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Guest Lancelot Arnold

The Origin and Diversification of Birds 2

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Guest Lancelot Arnold

Figure 5. Montage of Mesozoic birds.

(A) The basal avian Sapeornis chaoyangensis (juvenile, photo by Huali Chang). (B) The enantiornithine Eopengornis martini. (C) The basal avian Jeholornis prima. (D) The basal ornithuromorph Iteravis huchzermeyeri. Photos in (B–D) by Jingmai O’Connor. All specimens from the Early Cretaceous (130.7–120 million years ago) Jehol Biota of Liaoning Province, China.

The Jehol biota provides a spectacular window into the early evolution of birds, and demonstrates that many major lineages were already well established in the Early Cretaceous [35]. The long bony-tailed Jeholornithiformes (Jeholornis and kin), only slightly more derived than Archaeopteryx, lived alongside the earliest birds with a pygostyle (a fused, reduced tail bone). These latter birds include Sapeornithiformes (Sapeornis and kin), the beaked Confuciusornithiformes (a clade of early birds including the abundantly found Confuciusornis), and the earliest members of the major early bird groups Enantiornithes and Ornithuromorpha [33]. These latter two groups together form the derived clade Ornithothoraces, whose members are characterized by several modifications to the flight apparatus that probably made them more powerful and efficient fliers, such as a keeled sternum (breastbone), elongate coracoid, narrow furcula (wishbone), and reduced hand [30]. The enantiornithines were the dominant group of Cretaceous birds, in terms of both numbers of fossils and taxonomic diversity (∼50 named species). These so-called ‘opposite birds’, named because they differ from modern birds in the construction of the shoulder girdle (ornithuromorphs have a concave scapular cotyla, whereas this surface is convex in enantiornithines), include such taxa as Gobipteryx and Sinornis and were distributed worldwide during the Cretaceous [36].

Ornithuromorphs include a slew of Cretaceous birds, such as Gansus, Patagopteryx, Yixianornis, and Apsaravis, which form a grade on the line to Ornithurae, a derived subgroup that includes modern birds and their closest fossil relatives. Among these close relatives are Ichthyornis, a gull-like species with nearly modern avian skeletal features except for the retention of large teeth in both jaws and the absence of a hypotarsus (a structure of the ankle in living birds that guides the pulley-like tendons of the toes), and the Hesperornithiformes, a group of large, flightless diving birds 30, 37. These basal ornithurines are restricted to the Late Cretaceous.

True modern birds — members of the crown group Neornithes — are a mostly post-Cretaceous radiation, although there is some fossil evidence for Cretaceous species [38]. This evidence mostly consists of extremely fragmentary specimens of tenuous taxonomic affinity. The single best record of a Cretaceous neornithine is the partial skeleton of Vegavis from the latest Cretaceous (around 68–66 million years ago) of Antarctica, which is assigned to the subgroup of modern birds including ducks and geese (Anseriformes) based on the morphology of the well-developed hypotarsus [39].

The Assembly of the Bird Body Plan and Classic Avian Behaviors

The ever-growing fossil record of early birds and their closest dinosaurian relatives, which can be placed in a well-resolved family tree (Figure 1), allow unprecedented insight into how the classic body plan and signature behavioral features of birds originated, evolved, and were related to the phenomenal success of the group (Figure 4). Over the past two decades of research, one overarching pattern has become clear: many features — such as feathers, wishbones, egg brooding, and perhaps even flight — that are seen only in birds among living animals first evolved in the dinosaurian ancestors of birds (Figures 4 and 5). Other features, such as rapid growth, a keeled sternum, pygostyle, and beak, are absent in the earliest birds and evolved, often multiple times, in more derived birds during the Cretaceous. Therefore, what we think of as the bird ‘blueprint’ was pieced together gradually over many tens of millions of years of evolution, not during one fell swoop (Figure 1) 2, 3, 19, 20. We describe the assembly of this ‘blueprint’ below.

Living birds are mostly small and have a highly distinct skeleton well suited for flight. This small body size is a culmination of an evolutionary trend spanning more than 50 million years, beginning in maniraptoran theropods distantly related to birds 40, 41, 42. The bipedal posture, hinge-like ankle, hollowed bones, and long S-shaped neck of birds were inherited from deep dinosaurian ancestors 43, 44, the wishbone (furcula) and three-fingered hands of birds first appeared in primitive theropods, the reversion of the pubis and associated forward movement of the center of mass occurred in maniraptoran theropods, and the ability to fold the forearm against the body evolved in paravians closely related to birds 3, 19, 20. Other classic avian features, such as the keeled breastbone to support flight muscles and highly reduced tail, evolved after the origin of birds, meaning that the earliest birds looked more like dinosaurs in lacking these features. Long-term trends in skeletal proportions and musculature across dinosaurs and early birds led to two of the most characteristic features of living birds: the elongated arms, which became wings in birds ([45], but see [46]); and the bizarre ‘crouched’ hindlimb posture, in which the femur is held nearly horizontal and most of the locomotory activity of the hindlimb occurs at the knee joint rather than the pelvic joint [47].

Perhaps the single most recognizable feature of birds is feathers, which are used to construct an airfoil for flight (the wing), and also for display, thermoregulation, and egg brooding. The evolution of feathers likely began in the earliest dinosaurs, or perhaps even in the closest relatives of dinosaurs 48, 49 (Figure 4A,B). A variety of primitive theropods, such as Sinosauropteryx and the tyrannosaurs Dilong and Yutyrannus[17], and a growing number of plant-eating ornithischian dinosaurs, such as Tianyulong and Kulindadromeus50, 51, are now known from spectacularly preserved fossils covered in simple, hair-like filaments called ‘protofeathers’ that are widely considered to be the earliest stage of feather evolution 48, 52. Elaboration of these structures into the more complex, branching, vaned feathers of modern birds occurred in maniraptoran theropods [48]. Some non-bird dinosaurs like Microraptor possess feathers basically indistinguishable from the flight feathers of living birds 53, 54, 55 (Figures 2 and 3). The story of feather evolution is becoming increasingly clear: the earliest feathers evolved in non-flying dinosaurs, likely for display and/or thermoregulation, and only later were they co-opted into flight structures in the earliest birds and their very closest dinosaurian relatives.

In many derived non-bird dinosaurs, vaned feathers are layered together to form wings on the arms, and in some cases the legs and tails 55, 56, 57, 58, 59. Whether these wings were capable of flight, or perhaps used for other functions, such as egg brooding or display [60], is difficult to answer at present, although there is some emerging evidence for multiple uses.

Some non-bird dinosaurs probably did use their wings to fly. Biomechanical study of the four-winged dromaeosaurid Microraptor suggests that it was a capable glider, although probably not capable of the kind of muscle-driven powered flight of living birds [61]. In further support of Microraptor’s volant capabilities, it is the only taxon with asymmetrical hindlimb feathers (flight feathers are asymmetrical with a short and stiff leading vane and are optimized to withstand the force of the airstream), and the only non-avian with an elongated coracoid, a feature of all early birds in which a sternum is present (Jeholornis, Confuciusornis, and ornithothoracines) [62].

Other non-bird dinosaurs may have used their wings for functions other than flight. Although hindlimb feathers are often regarded as evidence that birds evolved flight through a four-wing stage [58], these feathers are symmetrical (i.e., not well constructed for flight) in all known species other than Microraptor. This suggests that their initial purpose was not for flight, but another function, such as display [63]. Similarly, a majority of tail morphologies of early birds and close dinosaurian relatives appear to be primarily ornamental in function, suggesting that sexual selection may have been the initial driving force in the evolution of complex paravian plumages, with their use as airfoils for flight coming later [35]. A display function for many of these complex feathers would also explain demonstrated increases in melanosome diversity in these dinosaurs, which would have caused the feathers to have a diversity of colors [64].

Therefore, we hold that the following is most likely, based on present evidence. First, much of the evolution of complex feathers and wings in paravian dinosaurs was driven by factors other than flight, such as display. Second, some paravians that evolved flightworthy plumage of large wings composed of asymmetrical feathers (such as Microraptor and perhaps other taxa that await discovery) evolved flight in parallel to flight in birds. This latter hypothesis is bolstered by the recent realization that flight probably evolved multiple times within maniraptoran dinosaurs, enabled by structures other than feathered wings: the enigmatic maniraptoran clade Scansoriopterygidae also evolved gliding flight through the use of fleshy patagia similar to flying squirrels [29]. If derived bird-like dinosaurs were experimenting with using different body structures to evolve flight in parallel, it follows that different dinosaurs may have evolved different flightworthy feathered wings in parallel as well. Third, although early birds and even some non-bird dinosaurs had volant capabilities, powered flight as we know it in modern birds most certainly developed after the origin of birds themselves.

The earliest birds lacked many key features related to powered flight in modern birds, and probably had primitive flight capabilities that varied substantially between groups. For example, unlike modern birds, Archaeopteryx lacked a bony sternum and even a compensatory specialized gastral basket for anchoring large flight muscles 62, 65. The slightly more derived Jeholornis possessed a curious mixture of features: it retained a primitive long, bony tail unlike that of extant birds, but had several derived flight-related features of modern birds, such as numerous fused sacral vertebrae, an elongated coracoid with a procoracoid process (important in creating the pulley-like system used to minimize effort in the upstroke, otherwise only present in the Ornithuromorpha), a complex sternum, a narrow excavated furcula with a short hypocleidium, and a curved scapula 66, 67. Jeholornis also had its own peculiarities: it possessed a unique fan-shaped tract of tail flight feathers that likely increased lift and allowed the long tail to be used as a stabilizer, thus producing its own unique and probably very effective form of flight [68].

It was only in birds much more derived than Archaeopteryx and Jeholornis that the fully modern style of avian flight developed, enabled by a keeled sternum supporting enormous flight muscles, a tail reduced to a fused plough-shaped pygostyle, and a complete triosseal canal in the shoulder (which encloses the pulley-like system that automates the upstroke). These innovations then combined with features evolved earlier in birds and their non-dinosaurian relatives, such as elongation of the feathered forelimbs and a narrow furcula, to produce the style of highly efficient, muscle-driven flight seen in today’s birds, which allows some species to fly at altitudes of ∼9,000 meters (such as some vultures and geese) and over distances of hundreds of kilometers [1]. This modern style of flight developed with or near the origin of Ornithuromorpha. Enantiornithines strongly resemble ornithuromorphs in many anatomical features of the flight apparatus, but a sternal keel was apparently lacking in the most basal members, only a single basal taxon appears to have had a triosseal canal [69], and their robust pygostyle appears to have been unable to support the muscles that control the flight feathers on the tail (retrices) in modern birds [70].

Other distinctive anatomical features of modern birds, relating to the sensory and respiratory systems, first evolved in their dinosaurian ancestors. Living birds are highly intelligent with keen senses, enabled in part by a forebrain that is expanded relative to body size [71]. This expansion began early in theropod evolution [72] and non-bird paravians had the highly expanded, and presumably ‘flight ready’, brain of early birds [73] (Figure 4). Modern birds also possess an efficient ‘flow through’ lung in which oxygen passes across the gas exchange tissues during inhalation and exhalation, and which is linked to a complex system of balloon-like air sacs that store air outside of the lungs [74]. Recent work has surprisingly shown that this system first began to evolve in reptiles, as extant crocodiles and monitor lizards exhibit unidirectional breathing 75, 76, but without a complex system of air sacs. The air sacs evolved in early dinosaurs, as shown by the distinctive foramina where the air sacs penetrate into vertebrae and other bones, and became more extensive and elaborate during the course of theropod evolution 77, 78, 79, 80 (Figure 4F,G). Most theropod dinosaurs at the very least, and possibly other dinosaurs, therefore possessed a ‘bird-like’ lung.

Extant birds grow remarkably fast, usually maturing from hatchling to adult within a few weeks or months, and have a high-powered endothermic (‘warm-blooded’) metabolism. As shown by studies of bone histology and growth curves based on counting lines of arrested growth in bones, non-bird dinosaurs grew much faster than previously realized, at a rate intermediate between that of reptiles and modern birds 81, 82. The oldest birds, such as Archaeopteryx, and Mesozoic bird groups, such as enantiornithines, had growth rates similar to derived non-bird dinosaurs [83], and the amplified rates and rapid maturation of modern birds probably evolved somewhere around the origin of Ornithurae 3, 84. Determining the physiology of dinosaurs is difficult and has been the source of considerable debate for decades 11, 13. What is certain, however, is that most dinosaurs had high metabolisms more similar to birds than to living reptiles [85]. A recent comprehensive study found that dinosaurs had so-called ‘mesothermic’ physiologies, intermediate between ‘cold-blooded’ ectotherms and endotherms [86]. The emerging consensus is that the endothermic physiology of living birds had its roots in the mesothermic physiologies of dinosaurs, but was absent in basal birds and developed later in avian history.

The reproductive system of living birds is remarkably derived compared to their closest living relatives (crocodilians) and other vertebrates. Birds possess only a single functional ovary and oviduct and have oocytes that mature rapidly, such that only a single oocyte (or none) is ovulated, shelled, and laid per 24-hour cycle (not numerous eggs en masse as in crocodilians and many dinosaurs). They lay small clutches of large, asymmetrical eggs formed by two or three crystal layers, which typically are actively brooded in the nest by one or both parents [1] (Figure 4). These features evolved incrementally: derived microstructural eggshell characteristics, smaller clutches, and sequential ovulation were acquired in maniraptoran dinosaurs closely related to birds 87, 88. However, derived near-bird dinosaurs apparently retained two functional ovaries [89], whereas Jeholornis and enantiornithines apparently had a single ovary, indicating that the left ovary was lost very close to the dinosaur–bird transition, perhaps related to body lightening during the evolution of flight [90]. Egg size progressively increased and clutch size decreased during early avian evolution [90].

This summary illustrates how the classic anatomical and behavioral features of birds (the bird ‘blueprint’) did not evolve in one or a few spurts of innovation, but more gradually over a long period of evolutionary time and across the dinosaur family tree (Figure 1). However, there apparently were some bursts of evolution in the early history of birds. Once a small flight-capable dinosaur had been assembled, there was a huge spike in rates of anatomical evolution in the earliest birds [2]. Later, the early evolution of short-tailed birds (Pygostylia) in the Cretaceous was associated with high rates of hindlimb evolution and greater than normal speciation [91].

Birds Dealt with a Crisis at the End of the Cretaceous

The course of avian history was dramatically affected by the mass extinction at the end of the Cretaceous, ∼66 million years ago, which wiped out all non-avian dinosaurs and many other groups 92, 93. The extinction was geologically rapid and most likely caused by the impact of a large asteroid or comet, which triggered a global cataclysm of climate and temperature change, acid rain, earthquakes, tsunamis, and wildfires 94, 95. It is possible that somewhat longer-term changes in the Earth system, including volcanism and sea-level fluctuations, may have also played a role in the extinction [96]. The emerging picture, however, is that the world changed suddenly at the end of the Cretaceous, killing off many once-dominant groups and giving other organisms an opportunity to radiate in the vacant ecospace.

Birds were diverse in the Late Cretaceous, with many of the characteristic lineages of ‘archaic’ birds from the Jehol Biota (species outside of the neornithine crown, such as enantiornithines and basal ornithuromorphs) living alongside what was probably a moderate diversity of early neornithines, as indicated by rare fossils and molecular phylogenetic studies tracing some modern lineages into the Cretaceous 4, 39, 97, 98. None of these ‘archaic’ non-neornithine birds, however, apparently survived past the Cretaceous and into the Paleogene. There has long been debate about whether the extinction of ‘archaic’ birds was gradual or sudden, but recent evidence shows that a diverse avifauna of enantiornithines and basal ornithuromorphs persisted until at least a few hundred thousand years before the end of the Cretaceous in western North America, suggesting that the extinction was sudden and directly linked to the end-Cretaceous impact [99]. This also indicates that birds were strongly affected by the end-Cretaceous extinction, with many major early groups going extinct, countering the stereotype that the mass extinction decimated the non-avian dinosaurs but largely spared birds (see reviews in 92, 99). However, because of the scrappy fossil record of the latest Cretaceous birds, which is mostly limited to isolated bones [99], it has been unclear why certain birds went extinct and others survived.

Multiple lineages of early neornithines must have endured the extinction, leaving them the only surviving members of the initial Mesozoic radiation of birds. Fossil 100, 101 and recent genetic [4] evidence supports this view and shows that these birds diversified rapidly in the post-apocalyptic world, probably taking advantage of the ecological release afforded by the extinction of both the ‘archaic’ birds and the very bird-like non-avian dinosaurs. Numerous groups of modern neornithines make their first appearance in the fossil record during the ∼10 million years after the end-Cretaceous extinction [102], and a genome-scale molecular phylogeny indicates that nearly all modern ordinal lineages formed within 15 million years after the extinction [4], suggesting a particularly rapid period of both genetic evolution and the formation of new species (Figure 6). We discuss this recent phylogenomic study further below.
Figure 6. Ordinal-level genome-scale family tree of modern birds.

The tree was generated from ∼30 million base pairs of genomic DNA consisting of exons, introns, and ultraconserved elements. Branch colors represent well-supported clades. All bootstrap values are 100% except where noted. Names on branches denote orders (-iformes) and English group terms (in parentheses). To the right are superorder (-imorphae) and higher unranked names. Text color denotes groups of species with broadly shared traits, whether by homology or convergence. The arrow at the bottom indicates the Cretaceous–Paleogene boundary at 66 million years ago, with the Cretaceous period shaded at left. The dashed line represents the approximate end time (50 million years ago) by which nearly all neoavian orders diverged. Horizontal gray bars on each node indicate the 95% credible interval of divergence time in millions of years. Figure used and modified with permission from [4].

Birds after the Cretaceous

The more than 10,000 species of birds living in today’s world are divided into two major groups: the Palaeognathae (which includes flightless forms, such as kiwis, ostriches, emus, and rheas) and the Neognathae, the speciose clade that includes the remainder of bird diversity. The Neognathae, in turn, is composed of the subgroup Galloanserae (the ‘fowls’, including ducks, chickens, and geese) and Neoaves (which includes everything from pigeons and owls to falcons and parrots) 4, 97, 98, 103 (Figure 6).

The phylogenetic relationships of Neoaves have been the subject of extensive work in recent years. The recent phylogenomic study by Jarvis et al.[4] is the most comprehensive genome-scale analysis of birds to date in terms of amount of DNA sequence (using up to ∼300 million nucleotides) and number of analyses, and attempted to resolve two main issues: firstly, the general branching patterns between the major orders on the bird family tree; and secondly, when these groups diverged, particularly which groups originated before the end-Cretaceous extinction and which arose afterwards. The study was able to resolve, with the highest level of certainty to date, the ordinal relationships of modern birds, and determine that the majority of these groups diverged immediately after the Chicxulub asteroid impact that ushered out the Cretaceous.

According to the dated phylogeny of Jarvis et al.[4], the common ancestor of Neoaves lived in the Cretaceous. The earliest divergence of this ancestor gave rise to the major subgroups Columbea (consisting of doves, flamingoes, grebes, and sandgrouse) and Passerea (consisting of all other neoavian species). We predict that this ancestor may have been ecologically similar to modern shorebirds, since the number of divergences after the Columbea and Passerea split, and thereby also after the Neognathae split, to obtain an aquatic or semi-aquatic versus terrestrial species are almost equal (Figure 6) [4]. At least four to six of these basal Neoaves lineages and several members of Palaeognathae and Galloanseres are predicted to have passed through the end-Cretaceous extinction. The subsequent burst of speciation after the extinction consisted of an initial rapid radiation of additional basal Neoaves orders, from grebes to hummingbirds, followed by two subsequent radiations of ‘core waterbirds’ (including penguins, pelicans, and loons) and ‘core landbirds’ (including birds of prey, woodpeckers, parrots, and songbirds). As mentioned above, nearly all of these ordinal divergences occurred within the first 15 million years after the mass extinction, with this pulse of evolution ending around 50 million years ago.

In general, the results of the Jarvis et al.[4] study are consistent with earlier studies proposing a major post-Cretaceous radiation of birds 99, 104 and the hypothesis that shorebird-type species were able to endure the extinction 100, 101 with traits that may have allowed them to live in diverse environments. However, these new results are at odds with previous molecular studies suggesting a major pre-Cretaceous divergence of Neoaves 20–100 million years earlier 97, 105, 106. The main differences with some previous molecular studies are that the Jarvis et al.[4] study used genomic-scale data and took a conservative approach of using non-ambiguous fossils for dating the tree. In sum, the new phylogenomic study supports a ‘short fuse’ hypothesis for modern bird diversity (e.g. [100]), in which some of the main extant lineages originated during the final few tens of millions of years of the Cretaceous, but the key interval of speciation and ordinal-level diversification was concentrated in the few million years after the end-Cretaceous extinction.

The new phylogenetic analysis revealed some surprising relationships among well-known living birds, which help to better understand the evolution of important anatomical and ecological traits. Among the Columbea, the flamingos and grebes (both waterbird orders) were found to be sister clades [107] and their closest relatives were inferred to be a landbird group consisting of pigeons, sandgrouse, and mesites (Figure 6). This suggests that the aquatic or terrestrial adaptations of these groups with the ‘core’ waterbirds and landbirds are convergent. Among the ‘core’ waterbird group, there appears to be a graded acquisition of aquatic traits, beginning with the sunbittern/tropicbird clade and culminating in penguins and pelicans amongst others, which are more obligate water-dwellers.

The common ancestor of the ‘core’ landbirds was inferred to be an apex predator, closely related to the extinct giant terror birds (Phorusrhacidae) that included human-sized apex predators in North and South America during much of the Cenozoic (around 62–2 million years ago) 107, 108. The species at the deepest branches of ‘core’ landbirds (vultures/eagles/owls and seriemas/falcons) are predatory, but within this group the raptorial trait appears to have been lost twice: once among the Afroaves clade, on the branch leading to Coraciimorphae (mousebirds to bee eaters), and again among the Australaves clade, on the branch leading to Passerimorphae (parrots to songbirds) (Figure 6). The names of Afroaves and Australaves imply their likely geographical origins [109], although more evidence is needed to confirm this. One interpretation of such independent losses of the raptorial trait is that being a predator is a costly lifestyle for modern birds and is being selected against over time. Another interpretation is that this trait was passively lost twice.

The new phylogeny also helps to better understand the evolution of one of the most intriguing traits of some living birds: vocal learning, including the ability of some species to imitate human speech. This is a very rare trait, seen in only in songbirds, parrots, and hummingbirds among birds and very few mammals (e.g. dolphins, bats, elephants, and humans) but not non-human primates. As such, avian vocal learners have become highly studied animal models of human speech 110, 111, 112. In contrast to long-standing inferences of three independent gains 103, 110, 113, the new analysis supports two independent gains of vocal learning amongst Neoaves: once in the hummingbirds and once in the common ancestor of parrots and songbirds, followed by two subsequent losses in New Zealand wrens and suboscines. However, it does not completely rule out independent evolution in parrots and songbirds (Figure 6) [4]. All three vocal-learning bird lineages and humans were found to have evolved convergent mutations and changes in gene expression in the regions of the brain that control song (bird) and speech (human) 98, 114. Overall, these findings reveal the great amount of diversity and convergence that occurred among birds (including some features convergent with mammals) during the post-Cretaceous revolution.

Conclusions

Modern birds achieved their enormous diversity over a more than 150 million year evolutionary journey, which began with their divergence from theropod dinosaurs, continued with the gradual and piecemeal acquisition of a flight-worthy body plan, and involved two bursts of diversification: first in the Mesozoic when a small, feathered, winged dinosaur was fully assembled, and second when surviving species had the freedom to thrive after the end-Cretaceous extinction. The origin of avian diversity reveals some greater truths about evolution over long timescales, namely that major living groups have a deep history, underwent long and often unpredictable paths of evolution, and were given unexpected opportunities to radiate if they were able to survive mass extinctions that decimated other groups. The flurry of recent work on avian evolution is a prime example of how fossil, morphological, genomic, phylogenetic, and statistical data can be combined to weave an evolutionary narrative, and explain how some of the modern world’s most familiar species became so successful.

Acknowledgments
This work is funded by NSF DEB 1110357, Marie Curie Career Integration Grant EC 630652, an NSF GRF, Columbia University, and the American Museum of Natural History to S.L.B.; and HHMI support to E.D.J. We thank R. Benson, J. Choiniere, A. Dececchi, G. Dyke, H. Larsson, M. Lee, G. Lloyd, P. Makovicky, M. Norell, A. Turner, S. Wang, and X. Xu for discussions with S.L.B.; and E.L. Braun, J. Cracraft, J. Fjeldsa, M.T.P. Gilbert, P. Houde, S. Ho, D. Mindell, S. Mirarab, T. Warnow, and G. Zhang for discussions with E.D.J.

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