Estimating Divergence Times from Molecular Data on Phylogenetic and Population Genetic Timescales

Arbogast, Brian S.; Edwards, Scott V.; Wakeley, John; Beerli, Peter; Slowinski, Joseph B.

doi:10.1146/annurev.ecolsys.33.010802.150500

Cited by 554 publications

(514 citation statements)

References 169 publications

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“…Dating nodes in molecular phylogenies is contentious and carries many assumptions (26,27), but our estimate based on a Pacific island age is supported by 2 independent dating measures. A separate study of regional white-eye diversification used a different set of taxa and genes, and used an Indian Ocean island for calibration (28), but the basal node in their Zosterops radiation is shared with our phylogeny and was estimated at 1.84 million years, just inside our CI for that node (1.40-1.89 million years).…”

Section: Resultsmentioning

confidence: 66%

Explosive Pleistocene diversification and hemispheric expansion of a “great speciator”

Moyle

Filardi

Smith

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

248

295

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Factors that influence speciation rates among groups of organisms are integral to deciphering macroevolutionary processes; however, they remain poorly understood. Here, we use molecular phylogenetic data and divergence time estimates to reconstruct the pattern and tempo of speciation within a widespread and homogeneous bird family (white-eyes, Zosteropidae) that contains an archetypal ''great speciator.'' Our analyses show that the majority of this species-rich family constitutes a clade that arose within the last 2 million years, yielding a per-lineage diversification rate among the highest reported for vertebrates (1.95-2.63 species per million years). However, unlike most rapid radiations reported to date, this burst of diversification was not limited in geographic scope, but instead spanned the entire Old World tropics, parts of temperate Asia, and numerous Atlantic, Pacific, and Indian Ocean archipelagos. The tempo and geographic breadth of this rapid radiation defy any single diversification paradigm, but implicate a prominent role for lineage-specific life-history traits (such as rapid evolutionary shifts in dispersal ability) that enabled white-eyes to respond rapidly and persistently to the geographic drivers of diversification.diversification rate ͉ speciation ͉ Zosterops ͉ white-eye ͉ evolution D isparity in diversification rates among groups of organisms is well documented and provides unique opportunities for studying evolutionary processes underlying the genesis of biological diversity (1-7). A few groups of organisms that diversified recently and rapidly have contributed disproportionately to speciation theory by providing comparatively accessible opportunities to evaluate factors that drive speciation (1-4). These groups are also characterized by a restricted geography (e.g., archipelagos, lakes, mountain tops, etc.) circumscribed by the more extensive distribution shared by the group and its close relatives. The reduced faunas, stark geographic boundaries, and limited set of earth history influences of these confined geographies make such systems attractive for studies of diversification.Island settings are especially well known for variable speciation rates. For example, some island bird taxa spread across scattered insular landscapes with little or no differentiation, whereas others appear to have diversified rapidly across the same geographies (8). In the wake of island biogeographic theory and its antecedents (9-11), recognition of this pattern in birds resulted in characterization of a set of ''great speciator'' lineages (12), as well as a famous paradox: how can these lineages show such high degrees of differentiation across oceanic islands when their excellent dispersal ability should limit differentiation?Discussions of this paradox have appealed to intermediate dispersal ability (8,12) or to evolutionary shifts in dispersal ability (12) to explain the seeming conflict between large geographic range, implying good dispersal ability, and the high degree of morphological differentiation be...

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Section: Resultsmentioning

confidence: 66%

Explosive Pleistocene diversification and hemispheric expansion of a “great speciator”

Moyle

Filardi

Smith

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

248

295

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“…The application of multiple fossil constraints should help to minimize such variability in divergence time estimates based on multiple gene regions. Similarly, data from multiple regions should help to minimize erroneous inferences based on a single locus (Arbogast et al, 2002;Yang and Yoder, 2003;Yoder and Yang, 2004). Although divergence time estimates from the combined and partitioned models were not identical, variance in divergence times between these models was less than that of models based on a single locus (Fig.…”

Section: Divergence Timesmentioning

confidence: 98%

“…4A), with most of the discordance occurring in the tribe Castilleae. The position of fossil constraints may have played a role, as Castilleae is the only tribe with no known fossils, and the accuracy of age estimates decreases with distance from the nearest calibration point (Arbogast et al, 2002). A possible explanation for the discrepancy in divergence date estimates between the diVerent gene regions is the taxonomic level at which each locus is informative and how nucleotide substitutions are distributed across branches of the tree (Fig.…”

Section: Divergence Timesmentioning

confidence: 99%

Biogeography and divergence times in the mulberry family (Moraceae)

Zerega

Clement

Datwyler

et al. 2005

Molecular Phylogenetics and Evolution

182

150

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The biogeographical history of the mulberry family (Moraceae) was investigated using phylogenetic inferences from nuclear and chloroplast DNA, molecular dating with multiple fossil calibrations, and independent geological evidence. The Moraceae are centered in the tropics which has invited the hypothesis that the family has Gondwanan origins and extant distribution is the result of vicariance due to the break-up of Gondwana. However, the cosmopolitan distribution of Moraceae suggests a more complicated biogeographical history. The timing and location of Moraceae diversiWcation also bears on the origin of the Wg pollination mutualism, a model for the study of coevolution and specialization. Recent molecular dating of pollinating Wg wasps suggested that an ancient Gondwanan origin coupled with vicariance and dispersal could account for the present day distribution of the mutualism. Here, we provide the Wrst assessment of this hypothesis based on dating of Wgs and their relatives. Minimum age estimates suggest that the Moraceae had diversiWed by at least the mid-Cretaceous and major clades including the Wgs may have radiated during the Tertiary after the break-up of Gondwanaland. Molecular evidence together with Eurasian fossils suggest that the early diversiWcation of Moraceae in Eurasia and subsequent migration into the southern hemisphere is at least as plausible as the Gondwanan hypothesis. These Wndings invite a reevaluation of the biogeography of Wg pollination and highlight the need for incorporating multiple sources of evidence in biogeographical reconstructions. 

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“…As the number of loci is crucial for estimating demographic parameters with less variance (Arbogast et al, 2002), we used sequences of 12 loci from 12 individuals that cover representative populations in East Asia and Alaska. C12 was excluded from the analysis because this locus exhibited a nonneutral pattern of polymorphisms (see Results).…”

Section: Estimating Demographic History and Examination Of Introgressionmentioning

confidence: 99%

Importance of demographic history for phylogeographic inference on the arctic–alpine plant Phyllodoce caerulea in East Asia

et al. 2015

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Arctic-alpine plants have enormous ranges in the Northern Hemisphere. Phylogeographic studies have provided insights into their glacial survival as well as their postglacial colonization history. However, our understanding of the population dynamics of disjunct alpine populations in temperate regions remains limited. During Pleistocene cold periods, alpine populations of arctic-alpine species in East Asia were either connected to an ice-free Beringia refugium or they persisted with prolonged isolation after their establishment. To estimate which of these scenarios is more likely, we elucidated the genetic structure of Phyllodoce caerulea (Ericaceae) in Beringia and northern Japan, East Asia. Sequence variation in multiple nuclear loci revealed that P. caerulea can be distinguished into northern and southern groups. A demographic analysis demonstrated that the north-south divergence did not predate the last glacial period and detected introgression from Phyllodoce aleutica, relative widely distributed in East Asia, exclusively into the southern group. Therefore, although there has been genetic divergence between northern Japan and Beringia in P. caerulea, the divergence is unlikely to have resulted from their prolonged geographic separation throughout several cycles of glacial and interglacial periods. Instead, our study suggests that the introgression contributed to the genetic divergence of P. caerulea and that the range of P. caerulea was plausibly connected between northern Japan and Beringia during the last glacial period. Overall, our study not only provides a biogeographic insight into alpine populations of arctic-alpine plants in East Asia but also emphasizes the importance of careful interpretation of genetic structure for inferring phylogeographic history.

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Estimating Divergence Times from Molecular Data on Phylogenetic and Population Genetic Timescales

Cited by 554 publications

References 169 publications

Explosive Pleistocene diversification and hemispheric expansion of a “great speciator”

Explosive Pleistocene diversification and hemispheric expansion of a “great speciator”

Biogeography and divergence times in the mulberry family (Moraceae)

Importance of demographic history for phylogeographic inference on the arctic–alpine plant Phyllodoce caerulea in East Asia

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