Alexander Zizka

Alexander Zizka
Philipps University of Marburg | PUM

Doctor of Philosophy

About

119
Publications
49,038
Reads
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1,972
Citations
Introduction
I am a postdoctoral researcher at the EA lab and synthesis group of the German Centre for Integrative Biodiversity Research (iDiv) in Leipzig, Germany. My primary research interest is the evolution of tropical biodiversity and the use of big data for biogeography and conservation. I integrate large-scale data sets of species distribution with molecular phylogenies and traits, to understand biodiversity over time and space, in particular of plants in the South American and African savannas. I am
Additional affiliations
November 2019 - November 2019
Physalia courses
Position
  • Professor
Description
  • 1-week block course "Big data Biogeography"
October 2019 - present
Naturalis Biodiversity Center
Position
  • Researcher
September 2019 - September 2019
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig
Position
  • Lecturer
Description
  • 2-day course "Writing R-packages"
Education
June 2013 - April 2018
University of Gothenburg
Field of study
  • Biology
September 2006 - February 2012

Publications

Publications (119)
Article
Full-text available
A large-scale analysis of bird diversity and evolution on mountains around the globe explores the relationships between elevation, species richness and the rate of formation of new species.
Article
Full-text available
The American tropics (the Neotropics) are the most species-rich realm on Earth, and for centuries, scientists have attempted to understand the origins and evolution of their biodiversity. It is now clear that different regions and taxonomic groups have responded differently to geological and climatic changes. However, we still lack a basic understa...
Article
Full-text available
Species occurrence records from online databases are an indispensable resource in ecological, biogeographical and palaeontological research. However, issues with data quality, especially incorrect geo-referencing or dating, can diminish their usefulness. Manual cleaning is time-consuming, error prone, difficult to reproduce and limited to known geo...
Article
Full-text available
Aim To provide distribution information and preliminary conservation assessments for all species of the pineapple family (Bromeliaceae), one of the most diverse and ecologically important plant groups of the American tropics—a global biodiversity hotspot. Furthermore, we aim to analyse patterns of diversity, endemism and the conservation status of...
Article
Species occurrence records provide the basis for many analyses in biodiversity research. They often derive from georeferenced specimens deposited in natural history collections or visual observations, such as those obtained through various mobile applications. Given the rapid increase in availability of such data, the control of quality and accurac...
Article
Full-text available
Aim: Central America is largely covered by hyperdiverse, yet poorly understood, rain forests. Understorey palms are diverse components of these forests, but little is known about their historical assembly. It is not clear when palms in Central America reached present diversity levels and whether most species arrived from neighbouring regions or evo...
Article
Full-text available
For many regions, such as in South America, it is unclear how well the existent protected areas network (PAs) covers different taxonomic groups and if there is a coverage bias of PAs towards certain biomes or species. Publicly available occurrence data along with ecological niche models might help to overcome this gap and to quantify the coverage o...
Article
Full-text available
Trees are fundamental for Earth's biodiversity as primary producers and ecosystem engineers and are responsible for many of nature's contributions to people. Yet, many tree species at present are threatened with extinction by human activities. Accurate identification of threatened tree species is necessary to quantify the current biodiversity crisi...
Article
1. In flowering plants (angiosperms), the herbaceous habit has evolved repeatedly from the ancestral woody state and herbs evolved repeatedly back to woody plants. Yet, how common these transitions were and which ecological conditions promote the herbaceous habit is poorly known. Several hypotheses exist, postulating an advantage of the herbaceous...
Preprint
Full-text available
Fungi play pivotal roles in ecosystem functioning, but little is known about their global patterns of diversity, endemicity, vulnerability to global change drivers and conservation priority areas. We applied the high-resolution PacBio sequencing technique to identify fungi based on a long DNA marker that revealed a high proportion of hitherto unkno...
Article
Full-text available
Aim The Red List (RL) from the International Union for the Conservation of Nature is the most comprehensive global quantification of extinction risk, and widely used in applied conservation as well as in biogeographic and ecological research. Yet, due to the time-consuming assessment process, the RL is biased taxonomically and geographically, which...
Preprint
Insular woodiness (IW)-the evolutionary transition from herbaceousness towards woodiness on islands-is one of the most iconic features of island floras. Since pioneering work by Darwin and Wallace, five IW drivers have been proposed: (i) favourable aseasonal climate and (ii) lack of large native herbivores promote plant longevity that (iii) results...
Article
The International Union for Conservation of Nature (IUCN) Red List of Threatened Species is central in biodiversity conservation, but insufficient resources hamper its long-term growth, updating, and consistency. Models or automated calculations can alleviate those challenges by providing standardised estimates required for assessments, or prioriti...
Article
Full-text available
The Andes are the world's most biodiverse mountain chain, encompassing a complex array of ecosystems from tropical rainforests to alpine habitats. We provide a synthesis of Andean vascular plant diversity by estimating a list of all species with publicly available records, which we integrate with a phylogenetic dataset of 14 501 Neotropical plant s...
Article
Full-text available
Due to increasing human transformation of virtually all habitats on Earth, setting global priorities for conservation is essential. The emerging disciplines of macroecology and macroevolution (MEE) can provide a global perspective and information for such prioritization but remain relatively separated from conservation prioritization, partly becaus...
Article
The palm tribe Lepidocaryeae (Arecaceae) comprises seven genera and 51 currently accepted species that are distributed in lowland tropical forests and savannas across Africa and the Americas. Subtribal relationships within Lepidocaryeae have been a persistent challenge,limiting our understanding of its systematics, morphology, and biogeography. Sev...
Article
Full-text available
p>Abandonment of agricultural land is widespread in many parts of the world, leading to shrub and tree encroachment. The increase of flammable plant biomass, that is, fuel load, increases the risk and intensity of wildfires. Fuel reduction by herbivores is a promising management strategy to avoid fuel build-up and mitigate wildfires. However, their...
Article
Full-text available
Aim Geo-referenced species occurrence records are a prime example of biodiversity data and a cornerstone of biodiversity research. Yet, their availability depends on non-biological factors, including the political framework in the region of collection. Here we present Bio-Dem (www.bio-dem.surge.sh), an open-source software to explore the relationsh...
Article
Full-text available
Insular woodiness (IW), referring to the evolutionary transition from herbaceousness toward woodiness on islands, has arisen more than 30 times on the Canary Islands (Atlantic Ocean). One of the IW hypotheses suggests that drought has been a major driver of wood formation, but we do not know in which palaeoclimatic conditions the insular woody line...
Preprint
Full-text available
Aim: The global Red List (RL) from the International Union for the Conservation of Nature is the most comprehensive global quantification of extinction risk, and widely used in applied conservation as well as in biogeographic and ecological research. Yet, due to the time-consuming assessment process, the RL is biased taxonomically and geographicall...
Article
Full-text available
Georeferenced biological data of species distributions, abundances, or traits are critical for ecological and evolutionary research. However, the accuracy (true vs. false records) and biogeographical status (native vs. alien) of individual georeferenced records are often unclear, which limits their use in species distribution modelling, analyses of...
Preprint
Full-text available
Published online in Frontiers of Biogeography's "in press" section (direct link: https://escholarship.org/uc/item/9wj3r67h).
Article
Full-text available
The lack of comprehensive and standardized taxonomic reference information is an impediment for robust plant research, e.g. in systematics, biogeography or macroecology. Here we provide an updated and much improved reference list of 1,315,562 scientific names for all described vascular plant species globally. The Leipzig Catalogue of Vascular Plant...
Article
Full-text available
The interchange between the previously disconnected faunas of North and South America was a massive experiment in biological invasion. A major gap in our understanding of this invasion is why there was a drastic increase in the proportion of mammals of North American origin found in South America. Four nonmutually exclusive mechanisms may explain t...
Article
Full-text available
Geo‐referenced species occurrences from public databases have become essential to biodiversity research and conservation. However, geographical biases are widely recognized as a factor limiting the usefulness of such data for understanding species diversity and distribution. In particular, differences in sampling intensity across a landscape due to...
Article
Full-text available
Species occurrence records provide the basis for many biodiversity studies. They derive from georeferenced specimens deposited in natural history collections and visual observations, such as those obtained through various mobile applications. Given the rapid increase in availability of such data, the control of quality and accuracy constitutes a pa...
Article
Full-text available
IUCN Red List assessments are essential for prioritizing conservation needs but are resource‐intensive and therefore only available for a fraction of global species richness. Automated conservation assessments based on digitally available geographic occurrence records can be a rapid alternative, but it is unclear how reliable these assessments are....
Article
Full-text available
The extinction of species can destabilize ecological processes. A way to assess the ecological consequences of species loss is by examining changes in functional diversity. The preservation of functional diversity depends on the range of ecological roles performed by species, or functional richness, and the number of species per role, or functional...
Preprint
Full-text available
IUCN Red List assessments are essential for prioritizing conservation needs but are resource-intensive and therefore only available for a fraction of global species richness. Tropical plant species are particularly under-represented on the IUCN Red List. Automated conservation assessments based on digitally available geographic occurrence records c...
Preprint
Full-text available
Aim: Insular woodiness, referring to the evolutionary transition from herbaceousness towards woodiness on islands, has arisen at least 38 times on the Canary Islands. Distribution patterns and physiological experiments have suggested a link between insular woodiness and increased drought stress resistance in current-day species, but we do not know...
Preprint
Full-text available
The lack of comprehensive and standardized taxonomic reference information is an impediment for robust plant research, e.g. in systematics, biogeography or macroecology. Here we provide an updated and much improved reference list of 1,315,479 scientific plant taxa names for all described vascular plant taxa names globally. The Leipzig Catalogue of...
Article
Full-text available
Palms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genus Raphia has 20 accepted species in Africa and one species endemic to the Neotropics. It is the most economically important genus of African palms with...
Preprint
Full-text available
Species occurrence records provide the basis for many biodiversity studies. They derive from geo-referenced specimens deposited in natural history collections and visual observations, such as those obtained through various mobile applications. Given the rapid increase in availability of such data, the control of quality and accuracy constitutes a p...
Preprint
Full-text available
National governments are the main actors responsible for mapping and protecting their biodiversity, but countries differ in their capacity, willingness, and effectiveness to do so. We quantify the global biodiversity managed by different regime types and developed a tool to explore the links between level of democracy and other key socio-economic v...
Article
Full-text available
Aim To quantify evolutionary transitions between tropical evergreen rain forest and seasonally dry biomes, to test whether biome transitions affect lineage diversification and to examine the robustness of these results to methodological choices. Location The tropics. Time period The Cenozoic. Major taxa studied The plant subfamily Bombacoideae (...
Preprint
Full-text available
Georeferenced species occurrences from public databases have become essential to biodiversity research and conservation. However, geographical biases are widely recognized as a limiting factor that could severely affect usefulness of such data for understanding species diversity and distributions. In particular, differences in sampling intensity ac...
Article
Full-text available
Most knowledge on biodiversity derives from the study of charismatic macro-organisms, such as birds and trees. However, the diversity of micro-organisms constitutes the majority of all life forms on Earth. Here, we ask if the patterns of richness inferred for macro-organisms are similar for micro-organisms. For this, we barcoded samples of soil, li...
Poster
Full-text available
Poster presented at the iDiv Annual Conference 2019, Leipzig, with some preliminary results of my master thesis.
Article
Full-text available
Increasing human pressure threatens plant and animal species with extinction worldwide. National political institutions constitute an important arena for biodiversity conservation. Yet, the relationship between how democratic these national institutions are and a country’s efforts towards and track-record for biodiversity conservation remains poorl...
Article
Full-text available
The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological d...
Article
Full-text available
Background Knowledge on the globally outstanding Amazonian biodiversity and its environmental determinants stems almost exclusively from aboveground organisms, notably plants. In contrast, the environmental factors and habitat preferences that drive diversity patterns for micro-organisms in the ground remain elusive, despite the fact that micro-org...
Data
Metadata Soil, coordinates and locality information of data collected in this study.
Data
Operational taxonomic units table for 18S used in this study
Data
Taxonomic assignment of 16S operational taxonomic units
Data
Taxonomic assignment of 18S operational taxonomic units
Data
Operational taxonomic units table for 16S used in this study
Article
Full-text available
Evolutionary biology has entered an era of unprecedented amounts of DNA sequence data, as new sequencing technologies such as Massive Parallel Sequencing (MPS) can generate billions of nucleotides within less than a day. The current bottleneck is how to efficiently handle, process, and analyze such large amounts of data in an automated and reproduc...
Data
Overview of recovered contigs The table shows which exon locus had a matching contig in each of the Geonoma samples.
Data
Example of phylogenetic tree inference from SECAPR output
Data
Biological data info Reported are the IDs of the Geonoma sample data and the locality and collector information about each sample.
Data
Library preparation and sequencing of Geonoma sample data Detailed description of the lab workflow.
Data
Overview of all contigs flagged by the find_traget_contigs function The document contains a list of all contigs that were flagged by the find_target_contigs function. Listed for each sample are all exons which were excluded because of possible paralogy (more than one matching contig). Further for each sample are listed all contig IDs, which matched...
Data
Overview of read-coverage for selected exon loci The table contains an overview of the read-depth information for all 97 exon loci that had an average read-depth of at least 3 reads across all Geonoma samples.
Data
Exon index legend for Fig. 4 This table contains an overview of which exon locus corresponds to which index in Fig. 4 of the manuscript.
Preprint
Full-text available
Background. Knowledge on the globally outstanding Amazonian biodiversity and its environmental determinants stems almost exclusively from aboveground organisms, notably plants. In contrast, the environmental factors and habitat preferences that drive diversity patterns for micro-organisms in the ground remain elusive, despite the fact that micro-or...
Preprint
Full-text available
Background. Knowledge on the globally outstanding Amazonian biodiversity and its environmental determinants stems almost exclusively from aboveground organisms, notably plants. In contrast, the environmental factors and habitat preferences that drive diversity patterns for micro-organisms in the ground remain elusive, despite the fact that micro-or...
Article
Full-text available
New World monkeys (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timin...
Article
Full-text available
The exceptional increase in molecular DNA sequence data in open repositories is mirrored by an ever-growing interest among evolutionary biologists to harvest and use those data for phylogenetic inference. Many quality issues, however, are known and the sheer amount and complexity of data available can pose considerable barriers to their usefulness....
Article
Full-text available
Amazonia is an environmentally heterogeneous and biologically megadiverse region, and its biodiversity varies considerably over space. However, existing knowledge on Amazonian biodiversity and its environmental determinants stems almost exclusively from studies of macroscopic above‐ground organisms, notably vertebrates and trees. In contrast, diver...
Preprint
The exceptional increase in molecular DNA sequence data in open repositories is mirrored by an ever-growing interest among evolutionary biologists to harvest and use those data for phylogenetic inference. Many quality issues, however, are known and the sheer amount and complexity of data available can pose considerable barriers to their usefulness....