The impact of fossil calibrations, codon positions and relaxed clocks on the divergence time estimates of the native Australian rodents (Conilurini)

Nilsson, Maria A.; Härlid, Anna; Kullberg, Morgan; Janke, Axel

doi:10.1016/j.gene.2010.02.002

Cited by 14 publications

(9 citation statements)

References 47 publications

(71 reference statements)

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“…Haplotype 1 has a world-wide distribution, including Antilles, Britain, Europe, French Polynesia, Guadeloupe, Mediterranean Basin, New Guinea, New Zealand, Polynesia, West Africa, and the USA (Robins et al 2007;Nilsson et al 2010;Tollenaere et al 2010;Colangelo et al 2015). It is common in New Zealand, but we did not find it on Stewart Island.…”

Section: Resultscontrasting

confidence: 62%

Where did the rats of Big South Cape Island come from?

Robins

Miller²,

Russell³

et al. 2016

NZ J Ecol

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Abstract:The ship rat invasion of Big South Cape Island/Taukihepa in the 1960s was an ecological catastrophe that marked a turning point for the management of rodents on offshore islands of New Zealand. Despite the importance of this event in the conservation history of New Zealand, and subsequent major advances in rodent eradication and biosecurity, the source and pathway of the rat invasion of Big South Cape Island has never been identified. Using modern molecular methods on contemporary and historical tissue samples, we identify the mitochondrial DNA (mtDNA) haplotype of ship rats (Rattus rattus) on Big South Cape Island and compare it to that of ship rats in the neighbouring regions of Stewart Island/Rakiura and southern New Zealand, all hypothesised as possible source sites for the invasion. We identify two haplotype clusters, each comprising three closely related haplotypes; one cluster unique to Stewart Island, and the other found in southern New Zealand and elsewhere. By a process of elimination we rule that the ship rat invasion of Big South Cape Island was neither by swimming nor boat transport from Stewart Island, and is unlikely to have come from the south coast ports of New Zealand. However, because the ship rat haplotype found on Big South Cape Island is cosmopolitan to New Zealand's South Island and elsewhere, we can only confirm that the invasion likely originated from some distance, but are not able to identify the invasion source more precisely. An unexpected consequence of our study is the discovery of five new mtDNA haplotypes for R. rattus that have not been previously reported.

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Section: Resultscontrasting

confidence: 62%

Where did the rats of Big South Cape Island come from?

Robins

Miller²,

Russell³

et al. 2016

NZ J Ecol

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“…The dating was performed solely by the NPRS-LOG method because previous studies showed virtually no differences relative to other algorithms (Roos et al 2007; Nilsson et al 2010). The numerous calibrating points are marked with circles.…”

Section: Resultsmentioning

confidence: 99%

Mammalian Evolution May not Be Strictly Bifurcating

Hallström

Janke²

2010

Molecular Biology and Evolution

131

146

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The massive amount of genomic sequence data that is now available for analyzing evolutionary relationships among 31 placental mammals reduces the stochastic error in phylogenetic analyses to virtually zero. One would expect that this would make it possible to finally resolve controversial branches in the placental mammalian tree. We analyzed a 2,863,797 nucleotide-long alignment (3,364 genes) from 31 placental mammals for reconstructing their evolution. Most placental mammalian relationships were resolved, and a consensus of their evolution is emerging. However, certain branches remain difficult or virtually impossible to resolve. These branches are characterized by short divergence times in the order of 1–4 million years. Computer simulations based on parameters from the real data show that as little as about 12,500 amino acid sites could be sufficient to confidently resolve short branches as old as about 90 million years ago (Ma). Thus, the amount of sequence data should no longer be a limiting factor in resolving the relationships among placental mammals. The timing of the early radiation of placental mammals coincides with a period of climate warming some 100–80 Ma and with continental fragmentation. These global processes may have triggered the rapid diversification of placental mammals. However, the rapid radiations of certain mammalian groups complicate phylogenetic analyses, possibly due to incomplete lineage sorting and introgression. These speciation-related processes led to a mosaic genome and conflicting phylogenetic signals. Split network methods are ideal for visualizing these problematic branches and can therefore depict data conflict and possibly the true evolutionary history better than strictly bifurcating trees. Given the timing of tectonics, of placental mammalian divergences, and the fossil record, a Laurasian rather than Gondwanan origin of placental mammals seems the most parsimonious explanation.

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“…Substitution saturation was reported to negatively influence the estimation of divergence time in deep branches and possibly effect estimated times of shallow nodes (Beaulieu, Oliver, O'meara, & Beaulieu, ; Nilsson et al., ; van Tuinen & Torres, ). The inclusion of COI third codon position led to different estimated ages of the basal nodes in comparison with divergence times predicted previously.…”

Section: Methodsmentioning

confidence: 99%

Diversification in tropics and subtropics following the mid‐Miocene climate change: A case study of the spider genusNesticella

Ballarin

2017

Global Change Biology

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Caves may offer suitable refugia for troglophilic invertebrates during periods of unfavourable climatic conditions because of their stable microclimates. As a consequence, allopatric divergence from their epigean counterparts may occur, leading to formation of truly hypogean communities (the Climatic Relict Hypothesis). Unlike the well-studied effects of Pleistocene glaciations, we know little about how ancient climate changes drove the development of cave-dwelling organisms living at both middle and lower latitudes. We investigate the evolutionary history of the troglophilic spider genus Nesticella (Araneae, Nesticidae) in relation to Asian Neogene (23-2.6 Ma) climatic changes. Our analyses discern clear differences in the evolution of the two main clades of Nesticella, which occur in temperate/subtropical and tropical latitudes. Eastern Asian Nesticella gradually evolved greater sedentariness and a strict subterranean lifestyle starting from the middle Miocene Epoch (~15-14 Ma) in conjunction with the progressive deterioration of the climate and vegetational shifts. Caves appear to have acted as refugia because of their internally uniform temperature and humidity, which allowed these spiders to survive increasing external seasonality and habitat loss. In contrast, a uniform accumulation of lineages, long-lasting times for dispersals and the lack of a comparable habitat shifting characterized the tropical lineage. This difference in pattern likely owes to the mild effects of climate change at low latitudes and the consequent lack of strong climatic drivers in tropical environments. Thus, the mid-Miocene climatic shift appears to be the major evolutionary force shaping the ecological differences between Asian troglophilic invertebrates and the driver of the permanent hypogean communities in middle latitudes.

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The impact of fossil calibrations, codon positions and relaxed clocks on the divergence time estimates of the native Australian rodents (Conilurini)

Cited by 14 publications

References 47 publications

Where did the rats of Big South Cape Island come from?

Where did the rats of Big South Cape Island come from?

Mammalian Evolution May not Be Strictly Bifurcating

Diversification in tropics and subtropics following the mid‐Miocene climate change: A case study of the spider genusNesticella

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