Research

Genomics

Comparative Phylogeography and adaptation of Penguins: Genome-Wide Single Nucleotide Polymorphism (SNP) Genotyping (FONDECYT 1150517)

(2015-2018, in progress)

Comparative phylogeography describes patterns of evolutionary divergence and whether they are consistent in co-distributed taxa populations. In this project we evaluate how historical processes such as barriers and climatic changes during the Pleistocene and signals of natural selection and adaptation of populations in different latitudes from the tropics of South America to Antarctica, affecting different species of penguins.

The use of advanced genomic technologies such as Next Generation Sequencing (NGS), has contributed to the study of SNPs (Single Nucleotide Polymorphism) in the complete genomes, allowing us to understand more fully phylogeographic and adaptive patterns, thanks to the large amount of data generated. This project combines different disciplines such as genetics, Remote Sensing and Geographic Information System.

Applying evolutionary principles to infer climate adaptation in marine species: Using a genomic approach (RT-12_14 Inach Project)

(2014-2017, in progress)

Antarctic species have manifested different responses to the current process of global climate change. In the Antarctic Peninsula, the Adelie Penguin population sizes have decreased, while Gentoo Penguins have increased.

Comparative phylogeography describes patterns of evolutionary divergence and whether they are consistent in taxa co-distributed populations. In this project we evaluate how historical processes such as barriers and climatic changes during the Pleistocene and signals of natural selection and adaptation of populations in different latitudes from the tropics of South America to Antarctica, affecting different species of penguins.

The use of advanced genomic technologies such as Next Generation Sequencing (NGS), has contributed to the study of SNPs (Single Nucleotide Polymorphism) in the complete genomes, allowing us to understand more fully phylogeographic and adaptive patterns, thanks to the large amount of data generated. This project combines different disciplines such as genetics, Remote Sensing and Geographic Information System.

Metagenomics soil in agricultural systems with different types of production management

Innovation Fund for Competitiveness (FIC), Región de O´Higgins. Integration of biodiversity to Fruticulture

(2015-2016, in progress)

The project will study soil biodiversity from metagenomics sequencing using DNA obtained from soil samples. This samples will be collected from farms with different agricultural practices in the region of O’Higgins,  from organic to pesticide use.

We will use primers for amplification and sequencing of ITS and 16S regions in bacteria, fungi and arthropods. Groups and species will be identified to compare biodiversity between the various agricultural areas of study. Additionally we will study the diversity of some functional genes of interest for subsequent application in the management of these areas.

Diseases

Associations between avian malaria, MHC genes diversity and Population structure in Humboldt penguin (Spheniscus humboldti) and Magellanic penguin (Spheniscus magellanicus)

FONDECYT PROJECT 11110060

(2011-2014, Completed)

Avian Malaria is a disease caused by species of the genus Haemoproteus, Leucocytozoon and Plasmodium. This affects various species of birds, causing a series of clinical signs, depending on the susceptibility of the host species. Although it has been detected a high mortality in captive penguins, epidemiological studies in wild colonies have been limited.

For this study 501 blood samples were obtained from adult specimens of Humbolt penguins and 360 samples from Magallanes penguin adults distributed in 13 colonies across South America. The identification of avian malaria was performed using molecular techniques. The results of this study showed that avian malaria was absent in most of the colonies analyzed, except for Punta San Juan in Peru, where two new lineages of Haemoproteus were found in three positive samples, resulting in a prevalence of 0.6% for Humboldt penguin. On the other hand, using ‘Next Generation Sequencing’ diversity of MHC I and II was evaluated in 100 Humboldt penguins and 75 Magallanes penguins from seven different colonies. High genetic diversity for MHC I and MHC II species were found for both species.

Evaluation of the prevalence of avian malaria in passerine birds of Chile.

FONDECYT PROJECT 1130948

(2013-2017, in progress)

There is a wide variety of protozoan blood parasites that infect birds, Plasmodium spp and Haempotroteus spp being the most prevalent . These have a worldwide distribution (except Antarctica) and marked cosmopolitan trend. In South America there are few studies involving avian malaria, concordant situation with Chile, with only five studies. However, only two of these studies have identified mitochondrial DNA lineages cytb in land birds. This study aims to determine the prevalence, geographic distribution and genetic lineages of blood parasites (Plasmodium spp and Haemoproteus spp) present in wild birds on the order of Passeriformes in Chile and Argentina, and compare them with those described in South America.

For this research birds have been captured from the far north, central and southern Chile, in a total of 15 ecoregions. To assess whether the Andes has influenced the distribution of the lineages of blood parasites, samples belonging to Argentina will be analyzed. Hemoparasites detection will be done through traditional diagnostic techniques (blood smear observation optical microscope) and molecular techniques (PCR). Prevalence and confidence intervals of certain lineages for each lineage and ecoregion will be determined.

With this data it is expected to determine if the lineages of the populations of blood parasites are dependent and/or restricted to a certain range. Besides determining if they present a higher specificity for some hosts, or conversely, if the lines having greater divergence, we aim to identify if they are able to adapt to a wide range of distribution and hosts.

Phylogeography, population genetics and climate change

Picaflor Chico Phylogeography (Sephanoides sephaniodes) in Chile and Argentina.

FONDECYT PROJECT 1130948

The current geographic distribution of species has been influenced by historical and ecological processes that cause expansion and contraction populations. The nature of these processes can be inferred by studying current patterns of genetic variation within and between populations. Climate changes during the late Pleistocene glacial period have differentially impacted the current geographical distribution and genetic diversity of vertebrates of the Southern Cone of South America. The coverage of the ice during the last glacial maximum covered the continent from 56ºS to 41ºS and the populations generating different patterns such as:

  1. They extinguished in the largest area of ice coverage with a post-glacial expansion by founder effect
  2. Persist in shelters with small population sizes accentuating the strength of genetic drift with a demographic expansion postglacial low genetic diversity or,
  3. Persist in the entire territory covered, presenting high current genetic diversity.

Few studies have explored paleoclimatic effects on birds in the Southern Cone.

Sephanoides sephaniodes are the most important vertebrate pollinator of temperate forests in Chile and Argentina, which extend from the 55 ° S to 30 ° S. Using the mitochondrial marker Cytochrome b and intron 7 of beta-fibrinogen nuclear gene, we will determine the effects of paleoclimatic events on the current genetic diversity of the species in order to elucidate the demographic and spatial history of the most important picaflor of the temperate forest in the Southern Cone of South America.

Comparative phylogeography of Lycalopex culpaeus and Lycalopex griseus

Phylogeography and genetic structure population of Pygoscelis antarctica and Pygoscelis papua in the Antarctic Peninsula and Sub-Antarctic Islands

| Laboratorio de Biodiversidad Molecular - Departamento de Ecosistemas y Medio Ambiente, Campus San Joaquín - Facultad de Agronomía e Ingeniería Forestal |
Pontificia Universidad Católica de Chile - Santiago, Chile - Oficina (56-2) 23547210 - Laboratorio (56-2) 23547210 | info@biodivmol-lab.com