Pierre-Henri Fabre

An Update of Wallace’s Zoogeographic Regions of the World

Next-Generation Biogeography In 1876, Alfred Russel Wallace mapped the zoogeographical regions of the world, based on the distributions and taxonomic relationships of broadly defined mammalian families. Wallaces classification of zoogeographical regions became a cornerstone of modern biogeography and a reference for a wide variety of biological disciplines, including global biodiversity and conservation sciences. Holt et al. (p. 74, published online 20 December) present a next-generation map of wallacean zoogeographic regions, incorporating phylogenetic data on >20,000 vertebrate species to discern and characterize their natural biogeographic patterns. Mapping the geographic distribution and phylogenetic relationships of 21,037 vertebrate species yields 11 realms. Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions of the world.

A glimpse on the pattern of rodent diversification: a phylogenetic approach

BackgroundDevelopment of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic groups such as the placentals (Mammalia). However, despite the increase of studies addressing the diversification patterns of organisms, no synthesis has addressed the case of the most diversified mammalian clade: the Rodentia.ResultsHere we present a rodent maximum likelihood phylogeny inferred from a molecular supermatrix. It is based on 11 mitochondrial and nuclear genes that covers 1,265 species, i.e., respectively 56% and 81% of the known specific and generic rodent diversity. The inferred topology recovered all Rodentia clades proposed by recent molecular works. A relaxed molecular clock dating approach provided a time framework for speciation events. We found that the Myomorpha clade shows a greater degree of variation in diversification rates than Sciuroidea, Caviomorpha, Castorimorpha and Anomaluromorpha. We identified a number of shifts in diversification rates within the major clades: two in Castorimorpha, three in Ctenohystrica, 6 within the squirrel-related clade and 24 in the Myomorpha clade. The majority of these shifts occurred within the most recent familial rodent radiations: the Cricetidae and Muridae clades. Using the topological imbalances and the time line we discuss the potential role of different diversification factors that might have shaped the rodents radiation.ConclusionsThe present glimpse on the diversification pattern of rodents can be used for further comparative meta-analyses. Muroid lineages have a greater degree of variation in their diversification rates than any other rodent group. Different topological signatures suggest distinct diversification processes among rodent lineages. In particular, Muroidea and Sciuroidea display widespread distribution and have undergone evolutionary and adaptive radiation on most of the continents. Our results show that rodents experienced shifts in diversification rate regularly through the Tertiary, but at different periods for each clade. A comparison between the rodent fossil record and our results suggest that extinction led to the loss of diversification signal for most of the Paleogene nodes.

Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA.

Here, we present a new primate phylogeny inferred from molecular supermatrix analyses of size 42 kb containing 70% of missing data, and representing 75% of primate species diversity. The supermatrix was analysed using a gene-partitioned maximum likelihood approach to obtain an exhaustive molecular phylogenetic framework. All clades recovered from recent molecular works were upheld in our analyses demonstrating that the presence of missing data did not bias our supermatrix inference. The resulting phylogenetic tree was subsequently dated with a molecular dating method to provide a timescale for speciation events. Results obtained from our relaxed molecular clock analyses concurred with previous works based on the same fossil constraints. The resulting dated tree allowed to infer of macroevolutionary processes among the primates. Shifts in diversification rate and speciation rates were determined using the SymmeTREE method and a birthdeath process. No significant asymmetry was detected for the primate clade, but significant shifts in diversification rate were identified for seven clades: Anthropoidea, Lemuriformes, Lemuridae, Galagidae, Callithrix genus, the Cercopithecinae and Asian Macaca. Comparisons with previous primate supertree results reveal that (i) there was a diversification event at the root of the Lemuriformes, (ii) a higher diversification rate is detected for Cercopithecidae and Anthropoidea and (iii) a shift in diversification is always recovered for Macaca genus. Macroevolutionary inferences and primate divergence dates show that major primate diversification events occurred after the Paleogene, suggesting the extinction of ancient primate lineages.

Major global radiation of corvoid birds originated in the proto-Papuan archipelago

A central paradigm in island biogeography has been the unidirectional “downstream” colonization of islands from continents (source to sink) based on the idea that less-diverse island communities are easier to invade than biologically more-diverse continental communities. Recently, several cases of “upstream” colonization (from islands to continents) have been documented, challenging the traditional view. However, all these cases have involved individual island species that have colonized mainland regions. Here, using molecular phylogenetic data, divergence time estimates, lineage diversity distributions, and ancestral area analyses, we reconstruct the spread of a species-rich (>700 species) passerine bird radiation (core Corvoidea) from its late Eocene/Oligocene origin in the emerging proto-Papuan archipelago north of Australia, including multiple colonizations from the archipelago to Southeast Asia. Thus, islands apparently provided the setting for the initiation of a major songbird radiation that subsequently invaded all other continents. Morphological and behavioral adaptations of the core Corvoidea as generalist feeders in open habitats, which facilitated dispersal and colonization, apparently evolved in the descendants of sedentary forest birds that invaded the proto-Papuan archipelago. The archipelago evidently provided islands of the right size, number, and proximity to continental areas to support the adaptation and diversification of vagile colonizers that went on to increase avian diversity on a global scale.

Connections between the Atlantic and the Amazonian forest avifaunas represent distinct historical events

AbstractThere is much evidence to support past contact between the Atlantic and the Amazon forests through the South American dry vegetation diagonal, but the spatiotemporal dynamics of this contact still need to be investigated to allow a better understanding of its biogeographic implications for birds. Here, we combined phylogenetic data with distributional data using a supermatrix approach in order to depict the historical connection dynamics between these biomes for New World suboscines. We examined the variation in divergence time and then compared the spatial distributions of taxon pairs representing old and recent divergences. Our results pointed to two distinct spatiotemporal pathways connecting the Atlantic and the Amazonian forests in the past: (1) old connections (middle to late Miocene) through the current southern Cerrado and Mato Grosso and the transition towards the Chaco and palm savannas of Bolivia and Paraguay; (2) young connections (Pliocene to Pleistocene) that possibly occurred through the Cerrado and Caatinga in northeastern Brazil. We suggest that the main events that played important roles in these connections were geotectonic events during the late Tertiary associated with the uplift of the Andes (old connections) and Quaternary climate changes that promoted the expansion of gallery forest through the Cerrado and Caatinga in northeastern Brazil (young connections). Our results provide the first general temporal and spatial model of how the Atlantic and Amazonian forests were connected in the past, which was derived using bird data.ZusammenfassungVerbindungen zwischen atlantischen und amazonischen Waldvogelfaunen spiegeln distinkte historische Ereignisse wider Zahlreiche Hinweise belegen ehemalige Kontakte zwischen atlantischen und amazonischen Wäldern über die diagonal durch Südamerika verlaufende Trockenvegetationszone hinweg, allerdings bedarf die raumzeitliche Dynamik dieser Kontakte noch näherer Untersuchung, um deren biogeografische Auswirkungen auf Vögel besser verstehen zu können. Hier fassten wir phylogenetische Daten mit Verbreitungsdaten in einer Supermatrix-Analyse zusammen, um so die Dynamik der historischen Verbindungen zwischen diesen Biomen für Neuwelt-Suboscine abzubilden. Wir untersuchten die Variation im Zeitpunkt der Artentrennung und verglichen dann die räumliche Verteilung von Taxonpaaren, die alte und rezente Trennungsereignisse repräsentieren. Unsere Ergebnisse deuten auf zwei distinkte raumzeitliche Verbindungswege zwischen atlantischen und amazonischen Wäldern in der Vergangenheit hin: (1) alte Verbindungen (Mittleres bis Oberes Miozän) durch den heutigen südlichen Cerrado und Mato Grosso sowie den Übergang zum Chaco und den Palmsavannen Boliviens und Perus; (2) junge Verbindungen (Pliozän bis Pleistozän), möglicherweise durch die Cerrados und die Caatinga im nordöstlichen Brasilien. Unserer Ansicht nach spielten die folgenden Hauptereignisse eine wichtige Rolle für diese Verbindungswege: geotektonische Ereignisse während des späten Tertiärs im Zusammenhang mit der Auffaltung der Anden (alte Verbindungen) sowie Klimaänderungen im Quartär, die die Ausbreitung von Galeriewäldern durch Cerrado und Caatinga im nordöstlichen Brasilien begünstigten (junge Verbindungen). Auf der Grundlage von Vogeldaten stellen unsere Ergebnisse die erste allgemeine Näherung für Zeiträume und die Art und Weise dar, wie atlantische und amazonische Wälder in der Vergangenheit in Verbindung standen.

Ecological and evolutionary determinants for the adaptive radiation of the Madagascan vangas

Adaptive radiation is the rapid diversification of a single lineage into many species that inhabit a variety of environments or use a variety of resources and differ in traits required to exploit these. Why some lineages undergo adaptive radiation is not well-understood, but filling unoccupied ecological space appears to be a common feature. We construct a complete, dated, species-level phylogeny of the endemic Vangidae of Madagascar. This passerine bird radiation represents a classic, but poorly known, avian adaptive radiation. Our results reveal an initial rapid increase in evolutionary lineages and diversification in morphospace after colonizing Madagascar in the late Oligocene some 25 Mya. A subsequent key innovation involving unique bill morphology was associated with a second increase in diversification rates about 10 Mya. The volume of morphospace occupied by contemporary Madagascan vangas is in many aspects as large (shape variation)—or even larger (size variation)—as that of other better-known avian adaptive radiations, including the much younger Galapagos Darwins finches and Hawaiian honeycreepers. Morphological space bears a close relationship to diet, substrate use, and foraging movements, and thus our results demonstrate the great extent of the evolutionary diversification of the Madagascan vangas.

Anthropoid versus strepsirhine status of the African Eocene primates Algeripithecus and Azibius: craniodental evidence.

Recent fossil discoveries have demonstrated that Africa and Asia were epicentres for the origin and/or early diversification of the major living primate lineages, including both anthropoids (monkeys, apes and humans) and crown strepsirhine primates (lemurs, lorises and galagos). Competing hypotheses favouring either an African or Asian origin for anthropoids rank among the most hotly contested issues in paleoprimatology. The Afrocentric model for anthropoid origins rests heavily on the >45 Myr old fossil Algeripithecus minutus from Algeria, which is widely acknowledged to be one of the oldest known anthropoids. However, the phylogenetic position of Algeripithecus with respect to other primates has been tenuous because of the highly fragmentary fossils that have documented this primate until now. Recently recovered and more nearly complete fossils of Algeripithecus and contemporaneous relatives reveal that they are not anthropoids. New data support the idea that Algeripithecus and its sister genus Azibius are the earliest offshoots of an Afro–Arabian strepsirhine clade that embraces extant toothcombed primates and their fossil relatives. Azibius exhibits anatomical evidence for nocturnality. Algeripithecus has a long, thin and forwardly inclined lower canine alveolus, a feature that is entirely compatible with the long and procumbent lower canine included in the toothcomb of crown strepsirhines. These results strengthen an ancient African origin for crown strepsirhines and, in turn, strongly challenge the role of Africa as the ancestral homeland for anthropoids.

PhySIC: A Veto Supertree Method with Desirable Properties

This paper focuses on veto supertree methods; i.e., methods that aim at producing a conservative synthesis of the relationships agreed upon by all source trees. We propose desirable properties that a supertree should satisfy in this framework, namely the non-contradiction property (PC) and the induction property (PI). The former requires that the supertree does not contain relationships that contradict one or a combination of the source topologies, whereas the latter requires that all topological information contained in the supertree is present in a source tree or collectively induced by several source trees. We provide simple examples to illustrate their relevance and that allow a comparison with previously advocated properties. We show that these properties can be checked in polynomial time for any given rooted supertree. Moreover, we introduce the PhySIC method (PHYlogenetic Signal with Induction and non-Contradiction). For k input trees spanning a set of n taxa, this method produces a supertree that satisfies the above-mentioned properties in O(kn(3) + n(4)) computing time. The polytomies of the produced supertree are also tagged by labels indicating areas of conflict as well as those with insufficient overlap. As a whole, PhySIC enables the user to quickly summarize consensual information of a set of trees and localize groups of taxa for which the data require consolidation. Lastly, we illustrate the behaviour of PhySIC on primate data sets of various sizes, and propose a supertree covering 95% of all primate extant genera. The PhySIC algorithm is available at http://atgc.lirmm.fr/cgi-bin/PhySIC.

Rodents of the Caribbean: Origin and diversification of hutias unravelled by next-generation museomics

The Capromyidae (hutias) are endemic rodents of the Caribbean and represent a model of dispersal for non-flying mammals in the Greater Antilles. This family has experienced severe extinctions during the Holocene and its phylogenetic affinities with respect to other caviomorph relatives are still debated as morphological and molecular data disagree. We used target enrichment and next-generation sequencing of mitochondrial and nuclear genes to infer the phylogenetic relationships of hutias, estimate their divergence ages, and understand their mode of dispersal in the Greater Antilles. We found that Capromyidae are nested within Echimyidae (spiny rats) and should be considered a subfamily thereof. We estimated that the split between hutias and Atlantic Forest spiny rats occurred 16.5 (14.8–18.2) million years ago (Ma), which is more recent than the GAARlandia land bridge hypothesis (34–35 Ma). This would suggest that during the Early Miocene, an echimyid-like ancestor colonized the Greater Antilles from an eastern South American source population via rafting. The basal divergence of the Hispaniolan Plagiodontia provides further support for a vicariant separation between Hispaniolan and western islands (Bahamas, Cuba, Jamaica) hutias. Recent divergences among these western hutias suggest Plio-Pleistocene dispersal waves associated with glacial cycles.

Brains, tools, innovation and biogeography in crows and ravens

BackgroundCrows and ravens (Passeriformes: Corvus) are large-brained birds with enhanced cognitive abilities relative to other birds. They are among the few non-hominid organisms on Earth to be considered intelligent and well-known examples exist of several crow species having evolved innovative strategies and even use of tools in their search for food. The 40 Corvus species have also been successful dispersers and are distributed on most continents and in remote archipelagos.ResultsThis study presents the first molecular phylogeny including all species and a number of subspecies within the genus Corvus. We date the phylogeny and determine ancestral areas to investigate historical biogeographical patterns of the crows. Additionally, we use data on brain size and a large database on innovative behaviour and tool use to test whether brain size (i) explains innovative behaviour and success in applying tools when foraging and (ii) has some correlative role in the success of colonization of islands. Our results demonstrate that crows originated in the Palaearctic in the Miocene from where they dispersed to North America and the Caribbean, Africa and Australasia. We find that relative brain size alone does not explain tool use, innovative feeding strategies and dispersal success within crows.ConclusionsOur study supports monophyly of the genus Corvus and further demonstrates the direction and timing of colonization from the area of origin in the Palaearctic to other continents and archipelagos. The Caribbean was probably colonized from North America, although some North American ancestor may have gone extinct, and the Pacific was colonized multiple times from Asia and Australia. We did not find a correlation between relative brain size, tool use, innovative feeding strategies and dispersal success. Hence, we propose that all crows and ravens have relatively large brains compared to other birds and thus the potential to be innovative if conditions and circumstances are right.