Dissertação(mestrado) - Universidade Federal do Rio Grande, Programa de Pós–Graduação em Oceanografia Biológica, Instituto de Oceanografia, 2013. / Submitted by Cristiane Gomides (cristiane_gomides@hotmail.com) on 2013-10-09T18:43:46Z No. of bitstreams: 1 Heloise.pdf: 1525937 bytes, checksum: 44441e69ced9544eaba26ec6b8f8e2d9 (MD5) / Approved for entry into archive by Sabrina Andrade (sabrinabeatriz@ibest.com.br) on 2013-10-17T03:12:06Z (GMT) No. of bitstreams: 1 Heloise.pdf: 1525937 bytes, checksum: 44441e69ced9544eaba26ec6b8f8e2d9 (MD5) / Made available in DSpace on 2013-10-17T03:12:06Z (GMT). No. of bitstreams: 1 Heloise.pdf: 1525937 bytes, checksum: 44441e69ced9544eaba26ec6b8f8e2d9 (MD5) Previous issue date: 2013 / População é a unidade fundamental da conservação e sua forma mais simples de monitoramento envolve a amostragem temporal regular para a determinação do status populacional. Uma das populações de baleia jubarte do Hemisfério Sul utiliza a costa do Brasil entre maio e dezembro para se reprodução e criação dos filhotes. Esta população, denominada “estoque reprodutivo A” pela Comissão Internacional da Baleia, tem mostrado sinais de recuperação após um marcado declínio devido a caça e um longo período de moratória. Esta população se concentra principalmente no Banco dos Abrolhos (BA), onde águas calmas e quentes parecem constituir um hábitat ideal. Este estudo teve o objetivo de estimar o tamanho da população de jubartes para o ano de 2011, bem como predizer a distribuição de grupos na costa brasileira. O método de amostragem de distâncias foi implementado, e modelos hierárquicos Bayesianos foram propostos para estimar a abundância. Modelos auto-regressivos condicionais foram aplicados para predizer a densidade em células de 0.5° de latitude e longitude. O tamanho da população foi estimado em 10,160 baleias (Cr.I.95%=6,607-17,692). As maiores densidades foram encontradas entre o Banco dos Abrolhos e a Baía de Todos os Santos (BA). Os resultados sugerem que o aumento populacional acarreta a expansão da população para além do Banco dos Abrolhos. / Population is the fundamental unit of conservation and its simplest monitoring tool involves regular sampling over time for population assessing status. One of the Southern Hemisphere humpback whale populations winters at the Brazilian coast typically from May to December where breeding and calving occur. This population, labeled as “breeding stock A” by International Whaling Commission, has shown signs of recovery after the long period of whaling. The goal of this study was to estimate the population size of humpback whales up to 2011, and predict group distribution along the Brazilian coast. Distance sampling methods were implemented and hierarchical Bayesian models were proposed to estimate abundance. Conditional auto-regressive models were used to predict the density in a lattice of 0.5° of latitude and longitude. Population size was estimated at 10,160 whales (Cr.I.95%=6,607-17,692). Highest densities were predicted to occur between Abrolhos Bank and Todos os Santos Bay (BA). The results suggest that the population increase leads to a population expansion beyond Abrolhos Bank.

A obtenção de genótipos superiores no melhoramento de plantas depende da existência de variabilidade genética. A existência de coleções de germoplasma representativas e a utilização de um tamanho adequado de amostra são fundamentais para a preservação das frequências alélicas e genotípicas, diminuindo a perda de variabilidade genética e postergando o aparecimento dos efeitos da deriva genética. Assim, teve-se como objetivo avaliar os efeitos da deriva genética em caracteres quantitativos em subpopulações de milho. Este estudo foi realizado a partir das populações originais BR-105 e BR-106, das quais 10 subpopulações foram obtidas em cada um dos cinco ciclos sucessivos de amostragem com tamanho efetivo reduzido, totalizando 50 subpopulações para cada população original, as quais foram posteriormente autofecundadas, gerando um nível a mais de endogamia. Os tratamentos foram constituídos de 10 amostras da população original sem autofecundação, 10 amostras com autofecundação, 50 subpopulações obtidas da população original e 50 subpopulações autofecundadas, totalizando 120 tratamentos para cada população, avaliados separadamente. Utilizou-se o delineamento em blocos casualizados no esquema de parcelas subdivididas em faixas hierárquico, em quatro ambientes com duas repetições por ambiente. Os caracteres avaliados foram produção de grãos (PG), prolificidade (PROL), comprimento e diâmetro de espigas (CE e DE), número de fileiras por espiga (NFE), número de grãos por fileira (NGF), altura de planta e espiga (AP e AE), florescimento masculino e feminino (FM e FF) e número de ramificações do pendão (NRP). Foram estimados os efeitos da deriva genética entre as médias das subpopulações nos dois níveis de endogamia e os efeitos da depressão por endogamia nas subpopulações dentro dos ciclos. Posteriormente, realizaram-se análises de regressão linear para as subpopulações nos dois níveis de endogamia, separadamente, e em conjunto. Foi verificada uma grande variação nas médias das subpopulações ao longo dos ciclos, indicando que a deriva genética causou diferenciação entre as mesmas e que estas se diferenciaram das populações originais. Detectaram-se efeitos significativos da deriva genética nas populações não autofecundadas para todos os caracteres avaliados, em maior número para PG, já que este caráter é mais sensível à deriva genética por possuir maior grau de dominância que os demais. Houve diminuição no número de estimativas de deriva significativas para as populações autofecundadas, incluindo mudanças na magnitude e no sinal das mesmas em relação às populações não autofecundadas. Para as estimativas de depressão por endogamia, os caracteres PG, NGF, FM e FF apresentaram maior quantidade de estimativas significativas que os demais. Para a maioria dos caracteres, a regressão linear explicou a maior parte da variação encontrada com o aumento dos coeficientes de endogamia. As populações BR-105 e BR-106, por terem estruturas genéticas distintas, apresentaram performances diferentes quanto aos efeitos da deriva genética. Enfim, como a deriva genética interfere na integridade genética das populações, torna-se importante considerar seus efeitos na coleta e manutenção dos bancos de germoplasma e nas populações utilizadas no melhoramento genético de plantas. / Obtaining superior genotypes in plant breeding depends on the existence of genetic variability. The existence of representative germplasm collections and the use of appropriate sample size are essential for preserving allelic and genotypic frequencies, reducing loss of genetic variability and delaying genetic drift effects. This study aimed to evaluate the effects of genetic drift in quantitative traits in subpopulations of maize. The original populations used were BR-105 and BR-106, of which 10 subpopulations were obtained in each five successive sample cycles with reduced effective size, accounting 50 subpopulations for each original population that were subsequently selfed to generate an additional level of inbreeding. The treatments consisted in 10 samples of the original population, 10 samples of the selfed original population, 50 non selfed subpopulations obtained from the original population and 50 selfed subpopulations, accounting 120 treatments for each population evaluated separately. It was used the randomized block strip-plot design, in four environments with two replications. The traits assessed were grain yield (GY), prolificacy (PROL), ear length and ear diameter (EL and ED), number of rows per ear (NRE), kernel-row number (KRN), plant and ear height (PH and EH), days to anthesis and silking (DA and DS), and number of tassel branches (NTB). It was estimated the effects of genetic drift between subpopulations means at both inbreeding levels, and the effect of the inbreeding depression in subpopulations within cycles. It was also performed linear regression analysis for subpopulations at both levels of inbreeding separately and together. A large variation was observed in the subpopulations means over cycles, indicating that genetic drift caused differentiation between them, and that they differed from the original populations. The effects of genetic drift were significant for all traits in the non selfed subpopulations, especially for GY, which is more sensitive to genetic drift effects by having a greater degree of dominance than the other traits. There was a decrease in the number of significant genetic drift estimates for selfed populations, including changes in magnitude and signs, compared to the non selfed populations. GY, KRN, DA and DS had higher number of significant inbreeding depression estimates than the other traits. Linear regression analysis explained most of the variation found with increasing homozygosity. As BR-105 and BR-106 populations have distinct genetic structures, they showed different performances regarding the effects of genetic drift. Therefore, genetic drift interferes in the genetic integrity of populations and it is important to consider its effect on the collection and maintenance of germplasm banks and populations used in plant breeding.

Abstract Many species and populations have perished as a consequence of human actions. During the last ~200 years, large carnivores have been almost completely extirpated from Western Europe. Large-scale wolf hunting started in Finland around the 1850s, and the population size quickly collapsed. The population was very small until the mid-1990s, when wolves started to regularly reproduce in Finland again. The wolf is an endangered species in Finland, and the biggest threat to the species’ survival is excessive hunting. In this doctoral thesis study, I inspected the genetic structure and diversity of the Finnish wolf population using neutral genetic markers. Almost 300 wolves from the contemporary Finnish population and over 50 wolves from the north-western Russia were analyzed with genetic methods. Additionally, the genetic history of the population was examined with the help of over 100 museum samples. The modern Finnish wolf population proved to be genetically as diverse as the non-endangered Eastern European and North American wolf populations. However, the genetic diversity decreased significantly during the study period (1995–2009), and was at its lowest level in the final phase of the examination. In tandem, the inbreeding coefficient rose to a relatively high level. Genetic sub-structures were observed due to social structures within wolf packs. The mean dispersal distances of wolves were approximately only 100 km. The Finnish wolf population is divided into neighbourhoods of related individuals, and their size substantially decreased during the study period. This pattern, together with the growth of the inbreeding coefficient, suggests that lost alpha individuals in wolf packs are replaced by their offspring. This study demonstrated that Russian and Finnish wolf populations are nowadays genetically differentiated. Gene flow between the populations is low, despite the geographic interconnection. Only a few possible immigrants from Russia into Finland were detected in the study. The effective size of the Finnish wolf population proved to be small, and was mainly below the often-considered critical size of 50. Historical analysis revealed that the Finnish wolf population was formerly genetically more diverse, more continuous with the Russian wolf population, and had a more than 90% larger effective size. On the basis of this study, the genetic status of the Finnish wolf population is worrying and needs to be monitored. The population should be substantially larger than today and/or the amount of gene flow higher, so that the population viability could be considered secured even in the short term. / Tiivistelmä Ihmisen toiminnan seurauksena lukuisat eliölajit ja –populaatiot ovat hävinneet. Viimeisten noin 200 vuoden aikana suurpedot hävitettiin lähes koko Länsi-Euroopasta. Laajamittainen sudenmetsästys alkoi Suomessa 1850-luvun paikkeilla ja kanta romahti nopeasti. Populaatio oli hyvin pieni lähes koko 1900-luvun, ja sudet ovat jälleen lisääntyneet yhtäjaksoisesti Suomessa vasta 1990-luvun puolivälistä. Susi on erittäin uhanalainen Suomessa ja merkittävin uhka lajin säilymiselle on liiallinen metsästys. Tarkastelen tässä väitöskirjatyössäni Suomen susipopulaation geneettistä rakennetta ja monimuotoisuutta neutraaleja geenimerkkejä käyttäen. Tutkimuksessa analysoitiin geneettisin menetelmin lähes 300 sutta nyky-Suomesta sekä yli 50 sutta Luoteis-Venäjältä. Lisäksi populaation geneettistä historiaa selvitettiin yli 100 museonäytteen avulla. Nykyinen Suomen susipopulaatio osoittautui tutkimuksessa geneettisesti yhtä monimuotoiseksi kuin ei-uhanalaiset susipopulaatiot Itä-Euroopassa ja Pohjois-Amerikassa. Geneettisen muuntelun määrä kuitenkin laski tutkimusajanjaksolla (1995–2009) merkitsevästi ollen matalin tarkastelujakson lopussa. Samanaikaisesti populaation sukusiitoskerroin nousi verrattain korkeaksi. Susipopulaatiossa havaittiin sosiaalisista rakenteista johtuvia geneettisiä alarakenteita. Susien dispersaalimatkat olivat keskimäärin vain noin 100 km. Suomen susipopulaatio on jakautunut toisilleen sukua olevien yksilöiden naapurustoiksi, joiden koko pieneni huomattavasti tutkimusajanjaksolla. Tämä yhdessä sukusiitoskertoimen kasvun kanssa viittaa susilaumojen menetettyjen alfayksilöiden korvautumiseen jälkeläisillään. Tutkimus osoitti, että Venäjän ja Suomen susipopulaatiot ovat nykyisin geneettisesti erilaistuneet. Geenivirta populaatioiden välillä on maantieteellisestä yhteydestä huolimatta vähäistä. Tutkimuksessa havaittiin vain muutamia todennäköisiä immigrantteja Venäjältä Suomeen. Suomen susipopulaation efektiivinen koko osoittautui pieneksi ollen pääosin alle kriittisenä rajana pidetyn 50:en. Historiallinen tarkastelu osoitti Suomen susipopulaation olleen aiemmin geneettisesti monimuotoisempi, yhtenäisempi Venäjän susipopulaation kanssa ja efektiiviseltä kooltaan yli 90 % nykyistä suurempi. Tutkimuksen perusteella Suomen susipopulaation geneettinen tila on huolestuttava ja tarvitsee seurantaa. Populaation tulisi olla nykyistä huomattavasti suurempi ja/tai geenivirran määrän korkeampi, jotta populaation elinvoimaisuuden voitaisiin katsoa olevan turvattu edes lyhyellä aikavälillä.

A wide majority of orchid populations are decreasing due to habitat fragmentation and to changes in land management. Population size, density and habitat quality are factors that are expected to be positively related to the viability and future growth of a population. We evaluated if population size, density and soil organic matter were good predictors of growth, survival, flowering, recruitment, and growth rate in 18 populations of the long-lived orchid Gymnadenia conopsea. We followed the populations for four years. Recruitment in 2020 increased with population size, and survival in 2018 was higher in denser populations. However, flowering probability and number of flowers both decreased with population size in 2018. Soil organic matter did not significantly influence any vital rate. In total, the studied population factors could explain very little of the variation in demography. The matrix modelling showed that 14 of the 18 populations had a positive stochastic growth rate, even with an increased probability of summer drought (scenario with 50% of the years equal to the dry summer of 2018). In the populations with negative growth rate, the probability of quasi-extinction in the next 50 years varied from 90 to 100%. Declining populations were characterized by low survival following the dry year. In sum, population size, density and soil organic matter did not convincingly explain variation in growth rate of G. conopsea, suggesting that other environmental factors are responsible of governing variation in vitals rates and population dynamics.

Prey s'appuie sur les décisions d'évasion lorsqu'il est confronté à des prédateurs pour maximiser les avantages de rester en place tout en réduisant les coûts de la prédation. Ce compromis de l'histoire de vie peut être reflété par la distance d'initiation de vol (FID), la distance à laquelle un individu prend son envol lorsqu'il est approché par un humain. J'ai abordé les facteurs potentiels expliquant la variation FID avec des données d'espèces d'oiseaux en Europe. La variabilité génétique était liée au risque de prédation FID; les espèces d'oiseaux menacées avaient généralement une FID plus longue que les espèces proches non menacées; le caractère distinctif de l'évolution (ED), un indicateur reflétant l'isolement phylogénétique des taxons, était positivement lié à la FID chez les oiseaux d'eau; La FID moyenne de différentes espèces d'oiseaux était positivement corrélée avec les niveaux spécifiques de MDA (malondialdéhyde qui est un indice de stress oxydatif) et UA (acide urique, qui est une mesure de la capacité antioxydante) et FID augmentée avec la taille du troupeau chez les espèces grégaires mais pas chez les espèces non grégaires. Ces résultats peuvent contribuer à la compréhension des causes et des conséquences des différences interspécifiques dans le comportement de fuite des prédateurs contre les prédateurs, et, plus important encore, ils peuvent fournir des moyens de résoudre les problèmes de conservation. Mots-clés : masse corporelle, taille du cerveau, taille effective de la population, modèle linéaire phylogénétique, stress oxydatif, comportement social / Prey rely on escape decisions when confronted with predators to maximize the benefits of staying put while reducing the costs of predation. This life history compromise can be reflected by flight initiation distance (FID), the distance at which an individual takes flight when approached by a human. I addressed potential factors explaining variation FID with data from bird species in Europe. Genetic variability was related to predation risk FID; threatened bird species generally had a longer FID than non-threatened closely related species; evolutionary distinctiveness (ED), an indicator reflecting the phylogenetic isolation of taxa, was positively related to FID in waterbirds; mean FID of different species of birds was positively correlated with species-specific levels of MDA (malondialdehyde which is an index of oxidative stress) and UA (uric acid, which is a metric of antioxidant capacity) and FID increased with flock size in gregarious species but not in non-gregarious species. These findings may contribute to the understanding of the causes and consequences of interspecific differences in anti-predator escape behavior of birds, and, more importantly they may provide means for resolving conservation problems. Key words: body mass, brain size, effective population size, phylogenetic linear model, oxidative stress, social behavior

The aim of this work was the construction of set of microsatellites for the Grey Partridge (Perdix perdix). I succeeded in isolation of seven new specific microsatellites. Another microsatellite markers were passed from close relative galliform species (Galliformes). On the whole I gained 18 microsatellite loci which were used for study of population charakteristics of three partridge populations from Stodůlky, Písecko and Milešín. The analysis showed conspicuous structuredness of these populations and surprisingly low values (less then 100) of their effective population sizes. Seven of the microsatellites were chosen for analysis of paternity. Indeed I found the evidence of extrapair paternity in this putatively monogamous bird. Finally I conclude, on the basis of sequenation of mitochondrial control region that our populations belong to the western linage of mitochondrial DNA.

Captive-breeding has been identified as an integral part of the conservation of threatened species. The black rhinoceros (Diceros bicornis) as a species is currently listed by the IUCN as critically endangered (CR), while the white rhinoceros’s (Ceratotherium simum) current status is near-threatened (NT). Three African rhinoceros subspecies currently occur in captive populations in regional population management programmes, namely the South-central black rhinoceros (Diceros bicornis minor), the Eastern black rhinoceros (Diceros bicornis michaeli) and the Southern white rhinoceros (Ceratotherium simum simum). Concerns have been raised, however, that these populations are not self-sustainable. This study aims to analyze the demographic parameters that contribute to the growth rates of the global captive populations of African rhinoceros. The study sets out to determine if these global captive populations are currently self-sustaining, which demographic factors have the most influence on the population growth rates, and whether or not 50- and 100- year targets set for the captive African rhinoceros populations are attainable. Demographic data from 1 January 2010 until 31 December 2010 were analysed through population census, life table and age structure analyses. Two additional concerns, namely poor reproductive performance of the female F1 generation and male-biased birth sex ratios, were also assessed. The results indicate that the captive populations of D. b. minor and C. s. simum are not self-sustainable, with population growth rates (λ) of 0.98 and 0.99, respectively. Diceros bicornis michaeli is the only subspecies with a growing population, with a population growth rate of 1.02. Sensitivity analyses conclude that fecundity rates, and not mortality rates, are the limiting factor to population growth in all three subspecies. While lifetime reproductive success values for D. b. minor and C. s. simum captive-born females are far lower than those of the founder generation, several factors need further investigation to determine the true cause of this. Birth sex ratio analysis shows no significant difference from parity for both black rhinoceros subspecies, however, quadratic logit regression conducted on the white rhinoceros data indicated a statistically significant male-bias. In all three subspecies, no significant link was found between maternal age and the sex of the offspring. Overall, the results of this study show that the 50 year and 100 year targets set at the GCAP workshop in 1992 are achievable. However, D. b. minor will only be able to achieve the target population sizes with an increase in fecundity rate of around 170% or alternatively, additional supplementation from the wild. Recommendations for the future include a global study of breeding husbandry at an institutional level, and the formalisation of a Global Species Management plan for D. b. minor. / Dissertation (MSc)--University of Pretoria, 2014. / I would like to acknowledge several organisations and people that have supported me throughout this MSc. The National Research Foundation (NRF), which provided me with the funding for my studies. My employer, The National Zoological Gardens of South Africa, a research facility of the NRF, and particularly the CEO, Dr Clifford Nxomani and my manager, Dr Abeda Dawood, who gave me support, encouragement and most importantly, time off to concentrate on this thesis. A special heartfelt thanks goes to my supervisors, Prof. Chris Chimimba, who never gave up on me, even though this study took a little bit longer than it was supposed to, and Dr Ed Stam, whose dedication, patience and endless comments (and good cappuccinos) helped shape this thesis. Lastly, my husband David, who always encourages me to do better and never allows me to become complacent; thank you, my love, for always pushing me to achieve. / Zoology and Entomology / MSc / Unrestricted

During the summer of 2008 and 2009, we studied the ecology of the Kittlitz’s Murrelet (Brachyramphus brevirostris), a small diving seabird and candidate for the U.S. Endangered Species List, in Prince William Sound (PWS), Alaska. At-sea survey data suggests that the population significantly increased from 2001 to 2009, however there is limited evidence of reproductive success. Habitat use models showed individuals were observed in shallower waters, closer to glaciers, the shoreline, and further from moraines than the available habitat during the daytime. Finer extent sampling from 2008 suggests temperature-depth profiles also influence Kittlitz’s Murrelet daytime habitat use. The associations between Kittlitz’s Murrelets and water column characteristics are likely an effect of prey availability. Stable isotope work in 2009 suggests birds were generalist foragers prior to the breeding season, becoming more specialized following the breeding season. This specialization may have been a response to strict foraging constraints during the flightless fall molt. Time budgets of radio-tagged individuals suggest birds may have been responding to ephemeral prey concentrations, and working near their maximum energetic limits. Remote monitoring of radio-tagged individuals showed birds left the glacial fjord system during the nighttime, possibly spending these hours near gillnet fishing areas, suggesting a new possible area of concern in evaluating potential threats to Kittlitz’s Murrelet populations.

Many wildlife populations globally are experiencing unprecedented declines, and without accurate and precise estimates of abundance, we will not be able to conserve these vulnerable species. Remote cameras have rapidly advanced as wildlife monitoring tools and may provide accurate and precise estimates of abundance that improve upon traditional methods. Using remote cameras to estimate abundance may be less expensive, less intrusive, less dangerous, and less time consuming than other methods. While it is apparent that remote cameras have a place in the future of wildlife monitoring, research, and management, many questions remain concerning the proper use of these tools. In an effort to answer some of these questions, we used remote cameras to study a population of Rocky Mountain bighorn sheep (Ovis canadensis) in Utah, USA from 2012 to 2014. In Chapter 1, we compared methods using remote cameras against 2 traditional methods of estimating abundance. In Chapter 2, we evaluated the relationship between deployment time of cameras and proportion of photos needed to be analyzed to obtain precise estimates of abundance. We found that methods using remote cameras compared favorably to traditional methods of estimating abundance, and provided a number of valuable advantages. In addition, we found that remote cameras can produce precise estimates of abundance in a relatively short sampling period. Finally, we identified the optimal sampling period to produce precise estimates of abundance for our study population. Our findings can help researchers better utilize the potential of remote cameras, making them a more suitable alternative to traditional wildlife monitoring.

Many wildlife populations globally are experiencing unprecedented declines, and without accurate and precise estimates of abundance, we will not be able to conserve these vulnerable species. Remote cameras have rapidly advanced as wildlife monitoring tools and may provide accurate and precise estimates of abundance that improve upon traditional methods. Using remote cameras to estimate abundance may be less expensive, less intrusive, less dangerous, and less time consuming than other methods. While it is apparent that remote cameras have a place in the future of wildlife monitoring, research, and management, many questions remain concerning the proper use of these tools. In an effort to answer some of these questions, we used remote cameras to study a population of Rocky Mountain bighorn sheep (Ovis canadensis) in Utah, USA from 2012 to 2014. In Chapter 1, we compared methods using remote cameras against 2 traditional methods of estimating abundance. In Chapter 2, we evaluated the relationship between deployment time of cameras and proportion of photos needed to be analyzed to obtain precise estimates of abundance. We found that methods using remote cameras compared favorably to traditional methods of estimating abundance, and provided a number of valuable advantages. In addition, we found that remote cameras can produce precise estimates of abundance in a relatively short sampling period. Finally, we identified the optimal sampling period to produce precise estimates of abundance for our study population. Our findings can help researchers better utilize the potential of remote cameras, making them a more suitable alternative to traditional wildlife monitoring.