Face the State

Article is Wrong about Status of Preble's Genetics

On April 20th, 2009 Duane says:

The genetics of Prebles is not a controversy. Rob Roy Ramey II provided junk science in a effort to thwart protection under the ESA. He and Julie McDonald have since been exposed for their abuse of science and politics.

A summary of and excerpts from the expert comments on
Rob Roy Ramey II's report:

Testing the Taxonomic Validity of
Preble's Meadow Jumping Mouse (Zapus hudsonius preblei)

Many of the expert comments gathered so far indicate that lumping Preble’s and Bear Lodge based on Ramey’s report is premature, and many commenters expressed support for continued conservation attention for Preble’s and/or Bear Lodge meadow jumping mice. Gaps in Ramey’s research that were commonly cited included the lack of analysis of potential ecological, behavioral, and geographical barriers causing these subspecies to be distinct and the use of only one molecular marker (mitochondrial DNA) in the analysis. Several commenters suggested that Ramey’s conclusions overreached the scope of his analysis, including his assessment that these mice do not warrant conservation attention.

David Armstrong, Professor of Environmental Biology, University of Colorado:
Armstrong does not comment on the molecular methods, but states that the limited scope of this study and the fact that it has not been published makes it unsuitable for taxonomic revision:

First, an agency report is not a publication and is therefore an inappropriate place to synonymize two subspecies. This report is private communication, or at most ‘gray literature,’ and it has no standing in zoological taxonomy. Second, the report seems not to recognize that this is a fairly small piece of the puzzle of geographic variation in the meadow jumping mouse. Absent a thorough taxonomic revision of subspecies of Zapus hudsonius, for example, I am not sure why Z. h. preblei should be considered a synonym of Z. h. campestris and not of Z. h. pallidus. And the authors have not investigated the distinctiveness of either Z. h. pallidus or Z. h. campestris relative to Z. h. intermedius, which is ascribed a range downstream in the Missouri-Mississippi watershed. And so forth.

In other words, a restricted, targeted investigation of this kind, laid out in an unpublished report, is not an appropriate vehicle for a taxonomic decision of the kind proposed. Rather, changes in intraspecific taxonomy and nomenclature should be based on thorough restudy of the species across its range – in other words, a study on the scale of Krutzsch (1954), but using the methods developed over the past 30-50 years to allow new and more sophisticated insights into evolutionary and ecological processes that any taxonomy ought to reflect. And they must be published in the peer-reviewed literature.

Armstrong also believes that Ramey’s call for definitive genetic testing prior to ESA listing is not practical:

I agree that it would be wonderful if there could be a modern systematic revision (based on phylogeographic analysis of molecular and morphological data) of all of the taxa that might be proposed for listing under the ESA. To be relevant, these would need to be on the scope of thorough revisions of whole species, not just the peripheral or disjunct populations that tend to populate the list of endangered species (and subspecies). I have not taken time to guess the numbers of taxa that would need to be evaluated but I suspect that the total enterprise (even at the rate of $57k per subspecies) would be prohibitively expensive. I do note that Hall (1981), listed 3607 subspecies and monotypic species of mammals in North America. Perhaps half of those are in the USA, and one would expect similar numbers of lissamphibians, squamate reptiles, and perhaps twice that many kinds of birds and even more kinds of fishes – and that considers only vertebrates, of course, not the whole biota. The total cost could exceed $1 billion.

Armstrong adds another critical point: "Beyond the financial cost, there is a huge opportunity cost. Conservation delayed is conservation denied.”

Mary Conner, Professor of Forest, Range, and Wildlife Sciences, Utah State University:
Conner does not support Ramey’s conclusions because other factors must be considered before determining that the subspecies are not different:

the conclusion that Z. h. preblei should be lumped with Z. h. campestris is not warranted by Ramey’s genetic and morphometric analyses. Changing the taxonomic identity of Z. h. preblei should not be done until determining whether ecological, behavioral, physiological, or physical barriers exist that may prevent Z. h. preblei from inbreeding [sic] with Z. hudsonius [campestris].

Conner also rejects Ramey’s assessment that Z. h. preblei cannot be considered a Distinct Population Segment:

the ‘discrete’ requirement that a DPS is ‘markedly separated from other populations of the same taxon by physical, physiological, ecological, or behavioral factors’ is key to the Z. h. preblei versus Z. hudsonius [campestris] issue. If you believe that only genetic evidence should be used to define a DPS, then Ramey et al.’s assessment of Z. h. preblei as not worth protecting is logical. However, if you believe that more than genetics should be used to define a DPS, then Ramey et al.’s assessment is not logical or valid.

Keith Crandall, Professor of Biology, Brigham Young University:
Crandall supports Ramey’s methods and conclusions but also states, “Indeed, it looks like you will have some more work to go to figure out an appropriate taxonomy for this group.”

Crandall also acknowledges that genetic differences are not the only test for distinctiveness:

If there were clear ecological differences that were persistent over evolutionary time and adaptively important, one might expect the evolution of morphological differences. In many cases, this occurs long before divergence of neutral genetic markers. For example, Polar Bears are obviously morphological [sic] distinct from Brown Bears, yet genetically they do not form distinct clades.

Marlis Douglas, Professor of Fishery and Wildlife Biology, Colorado State University:
Douglas questions Ramey’s methods based on the possibility of DNA becoming contaminated when using older museum specimens, the small size of the DNA sequence analyzed, the region of the mitochondrial DNA analyzed, the exclusion of certain specimens from analysis, the choice of statistical tests, and the reliance on a single marker. Her summary comments state in part:

The overall tone of the manuscript lacks objectivity. Conclusions would be more convincing if data and results were presented from a less biased perspective….The molecular data are quite limited (only 355 base pairs of sequence) and these provide insufficient resolution. Thus, results are inconclusive.

Douglas also comments on the different frequencies of the mitochondrial DNA sequence patterns (or haplotypes) observed in Z. h. preblei vs. Z. h. campestris: “the presence of different haplotype frequencies suggests that Z. h. preblei is on its own [evolutionary] trajectory and could warrant DPS (‘distinct population status’) if indeed corroborated with a more comprehensive genetic evaluation.”

David Hafner, Chair of the Science Division, New Mexico Museum of Natural History:
Hafner supports Ramey’s methods and recommendation to synonymize the subspecies, but disagrees with Ramey’s characterization of the status of the combined subspecies: “although the expanded campestris enjoys a larger geographic range, it (including populations previously assigned to preblei) is of conservation concern throughout its range.”

Hafner also writes, “I believe that Z. h. campestris (including preblei) remains imperiled.”

Carron Meaney, Research Associate, Denver Museum of Nature and Science and Curator Adjoint, University of Colorado Museum:
Meaney supports Ramey’s methods but believes that potential ecological differences should be examined:

Although there appears to be a lack of readily-available published information, I find the important question of potential ecological differences between the two taxa, or between the combined Z. h. preblei and Z. h. campestris and the remaining subspecies, nonetheless unanswered. The Front Range likely has less moisture than the Black Hills area, and the combined Front Range/Black Hills area has less moisture than the more eastern range of the species. The potential ecological (and associated behavioral) uniqueness of Z. h. preblei in being restricted to riparian habitats is worthy of further investigation, and a better understanding of how Z. h. campestris fits into this ecological paradigm is of considerable interest.

Meaney continues:

I recognize that, following the guidelines of Crandall et al. (2000), ecological exchangeability should be demonstrably heritable. This may be difficult to show for the potential habitat differences described above. Furthermore, Crandall et al. (2000) indicate that in their review of 98 studies, ecological data were frequently lacking.

I think the status of Z. h. campestris now becomes an important biological question, as very little is known about this subspecies. This taxon is categorized as vulnerable by the International Union on the Conservation of Nature. Thus although Z. h. preblei may not be distinct, there is the possibility that the two subspecies together may be imperiled.

Jeffry Mitton, Professor of Ecology and Evolutionary Biology, University of Colorado:
Mitton supports Ramey’s methods and conclusions, but also comments on the lack of ecological information available on these subspecies: “It sounds like there have not been any comparative studies of the life history variation or habitats of Z. h. campestris and Z. h. preblei.”

Mitton also writes, “no one has reported adaptive or ecological differences, but it is not clear that anyone has looked.”

Sara Oyler-McCance, Professor of Biological Sciences, University of Denver and Rocky Mountain Center for Conservation Genetics and Systematics:
Oyler-McCance generally supports Ramey’s methods, but she questions his conclusions: “I do not feel, however, that this study by any means resolves the taxonomic question. Further, I feel that some of the conclusions made by the authors are debatable.” She believes that nuclear DNA should be analyzed as well and that their use of AMOVA (a statistical method using molecular DNA) to test for genetic uniqueness may be misleading.

Oyler-McCance elaborates as follows:

I have no problems with the study itself except for some of the conclusions made by the authors. I feel that in some cases they have made recommendations based on an incomplete data set. Their data may suggest that Z. h. preblei and Z. h. campestris are synonymous yet without collecting data from nuclear loci, I would not say definitively that they are and I feel it is wrong to suggest reclassifying Z. h. preblei without collecting nuclear data and doing a more complete population level analysis first.

Gary White, Professor of Fishery and Wildlife Biology, Colorado State University:
White confines his comments to the logic behind Ramey’s conclusions:

this report concludes that there is no basis to distinguish between Z. h. campestris and Z. h. preblei because the authors did not find a difference with the tools they used. This conclusion is equivalent to stating that a Chevy 4-door wagen [sic] is equivalent to a Corvette because both use gasoline, both are shiny, both have windows, and both run on rubber tires. Both vehicles share many, many similar qualities, but are still very different vehicles.

White continues:

This report concludes that the two subspecies are the same, based on a limited suite of measurements. In reality, the report should conclude that no differences were detected given the measurements conducted, and should not jump to the unfounded conclusion that the two subspecies are identical. The conclusions presented in the report are much too strong given the necessarily limited set of measurements used.