Author
Leo Joseph
Other affiliations: Academy of Natural Sciences of Drexel University, Griffith University, University of Queensland
Bio: Leo Joseph is an academic researcher from Commonwealth Scientific and Industrial Research Organisation. The author has contributed to research in topics: Population & Subspecies. The author has an hindex of 39, co-authored 168 publications receiving 6141 citations. Previous affiliations of Leo Joseph include Academy of Natural Sciences of Drexel University & Griffith University.
Topics: Population, Subspecies, Phylogeography, Coalescent theory, Biogeography
Papers published on a yearly basis
Papers
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TL;DR: A review of recent studies shows heterogeneity in the magnitude and direction of size responses, exposing a need for large-scale phylogenetically controlled comparative analyses of temporal size change as mentioned in this paper, which will increase both understanding of the underlying mechanisms and physiological consequences of size shifts and therefore, the ability to predict the sensitivities of species to climate change.
Abstract: A recently documented correlate of anthropogenic climate change involves reductions in body size, the nature and scale of the pattern leading to suggestions of a third universal response to climate warming. Because body size affects thermoregulation and energetics, changing body size has implications for resilience in the face of climate change. A review of recent studies shows heterogeneity in the magnitude and direction of size responses, exposing a need for large-scale phylogenetically controlled comparative analyses of temporal size change. Integrative analyses of museum data combined with new theoretical models of size-dependent thermoregulatory and metabolic responses will increase both understanding of the underlying mechanisms and physiological consequences of size shifts and, therefore, the ability to predict the sensitivities of species to climate change.
830 citations
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TL;DR: This review highlights the opportunities that development of arid conditions provides for rapid and diverse evolutionary radiations, and re-enforces the emerging view that Pleistocene environmental change can have diverse impacts on genetic structure and diversity in different biomes.
Abstract: The integration of phylogenetics, phylogeography and palaeoenvironmental studies is providing major insights into the historical forces that have shaped the Earth's biomes. Yet our present view is biased towards arctic and temperate/tropical forest regions, with very little focus on the extensive arid regions of the planet. The Australian arid zone is one of the largest desert landform systems in the world, with a unique, diverse and relatively well-studied biota. With foci on palaeoenvironmental and molecular data, we here review what is known about the assembly and maintenance of this biome in the context of its physical history, and in comparison with other mesic biomes. Aridification of Australia began in the Mid-Miocene, around 15 million years, but fully arid landforms in central Australia appeared much later, around 1-4 million years. Dated molecular phylogenies of diverse taxa show the deepest divergences of arid-adapted taxa from the Mid-Miocene, consistent with the onset of desiccation. There is evidence of arid-adapted taxa evolving from mesic-adapted ancestors, and also of speciation within the arid zone. There is no evidence for an increase in speciation rate during the Pleistocene, and most arid-zone species lineages date to the Pliocene or earlier. The last 0.8 million years have seen major fluctuations of the arid zone, with large areas covered by mobile sand dunes during glacial maxima. Some large, vagile taxa show patterns of recent expansion and migration throughout the arid zone, in parallel with the ice sheet-imposed range shifts in Northern Hemisphere taxa. Yet other taxa show high lineage diversity and strong phylogeographical structure, indicating persistence in multiple localised refugia over several glacial maxima. Similar to the Northern Hemisphere, Pleistocene range shifts have produced suture zones, creating the opportunity for diversification and speciation through hybridisation, polyploidy and parthenogenesis. This review highlights the opportunities that development of arid conditions provides for rapid and diverse evolutionary radiations, and re-enforces the emerging view that Pleistocene environmental change can have diverse impacts on genetic structure and diversity in different biomes. There is a clear need for more detailed and targeted phylogeographical studies of Australia's arid biota and we suggest a framework and a set of a priori hypotheses by which to proceed.
595 citations
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University of California, Santa Cruz1, National Institutes of Health2, Broad Institute3, University of Los Andes4, University of Guelph5, University of Nottingham6, University of California, Berkeley7, Pennsylvania State University8, Royal Ontario Museum9, Texas A&M University10, Louisiana State University11, Agency for Science, Technology and Research12, University of Kansas13, University of Montana14, American Museum of Natural History15, Oregon State University16, Villanova University17, University of Porto18, Smithsonian Institution19, Oswaldo Cruz Foundation20, Okinawa Institute of Science and Technology21, University of Sheffield22, Harvard University23, Swedish Museum of Natural History24, University of Copenhagen25, Novosibirsk State University26, Australian National University27, Max Planck Society28, Field Museum of Natural History29, Commonwealth Scientific and Industrial Research Organisation30, Science Applications International Corporation31, Stanford University32, University of Illinois at Urbana–Champaign33, George Washington University34, Global Viral35, University of Bedfordshire36, Federal University of Rio de Janeiro37, University of California, Davis38, University of California, Riverside39, Museum Victoria40, University College Dublin41, Monterey Bay Aquarium Research Institute42, Washington University in St. Louis43, University of California, Los Angeles44, Kunming Institute of Zoology45
TL;DR: A precipitous drop in costs and increase in sequencing efficiency is anticipated, with concomitant development of improved annotation technology, and it is proposed to create a collection of tissue and DNA specimens for 10,000 vertebrate species specifically designated for whole-genome sequencing in the very near future.
Abstract: American Genetic Association, Gordon and Betty Moore Foundation, NHGRI Intramural Sequencing Center, and UCSC Alumni Association to cost of the Genome 10K workshop; Howard Hughes Medical Institute to D. H.; Gordon and Betty Moore Foundation to S. C. S.; A
545 citations
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Department of Environment and Conservation1, University of Tasmania2, Commonwealth Scientific and Industrial Research Organisation3, James Cook University4, Royal Botanic Gardens5, University of Queensland6, Australian National University7, Museum Victoria8, Museum of Vertebrate Zoology9, Deakin University10, Monash University11
TL;DR: The aims are to review and refine key hypotheses derived from palaeoclimatic data and the fossil record that are critical to understanding the evolution of the Australian mesic biota and examine predictions arising from these hypotheses using available molecular phylogenetic and phylogeographical data.
Abstract: Aim: The mesic biome, encompassing both rain forest and open sclerophyllous forests, is central to understanding the evolution of Australia’s terrestrial biota and has long been considered the ancestral biome of the continent. Our aims are to review and refine key hypotheses derived from palaeoclimatic data and the fossil record that are critical to understanding the evolution of the Australian mesic biota. We examine predictions arising from these hypotheses using available molecular phylogenetic and phylogeographical data. In doing so, we increase understanding of the mesic biota and highlight data deficiencies and fruitful areas for future research.
Location: The mesic biome of Australia, along the eastern coast of Australia, and in the south-east and south-west, including its rain forest and sclerophyllous, often eucalypt-dominated, habitats.
Methods: We derived five hypotheses based on palaeoclimatic and fossil data regarding the evolution of the Australian mesic biota, particularly as it relates to the mesic biome. We evaluated predictions formulated from these hypotheses using suitable molecular phylogenies of terrestrial plants and animals and freshwater invertebrates.
Results: There was support for the ancestral position of mesic habitat in most clades, with support for rain forest habitat ancestry in some groups, while evidence of ancestry in mesic sclerophyllous habitats was also demonstrated for some plants and herpetofauna. Contraction of mesic habitats has led to extinction of numerous lineages in many clades and this is particularly evident in the rain forest component. Species richness was generally higher in sclerophyllous clades than in rain forest clades, probably due to higher rates of net speciation in the former and extinction in the latter. Although extinction has been prominent in rain forest communities, tropical rain forests appear to have experienced extensive immigration from northern neighbours. Pleistocene climatic oscillations have left genetic signatures at multiple levels of divergence and with complex geographical structuring, even in areas with low topographical relief and few obvious geographical barriers.
Main conclusions: Our review confirms long-held views of the ancestral position of the Australian mesic biome but also reveals new insights into the complexity of the processes of contraction, fragmentation, extinction and invasion during the evolution of this biome.
326 citations
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TL;DR: The Australian monsoon is a component of a single global climate system, characterized by a dominant equator-spanning Hadley cell, and future palaeoecological and phylogenetic investigations will illuminate the evolution of the AMT biome.
Abstract: Aim This paper reviews the biogeography of the Australian monsoon tropical
biome to highlight general patterns in the distribution of a range of organisms
and their environmental correlates and evolutionary history, as well as to identify
knowledge gaps.
Location Northern Australia, Australian Monsoon Tropics (AMT). The AMT
is defined by areas that receive more than 85% of rainfall between November
and April.
Methods Literature is summarized, including the origin of the monsoon
climate, present-day environment, biota and habitat types, and phylogenetic and
geographical relationships of selected organisms.
Results Some species are widespread throughout the AMT while others are
narrow-range endemics. Such contrasting distributions correspond to presentday
climates, hydrologies (particularly floodplains), geological features (such as
sandstone plateaux), fire regimes, and vegetation types (ranging from rain forest
to savanna). Biogeographical and phylogenetic studies of terrestrial plants
(e.g. eucalypts) and animals (vertebrates and invertebrates) suggest that distinct
bioregions within the AMT reflect the aggregated effects of landscape and
environmental history, although more research is required to determine and
refine the boundaries of biogeographical zones within the AMT. Phylogenetic
analyses of aquatic organisms (fishes and prawns) suggest histories of associations
with drainage systems, dispersal barriers, links to New Guinea, and the existence
of Lake Carpentaria, now submerged by the Gulf of Carpentaria. Complex
adaptations to the landscape and climate in the AMT are illustrated by a number
of species.
Main conclusions The Australian monsoon is a component of a single global
climate system, characterized by a dominant equator-spanning Hadley cell.
Evidence of hot, seasonally moist climates dates back to the Late Eocene, implying
that certain endemic elements of the AMT biota have a long history. Vicariant
differentiation is inferred to have separated the Kimberley and Arnhem Land
bioregions from Cape York Peninsula/northern Queensland. Such older patterns
are overlaid by younger events, including dispersal from Southeast Asia, and
range expansions and contractions. Future palaeoecological and phylogenetic
investigations will illuminate the evolution of the AMT biome. Understanding the
biogeography of the AMT is essential to provide a framework for ecological
studies and the sustainable development of the region.
286 citations
Cited by
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TL;DR: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols used xiii 1.
Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201
14,171 citations
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TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
11,521 citations
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TL;DR: Primer3’s current capabilities are described, including more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers.
Abstract: Polymerase chain reaction (PCR) is a basic molecular biology technique with a multiplicity of uses, including deoxyribonucleic acid cloning and sequencing, functional analysis of genes, diagnosis of diseases, genotyping and discovery of genetic variants. Reliable primer design is crucial for successful PCR, and for over a decade, the open-source Primer3 software has been widely used for primer design, often in high-throughput genomics applications. It has also been incorporated into numerous publicly available software packages and web services. During this period, we have greatly expanded Primer3’s functionality. In this article, we describe Primer3’s current capabilities, emphasizing recent improvements. The most notable enhancements incorporate more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers. Additional enhancements include more precise control of primer placement—a change motivated partly by opportunities to use whole-genome sequences to improve primer specificity. We also added features to increase ease of use, including the ability to save and re-use parameter settings and the ability to require that individual primers not be used in more than one primer pair. We have made the core code more modular and provided cleaner programming interfaces to further ease integration with other software. These improvements position Primer3 for continued use with genome-scale data in the decade ahead.
7,286 citations
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TL;DR: A Brooks parsimony analysis produced an unrooted area phylogram, showing that: (i) the northern regions were colonized generally from the Iberic and Balkanic refugia; and (ii) the Italian lineages were often isolated due to the presence of the Alpine barrier.
Abstract: The Quaternary cold periods in Europe are thought to have heavily influenced the amount and distribution of intraspecific genetic variation in both animals and plants. The phylogeographies of 10 taxa, including mammals (Ursus arctos, Sorex spp., Crocidura suaveolens, Arvicola spp.), amphibians (Triturus spp.), arthropods (Chorthippus parallelus), and plants (Abies alba, Picea abies, Fagus sylvatica, Quercus spp.), were analysed to elucidate general trends across Europe. Only a small degree of congruence was found amongst the phylogeographies of the 10 taxa, but the likely postglacial colonization routes exhibit some similarities. A Brooks parsimony analysis produced an unrooted area phylogram, showing that: (i) the northern regions were colonized generally from the Iberic and Balkanic refugia; and (ii) the Italian lineages were often isolated due to the presence of the Alpine barrier. The comparison of colonization routes highlighted four main suture-zones where lineages from the different refugia meet. Some of the intraspecific genetic distances among lineages indicated a prequaternary divergence that cannot be connected to any particular cold period, but are probably related mainly to the date of arrival of each taxon in the European continent. As a consequence, molecular genetics so far appears to be of limited use in dating Quaternary events.
2,855 citations
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TL;DR: In this paper, a test based on two conserved CHD (chromo-helicase-DNA-binding) genes that are located on the avian sex chromosomes of all birds, with the possible exception of the ratites (ostriches, etc.).
2,554 citations