Only thirty known species have populations at high latitudes in both hemispheres, this is, a bipolar distribution. Five of them belong to the genus Carex. Before attempting to elucidate the origins of such distributions, we need to resolve taxonomical problems that are typically encountered in such species. We focus on the Carex capitata complex, which includes Carex arctogena as a bipolar species, in worldwide scope sampling. A morphometric study and phylogenetic analyses based on maximum parsimony, Bayesian inference and Statistical Parsimony have revealed: a) C. capitata and C. arctogena are different species; b) C. anctarctogena is a synonym of C. arctogena and c) a great biodiversity previously undetected in western North America that could lead to the description of three new taxa (“Carex cayouetteana”, Carex sp. nov. 1 and 2) comprised in the so called “C. cayouetteana” lineage. More studies are needed in some C. capitata samples from Russia that appears in the molecular analyses in a strongly supported clade.

Orientador: Vera Nisaka Solferini / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-26T20:50:57Z (GMT). No. of bitstreams: 1 Peres_ElenArroyo_D.pdf: 4419188 bytes, checksum: 1e99ff3fa29d44a021ecf49304ad863b (MD5) Previous issue date: 2015 / Resumo: Neste trabalho estudamos os padrões filogeográficos de duas espécies de aranhas do gênero Araneus (Araneidae) visando contribuir para o entendimento da biogeografia da região Neotropical. Para as duas espécies, realizamos estimativas de diversidade e estrutura genética, redes de haplótipos, inferências filogenéticas e análises demográficas utilizando um marcador mitocondrial (Citocromo Oxidase I, COI) e um nuclear (Internal Transcribed Subunit II, ITS2); e apresentamos os resultados em dois manuscritos. No primeiro, "Pleistocene niche stability and lineage diversification in the subtropical spider Araneus omnicolor", testamos a influência das oscilações climáticas do Quaternário sobre a demografia de A. omnicolor, uma espécie restrita à porção subtropical da América do Sul. Modelagens paleoclimáticas indicaram que a distribuição de A. omnicolor permaneceu estável ao longo do Pleistoceno tardio. Além disso, a comparação entre 14 modelos demográficos por meio de Approximate Bayesian Computation (ABC) apontou como mais provável o modelo de panmixia com estabilidade, embora as demais análises demográficas tenham indicado expansão recente, sugerindo um cenário complexo para a espécie. No segundo manuscrito, "Conexões entre Amazônia e Mata Atlântica reveladas por Araneus venatrix", analisamos os padrões filogeográficos de A. venatrix, que ocorre em ambientes úmidos em toda a região Neotropical (Amazônia, Mata Atlântica e matas de galeria localizadas na diagonal seca entre esses biomas). Detectamos uma profunda divergência entre um clado restrito ao sul da Mata Atlântica e outro distribuído em todo o restante do Brasil datada do Mioceno tardio. Os resultados indicam que a expansão do Cerrado e consequente separação das florestas úmidas coincidem com um progressivo esfriamento e ressecamento ao longo do Terciário, ainda que certa conectividade entre esses biomas tenha permanecido. As análises mostraram que as populações da porção norte na Mata Atlântica são geneticamente mais semelhantes às da Amazônia do que às da porção sul, indicando que os processos ligados à diversificação de linhagens desses dois biomas não são completamente independentes. Este trabalho mostrou que estudos com táxons de ampla ocorrência geográfica contribuem com informações importantes sobre a história das florestas úmidas Neotropicais. Os dois manuscritos sugeriram cenários intrigantes para a América do Sul e revelam a importância de mais trabalhos com organismos como as aranhas, muito abundantes e ainda pouco explorados nos Neotrópicos. Nossos resultados contribuem para o conhecimento geral do grupo e também a compreensão da história biogeográfica da região Neotropical / Abstract: In this work, we have studied the phylogeographic patterns of two spiders of the genus Araneus (Araneidae) to contribute to the knowledge about the biogeography of the Neotropical region. For both species, we estimated the genetic diversity, the population structure, haplotype networks, phylogenetic inferences and the demographic history using one mitochondrial (Cytochrome Oxidase I, COI) and one nuclear (Internal Transcribed Subunit II, ITS2) marker; and presented the results in two separate manuscripts. In the first, "Pleistocene niche stability and lineage diversification in the subtropical spider Araneus omnicolor", we have tested the influence of the Quaternary climatic oscillations on the demography of A. omnicolor, a species restricted to South American subtropical region. The paleoclimatic modeling indicated that A. omnicolor¿s distribution remained stable during the Late Pleistocene. Besides, the comparison among 14 demographic models through an Approximate Bayesian Computation (ABC) approach pointed to panmixia with stability as the most probable model, although the other demographic analyses had indicated recent expansion, suggesting a complex scenario for this species. In the second manuscript, "Conexões entre Amazônia e Mata Atlântica reveladas por Araneus venatrix", we have analyzed the patterns of A. venatrix, a species that occurs in humid Neotropical environments (Amazonia, Atlantic Forest and gallery forests located in the dry diagonal between these biomes). We have detected a deep divergence between a clade restricted to Southern Atlantic Forest and the other, distributed in all other Brazilian regions, on Late Miocene. These results suggest that the expansion of Cerrado biome and the consequent split of rainforests are coincident with a progressive cooling and dryness that occurred during the Tertiary, although some degree of connectivity between these biomes had remained until today. The analyses showed that the northern Atlantic Forest populations are genetically more similar to Amazonian populations than to the ones from southern Atlantic Forest, indicating that the processes related to the lineages diversification in these biomes are not completely independent. This work has showed that studies focused on widely distributed taxa contribute with important information regarding the history of Neotropical Rainforests. Both manuscripts suggest intriguing scenarios for South America and reveal the importance of more research with organisms as spiders, which are abundant but scarcely explored in Neotropics. Our results contribute to the general knowledge of the group and also to a better comprehension of the biogeographic history of Neotropical region / Doutorado / Genetica Animal e Evolução / Doutora em Genética e Biologia Molecular

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第22480号 / 農博第2384号 / 新制||農||1075(附属図書館) / 学位論文||R2||N5260(農学部図書室) / 京都大学大学院農学研究科森林科学専攻 / (主査)教授 吉村 剛, 教授 井鷺 裕司, 講師 YANG Chin-Cheng / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Bobcats (Lynx rufus) are generalist carnivores with an expansive range from southern Canada to northern Mexico, in which 11 - 12 subspecies have been described. Since European settlement, bobcat habitat has become increasingly fragmented due to urbanization and development of agricultural land. Presently, there is little information on the genetic structure of bobcat populations at large spatial scales. Furthermore, it is unknown whether the current isolation of bobcat populations is a historic feature or whether recent landscape alterations have disrupted dispersal among previously connected populations. To address these questions, microsatellite and mitochondrial DNA data were used for relatedness measurements, spatial autocorrelation examinations, Bayesian assignment testing and sequence analysis of bobcats across their range. These analyses showed that, within southern Illinois, females were closely related to one another and males tended to disperse from their natal area. On a regional scale, microsatellite data revealed several distinct genetic groups within the midwest, notably eastern and western bobcat populations. In contrast, mitochondrial DNA analyses resolved little differentiation among bobcat populations, elucidating two-three phylogeographic groups. Taken together, these data reveal that bobcats have not historically, experienced large barriers to dispersal. Rather, recent habitat alterations may be disrupting dispersal over large scales. Genetically defined groups are potential conservation units and should be used for regional management of bobcats.

There are seven living species of gars in two genera (Lepisosteiformes: Actinopterygii). In my first chapter, I estimate phylogenetic relationships among six of them using DNA data generated from four complete mitochondrial loci (cytb, CR, 12S, and 16S) and a single, partial nuclear locus--recombination activating protein 1 (RAG1) intron. A single outgroup taxon, the bowfin (Amia calva), was included in my analyses. Regardless of optimality criterion (genetic distance, parsimony, maximum likelihood, and Bayesian inference), a single, well-supported phylogeny estimate emerged. Both sister genera (Atractosteus and Lepisosteus) were monophyletic. Within Atractosteus, A. spatula paired with A. tropicus in the absence of data from A. tristoechus. Within Lepisosteus I recovered two sister pairings of species: L. platyrhincus and L. oculatus; and L. ossues and L. platostomus. I estimated the phylogenetic position of the seventh gar species, A. tristoechus, using DNA data generated from several partial mitochondrial loci and 105 morphological characters. In this analysis, within a monophyletic Atractosteus I recovered a well-supported sister pairing between A. spatula and A. tristoechus, with A. tropicus sister to the pair. My molecular phylogenies largely agree with recent morphologically-based phylogenies aside from the positions of L. ossues and L. platostomus. Using dates associated with the best fossil data available (244 Ma minimal age of the node joining bowfins to gars, and 100 Ma for Lepisosteidae), I estimated divergence dates under a relaxed molecular clock model in a Bayesian framework. Estimated ages for lineages ranged from approximately 50 Ma for Lepisosteus, 23 Ma for the split between L. oculatus and L. platyrhincus, 28 Ma on the L. osseus and L. platostoms divergence, and 30 Ma for the node uniting A. spatula and A. tropicus--dates ranging from the Early Eocene to the Early Miocene. In my second chapter, I conducted basic phylogeographic investigations into the geographical structuring of gene genealogies built with mitochondrial D-loop sequences from 115 individual gars, belonging to five species (A. spatula, L. osseus, L. platostomus, L. platyrhincus and L. oculatus) and collected from a broad array of localities. Across species, across localities, I found some phylogeographic structuring in L. osseus and L. oculatus. I found one unique set of haplotypes confined to L. osseus in the Pee Dee River drainage of North Carolina. The level of molecular divergence between these and other L. osseus haplotypes was similar to that among gar species. I found evidence that there might be mixing of haplotypes across a contact zone between L. platyrhincus and L. oculatus in the Florida Panhandle. I found significant molecular divergence among populations of L. osseus and L. oculatus distributed among drainages to the Gulf of Mexico. However little genetic divergence was detected among populations of L. osseus, L. platostomus and L. oculatus within the Mississippi River basin. In my third chapter I present pilot work into characterizing the origins of a population of morphologically unusual gars in eastern Wisconsin. The longnose gar, Lepisosteus osseus, and the shortnose gar Lepisosteus platostomus are native to Wisconsin. In the Fox and Wolf River systems in eastern Wisconsin there is a third form that superficially resembles the spotted gar, L. oculatus (not previously reported to occur in Wisconsin) in that is exhibits heavy head and body pigmentation and a relatively short, broad snout. After initial molecular phylogenetic analyses showed that these gars did not belong to L. oculatus, results of more detailed molecular investigations, coupled with simple morphological findings, are consistent with the hypothesis that these unusual gars may be hybrids of L. platostomus and L. osseus. Further molecular and morphological investigations must be conducted to definitively infer hybrid status for these unusual gars.

One of the original goals of phylogeography was to use genetic data to identify historical events that might contribute to breaks among biotic communities. In this study, we examine the phylogeography of a common livebearing fish (Poecilia gillii) from Costa Rica. Our goal was to see if phylogeographic breaks in this species were congruent with previously-defined boundaries among four fish community provinces. We hypothesized that if abiotic factors influence both community boundaries and genetic structuring in P. gillii then we would find four monophyletic clades within our focal species that were geographically separated along community boundary lines. Similarly, we expected to find most of the genetic variation in P. gillii partitioned among these four geographic regions. We generated DNA sequence data (mitochondrial cyt b and nuclear S7 small ribosomal subunit) for 260 individuals from 42 populations distributed across Costa Rica. We analyzed these data using phylogenetic (parsimony and likelihood) and coalescent approaches to estimate phylogenetic relationships among haplotypes, patterns of gene flow, and effective population size. Contrary to our expectations, we did not find four monophyletic groups that mapped cleanly to our geographic community provinces. However, one of our clades was restricted to a single province, suggesting that common earth history events could be responsible for both genetic structuring in P. gillii and fish community composition in this area. However, our results show a complex pattern of gene flow throughout other regions in Costa Rica where genetic structuring is not governed by community province boundaries.

Cave systems and their unique biota are widely viewed as highly endangered, yet very little is known about basic life history, ecology, distributions, habitat requirements, and evolutionary relationships of subterranean species. The crux of the problem in cave studies is the assumption that traditionally defined morpho-species represent distinct evolutionary lineages. Convergence is exhibited in the morphologies of many animal groups, vertebrate and invertebrate, which leads to confusion in diagnosing species' boundaries, geographic distributions, gene flow routes, and imperilment. This dissertation research includes phylogeographic analyses of freshwater cave-dwelling crayfishes in the Southern Appalachians, a global hotspot of subterranean biodiversity. By examining population structure in light of habitat, geology, geography, and hydrology, we can better provide conservation direction for these groundwater species. Chapter one introduces a method, Nested Clade Phylogeographic Analysis (NCPA), used to investigate hypotheses about historical and current population structures within species. Using a statistically-testable framework, NCPA can elucidate historical speciation patterns and current routes of gene flow using genetic sequence data of thoroughly-sampled species. Using diverse examples, the chapter details the methodology of building haplotype networks, performing the geographic analyses, inferring past and contemporary evolutionary patterns and processes, and delineating species' boundaries. Chapter two examines two competing hypotheses regarding conservation status of cave-dwelling species using a wide-ranging group of obligate subterranean crayfish species on the Cumberland Plateau's western escarpment. Using a population genetic approach, cave crayfish exhibited moderate to high levels of genetic diversity and attained large population sizes over their evolutionary histories. Phylogeographic analyses revealed that this crayfish assemblage originated along the northern end of the Cumberland Plateau and in leading-edge small steps, colonized southward and accumulated diversity along the way. Current species' boundaries do not match traditional morpho-species designations and also do not match current hydrological units. Chapter three explores phylogeography and habitat differences within the facultative cave-dwelling crayfish species Cambarus tenebrosus. This freshwater species is unique in that it inhabits surface and subsurface karst environments, has an unusually large distribution, and exhibits troglomorphism with reduced eyes and elongated limbs. Using sequence data from over 100 sampled localities, mostly along the Cumberland Plateau, C. tenebrosus appears to have inhabited surface and subsurface biomes throughout its evolutionary history. Additionally, this species shows extremely high levels of genetic diversity and NCA revealed significant phylogeographic structure within the species, but there was no significant relationship between habitat and genetic structure. Chapter four examines the obligate cave crayfish assemblage, genus Cambarus, subgenus Aviticambarus, which ranges across the southernmost area of the Southern Appalachians, which is known to contain the highest species diversity of obligate terrestrial animals in the United States. The Aviticambarus assemblage is only currently known from 58 caves in Alabama and Tennessee, and with samples from half of the known sites, this study uncovered additional lineages previously obscured by convergent morphology. These species show low levels of genetic diversity and populations that do not appear to be expanding. Species' boundaries are supported by geologic and phylogeographic information, but not current drainage basin boundaries.

Canary grasses (Phalaris, Poaceae) include 21 species widely distributed throughout temperate and subtropical regions of the world with centers of diversity in the Mediterranean Basin and western North America. The genus contains annual/perennial, endemic/cosmopolitan, wild, and invasive species with basic numbers of x=6 (diploid) and x=7 (diploid/tetraploid/hexaploid). The latter display vastly greater speciation and geographic distribution. These attributes make Phalaris an ideal platform to study species diversification, dispersal, historic hybridization, polyploidy events, and chromosome evolution in the grasses. This body of research presents the first molecular phylogenetic and phylogeographic reconstruction of the genus based on the nuclear ITS and plastid trnT-F DNA regions allowing species relationships and the importance of polyploidy in speciation to be assessed. Divergence dates for the genus were determined using Bayesian methods (BEAST, version 1.6.2) and historic patterns of dispersal were analyzed with RASP (version 2.1b). Self-incompatibility and the feasibility of hybridization between major groups within the genus were studied with a series of greenhouse experiments. Acetocarmine and fluorescent staining techniques were used to study the morphology of the chromosomes in a phylogenetic context and the nuclear DNA content (C values) was quantified using flow cytometry. Four major clades were revealed in the genus with cytological and geographic affinities leading to the establishment of two subgenera and four sections in the first comprehensive infrageneric treatment of Phalaris. Divergence dating revealed a Miocene emergence (20.6-8.4 MYA) for the genus which is concurrent with studies of other genera in the Aveneae tribe. The hypothesis stating that Phalaris originated in the Mediterranean Basin and dispersed to the New World via a western route leading to a secondary center of diversification in western North America was supported by phylogeographic and cytological analyses. An empirical study comparing the weight, length, and width of the florets by morphological type and cytotype revealed significant differences that support a dispersal advantage among the New World and Arundinacea species. The x=6 species displayed greater intraspecific C value variation, higher DNA content per haploid chromosome set, and a distinct karyotype compared with the x=7 species indicating a complex history of chromosome evolution. / Ph. D.

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