How Science Works - Giraffes - A single Pan-African Species Or Several Distinct Species?

Giraffe trio crossing plain, Etosha, Namibia

Photo: Mogens Trolle

Reticulated giraffe, Buffalo Springs, Kenya. Photo: Mogens Trolle

Photo: Mogens Trolle

Gene flow in giraffes and what it means for their conservation – Department of Biology - University of Copenhagen

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:

Creationism in Crisis - Evolution of Rock Doves & Domestic Pigeons

Rock dove, Colmba livia neglecta (Iran)

Picture: Γεωργός via Wikimedia (CC BY-SA 4.0)

Rock dove, Columba livia.
The wild ancestor of the domestic or town pigeon

Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences | Molecular Biology and Evolution | Oxford Academic

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:

Malevolent Designer News - 16 More Nasties For Devotees of the Divine Sadist To Enjoy

Figure 1.16 new species of endoparasitic wasps have been added to the group, Loboscelidia, based on their unique physical characteristics. Scale bar = 0.5 mmc

Credit: Yu Hisasue et al. (2023)
European Journal of Taxonomy

Male wasp of the Loboscelidia genus, a relative of the 16 newly-described Vietnamese species or endoparasitic wasps.

16 strange new parasitoid wasp species discovered in Vietnam | Research Results | KYUSHU UNIVERSITY

Creationist devotees of the divine sadist whom they believe creates all the parasites that increase the suffering in the world, will be thrilled to learn that 16 more endoparasitic wasps have been discovered.

These are all endoparasitic on other insects and lay their eggs inside their victims' eggs where their grubs can then consume the growing embryo. Their strange appearance is thought to be because they have evolved from a myrmecophilous species that mimicked the appearance or ants.

All these were discovered in Vietnam by entomologists from Kyushu University, Japan, and Vietnam’s National Museum of Nature. Their discovery is described in a Kyushu University news release:

Creationism in Crisis - Scientists Have Shown How Mosquitoes Evolved in Another Casual Refutation of Creationism With Facts

Researchers scoured academic literature and used new genomic techniques to create the mosquito family tree.

Photo credit: Matt Bertone, NC State University.

Aedes eagypti

Anopheles stephensi

Anopheles albimanus

Ochlerotatus notoscriptus

Study Elucidates Evolution of Mosquitoes and Their Hosts | NC State News

It's proving to be another terrible week for the creation cult with yet another science paper that casually, and without any intention on the part of the authors, utterly refutes some basic creationist cult dogmas.

This paper deal with the evolution of the mosquitoes and the parasite-host relationship that refute intelligent design ideas with their arms races, needless complexity and prolific waste, in addition to their refutation of the notion of an omnibenevolent designer.

And of course, as we've come to expect, almost all that evolutionary history occurred millions of years before creationists think the Universe was magically created out of nothing by a magic man made of nothing who popped up from nowhere, in the days when nothing was something that existed. This magic, invisible man then allegedly created every living thing without ancestors, pretty much as we find it today, but on a flat Earth with a dome over it to keep the water above the sky out. Seriously!

The point has already been made by others many times before: creationism is not a problem for science; science is a problem for creationism; and this paper is just one more drop in the tsunami engulfing the cult.

First, a little AI background on mosquitoes:

Creationism in Crisis - Rhino Retroviruses Provide Evidence of Evolution

Slideshow code developed in collaboration with ChatGPT3 at https://chat.openai.com/

Female black rhinoceros, Diceros bicornis bicornis.

Wikipedia
User: Bernard DUPONT

African rhinos share retroviruses not found in Asian rhinos or other related species - Leibniz Institute for Zoo and Wildlife Research

Endogenous retroviruses have long been a bugbear for creationists in that they show convincing evidence of evolutionary phylogeny and common ancestry, so this paper which reveals the recent entry into the genome of the African rhinoceroses but not the Asian rhinoceroses, shows that the African rhinos share a common ancestor more recently than they share a common ancestor with the Asian species. That African ancestor became infected after it split from the common ancestor of the African and Asian rhinos.
The research team was led by Alex D. Greenwood of the Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany.

First, a little about ERV's:

Endogenous retroviruses (ERVs) Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections that have become permanently integrated into the genome of the host organism. They are found in the genomes of most vertebrates, including humans. ERVs are considered "endogenous" because they are passed from generation to generation and are inherited in a Mendelian fashion, just like other genes. The life cycle of a retrovirus involves the reverse transcription of its RNA genome into DNA, which is then integrated into the host genome. Occasionally, retroviruses infect germ cells (cells that give rise to eggs or sperm) and their DNA is inserted into the genome of the offspring. Over time, these integrated viral sequences can become fixed in the population and passed on to future generations.

ERVs provide evidence for evolution in several ways:

1. Shared ERVs among species: ERVs are found in the genomes of different species, and the presence of the same ERV at the same genomic location in different species suggests a common ancestor. For example, scientists have identified a specific retroviral sequence called "HERV-K" that is present in the genomes of humans, chimpanzees, and other primates. The shared presence of this ERV provides strong evidence for a common evolutionary history.
2. ERV distribution and phylogenetic relationships: The distribution of ERVs across different species can be used to construct phylogenetic trees, which illustrate the evolutionary relationships between species. By comparing the presence or absence of specific ERVs in different genomes, scientists can infer the evolutionary history and relatedness of species. This approach has been used to study the evolutionary relationships between primates and other mammals.
3. ERVs as "molecular fossils": ERVs can act as "molecular fossils" that provide insights into ancient viral infections and evolutionary events. By studying the DNA sequences of ERVs, scientists can gain information about the timing of viral integration events and the evolutionary relationships between different ERVs. This information helps reconstruct the evolutionary history of the host species.
4. Functional remnants of ERVs: Although most ERVs have accumulated mutations over time and lost their ability to produce functional viral particles, some ERVs retain functional elements. These functional remnants can have important roles in the regulation of gene expression and embryonic development. For example, certain ERVs have been co-opted by the host organism to play a role in placenta formation in mammals. This co-option of ERV sequences for new functions illustrates the process of exaptation, where existing genetic material is repurposed for novel functions during evolution.

References:

1. Mager, D. L., & Stoye, J. P. (2015). Mammalian endogenous retroviruses. Microbiology spectrum, 3(1), MDNA3-0009-2014. doi: 10.1128/microbiolspec.MDNA3-0009-2014
2. Griffiths, D. J. (2001). Endogenous retroviruses in the human genome sequence. Genome biology, 2(6), reviews1017.1. doi: 10.1186/gb-2001-2-6-reviews1017

chatGPT3, "Tell me all about endogenous retroviruses (ERV's), how they enter the genome and why they are evidence for evolution, with references, please. [Response to user question]
Retrieved from https://chat.openai.com

The press release from the Leibniz Institute for Zoo and Wildlife Research explains the research and its significance:

Rhinoceros belong to a mammalian order called odd-toed ungulates that also include horses and tapirs. They are found in Africa and Asia. Until recently, evidence suggested that throughout their evolutionary history, gammaretroviruses such as Murine leukemia virus had not colonised their genomes, unlike most other mammalian orders. The colonisation process is called retroviral endogenisation and has resulted in most mammalian genomes being comprised of up to ten percent retroviral like sequences. An analysis of modern and extinct rhino genomes headed by the German Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW) now found that African rhinos have dozens of gammaretroviruses in their genomes absent from the genomes of Asian rhino species, such as the Sumatran and Javan rhino, and that the African black rhino has two related groups, one missing from the white rhinos. The restriction of gammaretroviruses to African rhinos and the close relatedness of the viruses to rodent viruses, particularly those of African rodents, suggests that African rhinos were infected by an exogenous viral variant and their genomes colonised in Africa. The work is published in the scientific “Journal of Virology”.

We had data from several rhino species where we kept finding large portions of gammaretroviruses. When we used much newer and more complete reference genomes from modern and extinct rhinos we found that only African rhinos had been colonised

Dr Kyriakos Tsangaras, lead author
Department of Life and Health Sciences
University of Nicosia, Nicosia, Cyprus

This ultimately comes down to lack of high-quality reference sequences of wildlife. While things have improved a lot since the first human genome was sequenced, you miss things such as viral history when the databases lack so many species or high-quality reference genomes from many species. It is really another example of why we need more genome reference sequences from wildlife because we don’t know what other things we are missing and which conclusions we draw about presence and absence of sequences that may turn out to be a consequence of too little information.

Professor Alex Greenwood, Senior author
Head of the Wildlife Disease Department. Leibniz Institute for Zoo and Wildlife Research
Berlin, Germany

Retroviruses such as the causal agent of aids, HIV-1, are unique among viruses in that they have to integrate into the DNA of the host as part of their replication cycle. If this happens in the germline in spermatocytes or oocytes, they can become a part of the host genome that is inherited by the following generation and then are present in every cell of offspring bodies. This evolutionary process has happened so often that on average up to ten per cent of the mammalian genome is made up of retroviruses or their remnants. A previous study of available genomes from horses and their relatives suggested that they, along with rhinos and tapirs, had not been invaded by gammaretroviruses, a group of viruses related to mouse and bird viruses that have successfully colonised most mammalian genomes.

Together with colleagues from Australia and Germany the scientific team found that in fact two different viral groups had colonised African rhinos. One of them had only colonised the black rhino (Diceros bicornis) and not the white rhino (Ceratotherium simum) and was evolutionarily younger than the one shared by both. As both groups are restricted to African rhinos the study suggests that the African rhino lineage was infected and their genomes colonised in Africa, and that is why the respective gammaretroviruses are not found in Asian rhinoceros and other rhino relatives.

More detail is given in the team's paper in the Journal of Virology, which sadly lies behind a paywall. However, the abstract is freely available:

ABSTRACT

High-throughput sequences were generated from DNA and cDNA from four Southern white rhinoceros (Ceratotherium simum simum) located in the Taronga Western Plain Zoo in Australia. Virome analysis identified reads that were similar to Mus caroli endogenous gammaretrovirus (McERV). Previous analysis of perissodactyl genomes did not recover gammaretroviruses. Our analysis, including the screening of the updated white rhinoceros (Ceratotherium simum) and black rhinoceros (Diceros bicornis) draft genomes identified high-copy orthologous gammaretroviral ERVs. Screening of Asian rhinoceros, extinct rhinoceros, domestic horse, and tapir genomes did not identify related gammaretroviral sequences in these species. The newly identified proviral sequences were designated SimumERV and DicerosERV for the white and black rhinoceros retroviruses, respectively. Two long terminal repeat (LTR) variants (LTR-A and LTR-B) were identified in the black rhinoceros, with different copy numbers associated with each (n = 101 and 373, respectively). Only the LTR-A lineage (n = 467) was found in the white rhinoceros. The African and Asian rhinoceros lineages diverged approximately 16 million years ago. Divergence age estimation of the identified proviruses suggests that the exogenous retroviral ancestor of the African rhinoceros ERVs colonized their genomes within the last 8 million years, a result consistent with the absence of these gammaretroviruses from Asian rhinoceros and other perissodactyls. The black rhinoceros germ line was colonized by two lineages of closely related retroviruses and white rhinoceros by one. Phylogenetic analysis indicates a close evolutionary relationship with ERVs of rodents including sympatric African rats, suggesting a possible African origin of the identified rhinoceros gammaretroviruses.

IMPORTANCE:Rhinoceros genomes were thought to be devoid of gammaretroviruses, as has been determined for other perissodactyls (horses, tapirs, and rhinoceros). While this may be true of most rhinoceros, the African white and black rhinoceros genomes have been colonized by evolutionarily young gammaretroviruses (SimumERV and DicerosERV for the white and black rhinoceros, respectively). These high-copy endogenous retroviruses (ERVs) may have expanded in multiple waves. The closest relative of SimumERV and DicerosERV is found in rodents, including African endemic species. Restriction of the ERVs to African rhinoceros suggests an African origin for the rhinoceros gammaretroviruses.

Tsangaras K, Mayer J, Mirza O, Dayaram A, Higgins DP, Bryant B, Campbell-Ward M, Sangster C, Casteriano A, Höper D, Beer M, Greenwood AD (2023)
Evolutionarily young African rhinoceros gammaretroviruses.
J VIROL 97, e0193222. https://doi.org/10.1128/jvi.01932-22.

© 2023 American Society for Microbiology.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

To any normal person, evidence like this would confirm evolutionary divergence, firstly between the African and Asian rhinoceroses, then, later between the African rhinoceroses.

It would also show that the scientists are in no doubt that evolution is the fundamental explanation for their findings, with no hint that they believe magic and supernatural magicians were involved, like creationist frauds fool their dupes into believing they increasingly are. Indeed, why would they? What rational, educated adult, with a mental age greater than about 9, believes in magic or supernatural magicians and thinks they should play any part in scientific explanations of real-world evidence?

Creationism in Crisis - So What 'Kind' is This Strange Thing?

Creationism in Crisis

So What 'Kind' is This Strange Thing?

George, Emma E., et al.(2023)

Evolutionary oddball has seven genomes inside a single cell | New Scientist

The Bible that creationists turn to for a source of scientific information, is of course, as hopelessly muddled and simplistic about biology as it is about cosmology, morality and medicine. For example, this is how it tries to classify the birds that it is forbidden to eat under the irrational food taboos it mandates for believers:

And these are they which ye shall have in abomination among the fowls; they shall not be eaten, they are an abomination: the eagle, and the ossifrage, and the ospray, and the vulture, and the kite after his kind; every raven after his kind; and the owl, and the night hawk, and the cuckow, and the hawk after his kind; the little owl, and the great owl, and the swan, and the pelican, and the gier eagle, and the cormorant; and the stork, the heron after her kind, and the lapwing, and the bat.

Leviticus 11:13-19

Not surprisingly, and not just because of the hilarious gaff of including 'the bat' in a list of birds, and the muddle over the different 'kinds' of owl, biologists soon realised how hopelessly inadequate the Biblical notion of 'kinds' is as a means of classifying biological taxons, so had the devise the modern classification system.

And, presumably because the authors didn't realise that plants are alive because they don't breath like vertebrates do, there is no attempt to classify plants. In fact, the author's show their muddle over plants by this strange piece from Genesis:

Then God said, 'Let the earth put forth vegetation: plants yielding seed, and fruit trees of every kind on earth that bear fruit with the seed in it. ' And it was so. The earth brought forth vegetation: plants yielding seed of every kind, and trees of every kind bearing fruit with the seed in it.

Genesis 1:11-12

Clearly the Bible's authors thought there were only angiosperms (the most advances plants) since they are the only ones mentioned. Incidentally, more of their muddle is illustrated by the fact that this creation of green plants occurs before the sun is created, showing the authors knew nothing of photosynthesis.

And of course, there is no hint that the authors were even aware of single-celled micro-organisms, otherwise they might have mentioned germ theory, of which there is not a single word. Imaging how many lives could have been saved and how much suffering would have been avoided if God had thought to mention bacteria and viruses and how to avoid being infected by them, assuming it didn't know what it had created them for in the first place...

But that's an aside. The real muddle comes with the authors attempt to come up with a classification system, as Bible-literalist creationists assume that's what they were trying to do.

So, here is a curveball inadvertently thrown to creationists by researchers led by Emma E. George, now of the Scripps Institution of Oceanography, Integrative Oceanography Division, University of California, San Diego, La Jolla, CA, USA, when working at the University of British Columbia in Canada.

Her team have discovered single-celled algae that are not single organisms at all, but a complex community of seven different organisms, each with its own genome, and each playing a part in a complex relationship within the algal cell body.

Figure 3
Microscopy of Cryptomonas gyropyrenoidosa SAG 25.80 with bacterial endosymbionts.

(A) DIC; (B) DAPI; (C) FISH-M. polyxenophila probe; (D) FISH-G. numerosa probe; (E) overlay of (C) and (D); (F) endosymbionts clustered in the host cytoplasm, including endosymbionts with virus-like particles (Sv); (G) endosymbiont with virus-like particles within the bacterial cytoplasm and attached to the bacterial cell’s surface (arrowhead); and (H) bacterial endosymbionts and a membrane-like structure (i.e., putative autolysosome vacuole) that potentially contains virus-like particles (arrowhead). See also Figures S4A and S4C and Table S2.

George, Emma E., et al.(2023)

Creationism in Crisis - Genetics Confirms Common Ancestry of 'Oddball' Fungi

Genome studies uncover a new branch in fungal evolution | Folio

The earth tongue is one of 600 “oddball” fungi that were found to share a common ancestor dating back 300 million years, according to University of Alberta researchers.

Photo: Alan Rockefeller, (CC-BY-SA-4.0)

In a stunning example of the power of the Theory of Evolution (TOE) to explain otherwise puzzling observations, a team of scientists led by principal investigator, Toby Spribille an associate professor in Alberta University's Department of Biological Sciences, has shown how some 600 'oddball' fungi share a common ancestor that lived about 300 million years ago.

The problem was that the usual Linnaean method of classification, using the appearance of organisms, some 600 strange fungi were difficult to fit into any single taxon.

In addition to this obvious confirmation that the TOE is the basis of biology, confirmed by genetics, there is the additional embarrassment for Creationists in the finding that the diversity of this group is due to a loss of genetic information, made possible by a symbiotic existence, where the co-symbiont has taken on some of the basic functions. That a loss of information is always detrimental and evolution requires an increase in information is now a central dogma of Creationism that flies in the face of evidence such as this.

The Alberta University news release explain the research:

Evolution News - How DNA Analysis is Adding to Our Knowledge of Evolutionary Biology

Source: OIST

Hidden in genetics: The evolutionary relationships of two groups of ancient invertebrates revealed | Okinawa Institute of Science and Technology Graduate University OIST

One of the things a study of modern biology teaches is an appreciation of just how much of an achievement was Darwin's and Wallace's Theory of Evolution by Natural Selection considering the relatively small amount of knowledge they had access to, compared to today. in fact, all they really had to go on was morphology - i.e., the outward appearance of organisms, albeit aided with a hand lens and low-powered light microscopes. They had no knowledge of genetics, nor any inkling of how information was modified in one generation and passed onto the next.

Not surprisingly, then, they got some things wrong, especially where convergent evolution gave some species the appearance of being related when in fact they were both the product of the same environmental selectors pushing their evolution towards similar solutions, but coming from different branches of the evolutionary tree. And some problems they left unresolved, because, although there reasons to suppose two very dissimilar taxons were related based on their positions in the geological column, there was no basis for placing them firmly in the tree of life as either sister groups, distant cousins, or only very distantly related as the descendants of much earlier forms that had diversified considerably over time so they were morphologically very dissimilar.

Just such a case was the relationship between two ancient groups, the Kamptozoa and Bryozoa, small marine invertebrates related to animal like snails, earthworms, leeches, and ribbon worms.