User:Doyle.280/sandbox

I feel this is vital information to understanding evolutionary relationships of elephants. I would like to add to the end paragraph of Evolution and Extinct Relatives - There has been some debate over the relationship of Mammuthus to Loxodonta or Elephas. Some DNA studies suggest Mammuthus is more closely related to the former,[42][43] while others point to the latter.[9] However, analysis of the complete mitochondrial genome profile of the woolly mammoth (sequenced in 2005) supports Mammuthus being more closely related to Elephas.[20][24][44] Morphological evidence supports Mammuthus and Elephas as sister taxa, while comparisons of protein albumin and collagen have concluded that all three genera are equally related to each other.[45] Some scientists believe a cloned mammoth embryo could one day be implanted in an Asian elephant's womb.[46] - the statement, "Later studies, using the American Mastodon Mammut americanum as an outgroup in phylogeny and mitochondrial genome studies has led to the determined 24-28 million years ago divergence of Mastodons from other Elephantidae, African elephant Loxodonta africa divergence of about 7.6 million years ago, and Mammoth Mammuthus primigenius and Asian elephant Elephas maximus divergence of about 6.7 million years ago." [Hofreiter, Michael, Anna-Sapfo Malaspinas, and et. al. (2007). Proboscidean Mitogenomics: Chronology and Mode of Elephant Evolution Using Mastodon as Outgroup. PLoS Biology, 5 (8), 1663-1671. DOI: 10.1371/journal.pbio.0050207]

Evolution Suggestions
This article is very good. After reviewing several scientific articles, I noted some things that could be added to this article under Evolution and Extinct Relatives. The dwarf elephant Palaeoloxodon antiquus falconeri found on the island of Tilos in Greece is part of a Palaeoloxodon-Elephas clade (with paleontology divergence evidence of about four million years ago), as Palaeoloxodon is more related to Mammuthus or Loxodonta. . More information on Elephantidae lineages divergences could be provided, such as the American Mastodon (Mammut americanum) divergence time of 24-28 million years ago, African elephant divergence about 7.6 million years ago, and Mammoth and Asian elephant divergence around 6.7 million years ago (using mitochondrial genome sequence of an American Mastodon sample).  Finally, mention of the family Deinotheres and others in the order Proboscidea, and their relation to elephants, would be beneficial to the article. Doyle.280 (talk) 03:09, 2 October 2014 (UTC)

Annotated Bibliography
Dubrovo, Irena A., Makoto Kato, and et. al. (1998) Molecular Phylogenetic Inference of the Woolly Mammoth Mammuthus primigenius, Based on Complete Sequences of Mitochondrial Cytochrome b and 12S Ribosomal RNA Genes. Journal of Molecular Evolution, 46 (3), 314-326. DOI: 10.1007/PL00006308 The authors determined the complete sequences of cytochrome b and 12S ribosomal RNA in mitochondrial DNA genes from the woolly mammoth (Mammuthus primigenius), African elephant (Loxodonta Africana), and Asian elephant (Elephas maximus) to analyze the phylogenetic relationship between them. Phylogenetic relationships and evolutionary divergences were reconstructed from previous analyses reporting that Mammuthus is more related to Elephas than Loxodonta by creating a Mammuthus-Loxodonta clade from the authors’ sequence data. The authors’ research methods were well described and thoroughly led to reaching their conclusions. Although this study suggests that Mammuthus is more closely related to Loxodonta, there were several base substitutions in the sequences that may have interfered with accurate analysis of the genera relationships. A larger sample size of the number of genes and specimens, and a greater sequence length would be beneficial to further the research on Elephantinae phylogenetic relationships. Harris, John M. (1975). Evolution of feeding mechanisms in the family Deinotheriidae (Mammalia: Proboscidea). Zoological Journal of the Linnean Society, 56 (4), 331-362. DOI: 10.1111/j.1096-3642.1975.tb00275.x	Deinotheriidae, an order of Proboscidae, was examined by these authors as previous knowledge of their relations with others in their order was uncertain. These mammals existing in the Neogene and Quaternary retained a single pair of lower tusks and had different morphology of cheek teeth than other Proboscidae. As other Proboscidae may have used their tusks for other functions, the authors suggest that Deinotheriidae used their tusks for stripping vegetation to provide room for their tapir-like probiscus and to individualize the mammals, rather than using them for digging. The authors concluded that Deinotheriidae experienced similar success in expansion as with other Proboscidae by information from their DNA, indicating these mammals existed in three continents and underwent minor morphological changes from the Miocene to the middle Pleistocene. Hofreiter, Michael, Anna-Sapfo Malaspinas, and et. al. (2007). Proboscidean Mitogenomics: Chronology and Mode of Elephant Evolution Using Mastodon as Outgroup. PLoS Biology, 5 (8), 1663-1671. DOI: 10.1371/journal.pbio.0050207

The authors sequenced the complete mitochondrial genome of the extinct American mastodon (Mammut americanum) from an Alaskan fossil 50,000-130,000 years old, which indicates a much different genome that previously reported mitochondrial sequences. Using the newly-found sequence of the Mastodon as an outgroup (showing divergence from other Elephantidae species 24-28 million years ago) the authors determined that African elephants diverged from mammoth and Asian elephant lineages around 7.6 million years ago. The authors also inferred that Asian elephants diverged from mammoths around 6.7 million years ago. Additionally, using the mastodon sequence, the African savannah and forest elephants showed divergence approximately 4 million years ago and supporting the fact that these elephants are different species. Mitochondrial mutation rate was also found to be twice as large in primates than in proboscideans in the last 24 million years, indicating a smaller time period between divergences of Elephantidae species.

Fleischer, Robert C., Kasinathan Muralidharan, et. al. (2001). Phylogeography of the Asian Elephant (Elephas maximus) Based on Mitochondrial DNA. Evolution, 55(9), 1882-1892. DOI: http://dx.doi.org/10.1554/0014-3820(2001)055[1882:POTAEE]2.0.CO;2

The authors described Asian elephant genetic variation and structure in relation to their population reductions and fragmentations in the past 3000-4000 years, partially due to humans. They sequenced mitochondrial DNA for the cytochrome b gene between Asian and African elephants and used a fossil-based age of divergence of about 5 million years ago. The data showed that Asian elephants grew in population in the Late Pleistocene, and are part of two major clades (A and B). All the Asian elephants from Indonesia and most from Malaysia form a well-supported clade of A, which evolutionarily significant for the authors. Clade A individuals decrease as elephants travel further North in Asia, suggesting loss of ancient lineages, recent mixing of two populations that were possibly isolated in the mid-Pleistocene, and/or impacts from human trade in Myanmar, Sri Lanka, and India. The authors use their scientific data to question whether humans should interfere with the evolution of elephants by attempting to reconstruct earlier age conditions, or to allow evolution to occur naturally with existing conditions.

Mylonas, Moysis, Nikos Poulakakis, and et. al. (2002). Molecular Phylogeny of the Extinct Pleistocene Dwarf Elephant Palaeoloxodon antiquus falconeri from Tilos Island, Dodekanisa, Greece. Journal of Molecular Evolution, 55 (3), 364-374. DOI: 10.1007/s00239-002-2337-x

The rib bones of the dwarf elephant Palaeoloxodon antiquus falconeri from the Charkadio cave of the island Tilos in Greece were examined to reveal a partial sequence of the cytochrome b gene of mitochondrial DNA to create the first report of its kind. The authors used this sequence to investigate phylogenetic relationships in Elephantidae using neighbor-joining and maximum parsimony methods. The results of the analysis indicate the existence of a “Palaeoloxodon-Elephas” clade which supports previous research on the closer relationship of Palaeoloxodon to Elephas rather than Loxodonta. The authors determine that the evolution of these different species were from their mass migrations starting in the middle Pleistocene. The authors were very descriptive with the biogeography of Elephantidae, along with the methods leading to their conclusions, involving extensive molecular analysis. The writers did indicate that their calculated divergence time between P. a. falconeri and E. maximus at 600-700 thousand years ago (based on genetic distance and the evolutionary rate of mitochondrial DNA) was not supported by the stratigraphic and paleontological data claiming the time was about four million years ago. Therefore, the phylogenetic relationships are still debatable.

Final Revisions to Wikipedia article
Evolution and extinct relatives

Elaboration on Evolution
Please add in the last paragraph before ====Dwarf species==== under ===Evolution and extinct relatives===, These claims are also based off the sequence analyses of cytochrome b and 12S ribosomal RNA of the species’ mitochondrial DNA. The Loxodonta-Mammuthus clade was supported by a 92% bootstrap value in the phylogenetic tree constructed. . The large bootstrap value is indicative of high relatedness of mammoth and African elephant based on these clades in hypothetical phylogenies reappearing in experimental studies. Contrarily, other scientists have argued that the Woolly Mammoth and the Asian elephant are more closely related, and therefore had a more recent evolutionary divergence time, based on similar dentition, hair, and immunology. . Based on using the American mastodon, Mammut americanum, as a phylogenetic outgroup (representing a more distant relative in a phylogenetic tree), an Elephas-Mammuthus clade would be more largely supported. . The partial sequences of mitochondrial DNA of fossils and living species were analyzed and compared, suggesting a divergence time between the American Mastodon and other Elephantidae of 24-28 million years ago, with African elephants diverging from Mammoths and the Asian elephant about 6.7 million years ago. . Additionally, using the Mastodon as an outgroup, the nuclear genomes suggested that African savannah and African forest elephants are different species, and had a divergence time of approximately 4.0 million years ago. If this were so, Elephantidae has experienced allopatric speciation based on changing African geography over time.

Please add in second paragraph of ====Dwarf species==== after Dwarf elephants of uncertain descent lived in Crete, Cyclades and Dodecanese, while dwarf mammoths are known to have lived in Sardinia.[49]: The Dwarf Elephant (Paleoloxodon antiquus falconeri) that existed during the Pleistocene and found on Mediterranean islands was determined to be more closely related to Elephas than Loxodonta or Mammuthus. Please add in ending of third paragraph under ===Evolution and extinct relatives===: Research has suggested that in Southern Levant, several proboscidean taxa related to Elephas in the late Early to Middle Pleistocene existed with a chronological overlap. Elephas hysudricus co-occurs in record with the Stegodon and the straight-tusked Palaeoloxodon, precedent for the idea that Asian elephants expanded to the near East in the Holocene and giving rise to their present-day existence in Southeast Asia. . Doyle.280 (talk) 03:05, 18 November 2014 (UTC)

Final Draft Starts Here
The African elephant (Loxodonta) and the Asian elephant (Elephas maximus) are the only surviving members in the order Proboscidea, with their closest phylogenetic outgroup as sirenians (manatees and dugongs) (Dubrovo et.al. 1998). The phylogenetic relationship of these species with their ancestors is a topic of debate among scientists, and has recently been given evidence to support certain relationships. The species’ evolution of specific characteristics can also be studied, as adaptation based on human interaction with elephants today may have an effect on their evolutionary future. The phylogenetic relationships – hypotheses on evolutionary divergences – of species in the family elephantidae and its extant genera, the African elephant (Loxodonta) and the Asian elephant (Elephas maximus), are a source for debate for scientists. The relationship of the Asian and African elephant to the mammoth or mastodon of America is most often used as a phylogenetic tool in Elephantidae lineage. For instance, Irena Dubrovo et. al. argues that there exists a Mammuthus-Loxodonta clade, suggesting that the Woolly Mammoth Mammuthus Primigenius is more closely related to Loxodonta africana than Elephas maximus (1998). This claim is based off the sequence analyses of cytochrome b and 12S ribosomal RNA of the species’ mitochondrial DNA. According to the data of Dubrovo et. al., the Loxodonta-Mammuthus clade was supported by a 92% bootstrap value in the phylogenetic tree constructed (1998). The large bootstrap value is indicative of high relatedness of mammoth and African elephant based on these clades in hypothetical phylogenies reappearing in experimental studies. Contrarily, other scientists have argued that the Woolly Mammoth and the Asian elephant are more closely related, and therefore had a more recent evolutionary divergence time, based on similar dentition, hair, and immunology (Dubrovo et. al. 1998). Hofreiter et. al. argues that based on using the American mastodon, Mammut americanum, as a phylogenetic outgroup (representing a more distant relative in a phylogenetic tree), an Elephas-Mammuthus clade would be more largely supported (2007). The partial sequences of mitochondrial DNA of fossils and living species were analyzed and compared, suggesting a divergence time between the American Mastodon and other Elephantidae of 24-28 million years ago, with African elephants diverging from Mammoths and the Asian elephant about 6.7 million years ago (Hofreiter et. al. 2007). Additionally, using the Mastodon as an outgroup, the nuclear genomes suggested that African savannah and African forest elephants are different species, and had a divergence time of approximately 4.0 million years ago (Hofreiter et. al. 2007). If this were so, Elephantidae has experienced allopatric speciation based on changing African geography over time. Moreover, after DNA analyses of African great apes and humans, researchers deduced that a change in environmental condition sparked speciation in these African mammals approximately 7.5-8 million years ago (Hofreiter et. al. 2007). Researchers have little knowledge of other extinct members of Elephantidae, and the Order Proboscidae (relatives with trunks, or a probiscus), but are beginning to discover more information from recently found fossils. This information helps to construct a more accurate phylogenetic tree, connecting extant Elephantidae species with extinct ones. The Dwarf Elephant (Paleoloxodon antiquus falconeri) that existed during the Pleistocene and found on Mediterranean islands was determined to be more closely related to Elephas than Loxodonta or Mammuthus (Mylonas et. al. 2002). Scientists again used mitochondrial DNA and the cytochrome b gene from the rib bones of a found Dwarf elephant excavated from Greece and compared it to the DNA of the Asian elephant. Based on the data, Elephas and Palaeoloxodon separated evolutionarily 600-700 thousand years ago, which competes with paleontological evidence – claiming divergence time is about four million years ago (Mylonas 2002). Evidently, there still occurs debate on phylogenetic relationships of Elephantidae – many based on differing dating methods of organism specimens and relationships in research. The Asian elephant additionally was thought to have the ancestor Elephas hysudricus of the Plio-Pleistocene based on dentition and other morphological characteristics, suggesting possible westward expansion of the Asian elephant (Applbaum et. al. 2013). Although the Asian elephant today only exists in the Indian subcontinent and Southeast Asia, it has lived from China’s Pacific Coast to west into Levant, as shown from remains and described in historical documentation (Applbaum et. al. 2013). This information was inferred by using fossil evidence from these locations. The research done by Applbaum et. al. may support this, suggesting that in Southern Levant, several proboscidean taxa related to Elephas in the late Early to Middle Pleistocene existed with a chronological overlap. Elephas hysudricus co-occurs with the Stegodon and the straight-tusked Palaeoloxodon, precedent for the idea that Asian elephants expanded to the near East in the Holocene and giving rise to their present-day existence in Southeast Asia (Applbaum et. al. 2013). The evidence from data collected from DNA sequence comparisons from different Elephantidae and Proboscidea species is crucial to creating an accurate phylogenetic tree. Additionally, research has been done to not only relate these species to each other, but also explain these species’ unique characteristics. For example, the family Deinotheriidae in the order Proboscidea also had lower tusks, seemingly obtained for adaptation to an environment – along with their probiscus. John Harris believes that Deinotheres used their tusks for scraping mud, but do the extant relatives use their tusks and other unique features the same as their ancestors? (1975) Research has been conducted recently in this topic – especially how human interaction may interfere with adaptations of extant relatives of Proboscidea. The evolutionary role of unique characteristics of Elephantidae and Proboscidea, such as tusks, has been questioned in science. Tusks, being elongated second upper incisors, have been in the Proboscidean record heavily. Chelliah et. al. studied Asian elephants and their use of tusks, and whether this adaptation is maladaptive (2013). Usually, only male elephants have tusks, contrary to African elephants, which makes Asian elephants useful in studying specific roles of tusks. Using this, Chelliah et. al. examined whether tusks invoke a greater dominance factor for Asian elephant males when there exists male-male competition – often for mating (2013). These researchers thought that tusk evolution is in fact for female-choice sexual selection, as using tusks to dig mud and tear off bark is seemingly a by-product of their evolution (2013). This is because musth (a heightened sexual drive in elephants) and body size overrides tusk status in male-male competition. Additionally, the tensile strength of the tusks is actually low, meaning physical usage of tusks may not be as important to elephants today as it was for earlier Proboscidea. Based on this, elephants may soon adapt to be tuskless (Chelliah et. al. 2013). The relationship of body parts of extant relatives of Proboscidea may be in fact different than their relatives. The evolution of elephants based on human interaction has been deemed important by scientists. Recently, a study was done that confirmed that Asian elephants actually make up two clades (which they called A and B), which were based geographically in Asia and diverged around 1.2 million years ago and were isolated during the mid-Pleistocene (Fleischer 2001). However, recent mixing of the clades has occurred as humans have used elephants for labor and war (Fleischer 2001). Additionally, with the loss of rainforest, elephants are experiencing lower fitness with decreased genetic diversity as populations are being separated in the wild - as a result of human conflict and forest resource usage (Archie and Chiyo 2012). Further studies need to be conducted on whether genetic diversity of elephants is in danger due to human interaction. Although elephants (and varieties thereof) have existed for millions of years, based on evidence that describe their relatives, there are only two extant species today. Further finds and studies of Proboscidea continue to give light on more detailed phylogenetic trees displaying this order and the family Elephantidae. The Elephantidae species living today may be in danger of extinction based on human interaction and geographical changes that would require elephants to continue their evolution and adaptation with lower genetic diversity and possibly lower fitness. Further studies on phylogeny and human interference of elephants need to be done to describe their diverse ancestors, along with their potential existence in the future. Doyle.280 (talk) 03:11, 18 November 2014 (UTC)