Comparative Phylogeography of Mesoamerican Highland Rodents: Concerted versus Independent Response to Past Climatic Fluctuations

Sullivan, Jack; Arellano, Elizabeth; Rogers, Donald E.

doi:10.1086/303362

Cited by 188 publications

(156 citation statements)

References 36 publications

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“…Concordance between phylogeographic patterns was also observed in other regions, such as central America, in several rodent species (ie Bermingham and Martin, 1998;Riddle et al, 2000;Sullivan et al, 2000), southern America in various bat, rodent and marsupial species (ie da Patton, 1993, 1998;Ditchfield, 2000) as well as in Australian birds, reptiles (Joseph et al, 1995) and snails (Hugall et al, 2002). Furthermore, Lessa et al (2003) detected a strong concordance of demographic expansion in North American mammals after the last ice age, 10 000 years ago.…”

Section: Introductionmentioning

confidence: 55%

So close and so different: comparative phylogeography of two small mammal species, the Yellow-necked fieldmouse (Apodemus flavicollis) and the Woodmouse (Apodemus sylvaticus) in the Western Palearctic region

2004

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In Europe, concordant geographical distribution among genetic lineages within different species is rare, which suggests distinct reactions to Quaternary ice ages. This study aims to determine whether such a discrepancy also affects a pair of sympatric species, which are morphologically and taxonomically closely related but which have slight differences in their ecological habits. The phylogeographic structures of two European rodents, the Yellow-necked fieldmouse (A. flavicollis) and the woodmouse (Apodemus sylvaticus) were, therefore, compared on the basis of mitochondrial DNA cytochrome b (mtDNA cyt b) sequences (965 base pairs) from 196 specimens collected from 59 European localities spread throughout the species distributions. The results indicate that the two species survived in different ways through the Quaternary glaciations. A. sylvaticus survived in the Iberian Peninsula from where it recolonized almost all Europe at the end of the last glaciation. Conversely, the refuge from which A. flavicollis recolonized Europe, including northern Spain, during the Holocene corresponds to the Italo-Balkan area, where A. sylvaticus suffered a serious genetic bottleneck. This study confirms that even closely related species may have highly different phylogeographic histories and shows the importance of ecological plasticity of the species for their survival through climate change. Finally, it suggests that phylogeographic distinctiveness may be a general feature of European species.

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Section: Introductionmentioning

confidence: 55%

So close and so different: comparative phylogeography of two small mammal species, the Yellow-necked fieldmouse (Apodemus flavicollis) and the Woodmouse (Apodemus sylvaticus) in the Western Palearctic region

2004

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“…Commonly used; applied to the most complex model before the model selection step Very rare; when used, applied to the best model after the model selection step [52] Model fitting algorithm…”

Section: Goodness Of Fit Testmentioning

confidence: 99%

Model selection in ecology and evolution

Johnson¹,

Omland²

2004

Trends in Ecology & Evolution

3,190

2,660

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Recently, researchers in several areas of ecology and evolution have begun to change the way in which they analyze data and make biological inferences. Rather than the traditional null hypothesis testing approach, they have adopted an approach called model selection, in which several competing hypotheses are simultaneously confronted with data. Model selection can be used to identify a single best model, thus lending support to one particular hypothesis, or it can be used to make inferences based on weighted support from a complete set of competing models. Model selection is widely accepted and well developed in certain fields, most notably in molecular systematics and markrecapture analysis. However, it is now gaining support in several other areas, from molecular evolution to landscape ecology. Here, we outline the steps of model selection and highlight several ways that it is now being implemented. By adopting this approach, researchers in ecology and evolution will find a valuable alternative to traditional null hypothesis testing, especially when more than one hypothesis is plausible.Science is a process for learning about nature in which competing ideas about how the world works are evaluated against observations [1]. These ideas are usually expressed first as verbal hypotheses, and then as mathematical equations, or models. Models depict biological processes in simplified and general ways that provide insight into factors that are responsible for observed patterns. Hence, the degree to which observed data support a model also reflects the relative support for the associated hypothesis.Two basic approaches have been used to draw biological inferences. The dominant paradigm is to generate a null hypothesis (typically one with little biological meaning [2]) and ask whether the hypothesis can be rejected in light of observed data. Rejection occurs when a test statistic generated from observed data falls beyond an arbitrary probability threshold (usually P , 0.05), which is interpreted as tacit support for a biologically more meaningful alternative hypothesis. Hence, the actual hypothesis of interest (the alternative hypothesis) is accepted only in the sense that the null hypothesis is rejected. By contrast, model selection offers a way to draw inferences from a set of multiple competing hypotheses. Model selection is grounded in likelihood theory, a robust framework that supports most modern statistical approaches. Moreover, this approach is rapidly gaining support across several fields in ecology and evolution as a preferred alternative to null hypothesis testing [1,3,4]. Advocates of model selection argue that it has three primary advantages. First, practitioners are not restricted to evaluating a single model where significance is measured against some arbitrary probability threshold. Instead, competing models are compared to one another by evaluating the relative support in the observed data for each model. Second, models can be ranked and weighted, thereby providing a quantitative measure of relative sup...

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“…We also tested the topological concordance of the gene trees with hypothesized population histories using parametric bootstraps (Goldman 1993;Sullivan et al 2000) in three lineages for which there was an appropriate outgroup. For Microtus, we used M. guatemalensis (AF410262; ), for Plethodon we used E. eschscholtzii (AY572108; Carstens et al 2004), and for Salix melanopsis we used the lowland race of the species (DQ060270, DQ060277).…”

Section: Tests Of Topologymentioning

confidence: 99%

“…Unlike descriptive approaches to phylogeography, these methods are primarily concerned with estimating parameters that quantify certain aspects of genetic variation and using these parameter estimates to test a priori hypotheses erected on the basis of independent data. Testing the same set of hypotheses with data gathered from codistributed taxa can lead to a better understanding of the formation of ecological communities (e.g., Zink 1996;Sullivan et al 2000) and allows for the expansion of the temporal and spatial scale studied to match the scale of the processes responsible for the evolution of ecosystems (Schluter and Ricklefs 1993).…”

mentioning

confidence: 99%

Investigating the Evolutionary History of the Pacific Northwest Mesic Forest Ecosystem: Hypothesis Testing Within a Comparative Phylogeographic Framework

et al. 2005

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Abstract. We examine the evolution of mesic forest ecosystems in the Pacific Northwest of North America using a statistical phylogeography approach in four animal and two plant lineages. Three a priori hypotheses, which explain the disjunction in the mesic forest ecosystem with either recent dispersal or ancient vicariance, are tested with phylogenetic and coalescent methods. We find strong support in three amphibian lineages (Ascaphus spp., and Dicampton spp., and Plethodon vandykei and P. idahoensis) for deep divergence between coastal and inland populations, as predicted by the ancient vicariance hypothesis. Unlike the amphibians, the disjunction in other Pacific Northwest lineages is likely due to recent dispersal along a northern route. Topological and population divergence tests support the northern dispersal hypothesis in the water vole (Microtus richardsoni) and northern dispersal has some support in both the dusky willow (Salix melanopsis) and whitebark pine (Pinus albicaulis). These analyses demonstrate that genetic data sampled from across an ecosystem can provide insight into the evolution of ecological communities and suggest that the advantages of a statistical phylogeographic approach are most pronounced in comparisons across multiple taxa in a particular ecosystem. Genetic patterns in organisms as diverse as willows and salamanders can be used to test general regional hypotheses, providing a consistent metric for comparison among members of an ecosystem with disparate life-history traits. Although studies in evolutionary biology often focus on particular ecological interactions (e.g., Pellmyr and LeebensMack 1999), evolutionary biologists have seldom directed investigations into the evolutionary history of an ecosystem itself. Ecosystem studies can be expanded into evolutionary time by considering abiotic factors that act on a deeper time scale, such as orogeny and climatic fluctuations, as well as the collection of data that are influenced by these deeper events. As community ecologists engage in studies across more extensive spatial and temporal scales (e.g., Ricklefs 1987) and focus on the roles of historical and geographical circumstances in community construction (e.g., Schluter and Ricklefs 1993), the field of comparative phylogeography is poised to contribute fundamental data on the formation and evolutionary history of ecosystems (e.g., Arbogast and Kenagy 2001; Wares 2002).Previous regional syntheses of phylogeographic patterns (e.g., Avise 2000), have focused on identifying genealogical concordance among taxa. Such congruence of genealogies has been considered to be evidence that similar environmental processes have structured the genetic diversity within a region. This approach is best suited for comparisons among closely related organisms, where factors that influence the shape of genealogies, such as mutation rates and effective

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Comparative Phylogeography of Mesoamerican Highland Rodents: Concerted versus Independent Response to Past Climatic Fluctuations

Cited by 188 publications

References 36 publications

So close and so different: comparative phylogeography of two small mammal species, the Yellow-necked fieldmouse (Apodemus flavicollis) and the Woodmouse (Apodemus sylvaticus) in the Western Palearctic region

So close and so different: comparative phylogeography of two small mammal species, the Yellow-necked fieldmouse (Apodemus flavicollis) and the Woodmouse (Apodemus sylvaticus) in the Western Palearctic region

Model selection in ecology and evolution

Investigating the Evolutionary History of the Pacific Northwest Mesic Forest Ecosystem: Hypothesis Testing Within a Comparative Phylogeographic Framework

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