Posts Tagged ‘molecular clock’

The Enigmatic Small Wolf Species of the Early-Mid Pleistocene of North America

August 6, 2017

There were at least 5 species of wolf-sized canids living in North America from about ~1.8 million years BP-~300,000 years BP.  Edward’s wolf (Canis edwardii) was a medium-sized canid, averaging about 75 pounds, that apparently occurred from coast to coast.  It’s the same species formerly known as Canis priscolatrans, and it was an evolutionary dead end–its extinction occurred about 300,000 years ago.  Armbruster’s wolf (Canis armbrusteri) co-occurred with Edward’s wolf but was a larger species, weighing on average 125 pounds.  Armbruster’s wolf is thought to be the evolutionary ancestor of the famous dire wolf (Canis dirus) which became extinct about 11,000 years ago.  Troxell’s dog (Protocyon texanus) was related to African hunting dogs.  Fossil evidence of this species has been found in Texas, the Yukon, and Alaska; and it probably had a wider range than the fossil record indicates.  Perhaps it lived in low numbers in geographic regions where processes of preservation were rare. The timber wolf (Canis lupus) was apparently confined to Alaska and Eurasia during the mid-Pleistocene and didn’t colonize North America until the late Pleistocene.  Finally, a mystery species nearly identical to the present day coyote (Canis latrans) left fossil evidence at sites in Nebraska, Colorado, California, Arkansas, Pennsylvania, Maryland, and West Virginia.  Some of the fossils at these sites are estimated to be 1 million years old.  Paleontologists identified these specimens as Canis latrans, though they cautiously also referred to them as coyote-like.  However, a recent study of wolf, coyote, and dog genetics determined the coyote is a recently evolved species no older than 50,000 years when it first diverged from timber wolves.  This result suggests the mid-Pleistocene species identified as Canis latrans may be an extinct mystery species.

In addition to the fossil record scientists can use a molecular clock to determine when 2 or more species diverged from a common ancestor.  A species has a fixed mutation rate, and scientists add up generations of mutational changes to determine the time of divergence from its closest related species.  (This is a vastly oversimplified explanation but will suffice for the purpose of this blog article.)  There are problems with using molecular clocks.  Different species have different rates of mutation, and the mutation rate can change over time.  Scientists try to calibrate the molecular clock with the fossil record by using various statistical methods.  An early study of wolf and coyote genetics determined the 2 species diverged about 1 million years ago, and this result is consistent with the fossil record, but the results of the newer study mentioned above totally contradict the fossil evidence.  There are 2 explanations for this discrepancy.  a) The new study is wrong.  Maybe the scientists used too many assumptions and dodgy statistics and just came up with the wrong number.  or b) The new study is right, and the mid-Pleistocene species identified as Canis latrans was an evolutionary dead end that went extinct.  The similarity between this mystery species and Canis latrans is just a remarkable example of convergent evolution. c) The new study is right and is not inconsistent with the fossil record.  Perhaps the common ancestor of the coyote and timber wolf was coyote-like.  Ice Age glaciers caused the divergence.  Populations north of the Cordilleran ice sheet evolved into timber wolves but populations south of it remained coyote-like.

Below are images of mid-Pleistocene  skull and jaw specimens identified as Canis latrans along with the skull and jaw of a present day coyote.  I can’t tell the difference, so I favor explanation a.  Even in a case of convergent evolution, there would have to be some notable anatomical differences between 2 different species.

Image result for irvingtonian Canis latrans skull

Genetic evidence from 1 study suggests coyotes diverged from gray wolves about 50,000 years ago.  However, this skull, assigned to Canis latrans (coyote) from Maryland dates to >300,000 years ago.  Is the genetic evidence incorrect or was there a species then so similar to modern coyotes it deceived paleontologists? Image from the below referenced paper by Tedford et. al.

Image result for Canis latrans skull

Present day skulls of Canis latrans.

Some zoologists think coyotes and dogs should now be classified as subspecies of timber wolf based on the data from the newer genetics study.  I don’t agree.  The behavioral characteristics of wolves, dogs, and coyotes are too dissimilar; and they don’t normally interbreed in natural conditions.  Humans can easily eradicate wolves from a region, but they can not eliminate coyotes because the latter are so much better adapted for living close to people.  Wolves and coyotes can survive in the wilderness, but they make terrible pets.  Most dogs make excellent companions for people but can’t survive in the wild.  In my opinion wolves, coyotes, and dogs are closely related but definitely different species.


Tedford, Richard; X. Wang, and B. Taylor

“Phylogenetic Systematics of the North American Fossil Caninae”

Bulletin of the American Museum of Natural History  2009

Von Holdt, Bridgett; et. al.

“Whole Genome Sequence Analysis Shows that Two Endemic Species of North American Wolf are Admixtures of Coyote and Gray Wolf”

Science Advances (27) July 2016

Wilson, Paul; et. al.

“DNA Profile of Eastern Canadian Wolf and Red Wolf Provide Evidence for a Common Evolutionary History Independent of the Gray Wolf”

Canadian Journal of Zoology 2000





The Evolutionary History of the Black Bass Genus (Micropterus sp.)

April 26, 2013

Scientists used a molecular clock to determine all 8 species of black bass share a common ancestor that lived 11 million years ago.  The molecular clock is a method scientists have of estimating the age of a species.  It’s especially helpful when studying the evolutionary history of organisms that are absent or rare in the fossil record.  It is based on the assumption that DNA  protein sequences evolve at a relatively constant rate.  Scientists assume a substitution rate of appearance of new mutations in each member of the population.  Scientists eventually learned the substitution rate varies among different kinds of organisms, so they calibrate the molecular clock with the fossil record and known geological events that may have caused species divergence.  This involves a lot of computer modeling and statistics, but they are confident that using a molecular clock is a reliable method of estimating evolutionary ages.

The oldest bass fossil ever found was unearthed in Texas and dated to 23 million BP.  Scientists estimate the Micropterus (black bass) genus originated about 26 million years ago, based on molecular clock data.  This suggests their findings are consistent with the fossil record.  Today, there are 8 species of bass that began to diverge from a common ancestor 11 million years ago when a marine transgression flooded most of the coastal plain in the southeast.  This dramatic rise in sea level isolated many populations of bass, resulting in allopatric speciation.  Scientists believe this is the most common type of speciation, and it occurs when founding populations become geographically isolated.

Marshall Forest 041

Range map of 8 species of black bass.  The dots represent collecting localities for specimens used in study.  From “Speciation in Micropterus” referenced below. Click to enlarge.

Marshall Forest 040

Time calibrated phylogram showing evolutionary history of black bass.  This is also from “Speciation in Micropterus.”  The scientific names translated to common names are: Micropterus punctulatus–spotted bass, M. dolomieu–smallmouth bass, M. coosae–redeye bass, M. cataractae–shoal bass, M. notius–Suwannee bass, M. treculi–Guadulupe bass, M. salmoides–largemouth bass, M. floridanus–Florida largemouth bass.

The common ancestor of smallmouth and spotted bass diverged from the ancestor of the other 6 species of bass during the marine transgression of 11 million BP.  Later rises in sea level between 8 million BP-2.5 million BP further resulted in the evolution of redeye, shoal, Suwannee, Guadalupe, largemouth, and Florida largemouth basses.  Before this study scientists thought speciation of bass occurred due to climate perturbations of the Pleistocene, but now they realize most Micropterus species evolved before Ice Ages began.  Only the divergence of spotted bass and smallmouth bass occurred during the Pleistocene about 1 million years BP. These sister species may have been isolated from each other by a glacier, but the other species of bass originated in warmer climates that remained glacier-free.

Most black bass species readily hybridize, showing just how closely related they are.  This can prove a problem when a common species is introduced to waters occupied by a rare species.  Shoal bass were formerly abundant in the rocky cataracts found in the Flint, Chattahoochee, and Appalachiacola Rivers, but most of those areas were inundated with reservoirs that make the habitat unsuitable.  Shoal bass became rare, and to make matters worse spotted bass were introduced.  Spotted bass compete for the same foods and hybridize with the remaining shoal bass.  

Comparison photos and illustrations between 4 species of bass.  The bottom photo is of a a redeye bass.  It has a curious distribution.  It’s found in 2 different river drainages–the Coosa and the upper Savannah.  At one time these 2 drainages must have been connected.

The below link has some nice photos comparing the shoal bass with other species of bass.

White bass (Morone chrysops), striped bass, (Morone saxatilis), and black sea bass (Centrophis stiata) are not closely related to the Micropterus genus, despite their common names.  Instead, the Micropterus genus is part of the Centrarchid family that includes sunfish and crappies.  Surprisingly, largemouth bass can hybridize with some of their distant sunfish and crappie relatives.

Adult largemouth bass prey on smaller fish, frogs, crayfish, and occasionally birds and mice.  Most of the largemouth bass’s sister species grow smaller and feed more on insects and small crayfish.  Smallmouth and spotted bass feed on prey intermediate in size between that taken by the largemouth and its 6 sister species.  The largemouth bass’s range overlaps with those of its sister species, but they occupy different ecological niches.  The introduction of intermediate feeders, like the smallmouth or spotted, may disrupt the ecosystems in southern rivers.

Largemouth bass are some times found in brackish waters located within salt marshes.  Anglers catching them here still call them by their archaic common name of “green trout.”


Near, T.J.; et. al.

“Speciation in North American black bass, Micropterus (Achioptergii: Centrarchidae)”

Evolution 57 (7) 2003

Simon, Ho

“The Molecular Clock and Estimating Species Divergence”

Nature Education 1 (1) 2008