Browsing by Subject "Biogeography"
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Item A sensitivity test for species distribution models used for gap analysis in New Mexico(Texas Tech University, 1996-12) Islas, Carlos Gonzalez-RebelesGap Analysis Program is a landscape-level evaluation of plant communities and animal richness and is useful in wildlife conservation. Models to predict species distributions are fundamental for Gap analysis to assess animal richness patterns. Basic models combine species' locality, together with their vegetation associations (base variables). Additional environmental variables (filter variables) are used for further adjustment and to represent particular habitat associations. However, there is a need to know the contribution that filter variables provide to the models. This research evaluated model sensitivity to simplification of habitat associations in the model, by systematically removing selected filter variables. This was done to quantify indirectly the value added by these variables and to examine if the response pattern was consistent with expected model performance. Distribution predictions from the New Mexico Gap Analysis Project (NMGAP) were used as baseline data for this study. A representative sample of species was evaluated by using subset combinations of filter variables as model input. Altered species distribution estimates were examined for differences in area relative to the full model. Model sensitivity to different single filter variables and combinations was found to be highly variable among different types of models (number of filter variables used) and the species they represented. Between extreme high and low values, results indicated that in general all filter variables presented some level of influence on the models (assumed adjustment). However, for those models formed with two or three filter variables most of their least influential variables did not differ (p>0.05) from a threshold value set as minimum acceptable change (5% change in area). This indicated that more risks of variables with no effect may occur when adding more than two filter variables (potential correlation). Consistent with model performance expectations, general response to perturbation suggested that each additional filter variable used in the model produced a cumulative effect for most models, and that this effect was greater (p<0.05) for models representing species with restricted distributions than for those with widespread species distributions. Sensitivity analysis is recommended at the stage of review of preliminary wildlife species distribution maps produced for Gap analysis to detect model weaknesses.Item Areographic fragmentation analysis of Texas mammal distributions: a fractal analysis(Texas Tech University, 2000-08) Allen, Kelly ElaineHabitat fragmentation, the leading cause in the decline of biodiversity, affects the geographic range distribution of Texas mammals through the loss of habitat and the disjunction of populations. The fragmentation of a distribution has been referred to as areographic fragmentation and the effects of fragmenting a distribution can be quantified by measurements of area and perimeter that are not affected by scale. Fractal theory provides an appropriate method of determining areographic fragmentation through the quantification of distribution shape, perimeter length, and patchiness via the fractal dimension. The sensitivity of the fractal dimension to changes in distribution morphology requires measurements of area and perimeter be determined from detailed maps. Through the use of geographic information systems, maps depicting distributions at greater spatial resolution than currently available were produced with reasonable accuracy. Fractal dimensions were used as a scale-invariant statistic to quantify shape (areato-perimeter), perimeter length (length-of-trail), and patchiness (Korcak's empirical law). Like other biological objects, the distributions of Texas mammals may be scale invariant at several separate scales; however, this phenomenon may actually represent a lack of fit by the areographic models with the data. Fractal dimensions of mammal distributions were examined for patterns in taxonomy, feeding preference, and spatial structure. No significant difference was found between taxonomic and feeding structure categories. However, differences between eastern and western distributions did exist. These differences were primarily based upon the perimeter length of distributions with western species exhibiting more complex boundaries. Maps have long been used as resources of data when collecting data in the field is too labor intensive or when the biological question being addressed is extremely complex. Yet, all maps are made with limitations that affect the data extracted from them. The effects of cartographic design, model impro\ement, and spatial resolution were examined. Fractal dimensions calculated from predicted distribution maps representing increased model complexit}- did not differ significantly from those dimensions calculated using simple mapping models for the length-of-rail and Korcak areographic methods. Significant differences were only found to exist for dimensions calculated from the areato-perimeter method. Further examination of the fractal dimensions calculated using increased model resolution revealed no differences exist between taxonomic, feeding preferences, and spatial categories. The results of this study indicate that Texas mammal distributions are the function of individualistic responses to environmental variables and evolutionary history.Item Biogeographic Patterns, Predator Identity, and Chemical Signals Influence the Occurrence and Magnitude of Non-lethal Predator Effects(2011-10-21) Large, Scott IsaacPredators can have large effects on prey populations and on the structure and function of communities. In addition to direct consumption of prey, predators often cause prey to alter their foraging behavior, habitat selection, and morphology. These non-lethal effects of predators can propagate to multiple trophic levels and often exert equal or larger effects upon communities than those of direct consumption. For non-lethal predatory effects to occur, prey must detect and respond to predation risk. While the importance of information transfer in this process has been realized, few studies explore how prey responses are influenced by predator characteristics and environmental conditions that influence the transmission of cues indicative of predation risk. In this dissertation I investigate factors that influence how a single prey species evaluates and responds to predation risk. Here, I examined: 1) the type and nature of cues prey use to evaluate predator risk; 2) how predator identity, predator diet, and the relative risk of predators influence prey response to predation risk; 3) how hydrodynamic conditions influence the delivery of predator cues; 4) how biogeographic trends in predator distribution influence prey response to predation risk; and 5) how genetic structure might vary according to prey geographic location and habitat. To address these questions, I used a common intertidal model system consisting of the rocky intertidal whelk Nucella lapillus (Linnaeus, 1758) and a suite of its predators, the native rock crab Cancer irroratus (Say, 1817), Jonah crab Cancer borealis (Stimpson, 1859), and the invasive green crab Carcinus maenas (Linnaeus, 1758). Nucella use chemical cues emanating from their most common predator (Carcinus maenas) and crushed conspecifics to evaluate predation risk. Nucella from different habitats experience different levels of predation risk, and Nucella from habitats with high levels of predation had larger antipredatory responses to predator risk cues than Nucella that experienced less predation. These chemical cues indicative of predation risk are influenced by hydrodynamic conditions, and Nucella have the strongest anti-predatory response in flow velocities of u= ~4- 8 cm s^-1. Furthermore, Nucella from geographic regions where green crabs are historically absent did not elicit anti-predatory responses, while Nucella from regions where green crabs are common frequently responded. Findings from my dissertation research demonstrate that prey detection and response to predation risk is highly dependent upon predator identity, predator diet, environmental forces, and biogeographic patterns in predator and prey distributions.Item Biogeography and evolution of widespread leafcutting ants, ata spp. (formicidae, attini)(2007) Solomon, Scott Even, 1979-; Mueller, Ulrich G.Leafcutter ants (Atta spp.) are Neotropical herbivores that play important ecological roles, but are also notorious pests, causing millions of dollars in annual damage to agriculture across their range. Three species, A. cephalotes, A. sexdens, and A. laevigata, stand out as the most widespread and economically important. Two studies were conducted using these three species to better understand their biogeography and evolutionary history. First, using a maximum entropy niche-based modeling approach, locality information for these three species was used to (1) accurately describe the current geographic range of each species, (2) determine what factors limit their respective ranges, and (3) identify areas where each species is capable of becoming established. By comparing the model's predictions with published records and targeted surveys, a more accurate picture of the current ranges of each species was obtained. Areas in which a species does not currently occur, but that are predicted to be suitable, may reveal the ecological factors limiting the spread of these species. Such areas may also represent potential sites for invasion by these ants, with potentially devastating results. Second, these species were used to test the leading biogeographic hypotheses on the origins of high Amazonian diversity, an issue that remains unresolved despite much research. The hypotheses are the riverine barrier, Pleistocene refugia, and marine incursion hypotheses, each of which has been tested almost exclusively on vertebrates. A comparative, molecular phylogeographic approach was combined for the first time with paleodistribution modeling for the last glacial maximum to test these hypotheses on an insect. All analyses rejected the predictions of the riverine barrier hypothesis for each species. Tests of gene tree topology could not reject the refugia hypothesis for A. sexdens, while population-genetic and historical demography analyses failed to reject both the refugia and marine incursion hypotheses for all three species. However, coalescent-based estimates of population divergences for each species suggest that current population structure formed recently, suggesting that Miocene marine incursions have not promoted diversification in these species. Therefore, of the hypotheses examined, only the Pleistocene refugia hypothesis can explain the current population structure of Amazonian leafcutter ants.Item Biogeography of upland bird communities in the Peruvian Amazon(2009-12) Pomara, Lazarus Yates; Young, Kenneth R.; Barth, Robert H.; Dull, Robert A.; Miller, Jennifer A.; Ruokolainen, KalleThe western Amazon is known to be one of the most biologically diverse regions in the world, yet information about the spatial distribution of that biodiversity and the processes governing its distribution remains scarce. An improved understanding of those biogeographic patterns and processes can inform conservation and development planning in areas where anthropogenic landscape change is ongoing. Spatial components of biodiversity are known to be influenced by historical and present-day physical and human geographic processes. There is evidence that major Amazonian rivers form the boundaries of biological regions, at least for birds. Other factors that may influence bird species composition include the dispersal limitations of individual species, forest plant species composition and structure, topography, forest fragmentation, and hunting. Sites where bird species composition was measured in this study represented mature, upland forest on both sides of the Amazon River, and a range of non-flooded forest types, as indicated by soil and plant surveys. Bird species compositional variation was closely correlated with variation in plant species composition, human disturbance associated with forest fragmentation, and position north or south of the Amazon River. The strongest differences were between opposite sides of the river, even though local environments, including plant composition, were not different on the two sides. This strongly suggests that historical biogeographic factors, rather than present-day environmental gradients, are responsible for bioregional boundaries at Amazonian rivers. The difference between plant and bird distributions at this scale underscores the pressing need to re-evaluate general notions of bioregional complexity and pattern in the Amazon basin. Locally, the influence of habitat fragmentation on animal communities, including reduced species richness, was confirmed. The influence of local floristic variation is of particular importance due to its ubiquity across western Amazonia. Thus, understanding the distributions of soils and vegetation is critical for explaining Amazonian animal diversity. The use of these factors to model bird community heterogeneity contradicts assumptions that the processes shaping Amazonian animal community diversity are too complex to measure efficiently, and their use contributes a new understanding of the dimensions of that diversity.Item Distribution of mammals in the davis mountains, texas and surrounding areas(Texas Tech University, 2008-08) DeBaca, Robert S.; Zak, John; Bravo, Jorge S.; Phillips, Carleton J.; Mulligan, Kevin; Bradley, Robert D.This project focused on the dispersal and distribution patterns of mammals in or near the Davis Mountains, Texas. Data were obtained from existing museum and literature records and from extensive field sampling of the region, which resulted in the acquisition of more than 2,000 museum specimens and related data (Appendix A). The purpose of this research was to investigate regional and local patterns of mammalian biodiversity as these relate to dispersal and distribution in montane ecosystems at a regional scale in the Trans-Pecos and at a local scale in and near the Davis Mountains. In the first chapter, paleontological data suggested that now isolated mountain ranges in the Trans-Pecos were once connected in a north-south network. Research in that chapter examined modern patterns of biodiversity in the mountains that could have resulted from patterns inherited from Pleistocene distributions and dispersal routes of species in mixed-conifer forests or piñon-juniper-oak woodlands. Evidence presented in chapter one indicated that connectivity to source areas could have improved dispersal opportunities through highland corridors and montane areas. The second research chapter evaluated an observed pattern of greater species richness at a middle elevation study site in the Davis Mountains that was about 15 percent the size of a larger study site in the highlands of this mountain range. Rodents were the focus of research to find a partial explanation for this pattern, in which a dispersal filter may have allowed dispersal of some species but hindered others along an elevational gradient from lowlands to highlands. This pattern suggested a decrease in the body size of a lowland group of species along this gradient in response to a substrate that becomes more unavailable to larger burrowing rodents. That pattern was not statistically significant, but an alternative investigation showed that the smaller mid-elevation site likely had greater habitat variety in comparison to the high elevation one, which could have provided more microhabitats for more species to coexist at the smaller, more diverse site. In the final research chapter, biodiversity patterns were investigated for bats in relation to broad-scaled ecological patterns and site-specific resource partitioning that could account for the observed spatial and temporal distribution patterns. Along an elevational gradient, five species were specific to a smaller series of elevations and habitat types; whereas, twelve species were either too rare to analyze or were widespread throughout the sampled array of environmental conditions. Five species also showed elevational segregation by sex, with females occupying a lower range of elevations than males, which was a surrogate measure of warmer macrohabitat utilization by females. Lastly the most prolific sampling site, a semi-perennial pool, was analyzed for temporal differences in its use by month and by time of night. The results showed that vespertilionid bats dominated use of this resource during mid-summer and during the first two hours of the night and that molossid bats dominated its use after the first two hours and during the latter part of the summer. This partitioning could result from the thermoregulation constraints of the main vespertilionid species that concentrated activity early in the evening and during the warmer months of the sampling period. In response to vespertilionid use and to prevent collisions, the fast-flying, less maneuverable molossid bats may avoid the area until use by other bats dwindles both during the night and warmer months of the season.Item Diversification and evolution of treefrogs in the Cerrado savanna of South America : from population structure to biogeographic patterns(2016-05) Vasconcellos, Mariana Mira; Cannatella, David C.; Wilke, C. (Claus); Bolnick, Daniel I.; Simpson, Beryl B.; Young, Kenneth R.; Ryan, Michael J.Historical and ecological factors underlying population structure and speciation of organisms are fundamental to uncover diversification mechanisms that lead to biogeographic patterns. The main goal of this dissertation is to determine the relative roles of geography and climate promoting diversification in a diverse group of treefrogs in the Cerrado savanna of South America, a hotspot of biodiversity. This dissertation approaches diversification at two different time-scales: from a macro-temporal scale of factors that promote species diversification in the Cerrado region, and from a micro-temporal scale of population divergence and recent cryptic speciation. Three main research goals were developed in separate chapters: (1) Phylogenetic and biogeographic analyses of the species in the Hypsiboas pulchellus group were used to quantify dispersal events between the Cerrado and other dry/open or humid/forested neighboring habitats, and to evaluate how this dynamic historical interchange affected diversification. The evolutionary relationships among the species in this group showed a pattern of multiple recent origins of the endemic Cerrado lineages, indicating recent colonization events. These analyses indicate an interesting pattern of recurrent dispersal among open and forest ecoregions accounting for the accelerated diversification in this group. (2) Species delimitation methods using molecular, morphological and mating call characters were used to study the recent speciation of a small clade of Cerrado endemics. This integrative approach allowed for a better resolution to detect species boundaries and the discovery of cryptic species in spite of conserved morphology and mating calls. (3) Population structure in a widespread Cerrado species was investigated using historical species distribution modeling and next generation sequencing data to evaluate the role of recent climatic fluctuations on population differentiation. Divergence among populations seems strongly affected by Pleistocene climatic instability, a pattern we call isolation-by-instability. In conclusion, this study highlights how diversification and biogeographic patterns in the Cerrado savanna can be affected by its historical dynamic climate and landscape.Item Ectoparasitic assemblages of Paraguayan bats: ecological and evolutionary parspectives(Texas Tech University, 2004-12) Presley, StevenNot availableItem Effect of topography on genetic divergence and phenotypic traits in tropical frogs(2011-08) Guarnizo, Carlos Enrique; Cannatella, David C.; Bull, James J.; Juenger, Thomas; Wilke, Claus; Perez, FranciscoComplex interactions between topographic heterogeneity and steep gradients in climate and environmental conditions are commonly assumed to promote biotic diversification. Using tropical frogs as a model, I investigate the nature of these interactions that disrupt migration between populations, causing genetic divergence and speciation. I determine the role of several putative factors that affect gene flow (Euclidean distances, Least Cost Path (LCP) distances, topographic complexity, and elevation difference) and promote genetic structure (FST) between populations of three tropical Andean frog species. Moreover, I investigate, from an intraspecific perspective, whether montane frog species display on average larger genetic distances per kilometer relative to lowland species. Finally, I test if recent genetic divergence caused by topographic barriers to gene flow is paralleled by independent character systems such as acoustics and morphological traits in the high Andean frog Dendropsophus labialis. Even though the effect of geographic features on migration (and conversely, FST) was species-specific, LCP and Euclidean distances had the strongest effect on migration rate. Topographic complexity also reduced migration rate whereas elevation difference did not have an effect. I found that indeed highland species show larger genetic distances per kilometer between haplotypes than do lowland species. Also, genetic divergence is strongly associated with topographic heterogeneity, which is an intrinsic characteristic of montane regions. Finally, I found that acoustic variation in D. labialis diverges according to genealogical history, but external morphology does not follow this relationship. Stochastic processes due to genetic drift appear to be a better explanatory mechanism for the divergence in calls than adaptive variation. The strong and congruent divergence observed in acoustic and genetic characters indicates that these two groups correspond to morphologically cryptic parapatric species. Overall, the results of this study suggest some of the mechanisms that allow tropical mountains to promote intraspecific genetic divergence. The combined effect of ridges (promoting allopatric differentiation) and environmental gradients across elevation (promoting parapatric differentiation) are effective forces that are present mostly in highland biomes. Unfortunately, such biomes are critically threatened by habitat destruction and climate change, possibly more than any other biome on earth.Item Evolution of microbial populations with spatial and environmental structure(2010-05) Miller, Eric Louis; Meyers, Lauren Ancel; Bennett, Philip C.; Bull, James J.; Hawkes, Christine V.; Hillis, David M.Rarely are natural conditions constant, but generally biologists study microbes in artificially constant environments in the laboratory. I relaxed these assumptions of constant environments through time and space as I investigated how microbial populations evolve. First, I examined how bacteriophage evolved in the presence of permissive and nonpermissive hosts. I found that bacteriophage evolved discrimina- tion in mixed environments as well as in one of two environments with homogeneous, permissive hosts. This showed the asymmetry of host-shifting in viruses as well as the possibility of large, and somewhat unpredictable, pleiotropic effects. Secondly, I reconstructed ancestral environmental conditions for soil bacteria groups using phy- logenetics and environmental variables of extant species’ habitats. These generaliza- tions suggested characteristic phenotypes for several phylogenetic groups, including uncultured Acidobacteria. Lastly, I collected genetic sequences and global collection information for 65 bacteria genera across the domain. In examining the relation- ship between genetic distance, environmental conditions, and geography, I observed positive relationships specifically between genetic distance and geography or genetic distance and environmental conditions for bacteria from land sites but not from wa- ter sites. Phylogenic classifications or phenotypes of the genera could not predict these correlations. In all of these projects, variations in the environment created evolutionary signals that hinted at past environments of microbial populations.Item Molecular phylogenetic studies in the Linaceae and Linum, with implications for their systematics and historical biogeography(2009-12) McDill, Joshua Robert; Linder, C. Randal; Simpson, Beryl Brintnall; Hillis, David; Jansen, Robert K.; Mauseth, James D.Best-known as the family of the cultivated flax, Linum usitatissimum L., the Linaceae is a small but ecologically diverse family of flowering plants, with approximately 250 species distributed throughout the temperate and tropical latitudes of the world. This work is an investigation of the systematics and biogeography of the family and a portion of its largest genus, Linum, using molecular phylogenetic methods. I collected DNA sequences of rbcL and matK genes from 51 species of Linaceae, representing all 14 genera, and combined them with data from 24 other families of the order Malpighiales in phylogenetic analyses. Results strongly support the monophyly of Linaceae and subfamily Linoideae in their current circumscriptions, but subfamily Hugonioideae is poorly supported. Molecular dating analysis suggests that the temperate Linoideae diversified in the Eocene or Oligocene, while tropical Hugonioideae diversified later, during the Miocene, perhaps ruling out Gondwanan vicariance as an explanation for their Pantropical distribution. Hugonia and Linum, the largest genera in their respective subfamilies, are each found have multiple segregate genera nested within them, indicating potential need for taxonomic revision of each subfamily. In Linoideae, I further investigate the phylogeny of a lineage that includes the yellow-flowered Linum sections Cathartolinum, Linopsis, and Syllinum, and the segregate genera Cliococca, Hesperolinon, Radiola, and Sclerolinon, to provide a framework in which to assess character evolution, classification, and biogeography. With data from four chloroplast markers (matK, ndhF, trnK 3’ intron, trnL-F region) and the nuclear ITS, and extensive sampling from Linum section Linopsis from Eurasia, Africa, and the Americas, Hesperolinon and Sclerolinon are shown to be related to a lineage of Central American linums including L. mexicanum Kunth and L. guatemalense Benth., while Cliococca is affiliated with South American Linum. The phylogeny supportes previous hypotheses of the evolution of some taxonomically important characters, and several well-supported lineages are identified which correspond to previously proposed taxonomic groupings. Results also provide evidence for a single trans-Atlantic disjunction and independent Old and New World colonizations of the southern hemisphere in yellow-flowered Linum, occurring during the Miocene.Item The molecular phylogeny of Pectis L. (Tageteae, Asteraceae), with implications for taxonomy, biogeography, and the evolution of C4 photosynthesis(2012-05) Hansen, Debra Rae; Jansen, Robert K., 1954-; Simpson, Beryl BrintnallThis study examines the evolutionary history of Pectis L., a neotropical genus of ~90 species of xeric-adapted, herbaceous, annuals and perennials. Pectis is rare among the Asteraceae, as it uses C₄ photosynthesis, a complex suite of traits that concentrates carbon around Rubisco. Plants with C₄ photosynthesis do well in environments of high light and high heat, and the C₄ syndrome is thought to have evolved as a response to such environments. Pectis is most diverse in Mexico, the Caribbean Islands, and South America, and its distribution mirrors the disjunctions of patches of desert, thornscrub, coastal plains, savanna, and openings in seasonally-dry tropical forests and oak-pine woodlands. Vicariance and long-distance dispersal theories can explain the patchy distribution of xeric-adapted plants, as well as the origin of Caribbean species. To answer evolutionary questions about a group, one must understand how its members are related. The most comprehensive taxonomic treatment of Pectis is over 100 years old, and includes only North American species. Recent revisions still leave half the species unassigned to section. Molecular studies have found Pectis sister to, or encompassing, the genus Porophyllum. To infer evolutionary relationships between and within Pectis and Porophyllum, DNA from the nuclear and chloroplast genomes of 78 Pectis and 22 Porophyllum species were sampled, sequenced, and analyzed. The molecular phylogeny was used to suggest updated sections based on monophyletic groups. To infer the photosynthetic pathway of Pectis and Porophyllum species, carbon isotope ratios were obtained from 62 Pectis and 18 Porophyllum species. The timing and location of the evolution of Pectis and Porophyllum has implications for the evolution of C₄ photosynthesis. The carbon isotope data were combined with the phylogeny to determine the extent and direction of the evolution of C₄ photosynthesis, and the timing of its evolution was inferred from a fossil-calibrated analysis using chloroplast data from species across the Asteraceae. Distribution data was combined with the Pectis phylogeny to answer questions regarding the biogeographical history of Pectis, including questions regarding its disjuncted distribution, the timing of the evolution of desert species, and the timing and pattern of dispersal to and from the Caribbean Islands.Item Molecular systematics and biogeography of Descurainia Webb & Berthel, (Brassicaceae)(2007) Goodson, Barbara Elizabeth; Jansen, Robert K.Descurainia is a genus in the Brassicaceae distributed throughout temperate areas of the Old and New World. The genus is well-known for its taxonomic complexity, especially within New World species, on account of its numerous intergrading forms coupled with circumscriptions dependent upon inconsistent and overlapping characters. Descurainia is most diverse in western North America and western South America, with a smaller center of distribution in the Canary Islands and three additional Old World species. This distribution makes the genus well-suited for addressing biogeographical issues related to New World intercontinental dispersal and evolution in island systems. A molecular-based analysis of Descurainia was conducted using DNA sequences from nuclear ribosomal internal transcribed spacer (ITS), single-copy nuclear Target of Rapamycin (TOR), and non-coding chloroplast regions. The genus, with the inclusion of the monotypic genera Hugueninia and possibly Robeschia, is strongly supported as monophyletic, and appears to be of Old World origin with recent diversification within the Canary Islands and the New World. A phylogeny recovered from combined ITS and chloroplast data is not well-resolved with respect to relationships between some major New World lineages, but suggests that multiple independent dispersals of Descurainia have taken place between North and South America. Substantial incongruence between ITS, chloroplast, and TOR phylogenies, as well as the presence of mixed ITS and TOR sequences, point to a complex evolutionary history involving extensive gene flow and hybridization for North American Descurainia. The molecular data highlight possible problems with current species circumscriptions, especially within North American taxa such as D. incisa, D. obtusa, and D. pinnata. ITS and chloroplast data indicate that species of Descurainia in the Canary Islands are derived via a single colonization event, most likely from southwestern Europe onto the lowland scrub zone on Tenerife. Both intra-island adaptive radiation and inter-island colonization have played a prominent role in the evolution of this genus in the islands. The results presented in this dissertation represent the first comprehensive molecular study of Descurainia, and may serve as a phylogenetic framework for future research on the genus as well as phenomena such as speciation and hybridization in recently-evolved groups.Item Molecular systematics and biogeography of Descurainia Webb & Berthel, (Brassicaceae)(2007-05) Goodson, Barbara Elizabeth, 1959-; Jansen, Robert K., 1954-Descurainia is a genus in the Brassicaceae distributed throughout temperate areas of the Old and New World. The genus is well-known for its taxonomic complexity, especially within New World species, on account of its numerous intergrading forms coupled with circumscriptions dependent upon inconsistent and overlapping characters. Descurainia is most diverse in western North America and western South America, with a smaller center of distribution in the Canary Islands and three additional Old World species. This distribution makes the genus well-suited for addressing biogeographical issues related to New World intercontinental dispersal and evolution in island systems. A molecular-based analysis of Descurainia was conducted using DNA sequences from nuclear ribosomal internal transcribed spacer (ITS), single-copy nuclear Target of Rapamycin (TOR), and non-coding chloroplast regions. The genus, with the inclusion of the monotypic genera Hugueninia and possibly Robeschia, is strongly supported as monophyletic, and appears to be of Old World origin with recent diversification within the Canary Islands and the New World. A phylogeny recovered from combined ITS and chloroplast data is not well-resolved with respect to relationships between some major New World lineages, but suggests that multiple independent dispersals of Descurainia have taken place between North and South America. Substantial incongruence between ITS, chloroplast, and TOR phylogenies, as well as the presence of mixed ITS and TOR sequences, point to a complex evolutionary history involving extensive gene flow and hybridization for North American Descurainia. The molecular data highlight possible problems with current species circumscriptions, especially within North American taxa such as D. incisa, D. obtusa, and D. pinnata. ITS and chloroplast data indicate that species of Descurainia in the Canary Islands are derived via a single colonization event, most likely from southwestern Europe onto the lowland scrub zone on Tenerife. Both intra-island adaptive radiation and inter-island colonization have played a prominent role in the evolution of this genus in the islands. The results presented in this dissertation represent the first comprehensive molecular study of Descurainia, and may serve as a phylogenetic framework for future research on the genus as well as phenomena such as speciation and hybridization in recently-evolved groups.Item Molecular systematics of Meconopsis Vig. (Papaveraceae): taxonomy, polyploidy evolution, and historical biogeography from a phylogenetic insight(2013-12) Xiao, Wei, active 2013; Simpson, Beryl BrintnallKnown as the Himalayan poppies or the blue poppies, Meconopsis is a genus with approximately 50 species distributed through the high altitude of the Himalaya and the Hengduan Mountains (SW China). This dissertation is a study of the systematics of Meconopsis primarily using molecular phylogenetic methods. DNA sequences of chloroplast matK, ndhF, trnL-trnF, rbcL, and nuclear ITS were collected to reconstruct the phylogenies of the genus. Results showed that traditional Meconopsis is a polyphyletic group and revealed extensive mismatches between the nuclear ITS tree and the chloroplast tree. Based on the phylogenies, the taxonomy of Meconopsis was revised, making Meconopsis monophyletic. Four new sections (sect. Meconopsis, sect. Aculeatae, sect. Primulinae, and sect. Grandes) were proposed as well as a species complex (M. horridula). The chloroplast phylogeny and a likelihood method (chromEvol) were applied to ancestral chromosome number estimation to reconstruct the polyploidy evolution history of the genus. The analysis recovered an ancient triploid ancestor shared by sect. Primulinae and sect. Grandes. A low-copy nuclear gene (GAPDH) network of Meconopsis was further reconstructed, which indicated that the ancient triploid ancestor was formed by hybridization. A hypothesis of reticulate history of Meconopsis was also proposed based on the GAPDH network. Using a reconstructed rbcL phylogeny of Ranunculales, the stem group of Meconopsis was estimated at ca. 22 Mya by molecular dating, which coincided with the time of Asian interior desertification and the onset of Asian monsoon. These climatic changes could possibly have been the impetus for the split between Meconopsis and its sister clade. Ancestral area reconstruction was further conducted using likelihood-based methods. The result indicated that Meconopsis originated in the Himalaya, most likely in the west Himalaya, followed by migration to the Hengduan Mountains.Item Phylogeny, biogeography and systematics of Menodora (oleaceae) and the chloroplast genome of Pelargonium × hortorum(2007-05) Chumley, Timothy Wayne; Jansen, Robert K., 1954-; Levin, Donald A.This dissertation presents the result of two separate research programs. The first elucidates the phylogeny, biogeography and systematics of the genus Menodora in the olive family. A phylogeny based on the internal transcribed spacer (ITS) of nuclear ribosomal DNA and the chloroplast rps16 and trnL introns and trnL-F intergenic spacer demonstrates that the genus is monophyletic. Within the genus, M. robusta of Patagonia is the first taxon to branch, followed by a monophyletic African clade and M. spinescens of California, though the placement of the latter does not have strong support. Most North American species are nested within the derived South Americans. A South American origin is hypothesized, with two independent dispersals to North America, and a single dispersal to Africa. The phylogeny provided new insights for the systematic treatment, where 24 species, one subspecies and six varieties are recognized, with major realignments of the intregrifolia and scabra species complexes, and a single new species described. In the second area of research, the chloroplast genome of Pelargonium × hortorum has been completely sequenced. At 217,942 base pairs (bp), it is both the largest and most rearranged land plant chloroplast genome yet sequenced. It features two copies of a greatly expanded inverted repeat (IR) of 75,741 bp each, and diminished single copy regions of 59,710 bp and 6,750 bp. Gene content is similar to other angiosperms, with the exceptions of a large number of pseudogenes, two open reading frames (ORF56 and ORF42), and the losses of accD, trnT-ggu, and possibly rpoA. The latter may be represented, however, by highly divergent set of rpoA-like ORFs. The IR expansion accounts for most of the size increase of the genome, but an additional 10% is related to the large number of repeats found. Most of these occur near rearrangement hotspots, and two different repeat associations (characterized by full or partial duplications of several genes) are localized in these regions. We propose simple models that account for the major rearrangements with a minimum of eight IR boundary changes and 12 inversions in addition to several sequence duplications.Item A re-evaluation of crinoid morphology and proposed relationship of crown groups, with insights from biogeography(2011-08) Womack, Kyle Richard; Sprinkle, James, 1943-; Molineux, Ann; Rowe, TimothyCrinoids are the most primitive living members of the Phylum Echinodermata. Though still present in reduced numbers today, crinoids were the dominant echinoderms from the Ordovician to the Permian. The crinoid body plan consists of three major regions, the column, the calyx, and the arms. Each region serves important functions in crinoids. The column raises the rest of the body into the water column for more efficient feeding. The calyx contains the visceral mass and mouth. Arms extend out from the top of the calyx to trap microorgansisms and suspended organic particles in the water column. A re-evaluation of these functional units is undertaken to understand the importance of various structures and to obtain discrete characters for use in a cladistic analysis. The relationship of crinoid crown groups has been an active area of research for the past couple of decades. With each proposed phylogenetic relationship, a new interpretation of thecal plate homology has been proposed. Here each study is re-examined in the light of new data. A review of functional morphology indicates a dual-reference system to be the most supported interpretation of plate homology. The two reference points in this system are the stem-cup and the cup-arm junctions, at the top and bottom of the calyx. The difference between a two-circlet and three-circlet crinoid is the presence or absence of the middle (basal) circlet. A new cladistic analysis is presented, with the topology of trees obtained giving support for the retention of Paleozoic crinoid stem and crown groups. Crinoids appear abruptly in the fossil record. Questions pertaining to origins and ancestral stock abound. A biogeography study is employed to look at the distribution of crinoids from the Early to Middle Ordovician. Locality information, combined with an understanding of the movement of major plates, paleoclimate data, an understanding of larval distribution, and a review of similar studies carried out on different taxa, gives insight into possible radiation and dispersal patterns of crinoids from the first half of the Ordovician.Item Scale and process : primate and non-primate mammal community composition and diversity in Madagascar(2015-05) Bannar-Martin, Katherine Hilary; Lewis, Rebecca J., 1972-; Leibold, Mathew A; Reed, Denne N; Di Fiore, Anthony; Hopkins, Mariah EThe study of community assembly, or the processes that shape the occurrence of species in an ecological community, is a fundamental area of inquiry in ecology. Patterns in community composition and diversity are attributed to the combined operation of deterministic (e.g., environmental sorting), stochastic (e.g., dispersal limitation), and biogeographic (e.g., dispersal barriers) processes. Environmental sorting results in communities composed of species that are ecologically adapted to their environment. Dispersal limitation results in communities shaped by the dispersal distance between sites. Biogeographic dispersal barriers prevent species dispersal between sites, and community membership is dependent upon site isolation. Community assembly is also dependent upon diversity type (taxonomic, functional, or phylogenetic) and spatial scale. I investigated the processes shaping the diversity of primate and nonvolant mammal communities using taxonomic, functional and phylogenetic diversity measures and a spatially explicit modelling approach. I described mammal diversity patterns at ecoregional, regional, and inter-regional scales within and across Madagascar and Australia. I tested the relationship of mammal community diversity to environmental, spatial, and biogeographic variables, indicating deterministic, stochastic, and biogeographic processes, in Madagascar and Australia. First, I found that arboreal mammal communities in Madagascar were more dispersal-limited than terrestrial mammal communities. Second, a combination of environmental sorting and dispersal limitation best explained primate taxonomic and functional diversity. Third, I tested for convergent diversity and assembly patterns in Madagascar and Australia, due to similar biogeographic and evolutionary histories, and found non-convergent patterns. Overall, biogeographic dispersal barriers were weak predictors of mammal diversity in Madagascar and Australia. Phylogenetic and functional diversity measures were weakly correlated, and phylogenetic diversity provided models with weak explanatory power. Environmental and spatial variables indicating the combined operation of environmental sorting and dispersal limitation variably shaped the taxonomic and functional diversity of mammal communities in Madagascar and Australia. Mammal community diversity was regionally specific, shaped by the unique historical and landscape components of each region, including ecoregional effects and the extinction of sympatric species. Macroscale studies of diversity should carefully investigate the influence of spatial scale and regional factors that can result in varied assembly patterns and unique ecological communities, such as those present for the nonvolant mammals of Madagascar and Australia.Item Species diversity of aquatic macroinvertebrates in playa lakes: island biogeographic and landscape influences(Texas Tech University, 1997-12) Hall, Dianne L.Patterns of species diversity have long intrigued ecologists. This fascination has resulted in numerous theories explaining differences among sites in species diversity. Two such theories are those pertaining to island biogeography and landscape ecology. They differ in the import placed on patch versus matrix characteristics. Island biogeographic theory suggests that patch characteristics are the foremost influences on diversity. Conversely, landscape ecology proposes that attributes of the surrounding matrix are of primary significance. Playas of the Southern High Plains are an excellent environment in which to study the relative influence of patch versus matrix characteristics. They are numerous and surrounded by a mosaic of landuse practices. These ephemeral lakes differ greatly in size and contain an abundance of aquatic macroinvertebrates. Macroinvertebrates were sampled three times over a two month period and were categorized as resident or transient species based on life history characteristics. Species richness and diversity were analyzed for the effects of landuse practices, basin size, and surface area via analysis of covariance. In addition, G-tests of independence were used to analyze the influence of landuse practices and surface area on species composition. Surrounding landuse practices were found to influence resident species richness and species composition; total species richness was sensitive to basin size. Surface area affected total, resident, and transient species richness, resident species diversity, and species composition. However, all relationships were contingent on sampling period. Regression analyses revealed that resident species richness and diversity were influenced more by island biogeographic characteristics than by landscape attributes. However, the converse was true for transient species richness and diversity. Neither resident nor transient species richness and diversity were related strongly to differences in water quality. Both island biogeographic and landscape characteristics affect the diversity of macroinvertebrates in playa lakes. However, the extent of the influence of these two factors is dependent on life history strategy of the biota and time since inundation. The idiosyncratic pattern of species diversity is a reflection of the stochastic nature of playa inundation overlain by the effects of island biogeographic and landscape processes.Item Use of Broad-scale data to assess changes of scaled quail populations in Texas(Texas Tech University, 2000-08) Leyva-Espinosa, Raquel IreneScaled quail {Callipepla squamata) is an upland species that has declined in areas of historical distribution in Texas. Potential causes for the present decline have been attributed to precipitation and changes in landscape characteristics. The effects of long-term landscape modification, precipitation variation, and scaled quail populations were evaluated using a Geographic Information System (GIS). Three databases were included in the construction of the GIS. The first database included records for precipitation for the state of Texas from 1968 through 1997. The second database consisted of Multispectral Scanner (MSS) satellite images for the state of Texas obtained during 1973, 1986, and 1991 to determine land use and land cover changes. Finally, the third database consisted of annual records for scaled quail population in Texas from 1968 through 1997. The objective of this project was to evaluate the use of broad-scale data to describe local reduction of scaled quail densities in Texas due to (1) changes in suitable habitat; (2) temporal precipitation variation; and (3) the combined effect of long-term habitat modifications and temporal climatic variation. The temporal distribution of precipitation was studied for two main rainy seasons, corresponding to the months of April-June (first rainy season) and July-September (second rainy season). Temporal precipitation variability and scaled quail population trends were analyzed using cross-spectral analysis for time series to determine whether or not these series were correlated. Scaled quail data were obtained from Breeding Bird Survey records for the 1968-1997 period. Long-linear models were used to determine scaled quail population trends at individual Breeding Bird Survey routes, ecoregions, and the area of scaled quail distribution in Texas. Two ecoregions were not included in the analysis due to the lack of data. A landscape gradient including rangelands, cultivated lands, water bodies, and urban areas was created to determine changes in suitable habitat during 1973, 1986, and 1991. Scaled quail population densities were compared at state, ecoregion, and Breeding Bird Survey route. Analysis of the temporal distribution of climatic parameters suggested the presence of annual trends plus lag-times that varied from 2 to 11 years; however, most sites presented periods ranging between 2 to 3 years. The use of cross-spectral analysis suggested that scaled quail populations in the Basin and Range and the Rolling Plains ecoregions were cross-correlated with precipitation. The Rio Grande Plain and the Texas High Plains ecoregions did not present strong correlations between scaled quail and either rainy season. Multiple regression indicated that changes in precipitation explained changes in scaled quail for ecoregions were the species is distributed; however, only the Basin and Range ecoregion presented statistically significant slopes. The combined effect of precipitation and vegetation did not explain changes in scaled quail populations in the Texas High Plains ecoregion. The combination of vegetation and precipitation influenced scaled quail only in the Rolling Plains but the slopes were not statistically significant. The lack of complete scaled quail records presented a big problem in the analysis of the population trends for the complete distributional range of the species. However, it provided a potential tool to determine changes at the ecoregion level. To develop state- wide management plans for scaled quail populations in Texas, the first step was to develop complete data sets. Scaled quail populations generally have declined in the past 3 decades. This negative trend may have been influenced by the combination of the temporal and spatial distribution of climatic parameters and habitat modification, however the lack of a strong data set may weaken results making them inconclusive and contradictory. The methodology used in this research provided alternatives to handle missing values and the presence of potential lag-effects in the data. These techniques in combination with more complete databases may provide, in the future better estimations of the relationships between scaled quail and long-term habitat modifications at different scales. Also the use of GIS allowed the integration of large databases to aid in the analysis of potential causes for scaled quail decline in the state of Texas. This approach may also provide the tools for management of other species.