Plant biogeography and conservation on a tropical island: Isla del Coco, Costa Rica

Isla del Coco (Cocos Island) is a small volcanic island located in the Pacific 500 km west of Costa Rica. Three collecting trips to Isla del Coco, in addition to herbarium research, were completed in order to assess the floristic diversity of the island. The current flora of Isla del Coco contains 262 plant species of which 37 (19.4%) are endemic. This study reports 58 species as new to the island. Seventy-one species (27.1%) were identified as introduced by humans. In addition, five potentially invasive plant species are identified. Seven vegetation types are identified on the island: bayshore, coastal cliff, riparian, low elevation humid forest, high elevation cloud forest, landslide and islet. ^ The biogeographic affinities of the native and endemic species are with Central America/northern South America and to a lesser extent, the Caribbean. Endemic species in the genus Epidendrum were investigated to determine whether an insular radiation event had produced two species found on Isla del Coco. Phylogenetic analysis of the internal transcribed spacer (ITS) of nuclear ribosomal DNA was not able to disprove that the endemic species in this genus are not sister species. Molecular biogeographic analyses of ITS sequence data determined that the Isla del Coco endemic species in the genera Epidendrum, Pilea and Psychotria are most closely related to Central American/northern South American taxa. No biogeographical links were found between the floras of Isla del Coco and the Galápagos Islands. ^ The native and endemic plant diversity of Isla del Coco is threatened with habitat degradation by introduced pigs and deer, and to a lesser extent, by exotic plant species. The IUCN Red List and RAREplants criteria were used to assess the extinction threat for the 37 endemic plant taxa found on the island. All of the endemic species are considered threatened with extinction at the Critically Endangered (CR) by the IUCN criteria or either CR or Endangered (EN) using RAREplants methodology. ^

Phylogenetics, conservation, and historical biogeography of the West Indian members of the Adelieae (Euphorbiaceae)

The Caribbean Island Biodiversity Hotspot is the largest insular system of the New World and a priority for biodiversity conservation worldwide. The tribe Adeliae (Euphorbiaceae) has over 35 species endemic to this hotspot, representing one of the most extraordinary cases of speciation in the West Indies, involving taxa from Cuba, Hispaniola, Jamaica, and the Bahamas. These species form a monophyletic group and traditionally have been accommodated in two endemic genera: Lasiocroton and Leucocroton. A study based on: (1) scanning electron microscopy of pollen and trichomes, (2) macromorphology, and (3) molecular data, was conducted to reveal generic relationships within this group. Phylogenies were based on parsimony and Bayesian analyses of nucleotide sequences of the ITS regions of the nuclear ribosomal DNA and the non-coding chloroplast DNA spacers psbM-trnD and ycf6-pcbM. One species, Lasiocroton trelawniensis, was transferred from the tribe into the genus Bernardia. Of the remaining species, three major monophyletic assemblages were revealed, one was restricted to limestone ares of Hispaniola and was sister to a clade with two monophyletic genera, Lasiocroton and Leucocroton. Morphological, biogeographical, and ecological data provided additional support for each of these three monophyletic assemblages. The Hispaniolan taxa were accommodated in a new genus with four species: Garciadelia. Leucocroton includes the nickel hyperaccumulating species from serpentine soils of Cuba, while the rest of the species were placed in Lasiocroton, a genus restricted to limestone areas. The geographic history of the islands as well as the phylogenetic placement of the Leucocroton-alliance, allows the research to include the historical biogeography of the alliance across the islands of the Caribbean based on a dispersal-vicariance analysis. The alliance arose on Eastern Cuba and Hispaniola, with Lasiocroton and Leucocroton diverging on Eastern Cuba according to soil type. Within Leucocroton, the analysis shows two migrations across the serpentine soils of Cuba. Additional morphological, ecological, and phylogenetic analyses support four new species in Cuba (Lasiocroton gutierrezii) and Hispaniola ( Garciadelia abbottii, G. castilloae, and G. mejiae). ^

Phylogenetic relationships among hadal amphipods of the Superfamily Lysianassoidea : Implications for taxonomy and biogeography

Date of Acceptance: 30/8/15 Acknowledgements We thank the chief scientists, crew and company of the Japanese RV Hakuho-Maru (KH0703 and KH0803), the RV Tansei-Maru (KT-09-03), the RV Kairei (KR0716), the German FS Sonne (SO197 and SO 209) and the New Zealand RV Kaharoa (KAH0190, KAH1109, KAH1202, KAH1301 and KAH1310). This work was supported by the HADEEP projects, funded by the Nippon Foundation, Japan (2009765188), the Natural Environmental Research Council, UK (NE/E007171/1) and the Total Foundation, France. We acknowledge additional support from the Marine Alliance for Science and Technology for Scotland (MASTS) funded by the Scottish Funding Council (Ref: HR09011) and contributing institutions. We also acknowledge support from the Leverhulme Research Fellowship granted to SBP. Additional sea time was supported by NIWA’s ‘Impact of Resource Use on Vulnerable Deep-Sea Communities’ project (CO1_0906). From NIWA we thank Malcolm Clark, Ashley Rowden, Kareen Schnabel, Sadie Mills for logistical support at the NIWA Invertebrate Collection. We also thank Fredrik Søreide from Promare, USA, for supply of the Puerto-Rico samples, Marius Wenzel for helpful comments on manuscript drafts, and Dr. Tammy Horton (NOCS, UK) for identifying some of the earlier amphipod samples

Early Carboniferous spiriferoid brachiopods from the Qaidam Basin, Northwest China: taxonomy, biostratigraphy and biogeography

Six Early Carboniferous brachiopod species in four genera of the Superfamily Spiriferoidea are described from the Qaidam Basin, northwestern China, including a new genus, Qaidamospirifer, and two new species: Grandispirifer qaidamensis and Qaidamospirifer elongatus. Additionally, a new genus, Triangulospirifer, is also proposed to replace Triangularia (Poletaev, 2001) that was preoccupied by a Devonian molluscan genus.

On the basis of the new material as well as published information, we have reviewed the taxonomic composition and the stratigraphic and palaeobiogeographic distributions of the three previously established genera from the viewpoint of palaeobiogeography. The study reveals that Grandispirifer has a relatively long stratigraphic range from the late Tournaisian to Serpukhovian. During this interval, the genus attained a wide geographical distribution, reaching Northwest China, western Yunnan of West China, Japan, as well as Iran and North Africa. Angiospirifer first occurred in western Europe in the Viséan, and later migrated to North Africa during the late Viséan. In the Serpukhovian, it migrated eastward, reaching the Donets Basin of Ukraine and the Qaidam Basin in Northwest China. Anthracothyrina evolved from Brachythyrina in North Africa in late Viséan, then dispersed north-westward to western and eastern Europe and, further eastward to the Qaidam Basin during the Serpukhovian.

Conservation biogeography of ecologically interacting species: The case of the Iberian lynx and the European rabbit

Aim To relate the recent Iberian lynx decline to changes in the distribution of the European rabbit after the haemorrhagic disease outbreak of 1989. As Iberian rabbits evolved in two geographically separated lineages, being the recent lynx range practically restricted to the southwestern lineage, we also test if differential range dynamics exists for these lineages, with the consequent implications for lynx conservation and reintroduction planning.

Converse Bergmann cline in a eucalyptus herbivore, paropsis atomaria olivier (coleoptera: chrysomelidae) : phenotypic plasticity or local adaptation?

Aim To measure latitude-related body size variation in field-collected Paropsis atomaria Olivier (Coleoptera: Chrysomelidae) individuals and to conduct common-garden experiments to determine whether such variation is due to phenotypic plasticity or local adaptation. Location Four collection sites from the east coast of Australia were selected for our present field collections: Canberra (latitude 35°19' S), Bangalow (latitude 28°43' S), Beerburrum (latitude 26°58' S) and Lowmead (latitude 24°29' S). Museum specimens collected over the past 100 years and covering the same geographical area as the present field collections came from one state, one national and one private collection. Methods Body size (pronotum width) was measured for 118 field-collected beetles and 302 specimens from collections. We then reared larvae from the latitudinal extremes (Canberra and Lowmead) to determine whether the size cline was the result of phenotypic plasticity or evolved differences (= local adaptation) between sites. Results Beetles decreased in size with increasing latitude, representing a converse Bergmann cline. A decrease in developmental temperature produced larger adults for both Lowmead (low latitude) and Canberra (high latitude) individuals, and those from Lowmead were larger than those from Canberra when reared under identical conditions. Main conclusions The converse Bergmann cline in P. atomaria is likely to be the result of local adaptation to season length.

Deeply divergent mitochondrial lineages reveal patterns of local endemism in chironomids of the Australian Wet Tropics

The Wet Tropics bioregion of north-eastern Australia has been subject to extensive fluctuations in climate throughout the late Pliocene and Pleistocene. Cycles of rainforest contraction and expansion of dry sclerophyll forest associated with such climatic fluctuations are postulated to have played a major role in driving geographical endemism in terrestrial rainforest taxa. Consequences for the distributions of aquatic organisms, however, are poorly understood.The Australian non-biting midge species Echinocladius martini Cranston (Diptera: Chironomidae), although restricted to cool, well-forested freshwater streams, has been considered to be able to disperse among populations located in isolated rainforest pockets during periods of sclerophyllous forest expansion, potentially limiting the effect of climatic fluctuations on patterns of endemism. In this study, mitochondrial COI and 16S data were analysed for E. martini collected from eight sites spanning theWet Tropics bioregion to assess the scale and extent of phylogeographic structure. Analyses of genetic structure showed several highly divergent cryptic lineages with restricted geographical distributions. Within one of the identified lineages, strong genetic structure implied that dispersal among proximate (<1 km apart) streams was extremely restricted. The results suggest that vicariant processes, most likely due to the systemic drying of the Australian continent during the Plio-Pleistocene, might have fragmented historical E. martini populations and, hence, promoted divergence in allopatry.

Hierarchical models for 2D presence/absence data having ambiguous zeroes: With a biogeographical case study on dingo behaviour

This dissertation is primarily an applied statistical modelling investigation, motivated by a case study comprising real data and real questions. Theoretical questions on modelling and computation of normalization constants arose from pursuit of these data analytic questions. The essence of the thesis can be described as follows. Consider binary data observed on a two-dimensional lattice. A common problem with such data is the ambiguity of zeroes recorded. These may represent zero response given some threshold (presence) or that the threshold has not been triggered (absence). Suppose that the researcher wishes to estimate the effects of covariates on the binary responses, whilst taking into account underlying spatial variation, which is itself of some interest. This situation arises in many contexts and the dingo, cypress and toad case studies described in the motivation chapter are examples of this. Two main approaches to modelling and inference are investigated in this thesis. The first is frequentist and based on generalized linear models, with spatial variation modelled by using a block structure or by smoothing the residuals spatially. The EM algorithm can be used to obtain point estimates, coupled with bootstrapping or asymptotic MLE estimates for standard errors. The second approach is Bayesian and based on a three- or four-tier hierarchical model, comprising a logistic regression with covariates for the data layer, a binary Markov Random field (MRF) for the underlying spatial process, and suitable priors for parameters in these main models. The three-parameter autologistic model is a particular MRF of interest. Markov chain Monte Carlo (MCMC) methods comprising hybrid Metropolis/Gibbs samplers is suitable for computation in this situation. Model performance can be gauged by MCMC diagnostics. Model choice can be assessed by incorporating another tier in the modelling hierarchy. This requires evaluation of a normalization constant, a notoriously difficult problem. Difficulty with estimating the normalization constant for the MRF can be overcome by using a path integral approach, although this is a highly computationally intensive method. Different methods of estimating ratios of normalization constants (N Cs) are investigated, including importance sampling Monte Carlo (ISMC), dependent Monte Carlo based on MCMC simulations (MCMC), and reverse logistic regression (RLR). I develop an idea present though not fully developed in the literature, and propose the Integrated mean canonical statistic (IMCS) method for estimating log NC ratios for binary MRFs. The IMCS method falls within the framework of the newly identified path sampling methods of Gelman & Meng (1998) and outperforms ISMC, MCMC and RLR. It also does not rely on simplifying assumptions, such as ignoring spatio-temporal dependence in the process. A thorough investigation is made of the application of IMCS to the three-parameter Autologistic model. This work introduces background computations required for the full implementation of the four-tier model in Chapter 7. Two different extensions of the three-tier model to a four-tier version are investigated. The first extension incorporates temporal dependence in the underlying spatio-temporal process. The second extensions allows the successes and failures in the data layer to depend on time. The MCMC computational method is extended to incorporate the extra layer. A major contribution of the thesis is the development of a fully Bayesian approach to inference for these hierarchical models for the first time. Note: The author of this thesis has agreed to make it open access but invites people downloading the thesis to send her an email via the 'Contact Author' function.

Influence of historical landscapes, drainage evolution and ecological traits on patterns of genetic diversity in Southeast Asian freshwater snakehead fishes

Snakehead fishes in the family Channidae are obligate freshwater fishes represented by two extant genera, the African Parachannna and the Asian Channa. These species prefer still or slow flowing water bodies, where they are top predators that exercise high levels of parental care, have the ability to breathe air, can tolerate poor water quality, and interestingly, can aestivate or traverse terrestrial habitat in response to seasonal changes in freshwater habitat availability. These attributes suggest that snakehead fishes may possess high dispersal potential, irrespective of the terrestrial barriers that would otherwise constrain the distribution of most freshwater fishes. A number of biogeographical hypotheses have been developed to account for the modern distributions of snakehead fishes across two continents, including ancient vicariance during Gondwanan break-up, or recent colonisation tracking the formation of suitable climatic conditions. Taxonomic uncertainty also surrounds some members of the Channa genus, as geographical distributions for some taxa across southern and Southeast (SE) Asia are very large, and in one case is highly disjunct. The current study adopted a molecular genetics approach to gain an understanding of the evolution of this group of fishes, and in particular how the phylogeography of two Asian species may have been influenced by contemporary versus historical levels of dispersal and vicariance. First, a molecular phylogeny was constructed based on multiple DNA loci and calibrated with fossil evidence to provide a dated chronology of divergence events among extant species, and also within species with widespread geographical distributions. The data provide strong evidence that trans-continental distribution of the Channidae arose as a result of dispersal out of Asia and into Africa in the mid–Eocene. Among Asian Channa, deep divergence among lineages indicates that the Oligocene-Miocene boundary was a time of significant species radiation, potentially associated with historical changes in climate and drainage geomorphology. Mid-Miocene divergence among lineages suggests that a taxonomic revision is warranted for two taxa. Deep intra-specific divergence (~8Mya) was also detected between C. striata lineages that occur sympatrically in the Mekong River Basin. The study then examined the phylogeography and population structure of two major taxa, Channa striata (the chevron snakehead) and the C. micropeltes (the giant snakehead), across SE Asia. Species specific microsatellite loci were developed and used in addition to a mitochondrial DNA marker (Cyt b) to screen neutral genetic variation within and among wild populations. C. striata individuals were sampled across SE Asia (n=988), with the major focus being the Mekong Basin, which is the largest drainage basin in the region. The distributions of two divergent lineages were identified and admixture analysis showed that where they co-occur they are interbreeding, indicating that after long periods of evolution in isolation, divergence has not resulted in reproductive isolation. One lineage is predominantly confined to upland areas of northern Lao PDR to the north of the Khorat Plateau, while the other, which is more closely related to individuals from southern India, has a widespread distribution across mainland SE Asian and Sumatra. The phylogeographical pattern recovered is associated with past river networks, and high diversity and divergence among all populations sampled reveal that contemporary dispersal is very low for this taxon, even where populations occur in contiguous freshwater habitats. C. micropeltes (n=280) were also sampled from across the Mekong River Basin, focusing on the lower basin where it constitutes an important wild fishery resource. In comparison with C. striata, allelic diversity and genetic divergence among populations were extremely low, suggesting very recent colonisation of the greater Mekong region. Populations were significantly structured into at least three discrete populations in the lower Mekong. Results of this study have implications for establishing effective conservation plans for managing both species, that represent economically important wild fishery resources for the region. For C. micropeltes, it is likely that a single fisheries stock in the Tonle Sap Great Lake is being exploited by multiple fisheries operations, and future management initiatives for this species in this region will need to account for this. For C. striata, conservation of natural levels of genetic variation will require management initiatives designed to promote population persistence at very localised spatial scales, as the high level of population structuring uncovered for this species indicates that significant unique diversity is present at this fine spatial scale.

Xiamen Hai Cang tourism project : landscape planning and design of five islands

International practice-led design research in landscape architecture has identified the need for addressing the loss of biodiversity in urban environments. China has lost much of its biodiversity in rural and urban environments over thousands of years. However some Chinese cities have attempted to conserve what remains and enhance existing vegetation communities in isolated pockets. Island biogeography has been used as the basis for planning and designing landscapes in Australia and North America but not as yet in China, as far as we know. A gap in landscape design knowledge exists regarding how to apply landscape ecology concepts to urban islands of remaining biodiversity being developed for heavy Chinese domestic tourism impacts in the future. This project responded to the demands for harbour-side tourism opportunities in Xiamen City, Fujian Province, by proposing a range of eco-design innovations using concepts of patch, edge and interior to interconnect people and nature in a Chinese setting.