Bonobos and Chimpanzees had a Human/Neandertal Like Fling

A new whole-genome analysis of chimpanzees and bonobos reveals that these two great ape species likely interbred several hundred thousand years ago. A better understanding of the genetic flow between humans' closest living relatives could shed light on processes that might have played a recurring role in great ape evolution. While chimpanzees and bonobos are known to interbreed in captivity, the historic genetic flow between the two species in the wild is less clear. To gain better insights into possible historical gene flow between them, Marc de Manuel et al. analyzed the complete genomes of 10 bonobos and 65 chimpanzees. Significantly, more chimpanzees were included in their analysis, and from various regions in Africa, because previous genetic studies have suggested that four distinct species of chimpanzee exist. Following their analysis, the researchers observed clear evidence for gene flow between the two species, occurring between 200 and 550 thousand years ago, they estimate. Central, eastern, and Nigeria-Cameroon chimpanzees share significantly more genetic information with bonobos than do western chimpanzees, they report. What's more, similar to Neanderthal genetic patterns in humans, some background bonobo genetic information has been deleted in the chimpanzee genome, suggesting that some bonobo genes may have been disadvantageous for chimpanzees.

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Humans Drive Speciation as well as Extinction

How humans drive speciation as well as extinction

Authors:

Bull et al

Abstract:

A central topic for conservation science is evaluating how human activities influence global species diversity. Humanity exacerbates extinction rates. But by what mechanisms does humanity drive the emergence of new species? We review human-mediated speciation, compare speciation and known extinctions, and discuss the challenges of using net species diversity as a conservation objective. Humans drive rapid evolution through relocation, domestication, hunting and novel ecosystem creation—and emerging technologies could eventually provide additional mechanisms. The number of species relocated, domesticated and hunted during the Holocene is of comparable magnitude to the number of observed extinctions. While instances of human-mediated speciation are known, the overall effect these mechanisms have upon speciation rates has not yet been quantified. We also explore the importance of anthropogenic influence upon divergence in microorganisms. Even if human activities resulted in no net loss of species diversity by balancing speciation and extinction rates, this would probably be deemed unacceptable. We discuss why, based upon ‘no net loss’ conservation literature—considering phylogenetic diversity and other metrics, risk aversion, taboo trade-offs and spatial heterogeneity. We conclude that evaluating speciation alongside extinction could result in more nuanced understanding of biosphere trends, clarifying what it is we actually value about biodiversity.

pop sci link.

A More Precise Method for Determining the Speciation and Extinction Rates

A more precise speciation and extinction rate estimator

Author:

Alroy

Abstract:

A new turnover rate metric is introduced that combines simplicity and precision. Like the related three-timer and gap-filler equations, it involves first identifying a cohort of taxa sampled in the time interval preceding the one of interest (call the intervals i 0 and i 1 ). Taxa sampled in i 0 and i 1 are two-timers (t 2 ); those sampled in i 0 and i 2 but not i 1 are part-timers (p); and taxa sampled only in either i 1 , i 2 , or i 3 are newly notated here as either s 1 , s 2 , or s 3 . The gap-filler extinction proportion can be reformulated as (s 1 −s 3 )/(t 2 +p). The method proposed here is to substitute s 3 with the second-highest of the three counts when the expected ordering s 1 ≥s 2 ≥s 3 is violated. In simulation, this new estimator yields values that are highly correlated with those produced by the gap-filler equation but more precise. In particular, it rarely produces highly negative values even when sample sizes are quite small. It is mildly upwards biased when sampling is extremely poor and turnover rates are extremely low, but it is otherwise highly accurate. Examples of Phanerozoic extinction rates for four major marine invertebrate groups are given to illustrate the method’s improved precision. Based on the results, the procedure is recommended for general use.

Horses, Equids Have a Complicated Evolutionary History

Speciation with gene flow in equids despite extensive chromosomal plasticity

Authors:

Jónsson et al

Abstract:

Horses, asses, and zebras belong to a single genus, Equus, which emerged 4.0–4.5 Mya. Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here we present six genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto represented only by the horse and the domestic donkey. In addition, we used a museum specimen to characterize the genome of the quagga zebra, which was driven to extinction in the early 1900s. We scan the genomes for lineage-specific adaptations and identify 48 genes that have evolved under positive selection and are involved in olfaction, immune response, development, locomotion, and behavior. Our extensive genome dataset reveals a highly dynamic demographic history with synchronous expansions and collapses on different continents during the last 400 ky after major climatic events. We show that the earliest speciation occurred with gene flow in Northern America, and that the ancestor of present-day asses and zebras dispersed into the Old World 2.1–3.4 Mya. Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 pairs to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation, and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow, and, ultimately, speciation.

Geology Influencing Mammal Evolution in Mioecene Neogene North America?

Possible regional tectonic controls on mammalian evolution in western North America

Authors:

1. Malinda L. Kent-Corson (a)
2. Anthony D. Barnosky (b)
3. Andreas Mulch (c, d, e)
4. Marc A. Carrasco (b)
5. C. Page Chamberlain (f)

Affiliations:

a. Division of Earth Sciences, Nanyang Technological University, 639798, Singapore

b. Department of Integrative Biology and Museum of Paleontology, University of California, Berkeley, CA 94709, USA

c. Biodiversity and Climate Research Centre (BiK-F), 60325 Frankfurt, Germany

d. Institute of Geosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany

e. Senckenberg Research Institute, 60325 Frankfurt, Germany

f. Department of Environmental Earth System Science, Stanford University, Stanford, CA 94305, USA

Abstract:

Previous work has suggested that tectonically active regions act as speciation pumps for mammals and plant species, but little is known about how fast or widespread tectonism must be in order to directly influence evolution. Here, we use oxygen and hydrogen isotopic data from Miocene sedimentary deposits to characterize the topographic evolution of the southern Columbia Plateau/Snake River Plain and northern Rocky Mountain regions during the Yellowstone hotspot passage, with the ultimate goal of understanding whether topographic changes caused by the hotspot influenced mammalian evolution within those regions. We conducted oxygen isotope analyses of 130 samples of lacustrine, and paleosol carbonate from Miocene stratigraphic sections that span much of the northern Rocky Mountain region, and combined these data with previously published isotopic records. Collectively these isotopic data show that caldera formation associated with the Yellowstone hotspot has modified regional topography and rearranged drainages along the track of the hotspot, and that the hotspot has left a topographic depression in its wake.

We explore the extent to which these topographic changes influenced or are decoupled from diversity changes exhibited by the local mammal faunas and conclude that the passage of the hotspot and consequent surface uplift created rainshadows in the lee of high-elevation calderas and/or generated large volumes of volcanic materials, influencing soils and vegetation. Collectively, that may explain a possible rise in mammal diversity in the CP/SRP region at ~ 14 Ma, coincident with a drop in diversity in the NRM. It is still unclear, however, how different taphonomic pathways and sample-standardization problems are influencing apparent diversity peaks at this temporal and geographic resolution.

New Phylogenetic Tree for Avians (Birds) Shows Speciation Rates Increasing

A Yale-led scientific team has produced the most comprehensive family tree for birds to date, connecting all living bird species — nearly 10,000 in total — and revealing surprising new details about their evolutionary history and its geographic context.

Analysis of the family tree shows when and where birds diversified — and that birds' diversification rate has increased over the last 50 million years, challenging the conventional wisdom of biodiversity experts.

"It's the first time that we have — for such a large group of species and with such a high degree of confidence — the full global picture of diversification in time and space," said biologist Walter Jetz of Yale, lead author of the team's research paper, published Oct. 31 online in the journal Nature.

He continued: "The research highlights how heterogeneously fast diversifying species groups are distributed throughout the family tree and over geographic space. Many parts of the globe have seen a variety of species groups diversify rapidly and recently. All this leads to a diversification rate in birds that has been increasing over the past 50 million years."

The researchers relied heavily on fossil and DNA data, combining them with geographical information to produce the exhaustive family tree, which includes 9,993 species known to be alive now.

"The current zeitgeist in biodiversity science is that the world can fill up quickly," says biologist and co-author Arne Mooers of Simon Fraser University in Canada. "A new distinctive group, like bumblebees or tunafish, first evolves, and, if conditions are right, it quickly radiates to produce a large number of species. These species fill up all the available niches, and then there is nowhere to go. Extinction catches up, and things begin to slow down or stall. For birds the pattern is the opposite: Speciation is actually speeding up, not slowing down."

The researchers attribute the growing rate of avian diversity to an abundance of group-specific adaptations. They hypothesize that the evolution of physical or behavioral innovations in certain groups, combined with the opening of new habitats, has enabled repeated bursts of diversification. Another likely factor has been birds' exceptional mobility, researchers said, which time and again has allowed them to colonize new regions and exploit novel ecological opportunities.

In their analysis, the researchers also expose significant geographic differences in diversification rates. They are higher in the Western Hemisphere than in the Eastern, and higher on islands than mainlands. But surprisingly, they said, there is little difference in rates between the tropics and high latitudes. Regions of especially intense recent diversification include northern North American and Eurasia and southern South America.

"This was one of the big surprises," Jetz said. "For a long time biologists have thought that the vast diversity of tropical species must at least partly be due to greater rates of net species production there. For birds we find no support for this, and groups with fast and slow diversification appear to occur there as much as in the high latitudes. Instead, the answer may lie in the tropics' older age, leading to a greater accumulation of species over time. Global phylogenies like ours will allow further tests of this and other basic hypotheses about life on Earth."