F Rosa Rubicondior: How Science Works - Giraffes - A single Pan-African Species Or Several Distinct Species?

Wednesday 13 March 2024

How Science Works - Giraffes - A single Pan-African Species Or Several Distinct Species?

Reticulated giraffe, Buffalo Springs, Kenya. Photo: Mogens Trolle

Photo: Mogens Trolle
Gene flow in giraffes and what it means for their conservation – Department of Biology - University of Copenhagen

In an evolutionary picture that resembles that of humans, giraffes appear to have speciated, or partially speciates at different times and in different parts of their range, then hybridized, before splitting again with regular gene-flow between the groups.

Similarly, though over a greater range, humans seems to have partially speciated into isolated populations in Africa before coming together again and spreading to Eurasia as Homo erectus which then split into Neanderthals, Denisovans and possibly others before meeting up with H. sapiens coming out of Africa in a second wave, to interbreed with the Eurasian species. The result is genetically distinct populations with evidence of ancient hybridization and gene flow.

Because conservation efforts tend to be directed at the species level, it is important for giraffe conservation to determine whether there is a single pan-African species with local sub-species or whether there are four or more species, each with a smaller population and therefore more vulnerable to habitat destruction and extinction.

To try to resolve this issue, as part of the African Wildlife Genomics research framework led by research groups at the Department of Biology at the University of Copenhagen, scientist carried out an extensive genome analysis to establish whether the different populations have been genetically isolated for long enough to be regarded as distinct species, even though, in captivity, they freely interbreed.

The results were a little surprising but highlight the difficulty in determining whether speciation has occurred within a population where differentiation is still in progress and few barriers to hybridisation have arisen. The problem is compounded by the fact that there is not a fixed definition of species, although biologists understand what the term means in a given context.

I've previously written blog posts about this problem, using the Eurasian crows as an example - an article incidentally which was recommended reading for Scottish biology students doing their 'Highers'.

The researchers have published their findings open access in the online Cell Press journal, Current Biology and explain it in a news item from the University of Copenhagen Biology Department:
EVOLUTION Giraffes, with their bizarre body plan, have always held a special place in the minds of evolutionary biologists and non-experts alike. In a new study, led by a team of researchers from the University of Copenhagen, whole-genome sequencing data was used to investigate the evolutionary processes occurring within giraffes. In particular, the authors were interested in establishing whether different populations of giraffes really have been isolated from each other for extended periods of time, which is normally a requirement before new species can arise.

Giraffes are a beautiful and powerful example of what adaptive evolution can achieve. However, in recent years they have attained notoriety for a completely different reason: it has been suggested that instead of one giraffe species, there might be no fewer than four different species. Such dramatic taxonomic reappraisals in highly conspicuous and well-known “flagship” taxa are very unusual. The suggestion caused some uproar in the scientific community and received a lot of media attention. Much is at stake, because the way that most nature conservation works is focused on species, meaning that each species must receive its own dedicated conservation action plan and must be monitored individually. If we recognize four rather than one species of giraffe, it follows that each of them will have a lower population size and be more vulnerable to extinction, not only raising the conservation stakes considerably, but also the conservation costs.

Giraffes form four distinct, but not isolated lineages - and some are even hybrids

The results of the new study, published today in Current Biology, confirm that giraffes are highly genetically structured, which means that populations tend to become differentiated from each other rather easily. It also means that giraffes do appear to be separated into evolutionary lineages that are quite genetically distinct from each other. But there were also some big surprises:

When we started getting results from our analyses of gene flow between different giraffe lineages, we had to check twice. The results showed not just a little gene flow here and there, but major hybridization events. For example, the reticulated giraffe, which occurs in Kenya, Ethiopia, and Somalia, appears to be the result of a 40%-60% mixture of an ancient northern lineage and an ancient southern lineage of giraffes, and therefore a hybrid. Today, the other descendants of these ancient northern and southern giraffes sit at either end of the giraffe tree and are highly genetically differentiated, but at some time in the past they evidently met and interbred, giving rise to the reticulated giraffe.

Dr. Laura D. Bertola, co-first authors Department of Biology
University of Copenhagen, Copenhagen, Denmark.
The team also found historical gene flow among several other branches of the giraffe tree, and in fact there are so many gene flow events among giraffe lineages that the evolutionary history within giraffes resembles a “reticulated” network rather than a tree.

What this means for giraffes and their conservation

Biologists do not agree on what the best definition of species is, nor how to resolve at what stage two populations are sufficiently different that they belong to two different species. However, it is often assumed that extensive gene flow can only take place between populations that belong to the same, and not different, species. Therefore, the finding of widespread historical gene flow between giraffe lineages that are today highly genetically differentiated raises important doubts about whether or not high genetic differentiation is necessarily a sure sign of speciation, at least in giraffes.

Our findings touch on a very delicate matter in biology, namely that we do not have a universally agreed species concept. Therefore, it can be very difficult to settle how many species there are within a group. However, we show something more tangible which has so far been overlooked in evolutionary studies on giraffes: namely that giraffe lineages have had extensive gene flow among them. Giraffes seem to have retained their ability to interbreed freely, which they also still do in captivity. So, instead of solving how many species of giraffes there are, we prefer to highlight that gene flow has occurred pretty freely among even the most genetically differentiated lineages of giraffes, whenever conditions were right for this to happen.

Associate Professor Rasmus Heller, co-senior author
Department of Biology
University of Copenhagen, Copenhagen, Denmark.
The study also concludes that regardless of the number of giraffe species, the different lineages are so genetically differentiated that they definitely deserve extensive protection in all parts of their range. If we want to protect biodiversity effectively, we cannot stop at the species level, but also need to look at the diversity within and between species.

Giraffes are such endlessly fascinating animals, and this study confirms just how much genetic variation there is even on small geographical scales. This provides a further incentive for conserving all the different lineages of giraffes, whether they be called species, subspecies, populations or whatever. Studies that focus on the whole complexity of the evolutionary process are needed, instead of studies focusing on answering simplified binary questions such as whether or not there is one, four or dozens of species, whatever that may be.

Yoshan Moodley, co-author
Department of Biological Sciences
University of Venda, Thohoyandou, Republic of South Africa.
The study is part of the African Wildlife Genomics research framework led by research groups at the Department of Biology at the University of Copenhagen. This research framework is an associated partner project of the African BioGenome Project - an African-led initiative to use genomics in the service of conservation and capacity building in Africa.

Find the article Current Biology
Graphical Abstract
  • Giraffes show exceptional genetic structure despite lack of physical barriers.
  • Giraffes have a complex evolutionary history, with high levels of gene flow.
  • Reticulated giraffes are a hybrid lineage.
  • For effective conservation, diversity within giraffes needs to be taken into account.

Strong genetic structure has prompted discussion regarding giraffe taxonomy,1,2,3 including a suggestion to split the giraffe into four species: Northern (Giraffa c. camelopardalis), Reticulated (G. c. reticulata), Masai (G. c. tippelskirchi), and Southern giraffes (G. c. giraffa).4,5,6 However, their evolutionary history is not yet fully resolved, as previous studies used a simple bifurcating model and did not explore the presence or extent of gene flow between lineages. We therefore inferred a model that incorporates various evolutionary processes to assess the drivers of contemporary giraffe diversity. We analyzed whole-genome sequencing data from 90 wild giraffes from 29 localities across their current distribution. The most basal divergence was dated to 280 kya. Genetic differentiation, FST, among major lineages ranged between 0.28 and 0.62, and we found significant levels of ancient gene flow between them. In particular, several analyses suggested that the Reticulated lineage evolved through admixture, with almost equal contribution from the Northern lineage and an ancestral lineage related to Masai and Southern giraffes. These new results highlight a scenario of strong differentiation despite gene flow, providing further context for the interpretation of giraffe diversity and the process of speciation in general. They also illustrate that conservation measures need to target various lineages and sublineages and that separate management strategies are needed to conserve giraffe diversity effectively. Given local extinctions and recent dramatic declines in many giraffe populations, this improved understanding of giraffe evolutionary history is relevant for conservation interventions, including reintroductions and reinforcements of existing populations.

Motivation and aims

In many species and species groups there is no obvious bifurcating tree that describes taxonomic relationships satisfactorily,7 and previous studies have shown that interspecific introgression is common and may even play a role in speciation in multiple mammalian lineages,8 including canids,9 felids,10,11 and bears.12 Giraffes (Giraffa sp.) provide an interesting case study, as these widely dispersed megaherbivores have been described as strongly diverged yet with a contested taxonomy.1 Although the IUCN (International Union for Conservation of Nature) only recognizes a single species with nine subspecies,13 in recent years there have been proposals to classify giraffes into four separate species.4,5,6 High levels of genetic differentiation, even between directly neighboring populations, have been central in this newly suggested classification. However, others have pointed out that different genetic markers do not show congruent results and that, depending on the methodology used, one, three, or six species could be distinguished.1,2,3

Historically, giraffes had a continent-wide range throughout savannah habitats in sub-Saharan Africa; however, their range has recently become severely fragmented as a result of anthropogenic habitat conversion and degradation.14,15 Giraffe populations are estimated to have declined 40% in the past 30 years, restricting them mostly to conservation areas.15,16 Assessing both historical and contemporary gene flow will help understand unresolved phylogeographic patterns but can also be used to inform conservation actions. This is particularly relevant since giraffes are frequently translocated,17 and insights into genetic relationships should be taken into account when selecting source and target populations for conservation translocations.18,19 Motivated by this, we aimed to explore the evolutionary and demographic history of giraffes using whole-genome data from across the range, covering all previously described major lineages.

Sequencing and quality control

We generated medium depth (≈20X) whole-genome sequencing data for 47 giraffes from 12 localities in six countries (Table S1). In addition, we obtained published whole-genome sequencing data for 43 other giraffes from 17 localities in 11 countries,4,20 as well as a giraffe21 and an okapi (Okapia johnstoni)20,22 reference genome and sequencing data from another okapi20,22 and a pronghorn (Antilocapra americana)22 as outgroups. After mapping, 11 samples were excluded due to low average depth (<6X) or highly skewed, i.e., non-symmetric, depth distributions. One individual from a pair of close (first degree) relatives was also removed, leaving 78 samples spanning 27 localities in 13 countries and all four major lineages (Figure 1A). Excluded samples are listed in Table S1 (light gray shading).
Figure 1 Sampling and population structure of giraffes

(A) Distribution of giraffe samples used in this study, colored according to inferred sublineages. Contemporary giraffe distribution, fragmented from a formerly more continuous distribution is shown in green.13

(B) ADMIXTURE results assuming K = 4 (upper barplot) and K = 10 (bottom barplot). EvalAdmix results, displaying the correlation of residuals for assessing model fit from ADMIXTURE, are shown as correlation plots above the K = 4 and below the K = 10 barplot. Gray asterisks (∗) highlight the related individuals within the Reticulated giraffe, and black asterisks indicate samples that have been excluded due to admixture signal (>10% ancestry proportion). Also see Figure S1.

(C) Neighbor-joining tree based on pairwise Identity-by-State (IBS), illustrating the substructure within the major lineages.

Figure 2 Genetic differentiation and migration rates of giraffes

(A) Table showing genetic differentiation between sublineages, expressed by pairwise Hudson FST derived from the site frequency spectrum (SFS).

(B) EEMS plot showing migration rates (log(m)) between sampling localities across the giraffe range, with high log(m) rates indicating increased gene flow and low log(m) rates indicating reduced gene flow under the null model of isolation by distance.

(C) EEMS plot showing migration rates inferred at a local scale in eastern Africa (black box), where three major giraffe lineages occur but appear geographically isolated.
Figure 4. Complex evolutionary history of giraffes, including admixture between major evolutionary lineages based on data mapped to an okapi reference genome

(A) f-branch (fb) heatmap for seven giraffe sublineages, excluding Nubian and Angolan, to reduce complexity as a result of intraspecific gene flow. The shading of the heatmap refers to excess allele sharing between branches located on the tree on the y axis (relative to its sister branch) and the sublineages identified on the x axis. Gray cells are combinations of branches and populations for which the f-branch cannot be calculated given the topology of the tree.

(B) Highest scoring admixture graph with two admixture events, including seven giraffe sublineages, exploring 0 to 5 admixture events. The gray triangles indicate that it is uncertain where along the branch these admixture events took place, as well as that introgression may not have occurred as a single pulse.

(C) f-branch (fb) heatmap for all nine giraffe sublineages. The shading of the heatmap refers to excess allele sharing between branches located on the tree on the y axis (relative to its sister branch) and the sublineage identified on the x axis. Gray cells are combinations of branches and populations for which the f-branch cannot be calculated given the topology of the tree.

(D) Highest scoring admixture graph with three admixture events, including nine giraffe sublineages. Another version of this figure based on giraffe data mapped to a giraffe reference genome is included as Data S1H. Original admixture graphs, including drift parameters, for two, three, and five admixture events are available as Data S1G for data mapped to okapi and Data S1I for data mapped to giraffe.

Bertola, Laura D.; Quinn, Liam; Hanghøj, Kristian; Garcia-Erill, Genís; et al.
Giraffe lineages are shaped by major ancient admixture events
Current Biology (2024); 10.1016/j.cub.2024.02.051

Copyright: © 2024 The authors.
Published by Elsevier Inc. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
As the authors point out, this problem is the result not of the Theory of Evolution (TOE) being wrong or inadequate, but because it is right; the giraffes are in the process of a prolonged evolution from a single pan-African species into possibly four or more genetically isolated populations that could then be classified as different species.

This problem is no comfort for creationists, firstly because it confirms the TOE and secondly because it confirms that the fuzzy definition of 'species' reflects the reality of how species form and how speciation is an ongoing process over sometimes very many years, particularly with a slow generation time, unlike the daft notion of 'kind' which seems to be a flexible as creationists need it to be.

Secondly, because the genetic evidence is that giraffes have been present and slowly differentiating in Africa for very much longer than creationists believe Earth has existed. This genetically diverse populations could not have formed within the last few thousand years from two survivors of a global flood.

Thirdly, because creating a species then giving different populations different genomes that just happen to look like the different populations evolved from a common ancestor millions of years ago and from an ancestor they share more remotely with the okapi, is not an act of intelligence but an act of deception, if the evidence of the genome is false.

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