Reply to Lessios and Marko et al.: Early and progressive migration across the Isthmus of Panama is robust to missing data and biases

Bacon, Christine D.; Silvestro, Daniele; Jaramillo, Carlos; Smith, Brian Tilston; Chakrabarty, Prosanta; Antonelli, Alexandre

doi:10.1073/pnas.1515451112

Cited by 36 publications

(39 citation statements)

References 12 publications

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“…This supports the hypothesis that lowland white sand areas may be where many Neotropical lineages first began to diversify(Frasier, Albert, & Struwe, 2008). The timing of this event has been much debated with most recent studies placing it in the early Miocene (e.g.,Montes et al, 2015) that has been supported by studies using dated phylogenies to suggest support for an earlier direct land connection (e.g.,Bacon et al, 2015aBacon et al, , 2015bBacon, Mora, Wagner, & Jaramillo, 2012;De Baets, Antonelli, & Donoghue, 2016;Jaramillo et al, 2017;Smith, Amei, & Klicka, 2012). A dated phylogeny of the families Bromeliaceae and Rapateaceae that are either epiphytic or largely restricted to sandstone substrates indicated that these families first evolved at low elevations in the Guayana Shield before extending their distributions more broadly throughout South America and into Africa(Givnish et al, 2004).…”

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confidence: 99%

Using dated molecular phylogenies to help reconstruct geological, climatic, and biological history: Examples from Colombia

et al. 2018

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Attempts at historical reconstruction are based on limited data. We are more likely to produce accurate historical reconstructions by utilizing information from diverse sources and pooling data within the relevant research communities which will allow us to build up a moving picture of the geological, climatic, and biological evolution of our planet. We suggest that dated phylogenies of plants can contribute greatly to a better understanding of Earth history. Timing of phylogenetic splits of lowland restricted lineages on either side of the Andes could provide information on the timing of montane uplift and associated climatic changes. The timing of the arrival and diversification of organisms restricted to specific climatic regimes at a particular altitude can provide information on the age at which mountains reached a height adequate for that climate once corrected for global climate changes. As a model for study, we discuss how dated phylogenies in biome rich Colombia may contribute to an understanding of geological and climatic change in north‐western South America. Lowland wet forest restricted lineages separated from the mid‐Miocene, whereas lineages primarily restricted to mid‐altitude cloud forests began to diversify from the mid‐ to late‐Miocene and the majority of high‐altitude Páramo lineages began to diversify during the Pliocene. The age of diversification of altitudinally restricted lineages therefore gives an indication of the age at which particular altitudes may have been reached.

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confidence: 99%

Using dated molecular phylogenies to help reconstruct geological, climatic, and biological history: Examples from Colombia

et al. 2018

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“…The timing of the emergence of a connection between North and South America and the timing of biotic interchanges are highly controversial (see, e.g., Bacon et al., ,b; Lessios, ). For some time, the dominant hypothesis was a very recent emergence of land masses above sea level and the closure of the Isthmus of Panama around 4–3 million years ago (Coates & Stallard, ; Coates et al., ).…”

Section: Discussionmentioning

confidence: 99%

Contrasting patterns of Andean diversification among three diverse clades of Neotropical clearwing butterflies

Chazot

De‐Silva

Willmott

et al. 2018

Ecology and Evolution

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The Neotropical region is the most biodiverse on Earth, in a large part due to the highly diverse tropical Andean biota. The Andes are a potentially important driver of diversification within the mountains and for neighboring regions. We compared the role of the Andes in diversification among three subtribes of Ithomiini butterflies endemic to the Neotropics, Dircennina, Oleriina, and Godyridina. The diversification patterns of Godyridina have been studied previously. Here, we generate the first time‐calibrated phylogeny for the largest ithomiine subtribe, Dircennina, and we reanalyze a published phylogeny of Oleriina to test different biogeographic scenarios involving the Andes within an identical framework. We found common diversification patterns across the three subtribes, as well as major differences. In Dircennina and Oleriina, our results reveal a congruent pattern of diversification related to the Andes with an Andean origin, which contrasts with the Amazonian origin and multiple Andean colonizations of Godyridina. In each of the three subtribes, a clade diversified in the Northern Andes at a faster rate. Diversification within Amazonia occurred in Oleriina and Godyridina, while virtually no speciation occurred in Dircennina in this region. Dircennina was therefore characterized by higher diversification rates within the Andes compared to non‐Andean regions, while in Oleriina and Godyridina, we found no difference between these regions. Our results and discussion highlight the importance of comparative approaches in biogeographic studies.

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“…20 and 6 Ma; marine vicariance at c . 23 and 7 Ma; see debate about “an early closure of the Isthmus of Panama”: Bacon et al., ; Lessios, ; Marko et al., ). On the contrary, the divergence time between the WN population and the EN population of A. litoralis estimated in this study could support both of these hypotheses, considering the 95% HPD intervals (3.28–7.06 Ma).…”

Section: Discussionmentioning

confidence: 99%

Species trees, temporal divergence and historical biogeography of coastal rove beetles (Coleoptera: Staphylinidae) reveal their early Miocene origin and show that most divergence events occurred in the early Pliocene along the Pacific coasts

Song

Ahn

2017

Cladistics

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We investigated the species trees, temporal divergence and historical biogeography of Emplenota Casey and Triochara Bernhauer (ET clade hereafter), subgenera of the Aleochara coastal staphylinid beetles, to determine their place of origin. We explored a multilocus dataset to infer gene trees and species trees based on traditional concatenated and multispecies coalescentbased approaches using both model-(maximum likelihood and Bayesian) and parsimony-based methods. The multilocus dataset comprised DNA sequences from five nuclear genes (ArgK, CAD, EF1-a, wg and 28S) and three mitochondrial genes (COI, COII and 16S). *BEAST analysis according to a coalescent-based approach resolved the following phylogenetic relationships: ((A. trisulcata (A. nubis + A. zerchei)) (A. obscurella ((A. pacifica (A. curtidens + A. litoralis)) (A. hayamai (A. yamato (A. fucicola (A. segregata + A. puetzi))))))). Using a relaxed molecular clock, we reconstructed a time-calibrated phylogeny for this group. Furthermore, to account for the historical biogeography of the ET clade at the ages of major divergences, we investigated the ancestral area based on a time-calibrated phylogeny. Biogeographical analyses suggested that the ancestor of the ET clade was widely distributed along the eastern and western Palearctic and the western Nearctic coasts in the early Miocene. According to reconstruction of the ancestral area, one dispersal and three vicariance events were required, and the analyses indicated that vicariance events were important in shaping its current distribution patterns. Most of the divergence events occurred in the late Miocene and early Pliocene along the Pacific coasts, and the East Asian seacoasts harboured the most species-rich fauna, including eight of the 13 species in the ET clade.

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Reply to Lessios and Marko et al.: Early and progressive migration across the Isthmus of Panama is robust to missing data and biases

Cited by 36 publications

References 12 publications

Using dated molecular phylogenies to help reconstruct geological, climatic, and biological history: Examples from Colombia

Using dated molecular phylogenies to help reconstruct geological, climatic, and biological history: Examples from Colombia

Contrasting patterns of Andean diversification among three diverse clades of Neotropical clearwing butterflies

Species trees, temporal divergence and historical biogeography of coastal rove beetles (Coleoptera: Staphylinidae) reveal their early Miocene origin and show that most divergence events occurred in the early Pliocene along the Pacific coasts

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