Population genetic structure of the prairie skink (Eumeces septentrionalis): Nested clade analysis of post Pleistocene populations

We sequenced two regions of the mitochondrial genome, ND4 and d-loop, from 64 Eumeces septentrionales to assess intra- and interspecific population differentiation. We constructed haplotype genealogies for nine Eumeces septentrionalis septentrionalis populations in previously glaciated regions and used nested clade analysis to examine the role of vicariance and dispersal in shaping the population structure of E. s. septentrionalis in the northern part of its range following Pleistocene paleoclimatological events. In addition, we used DNA sequence data to compare populations of the northern subspecies (E. s. septentrionalis) with the southern subspecies (Eumeces septentrionalis obtusirostris) to determine whether specific level differentiation is evident. For populations of E. septentrionalis in previously glaciated areas, nested clade analyses revealed isolation by distance with restricted gene flow at both haplolype and upper clade levels as the inferred geographical pattern reflecting the lack of overlapping haplotypes in distant populations. These results suggest that colonization of E. septentrionalis into previously glaciated areas was from a single source with restricted gene flow. These results do not support past population fragmentation or colonization from multiple, genetically distinct source populations. Parsimony and maximum likelihood phylogenetic analyses showed reciprocal monophyly between northern (E. s. septentrionalis) and southern (E. s. obtusirostris) subspecies with unconnected sequence divergence ranging from 6.7-7.0%. These results, combined with the morphological differences found in previous studies, suggest that these allopatric populations are on separate evolutionary trajectories

Establishment limitation reduces species recruitment and species richness as soil resources rise

At local spatial scales, species richness tends to fall as productivity rises. Most explanations have focused on increased extinction, but, instead, we test experimentally whether increased soil fertility reduces recruitment. Specifically, we test whether variation in recruitment is due to source limitation, germination limitation or establishment limitation, and how litter accumulation and seed predation contribute to these processes. We established four crossed experimental treatments in a perennial‐dominated early successional plant community over 3 years. We added seed of 30 species, manipulated access by selected seed predators, removed litter and added slow release fertilizer at four levels (0, 8, 16 and 32 g N m−2). Species recruitment and richness both decreased with increasing fertility, but, counter to our expectations, we found that neither seed additions nor litter removal could counteract the negative effects of fertilizer. Seed additions increased seedling density at all fertilizer levels, and seed predation appeared to have no influence on seedling densities. In spite of high seedling densities at all fertilizer levels, final stem density declined by 70% as fertilizer increased. A strong stem density–species richness relationship suggests that declines in final stem density caused more than half of the decline in species richness along this fertility gradient. These results suggest that establishment limitation, i.e. the reduction of growth and survival from seedling to adult, controls species recruitment in highly fertile sites. The high degree of recruitment limitation commonly observed in productive habitats suggests that high productivity causes establishment limitation, thereby isolating these communities from the regional species pool. We suggest that such isolation provides a mechanism to explain why the species composition of productive communities exhibits higher variability than the composition of less productive communities within the same regional source pool

Evolution and Biogeography of the Slipper Orchids: Eocene Vicariance of the Conduplicate Genera in the Old and New World Tropics

Intercontinental disjunctions between tropical regions, which harbor two-thirds of the flowering plants, have drawn great interest from biologists and biogeographers. Most previous studies on these distribution patterns focused on woody plants, and paid little attention to herbs. The Orchidaceae is one of the largest families of angiosperms, with a herbaceous habit and a high species diversity in the Tropics. Here we investigate the evolutionary and biogeographical history of the slipper orchids, which represents a monophyletic subfamily (Cypripedioideae) of the orchid family and comprises five genera that are disjunctly distributed in tropical to temperate regions. A relatively well-resolved and highly supported phylogeny of slipper orchids was reconstructed based on sequence analyses of six maternally inherited chloroplast and two low-copy nuclear genes (LFY and ACO). We found that the genus Cypripedium with a wide distribution in the northern temperate and subtropical zones diverged first, followed by Selenipedium endemic to South America, and finally conduplicate-leaved genera in the Tropics. Mexipedium and Phragmipedium from the neotropics are most closely related, and form a clade sister to Paphiopedilum from tropical Asia. According to molecular clock estimates, the genus Selenipedium originated in Palaeocene, while the most recent common ancestor of conduplicate-leaved slipper orchids could be dated back to the Eocene. Ancestral area reconstruction indicates that vicariance is responsible for the disjunct distribution of conduplicate slipper orchids in palaeotropical and neotropical regions. Our study sheds some light on mechanisms underlying generic and species diversification in the orchid family and tropical disjunctions of herbaceous plant groups. In addition, we suggest that the biogeographical study should sample both regional endemics and their widespread relatives

Molecular systematics, biogeography and dating of the tribe Haemantheae (Amaryllidaceae) and the phylogeography of Clivia

Includes abstract.Includes bibliographical references (leaves 121-140).The African tribe Haemantheae, belonging to the monocotyledonous family Amaryllidaceae, comprises six genera (Gethyllis, Apodolirion, Haemanthus, Scadoxus, Clivia and Cryptostephanus) with ca. 90 species. A phylogenetic hypothesis for the Haemantheae is presented as a basis for an enquiry into the generic and species relationships within the tribe. DNA sequence data from five plastid regions: the rpoB-trnC intergenic spacer, trnL intron, trnL-F intergenic spacer, the rps16 intron, the psbA-trnH intergenic spacer and internal transcribed spacer region (ITS) have been collected and analysed for 62 taxa within this tribe using two outgroups within Amaryllidaceae. Combined parsimony and Bayesian analyses of the five plastid and one nuclear region indicated that Scadoxus and Haemanthus are monophyletic and resolved as sister clades to one another. The summer rainfall group of species within the genus Haemanthus is monophyletic. The genus Apodolirion is embedded within Gethyllis as has been previously suggested on morphological grounds. Both Clivia and Cryptostephanus resolved as monophyletic groups with Cryptostephanus placed as sister to Clivia. Character optimizations of 15 morphological characters were carried out and optimization of the character ‘anther number’ revealed the strongest evidence so far for not recognising the informally recognized Gethyllis ‘villosa’ group. Biogeographic analyses using the divergence/vicariance (DIVA) method were inconclusive in determining the ancestral node of Haemantheae as the phytogeographic areas occupied by the taxa were too widespread. Two methods, non parametric rate smoothing (NPRS) and a Bayesian method (implemented in BEAST) were used in the assessment of age estimates and divergence times within the Haemantheae. Due to a lack of fossil record for this group, a calibration point from Wikström et al. (2001) of 33 Ma was used, based on the split of Haemantheae and Hippeastreae. Results indicate a rapid diversification for the winter rainfall lineages of Haemanthus at around 5 Ma coinciding with the late Miocene/Pliocene and the aridification and formation of a Mediterranean-type climate in southwestern Africa. In contrast, Gethyllis reflects a gradual diversification from 20-8Ma before the onset of aridification and the establishment of the Mediterranean-type climate. Analyses of the Clivia populations reveal occasional haplotype sharing between Clivia species in those parts of the distribution range where they are sympatric. The interconnectedness of C. gardenii and C. robusta brings into question the recognition of these two entities as discrete species

β-Diversity and Species Accumulation in Antarctic Coastal Benthos: Influence of Habitat, Distance and Productivity on Ecological Connectivity

High Antarctic coastal marine environments are comparatively pristine with strong environmental gradients, which make them important places to investigate biodiversity relationships. Defining how different environmental features contribute to shifts in β-diversity is especially important as these shifts reflect both spatio-temporal variations in species richness and the degree of ecological separation between local and regional species pools. We used complementary techniques (species accumulation models, multivariate variance partitioning and generalized linear models) to assess how the roles of productivity, bio-physical habitat heterogeneity and connectivity change with spatial scales from metres to 100's of km. Our results demonstrated that the relative importance of specific processes influencing species accumulation and β–diversity changed with increasing spatial scale, and that patterns were never driven by only one factor. Bio-physical habitat heterogeneity had a strong influence on β-diversity at scales <290 km, while the effects of productivity were low and significant only at scales >40 km. Our analysis supports the emphasis on the analysis of diversity relationships across multiple spatial scales and highlights the unequal connectivity of individual sites to the regional species pool. This has important implications for resilience to habitat loss and community homogenisation, especially for Antarctic benthic communities where rates of recovery from disturbance are slow, there is a high ratio of poor-dispersing and brooding species, and high biogenic habitat heterogeneity and spatio-temporal variability in primary production make the system vulnerable to disturbance. Consequently, large areas need to be included within marine protected areas for effective management and conservation of these special ecosystems in the face of increasing anthropogenic disturbance

Demographic and genetic variability in Cape Dwarf Chameleons, Bradypodion pumilum, withink a fragmented, urban habitat

Includes bibliographical references.Habitat fragmentation is recognized as a primary cause of biodiversity loss. To maximize biodiversity maintenance, researchers in the field of conservation biology often investigate population demography and genetic variability for species inhabiting fragmented landscapes. Findings from such work enable effective conservation management, maximizing viability for potentially imperiled populations. Previous research has relied predominately on spatial analysis when investigating population demography and genetic variability; however, temporal analysis is also important to species conservation. As of 2006, reptiles and amphibians had the highest threat status among small, terrestrial vertebrates, warranting continual investigation of herpetofaunal species inhabiting fragmented landscapes. Of the two, reptiles are the more poorly studied, though are suggested to be equally or more threatened than amphibians. The Cape Dwarf Chameleon, Bradypodion pumilum, exemplifies one potentially threatened reptile species which has suffered habitat loss, due to urbanization, inducing fragmentation and transformation among much of its habitat. As a result, many B. pumilum populations currently exist as a collection of isolated groups inhabiting critically endangered ecosystems

The phylogenetics and evolutionary history of the northern latitude plant genus Therorhodion (Maxim.) small (Ericaceae)

Thesis (M.S.) University of Alaska Fairbanks, 2017Taxonomic uncertainty in the Arctic-alpine flowering plant genus Therorhodion (Maxim.) Small (Ericaceae) can be attributed to two distinctly different viewpoints representing the taxonomic diversity. Russian taxonomists recognize two species, one with two subspecies, whereas three distinct species are recognized in North America following a broader species concept. Therorhodion redowskianum Hutch. is restricted to Asia, and is unambiguously recognized by both viewpoints. Therorhodion camtschaticum Small and T. glandulosum Standl. ex Small have an amphiberingian distribution in eastern Asia and Alaska with T. glandulosum sometimes recognized as a subspecies of T. camtschaticum. Investigating this taxonomic disagreement creates an opportunity to learn more about the diversification of Beringian taxa and how past glacial events have influenced speciation and the exchange of biota between the continents. I set out to unravel the taxonomic relationships within Therorhodion and the likely dispersal route/s of these amphiberingian taxa through the measurement of macromorphological characteristics from voucher specimens, phylogenetic analyses using plastid and nuclear DNA markers, and divergence time analyses. A comparison of age estimates was also performed based on secondary constraints versus fossil constraints. Although leaf length and width measurements were not reliable delimiting characters, there is strong molecular support for Therorhodion as the sister clade to Rhododendron, and within Therorhodion three strongly supported monophyletic clades representing three species were recovered. The use of secondary constraints in the divergence time analyses resulted in younger age estimates than when fossil constraints were applied, corroborating previous studies. Using fossil constraints I inferred a divergence of Therorhodion from Rhododendron in the late Paleocene with the Asian-restricted species diverging first from the T. camtschaticum/ T. glandulosum clade during the middle Miocene, supporting an Asian origin for the genus. Subsequently, the remaining two species are inferred to have diverged in the middle to late Miocene and further dispersed throughout the Pliocene and Pleistocene as suitable habitat became available through a cooling climate

Phylogeography and Population Structure of the Prairie Skink (Eumeces Septentrionalis)

The geographical and geneological limits of species are firmly rooted in historical and current processes. Phylogenetic studies focus on the historical aspect and examine character states to estimate ancestor-descendent relationships. The number of described species in the world has been estimated at 1.4 to 1.8 million and other estimates suggest that as many as 30 million species may exist (May, 1990; Wilson, 1992). Phylogenetic studies provide the information needed to delimit and classify these species based on their historical relationships. Studies on species population structure focus on the current and historical processes acting on a species. These studies use a variety of methods and estimate gene flow and allele frequencies across the species range. This thesis is composed of three chapters that examine the phylogeny and population structure of the prairie skink, Eumeces septentrionalis. Chapter 1 reviews some of the current methods available for examining population structure and justifies the m ethods used in this study. Chapter 2 examines the phylogenetic relationships within Eumeces septentrionalis using DMA sequence data from two portions of the mitochondrial genome. Specifically, populations from the northern subspecies, E. s. septentrionalis, are compared with the southern subspecies, E. s. obtusirostris. These data along with the phylogenetic species concept are then used to examine the placement of E. s. septentrionalis and E. s. obtusirostris as one or two distinct species. Chapter 3 focuses on the population structure of E. septentrionalis specifically with respect to the northern populations to examine the recolonization pattern following Pleistocene glaciation events. Two field seasons in the spring and summer of 2001 and 2002 were conducted for this study during which sixty-four tissue samples were collected from individuals in Canada, North Dakota, South Dakota, Minnesota, Wisconsin, and Kansas. ND4 (807 bp) and d-loop (~747 bp) regions of the mitochondrial genome (ND4 and d-loop) were sequenced from the collected samples, and these data were used in both phylogenetic and population structure analyses. Phylogenetic analyses demonstrated a substantial sequence divergence and reciprocal monophyly between the northern and southern subspecies of E. septentrionalis. Uncorrected pairwise distance values between the northern and southern subspecies ranged from 6.7 - 7.0%, and the monophyly of the northern and southern subspecies, E. s. septentrionalis and E. s. obtusirostris, were strongly supported by both maximum parsimony (bootstrap = 100) and maximum likelihood analyses. These results support the morphological differences found in previous studies and suggest that these two subspecies may be on separate evolutionary trajectories. The population structure of the prairie skink, E. septentrionalis, was examined using nested clade analyses, which revealed isolation by distance with restricted gene flow as the inferred geographical pattern for northern populations (E. s. septentrionalis). This pattern reflects the lack of overlapping haplotypes in distant populations and was found at both the hapiotype and upper clade levels. These results indicate that E. septentrionalis was likely subject to one or more vicariant events, and subsequently several localities probably acted as refugia and source populations during times of glacial advance and retreat

Dynamic modulation of neural feedback processing and attention during spatial probabilistic learning

Learned stimulus-reward associations can modulate behavior and the underlying neural processing of information. We investigated the cascade of these neurocognitive mechanisms involved in the learning of spatial stimulus-reward associations. Using electroencephalogram recordings while participants performed a probabilistic spatial reward learning task, we observed that the feedback-related negativity component was more negative in response to loss feedback compared to gain feedback but showed no modulation by learning. The late positive component became larger in response to losses as the learning set progressed but smaller in response to gains. In addition, feedback-locked alpha frequency oscillations measured over occipital sites were predictive of N2pc amplitudes—a marker of spatial attention orienting—observed on the next trial. This relationship was found to become stronger with learning set progression. Taken together, we elucidated neurocognitive dynamics underlying feedback processing during spatial reward learning, and the subsequent effects of these learned spatial stimulus-reward associations on spatial attention