Archive for April, 2009

Global warming

One sent me this video and it remembered me our biogeography class…

What is Phylogeography?

Wikipedia (the one who knows everything!) defines phylogeography as “the study of the historical processes that may be responsible for the contemporary geographic distributions of individuals … distribution of individuals in light of the patterns associated with a gene genealogy”. I have found more complex definitions, from renamed authors, and even using different words, all authors agree that phylogeography is concerned with processes driving distributions of genealogical lineages (population or intraspecific levels). Moreover, they agree that phylogeography is positively related to the development of recent molecular techniques. Finally, I will define phylogeography as a field of study concerned in understands microevolution and speciation in its geographic or spatiotemporal context based on molecular studies.


The phylogeography approach began in the late 1980s, with the development of the molecular techniques. With the advanced of the polymerase chain reaction (PCR), phylogenetic and population genetic studies have increased fast in the last years. The newly developing molecular approaches provide bases for mapping the spread of lineages (within populations or close related species) during the evolution.


The studies are based mainly on mitochondrial DNA, this DNA is small (about 16,500 bases), circular, and has high rate of evolution. Also, it is usually passed without recombination to the next generation, making it perfect for intraspecific studies. (In the majority of the species).


Organellar genomes (as mitochondrial or chloroplast ones) exist as haploid rather than diploid. Individuals within species have different genotypes, or in this case called haplotype and transmitted between generations exclusively through the female. The analysis of the haplotype distribution, frequencies across different geographical regions, quantification of the genetic divergence between haplotypes, and the evaluation of genetic relationship between haplotypes will be the base of phylogeographic studies (Weising et al.  .


Phylogeographyc has been used not only in taxa distribution and lineage studies, but deeper studies have come out in the last years.


Carstens & Richards (2007) studied the influence of stochastic variance inherent to genetic processes that could interfere in formation of population genetic structure. Statistical approaches to testing phylogeography hypotheses accommodate this stochasticity by evaluating competing models of putative historical population structure.


Hewitt (2001) provides many examples of studies using mtDNA for biogeography applications. For example: DNA sequences that have been used for the phylogeography of volcanic archipelagos like Hawaii and Canaries. He cites the studied conducted by Carson, in 1983, based on Hawaiian Drosophila. Others like Remington used the technique in understanding hybrid zones in Europe. Moreover, Hewitt (2001) affirms that advances in molecular genetics providing DNA markers for the study of subspecific divergence there has been much progress in paleoclimatology. In southem Europe and south-east USA molecular phylogeographies reveal that species contain divergent genomes and are often greatly subdivided geographically, in marked contrast to northward expansions. Climatic changes in Pleistocene are also cleared in light of phylogeography.


In conclusion, phylogeography is a rapidly growing discipline that aims at studying the principles and historical processes governing the geographical distributions of genealogical lineages. In contrast to classical population genetics, which is based on allele frequency distributions, phylogeographic procedures are supposed to separate population structure from population history (Weising et al. 2005).




Weising, K., Nybom, H., Wolff, K. & Kahl, G. (2005). DNA Fingerprinting in plants: Principles, methods, and applications. Second edition. CRC Press, Taylor & Francis Group. 470pp


Hewitt, G. (2001). Speciation, hybrid zones and phylogeography – or seeing genes in space and time. Molecular Ecology, 10, 537-549.


Carstens, B. C. & Richards, C. L. (2007). Integrating coalescent and Ecological niche modeling in comparative phylogeography. Evolution, 61 (6), 1439-1454.




Text book.

DIVA: Reconstructing the Ancestral Range Distribution

Since the beginning of the semester, we have been learned that the geographic distributions of organisms are determined by historical and ecological mechanisms. We also have learned some of the methodology that has been applied in historical biogeography studies. My last two posts were dedicated to historical biogeography, its pattern-based methodology, and assumptions. But I have not yet described an event-based methodology…


In event-based approaches, the processes responsible for taxa distribution are analyzed and the events are weight modeled.  One example of event-based approach is the Dispersal-vicariance analysis –DIVA. It reconstructs the ancestral range distribution of a particular group of organisms, minimizing the dispersal events needed for explaining the distributions. In this approach, the vicariance events have no cost, while the dispersals and extinctions cost one per area unit added to the distribution (Gomez & Lobo, 2006). This method was first applied to the theory of coevolutionary inference, and it uses the computer program DIVA (Ronquist, 1997).

Event-based methods have been criticized because the accuracy of the result depends on the validity of the model, and is necessary to specify a relative cost for each event in the model. Based on the model, the program will do a parsimony analysis and will provide the minimum-cost reconstruction.

To run the analysis, a three-dimension step matrix is needed (due to one ancestor can have two direct descents). The input information comprehends of the taxon relationship cladogram, the area cladogram, and the studied areas. Dispersal-vicariance, however, does not take general area relationships into account. It is just related to taxa cladogram and their current distribution. Thus, it is possible to use DIVA in taxon biogeography studies, even when no general area cladogram is available. 

Since the Ronquist (1997), many studies have used DIVA to reconstruct taxa ancestral areas. In Alberti et al. (2007), for example, proboscids (Mammalia) were studied applying dispersion-vicariance analysis. They used DIVA 1.1 (Ronquist, 1996), applying an exact search according to the default program. The genera of Gomphotheriidae ancestral distributions were given in an exact solution requiring 15 dispersal events. They discussed each processes (e. g. vicariance, dispersal, extinction) and each node, concluding that the ancestral distribution for the group included Africa-Europe-Asia-North America. The distribution could be achieved during earliest Miocene, a time of low sea-levels and low temperatures (Alberdi et al. 2007).

Gomes & Lobo (2006) studied Iguania using Dispersal-vicariance, Fitch Optimisation, and Weighted Ancestral Area Analysis. All their results were congruent. The ancestral area analyses agreed in an Andean-Patagonian origin for the studies clade, and were congruent with previous hypotheses and paleontological data.

One problem that I see in DIVA is that we do not have probabilities to base on. Each node received a hypothesis of ancestral area and can have many ambiguous results, which difficult our interpretation. The researcher or specialist interprets and proposes historic factors and processes for the under studied taxa distribution. Fortunately, other programs and approaches have been developed based on maximum likelihood and Bayesian analyses that given statistical results.




Alberdi, M.T.; Prado, J.L.; Ortiz-Jaureguizar, E.; Posadas, P. & Donato, M. (2007). Historical Biogeography of Trilophodont Gomphotheres (Mammalia, Proboscidea) reconstructed applying dispersion-vicariance analysis. Cuadernos del Museo Geominero (8), 4th European Meeting on the Palaeontology and Stratigraphy of Latin America. Instituto Geológico y Minero de España, Madrid.

Gómez, J. M. D. & Lobo, F. (2006). Historical Biogeography of a clade of Liolaemus (Iguania: Liolaemidae) based on ancestral areas and dispersal-vicariance analyis (DIVA). Papéis Avulsos de Zoologia (São Paulo) 46 (24): 261-274.



Other references:


DIVA v1.1 User’s manual