Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

Reis, Mario dos; Inoue, Jun; Hasegawa, Masami; Asher, Robert J.; Donoghue, Philip C. J.; Yang, Ziheng

doi:10.1098/rspb.2012.0683

Cited by 476 publications

(586 citation statements)

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“…In fact, this is probably an underestimate because: (1) the peak species richness in the Cenozoic may well have been higher than today's richness, based on their Cenozoic diversity trajectory 12 ; (2) it appears that the biome today that has the highest species richness (that is, the tropical moist forests 17 ) has shrunk considerably in the past dozen Myr 18 , which further supports the idea that the diversity of mammals may have been higher in the early to mid Miocene 12 (15)(16)(17)(18)(19)(20)(21)(22)(23) Myr ago) than today.…”

Section: The Second Law Of Palaeobiologymentioning

confidence: 84%

Five palaeobiological laws needed to understand the evolution of the living biota

Marshall

2017

Nat Ecol Evol

179

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TitleFive palaeobiological laws needed to understand the evolution of the living biota O ne of the cornerstones of evolutionary theory is the idea of differential survival. The fact of death, the termination of the lives of individuals, is central to evolutionary change. For biologists working on the timescales of generations, the importance of differential survival has been well understood and well studied since Darwin. On longer timescales, however, although it is well recognized that there has been extensive termination of unique morphologies and lineages, study of the living biota alone offers relatively little when trying to determine the importance of these extinctions, given that among the living we only have direct data on the survivors. This presents significant challenges when trying to elucidate the evolutionary process that produced the living biota.Fortunately, the fossil record provides unique and invaluable data on the nature of extinction, including its selectivity, recurrence times, magnitudes and causes. While there has been a dramatic increase in the number of integrated palaeontological and neontological studies [1][2][3][4] , from a palaeobiological perspective, the field of biology has not yet fully assimilated the fundamental findings from the fossil record. Here I summarize these findings in the context of their relevance to our understanding of the living biota. I express this knowledge in the form of simple laws (Box 1), in the hope of facilitating the incorporation of the longstanding and fundamental discoveries of palaeontology into the foundations of thinking in evolutionary biology and ecology, something that has yet to be fully realized. The first law of palaeobiologyLineages become extinct. While the notion of immortality at the level of individuals has been rejected for millennia, it was not until around 1800 that the idea that species could become extinct was established through the discovery of fossils that could not be ascribed to any living species 5 . More formally, the first law can be expressed in terms of the probability that clade will ultimately go extinct, P e :Five palaeobiological laws needed to understand the evolution of the living biota Charles R. MarshallThe foundations of several disciplines can be expressed as simple quantitative laws, for example, Newton's laws or the laws of thermodynamics. Here I present five laws derived from fossil data that describe the relationships among species extinc tion and longevity, species richness, origination rates, extinction rates and diversification. These statements of our palaeo biological knowledge constitute a dimension largely hidden from view when studying the living biota, which are nonetheless crucial to the study of evolution and ecology even for groups with poor or non existent fossil records. These laws encapsulate: the critical fact of extinction; that species are typically geologically short lived, and thus that the number of extinct species typically dwarfs the number of living species; that extinction and orig...

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Section: The Second Law Of Palaeobiologymentioning

confidence: 84%

Five palaeobiological laws needed to understand the evolution of the living biota

Marshall

2017

Nat Ecol Evol

179

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“…The development of 'relaxed' clock models [18] that allow molecular evolutionary rates to vary across branches has somewhat reduced the discrepancy with the fossil record [4,5]. However, recent molecular studies typically place the origin of Placentalia in the Middle-to-Late Cretaceous and indicate that several divergences (including those between most extant orders) occurred well before the K-Pg boundary [3][4][5]19].…”

Section: Introductionmentioning

confidence: 99%

“…(2) In the second, we added 16 plausible but conservative age constraints on internal nodes, based on the fossil record; of these, 14 are within Placentalia. (3) In the third, we constrained the age of Placentalia to be less than 93.8 Ma; this represents the older limit (95% confidence interval) of the age of Placentalia based on extensive DNA data [5], and so investigates the impact of enforcing a younger, molecular-based estimate for the age of the crown radiation of eutherians. (4) The fourth was similar to (3), except that we constrained the age of Placentalia even further to be less than 66 Ma, ensuring the crown radiation of eutherians post-dates the K-Pg boundary, and thus enforcing the 'explosive' model.…”

Section: (F ) Node Age Constraintsmentioning

confidence: 99%

“…As all of these morphological and TE analyses infer divergence dates deep in the Mesozoic, we then constrain the origin of Placentalia to post-date the K -Pg boundary (66 Ma), and thus generate quantitative estimates for rates of evolution required to accommodate the 'explosive' model of placental origins. We also investigate the effect of constraining the origin of Placentalia to be no older than 93.8 Ma, to match the estimated 95% maximum upper bound for this node from a recent molecular dating study [5].…”

Section: Introductionmentioning

confidence: 99%

“…The timing of the origin and early diversification of placentals has been the focus of intensive research, yet remains controversial [1][2][3][4][5]. Palaeontological studies typically place the origin and early diversification of Placentalia at, or at most slightly before, the Cretaceous-Palaeogene (K-Pg) boundary at 66 Ma [2,[6][7][8].…”

Section: Introductionmentioning

confidence: 99%

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Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals

2014

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Analyses of a comprehensive morphological character matrix of mammals using 'relaxed' clock models (which simultaneously estimate topology, divergence dates and evolutionary rates), either alone or in combination with an 8.5 kb nuclear sequence dataset, retrieve implausibly ancient, Late JurassicEarly Cretaceous estimates for the initial diversification of Placentalia (crown-group Eutheria). These dates are much older than all recent molecular and palaeontological estimates. They are recovered using two very different clock models, and regardless of whether the tree topology is freely estimated or constrained using scaffolds to match the current consensus placental phylogeny. This raises the possibility that divergence dates have been overestimated in previous analyses that have applied such clock models to morphological and total evidence datasets. Enforcing additional age constraints on selected internal divergences results in only a slight reduction of the age of Placentalia. Constraining Placentalia to less than 93.8 Ma, congruent with recent molecular estimates, does not require major changes in morphological or molecular evolutionary rates. Even constraining Placentalia to less than 66 Ma to match the 'explosive' palaeontological model results in only a 10-to 20-fold increase in maximum evolutionary rate for morphology, and fivefold for molecules. The large discrepancies between clock-and fossil-based estimates for divergence dates might therefore be attributable to relatively small changes in evolutionary rates through time, although other explanations (such as overly simplistic models of morphological evolution) need to be investigated. Conversely, dates inferred using relaxed clock models (especially with discrete morphological data and MRBAYES) should be treated cautiously, as relatively minor deviations in rate patterns can generate large effects on estimated divergence dates.

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Primates (Lemurs, Lorises, Tarsiers, Monkeys and Apes)

Rosenberger

Hartwig

2013

Encyclopedia of Life Sciences

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The modern primates are a diverse order of mammals that includes lemurs, lorises, tarsiers, monkeys, apes and humans. They are united by a 65 My evolutionary history originally built on an adaptive foundation of tropical arboreality and so they share a collection of traits that are unique among mammals, such as an excellent sense of balance, acute vision, good hand–eye coordination, a large grasping first toe, prehensile feet and hands and a flexible, athletic limb anatomy. Primates also tend to live in relatively large social groups and often have correlatively enlarged brains. They almost always give birth to singletons that grow over a prolonged period, which is advantageous to cognitive development, learning and socialisation. Fossil nonhuman primates have been found on all continents but Australia and Antarctica. Primates have been important elements of tropical and subtropical faunas since mammals rebounded following the mass extinction that also promoted the demise of dinosaurs. Key Concepts: Primates are a highly diversified and successful order of mammals adapted to an arboreal, tropical lifestyle. There are three major surviving radiations – lemurs and lorises (strepsirhines) and Old World monkeys and apes (catarrhines) occur in Africa and Asia, and New World monkeys (platyrrhines) live in Central and South America – but many species are now threatened with extinction and the fourth radiation consists of only one genus, the tarsiers of eastern Asia. Although they arose from different ancestral stocks and display their own distinctive character, each radiation exhibits parallel evolution in dietary, locomotory and social adaptation to a treed environment, and all exhibit the universal primate characteristics of grasping big toes, some form of manual prehension and a preference for eating fruits – except for the exclusively predaceous tarsiers. Fossil primates are fairly well known and modern in appearance as early as the Eocene epoch, when many existing orders of mammals are also prevalent, but there is controversy as to where to set the primate–nonprimate boundary that influences how the older plesiadapiforms should be classified – in or outside of the primate order. The two largest primate clades, strepsirhines and haplorhines, one heavily reliant on the sense of smell and basically nocturnal and the other depending on vision and essentially diurnal, already existed approximately 55 Ma, but where and when anthropoids split from early haplorhines, and how the earliest members can be identified from limited sets of fossils, has not been determined. The New World platyrrhine monkeys are an early offshoot of anthropoids and only distantly related to Old World monkeys, a group that is more closely related to apes and humans. Increasing brain size as a correlate of increasing social group size is a pattern that evolved multiple times among anthropoids, irrespective of dietary preferences. The prolific early apes of the Miocene were eclipsed by the diversification of Old World monkeys in forested and open country habitats, especially in sub‐Saharan Africa.

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Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

Cited by 476 publications

References 49 publications

Five palaeobiological laws needed to understand the evolution of the living biota

Five palaeobiological laws needed to understand the evolution of the living biota

Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals

Primates (Lemurs, Lorises, Tarsiers, Monkeys and Apes)

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