An international research team have discovered seven new species of tree frog in Madagascar, all members of the Boophis genus, previously thought to be a single species. They are characterized by their distinctive sounds. Their high-pitched whistles are unlike the sounds normally associated with frogs and sounding more like something from science fiction prompted their discoverers to give them all names based on Star Trek captains: Boophis archeri (Archer), Boophis burnhamae (Burnham), Boophis janewayae (Janeway), Boophis kirki (Kirk), Boophis picardi (Picard), Boophis pikei (Pike), Boophis siskoi (Sisko).
The basis for the revised taxonomy is two-fold - genetic and bioacoustic. Although there are all morphologically similar, differing mainly in size, the genetic evidence shows they have diverged into genetically isolated populations and the acoustic evidence shows how genetic separation is maintained by a prezygotic barrier to hybridization. The high pitch of their calls is believed to make them audible above the sound of running water in their normal environment.
Tell a creationists that humans and chimpanzees have 98% of their genomes in common, and they'll tell you this doesn't prove common origins or 'macro-evolution', but show them evidence that two bacteria have evolved from a common ancestor because they have 80% of their genome in common and they'll tell you this doesn't mean they've evolved because they are both still 'bacteria kind'.
So, why doesn't 98% commonality mean humans and chimpanzees are both still 'ape kind'?
But the evidence that the two bacteria, Mycobacterium tuberculosis, and the newly-discovered M. spongiae is compelling, and gives a clue as to the origins of M. tuberculosis, one of the most deadly pathogenic bacteria, possibly from marine origins.
News that a team of evolutionary biologists are reassessing what we thought we knew about the dodo, Raphus cucullatus, is a good excuse to look at what the dodo teaches us about evolution.
The dodo was a species of pigeon which had spread to the Indian Ocean island of Mauritius, where in common with many island birds had lost the ability to fly. In the context of an island with no mammalian predators, any advantage of flight is balanced against the greater disadvantage of occasionally being blown out to sea. Natural selection, with no foresight and no plan, results in a flightless bird, and, as events transpire, extinction.
The arrival of Europeans with their rats, cats and dogs and need for supplies for a long sea voyage, was an environmental change that the dodo could not adapt to because evolution has no reverse gear and rarely reinvents what was lost earlier. The ground-nesting dodo like its close relative, on a neighbouring island, the Rodriguez Island Solitaire, Pezophaps solitaria, were doomed. They were extinct by the late 17th century.
Evolution is an unintelligent process. This would not be so, if species like the dodo had been intelligently designed by an omniscient designer, who could have foreseen and prepared for the coming of Europeans with their rats, cats and dogs. It is not an intelligent act to design a species headed for inevitable extinction because it can't adapt to what can be anticipated.
What information do you have on the 'Oxford dodo' and it's role in literature and biology?
The "Oxford dodo" is a significant artifact in both biological and literary history. Here's an overview of its importance:
Historical Background
The Dodo: The dodo (Raphus cucullatus) was a flightless bird native to Mauritius, an island in the Indian Ocean. It became extinct in the late 17th century due to overhunting by humans and the introduction of non-native animals.
Oxford Dodo: The Oxford dodo refers to the most complete known specimen of the dodo, which is housed at the Oxford University Museum of Natural History. This specimen includes the only remaining soft tissue (a dried head and a foot) from any dodo in the world.
Role in Biology
Scientific Study: The Oxford dodo has played a crucial role in scientific studies on the species. Since it includes soft tissue, researchers have been able to extract DNA, providing insights into the dodo's genetic makeup and its relationship to other bird species.
Extinction Studies: The dodo is often cited as one of the earliest recorded examples of human-caused extinction. The Oxford specimen has contributed to studies on extinction, illustrating the impact of human activity on isolated ecosystems.
Role in Literature
Lewis Carroll's "Alice's Adventures in Wonderland": One of the most famous literary references to the dodo is in Lewis Carroll's 1865 novel *Alice's Adventures in Wonderland*. The dodo in the story is believed to represent Carroll himself, who had a stammer and sometimes introduced himself as "Do-do-Dodgson" (Carroll's real name was Charles Dodgson). The character of the dodo in the story is depicted as a wise figure who proposes the "Caucus-race," where everyone wins and all must have prizes—a satire on political processes.
Symbol of Extinction: In literature and popular culture, the dodo has come to symbolize obsolescence and extinction, often representing something that is outdated or doomed to disappear. The Oxford dodo, as a physical reminder of a lost species, has reinforced this symbolism.
Cultural and Educational Impact
Exhibitions: The Oxford dodo has been featured in various exhibitions, not just as a scientific specimen but also as a cultural icon. It serves as a powerful educational tool about biodiversity loss and conservation.
Inspiration for Research and Art: The dodo has inspired a wide range of research, from studies in paleontology and conservation biology to its portrayal in art, literature, and even in discussions about colonialism and its impact on indigenous species.
Recent Developments
DNA Analysis: Advances in DNA technology have allowed scientists to conduct more detailed studies on the Oxford dodo's remains, leading to a better understanding of its biology and the causes of its extinction. These studies are crucial for understanding the dynamics of extinction and the evolution of island species.
Conservation Lessons: The story of the dodo, as illustrated by the Oxford specimen, is frequently used in discussions about conservation and the need to protect endangered species today. It serves as a cautionary tale about the consequences of human activity on the environment.
In summary, the Oxford dodo is more than just a biological specimen; it is a symbol of extinction and a cultural icon that has influenced literature, conservation science, and our understanding of human impact on the natural world.
Is there any evidence for the story that it was rescued from a bonfire of 'rubbish' at either the Ashmolean or the Oxford University Natural History Museum?
The story that the Oxford dodo was rescued from a bonfire of "rubbish" at the Ashmolean Museum, or the Oxford University Museum of Natural History is a widely circulated anecdote, but its accuracy is somewhat debated. Here's what is known:
Origins of the Story
Historical Context: The story typically claims that the dodo specimen, or parts of it, were nearly discarded during a clean-up or reorganization at one of the Oxford museums, likely the Ashmolean Museum, where the dodo was initially housed. The account suggests that someone recognized the value of the remains just in time to save them from being burned as rubbish.
Attribution: This anecdote is often linked to John Tradescant the Younger, an early naturalist and collector, whose collection formed the core of the Ashmolean Museum's early holdings. It is also sometimes associated with Elias Ashmole, the museum's founder.
Supporting Evidence
Lack of Concrete Records: There is no definitive archival evidence or documentation to substantiate the bonfire rescue story. The tale seems to have been passed down through oral history and later written accounts, but without solid documentary support.
Museum Records: Some records suggest that by the late 18th century, parts of the dodo specimen were discarded because they had decayed. The surviving head and foot were kept, while the rest of the body, which had likely decomposed significantly, was disposed of. This might have contributed to the myth that the specimen was almost entirely lost.
Plausibility and Scholarly Opinions
Scholarly Views: Historians and museum curators generally agree that while the story is plausible, it is likely an exaggeration or a simplification of events. It is plausible that during a period of reorganization or decay of the specimen, parts of the dodo were discarded, and someone recognized the importance of preserving the head and foot.
Interpretation: The bonfire story has become part of the dodo's lore, serving as a dramatic reminder of how close we came to losing this invaluable specimen. Whether or not it is literally true, the story underscores the precarious nature of historical artifacts and the importance of preservation.
Cultural Impact
Moral of the Story: The bonfire rescue tale is often used to highlight the fragility of historical artifacts and the importance of vigilance in preservation. It also serves to enhance the mystique of the dodo, a species already surrounded by a sense of loss and extinction.
In summary, while the story of the Oxford dodo being rescued from a bonfire at either the Ashmolean or the Oxford University Museum of Natural History is an intriguing one, it remains an anecdote with limited concrete evidence. The story has likely been embellished over time, though it reflects the real dangers historical specimens face when not properly cared for.
The extinction of the dodo on Mauritius had a long-lasting effect on the island's ecosystem of which the dodo was an essential part, but its contribution to the history of Oxford and it's literary heritage that is perhaps as interesting, coming as it does from the fact that the 'New' Ashmolean Museum became the depository of the only known remains of a dodo, which, when the collection in the Ashmolean was shared with the Oxford University Natural History Museum, and Pitt Rivers museum, was housed there, where it fascinated the Oxford Academic, Charles Ludwig Dodgson, aka Lewis Carroll (the Latinized form of Charles Ludwig).
Dodgson had a stammer and would introduce himself as Charles Do-Do-Dodgson, earning him the nickname Dodo Dodgson. When he wrote Alice in Wonderland, he based the Dodo on the 'Oxford dodo' and himself.
Part of the Oxford story concerning the Oxford dodo is probably apocryphal but serves to illustrate the importance of conservation, the fragility of specimens and recognising the importance of specimens which may not seem important at the time. The story is that it was saved from destruction at the last minute when it was destined for a bonfire of 'rubbish' that was being thrown out. The story varies as to who rescued it and whether it was the Ashmolean or the Natural History Museum that was about to burn it. What is probably true, and probably contributed to the story, is the fact that there was initially much more of the dodo but much of it decayed and was destroyed, leaving only the beak, feet and skin of the head and face.
The new study by researchers from the University of Southampton and Oxford University Museum is the subject of an open access paper in the Zoological Journal of the Linnean Society, and a University of Southampton News release:
Rethinking the Dodo Researchers are setting out to challenge our misconceptions about the Dodo, one of the most well-known but poorly understood species of bird.
In a paper published today in the Zoological Journal of the Linnean Society researchers from the University of Southampton, Natural History Museum (NHM) and Oxford University Museum of Natural History have undertaken the most comprehensive review of the taxonomy of the Dodo and its closest relative, the Rodriguez Island Solitaire.
They’ve painstakingly gone through 400 years’ worth of scientific literature and visited collections around the UK to ensure this iconic species, embodying humanity’s destructive potential, is correctly classified.
The Dodo was the first living thing that was recorded as being present and then disappeared. Before this, it hadn’t been thought possible for human beings to influence God’s creation in such a way. This was a time before the scientific principles and systems we rely on to label and classify a species were in place. Both the Dodo and the Solitaire were gone before we had a chance to understand what we were looking at.
Dr Neil J. Gostling, co-corresponding author
School of Biological Sciences
Faculty of Environmental and Life Sciences
University of Southampton, Southampton, UK.
Correcting the record
Much of what was written about the Dodo and the Solitaire was based on accounts from Dutch sailors, representations by artists, and incomplete remains.
The lack of a definitive reference point (type specimen) or convention to label species (zoological nomenclature) led to a series of misidentifications in the centuries following their extinction. New species such as the Nazarene Dodo, the White Dodo, and the White Solitaire were named, but the paper confirms that none of these creatures existed. Still, these erroneous ‘pebbles’ sent ripples through the waters of zoological literature.
By the 18th and early 19th centuries, the Dodo and the Solitaire were considered to be mythological beasts. It was the hard work of Victorian-era scientists who finally proved that the Dodo and the Solitaire were not mythological but were giant ground doves. Unfortunately, no one could agree how many species there had been. Throughout most of the 19th and 20th centuries, researchers thought there were three different species, although some people thought there had been four or even five different species.
Dr. Mark T. Young, co-corresponding author
School of Biological Sciences
Faculty of Environmental and Life Sciences
University of Southampton, Southampton, UK.
To unpick this confusion, researchers went through all the literature on the Dodo and Rodriguez Solitaire encompassing hundreds of accounts dating back to 1598 and visited specimens around the UK, including the world’s only surviving soft tissue from the Dodo, in the Oxford Museum.
More has been written about the Dodo than any other bird, yet virtually nothing is known about it in life. Based on centuries of nomenclatural confusion, and some 400 years after its extinction, the Dodo and Solitaire, continue to prompt heated debate. We’ve gone from where the first statements were made, seen how these have developed, and identified various rabbit holes to correct the record, as best we can.
Dr Julian Hume, co-author
Bird Group
Natural History Museum
Tring Hertfordshire, UK.
Through this work, researchers were able to confirm that both birds were members of the columbid (pigeon and dove) family.
Understanding its wider relationships with other pigeons is of taxonomic importance, but from the perspective of conservation, the loss of the dodo and the solitaire a few decades later means a unique branch of the pigeon family tree was lost. There are no other birds alive today like these two species of giant ground dove.
Dr Neil J. Gostling.
Challenging our misconceptions
The Dodo was an integral part of the ecosystem of Mauritius.
Artwork by Julian Pender Hume.
The researchers believe the popular idea of the Dodo as a fat, slow animal, predestined for extinction is flawed.
Even four centuries later, we have so much to learn about these remarkable birds. Was the Dodo really the dumb, slow animal we’ve been brought up to believe it was? The few written accounts of live Dodos say it was a fast-moving animal that loved the forest.
Dr. Mark T. Young.
Evidence from bone specimens suggests that the Dodo’s tendon which closed its toes was exceptionally powerful, analogous to climbing and running birds alive today. The dodo was almost certainly a very active, very fast animal. These creatures were perfectly adapted to their environment, but the islands they lived on lacked mammalian predators. So, when humans arrived, bringing rats, cats, and pigs, the Dodo and the Solitaire never stood a chance.
Dodos held an integral place in their ecosystems. If we understand them, we might be able to support ecosystem recovery in Mauritius, perhaps starting to undo the damage that began with the arrival of humans nearly half a millennium ago.
Dr Neil J. Gostling.
Learning ‘valuable lessons’
The study marks the beginning of a wider project to understand the biology of these iconic animals.
The mystery of the Dodo bird is about to be cracked wide open. We have assembled a fantastic team of scientists to uncover the true nature of this famous extinct bird. But we are not just looking back in time - our research could help save today's endangered birds too.
Using cutting-edge computer technology, we are piecing together how the Dodo lived and moved. This isn't just about satisfying our curiosity. By understanding how birds evolved in the past, we are learning valuable lessons that could help protect bird species today. It's like solving a 300-year-old puzzle, and the solution might just help us prevent more birds from going the way of the Dodo.
Professor Marcus O Heller, co-author
Bioengineering Research Group
Faculty of Engineering and Physical Sciences
University of Southampton, Southampton, UK.
Palaeoartist Karen Fawcett’s Dodo sculpture
The project will include work with palaeoartist Karen Fawcett , who has created a detailed, life-size model of the Dodo to bring the words on the pages of books and journal articles to life.
This work has been the merging of science and art to achieve accuracy and realism so that these creatures come back from the dead, real and tangible for people to touch and see.
Karen Fawcett
Palaeoartist
The work is supported by the University of Southampton’s Institute for Life Sciences.
The Institute was delighted to support this exciting work which exemplifies Southampton’s strength in interdisciplinary research and advanced scholarship.
Professor Max Crispin.
Director
Institute for Life Sciences.
University of Southampton, Southampton, UK.
Creationists might want to ignore or prepare to lie about the following, especially the section on the terminology and nomenclature background, which contains a description of how taxonomy has adapted to the modern synthesis of evolutionary theory, cladistics, shared common ancestry and monophyletics as it will make distressing reading for those who have been fooled into believing that biologists are abandoning the TOE as not fit for purpose, since nothing could be further from the truth, as this paper shows:
Abstract
The Dodo and its extinct sister species, the Solitaire, are iconic exemplars of the destructive capabilities of humanity. These secondarily terrestrial columbids became extinct within a century of their first encounter with humanity. Their rapid extinction, with little material retained in natural history collections, led 18th and some early 19th century naturalists to believe that these aberrant birds were mythological. This meant that the nomenclatural publications in which their scientific nomina were established were based on accounts written before the species became extinct. As such, no type specimens were designated for either the Dodo or the Solitaire. Our in-depth historical overview of both species and associated family-group nomina found that the nominal authority of the Dodo-based family group is not what is reported in the literature. Moreover, our detailed review of the family-group nomina based on columbid genera ensures that the current columbid family-group systematization is valid. Changing nomenclatural norms between the 19th and 20th centuries had a profound impact on Dodo nomenclature; so much so that the Dodo is an example of how pervasive nomenclatural ‘ripples’ can be and a warning for our current world of multiple nomenclatural codes.
INTRODUCTION
The Mauritian Dodo, †Raphus cucullatus (Linnaeus, 1758) (Fig. 1), and the Rodrigues Solitaire, †Pezophaps solitaria (Gmelin, 1789) (Fig. 2), are textbook examples of evolutionary transitions and of human-made extinctions. Their morphologies were so aberrant that for a time, during the 18th and early 19th centuries, they were considered mythological (Duncan 1828, de Blainville 1835, Strickland 1844, 1848, Hume 2006; see Figs 1, 2). As said by Strickland (1848: 4): ‘So rapid and so complete was their extinction that the vague descriptions given of them [Dodo and Solitaire] by early navigators were long regarded as fabulous or exaggerated, and these birds, almost contemporaries of our great-grandfathers, became associated in the minds of many persons with the Griffin and the Phœnix of mythological antiquity’. The existence of the Solitaire, in particular, was long doubted, because for several decades it was known solely from the descriptions by Leguat (1708). Strickland (1844: 324) mentioned that the Solitaire had been considered either ‘fictitious, or to be founded on an imperfect description of the true Dodo’.
Dodo (†Raphus cucullatus) mounted composite skeleton [NHMUK S/1988.50.1 (PV A 3302)]. A, cranial view. B, left lateral view.
Solitaire (†Pezophaps solitaria) mounted skeletons (on display at the Royal College of Surgeons, London, UK in 2023). A, female individual. B, male individual. Note the difference in skeleton size and robusticity between the sexes.
A series of key papers during the early 19th century ‘resurrected’ the Dodo and the Solitaire from the realm of the mythological to the material (Duncan 1828, de Blainville 1835, Strickland 1844). The seminal work of Strickland (1848) and Melville (1848.1), in their shared volume, described in detail the anatomy of specimens still found in European collections at that time, in addition to giving an authoritative account of the history of the two species. However, it was not until new expeditions to the islands of Mauritius and Rodrigues during the 1860s that new incomplete skeletons of both species were discovered. The skeletal remains discovered in the ‘Mare aux Songes’ marsh during 1865 (Clark 1866, Hume et al. 2009) allowed the Dodo to be described more fully (Owen 1866.1), and the Solitaire was described by Newton and Newton (1868, 1869) after the Jenner excavations of 1865 discovered skeletal remains (Parish 2013: 234; Hume et al. 2015).
There has been renewed interest in the biology of the Dodo and the Solitaire in the 21st century. Studies have explored Dodo body mass (Brassey et al. 2016, van Heteren et al. 2017) and bone histology (Angst et al. 2017.1), and the endocranial anatomy of both species has been reconstructed digitally from computed tomography scans (Gold et al. 2016.1). New Dodo material has been discovered from Mare aux Songes, and the ecosystem of the Mare aux Songes Lagerstätte has been studied (see Rijsdijk et al. 2009.1, 2015.1, Meijer et al. 2012). The remarkable ‘Thirioux Dodos’ have been described in-depth, which includes the most complete Dodo skeleton known (Claessens and Hume 2015.2; Claessens et al. 2015.3). There have even been attempts to reconstruct digitally how these animals would have looked (Rodríguez-Pontes 2016.2). With each decade, our understanding of these aberrant birds is being revolutionized. To ensure that this work is on a firm basis, we need to ensure that the alpha and beta taxonomy (and accompanying nomenclature) of both species is stable. As we will show, there are no known type specimens for either species. Moreover, given that the use of Dodo-based (i.e. †Raphus) family-group nomina is now accepted within columbid systematics, we need to ensure that these names are themselves valid, in order to maintain the nomenclatural stability of extant pigeons and doves. To those ends, we provide an in-depth historical overview of the Dodo, the Solitaire, and the family-group nomina based upon them. We also establish a new nomen to unite both species: †Raphina.
Terminology and nomenclatural background
Before starting our historical overview, it is worth stating that the current rules of zoological nomenclatural are ‘relatively’ recent and have evolved from prior rules/suggestions made during the 19th century. We wish this to be clear from the outset, in order that readers will not mistake our comments hereafter as undue criticisms of past workers. There have also been dramatic shifts in both systematics (the paradigms and methods used to hypothesize clades) and nomenclature (the establishment of names for said clades, and the rules governing those names) between the 18th and 21st centuries. During the 18th and 19th centuries, the rules and norms of zoological nomenclature were being developed (e.g. Linnaeus 1758, Kirby 1815, Westwood 1836, 1837a, 1837.1b, Strickland 1837.2, 1878, Strickland et al. 1843, Dall 1878.1, Société Zoologique de France 1881, Douvillé 1882, American Ornithologists’ Union 1886, Blanchard 1889, Bütschli et al. 1893), prior to their widespread formulation and promulgation during the 20th century (ICZN 1905, 1961, 1964, 1985, 1999). Moreover, the paradigms used to hypothesize taxa were distinctly different, with the transition from a pre-evolutionary paradigm to an acceptance of paraphyletic groupings and groups united based on shared similarity, which then shifted to our current paradigm based on shared common ancestry and monophyletic groups (for a general overview of thought, see Mayr 1942, 1965, 1982, Hennig 1966, Nelson 1973, de Queiroz 1988, Mishler 2009.2; and for some clade-specific examples, see Allard et al. 1999.1, Dornburg and Near 2021, Cotterill et al. 2014 and the references therein).
The current International Code of Zoological Nomenclature (the Fourth Edition, ICZN 1999, 2003, 2012.1, 2016.3; ‘Zoological Code’ hereafter) is a direct descendent of ‘Blanchard’s Code’ (Blanchard 1889) via the Règles Internationales de la Nomenclature Zoologique [International Rules of Zoological Nomenclature] (ICZN 1905). Raphaël Blanchard, the ‘father of International Zoological Nomenclature’ (Bock 1994: 33), was the Chair of the nomenclatural committee of the International Congress of Zoology, the first President of the International Committee on Zoological Nomenclature, and the Editor of the French edition of the Règles Internationales. For the first International Congress of Zoology, he wrote an overview of zoological nomenclature and outlined what he believed would be an acceptable set of rules for the international corpus of zoologists (‘Blanchard’s Code’; Blanchard 1889). ‘Blanchard’s Code’ did not exist in a vacuum, because a plethora of nomenclatural codes for zoology had been proposed during the 19th century, with the earliest comprehensive code being proposed by the British Association for the Advancement of Science (‘Strickland’s Code’).
‘Strickland’s Code’ (Strickland et al. 1843) was formulated by a committee of British zoologists and palaeontologists (including famous individuals, such as Charles Darwin and Richard Owen, in addition to Hugh Strickland, who was pivotal in our understanding of the Dodo and the Solitaire), who set down many of the norms we recognize today; norms of the so-called ‘Linnean’ system of nomenclature, although this is perhaps more accurately called ‘Linnean–Westwoodian–Stricklandian’ nomenclature (sensuDubois 2011: 4–5). However, there were some important differences between ‘Strickland’s Code’ and the current Zoological Code (ICZN 1999), such as the proposed ‘start date’ for zoological nomenclature, which in ‘Strickland’s Code’ was 1766, beginning with the publication of the 12th edition of Systema Naturæ (Linnaeus 1766). The ensuing controversy over the ‘start date’ for zoological nomenclature cost ‘Strickland’s Code’ support amongst zoologists (Linsley and Usinger 1959: 41), with Dall (1878.1: 15) noting that the starting point used by the British Association had begun ‘admitting to recognition some ichthyological works printed between the dates of the tenth and twelfth editions [of Systema Naturæ]’. Other national societies began proposing their own nomenclatural codes, including the American Association for the Advancement of Science (Dall 1878.1), the Société Zoologique de France (Société Zoologique de France 1881), the American Ornithologists’ Union (American Ornithologists’ Union 1886), and the Deutsche Zoologische Gesellschaft (Bütschli et al. 1893), as did the Congrès international de géologie [International Congress of Geology] (Douvillé 1882). It was ‘Blanchard’s Code’ (Blanchard 1889) and the subsequent Règles Internationales (ICZN 1905) that would begin to bring international stability to zoological nomenclature (for further details, see Linsley and Usinger 1959, Bock 1994).
Zoological nomenclature of the 18th and early 19th centuries did not adhere to the quasi-legal system in place today. The renaming of pre-existing genera and specific epithets was commonplace (particularly up to the 1840s–1850s). Therefore, readers should not be surprised that the principal of priority with regard to nominal authority was not adhered to in Dodo nomenclature during this time period or that the formulation of names does not meet the requirements on the Zoological Code as we understand it today (ICZN 1999). It is also worth noting that when the Dodo and Solitaire were first named (Linnaeus 1766, Gmelin 1789), the concept of nomenclatural types did not exist. Witteveen (2016.4: 156) credited Westwood (1837a) as the originator of this concept, which then became incorporated into ‘Strickland’s Code’ (and subsequent nomenclatural codes). As such, type specimens were not designated for the Dodo or the Solitaire.
Before continuing, we also need to define the terminology we will be using. We will follow the suggestions and recommendations of Dubois and Fitzhugh. Dubois (2021.1: 39) noted that, ‘the term taxonomy is traditionally used in two distinct senses, to designate either a scientific discipline, or any scientific classification of organisms produced by this discipline and adopted as valid by taxonomists’. In order to distinguish between both meanings, Dubois (2005: 406) erected the term ergotaxonomy for the latter (‘classification used by a given author in a given work’, Dubois 2006.1: 250). To remove any ambiguity, we use the term ergotaxonomy to refer to any ‘taxonomic framework’ considered valid by their proposer.
We will use the term ‘systematics’ rather than ‘taxonomy’ throughout. There is disagreement within the field of evolutionary biology regarding whether taxonomy and systematics are different subfields (e.g. Simpson 1961.1, Wiley and Lieberman 2011.1), whether taxonomy is a subdiscipline within systematics (e.g. Michener et al. 1970, Dubois 2006.1, Pavlinov 2013.1, Winsor 2023 and the references therein), or whether systematics is a subfield of taxonomy (e.g. Toepfer 2011.2). However, others, such as Mayr and Ashlock (1991) and Fitzhugh (2008), have proposed that taxonomy is a synonym of systematics. We will follow Fitzhugh (2008: 54) and use the term ‘systematics’ throughout.
We also use the term ‘systematization’ in preference to ‘classification’ following Fitzhugh (2008). Fitzhugh (2008: 54) defined classification as the ‘segregation of objects into classes based on specified properties’, whereas systematization is ‘the organization of observations into a system of concepts, in the form of hypotheses, according to theory’ (the definitions of these terms given by de Queiroz 1988: 241 was similar). We consider the latter to be the best description of systematics, because both species and ‘higher-level’ clades are explanatory hypotheses rather than objects (e.g. see Fitzhugh 2005.1, 2008, Mortimer et al. 2021.2).
Herein, we follow ornithological convention and capitalize English vernacular names of species (Parkes 1978; and the International Ornithological Committee World Bird List v.13.2; https://www.worldbirdnames.org/english-names/spelling-rules/). Moreover, we use the English vernacular names for columbid species that appear in the International Ornithological Committee World Bird List v.13.2 (https://www.worldbirdnames.org/new/bow/pigeons/), but with the following exceptions: (i) Didunculus strigirostris (Jardine, 1845) is referred to as the Samoan Tooth-billed Pigeon, because another species (†Didunculus placopedetesSteadman, 2006.2) was present throughout the islands that constitute the Kingdom of Tonga until ~2850 years ago (Steadman 2006.2; Worthy and Burley 2020) and was also present on Efate Island, Vanuatu (Worthy et al. 2015.4); and (ii) we generally refer to †Pezophaps solitaria as the Solitaire rather than the Rodrigues Solitaire, in order that it is consistent with the use of ‘the Dodo’ for †Raphus cucullatus (i.e. not using Mauritian Dodo). We follow Dubois (2000: 39) in using the term nomen (plural nomina) for any ‘scientific name’ that is formulated in compliance with a nomenclatural code, which, in this case, is the Zoological Code (ICZN 1999, 2003, 2012.2, 2016.5).
Our open nomenclature and synonymy lists follow the recommendations of Richter (1948) (see: Matthews 1973.1, who outlined them in English, and Becker 2001, who gave a recent overview in German), Sigovini et al. (2016.6), and Horton et al. (2021.3). Finally, we use the dagger (†) symbol in front of nomenclatural nomina that denote extinct taxa (except when they appear in quotations).
The dodo was named before biologists understood about evolution and believed species were created without ancestors, so the idea of a systematic nomenclature which reflected the evolutionary relationships between species had not occurred to them, so the dodo and its close relative, the Rodriguez Island Solitaire, were given different family names. This new study proposes a new family name, Raphina, for both species which reflects their evolutionary relationship and puts them in their correct position in the evolutionary tree of the pigeons and doves (the columbids) based on a DNA analysis.
The fact that human agency could drive a species to extinction was a shock to the early biologists who subscribed to the 'creation' mythos and assumed that what God had created mankind would be unable to destroy. We now know that both parts of the superstition were wrong and disastrously so. Not only are species the product of their environment but can be destroyed simply by changing that environment. There is no god playing any part in the process and least of all protecting its 'creation'.
This realisation made the Oxford dodo an object of fascination especially for academics like Do-Do-Dodgson who saw in it a metaphor for revealed wisdom about the nature of reality and the difference between it and human expectations, based on religious mythology.
Creationists might find it distressing to read how modern taxonomy has been revised to reflect the modern evolutionary synthesis, recognising that species can be arranged in clades and family trees based on how they evolved and diversified from common ancestors which themselves were the result of diversification from earlier common ancestors. They will probably find it distressing too how a DNA analysis of an extinct species like the dodo is confirming that view of the origins of biodiversity and no sign of that impending abandonment of the Theory of Evolution that their cult leaders have been assuring them is about to happen, any day now, real soon.
The Solanaceae is a large family of plants which includes potatoes, tomatoes, aubergines and peppers/capsicums, and some highly poisonous plants such as deadly nightshade and thornapple. Some of them are economically and nutritionally important food crops.
A feature of the family is the high level of toxicity of most parts of the plants, even important crops like potatoes, all parts of which, apart from the tubers, are highly poisonous, even the small green tomato-like fruits. Similarly, all parts of the closely related tomato plant, apart from the fruits, are highly toxic.
What can you tell me about the Solanaceae and the time-scale of their evolution?
The Solanaceae, commonly known as the nightshade family, is a diverse and economically significant family of flowering plants. This family includes well-known species such as tomatoes, potatoes, eggplants, bell peppers, and tobacco. Understanding the evolution and diversification of the Solanaceae involves looking at their origin, diversification events, and the adaptive radiation that led to the variety of species we see today.
Evolutionary Origin and Timeline
Early Origins: The Solanaceae family is believed to have originated during the late Cretaceous period, around 80-90 million years ago (mya). This timing is based on molecular clock estimates and fossil records.
Diversification: Significant diversification within the family occurred during the Paleocene and Eocene epochs (about 66-34 mya), likely driven by climatic changes and the availability of new ecological niches.
Key Evolutionary Events
Initial Diversification: The early diversification of Solanaceae likely took place in South America, which is considered the primary center of origin for the family. The varied climates and geographies of this region provided multiple ecological niches.
Dispersal and Adaptation: As members of the Solanaceae spread to different parts of the world, they adapted to a wide range of environments. This includes the arid regions of Australia and the temperate climates of North America and Europe.
Radiation of Major Genera: Key genera within the family, such as Solanum (which includes tomatoes and potatoes), diversified significantly during the Miocene epoch (23-5 mya). This period was marked by further climatic changes that created new habitats.
Morphological and Genetic Diversification
Morphological Adaptations: Solanaceae species exhibit a wide range of growth forms, from herbaceous plants to shrubs and small trees. They have also developed various fruit types, including berries, capsules, and drupes.
Genetic Studies: Advances in molecular genetics have provided insights into the evolutionary relationships within the family. Phylogenetic studies based on DNA sequencing have helped clarify the lineage and divergence times of different genera and species.
Ecological and Economic Importance
Agricultural Significance: Many Solanaceae species are essential crops with significant agricultural value. Tomatoes, potatoes, and peppers are staple foods in many cultures.
Medicinal and Toxic Properties: Some members of the Solanaceae family produce alkaloids that have medicinal properties, such as atropine and scopolamine, used in various treatments. However, some species are also toxic and have been used historically as poisons.
Evolutionary Challenges and Research Directions
Hybridization and Polyploidy: Hybridization and polyploidy (having multiple sets of chromosomes) have played a role in the evolution of some Solanaceae species, contributing to their genetic diversity.
Conservation and Study: Preserving the genetic diversity of wild Solanaceae species is important for both conservation and potential agricultural benefits. Continued research on their genetics and evolutionary history can provide valuable insights into plant evolution and adaptation.
In summary, the Solanaceae family has a rich evolutionary history that spans tens of millions of years. Its members have adapted to a wide range of ecological niches, leading to the diverse array of species we see today. This evolutionary journey has been shaped by climatic changes, geographical dispersal, and genetic diversification.
Which species are the result of hybridization and/or polyploidy?
Hybridization and polyploidy have played significant roles in the evolution of many species within the Solanaceae family. Here are some notable examples:
Hybridization
Hybridization has contributed to the genetic diversity and speciation within the Solanaceae family. Some examples include:
Tomato (Solanum lycopersicum):
The cultivated tomato (Solanum lycopersicum) has undergone hybridization with wild relatives, leading to the development of various cultivars with different desirable traits such as disease resistance, fruit size, and flavor.
Wild species such as Solanum pimpinellifolium and Solanum cheesmaniae have contributed genetic material to cultivated tomatoes through both natural hybridization and intentional breeding.
Potato (Solanum tuberosum):
The cultivated potato (Solanum tuberosum) is a complex hybrid species. It has hybridized with various wild potato species, such as Solanum demissum and Solanum acaule, which have contributed to its genetic makeup and provided resistance to diseases like late blight.
Pepper (Capsicum species):
Hybridization among different Capsicum species has been common in the cultivation of peppers. For instance, Capsicum annuum (bell pepper, chili pepper) has hybridized with other species such as Capsicum frutescens and Capsicum chinense to produce new varieties with different heat levels and flavors.
Polyploidy
Polyploidy has been an important mechanism in the evolution of certain Solanaceae species. Polyploid species often exhibit greater genetic diversity and adaptability.
Potato (Solanum tuberosum):
The cultivated potato is a tetraploid species (4 sets of chromosomes, 2n = 4x = 48), resulting from the polyploidization of diploid ancestors. This polyploid nature has contributed to its genetic complexity and adaptability.
Tobacco (Nicotiana tabacum):
Nicotiana tabacum, the species used for commercial tobacco, is an allotetraploid (4 sets of chromosomes, 2n = 4x = 48). It originated from the hybridization of two diploid species, Nicotiana sylvestris and Nicotiana tomentosiformis, followed by chromosome doubling.
Wild Potatoes:
Several wild potato species are polyploids. For example, Solanum demissum is a hexaploid species (6 sets of chromosomes, 2n = 6x = 72), and it has been used in breeding programs to introduce disease resistance genes into cultivated potatoes.
Importance of Hybridization and Polyploidy
Genetic Diversity: Both hybridization and polyploidy contribute to genetic diversity, providing a broader range of traits that can be selected for in breeding programs.
Adaptability: Polyploid species often have greater genetic variability, which can enhance their adaptability to different environmental conditions and stresses.
Crop Improvement: Understanding the genetic contributions from hybridization and polyploidy is crucial for crop improvement efforts, allowing for the development of new varieties with desirable traits such as increased yield, disease resistance, and improved nutritional content.
Overall, hybridization and polyploidy have been vital in shaping the evolution and diversity of the Solanaceae family, leading to the development of many economically important species and cultivars.
Now researchers at Penn State University, have produced a new evolutionary tree of the family which explains how the fruits of the plants evolved their size and colour together and that fruit-eating animals were probably not the main drivers of their evolution, as was previously thought.
The team have just published their findings, open access, in the journal New Phytologist. It is explained in the press release from Penn State:
Fruits of Solanum plants, a group in the nightshade family, are incredibly diverse, ranging from sizable red tomatoes and purple eggplants to the poisonous green berries on potato plants. A new and improved family tree of this group, produced by an international team led by researchers at Penn State, helps explain the striking diversity of fruit colors and sizes and how they might have evolved.
The team found that the size and color of fruits evolved together and that fruit-eating animals were like not the primary drivers of the fruits’ evolution, as had been previously thought. The study, published in the journal New Phytologist, may also provide insight into breeding agriculturally important plants with more desirable traits, the researchers said.
“There are about 1,300 species in the genus Solanum, making it one of the most diverse plant genera in the world,” said João Vitor Messeder, graduate student in ecology and biology in the Penn State Eberly College of Science and Huck Institutes for the Life Sciences and lead author of the paper. “Since the 1970s and ‘80s, researchers have suggested that birds, bats and other fruit-eating animals have driven the evolution of fruits like those in Solanum. However, the importance of the evolutionary history of the plants has been underestimated or rarely considered when evaluating the diversification of fleshy fruits. To better test this hypothesis, we needed first to produce a more robust phylogeny, or family tree, of this plant group to improve our understanding of the relationships between species.”
Plants in the genus Solanum produce fruits with a wide variety of sizes, colors and nutritional values. They can appear black, purple, red, green, yellow or orange and range in size from less than a quarter of an inch to as much as 8 inches, or 0.5 to 20 centimeters. In addition to agriculturally important plants, some plants in the group are cultivated for their ornamental flowers, and the fruits of many of these plants are eaten by humans and a large diversity of animals, including birds, bats, reptiles, primates and other land mammals.
The researchers collected samples of plants from across the world, including wild plants from Brazil, Peru and Puerto Rico and plants from botanical gardens, and sequenced their genes from RNA. They supplemented with previously collected samples and publicly available data, ultimately comparing the sequences of 1,786 genes from a total of 247 species to reconstruct the Solanum family tree. This included representatives from all 10 of the major clades — the branches of the tree — and 39 of 47 minor clades within the genus.
“By using thousands of genes shared among species that effectively represented the entire genus, we significantly improved the Solanum family tree, making it the most comprehensive to date,” said Messeder, who conducted the research in the lab of Hong Ma, Huck Chair in Plant Reproductive Development and Evolution and professor of biology at Penn State and a co-corresponding author of the paper. “Recent advances in technology allowed us to use more genes than previous studies, which faced many challenges in resolving relationships between species and clades. This improved tree helps us understand when different fruit colors and sizes originated or how they changed as new plant species came about.”
The researchers added considerable resolution of the smaller branches in the group that includes potatoes and tomatoes, as well as their closely and more distantly related wild species. The insights gained, the researchers said, could support crop improvement programs for these species and other crops in the genus.
“If the closest wild relatives of important agricultural crops have desirable traits, it is possible to breed crops with those species or borrow their genes, for example to improve resistance to temperature or pests or to produce larger fruits or fruits of a certain color,” Messeder said.
The researchers found that the color and size of Solanum fruits was fairly conserved over evolutionary history, meaning that closely related species tend to have similar fruits. The evolution of fruit color and size is also correlated, with changes in one trait often corresponding to changes in the other, leading fruits of certain colors to be bigger than fruits of other colors.
“These results suggest that physiological and molecular mechanisms may play a role in keeping the evolution of fruit color and size tied together,” Messeder said. “While frugivores — or animals that primarily eat fruit — and seed dispersers may influence diversification, we need to consider all of the possibilities when studying how fruits became so diverse.”
The researchers also clarified the origin and diversification timeline of this genus, in part by including recent information from the oldest nightshade family fossil — from a different genus in the Nightshade family whose fossil was dated to about 52 million years ago — and from particular genes that improved estimates of the length of evolutionary branches. The researchers dated the origin of Solanum to about 53.1 million years ago — a full 30 million years earlier than prior estimates that were based on genes from other parts of the plant cell. This paints a new picture of the environment that might have shaped how these plants diversified into new groups and species.
“The Earth’s environment changed dramatically during the 30 million years in terms of temperature, carbon dioxide in the atmosphere, geography and animal diversity,” Messeder said. “Now that we know when Solanum and its subgroups originated, we can think about the conditions that might have promoted the diversification of that group, as well as how other organisms might have played a role.”
The team found that the earliest members of Solanum had medium-sized berries that remained green when ripe, and that green and yellow fruits of this group became more diverse around 14 million years ago. The researchers speculated that bats might have played a role in this diversification, given their similar evolutionary timeline and that they are the primary dispersers of modern green and yellow Solanum fruits. As new bat species arose and expanded where they were living during this time, they ate Solanum fruits and carried their seeds to new environments.
Next, the researchers plan to explore how modern interactions between animals and the fruit they eat may shed light on the evolution of both groups as well as explore the evolution of certain genes relevant to fruit color and size.
In addition to Messeder and Ma, the research team includes Tomás Carlo, professor of biology at Penn State; Guojin Zhang, postdoctoral researcher at Penn State at the time of the research; Juan David Tovar at the National Institute of Amazonian Research in Brazil; César Arana at the National University of San Marcos in Peru; and Jie Huang and Chien-Hsun Huang at Fudan University in China.
Summary
Mutualisms between plants and fruit-eating animals were key to the radiation of angiosperms. Still, phylogenetic uncertainties limit our understanding of fleshy-fruit evolution, as in the case of Solanum, a genus with remarkable fleshy-fruit diversity, but with unresolved phylogenetic relationships.
We used 1786 nuclear genes from 247 species, including 122 newly generated transcriptomes/genomes, to reconstruct the Solanum phylogeny and examine the tempo and mode of the evolution of fruit color and size.
Our analysis resolved the backbone phylogeny of Solanum, providing high support for its clades. Our results pushed back the origin of Solanum to 53.1 million years ago (Ma), with most major clades diverging between 35 and 27 Ma. Evolution of Solanum fruit color and size revealed high levels of trait conservatism, where medium-sized berries that remain green when ripe are the likely ancestral form. Our analyses revealed that fruit size and color are evolutionary correlated, where dull-colored fruits are two times larger than black/purple and red fruits.
We conclude that the strong phylogenetic conservatism shown in the color and size of Solanum fruits could limit the influences of fruit-eating animals on fleshy-fruit evolution. Our findings highlight the importance of phylogenetic constraints on the diversification of fleshy-fruit functional traits.
Introduction
The fleshy fruits of angiosperms are key innovations that mediate mutualistic seed dispersal by fruit-eating animals (i.e. frugivores) (Eriksson, 2016). This plant–animal interdependence is central to the development and organization of terrestrial communities (Bascompte & Jordano, 2007; Fleming & Kress, 2013). By encapsulating seeds within nutritious pulp, plants take advantage of foraging animals to effectively disseminate their seeds (Schupp et al., 2010). Thus, frugivores can increase plant fitness, and drive the evolution of fruit types (e.g. fleshy fruits) and fleshy-fruit traits (e.g. color) (Lomáscolo et al., 2010.1; Eriksson, 2016; Xiang et al., 2024). Still, it remains unclear how shared evolutionary history influences the evolution of the functional traits of fleshy fruits among related species. Specifically, to examine how frugivores may affect the evolution of fruit traits, it is crucial to assess whether a trait is conserved and has evolved a few or multiple times within a lineage (Ackerly, 2009).
Differences in fruit traits such as size and color when ripe have been interpreted as adaptations to different types of frugivores (Van Der Pijl, 1982; Valenta & Nevo, 2020). For example, birds typically feed on small brightly colored fruits given their highly developed color vision and narrow bill gapes (Janson, 1983; Wheelwright, 1985; Wheelwright & Janson, 1985.1). In comparison with birds, mammals have more limited color vision but highly developed olfaction, teeth, and forelimbs that aid in the manipulation and use of fruits that are large, tough, dull-colored, and odoriferous (Janson, 1983; Nevo et al., 2018). Such trait-matching suggests that frugivores could drive the evolution of fruit traits through natural selection (i.e. dispersal syndrome hypothesis) (Van Der Pijl, 1982; Janson, 1983; Valenta & Nevo, 2020). For instance, fruit traits of figs (Ficus spp., Moraceae) converge to small brightly colored fruits when birds are the main frugivores, or to larger dull-colored fruits when bats and other mammals are the main frugivores (Lomáscolo et al., 2008, 2010.1). Similarly, other phylogenetic comparative studies have also suggested that frugivores are the main drivers shaping fruit characteristics that lead to general ‘syndromes’ that match distinct frugivore groups (Valenta et al., 2018.1; Nevo et al., 2018; do Nascimento et al., 2020.1; Barnett et al., 2023a,2023.1b). It is expected that when selective pressures from frugivores are convergent, the characteristics of fleshy fruits might be less predictable by phylogenetic relationships (Ackerly, 2009; Valenta & Nevo, 2020).
Although the dispersal syndrome hypothesis offers a compelling explanation for fruit trait diversity rooted in selection theory and adaptation, the evidence remains inconclusive (Valenta & Nevo, 2020). This is because many plant species can be effectively dispersed by animals with distinct morphologies and physiologies, leading to diffuse selective pressures that may preclude adaptation to specific frugivores (Herrera, 1985.2). Furthermore, fruit traits may be phylogenetically determined, limiting the selective pressures from frugivores on fruit trait evolution (Fischer & Chapman, 1993; Jordano, 1995; Ackerly, 2009). In such cases, trait matching is more likely the result of ecological fitting (i.e. pre-existing traits fitting new ecological niches without further modification) rather than the evolution of new traits due to selection (Janzen, 1985.3; Agosta & Klemens, 2008.1). Thus, how much fruit traits are the result of adaptations or of phylogenetic constraints and ecological fitting remains unclear. Advance in this field has been constrained by the use of limited phylogenetic frameworks, poorly resolved phylogenies, and additional challenges posed by hybridization and introgression events among species (e.g. Gardner et al., 2023.2).
Recent studies merging phylogenetics and trait evolution have provided important insights into fleshy-fruit evolution. Fleshy fruits have independently evolved multiple times across angiosperms (Xiang et al., 2017, 2024; Frost et al., 2021; Hilgenhof et al., 2023.3). Studies have shown that fruit color can be associated with long-distance dispersal patterns (Lu et al., 2019) and diversification rates (Spriggs et al., 2015; Lu et al., 2019; L. Zhang et al., 2023.4). Fruit developmental processes have been identified as a mechanism underlying the origin of syndromes (Sinnott-Armstrong et al., 2020.2). Still, in-depth studies assessing the role of shared evolutionary histories on fruit trait evolution remain scarce, especially within highly diverse plant groups.
The genus Solanum L. comprises c. 1300 fleshy-fruited species and is the largest genera of Solanaceae and the second largest genus of fleshy-fruited plants (Frodin, 2004). Regarding fruit traits, Solanum shows a remarkably high diversity, producing berries of various sizes, colors, and pulp with different nutritional and chemical profiles (Cipollini et al., 2002; Knapp et al., 2004.1; Hilgenhof et al., 2023.3). For instance, berry size ranges between 0.5 and 20.0 cm, ripening in many colors, including black, purple, red, green, yellow, and orange. Additionally, Solanum fruits with different colors and sizes are eaten and dispersed by distinct animal groups, including reptiles, birds, bats, primates, and terrestrial mammals (Symon, 1979; Cáceres & Moura, 2003; Arruda Bueno & Motta-Junior, 2004.2; Vasconcellos-Neto et al., 2009.1; Jacomassa & Pizo, 2010.2). This unusual fruit diversity within a single genus makes Solanum an excellent group to investigate a wide range of eco-evolutionary questions (Knapp et al., 2004.1; Moyle, 2008.2). Furthermore, humans have cultivated and domesticated many Solanum species, such as the potato (S. tuberosum), tomato (S. lycopersicum), eggplant (S. melongena), and others (S. betaceum, S. muricatum, and S. quitoense), contributing to the global agriculture (Knapp et al., 2004.1). However, uncertainties in the phylogeny of Solanum limit our understanding of the evolution and diversification patterns of fruit traits relevant to plant–frugivore interactions and agriculture. Unclear phylogenetic relationships make it challenging to determine the ancestral form of a trait and track the number of times and the direction of transitions of the fruit trait over time. Furthermore, assessing the lability of a trait may facilitate its manipulation for agriculture.
Previous studies have made significant progress toward reconstructing the evolutionary history of Solanum (Weese & Bohs, 2007.1; Särkinen et al., 2013.1; Gagnon et al., 2022; Huang et al., 2023.5), with the identification of three deep lineages (we adopted the informal clade nomenclature proposed in previous molecular phylogenetic studies – Bohs, 2005; Stern et al., 2011; Särkinen et al., 2013.1; Tepe et al., 2016.1; Gagnon et al., 2022). The Thelopodium Clade, comprising three species, diverges first, while the remaining species are divided into Clades I and II. Clade I contains c. 350 species, including tomato and potato, whereas Clade II, with c. 900 species, has many spiny shrubs, including eggplant. Clades I and II were further subdivided into nine major and 47 minor clades (Särkinen et al., 2013.1). However, the placement of many clades is inconsistent among studies using various taxa and genes (Särkinen et al., 2013.1; Gagnon et al., 2022; Huang et al., 2023.5) (Supporting Information Fig. S1). Recently, a comprehensive phylogenetic study of 742 Solanum species still found major clades with unresolved relationships (Fig. S1) (Gagnon et al., 2022). For example, the monophyly of Clade I was supported by some analyses using plastid sequences (Fig. S1a–c) but not others using nuclear genes (Fig. S1d,e), and placement of its major clades – especially Regmandra – was uncertain (Fig. S1c–e). These inconsistencies have been described as polytomies near the crown node and reflect difficulties for resolving the deep Solanum relationships (Gagnon et al., 2022). Another recent study (Huang et al., 2023.5) using 1699 genes from 81 Solanum species, along with other members of Solanaceae, presented a well-supported phylogeny, but lacked the Thelopodium Clade and some major clades in Clades I and II, including Regmandra (Fig. S1f–k) and many minor clades. Consequently, a Solanum phylogeny with a more complete lineage representation and well-supported relationships is needed to further understand the ecological factors that shape its evolution, including the drivers behind its remarkable diversity of fruit sizes, shapes, and colors.
Here, we bridge the gap between ecology and phylogenomics using Solanum as study group to examine the tempo and mode of the evolution of fruit traits that are both agriculturally relevant and mediate frugivory and seed dispersal interactions. We used 1786 low-copy nuclear genes across 247 species to reconstruct a highly resolved Solanum phylogeny. We explored the temporal aspects of Solanum's evolutionary history and investigated the phylogenetic effects on the diversification patterns of two important fruit functional traits: size and color when ripe. We evaluated how evolutionarily constrained are fruit size and color in Solanum and discussed implications for the ecology and evolution of seed dispersal mutualisms.
Fig. 2
Divergence time estimation for Solanum indicating its origin in early Eocene and divergence among extant species starting in the middle Eocene. Relevant estimated divergence times of major clade lineages are marked at corresponding nodes. Branch colors match major clade colors of Fig. 1, with their respective names on the right side. Fruit colors and sizes are mapped on terminal tips. At the bottom of the chronogram, geological timescale is shown with periods delimited by vertical lines, the estimated temperature variation for the Cenozoic, and arrows indicating the Mid-Eocene Climatic Optimum and Mid-Miocene Climatic Optimum. Eo, Eocene; LC, late Cretaceous; Mio, Miocene; Ol, Oligocene; Pal, Paleocene; Pli, Pliocene; Q, Quaternary. On the right side, pictures demonstrate some of the variety of colors, sizes, and shapes that can be found in Solanum fruits. Pictures were taken by the authors or downloaded from the internet (Supporting Information Table S6). (Detailed divergence times with species names are shown in Figs S6, S7).
Of special concern for creationists, is not the technical details, which few would understand even if they read it, but the timeline and the fact that the scientists show no hint of giving up on the Theory of Evolution but instead, use it to explain their findings, with no hint that a magic supernatural entity intervened anywhere in the divergence process.
Additionally, the Introduction section contains links to lots of references to papers dealing with the same or related subjects. None of them show any signs of adopting creationism because the TOE isn't up to the task, either.
The entire range of Solanum species, including many important foods, is the result of evolution, with new genetic information being created by the natural processes of gene and whole genome duplication to give polyploidy, and hybridization. The potatoes, tomatoes, peppers, chilis and aubergines we eat contain evidence of evolution in their genomes.
Many of these plants are the product of cultivation and human selective breeding of course, so creationists might like to explain why plants, like domestic animals, which are the descendants of species the Bible says were created for humankind, have had to be improved to make them fit for purpose. Did their designer not know what humans would need, or did the authors of the Bible not understand about domestication, cultivation and selective breeding to improve on the wild type?
In case any creationists are still under the delusion that mainstream biologists are abandoning the scientific Theory of Evolution (TOE) in favour of their childish magical story involving a magic man made of nothing who magicked everything into existence out of nothing with some magic words, here is an example of how the TOE is used to understand and make sense of the observable facts.
It addresses the question of how the ability to learn and imitate sounds evolved in birds.
Basically, ornithologists had thought that birds could be divided into two groups - those which can learn sounds (parrots, songbirds, and hummingbirds) and those which can’t - and that this ability in the former group had evolved sometime after modern birds had diversified from their avian dinosaur ancestors, but the fact that a small New Zealand bird, the titipounamu or rifleman, Acanthisitta chloris, has the rudiments of this ability suggests it may have been present in the common ancestor of both groups.
In other words, the ability to learn and imitate sounds may be evidence of common descent.
In an evolutionary picture that resembles that of humans, giraffes appear to have speciated, or partially speciates at different times and in different parts of their range, then hybridized, before splitting again with regular gene-flow between the groups.
Similarly, though over a greater range, humans seems to have partially speciated into isolated populations in Africa before coming together again and spreading to Eurasia as Homo erectus which then split into Neanderthals, Denisovans and possibly others before meeting up with H. sapiens coming out of Africa in a second wave, to interbreed with the Eurasian species. The result is genetically distinct populations with evidence of ancient hybridization and gene flow.
Because conservation efforts tend to be directed at the species level, it is important for giraffe conservation to determine whether there is a single pan-African species with local sub-species or whether there are four or more species, each with a smaller population and therefore more vulnerable to habitat destruction and extinction.
To try to resolve this issue, as part of the African Wildlife Genomics research framework led by research groups at the Department of Biology at the University of Copenhagen, scientist carried out an extensive genome analysis to establish whether the different populations have been genetically isolated for long enough to be regarded as distinct species, even though, in captivity, they freely interbreed.
The results were a little surprising but highlight the difficulty in determining whether speciation has occurred within a population where differentiation is still in progress and few barriers to hybridisation have arisen. The problem is compounded by the fact that there is not a fixed definition of species, although biologists understand what the term means in a given context.
I've previously written blog posts about this problem, using the Eurasian crows as an example - an article incidentally which was recommended reading for Scottish biology students doing their 'Highers'.
The researchers have published their findings open access in the online Cell Press journal, Current Biology and explain it in a news item from the University of Copenhagen Biology Department:
A great deal is understood about how the many different varieties of domestic pigeon were produced ever since Charles Darwin used them to illustrate the role of selection in evolution. In this case, selection is human selection rather than natural selection, although the difference is a matter of semantics if you regard human selective breeders as part of the domestic pigeon's environment.
Incidentally, creationists should note that Darwin never claimed evolution always resulted in new species. As he showed with his selective breeding examples, it produced new varieties too. Some of these have become so far removed from their wild ancestors that they rank as subspecies, like the domestic pigeon, Columba livia domestica
Although the radiation of domestic varieties is now well understood, the wild ancestors, the rock doves, have received far less attention until now. Now a paper by a team led by Germán Hernández-Alonso of the Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark, redresses that discrepancy by analysing the entire genomes of 65 historical rock doves that represent all currently recognized subspecies and span the species’ original geographic distribution. 3 of these specimens were from Charles Darwin's collection.
This works shows that rock doves have diversified into a number of subspecies across their range, stemming from a subspecies now restricted to a small coastal strip of Northwest Africa, C. livia gymnocyclus. One of these subspecies received a substantial ingression of genes from a related species, C. rupestris after it split from the West African population but before it became domesticated. The result is that C. livia gymnocyclus should now probably rank as a species in its own right, C. gymnocyclus.
First a little about the evolution of domestic pigeons:
