There are large gaps in the coverage of critical ecological processes related to the movement of individuals or genes (i.e. dispersal), which is critical for determining the spread and persistence of populations across space. In this dissertation we investigate understudied but important aspects of the dispersal process in mangroves, with as the main objective the reduction of parameter and model uncertainty. Models rarely incorporate realism and complexity at the level of emigration, transfer and immigration phases, hampering reliable predictions of dispersal patterns and long-term population dynamics under different climate change scenarios. <p><p>Mangrove ecosystems function at the edge of land and sea, often covering large intertidal areas along (sub)tropical coastal regions worldwide. Mangroves can live in these highly dynamic and demanding environmental conditions via a series of remarkable adaptations. They produce buoyant seeds and fruits (propagules) that disperse at the ocean surface (i.e. hydrochory - see cover image). <p><p>Despite their ecological and economical value, about 40 % of original mangroves have been lost worldwide during the last 50 years due to excessive exploitation and development. Deforestation, degradation and conversion to other land uses like intensive shrimp farming and agriculture have reduced and fragmented these ecosystems at an alarming rate. Climate change, probably most pronouncedly via changes in sea level, poses another important threat. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

In this thesis, the biogeography of the centipede family Scolopendridae of the Western Ghats (WG)was studied. First, a novel limited sampling approach to identify putative Gondwanan origin wherein sampling of was confined to one of the Gondwanan fragments, i.e. the WG was developed. The results indicated that at least four genera, Scolopendra, Cormocephalus, Rhysida and Digitipes of Scolopendridae, have diversified on the drifting peninsular Indian plate, and thus might have a Gondwanan origin. Three of these genera, Cormocephalus, Scolopendra and Rhysida, might have dispersed out of India and Digitipes has remained a Gondwanan relict. Second, an integrative frame work was used to delimit species boundaries in the genus Digitipes which was characterized as an ancient, endemic and monophyletic group. A new phylogenetic hypothesis was proposed for the genus Digitipes, with eight sampled species of which three were described and five were potentially new species. Among the five potentially un-described species, three were morphologically cryptic, emphasizing the effectiveness of this approach in revealing cryptic diversity. Third, historical biogeography of wet evergreen species of WG was evaluated using the genus Digitipes from the WG. Biogeographic and divergence date estimation suggest that the southern WG was indeed a refuge for Digitipes species of the WG during Cretaceous volcanism. The dated molecular phylogeny of family Scolopendridae as well as of genus Digitipes obtained in the current study will be useful in future comparative biogeography and diversification studies in the WG.

The Leon River, a small-medium river in central Texas, is highly impacted by multiple impoundments, enrichment from agricultural runoff, and decreased dissolved oxygen levels. This degraded river contains sixteen unionid species, two of which are both endemic to the region and candidates for the federal endangered species listing (Quadrula houstonensis and Truncilla macrodon). While there is a short historical record for this river basin and a recent modern survey completed in 2011, zooarchaeological data adds evidence for conservation efforts by increasing the time depth of data available and providing another conservation baseline. Zooarchaeological data for the Leon River is available from the two Late Holocene archaeological sites: 41HM61 and the Belton Lake Assemblages. Data generated from these assemblages describe the prehistoric freshwater mussel community of the Leon River in terms of taxonomic composition and structure. By comparing this zooarchaeological data to the data generated by the longitudinal modern survey of the Leon River, long term changes within the freshwater mussel community can be detected. A conceptual model is constructed to evaluate how robusticity, identifiability, and life history ecology affect unionid taxonomic abundances in zooarchaeological data. This conceptual model functions as an interpretive tool for zooarchaeologists to evaluate forms of equifinality in zooarchaeological assemblages. This thesis determines differences between the late Holocene and modern freshwater community of the Leon River, explores how different alternative mechanisms influence zooarchaeological data, and exemplifies of how zooarchaeological data can be used for conservation biology.

[Truncated abstract] Southwestern Australia is a global biodiversity hotspot. The region contains a high number of endemic species, ranging from Gondwanan relicts to more recently evolved plant and animal species. Biogeographic models developed primarily for plants suggest a prominent role of Quaternary climatic fluctuations in the rampant speciation of endemic plants. Those models were not based on explicit spatial analysis of genetic structure, did not estimate divergence dates and may be a poor predictor of patterns in endemic vertebrates. Myobatrachid frogs have featured heavily in the limited investigations of the biogeography of the regions fauna. Myobatrachid frogs are diverse in southwestern Australia, and while we know they have speciated in situ, we know little about the temporal and spatial patterning of speciation events. In order to gain insight into the biogeographic history and potential speciation patterns of Myobatrachid frogs in the southwest I conducted a comparative phylogeography of four frog species spanning three life history strategies. I aimed to: 1) assess the biogeographic history of individual species, 2) determine where patterns of regional diversity exist using a comparative framework, 3) determine whether congruent patterns across species enable the development of explicit biogeographic hypotheses for frogs, and 4) compare patterns of diversity in plants with the models I developed for frogs. I conducted fine-scale intraspecific phylogeographies on four species. ... Geocrinia leai: deep divergences, coincident with late Miocene arid onset, divide this species into western and southeast coastal lineages, with a third only found within the Shannon-Gardner River catchments. Phylogeographic history within each lineage has been shaped by climatic fluctuations from the Pliocene through to the present. Arenophryne shows the first evidence of geological activity in speciation of a Shark Bay endemic. Divergence patterns between the High Rainfall and Southeast Coastal Provinces within C. georgiana are consistent with patterns between Litoria moorei and L. cyclorhynchus and plant biogeographic regions. Subdivision between drainage systems along the southern coast (in M. nichollsi, G. leai and the G. rosea species complex) reflect the relative importance of distinct catchments as refuges during arid maxima, similarly the northern Darling Escarpment is identified as a potential refugium (C. georgiana and G. leai). Divergences in Myobatrachid frogs are far older than those inferred for plants with the late Miocene apparently an important time for speciation of southwestern frogs. Speciation of Myobatrachids broadly relates to the onset of aridity in Australia in the late Miocene, with the exception of earlier/contemporaneous geological activity in Arenophryne. The origins of subsequent intraspecific phylogeographic structure are coincident with subsequent climatic fluctuations and correlated landscape evolution. Divergence within frogs in the forest system may be far older than the Pleistocene models developed for plants because of the heavy reliance on wet systems by relictual frog species persisting in the southwestern corner of Australia.

The Wolf Willow site (FbNp-26) is a multicomponent Precontact site located within the confines of Wanuskewin Heritage Park approximately 2 km north of the city of Saskatoon Saskatchewan. The site was excavated during 2010 and 2011 field seasons with the participation of The University of Saskatchewan’s archaeological field school and the Saskatchewan Archaeological Society’s field school. As a result of these excavations, 30 m2 were exposed and four distinct cultural levels were identified. These include the Plains Side-Notched complex, Prairie Side-Notched complex, McKean series, and Oxbow complex cultures. An analysis of artifacts, ecofacts, and features from each cultural level was undertaken in order to determine site usage for each time period. Ecological concepts are often used as heuristic devices in archeological studies. The theory of island biogeography and the study of patch dynamics are two concepts that can lend themselves to the archeological study of past human groups. Island biogeography was developed to explain speciation in insular environments. In archeological studies, the same mechanisms affecting speciation can be employed to study the development of culture. Patch dynamics can be used to hypothesize how resource availability affected the behavior of past populations. Using the aforementioned concepts, the Wanuskewin/Opimihaw Valley area can be viewed as a terrestrial island. The unique combination of resources both tangible and intangible combined to make the area a draw for Precontact populations for the past 6000 years. Wanuskewin continues to attract people from around the world as a centre of spiritual and cultural renewal, a world class tourism destination, and an educational facility.

Biological diversity is controlled by an array of factors and processes all active at different spatial and temporal scales. Regional factors control what species are available to occur locally, whereas the local factors determine what species are actually capable of colonizing the locality. I have investigated how these local and regional factors affect species richness and diversity, mainly of fish in Swedish lakes and in order to assess the impact of dispersal mode one study on bacteria was also performed. In addition, potential first steps towards speciation were investigated in perch (Perca fluviatilis) from two different habitats. Fish species richness and diversity were found to be regulated by history, dispersal limitation and the local environment. In addition, striking similarities were found in the control of community composition for fish and bacteria. Both were regulated by nearly equal parts regional and local factors. The study of morphological and genetical variation in perch (Perca fluviatilis) revealed genetic differentiation at small spatial scales, suggesting that genetic differences can evolve between groups at strikingly small spatial scales, which might have implications for speciation in a long time perspective. Based on these findings I conclude that space and time matter. Space has the potential to isolate sites. And both dispersal and local extinctions, it seems, might take a long time, as effects of the last ice-age can still be seen on the contemporary fish community richness and composition.

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Freshwater organisms, such as crabs (Crustacea: Decapoda: Brachyura), are useful in studies examining inland historical biogeographic patterns and speciation because they are isolated to specific drainage systems, which often serve as barriers to gene flow. The Afrotropical freshwater crab fauna (Potamonautidae) present ideal organisms for investigating hypothesis relating to evolutionary histories because they occur on continental Africa (sub-Sahara) and islands. However, there is a great deal of undiscovered freshwater crab diversity, especially with the prevalence of undiscovered cryptic lineages, which are poorly studied among freshwater crabs, leading to uncertain regional diversity. In this research, multiple genetic (mt- and nuDNA) markers were used to infer the phylogenetic relationships and the biogeographical histories of the Afrotropical freshwater crab superfamily, Potamonautidae. Divergence time estimations were used to infer biogeographic histories, to ascertain whether speciation could be linked to past geologic and / or climatic events. Two widely distributed Potamonautes species complexes were targeted for the investigation of regional cryptic species diversity. In Chapter 2, the intraspecific phylogenetic variability within Potamonautes perlatus sensu lato occurring on the Cape Fold Mountain range (South Africa) was examined, with sampling localities occurring in western- and southern flowing drainages. Previous research suggested possible cryptic speciation within this species complex; however, no tangible inferences could be made because of analytical constraints. Two major clades were recovered: one corresponding to western flowing drainages and another to southern flowing drainages. Moreover, three cryptic lineages were recovered: P. perlatus sensu stricto, restricted to western flowing drainages, and two geographically discrete novel cryptic lineages from the southern flowing drainages, described as P. barbarai sp. nov and P. barnardi sp. nov., with divergence (±2.61 Mya) linked to Pleistocene climatic events. Subsequent to the recovery of the two novel lineages from the Cape Fold Mountain range, the Pleistocene climatic events. Subsequent to the recovery of the two novel lineages from the Cape Fold Mountain range, the revision of the P. clarus / P. depressus species complex from the Tugela and uMkomazi drainages (Drakensberg Mountain range, South Africa) was conducted. This species complex was previously found to comprise at least five cryptic lineages (Chapter 3). A coalescent multilocus (three mt- and three nuDNA) Bayesian species delimitation method was used, and an additional three cryptic lineages were recovered, bringing the total to eight species (two already described as P. clarus and P. depressus), with divergence having occurred approximately 10.3 Mya. Following the recent discovery of novel freshwater crab lineages in the mountainous areas of Mozambique and Malawi, a sampling trip to the Zimbabwean Highlands was undertaken, where a novel freshwater crab species was discovered and described as P. mutareensis, highlighting the need to sample high-lying regions (Chapter 4). Furthermore, two additional novel lineages from Mozambique (P. bellarussus sp. nov.) and the Mpumalanga Province in South Africa (P. flavusjo sp. nov) were described (Chapter 5). In Chapter 6, increased taxon sampling, with additional specimens acquired from various museums and personal collections was used to obtain a better resolution of the phylogeny of the Afrotropical Potamonautidae and to infer the ancestral affinities of the two sub-families, Deckeniinae and Potamonautinae. The Potamonautidae were found to have speciated eastward from West Africa, with a late Cretaceous divergence (±107 – 96.04 Mya). The Potamonautinae originated in West Africa (three genera), while the paraphyletic Potamonautes and Platythelphusa had East African affinities. Potamonautes was not monophyletic, comprising several fragmented geographic clades, which may suggest that this genus requires revision. Nevertheless, the overall speciation within the Potamonautidae reflects past geological and climatic events, such as rifting and uplift episodes and the contraction of forests, which occurred from the Tertiary onwards.

The 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. / text

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. / text

Axelrod (1958) suggested that the late Tertiary shift in regional climate -- the elimination of summer rains -- had a profound influence on the evolution of biotic provinces in the American southwest. In particular, the taxa endemic to biotic provinces characterized by summer drought, e.g., the Mojave Desert, should be derived from ancestors that likely inhabited regions of summer rain, e.g., the Chihuahuan Desert. Further, the derived features of summer-drought taxa should be related to water stress. I examined Axelrod's thesis, using a combination of phylogenetic systematics, physiological ecology, and vicariance biogeography. The first chapter is a cladistic study of the pinyon pines, 13 taxa of small trees that range from the summer-wet regions of Mexico to the summer drought regions of Nevada and California. A parsimony analysis using twenty morphological characters showed that the most recently derived pinyons are from regions of summer drought. The "summer-drought" taxa are characterized by relatively few needles per fascicle. Because fewer needles per fascicle results in a reduction in the needle surface-to-volume ratio, Haller (1965) hypothesized that fewer needles in pines is an adaptation to reduce transpirational water loss. The second chapter reports on a two year study of the xylem pressure potentials of single- and double-needled fascicles of hybrid pinyons in central Arizona. The results showed no significant differences between single- and double-needles. I concluded that either needle morphology does not effect water relations, or that the relatively high precipitation during the study did not allow significant water stress to occur. The third chapter uses the methods of vicariance biogeography to search for a common pattern of relationship between southwestern biotic provinces, as indicated by the relationships of their endemic taxa. Using a biogeographic parsimony analysis, I compared the area cladograms of six taxa -- junipers, pinyon pines, the composite Palafoxia, hedgehog cactus, desert tortoises, and gecko lizards. The most parsimonious area cladogram supports Axelrod's (1958) hypothesis, but also shows that some taxa, notably the junipers, support other patterns of area relationships, e.g., summer-drought primitive. I suggest that there is no single pattern of area relationships because of the effects of the Pleistocene (including dispersal and extinction) and vicariance events other than the Tertiary climatic change, e.g., the separation of the Baja peninsula from mainland Mexico during the Miocene.