Saturday, 22 June 2019

Terrible News for Creationists - Evolution of Ruminants Now Known

Lesser Mouse Deer, Tragulus kanchil
By Seshadri.K.S. - Own work,
CC BY-SA 4.0, Link
Masai giraffe, G. c. tippelskirchi
By © Hans Hillewaert,
CC BY-SA 3.0, Link
From Sheep and Cattle to Giraffes, Genome Study Reveals Evolution of Ruminants | UC Davis

The ruminants are a large and very successful group of mammals ranging in size from the tiny lesser mouse deer of Malaysia to the giant African giraffes, and occupying a wide range of ecosystems. A characteristic of this group is a four-chambered stomach modified to digest a high-cellulose diet with the aid of specialist microorganisms, regurgitation and re-chewing of the food (chewing the cud), a pair of horns or antlers used for defence and sexual display and teeth adapted for eating grass and leaves.

This group emerged between 32 and 39 million years ago and has provided several important domesticated animals such as cattle, sheep and goats, but how exactly they are related had not before been fully worked out.

Now a team of scientists led by Wen Wang and Guojie Zhang at the Kunming Institute of Zoology, China, and Rasmus Heller at the University of Copenhagen, Denmark, and including Professor Harris Lewin at the UC Davis Department of Evolution and Ecology and Genome Center, Davis California, has gone some considerable way to working out a phylogenic tree for this group.

To do this, they sequenced the genomes of 44 species, representing 36 genera from all 6 ruminant families, and comprising some 40 trillion base pairs of raw DNA. They combined this with data from five previously published bovid genomes, two published cervid genomes, and recently-updated fossil evidence.

Phylogeny and trait evolution of ruminants.
The phylogenic tree of ruminants is presented with the species within same families and subfamilies collapsed. The ruminants have many textbook examples of distinct traits. The four-chambered stomach with omasum chamber is a key innovation evolved in pecoran ruminants. Headgear keratinous sheath only appear in Bovidae and Antilocapridae lineages. Many ruminants have evolved high-crowned or hypsodont teethes. The Antilocapridae and two bovid lineages are among the mammals with highest cursorial locomotion ability.

Structured Abstract

The ruminants are one of the most successful mammalian lineages, exhibiting extensive morphological and ecological diversity and containing several key livestock species, such as cattle, buffalo, yak, sheep, and goat. Ruminants have evolved several distinct characteristics such as a multichambered stomach, cranial appendages (headgear), specialized dentition, a highly cursorial locomotion, and a wide range of body size variations. Despite their biological prominence and value to human societies, the evolutionary history of ruminants has not been fully resolved, and the molecular mechanisms underlying their particular characteristics remains largely unknown.

We seek to resolve the controversies in the ruminant phylogeny and reveal the genetic basis underpinning the evolutionary innovations in ruminants. Here, we report the newly sequenced genomes of 44 ruminant species, covering about half the genera and all six extant Ruminantia families. We included seven published ruminant genomes (five bovids and two cervids) to reconstruct the phylogenetic tree by using improved time calibrations. We also reconstructed the Pleistocene demographic histories of these ruminant species using whole-genome heterozygosity information. Together with transcriptomic data of 516 samples from 68 tissues of four species, we conducted comparative genomic analyses to reveal candidate genes and regulatory elements that might have contributed to the evolution of the distinct ruminant characteristics.

Using whole-genome orthologous sequences obtained from 51 ruminants, we have produced a new well-supported ruminant phylogenetic tree. The new tree resolves previous controversies over the deep branches of ruminant families, as well as the highly radiated Bovidae family. We estimated the emergence of crown Ruminantia to the late Oligocene (39.1 million to 32.3 million years ago) and that of Pecora to the Neocene (23.3 million to 20.8 million years ago). Investigations of demographic history revealed massive population decline events that occurred in most ruminant species, starting from ~100,000 to 50,000 years ago, which was temporally and spatially concurrent with the increased human activities on different continents during this period. We further identified many genomic changes that associate with important evolutionary innovations, such as the multichambered stomach, headgear, body size variation, cursorial locomotion, and dentition.

Our results demonstrate the power of using comparative phylogenomic approaches in resolving the deep branches of phylogeny that result from rapid radiations. The data and results presented in this study provide valuable resources and insights into the evolution of ruminant and mammalian biology.

The key points they found were:
  1. 295 of the newly-evolved genes were associated with the structure and function of the digestive system.
  2. A number of the genes were associated with horns and antlers.
  3. Of the 366 genes related to bone development, 115 were specific to giraffes.
  4. The gene ENAM which is involved in mineralisation of tooth enamel, had two amino-acid insertions and several mutations that are specific to ruminants.

The team also found evidence of the impact of the spread of humans out of Africa, with evidence of a massive decline in more than half the ruminant species between 100,000 and 50,000 years ago.

The significance of this research for creationists is that it refutes their key dogmas. The evolution of the genes that gave rise to this group of mammals not only resulted in very many different sub-taxons - families and species - but they all resulted from mutations or de novo genes originating from gene duplication and co-option by natural selection as developments enabled new ecological niches to be exploited. Specific mutations, including amino-acid insertions have been involved in the evolution of specialised ruminant teeth.

This research identifies how a major taxon has evolved and diversified over time, and shows how a genetic phylogeny maps accurately onto the anatomical, physiological and palaeontological phylogeny, and maps onto known climatological and geological changes over the same time scale.

200 species, 6 families and a whole order, all the result of evolution by natural selection of beneficial mutations. And now we know how.

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