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

Just a little more information…

Historical Biogeography is concerned with relationships among and between species —the true genetic relationship of taxa. It deals with evolutionary processes occurring over millions of years on a large scale.

The five biogeographic methods are: dispersalism, phylogenetic biogeography, panbiogeography, Cladistic biogeography, and parsimony analysis of endemicity.

Cladistic biogeography assumes a correspondence between taxonomic relationships and area relationships, where comparisons between area cladograms derived from different taxa allow one to obtain general area cladograms. The most important Cladistic biogeographic procedures are: component analysis, Brooks’s parsimony analysis, three-area statements, and reconciled trees.



Introduction to BPA concepts

Brooks Parcimony Analysis (BPA), as other methods used in historical biogeography, has been received criticism from some authors. BPA does not have a computer program to be performed, and the data are prepared manually.

The historical biogeography methods of analyses are divided in two categories: a priori and a posteriori methods. BPA is considered a posteriori method. The major difference between those methods is the sister group relation. A posteriori methodology forbids changes or distortion of the area sister group. This information is gotten from the taxon phylogenetic tree.

Both methods have the same null hypothesis – vicariant speciation – and make the assumption that phylogenetic and distribution data of taxa are informative for the reconstruction of the historical relationships among their areas of distribution. However, I wondered how they work with sympatric species…

The answer for my question has not consolidated yet in my mind, but Platnick & Nelson (1978) proposed two assumptions that were improved by other authors. Actually those assumptions have been proposed to sympatric and widespread species.


I still need to read more about it and look for more papers related to.


Any help or comments are welcome.  J


Platnick, NI & Nelson, G. 1978. A method of analysis for historical biogeography. Systematic Zoology 27: 1-16.

Atlantic Rain Forest domain



100 years ago and nowadays.

Brazilian hotspots and refugia

Brazilianforests are widely known for their high biodiversity. Two hotspots were identified in Brazil by Myers et al.(2000): the Biome of Cerrado and the Biome of Atlantic Forest. Hotspots are regions or areas with high endemism and exceptional loss of habitat, that make them priority in conservation politics.

                The Atlantic Forest has been deforested along the last 500 years. Nowadays, less than 8% of the original cover is rested. Despite its diminished state, the Atlantic Foreststill ranks as a global conservation priority. Although it is just a small fraction of the size of the huge Amazon rainforest, the Atlantic Forest still harbors of a range of biological diversity similar to that of the Amazon. Not only similar in richness, but following Costa (2003), both forests were connected during the Pleistocene, and the Atlantic and Amazon’s fauna are relative.

We have seen that the Late Quaternary climate fluctuations helped to shape present-day diversity, providing a general context for understanding current patterns of endemism. Carnaval et al. (2009) related refuge areas and biodiversity in Brazilian Atlantic forest hotspot. In the study, the authors used frogs as indicators; ecological niche models under paleoclimates; and simultaneous Bayesian analyses of multispecies molecular data to compare alternative hypotheses of assemblage-scale response to late Quaternary climate change.

In a regional scale, biodiversity species should consistently show higher genetic diversity within and among populations in refugia relative to recent colonized areas. This is explained by the long-term persistence and population structure. The genetic signature of population expansion in unstable (recent colonized) areas, should reflect multispecies colonization from adjacent refugial regions after the Last Glacial Maximum (Carnaval et al. 2009).

Besides, the absence of genetic patterns of isolation-by-distance in recent colonized areas is due to colonization has been too recent to permit restoration of equilibrium between migration and genetic drift.

Following all predicts, the authors supposed a large central refugium throughout the Late Quarternary – Bahia refugium; a second much smaller in the northeastern most of forest – Pernambuco refugium; and a southeastern refugium of intermediate size – São Paulorefugium. The authors also supposed that these areas received a significant influx of migrants from adjacent, large refugial populations after Late Quaternary Maximum. The southern Atlantic forest was climatically unstable relative to the central part (Bahia).

I am from Espírito Santo, a state between São Paulo and Bahia and, following the article, it is included in Bahiarefugium. During my on field works, I could realize the difference among the forests. The Bahia Atlantic Forest (northern of my state) is drier and the fauna, generally, is less related to animals from the southernmost (more humid and high altitude). Otherwise, São Paulo has humid and high altitude forests, as the southern of my state.

Finally, this paper was quite interesting for my, because actually, the highest diversity that we have been found for a wasp family (Bethylidae) in Brazil occurs in the central part of the Atlantic Forest, which the authors called Bahia refugium. 




Carnaval AC et al. 2009. Stability Predicts Genetic Diversity in the Brazilian Atlantic ForestHotspot.

Costa LP. 2003. The historical brigde between the Amazon Forest of Brazil: a study of molecular phylogeography with small mammals. Journal of Biogeography 30: 71-86.

Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J. 2000. Biodiversity hotspots for conservation priorities. Nature 403: 853-858.

Science 323: 785-789.

Chaos Theory

It’s not really biogeography, but the Ethan’s class and Ken’s blog, remembered me my brother trying to explain me the Chaos Theory. 

“Chaos theory describes the behaviour of certain dynamical systems – that is, systems whose states evolve with time – that may exhibit dynamics that are highly sensitive to initial conditions (popularly referred to as the butterfly effect). As a result of this sensitivity, which manifests itself as an exponential growth of perturbations in the initial conditions, the behavior of chaotic systems appears to be random. This happens even though these systems are deterministic, meaning that their future dynamics are fully defined by their initial conditions, with no random elements involved. This behavior is known as deterministic chaos, or simply chaos.”


Considering the fractal definition  (a rough or fragmented geometric shape that can be split into parts, each of which is a reduced-size copy of the whole), you can ask: where is the relation? Chaos system is about dynamic systems and deterministic factors, such as the film that many of you have watched, The Butterfly effect. Otherwise, fractal is about static geometric traces.  Biological and physical models, e.g. weather, are explained or based on Chaos Theory, and fractal models can be kind of measurements in works on Chaos Theory. Well, the whole theory is complicated but, if I wasn’t persuasive in the relationship between them, I’ll let the pictures tell for me.

Fractal fern created using chaos game. Natural forms (ferns, clouds, mountains, etc.) may be recreated through an Iterated function system.

Fractal fern created using chaos game. Natural forms (ferns, clouds, mountains, etc.) may be recreated through an Iterated function system.

New Page

I’ve just added a new page related to my research proposal for Biogeography. Any ideas are welcome!

Last week on Nature…

I came out with this highlight today and I though it was interesting to post it here:

Two conflicting theories explain the heritage of New Zealand’s current flora and fauna.

Sea levels rose 25 million–22 million years ago, and some believe that the landmass was completely submerged during this time and then repopulated later by transoceanic voyagers. Others hold that the land was only ever partly submerged, and that the ancestors of some of today’s resident species have been there since New Zealand separated from other continents, 82 million–60 million years ago.

Marc Jones of University College London and his colleagues identified fossil jaw bones and teeth (pictured) of a rhynchocephalian reptile, a relative of the extant New Zealand tuatara. Given the fossil’s age — 19 million–16 million years — these lizard-like creatures would have had less time to repopulate the landmass than had previously been thought, suggesting that New Zealand was never fully underwater and has been home to the tuatara’s ancestors since the time of the dinosaurs.


The paper can be found in:

Proc. R. Soc. B. doi:10.1098/rspb.2008.1785 (2009)



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