A new paper confidently

claims that there are four

giraffe species rather than
one, but I’m not so sure
by whyevolutionistrue September 11, 2016 • 10:00 am

The giraffe, Giraffa cameleopardalis, was first described

by Linnaeus, and gets its species name from its fancied
resemblance to a hybrid beast (as Wikipedia notes, the
name comes from the Greek καµηλοπάρδαλις” meaning
“giraffe”, from “κάµηλος” (kamēlos), “camel” + “πάρδαλις”
(pardalis), “leopard”, due to its having a long neck like a
camel and spots like a leopard). It’s always been
considered a single species, but divided into about a half
dozen subspecies that live in different areas and are
distinguishable by different patterns of reticulation in their
coats. Here’s an old subspecies designation and map;
note that the populations included in each of the six
subspecies live in different areas:
Here’s a classification of nine subspecies based on
pattern (the number of named subspecies has been
between four and about nine (I haven’t searched
extensively).
Note that this classification is more or less arbitrary
because the populations are geographically isolated and
so one can’t use the classical “biological species
definition” (BSC), in which members of the same species
are able to interbreed in nature and produce fertile
hybrids, while members of different species, when
present in the same area, either do not mate with each
other, or, if they do mate, do not produce hybrids that are
fertile. Note that to use the BSC, putatively different (or
identical) species have to be “tested” when living in the
same area (“sympatric”). If they do not encounter each
other in nature, there’s little you can do to apply the BSC.
One way around this is to hybridize them in zoos. If
different “subspecies” do not mate with each other, or
can’t produce fertile hybrids when they do mate in
captivity, they’re almost certainly unlikely to do so in
nature, and can be considered members of different
species. However, if two different types do hybridize and
produce fertile offspring in captivity, that doesn’t mean
they’re members of the same species, for in nature other
“isolating barriers”, like different breeding times or a
genetically-based aversion for mating with other types,
could keep them genetically separated even
though barriers could break down in the artificial
environment of zoos.

“Ligers“, for instance, are hybrids between male lions and

female tigers, made famous in the movie Napoleon
Bonaparte. Lions and tigers will mate in captivity, and
some liger hybrids are fertile. But we don’t consider lions
and tigers to be members of the same biological species
because, when they were living in the same place in
nature—in India, though they no longer are “sympatric”
there—no hybrids were produced.

Allen Orr and I discuss the rationale for using the BSC for
investigating how species originate in Chapter 1 of our
book Speciation (2004), and conclude that if you want to
understand “the species problem”—why animals and
plants in a given area divide into clumps and are not
simply a schmear)—the BSC is the concept to use. But if
you merely want to name species, rather than understand
how discrete cluster originate, then you’ll have to engage
in a subjective classification if those groups don’t live in
the same area.

This is the problem with a new paper in Current Biology

by Julian Fennessy and coauthors (reference and free link
below). This paper tries to determine the number of
giraffe species that really do exist, but since the
subpopulations live in different places and don’t
encounter each other (see below), they’re forced to
use another criterion to determine the number of giraffe
“species”. They use genetic divergence, as measured by
the amount of sequence difference in the DNA.

Fennessy et al. sequenced eight genes: 7 nuclear genes

and the mitochondrial DNA (effectively a single gene) in
nine previously-described subspecies of the giraffe.
Phylogenetic analysis of the sequences, shown below,
showed that populations fell into four distinct clusters,
which they decided to call “four species”. Here are the
new species they distinguish and name:

southern giraffe (Giraffa giraffa),

Masai giraffe (G. tippelskirchi),
reticulated giraffe (G. reticulata)
northern giraffe (G. camelopardalis), which includes
the Nubian giraffe (G. c. camelopardalis) as a distinct
but related subspecies.

Here’s the phylogenetic analysis (turn sideways); the

colors of the populations correspond to colors on the map
below (note again that the subspecies do not inhabit the
same areas, though they may have in the past; we just
don’t know!) Note too that each species is “monophyletic”,
containing all the individuals that descend from a single
common ancestral population.
Here are some of the populations they sampled; the
colors correspond to the dots in the phylogeny above.

(From the paper): Figure 1 Distribution and Sampling Locations of Different Giraffe
Subspecies in Africa (A) Distribution ranges (colored shading) provided by the Giraffe
Conservation Foundation [7], plotted on a map of Africa
(http://www.naturalearthdata.com/). Circles represent sampling locations; for coding,
see Figure 2. (B) Enlarged view of the South Sudan region. Note that the samples of the
putative Nubian giraffe were taken west and east of the Nile River.

Finally, the authors do a genetic “STRUCTURE” analysis,

which assumes the presence of different groups (varying
how many groups they preconceive) and tries to see,
using genetic differences, how distinct those groups. The
assumption of both three and four groups (the latter
corresponding to the four species they name) were the
most useful for giraffes. At the top of the figure below you
can see how well the clusters are demarcated with a K
(group number) of four, and how the demarcation
becomes marginally worse when you assume five
clusters.

Also, below the cluster diagram is a DNA-based estimate

of giraffe “species” divergence times calibrated from the
fossil record of other mammals. You can see that the four
groups diverged from each other between 1 and 2 million
years ago.
So everybody seems to be happy with the conclusion that
we have four species instead of one.

Everybody, that is, but Matthew Cobb and I. But more on

that in a second.

The breathless conclusion that we have four species was

accepted not only by the journal Current Biology, which
published the paper (note the title), but by major news
outlets, including the New York Times, the BBC, Science
magazine, and so on. I haven’t found a word of criticism of
this conclusion. So here’s some.

Dividing up geographically isolated groups into species is

an exercise in naming and classification rather than
understanding the problem of why nature is discontinuous
—and by “discontinuous”, I mean the answer to the
fascinating question “Why, in one area, are animals and
plants divided into discrete groups rather than forming a
continuum?” Using a genetic-distance measure, as the
authors did in this paper, simply tells you how long the
groups have been separated rather than whether they’d
remain discrete were they to meet in nature. It tells you
about evolutionary history but not about speciation.

So yes, we know the four groups they call species

have been separated for 1-2 million years, and have
developed coat color differences. But human “races” have
also developed coat-color differences (and other genetic
differences) over a period of about 60,000-100,000 years,
also largely among geographically isolated groups. Now
human populations cannot be distinguished from their
DNA sequences nearly as unambiguously as can these
giraffe subspecies, but if you gave them another million
years of geographic isolation (now impossible because of
travel), they might well have separated genetically to the
same extent as these giraffes. Would you then be happy
to call human populations different “species”? What if a
human population became marooned on an island for a
million years, and changed its hair color and became
genetically distinguishable using sequencing of largely
neutral sites. Would you be happy to say, unambiguously,
that here was have a new species: Homo islandensis?

Also note that genetic STRUCTURE analysis of human

populations shows a pretty neat division into six groups
(Rosenberg et al. 2002), corresponding well with 5
geographic regions. (Using other assumptions of group
numbers, with K = 2, 3, and 4, doesn’t give as clean a
resolution, as shown by areas with mixed colors). The
groups are from Africa, East Africa, Europe + Middle East,
Central/South Asia, Oceania, and the Americas.
Do we have five human species here, based on genetic
clustering? How much genetic difference would be
sufficient to call them different human species? (These
problems are all discussed in the Appendix of Speciation).

The correlation of genetic differences with geographic

isolation, of course, reflects the fact that populations that
don’t get a chance to exchange genes become more and
more different through time via natural selection and—
probably the major force in this case—genetic drift. But
how much difference do we need to diagnose species?
It’s arbitrary, since populations can become “reciprocally”
monophyletic for even a single gene. Okay, so how many
genes do you need?

So the designation that there are four genetic clusters of

giraffes is sound, but do they correspond to what
evolutionary biologists call “species”? Who knows? We
don’t know whether these groups are reproductively
isolated. I can find no evidence that these groups ever
lived in the same area of Africa at breeding time—or any
time. Further, they can apparently hybridize in zoos (see
reference 20 for THE GIRAFFE STUD BOOK; the fertility of
hybrids isn’t mentioned). So while these are “genetic
clusters”, we have no idea whether they’re biological
species.

Matthew in fact was quoted in the BBC piece from an

email he sent them, but they left out his caveat about
reproductive isolation. Here’s what the article said:
 Matthew Cobb, professor of zoology at the University
of Manchester explained that the “four groups of
giraffes had “been separated for 1-2 million years, with
no evidence of genes being exchanged between
them”.

Here’s what the BBC chose not to quote from Matthew’s

email (reproduced with permission):

Defining species is difficult, and neither number of

genetic differences between two groups, nor the time
they have been separated, are necessarily relevant.
The key point is what is called the biological species
concept – does mating between these groups produce
fertile offspring? If not, they are species. If they can
produce fertile offspring, then no matter how long they
have not done so in the wild, they are still not true
species. However, this technical aspect is probably the
least interesting point about this study. Instead, we
should be focusing on developing appropriate
conservation strategies for the four groups identified in
this study. Whatever we call them, these four groups
have distinct genes and have had distinct histories for
over a million years.

I agree almost completely with Matthew, though I have

one quibble. Yes, Fennessy et al. have identified groups
that we can use for conservation purposes—if we want to
conserve the phenotypic and genetic diversity in what
was once considered a single species. But do we want to
do that? This question is never really discussed. ‘

If we’re trying to save the coat color genes, well, they’re

probably segregating at low frequency in other “species”
of giraffes, and we could reconstruct any extinct pattern
through artificial selection. If we’re trying to save the DNA
diversity, most of which probably involves nucleotide
bases whose differences among the “species” is of no
biological consequence, why are we trying to do that? My
point here is that—and I may be missing some literature—
is I have never seen a detailed and critical discussion
of what exactly conservationists are trying to accomplish
when they decide to preserve populations X, Y, and Z. As
Dick Lewontin pointed out long ago, a single fertilized
female within a species contains half of all the “additive
genetic variation” (selectable genetic variation for various
traits) of the entire species, and that kind of latent
variation is probably present in several or all of the four
“distinct” giraffe species. When we say “we have to save
all four giraffe species”, we don’t consider what we’re
trying to save? The populations themselves? The
phenotypic differences that distinguish them? Or the
genes that distinguish them? (My own view is that we
should save everything just out of respect for animals and
plants that were here before us.)

I’ve been hard on this study because I study species using

the BSC, but I want to finish by saying out that the study
of Fennessy et al. is indeed very good, except for its
certainty that we have four “species”. They don’t discuss
the difficult problem of what, exactly, a “species” is—
something that Matthew summarized in one paragraph.
That aside, Fennessy et al. have done great work. They
have identified four distinct genetic clusters, which tells us
about the evolutionary history of these groups and may
ultimately give a key to their degree of reproductive
isolation if the giraffes move around (perhaps due to
climate change). It also gives us an idea of which groups
were geographically isolated for long enough to allow
such genetic differences to accumulate, and thus raises
questions about biogeography of these populations.

But four species for sure? I can’t say. And I’m surprised
that the major science journals and newspaper sections
have accepted the authors’ conclusions uncritically.

__________

Fennessy, J. et al. 2016. Multi-locus analyses reveal four

giraffe species instead of one. Current Biology 26:1-7,
online doi.org/10.1016/j.cub2016.07.036