Evolutionary history of the endangered fish Zoogoneticus quitzeoensis (Bean, 1898) (Cyprinodontiformes: Goodeidae) using a sequential approach to phylogeography based on mitochondrial and nuclear DNA data

<p>Abstract</p> <p>Background</p> <p>Tectonic, volcanic and climatic events that produce changes in hydrographic systems are the main causes of diversification and speciation of freshwater fishes. Elucidate the evolutionary history of freshwater fishes permits to infer theories on the biotic and geological evolution of a region, which can further be applied to understand processes of population divergence, speciation and for conservation purposes. The freshwater ecosystems in Central Mexico are characterized by their genesis dynamism, destruction, and compartmentalization induced by intense geologic activity and climatic changes since the early Miocene. The endangered goodeid <it>Zoogoneticus quitzeoensis </it>is widely distributed across Central México, thus making it a good model for phylogeographic analyses in this area.</p> <p>Results</p> <p>We addressed the phylogeography, evolutionary history and genetic structure of populations of <it>Z. quitzeoensis </it>through a sequential approach, based on both microsatellite and mitochondrial cytochrome <it>b </it>sequences. Most haplotypes were private to particular locations. All the populations analysed showed a remarkable number of haplotypes. The level of gene diversity within populations was <inline-formula><m:math name="1471-2148-8-161-i1" xmlns:m="http://www.w3.org/1998/Math/MathML"><m:semantics><m:mover accent="true"><m:mi>H</m:mi><m:mo>¯</m:mo></m:mover><m:annotation encoding="MathType-MTEF"> MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGafmisaGKbaebaaaa@2D06@</m:annotation></m:semantics></m:math></inline-formula>_{<it>d </it>}= 0.987 (0.714 – 1.00). However, in general the nucleotide diversity was low, π = 0.0173 (0.0015 – 0.0049). Significant genetic structure was found among populations at the mitochondrial and nuclear level (Φ_ST= 0.836 and <it>F</it>_{<it>ST </it>}= 0.262, respectively). We distinguished two well-defined mitochondrial lineages that were separated <it>ca</it>. 3.3 million years ago (Mya). The time since expansion was <it>ca</it>. 1.5 × 10⁶years ago for Lineage I and <it>ca</it>. 860,000 years ago for Lineage II. Also, genetic patterns of differentiation, between and within lineages, are described at different historical timescales.</p> <p>Conclusion</p> <p>Our mtDNA data indicates that the evolution of the different genetic groups is more related to ancient geological and climatic events (Middle Pliocene, <it>ca</it>. 3.3 Mya) than to the current hydrographic configuration of the basins. In general, mitochondrial and nuclear data supported the same relationships between populations, with the exception of some reduced populations in highly polluted basins (Lower Lerma River), where the effects of genetic drift are suggested by the different analyses at the nuclear and mitochondrial level. Further, our findings are of special interest for the conservation of this endangered species.</p

Evolutionary history of the endangered fish (Bean, 1898) (Cyprinodontiformes: Goodeidae) using a sequential approach to phylogeography based on mitochondrial and nuclear DNA data-4

Tre: Bar plot obtained using STRUCTURE for the most likely number of clusters = 5. LUZ: La Luz, ORA: Orandino, MAG: Magdalena, MOL: Moloya, PLA: La Platanera, SFR: San Francisco del Rincón, BEL: Belisario, MIN: Mintzita, ZAC: Zacapu, SCR: San Cristóbal. Colours represent clades defined in Figures 2 and 3, except Orandino, in yellow, which appears differentiated from La Luz and clustered with El Moloya and Magdalena populations at the nuclear level.<p><b>Copyright information:</b></p><p>Taken from "Evolutionary history of the endangered fish (Bean, 1898) (Cyprinodontiformes: Goodeidae) using a sequential approach to phylogeography based on mitochondrial and nuclear DNA data"</p><p>http://www.biomedcentral.com/1471-2148/8/161</p><p>BMC Evolutionary Biology 2008;8():161-161.</p><p>Published online 26 May 2008</p><p>PMCID:PMC2435552.</p><p></p

Evolutionary history of the endangered fish (Bean, 1898) (Cyprinodontiformes: Goodeidae) using a sequential approach to phylogeography based on mitochondrial and nuclear DNA data-1

As outgroup (not shown).<p><b>Copyright information:</b></p><p>Taken from "Evolutionary history of the endangered fish (Bean, 1898) (Cyprinodontiformes: Goodeidae) using a sequential approach to phylogeography based on mitochondrial and nuclear DNA data"</p><p>http://www.biomedcentral.com/1471-2148/8/161</p><p>BMC Evolutionary Biology 2008;8():161-161.</p><p>Published online 26 May 2008</p><p>PMCID:PMC2435552.</p><p></p

Evolutionary history of the endangered fish (Bean, 1898) (Cyprinodontiformes: Goodeidae) using a sequential approach to phylogeography based on mitochondrial and nuclear DNA data-3

Are shown.<p><b>Copyright information:</b></p><p>Taken from "Evolutionary history of the endangered fish (Bean, 1898) (Cyprinodontiformes: Goodeidae) using a sequential approach to phylogeography based on mitochondrial and nuclear DNA data"</p><p>http://www.biomedcentral.com/1471-2148/8/161</p><p>BMC Evolutionary Biology 2008;8():161-161.</p><p>Published online 26 May 2008</p><p>PMCID:PMC2435552.</p><p></p

Evolutionary history of the endangered fish (Bean, 1898) (Cyprinodontiformes: Goodeidae) using a sequential approach to phylogeography based on mitochondrial and nuclear DNA data-7

As outgroup (not shown).<p><b>Copyright information:</b></p><p>Taken from "Evolutionary history of the endangered fish (Bean, 1898) (Cyprinodontiformes: Goodeidae) using a sequential approach to phylogeography based on mitochondrial and nuclear DNA data"</p><p>http://www.biomedcentral.com/1471-2148/8/161</p><p>BMC Evolutionary Biology 2008;8():161-161.</p><p>Published online 26 May 2008</p><p>PMCID:PMC2435552.</p><p></p

Evolutionary history of the endangered fish (Bean, 1898) (Cyprinodontiformes: Goodeidae) using a sequential approach to phylogeography based on mitochondrial and nuclear DNA data-0

, 12) Zacapu. Light blue outlines represent the areas of the paleolakes that developed in Central Mexico during the Miocene-Pleistocene: A) Sayula, B) Magdalena, C) Zacoalco-Ameca. Arrows represent proposed routes of colonisations. Black dotted lines represent geologic faults and grabens: Am: Ameca Fault, SM: San Marcos Fault, PG: Penjamillo Graben, CT: Chapala-Tula Fault, TC and dotted area: Corredor Tarasco volcanic field. The colours in the water bodies represent clades defined in Figures 2 and 3.<p><b>Copyright information:</b></p><p>Taken from "Evolutionary history of the endangered fish (Bean, 1898) (Cyprinodontiformes: Goodeidae) using a sequential approach to phylogeography based on mitochondrial and nuclear DNA data"</p><p>http://www.biomedcentral.com/1471-2148/8/161</p><p>BMC Evolutionary Biology 2008;8():161-161.</p><p>Published online 26 May 2008</p><p>PMCID:PMC2435552.</p><p></p

Evolutionary history of the endangered fish (Bean, 1898) (Cyprinodontiformes: Goodeidae) using a sequential approach to phylogeography based on mitochondrial and nuclear DNA data-5

<p><b>Copyright information:</b></p><p>Taken from "Evolutionary history of the endangered fish (Bean, 1898) (Cyprinodontiformes: Goodeidae) using a sequential approach to phylogeography based on mitochondrial and nuclear DNA data"</p><p>http://www.biomedcentral.com/1471-2148/8/161</p><p>BMC Evolutionary Biology 2008;8():161-161.</p><p>Published online 26 May 2008</p><p>PMCID:PMC2435552.</p><p></p

Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos)

The endangered brown bear populations (Ursus arctos) in Iberia have been suggested to be the last fragments of the brown bear population that served as recolonization stock for large parts of Europe during the Pleistocene. Conservation efforts are intense, and results are closely monitored. However, the efforts are based on the assumption that the Iberian bears are a unique unit that has evolved locally for an extended period. We have sequenced mitochondrial DNA (mtDNA) from ancient Iberian bear remains and analyzed them as a serial dataset, monitoring changes in diversity and occurrence of European haplogroups over time. Using these data, we show that the Iberian bear population has experienced a dynamic, recent evolutionary history. Not only has the population undergone mitochondrial gene flow from other European brown bears, but the effective population size also has fluctuated substantially. We conclude that the Iberian bear population has been a fluid evolutionary unit, developed by gene flow from other populations and population bottlenecks, far from being in genetic equilibrium or isolated from other brown bear populations. Thus, the current situation is highly unusual and the population may in fact be isolated for the first time in its history