Botany is hard

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So, in the post below, and probably in a number of posts that will follow, I criticize the results of or approaches to research that relies on field botany and plant identification. I should say now: it’s hard. None of us always get it right and mistakes will be made. A major target of my ire tends not to be that people aren’t perfect botanists, but that I think there is a systematic undervaluation of botanical expertise. Field personnel whose work requires them to be able to identify plants are often poorly trained and poorly paid, because the difficulty of the work is not appreciated. So far as I can tell, land management agencies and ecological research stations assume that someone who’s taken a couple of courses in plant taxonomy can be sent into the field and will bring back reliable data. Well, I’ve taken those courses, I’ve taught those courses, I’ve botanized extensively across much of the western United States, and I can tell you (assuming, hypothetically, a reader) now: this simply is not the case.

Someone who’s taken the courses available at NMSU (Rangeland Plants, Rangeland Grasses, Plant Taxonomy), done well and studied conscientiously, should be able to sight-ID a fair number of the common species (but few of those uncommon species that make up most of the biodiversity), and should be able to key out most plants assuming there is flowering and/or fruiting material available (and there often isn’t, but field crews don’t tend to have the luxury of waiting for good conditions). But that’s it. Don’t expect or rely on sight-IDs of most of the plants in the area, and don’t expect that any kind of identification will be possible for most species if the plants are in poor shape and many or most of the diagnostic characters are absent.

Suppose you want to answer a simple question: is plant diversity higher in grasslands or shrublands in southern New Mexico? Well, if you want reliable data, you need a field crew of people who already have several years of experience–probably voluntary / recreational since, AFAICT, no one will pay you to learn plants–botanizing in the area. Those people are scarce, and most of them have Masters or PhD degrees (and many are retired!); you probably can’t (and, ethically, shouldn’t) hire them for crappy minimum or near-minimum wage temporary positions. If, on the other hand, you hire a field crew of people fresh from their undergrad degrees whose experience is limited to two or three courses in plant ID or taxonomy, either that crew is going to be spending 90% of its time learning plant ID, or you’re going to get crappy, unreliable data. (As for the simple question, so far as I know there is no reliable answer! More on that some time later.)

One way to minimize the expertise required is to only focus on a few of the dominant plant species (as in the vegetation maps discussed in the post below). It is better to recognize one’s limitations and work within them, but this approach means you’re ignoring most of the botanical diversity in the area… not exactly ideal, in my opinion.

The gist is, if you try to fill botanical field crews on the cheap, rather than hiring highly trained botanists with extensive experience, you have a few options, none of them particularly good: deal with poor accuracy of identifications; get very little data back because your field crews are spending most of their time learning the plants; adopt a very myopic view of plant communities.

Floral inventory of my apartment

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An inventory of the plants presently living in my apartment. Some identifications are very approximate, as a number of these were acquired through greenhouses that don’t label plants and so forth… and I don’t exactly have, say, a key to all the species of Aechmea, Neoregelia, all the myriad cultivated varieties in genera like Saintpaulia, etc. Listed in alphabetical order by family, genus, then species.

Asteraceae:

Senecio articulatus
Senecio stapeliiformis

Bromeliaceae (I have a particular fondness for terrestrial bromeliads, as you may notice):

Acanthostachys pitcairnoides
Acanthostachys strobilacea
Aechmea sp. (not one of the obnoxious cultivars; alas, I’ve lost the tag indicating which species)
Billbergia chiapensis
Billbergia zebrina (thought this thing was dead for a good while!)
Deuterocohnia brevifolia
Dyckia platyphylla
Fosterella kroemeri (or perhaps F. windischii; I need to wait for flowers to tell; sold to me as Fosterella albicans)
Fosterella latifolia (sold as Fosterella villosula; Fosterella latifolia is placed in synonymy of Fosterella penduliflora in a revision by Jule Peters but it looks different so, what the hell, I’ll list it separately)
Fosterella penduliflora (I’ve had these for something like 15 years; they reseed readily and are hard to kill)
Fosterella petiolata (I think)
Fosterella spectabilis
Neoregelia sp. (not one of the obnoxious cultivars; alas, I’ve lost the tag indicating which species)
Orthophytum saxicola
Pitcairnia cf. punicea

Cactaceae (I don’t particularly like cacti, but somehow I end up with them anyways!):

x Disophyllum, unknown cultivar
Echinops, unknown hybrid
Mammillaria elongata
Mammillaria hernandesi
Rhipsalis baccifera
Rhipsalis paradoxa
Schlumbergera, unknown cultivar (white flowers)
Stenocactus zacatecasensis

Commelinaceae:

Tradescantia spathacea

Crassulaceae:

Sedum wrightii

Euphorbiaceae:

Euphorbia horrida
Euphorbia obesa (although it doesn’t look particularly happy…)

Gesneriaceae:

Saintpaulia, unknown cultivar (single purple flowers)

Hypnaceae:

Hypnum sp.

Isoëtaceae:

Isoëtes louisianensis
Isoëtes melanopoda

Marchantiaceae:

Marchantia polymorpha

Marsileaceae:

Marsilea vestita

Moraceae:

Dorstenia foetida
Ficus sansibarica

mosses (unknown family):

several species that I have not identified

Ophioglossaceae:

Botrychium lunarioides
Ophioglossum crotalophoroides

Polypodiaceae:

Davallia sp.

Polytrichaceae:

Atrichum sp.
Polytrichum sp.

Porellaceae:

Porella sp.

Psilotaceae:

Psilotum nudum

Pteridaceae:

Astrolepis sinuata (it volunteered in a terrarium, of all things)
Astrolepis windhamii
Bommeria hispida
Cheilanthes eatonii
Cheilanthes fendleri
Cheilanthes lindheimeri
Cheilanthes yavapensis
Pellaea atropurpurea
Pellaea gastonyi
Pellaea truncata
Pellaea wrightiana
Pteris cretica

Selaginellaceae:

Selaginella erythropoda
Selaginella moellendorfii
Selaginella rupincola

Sphagnaceae:

Sphagnum sp. (not really sure why I bought this… online biological supply stores are dangerous)

Vitaceae:

Cissus quadrangularis

Welwitschiaceae:

Welwitschia mirabilis

Xanthorrhoeaceae:

Haworthia herbacea

[updated 30 Jan 2014]

Plant diversity in New Mexico

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From 14 Oct 2010.

Out of curiosity, I decided to find out how many taxa (species + varieties or subspecies as applicable) are recorded from each of the counties of New Mexico. I searched the herbarium records at swbiodiversity.org & ran the results through the ASU taxonomic database, which will keep the same taxon from showing up multiple times if it’s listed under several synonyms. Of course, the taxonomic filter only works if the ASU database contains the appropriate names and synonymies; generally speaking it probably does, but there are certainly omissions and errors as well. There’s also some error in specimens being recorded for the wrong county due either to error when databasing, the collector not really knowing where he or she was, or changing county boundaries. So, the numbers are quite approximate but as good as can be done without devoting considerable time to the project. That said, here are the results on a map:

Now, one reason for doing this is that I had heard, from Dr. Heil at San Juan College, that Rio Arriba was the most diverse county in the state botanically. I was skeptical, but didn’t really know any better, but now I at least have some basis to believe otherwise; Grant County appears to be most diverse, with Rio Arriba in seventh. My initial guess was that Doña Ana or Hidalgo County would come out on top; with Doña Ana in third I guess that’s not bad, though Hidalgo’s a bit further down. Differing results between myself and Dr. Heil may be due to his use of the NMBCC (New Mexico Biodiversity Consortium) database at nmbcc.org; this database includes only the holdings of New Mexico herbaria, while swbiodiversity.org includes New Mexico holdings from the Arizona herbaria and a few others.

It’s also worth mentioning that there are some obvious biases in collecting. The eastern counties, in particular, are poorly collected. However, this alone is unlikely to account for their low diversity. For instance, there have been at least one or two floristic inventory projects in Roosevelt County (including a flora of Milnesands by Rob Strahan), and so it has about twice as many species recorded from it as most of the surrounding counties. However, the total of 651 is still unimpressive.

Gonochorism, a neglected term

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From 11 Oct 2010.

I’ve been reading a few papers recently on the evolution of sex and it seems to me that an important distinction is often overlooked, the distinction between sex and gonochorism. Theoretical work on the evolution of sex often contrasts gonochoristic sexuality, i.e., having separate male and female individuals, with asexuality. If females have a constant number of offspring in gonochoristically sexual and asexual lineages, the asexual lineage will have twice the reproductive output. Suppose all females have four offspring; a gonochoristically sexual female will have two sons and two daughters, while an asexual female will have four daughters. Those four daughters will have four daughters, while the gonochoristically sexual female’s two daughters will each have two daughters. There are some simplifying assumptions here that may not hold–i.e., the sex ratio is 1:1, males are assumed to make only a genetic and not a material contribution to reproduction, and it is assumed that no physiological reliance on sexuality exists. The second is apparently the most problematic; if males provide food or other resources that can increase the per-female reproductive rate in a gonochoristically sexual species, a competing asexual female will not be able to achieve the theoretical doubling in reproductive rate. This is likely to be a factor to some extent among many mammals and birds, but presumably not in reptiles & insects. The third assumption has also been shown not to hold in some cases. Whiptail lizards (genus Aspidoscelis) have a hormonal reliance on mating behavior, and engage in pseudosexual behavior. This apparently reduces the efficiency of reproduction and prevents asexual whiptails from maintaining an equal per-female reproductive rate compared to their gonochoristically sexual relatives.

In any case, apart from the violations of simplifying assumptions that mitigate the potential doubling reproductive output of asexuals in some cases, the potential reproductive inequality between gonochoristically sexual and asexual lineages presents presents a significant challenge to any account of how sexuality could have evolved and how it could be maintained. Resolving this difficulty has been the focus of extensive research. However, as I suggested initially, I think the problem is in part poorly framed. The reproductive inequality that papers on the evolution of sex seek to address is not specifically one relating to sexuality vs. asexuality, but a result of the division of the sexes into separate individuals, i.e., gonochorism. If we compare hermaphroditic (loosely speaking… in plants this term and ‘gonochoristic’ can be misleading, see the post regarding Pollan’s “Botany of Desire” on PBS) lineages with asexual lineages there isn’t any general theoretical reason to expect a strong reproductive inequality between the two. All offspring in each case will be reproductive. We might expect marginally lower reproduction in hermaphrodites because some of their energy is devoted to male functionality, but, as the biological cliché goes, sperm are cheap; this should not be a major factor. We might still expect asexuality to be favored under certain circumstances, particularly if gamete (or, in flowering plants, pollen) transfer is inefficient. If populations are sparse and encountering other individuals of the species is infrequent or energy-intensive (or, in flowering plants, if pollinators are scarce or inefficient)–i.e., if it is difficult to engage in sexual activity–this should tend to favor asexuality. That aside, in general it seems to me that the arguments already advanced to explain the evolution of sex, which focus in various different ways on the fact that sex encourages genetic diversity, both in terms of numbers of alleles present and in their ability to be assorted in offspring independently of each other. Genetic diversity provides the substrate on which natural selection can act, and is thus a prerequisite for an evolutionary response to selective pressure. If either abiotic or biotic conditions change, a sexual species should be able to adapt to that change much more quickly and effectively.

Sexuality seems to me to be relatively easy to explain. Gonochorism, on the other hand, is very difficult to explain. Compare a gonochoristic and a hermaphroditic lineage; the latter should have twice (more or less) the reproductive output, but both have the genetic advantages of sexuality. The hermaphrodites should win easily. So, why are there so many gonochoristic species? I’m sure there must be literature that addresses this specific point, although I haven’t run across any in my own fairly cursory reading in the field, but I think many miss this point and simply take gonochoristic sexuality and asexuality to be the two available options. They are not.

(Parenthetically, a further confusion that I’m ignoring for present purposes is that between self-fertilization (or self-pollination…) and outcrossing. Self-fertilization is sexual, but has broadly similar detrimental genetic consequences to those asexuality. In plants, the evolutionary dynamics of self-compatibility / self-pollination vs. self-incompatibility are subject to some of the same general considerations as the evolution of asexuality vs. sexuality (which in plants is generally ‘hermaphroditic’, but occasionally ‘gonochoristic’…), but of course it isn’t quite the same. The main complication added is that selfing plants can be either facultatively or obligately selfing… anyways, enough for one day.)

Seasons

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From 1 Jan 2010.

I’ve always been bothered by the traditional definitions of seasons, because seasonality is essentially a meteorological phenomenon and these definitions are based on astronomical rather than meteorological events. Clearly the amount of sunlight we receive plays the main role in determining meteorological seasons and hence the astronomical phenomena are important. However, the link between, for instance, the winter solstice and thermal minimum is somewhat complicated. If insolation directly and instantaneously determined terrestrial temperatures, the solstice and thermal minimum should coincide. If we assume a naïve astronomical determinism, winter solstice should be the middle of winter, not its beginning. However, thermal inertia places the temperature minimum after the winter solstice, sometimes long after. Consequently, an astronomically coherent view of seasons does not make sense meteorologically. Placing the beginning of winter at the solstice to account for this lag both removes the astronomical credibility of seasonal definition and entails an assumption that the thermal minimum lags about 45 days behind the winter solstice. This may happen in very cold climates (e.g., the North Slope of Alaska & high elevations in the Sierra Nevada), but more typically the thermal minimum lags 10-30 days after the solstice. The dominant view of seasons as beginning at the solstices and equinoxes does not make sense either astronomically or meteorologically. Like most compromises, it fails on both counts. So, in my opinion, either we should define seasons astronomically, or meteorologically. Since I view seasons as a fundamentally meteorological phenomenon, I will opt for the latter. Perusing weather data for El Paso on wunderground.com, I have defined the seasons for southern New Mexico and west Texas as follows: the coldest 91 days are winter; the warmest 91 days are summer; the days falling after winter & before summer are spring; the days falling after summer and before winter are fall. This gives the following dates:

Spring begins on February 19th.
Summer begins on June 1st.
Fall begins on August 31st.
Winter begins on November 20th.

For comparison, here are graphs showing the various options with temperatures at El Paso (modified from wunderground.com). First, astronomically defined seasons; i.e., solstices & equinoxes are centered in each season:

Second, traditionally defined seasons with the solstices and equinoxes beginning seasons:

Third, my meteorologically defined seasons:

Note that the astronomical seasons are too early (because they do not incorporate lag) and the traditional seasons are too late (because they incorporate too much lag). June 1st and August 30th both have average mean temperatures of 79 degrees Fahrenheit. November 20th and February 18th both have mean temperatures of 51 degrees Fahrenheit. Dates would probably move slightly based on a more precise analysis, but these should be pretty close. Lag for thermal minima and maxima is about 10-15 days, although the thermal maximum is not centered within summer due to the influence of the average onset of monsoonal rains around the beginning of July, which depresses daily maximum temperatures while apparently having no strong effect on daily minima. Spring ends up being longer than fall (102 vs. 81 days), but this reflects the meteorological reality that warming in the area is more gradual in spring than is cooling in fall.

Doing the same thing for Indiana (using weather data from the Indianapolis airport), we get:

Spring begins on March 3rd.
Summer begins on June 5th.
Fall begins on September 5th.
Winter begins on December 5th.

And more graphs; astronomically defined seasons:

Traditionally defined seasons:

Meteorologically defined seasons:

Indiana lacks the significant asymmetry of southern New Mexico & western Texas, presumably because there is no monsoon season. Maxima & minima lag about 28-30 days behind the solstices.

Comparing the two also brings to light another detail worth mentioning: placing the beginnings and endings of seasons at uniform dates across even the climates of the United States is a normative cultural concept that does not accurately meteorological reality. Indiana and southern New Mexico are by no means the most divergent climates one could choose in this respect; I chose them simply because these are the two places I have lived.

Getting plant sex wrong

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From 28 Oct 2009.

Watching “Botany of Desire” on PBS. I’ve generally been a bit ambivalent about Michael Pollan, but about 36 minutes in he veers into “just plain wrong” territory. “Before that [before the evolution of angiosperms] you had this greener, sleepier world where things reproduce usually by cloning, by spores that were genetically identical to their parents”. Regarding cloning–yes, there were a fair number of clonal plants before angiosperms evolved, but there are also plenty of clonal angiosperms. Regarding spores–he is right that sexual recombination isn’t involved in producing spores but: 1) this does not mean the spores are genetically identical to the parent–they aren’t; 2) angiosperm reproduction involves the production of spores as well, so this is not a difference between angiosperms & non-angiosperms.

Brief recap of plant life cycles: the dominant portion of the vascular plant life cycle is the sporophyte (on the other hand, gametophytes are dominant in non-vascular plants: mosses, liverworts, hornworts), which is diploid (has two sets of chromosomes, just like all stages of the human life cycle except sperm & eggs). The diploid sporophyte produces spores by meiosis. Meiosis halves the chromosome number, so the spores are haploid. Whereas the sporophyte has two copies of each gene (excluding the rare cases in which plants have sex chromosomes), each spore has one copy of each gene. It’s the same as the relationship between, for instance, a human male and one of his sperm cells (except, for the sake of nit-picking, that humans have sex chromosomes and most plants don’t), and is not genetic identity. However, whereas human sperm & egg cells do nothing more than unite to form a zygote, plant spores undergo cell divisions to produce gametophytes. Gametophytes are a multicellular haploid stage in a vascular plant’s life cycle, and they produce gametes (sperm and eggs) through mitosis. Gametophytes exist in all plants, but are quite small and dependent on the sporophytes in angiosperms. Pollen grains are male gametophytes. Inside each ovule lives a female gametophyte. When the sperm and eggs produced by gametophytes join in fertilization, we are back at the diploid sporophyte level. Very short version: diploid sporophyte produces spores; spores grow into haploid gametophyes; gametophytes produce sperm & eggs; fertilization takes us back to a diploid sporophyte. Although (with minor exceptions; e.g., the genus Vittaria, some species of which exist solely as gametophytes) all plants produce spores, in no plants is the production of spores itself sexual. The production of spores is part of the sexual process, however; without the gametophytes they give rise to, you can’t get gametes. Lest you think Pollan just misplaced a word or two, he continues: “And then you have this incredible explosion of diversity that happens with this new strategy. It was an incredibly successful strategy. It allowed you [by which he means angiosperms] to move your genes around, it allowed you to evolve much quicker because sex creates variation.” Nope, he didn’t just misplace a word or two, he’s really saying that the key innovation of angiosperms relative to earlier plants was sex.

Eryngium

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From 7 Oct 2007

How to distinguish Eryngium heterophyllum and Eryngium lemmoni
or
Why I don’t like to use the Kearney & Peebles Flora of Arizona

Here is how Kearney & Peebles distinguish these two species:
“3. Plants from a cylindric taproot; lower cauline leaves pinnatifid to bipinnatisect; inflorescence paniculately branched, the heads comate; bracts linear-lanceolate to lanceolate, entire or with 1 or 2 pairs of lateral spines near the middle, commonly yellowish above . . . . . . . 3. E. heterophyllum
3. Plants from a fascicle of fibrous or fleshy roots; lower cauline leaves spinose-serrate; inflorescence successively trifurcate, the heads not comate; bracts broadly lanceolate to oblanceolate, spinose-serrate with 2 or 3 pairs of teeth, silvery-white above . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4. E. Lemmoni”

And here are my observations on the various characters:
“Plants from a cylindric taproot” vs. “plants from a fascicle of fibrous or fleshy roots”. This appears to be accurate and, although not necessarily a useful field character, this can be a useful distinction with good herbarium specimens.
“Lower cauline leaves pinnatifid to bipinnatisect” vs. “lower cauline leaves spinose-serrate”. This is also essentially accurate, although it could be better worded, for instance by including a more quantifiable distinction rather than descriptive terms that can be somewhat subjective (how deep must the divisions be before the leaf is pinnatifid?).
“Inflorescence paniculately branched” vs. “inflorescence successively trifurcate”. This is simply inaccurate. Inflorescences of the two species are quite similar. In both, as we move up the plant we have first several alternately arranged primary inflorescence branches, then a whorl of ca. 3-7 primary branches. Each primary branch of the inflorescence is determinate, and may either terminate in 2-3 heads arising from a single node, or the lateral head(s) may be replaced by secondary branches terminating in groups of 2-3 heads. It seems to be more common for E. heterophyllum to have the terminal groups with only 2 heads, and E. lemmoni to have groups of 3 heads. However, this is by no means a uniformly applicable identifying characteristic, and neither species has an inflorescence that is accurately characterized as “paniculately branched” or as “successively trifurcate”, although the primary branches of the inflorescences of either species may (or may not) be “successively trifurcate”.
“The heads comate” vs. “the heads not comate”. “Comate” is, first, a needlessly obscure term. I do not recall having heard it before, in any context, and although it sounds much like the more commonly used “comose” the meaning is quite different. In any case, a comate head is one in which the bracts of the head are greatly enlarged at the apex of the head and form a leafy projection beyond the flowers. Pineapples are comate. The heads of E. lemmoni are indeed not comate and most heads on most specimens of E. heterophyllum are indeed comate. But some heads on many specimens, and all heads on rare specimens of E. heterophyllum are not comate, or at best indistinctly so. So this is a one-directional character; plants with comate heads must be E. heterophyllum, but plants with non-comate heads could be either species.
“Bracts linear-lanceolate to lanceolate, entire or with 1 or 2 pairs of lateral spines near the middle” vs. “bracts broadly lanceolate to oblanceolate, spinose-serrate with 2 or 3 pairs of teeth”. This is accurate, although unfortunately there is overlap in the descriptions.
Bracts “commonly yellowish above” vs. “silvery-white above”. I cannot tell if this character is inaccurate, or simply variable and of limited utility. I have only seen E. heterophyllum in the field at two locations (Rucker Canyon in the Chiricahua Mts. and Clanton Draw in the Peloncillo Mts.), but both times the bracts were silvery-white above. No difference in bract coloration is apparent from the herbarium specimens I looked at earlier today, but colors are often unreliable in dried material. Presumably any specimens that did clearly have yellowish bracts could be readily identified but, as with non-comate heads, specimens with silvery-white bracts (which appear to be the overwhelming majority) could be either species.

Although this is the most annoying example I have encountered recently (since this key has resulted in my misidentifying E. heterophyllum as E. lemmoni not once but twice), it is unfortunately not an isolated example. Most keys in the Kearney & Peebles flora are well written and eminently usable. However, a significant minority are not, and while these keys will still usually yield correct identifications if used carefully while comparing specimens of all of the relevant taxa, they often make me feel rather confused and can easily lead to misidentifications if used incautiously.

Plants in washing machines

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I’ve put compact flash cards through the wash a few times with no ill effect, but I discovered a stem of Senecio pendulus that had made it through the washing machine. This is a succulent species, with jointed stems and no leaves, similar in some ways to Cylindropuntia (but without spines). The joints break off readily, and one apparently fell among my dirty laundry. In any case, it is apparently no worse for wear and I’ve planted it. We’ll see if it survives.

Quotes from Stebbins

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A collection of edifying (or, at least, interesting to me) quotations from G.L. Stebbins’ Variation and Evolution in Plants, originally posted in Sep 2006.

p. 1:
“The hierarchy of categories is a multidimensional pattern of variation in nature, and the gaps or discontinuities give reality to the various categories.”

I think (and hope) he means taxa by “categories”. This seems to be his usage elsewhere. There are several other interesting quotes in the first few dozen pages that I may put up later.

p. 34:
“All [Dobzhansky, Mayr, & Huxley] agree that species must consist of systems of populations that are separated from each other by complete or at least sharp discontinuities in the variation pattern, and that these discontinuities must have a genetic basis.”

This remains essentially the case with modern disagreements on species concepts. The disagreements are not in what species are, but in what is the best axis on which to look for discontinuities.

p. 35:
“In fact, it is likely that most families in which the genera are well-defined have suffered the extinction of many species, and further that most boundaries between neighboring genera represent gaps left by species which have perished.”

The importance of extinction in observed patterns remains often overlooked and misunderstood. In most cases monophyletic taxa, for instance, were probably previously paraphyletic groups in which sufficient lineages have subsequently become extinct.

Stebbins continues:
“If this fact is kept in mind, then the search for natural boundaries to genera has some meaning to the evolutionist and is not entirely a matter of convenience.”

pp. 189-190:

“The common ground of agreement between these definitions may be expressed as follows. In sexually reproducing organisms, a species is a system consisting of one or more genetically, morphologically, and physiological different kinds of organisms which possess an essential continuity maintained y the similarity of genes or the more or less free interchange of genes between its members. Species are separated from each other by gaps of genetic discontinuity in morphological and physiological characteristics which are maintained by the absence or rarity of gene interchange between members of different species. The above sentences are not to be construed as this authors definition of a species, since several different species definitions are possible within the framework of their meaning.”

But–isn’t it precisely the problem of existing species concepts that they try to limit us to a single axis for discerning species, rather than admitting of several different axes, as Stebbins’ sentences above do? Why not embrace such a broad and inclusive definition–merely because it could be subdivided?

p. 202:
“The second alternative [the first was multiple species concepts] would be to recognize that at any given moment in the evolutionary time sale, reproductive isolation is important in keeping distinct only those populations which are sympatric or which overlap in their distributions.”

In other words… Mayr’s Biological Species Concept is applicable only to sympatric or overlapping populations. This criticism has been hemmed and hawed over for five decades now, but has never been addressed in a coherent fashion. And it is precisely a multidimensional species concept that will allow us to overcome this problem, as well as those that plague the other species concepts. Why, after all, would we expect groups in multi-dimensional space to always be identifiable along a single axis, like that of reproductive isolation?

More bits of Stebbins; p. 262:

“Hybridization between well-established and well-adapted species in a stable environment will have no significant outcome or will be detrimental to the species populations. But if the crossing occurs under rapidly changing conditions or in a region which offers new habitats to the segregating offspring, many of these segregates may survive and contribute to a greater or lesser degree to the evolutionary progress of the group concerned.”

p. 270:

“There is little doubt, therefore, that the majority of the examples of hybridization and introgression which can be found in plant populations at the present time are associate with the disturbance of old habitats and the opening up of new ones through human activity.”

White sands lizards

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Another old post, from 19 Jul 2007.

Now, there’s nothing some scientists like better than pointing out the gaping flaws in the work of others. I happen to be one of those scientists, and, with that in mind, here are my thoughts on a recent paper by E.B. Rosenblum: Convergent Evolution and Divergent Selection: Lizards at the White Sands Ecotone. First, a brief summary, taken from portions of the abstract:
“Three lizard species [Aspidoscelis inornata, Holbrookia maculata, and Sceloporus undulatus], distributed along a dramatic environmental gradient in substrate color, display convergent adaptation of blanched coloration on the gypsum dunes of White Sands National Monument.” … “I find species differences in degree of background matching and in genetic connectivity of populations across the ecotone. Differences among species in phenotypic response to selection scale precisely to levels of genetic isolation. Species with higher levels of gene flow across the ecotone exhibit less dramatic responses to selection. Results also reveal a strong signal of ecologically mediated divergence for White Sands lizards. For all species, phenotypic variation is better explained by habitat similarity than genetic similarity. Convergent evolution of blanched coloration at White Sands clearly reflects the action of strong divergent selection; however, adaptive response appears to be modulated by gene flow and demographic history and can be predicted by divergence-with-gene-flow models.”

The problems in this study show the importance of basic biology & knowledge of ecology. First off, this is based on mitochondrial DNA and the results show higher gene flow between sample sites for the teiid Aspidoscelis inornata than the two phrynosomatid species, Holbrookia inornata and Sceloporus undulatus. Mitochondrial DNA is, however, a biased marker; since it shows only matrilineal relationships, it will consistently underestimate gene-flow in species with male-biased dispersal. Not a terribly good choice, then, but perhaps defensible because it is far easier to work with than any of the alternatives; however, the deficiencies need to be addressed and they aren’t. Most lizards, including phrynosomatids, do have male-biased dispersal; but teiid lizards don’t. So we would expect that, even under similar patterns of overall gene flow, phrynosomatids should show more geographic structure than teiids because of differences in sex-biased dispersal.

Second, differences in microhabitat use & behavior, although mentioned, are given short shrift. From the paper:
“A previous study comparing activity patterns between H. maculata and S. undulatus at White Sands found that H. maculata spent more time in open areas and was less closely associated with vegetation than S. undulatus (Hager 2001a).” … “Therefore, it is plausible that H. maculata is more visible to predators and that selection pressure for substrate matching is higher in this species.”
This is an important point. If we want to look at background matching, we need to measure the backgrounds relevant for the lizards. A lizard that spends a lot of its time under bushes needs to be cryptic under bushes, not merely on open sand; even if it matches its background just as well as a lizard spending most of its time on open sand, it will be darker and more strongly patterned. And, guess what, the species that spends most of its time on sand, Holbrookia maculata, is indeed lighter and less-patterned than the other two, and so the observed results fit perfectly with expectations based on what we know of the ecology of these lizards. Moreover, ordering of taxa in order of brightness is the same on White Sands and off: Holbrookia maculata is always brightest, Aspidoscelis inornata is always darkest, and Sceloporus undulatus is always intermediate–a good indication that something more than different facility in matching White Sands substrates is going on. But an important role for microhabitat use and behavior is rejected for, so far as I can tell, no particularly good reason.

A third, and related, problem is poor knowledge of White Sands:

“Second, intermediately colored S. undulatus [and A. inornata!] could be locally adapted to the intermediate substrate color at the margin of the dune field. However, in contrast to the large expanse of pure gypsum habitat, the band of intermediately colored ecotonal substrate is extremely narrow, often only meters wide. Given the likelihood of gene flow across the ecotone in this species and the restricted area of the ecotone, natural selection would need to be implausibly strong to provide an adaptive explanation for maintenance of intermediate color morphs.”
I’ve spent some time wandering White Sands. The basic situation is this: there’s a large active dune field with very white sand and small, slightly darker interdunal areas; to the west of this area there are flat, crusty, white, alkali flats; to the north, east, and south, the dunes get progressively smaller, narrower, more vegetated, and slightly darker in color while the interdunes get much larger and significantly darker. These large interdunes toward the edge of the dune area are a major portion of the White Sands area, and are intermediate in color between the active dune field and the soil of the surrounding flats of Tularosa Basin. The “extremely narrow” ecotone is exactly what you see along the road at White Sands National Monument in the area of the Big Dunes Trail, one of E.B. Rosenblum’s collection sites, but it is not at all an accurate representation of the situation otherwise. Importantly, Aspidoscelis inornata is very abundant in these large interdunal areas, whereas Holbrookia maculata is not (I haven’t seen enough Sceloporus undulatus, OTOH, to have any idea of their distribution). This comes back to the point above: what background is relevant to the lizards? This is determined by behavior and abundance across habitat types and cannot be estimated by simply choosing a half-dozen sites, treating them as monoliths, and seeing how well the lizards at each site match open soil or sand.

And then we have another problem: phenotypic plasticity. We don’t know whether or not color differences between White Sands and other populations of these lizards are heritable, and we do know that most lizards, including phrynosomatids, have some level of plasticity in coloration. For instance, a 1958 study by R.E. Bundy & J. Neess suggests that the major factor in background matching by the phrynosomatid Phrynosoma modesta is plasticity.

And now we’re down to nit-picking. There are more than three lizards with light-colored populations on White Sands, but the “other two” are never mentioned: Phrynosoma cornuta and Uta stansburiana. I wouldn’t bother mentioning this, except that E.B. Rosenblum says: “In this study, I ask how the complete lizard fauna at White Sands has responded to natural selection across a common ecotone.” No, this study examines how 3/5 of the lizard fauna at White Sands responds to selection.

In conclusion:
1. The genetic markers used do not provide a neutral estimate of gene flow, and this bias, although fundamental in interpretation of the results, is ignored.
2. Alternative explanations that fit the data at least as well as the preferred hypothesis, that gene flow limits crypsis, are rejected either without good cause or due to poor knowledge of the area.