Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Limited dispersal, territoriality and the occupation of patchy habitats; characters that typify most African rock-dwelling (saxicolous or rupicolous) species, often result in structured genetic patterns with little or no gene-flow among populations (e.g., velvet worms, net-winged midges, elephant shrews, red rock rabbits and a variety of lizards and agamas). In an attempt to deepen our understanding of taxa that inhabit these “terrestrial islands” the distribution of genetic variation was studied at several spatial scales in the rock hyrax, Procavia capensis. This species has a polygynous social system that is unusual among taxa with similar ecological requirements, and a morphology that would intuitively be associated with poor dispersal capabilities (short limbs and a squat, heavy body). Possibly as a consequence of these considerations, few studies have attempted to determine the distance of migration by rock hyraxes and the influence that their social system and the surrounding landscape has on dispersal success. This investigation therefore tests hypotheses of how the ecology, distribution, social structure and the connectivity of the surrounding landscape have contributed to shaping the structure of rock hyrax genetic variation across the Namaqualand and western Fynbos regions. To do so, mitochondrial and microsatellite markers were used to document gene-flow at a fine spatial scale (an isolated population comprising 5 koppies), an intermediate spatial scale (across known geographic barriers to saxicolous taxa - the Cape Flats and Knersvlakte), and a regional spatial scale (across the Namaqualand/western Fynbos regions of South Africa - regions exhibiting contrasting landscape connectivity). In addition the genetic diversity, spatial clustering, sex-biased dispersal and relatedness (fine-scale) of colonies is described and the major genetic breaks detected in the investigation dated using a relaxed molecular clock approach. Finally, these results were compared to other studies that identified the Cape Flats and Knersvlakte as phylogeographic disruptors. The genetic patterns at a fine spatial scale were complex: Gene-flow was restricted by the social structure of the rock hyrax rather than geographic distance, dispersal was female-biased and there was significant genetic structure. Genetic structure was also evident at the intermediate and regional spatial scales. In the Hottentots Holland Mountains and Cape Peninsula gene-flow was restricted (in both data sets) in comparison to localities that traversed the Cape Flats. In contrast, gene-flow across the Knersvlakte was restricted in the mitochondrial DNA data set but not so with microsatellites. A similar pattern was observed at a regional scale pointing to male-biased dispersal within this species - a result of its polygynous social structure. In addition to sex-biased dispersal, landscape connectivity also influenced gene-flow on a regional spatial scale as the Namaqualand region, which has greater intermediate suitable habitat compared to the western Fynbos region, displayed significantly higher levels of gene-flow between sampling localities. Consequently, colonies in Namaqualand were genetically more diverse compared to those of the western Fynbos region. Two major matrilineal clades were evident on both side of the Knersvlakte - one to the north of this biogeographic break (Namaqualand), and the other to the south (western Fynbos). This was not, however, evident from the microsatellite data (reflecting the influence of male dispersal) where seven nuclear clusters were found. In keeping with other studies on saxicolous vertebrate taxa straddling the same region, this area of low connectivity has acted (and probably still does) as a barrier to gene-flow. Importantly, unlike in many other (admittedly invertebrate) species, no evidence of a genetic break was detected among hyrax populations across the Cape Flats. Colonies across the Hottentots Holland Mountains and Cape Peninsula regions may have been subject to founder-events and breeding isolation. This investigation demonstrated the importance of using a well-structured sampling regime that included both mitochondrial and nuclear markers and it underscores the need to apply appropriate statistical programmes for inferring genetic patterns. It shows that landscape genetics may be useful in a conservation context and should be taken into account when planning conservation initiatives that include the implementation of corridors. In brief, the information contained in this study advances our knowledge of the dispersal capability and genetic diversity of contemporary rock hyrax populations. / AFRIKAANSE OPSOMMING: ‘n Beperkte spreidingsvermoë, territorialiteit en die bewoning van yl-verspreide habitat is kenmerkend van die meeste klip-bewonende spesies in Afrika en dit veroorsaak gereeld gestruktureerde genetiese patrone met min of geen genevloei tussen populasies (bv., die velvetwurms, net-vlerk muggies, klipklaasneuse, klipkonyne en ‘n verskeidenheid akkedisse en koggelmanders). In ‘n poging om kennis oor taksa wat hierdie “terrestriële eilande” bewoon te verdiep, het ons die die verspreiding van genetiese variasie bestudeer oor verskeie ruimtelike skale in die klipdassie, Procavia capensis. Hierdie spesie het ‘n veelwywige sosiale sisteem, wat vreemd is onder taksa met soortgelyke ekologiese vereistes, en ‘n morfologie wat intuïtief verbind kan word met swak spreidingsvermoëns (kort bene en ‘n kort, dik liggaam). As ‘n moontlike resultaat van hierdie oorwegings het min studies tot dusver daarop gefokus om die migrasie-afstand van klipdassies en die invloede van hulle sosiale sisteem en die omliggende landskap op spreidings-sukses te bepaal. Hierdie studie toets daarom hipoteses oor hoe die ekologie, verspreiding, sosiale struktuur en die konnektiwiteit (verbindheid) van die omliggende landskap bydra om die struktuur van genetiese variasie in klipdassies oor die Namakwaland en westelike Fynbos streke te beïnvloed. Derhalwe is mitochondriale en mikrosatelliet merkers gebruik om genevloei te bepaal op ‘n fyn ruimtelike skaal (‘n geïsoleerde populasie bestaande uit 5 koppies), ‘n gemiddelde ruimtelike skaal (oor bekende geografiese grense vir klipbewonende taksa - die Kaapse Vlakte en die Knersvlakte), en op ‘n streeks (groot) ruimtelike skaal (oor die Namakwaland/westelike Fynbos streke van Suid-Afrika - streke met kontrasterende konnektiwiteit van die landskap). Bykomend is die genetiese diversiteit, ruimtelike groepering, seksuele eensydigheid in spreiding en genetiese verwantskappe (fyn skaal) van kolonies beskryf en die hoof genetiese skeiding gedateer deur gebruik te maak van ‘n ontspanne molekulêre klok. Laastens het is die resultate van hierdie studie vergelyk met dié van ander studies wat die Kaapse Vlakte en Knersvlakte as filogeografiese skeidings gevind het. Die genetiese patrone op ‘n fyn ruimtelike skaal was kompleks: Genevloei is beperk deur die sosiale struktuur van die klipdassie eerder as geografiese afstand, migrasie was wyfie-spesifiek en daar was beduidende genetiese struktuur tussen kolonies. Genevloei was beperk in die Hottentots Holland berge en die Kaapse Skiereiland (in beide datastelle) in vergelyking met lokaliteite oor die Kaapse Vlakte. In kontras was genevloei oor die Knersvlakte beperk in die mitochondriale DNA, maar nie in die mikrosatelliete nie. ‘n Soortgelyke patroon is waargeneem op ‘n streeks skaal wat dui op mannetjie-spesifieke spreiding in hiérdie spesie - ‘n resultaat van die veelwywige sosiale struktuur. Bykomend, saam met geslag-spesifieke spreiding, het landskaps konnektiwiteit ook genevloei beïnvloed op ‘n streeks skaal omdat die Namakwaland streek, wat meer tussenleggende geskikte habitat bevat in vergelyking met die westelike Fynbos streek, beduidende hoër vlakke van genevloei tussen lokaliteite getoon het. Gevolglik was kolonies in Namakwaland geneties meer divers in vergelyking met dié van die westelike Fynbos streek. Twee hoof moederlike genetiese groepe is waargeneem op elke kant van die Knersvlakte - een aan die noorde van hierdie biogeografiese skeiding (Namakwaland) en een in die suide (westelike Fynbos). Dieselfde patroon was egter nie waarneembaar in die mikrosatelliet data nie (wat die invloed van mannetjie-spesifieke spreiding toon) waar sewe nukluêre groepe gevind is. In ag genome ander studies op klipbewonende gewerwelde taksa oor dieselfde verspreiding, het hierdie area van lae konnektiwiteit histories (en heelmoontlik ook huidiglik) as ‘n grens vir genevloei gedien. Belangrik, anders as in ander (hoewel ongewerwelde) spesies, kon ons geen bewyse verskaf van ‘n genetiese skeiding tussen klipdassie populasies oor die Kaapse Vlakte nie. Kolonies in die Hottentots Holland berge en Kaapse Skiereiland is dus onderhewig aan moontlike vestigings-effekte en telings-isolasie. Hiérdie studie demonstreer die belang van die gebruik van ‘n goed-gestruktureerde monsternemingskema, die insluiting van beide mitochondriale en nukluêre merkers en dit beklemtoon ook die noodsaaklikheid van die gebruik van toepaslike statistiese programme vir gevolgtrekkings oor genetiese patrone. Dit toon ook dat landskapsgenetika nuttig mag wees in ‘n bewaringskonteks en in ag geneem moet word in die beplanning van bewarings inisiatiewe wat die implementering van korridors insluit. Kortliks, die informasie in hierdie studie bevorder ons kennis oor die spreidingsvermoë en genetiese diversiteit van kontemporêre klipdassie populasies.

abstract: Human land use and land cover change alter key features of the landscape that may favor habitat selection by some species. Lizards are especially sensitive to these alterations because they rely on their external environment for regulating their body temperature. However, because of their diverse life-history traits and strategies, some are able to respond well to disturbance by using their habitat in various ways. To understand how they use their habitat and how human modifications may impact their ability to do this, biologists must identify where they occur and the habitat characteristics on which they depend. Therefore, I used species occupancy modeling to determine (1) whether disturbance predicts the presence of two sympatric congeneric (species of the same genus) lizard species Sceloporus grammicus and S. torquatus, and (2) which habitat characteristics are essential for predicting their occupancy and detection. I focused my study in central Mexico, a region of prevalent land use and land cover change. Here, I conducted visual encounter and habitat surveys at 100 1-hectare sites during the spring of 2019. I measured vegetation and ground cover, average tree diameter, and abundance of refuges. I recorded air temperature, relative humidity, and elevation. I summarized sites as either undisturbed or disturbed, based on the presence of human development. I also summarized sites by ecosystem type, desert or forest, based on vegetation composition (i.e., desert-adapted vs. non-desert-adapted plants), evidence of remnant forest, air temperature, and relative humidity. I found that S. torquatus was more likely to be present in disturbed habitat, whereas S. grammicus was more likely to be present in areas with leaf litter, tree cover, and woody debris. S. torquatus was twice as likely to be detected in forests than deserts, and S. grammicus was more likely to be detected at sites with high elevation and high relative humidity, low temperature, and herbaceous and grass cover. These results emphasize the utility of species occupancy modeling for estimating detection and occupancy in dynamic landscapes. / Dissertation/Thesis / Masters Thesis Biology 2020

A Caatinga é um ecossistema brasileiro análogo as savanas africanas apresentando escassez de chuvas e temperaturas altas. O mocó apresenta, importantes adaptações ao microambiente dos afloramentos rochosos. Esse roedor caviomorfo, abandonou o hábito pastador comum a outros roedores cavíneos, como preá e a capivara, pela capacidade de escalar árvores e se alimentar de folhas e frutos. Alongou o período de gestação e adotou o cuidado paterno. Interessados em entender de que forma a comunicação acústica teria se ajustado ao ambiente isolado dos rochedos da caatinga, gravamos e analisamos as emissões sonoras dos mocós. Foram 90 dias de trabalho de campo nas Fazendas Tamanduá e São Francisco, na cidade de Patos, Paraíba. Capturamos 13 animais (6 machos e 7 fêmeas) e fizemos registros em áudio e vídeo em três situações: 1) pareamentos em caixa teste, nas condições macho x macho, macho x fêmea e fêmea x fêmea, 2) animais em grupo em cativeiro, e 3) animais em vida livre. Encontramos um repertório de 11 sinais sonoros, registrados em 3 categorias amplas de comportamento: (1) Exploração/Forrageamento: Có de contato, Estalido, Chorinho e Drrr; (2) Alerta: Assobio de alarme, Drrr e Silvo; (3) Interação Agonística: Ganido, Grito, Ronco, Arfar, Assobio de alarme e o Baterdedentes. O repertório mostrouse mais rico do que o de outros caviomorfos, como o preá. Discutimos esse resultado em relação ao tipo de vida social da espécie em comparação com a de outros caviníneos e à vida nos rochedos da caatinga. Também sugerimos que o Assobio de alarme seja um comportamento compartilhado entre o mocó e outras espécies de roedores 10 de rochedos. Há uma perspectiva de continuidade da pesquisa em busca de uma maior compreensão da função biológica desse sinal e da riqueza desse repertório acústico / The environment of Brazilian Caatinga ecosystem is similar to African Savannah with low level of rain and high temperature. The Moco shows important adaptation at the microenvironment of rock outcrops. This caviomorph rodent abandoned grazing habit, commom at others Caviinae species such as the Cavy and the Capybara for the capacity of climbing trees feeding of leaves and fruits. It also lengthened the gestation period and adopted paternal care. Interested in understanding how acoustic communication would have adjusted to the isolated environment of Caatinga rock piles, we recorded and analyzed the signals songs of Moco. Past through 90 days in field at Fazenda Tamanduá and Sítio São Francisco located at Patos city Paraiba State in Brazil. We captured 13 animals (6 males and 7 females), acquired audio and video of animals in three different situations: 1) paired in tests boxes under conditions: male x male, female x male and female x female; 2) captivity group and 3) Living free. We found a repertoire with 11 acoustic signals registered in 3 broad behavioral categories: (1) Exploration/ Foraging: Contact call, Co, Clicking (Estalido), Whine (Chorinho) and Drrr call, (2) Warning: Alarm whistle, Drrr call and Silvo, (3) Agonistic Interaction: yelp (Ganido), scream (Grito), grunt (Ronco), a breathless like sound (Arfar), Alarm Whistle and ToothChatter. This repertoire showed more rich that other caviomorph as a cavy. eu escreveria esse parágrafo dessa forma: This repertoire seemed better than other caviomorph as a Cavy. We discussed those results comparing the social life of species with social life of others Caviinae and the life at the rock piles of Caatinga. We also suggested that the Alarm whistle is shared between the 12 Moco and others rock rodents. There is a perspective to continue this research looking for a better comprehension of the biologic function of this signal and acoustic repertoire richness

A Caatinga é um ecossistema brasileiro análogo as savanas africanas apresentando escassez de chuvas e temperaturas altas. O mocó apresenta, importantes adaptações ao microambiente dos afloramentos rochosos. Esse roedor caviomorfo, abandonou o hábito pastador comum a outros roedores cavíneos, como preá e a capivara, pela capacidade de escalar árvores e se alimentar de folhas e frutos. Alongou o período de gestação e adotou o cuidado paterno. Interessados em entender de que forma a comunicação acústica teria se ajustado ao ambiente isolado dos rochedos da caatinga, gravamos e analisamos as emissões sonoras dos mocós. Foram 90 dias de trabalho de campo nas Fazendas Tamanduá e São Francisco, na cidade de Patos, Paraíba. Capturamos 13 animais (6 machos e 7 fêmeas) e fizemos registros em áudio e vídeo em três situações: 1) pareamentos em caixa teste, nas condições macho x macho, macho x fêmea e fêmea x fêmea, 2) animais em grupo em cativeiro, e 3) animais em vida livre. Encontramos um repertório de 11 sinais sonoros, registrados em 3 categorias amplas de comportamento: (1) Exploração/Forrageamento: Có de contato, Estalido, Chorinho e Drrr; (2) Alerta: Assobio de alarme, Drrr e Silvo; (3) Interação Agonística: Ganido, Grito, Ronco, Arfar, Assobio de alarme e o Baterdedentes. O repertório mostrouse mais rico do que o de outros caviomorfos, como o preá. Discutimos esse resultado em relação ao tipo de vida social da espécie em comparação com a de outros caviníneos e à vida nos rochedos da caatinga. Também sugerimos que o Assobio de alarme seja um comportamento compartilhado entre o mocó e outras espécies de roedores 10 de rochedos. Há uma perspectiva de continuidade da pesquisa em busca de uma maior compreensão da função biológica desse sinal e da riqueza desse repertório acústico / The environment of Brazilian Caatinga ecosystem is similar to African Savannah with low level of rain and high temperature. The Moco shows important adaptation at the microenvironment of rock outcrops. This caviomorph rodent abandoned grazing habit, commom at others Caviinae species such as the Cavy and the Capybara for the capacity of climbing trees feeding of leaves and fruits. It also lengthened the gestation period and adopted paternal care. Interested in understanding how acoustic communication would have adjusted to the isolated environment of Caatinga rock piles, we recorded and analyzed the signals songs of Moco. Past through 90 days in field at Fazenda Tamanduá and Sítio São Francisco located at Patos city Paraiba State in Brazil. We captured 13 animals (6 males and 7 females), acquired audio and video of animals in three different situations: 1) paired in tests boxes under conditions: male x male, female x male and female x female; 2) captivity group and 3) Living free. We found a repertoire with 11 acoustic signals registered in 3 broad behavioral categories: (1) Exploration/ Foraging: Contact call, Co, Clicking (Estalido), Whine (Chorinho) and Drrr call, (2) Warning: Alarm whistle, Drrr call and Silvo, (3) Agonistic Interaction: yelp (Ganido), scream (Grito), grunt (Ronco), a breathless like sound (Arfar), Alarm Whistle and ToothChatter. This repertoire showed more rich that other caviomorph as a cavy. eu escreveria esse parágrafo dessa forma: This repertoire seemed better than other caviomorph as a Cavy. We discussed those results comparing the social life of species with social life of others Caviinae and the life at the rock piles of Caatinga. We also suggested that the Alarm whistle is shared between the 12 Moco and others rock rodents. There is a perspective to continue this research looking for a better comprehension of the biologic function of this signal and acoustic repertoire richness