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Ego sum Daniel

You've reached Daniel Ocampo Daza, resident of Uppsala, Sweden, enfant terrible, glasses-wearer, beard enthusiast, musicophile, evol biologist and PhD in medical science.

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About Me

Bio

January 6th 1984, Valledupar, Colombia

Swedish citizen; Resident of Uppsala, Sweden

Interests

Music, Painting, Science, Illustration & Web design, Baking

Contact

Address:
Evolutionary Biology Centre, EBC
Norbyvägen 18A
752 36 Uppsala
Sweden

E-mail: daniel.ocampo.daza /at/ gmail.com

Current position

2017 - Postdoctoral research fellow
Uppsala University, Department of Organismal Biology - Evolution and Development. Funded by the Swedish Research Council.

Experience

I received my M.Sc. in biology from Uppsala University in 2007 and subsequently pursued a doctorate under the supervision of prof. Dan Larhammar at the Department of Neuroscience, Uppsala University. I defended my thesis "Evolution of Vertebrate Endocrine and Neuronal Gene Families: Focus on Pituitary and Retina" on 1 March 2013, receiving a Ph.D. in medical science.

Awards and honors

The Royal Society of Sciences in Uppsala awarded me the 2015 Benzelius prize in the Biology-Medicine class, with the motivation - "For your pre-eminent studies of vertebrate genomes". The prize was confered at a public ceremony in Uppsala on September 1, 2015.

The Royal Society of Sciences in Uppsala is Sweden's oldest scientific academy, founded in 1710, and counts Carl Linnaeus, Olof Rudbeck the younger and Anders Celsius among its early members. The Benzelius award, named for the founder of the society, Erik Benzelius the younger, was founded in the 1980's to promote and reward young researchers.

Skills summary

Evolution, Neuroscience, Comparative endocrinology, Scientific writing, Molecular evolution, Sequence analysis, Phylogenetics, Genome Analysis, Gene prediction and annotation, Bioinformatics

Languages

  • Native/bilingual proficiency in Spanish and Swedish
  • Full professional proficiency in English

Education

2013 — Ph.D. in Medical Science
Uppsala University, Department of Neuroscience

2007 — M.Sc. in Biology
Uppsala University

Bio

January 6th 1984, Valledupar, Colombia
Swedish citizen; Resident of Uppsala, Sweden

Interests

Music, Painting, Science, Illustration & Web design, Baking

Contact

Address:
Evolutionary Biology Centre, EBC
Norbyvägen 18A
752 36 Uppsala
Sweden

E-mail: daniel.ocampo.daza /at/ gmail.com

Bioinformatics is simultaneously a scientific field and a set of methods for the analysis of biological data using computational tools. The study of how organisms or biological molecules are related through evolution is called phylogenetics, and evolutionary relationships are visualised through diagrams called phylogenetic trees.

Research

Understanding our evolutionary past through the language of our genes

As vertebrates, we are united by a common ancestry that stretches back to the Cambrian period, some 500 million years ago. Since then, vertebrates have occupied an astonishingly diverse set of ecological niches. Vertebrates live on almost every place on earth; from deep ocean trenches to arid deserts. The early evolution of vertebrates was a period of great innovation. It set the foundation for the great variety of complex and specialised functions that have allowed us to diversify and spread. Our mineralised bone structures and complex nervous systems stem back to this period, for example.

There is now convincing evidence that a group of our early ancestors doubled their genetic material twice during this period. This happened through a process called whole-genome duplication. It is the most drastic mutation possible: The doubling of the total genetic content, including genes, regulatory sequences, and non-functional DNA. We know that this had a great impact on vertebrate evolution because we can still find many of those twice duplicated genes in now-living vertebrates. A third whole-genome duplication occurred in the early evolution of teleost fishes. Similarly, we can find additional gene copies in teleosts resulting from this event.

What is a fish? When describing evolutionary relationships the word "fish" is almost entirely useless. What we call "fish" usually belongs to the group of teleost fishes, the most numerous group, like the pike in the image above. Or perhaps we refer to a shark, a cartilaginous fish, like the dogfish above. In actual fact these species are not closely related. Teleost fishes are more closely related to us four-limbed land vertebrates, or tetrapods, marked in red above. Every branch of the vertebrate evolutionary tree contains animals we might call "fish" - "any aquatic vertebrate that possesses gills and fins (if any appendages)". Speaking inclusively, all vertebrates are fish, and some of them are more closely related to you than to the "fish" you might have for lunch.

Duplication, be it of individual genes, segments of chromosomes, or of whole genomes, is one of evolution's driving forces. It is how families of related genes arise in evolution. Duplication generates new genetic material that mutation and selection can act upon to generate new functions while still keeping the original function in one of the copies. In this way, evolution can add new genetic building blocks on top of a previously laid foundation. In On the Origin of Species, Darwin hinted at this: "it is quite probable that natural selection, during a long-continued course of modification, should have seized on a certain number of the primordially similar elements, many times repeated, and have adapted them to the most diverse purposes." Of course Darwin did not know about genes, but the fundamental principle is the same.

As genome sequences began to fill the literature, even the most molecular and computational of biologists have become like naturalists. They wander through diverse landscapes of As, Ts, Gs and Cs, comparing genomes and wonder about the origin of the distinct classes of variation found there.

BioEssays 31:700-2

As genome sequences began to fill the literature, even the most molecular and computational of biologists have become like naturalists. They wander through diverse landscapes of As, Ts, Gs and Cs, comparing genomes and wonder about the origin of the distinct classes of variation found there.

BioEssays 31:700-2

Since the publication of the first draft of the human genome in 2001, we have seen an unprecedented advance in DNA sequencing technologies and bioinformatics tools. There is now openly available genome data from an ever growing number of organisms, including many vertebrates. This allows us to study the consequences of ancient whole-genome duplications, as well as other genomic events, with greater accuracy and resolution than ever before. Because we share a common ancestry, we can explore the evolution of vertebrates by comparing DNA sequences across different vertebrate groups. Like archaeologists looking for clues to the past in the soil, or naturalists exploring new and unknown environments, we can wade through the vast stretches of DNA and explore the contents of different genomes; trying to identify genes and figuring out how they are related to each other and how they have evolved.

This has been the backdrop for my research in the past ten years, which has explored the evolution of neurobiological and endocrine gene families in vertebrates. That is, families of genes involved in the nervous system and the hormonal control of bodily functions. By combining genomic analyses with molecular phylogenetics, my research has shown that the ancient whole-genome duplications in vertebrates likely contributed greatly to the evolution of processes such as vision, neural communication, body growth, the control of water balance, and social behaviours. Currently, I am also working on understanding the evolution of the ampullae of Lorenzini. These are small electro-sensory organs on the heads of cartilaginous fishes which allow them to detect weak electromagnetic fields generated by the muscular activity of their prey.

Understanding our evolution through the language of our genes is not only an interesting evolutionary puzzle. It also benefits applied biological and biomedical research. Functional studies can profit greatly from the combination of genomic and evolutionary approaches. Not least through the discovery of novel genes and functions, and through the increased understanding of model organisms used in laboratories to understand human diseases. But at its core, knowing more about our evolutionary past, where we come from and how we got here, is a fundamental human pursuit. It gives us context and binds us to other beings. As we move towards increasing climate change and a possible sixth mass extinction, including of many vertebrate species, this is more important than ever.

Publications

Publication Stats

Citations: 310
h-index: 9
Excluding self-citations

73% of my research is free to read online (top 21% of researchers), and 27% of my papers are published under a fully Open license like CC-BY, making them available for a wide range of reuse (not just reading).
Source: Impactstory

I have reviewed 5 pre-publication manuscripts for 3 journals.
Source: Publons

Links

Google Scholar profile
Scopus Author Details
My Impactstory
Mendeley profile
ORCID profile
ResearcherID: E-4635-2011
Publons profile

Publication Stats

Citations: 310
h-index: 9
Excluding self-citations

73% of my research is free to read online (top 21% of researchers), and 27% of my papers are published under a fully Open license like CC-BY, making them available for a wide range of reuse (not just reading).
Source: Impactstory

I have reviewed 5 pre-publication manuscripts for 3 journals.
Source: Publons

Peer-reviewed articles

NEW: Evolution of the receptors for growth hormone, prolactin, erythropoietin and thrombopoietin in relation to the vertebrate tetraploidizations
D Ocampo Daza, D Larhammar
General and Comparative Endocrinology, In Press N/D

Molecular evolution of GPCRs: Somatostatin/urotensin II receptors
H Tostivint, D Ocampo Daza, CA Bergqvist, FB Quan, M Bougerol, I Lihrmann & D Larhammar
Journal of Molecular Endocrinology 52(3): T61-T86 (2014) Cited by 18

The vertebrate ancestral repertoire of visual opsins, transducin alpha subunits and oxytocin/vasopressin receptors was established by duplication of their shared genomic region in the two rounds of early vertebrate genome duplications
D Lagman, D Ocampo Daza, J Widmark, XM Abalo, G Sundström, D Larhammar
BMC Evolutionary Biology 13:238 (2013) Cited by 44

The evolution of vertebrate somatostatin receptors and their gene regions involves extensive chromosomal rearrangements
D Ocampo Daza, G Sundström, CA Bergqvist, D Larhammar
BMC Evolutionary Biology 12:231 (2012) Cited by 18

Evolution of the vertebrate paralemmin gene family: ancient origin of gene duplicates suggests distinct functions
G Hultqvist, D Ocampo Daza, D Larhammar, MW Kilimann
PLoS ONE 7 (7), e41850 (2012) Cited by 13

Expansion of transducin subunit gene families in early vertebrate tetraploidizations
D Lagman, G Sundström, D Ocampo Daza, XM Abalo, D Larhammar
Genomics, 100(4): 203-11 (2012) Cited by 16

The oxytocin/vasopressin receptor family has at least five members in the gnathostome lineage, including two distinct V2 subtypes
D Ocampo Daza, M Lewicka, D Larhammar
General and Comparative Endocrinology 175(1): 135-43 (2012) Cited by 47
Free author's copy

Evolution of the insulin-like growth factor binding protein (IGFBP) family
D Ocampo Daza, G Sundström, CA Bergqvist, C Duan, D Larhammar
Endocrinology, 152(6): 2278-89 (2011) Cited by 63

Differential evolution of voltage-gated sodium channels in tetrapods and teleost fishes
J Widmark, G Sundström, D Ocampo Daza, D Larhammar
Molecular Biology and Evolution, 28(1): 859-71 (2011) Cited by 53

Major genomic events and their consequences for vertebrate evolution and endocrinology
D Ocampo Daza, G Sundström, TA Larsson, D Larhammar
Annals of the New York Academy of Sciences, 1163: 201-8 (2009) Cited by 32

Evolution of the Growth Hormone-Prolactin-Somatolactin System in Relation to Vertebrate Tetraploidizations
D Larhammar, G Sundström, S Dreborg, D Ocampo Daza, TA Larsson
Annals of the New York Academy of Sciences, 1163: 491-3 (2009) Cited by 6

Conference contributions (Selected)

Complex evolution of somatostatin and urotensin II receptors: Eleven ancestral gnathostome genes of which only six remain in mammals
D Larhammar, CA Bergqvist, G Sundström, Daniel Ocampo Daza
Frontiers in Endocrinology 100 (2011) Conference Abstract: NASCE 2011: The inaugural meeting of the North American Society for Comparative Endocrinology

The oxytocin/vasopressin receptor family has at least five members in the gnathostome lineage
D Ocampo Daza, M Lewicka, B Venkatesh, D Larhammar
Frontiers in Endocrinology 83 (2011) Conference Abstract: NASCE 2011: The inaugural meeting of the North American Society for Comparative Endocrinology

Evolution of the insulin-like growth factor binding protein (IGFBP) family in vertebrates
D Larhammar, G Sundström, CA Bergqvist, C Duan, D Ocampo Daza
Frontiers in Endocrinology 46 (2010) Conference Abstract: 25th Conference of the European Comparative Endocrinologists

Evolution of vertebrate neuropeptide receptors
D Larhammar, D Ocampo Daza, CA Bergqvist, G Sundström
Regulatory Peptides 164(1): 20 (2010) Conference Abstract: 18th International Symposium on Regulatory Peptides

Open science

Figshare Stats

Views: 6008
Downloads: 3900
Citations: 6

Figshare profile

Contact

Do you want additional data not found in figshare? Have you used any of my data or supporting information? Contact me at daniel.ocampo.daza /at/ gmail.com.

Figshare Stats

Views: 6008
Downloads: 3900
Citations: 6

Figshare profile

Contact

Do you want additional data not found in figshare? Have you used any of my data or supporting information? Contact me at daniel.ocampo.daza /at/ gmail.com.

I have shared all data and supporting information that underlie my published research under Open Science principles and a CC-BY license. This gives anyone the right to use, reuse and redistribute the data freely. It also enables post-publication peer review of my findings and ensures scientific transparency. Learn more about open science at the Open Knowledge Foundation and the CC-BY license at Creative Commons.

Visit my figshare profile to access my data. You can see an example fileset below. Learn more about figshare here.

Illustration

Illustration

Free Download

These are clipart-type illustrations of vertebrate species whose genomes have been sequenced, as well as a few others of taxonomic interest. I created these to use in presentations, lectures, posters et c. You can preview the illustrations above and see some examples of how I've used them in the past here and here.

I have licensed most of them under a Free Culture License by Creative Commons. This means that, with some exceptions*, you are free to use them for any purpose without asking for permission as long as you attribute them to Daniel Ocampo Daza, including a link to www.egosumdaniel.se. Find detailed information under Credits & License below. I took precautions to use only non-copyrighted/non-restricted images as references. However, if you think a photo that you own the rights to or license exclusively has been used as a reference for any of the illustrations, please contact me.

I'm constantly adding more species to the collection, and I've been known to make new species by request. If you're a researcher or student and you miss an illustration for your poster or publication, don't hesitate to contact me.

Contact

Credits & License

All original work by Daniel Ocampo Daza on www.egosumdaniel.se is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License. A share-alike license prevents you from using this work in anything you or someone else will retain full copyright on. Learn more about Creative Commons here. This license does not apply to any material posted from outside sources. *Zebrafish illustration based on a photo by Dries Knapen, used by kind permission and shared under a separate Creative Commons license. Sea lamprey illustration based on a photo by Jan Yde Poulsen.

Langdon typeface by xIntelecom. Quicksand typeface by Andrew Paglinawan. Carrois Gothic typeface by Carrois Type Design. Source Sans Pro typeface by Adobe.

Creative Commons License