, respectively. However, the overall resolution of the simple maximum-parsimony and the Bayesian trees were very low. In addition, the branch support for most nodes is also very low. This result might be due to the nature of the genitalic characters of Cernotina, being extremely variable on all its components, making the task of finding character congruence difficult. With additional data such as DNA sequence and geometric morphometrics, such issues could be alleviated. In Chapter 2, I revised the genus Cernotina at species-level. I discussed the complex homology of the morphological characters of the male genitalia, especially concerning the intermediate appendage and its relation to the Xth tergum and the preanal appendage, produced illustrations and comparative diagnoses for each species in the genus, and taxonomic descriptions for 64 species. In addition, I described 16 new species. I also proposed 2 synonymies considering the phylogenetic data from Chapter 1: Ce. lanceolata as junior synonym of Ce. perpendicularis, and Ce. nigridentata as junior synonym of Ce. hastilis. In Chapter 3, I revised the genus Cyrnellus at species-level. I also discussed the homology of the morphological characters of the much simpler male genitalia of the genus, produced a key to species of Cyrnellus, provided illustrations, and full taxonomic descriptions for 11 species. In addition, I reinstated the validity of Cy. minimus based on the morphology of the inferior appendage in ventral view. I also synonymized 2 species based on morphological similarity and high variability among specimens: Cy. keskes as junior synonym of Cy. minimus, and Cy. kozepes as junior synonym of Cy. ulmeri.
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    Systematics of the family Polycentropodidae (Inseecta:Trichoptera: Psychomyioidea) and taxonomic revisions of New World Polyplectropus Ulmer.
    (2009-01) Chamorro, Maria Lourdes
    The monophyly and phylogenetic relationships of subfamilies and genera traditionally classified in Polycentropodidae Ulmer, 1903, one of the most diverse families in the suborder Annulipalpia, with more than 700 species in 3 subfamilies, were tested. Particular emphasis was placed on testing the monophyly of the cosmopolitan genus Polyplectropus. Larval information is unknown for 46% of the taxa included in this study. To understand the effects of including characters with large sets of missing data, three alternative datasets [TOTAL (all available data for all taxa)= 49 ingroup taxa, 122 characters (including highly incomplete characters); LPA (larval, pupal, adult) = 20 ingroup taxa, 122 characters; ADULT (only adult characters) = 49 ingroup taxa, 86 adult characters] were analyzed under parsimony and Bayesian methods. The five outgroup taxa, representing all four extant families in the Psychomyioidea and the single family in the Hydropsychoidea, remained constant in all datasets. The TOTAL and ADULT datasets included all 20 currently recognized polycentropodid genera placed in 3 subfamilies, and the LPA and TOTAL datasets included characters interpreted from structures of the larvae, pupae, and adults. Results rejected the monophyly of Polycentropodidae, as currently defined; however, the monophyly of the three largest cosmopolitan genera, Polycentropus, Polyplectropus, and Nyctiophylax, could not be rejected nor confirmed. The monophyly of the following taxa was strongly supported in all analyses: Cernotina, Cyrnellus, Kambaitipsyche, Neureclipsis, Paranyctiophylax, New World Polyplectropus sensu stricto, Placocentropus, Neotropical Nyctiophylax, and in the outgroup, Psychomyia + Xiphocentron; while monophyly was strongly supported in some, but not all analyses for the following taxa: Cyrnus, Antillopsyche, Pseudoneureclipsis, Polycentropus sensu stricto, Pseudoneureclipsinae, New Zealand Polyplectropus, Polycentropodinae, Cyrnodes scotti + Pahamunaya jihmita. The implementation of two different analytical methods revealed some areas of conflict which would not have been detected under a single method of analysis. Contradictory results among the datasets were primarily due to either inclusion or exclusion of key sets of characters (i.e., immature characters); and second, missing data negatively affected phylogenetic reconstruction when proportions of characters with missing data were high and characters without missing data were unable to provide adequate phylogenetic signal due to high variation in rates of evolution among characters. Therefore, a combination of few overall characters that have high variation in rates of change, plus an abundance of missing data may be problematic and may lead to poorly resolved trees, thus decreased accuracy. This study also emphasized the importance in phylogenetic reconstruction of including data from all available sources. Several taxonomic changes were necessary in order for classification to properly reflect phylogeny. Three new genera, all from the Neotropical region, will be described in future publications. The redefinition of Paranyctiophylax as a valid genus in Polycentropodinae was confirmed. Additionally, the recommendation was made that North American Polycentropus species previously belonging in Plectrocnemia or Holocentropus be recognized as such (either Plectrocnemia or Holocentropus depending on original designation) and not as belonging in Polycentropus. Furthermore, species described in Polycentropus post-1944 in North America are transferred to either Holocentropus or Plectrocnemia to reflect previously hypothesized sister relationships. The following new or reinstated combinations were proposed: Plectrocnemia albipuncta Banks, 1930 combinatio revivisco; Plectrocnemia aureola Banks, 1930 comb. rev.; Plectrocnemia cinerea (Hagen), 1861 comb. rev.; Plectrocnemia clinei Milne, 1936 comb. rev.; Plectrocnemia crassicornis (Walker), 1852 comb. rev.; Plectrocnemia jenula (Denning), in Denning & Sykora, 1966 combinatio nova; Plectrocnemia icula (Ross), 1941 comb. nov.; Plectrocnemia nascotia (Ross), 1941 comb. nov.; Plectrocnemia remota (Banks), 1911 comb. rev.; Plectrocnemia sabulosa (Leonard & Leonard), 1949 comb. nov.; Plectrocnemia smithae (Denning), 1949 comb. nov.; Plectrocnemia vigilatrix Navás, 1933 comb. rev.; Plectrocnemia weedi (Blickle & Morse), 1955 comb. nov.; Holocentropus chellus (Denning), 1964 comb. nov.; Holocentropus flavus Banks, 1908 comb. rev.; Holocentropus glacialis Ross, 1938 comb. rev.; Holocentropus grellus Milne, 1936 comb. rev.; Holocentropus interruptus Banks, 1914 comb. rev.; Holocentropus melanae Ross, 1938 comb. rev.; Holocentropus milaca (Etnier), 1968 comb. nov.; Holocentropus picicornis (Stephens), 1836 comb. rev. Additional taxonomic changes proposed based on current findings were: 1) the elevation of Pseudoneureclipsinae to family status: Pseudoneureclipsidae Ulmer status novus; and 2) the resurrection of Placocentropus Schmid, nomen revivisco, to include the following species: Placocentropus aspinosus (Schmid), 1964 comb. nov.; Placocentropus chilensis (Yamamoto), 1966 comb. nov.; Placocentropus obtusus Schmid, 1955 comb. rev.; Placocentropus quadriappendiculatus (Schmid), 1964 comb. nov.; Placocentropus quadrispinosus (Schmid), 1964 comb. nov.; Placocentropus tuberculatus (Flint), 1983 comb. nov.; Placocentropus valdiviensis (Flint), 1983 comb. nov. A phylogeny of New World Polyplectropus species was inferred. Characters were interpreted from structures of the male and female genitalia as well as the fore- and hind wings. Parsimony and Bayesian phylogenetic analyses of 89 ingroup taxa (97% of the known New World diversity in the genus), two outgroup taxa, and 59 morphological characters were performed. Results of the parsimony and Bayesian analyses were similar, although the Bayesian tree was less resolved. Monophyly of the panamensis and charlesi Groups, as currently defined, was rejected. A total of 10 lineages, with varying amounts of support, were recognized. These groups are the alienus Group (2 species), annulicornis Group (11 species, 8 new), bredini Group (19, 7), charlesi Group (3), fuscatus Group (3, 2), guyanae Group (2, 2), manuensis Group (3, 3), narifer Group (5, 3), santiago Group (25, 6), and thilus Group (15, 7). Four species remain unassigned to any species-group: P. beccus, P. beutelspacheri, P. kanukarum, and P. nayaritensis. The distribution of the genus is mostly restricted to the Mexican and Brazilian subregions of the Neotropics. Most of the species and species-groups are regional endemics. The taxonomy of New World species of Polyplectropus Ulmer, 1905 was revised to include detailed male and female diagnoses, descriptions, illustrations, distribution records, and keys to males of all species and species-groups. A key to genera of New World Polycentropodidae, including a redescription of Polyplectropus, was provided. The homology of the male genitalia of species in the genus was discussed, as well as reassessment and diagnoses of 10 species groups, 6 newly established. A total of 92 species were treated, 39 described as new: Polyplectropus adamsae, sp. nov. (Peru), P. alatespinus, sp. nov. (Brazil), P. amazonicus, sp. nov. (Brazil), P. andinensis, sp. nov. (Argentina, Bolivia), P. blahniki, sp. nov. (Venezuela), P. bolivianus, sp. nov. (Bolivia), P. brasilensis, sp. nov. (Brazil), P. vii brborichorum, sp. nov. (Ecuador), P. cressae, sp. nov. (Venezuela), P. colombianus, sp. nov. (Colombia), P. corniculatus, sp. nov. (Peru), P. cuzcoensis, sp. nov. (Peru), P. ecuadoriensis, sp. nov. (Ecuador), P. flintorum, sp. nov. (Venezuela), P. gaesum, sp. nov. (Brazil), P. guyanae, sp. nov. (Guyana, Venezuela), P. holzenthali, sp. nov. (Brazil), P. hystricosus, sp. nov. (Brazil), P. insularis, sp. nov. (Panama), P. julitoi, sp. nov. (Brazil), P. kanukarum, sp. nov. (Guyana), P. maculatus, sp. nov. (Venezuela), P. manuensis, sp. nov. (Peru), P. matatlanticus, sp. nov. (Brazil), P. minensium, sp. nov. (Brazil), P. novafriburgensis, sp. nov. (Brazil), P. peruvianus, sp. nov. (Peru), P. petrae, sp. nov. (Brazil), P. pratherae, sp. nov. (Brazil), P. puyoensis, sp. nov. (Ecuador), P. robertsonae, sp. nov. (Bolivia), P. rodmani, sp. nov. (Brazil), P. rondoniensis, sp. nov. (Brazil), P. tragularius, sp. nov. (Brazil), P. tripunctatum, sp. nov. (Peru), P. venezolanus, sp. nov. (Venezuela), P. woldai, sp. nov. (Panama), P. zamoranoensis, sp. nov. (Honduras), and P. zuliae, sp. nov. (Venezuela). Polyplectropus buchwaldi is designated as a nomen dubium.