Evolutionary history of the thicket rats (genus Grammomys) mirrors the evolution of African forests since late Miocene

TLDR: In this article, the authors inferred the molecular phylogeny of Grammomys using Bayesian and maximum likelihood methods and DNA sequences of 351 specimens collected from across the distribution of the genus.

Abstract: Aim Grammomys are mostly arboreal rodents occurring in forests, woodlands and thickets throughout sub-Saharan Africa. We investigated whether the divergence events within the genus follow the existing evolutionary scenario for the development of African forests since the late Miocene. Location Sub-Saharan African forests and woodlands. Methods We inferred the molecular phylogeny of Grammomys using Bayesian and maximum likelihood methods and DNA sequences of 351 specimens collected from across the distribution of the genus. We mapped the genetic diversity, estimated the divergence times by a relaxed clock model and compared evolution of the genus with forest history. Results Phylogenetic analysis confirms the monophyly of Grammomys and reveals five main Grammomys lineages with mainly parapatric distributions: (1) the poensis group in Guineo-Congolese forests; (2) the selousi group with a distribution mainly in coastal forests of southern and eastern Africa; (3) the dolichurus group restricted to the easternmost part of South Africa; (4) the macmillani group in the northern part of eastern and Central Africa with one isolated species in Guinean forests; and (5) the surdaster group, widely distributed in eastern Africa south of the equator. Every group contains well supported sublineages suggesting the existence of undescribed species. The earliest split within the genus (groups 1 vs. 2–5) occurred in the late Miocene and coincides with the formation of the Rift Valley which resulted in the east–west division of the initially pan-African forest. The subsequent separation between groups (2 vs. 3–5) also dates to the end of the Miocene and suggests the split between Grammomys from coastal to upland forests in eastern Africa followed by a single dispersal event into western Africa during the Pleistocene. Conclusions The evolutionary history of the genus Grammomys closely reflects the accepted scenario of major historical changes in the distribution of tropical African forests since the late Miocene.

Figures

Table 1 Minimum and maximum genetic distances (K2P-corrected and uncorrected p-797 distances) among lineages in four main Grammomys groups. Genetic variation within the 798 dolichurus group was not analysed because of the low number of available sequences. 799 800

Full text

This item is the archived peer-reviewed author-version of:
Evolutionary history of the thicket rats (genus **Grammomys**) mirrors the evolution of African forests since
late Miocene
Reference:
Bryja Josef, Šumbera Radim, Kerbis Peterhans Julian C., Aghová Tatiana, Bryjová Anna, Mikula Ondřej, Nicolas Violaine, Denys Christiane, Verheyen Erik K..-
Evolutionary history of the thicket rats (genus **Grammomys**) mirrors the evolution of African forests since late Miocene
Journal of biogeography - ISSN 0305-0270 - 44:1(2017), p. 182-194
Full text (Publisher's DOI): http://dx.doi.org/doi:10.1111/JBI.12890
To cite this reference: http://hdl.handle.net/10067/1396060151162165141
Institutional repository IRUA

1
1
Original Article
1
Evolutionary history of the thicket rats (genus Grammomys) mirrors the evolution of
2
African forests since late Miocene
3
4
Josef Bryja
1,2*
, Radim Šumbera
3
, Julian C. Kerbis Peterhans
4,5
, Tatiana Aghová
1,2
, Anna
5
Bryjová
1
, Ondřej Mikula
1,6
, Violaine Nicolas
7
, Christiane Denys
7
and Erik Verheyen
8,9
6
7
1
Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65, Brno, Czech
8
Republic
9
2
Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37,
10
Brno, Czech Republic
11
3
Department of Zoology, Faculty of Science, University of South Bohemia, 370 05,
12
České Budějovice, Czech Republic
13
4
College of Professional Studies, Roosevelt University, 60605, Chicago IL, USA
14
5
Field Museum of Natural History, 60605, Chicago, IL, USA
15
6
Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, 602
16
00, Brno, Czech Republic
17
7
Institute of Systematics and Evolution, UMR7205 CNRS-MNHN-EPHE-Sorbonne
18
Universités, 75005, Paris, France
19
8
Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and
20
Phylogeny, 1000, Brussels, Belgium
21
9
Evolutionary Ecology Group, Biology Department, University of Antwerp, 2020,
22
Antwerp, Belgium
23

2
2
24
*Correspondence: Josef Bryja, Institute of Vertebrate Biology of the Czech Academy of
25
Sciences, Research Facility Studenec, Studenec 122, 675 02 Koněšín, Czech Republic; E-
26
mail: bryja@brno.cas.cz
27
28
Running head: Evolution of climbing rats and African forests
29
30
Keywords: Arvicanthini, coastal forests, late Miocene, lowland forests, mountain forests,
31
phylogeography, Plio-Pleistocene climate changes, Rodentia, tropical Africa
32
33
34

3
3
ABSTRACT
35
Aim Grammomys are mostly arboreal rodents occurring in forests, woodlands and
36
thickets throughout sub-Saharan Africa. We investigated whether the divergence events
37
within the genus follow the existing evolutionary scenario for the development of African
38
forests since the late Miocene.
39
Location Sub-Saharan African forests and woodlands.
40
Methods We inferred the molecular phylogeny of Grammomys using Bayesian and
41
maximum likelihood methods and DNA sequences of 351 specimens collected from
42
across the distribution of the genus. We mapped the genetic diversity, estimated the
43
divergence times by a relaxed clock model and compared evolution of the genus with
44
forest history.
45
Results Phylogenetic analysis confirms the monophyly of Grammomys and reveals five
46
main Grammomys lineages with mainly parapatric distributions: (1) the poensis group in
47
Guineo-Congolese forests; (2) the selousi group with a distribution mainly in coastal
48
forests of southern and eastern Africa; (3) the dolichurus group restricted to the
49
easternmost part of South Africa; (4) the macmillani group in the northern part of eastern
50
and Central Africa with one isolated species in Guinean forests; and (5) the surdaster
51
group, widely distributed in eastern Africa south of the equator. Every group contains
52
well supported sublineages suggesting the existence of undescribed species. The earliest
53
split within the genus (groups 1 versus 2-5) occurred in the late Miocene, and coincides
54
with the formation of the Rift Valley which resulted in the east-west division of the
55
initially pan-African forest. The subsequent separation between groups (2 versus 3-5)
56
also dates to the end of the Miocene and suggests the split between Grammomys from
57

4
4
coastal to upland forests in eastern Africa followed by a single dispersal event into
58
western Africa during the Pleistocene.
59
Conclusions The evolutionary history of the genus Grammomys reflects closely the
60
accepted scenario of major historical changes in the distribution of tropical African
61
forests since the late Miocene.
62
63

Frequently asked questions

Q1. What are the contributions in "Evolutionary history of the thicket rats (genus **grammomys**) mirrors the evolution of african forests since late miocene reference:" ?

In this paper, the evolution history of the thicket rats ( genus Grammomys ) mirrors the evolution of African forests since late Miocene. 

Q2. What is the probable clade of the grammomys?

(D) Pleistocene climatic cycles 787 caused repeated fragmentations and expansions of forest habitats leading to 788 diversification within all five main clades. 

Q3. What is the main characteristic of the African rain forest?

The African rain forest – main characteristics of changes in vegetation 646 and climate from the Upper Cretaceous to the Quaternary. 

Q4. What is the probable ancestral area of the genus?

(A) The 780 fragmentation of Late Miocene pan-African forest into the ancestors of current Guineo-781 Congolese forests (green) and East African montane and coastal forests (purple). 

Q5. What is the origin of the macmillani clade?

One of the expansions of the macmillani clade 789 involved the colonization of Guinean forests (m3 lineage) by the "northern route", i.e. 790 north of the Congolese forests. 

Q6. What is the ancestor of the dolichurus?

(C) During the Pliocene the ancestors of the dolichurus (orange), surdaster (red) 784 and macmillani (blue) groups split along a south-north trajectory. 

Q7. Where were the long-term forest 785 refugia located?

The long-term forest 785 refugia for the surdaster and macmillani groups were probably located in the EAM + 786 SRM for the former and in KH + ARM for the latter. 

Q8. who is the head of the molecular ecology group at the institute?

738 Josef Bryja is head of the molecular ecology group at the Institute of Vertebrate Biology 739 ASCR, and has a general interest in factors affecting the evolution of vertebrate 740 populations. 

Q9. How many trees are represented by the circles?

The circles indicate statistical support for nodes, 763 specifically 1000 bootstraps in maximum likelihood analysis (BS)/posterior probability 764 from Bayesian analysis (PP). 

Q10. What is the name of the main mountain 754 blocks?

Main mountain 754 blocks mentioned in the text are schematically demarcated by dashed lines: KH = Kenyan 755 Highlands, ARM = Albertine Rift Mountains, EAM = Eastern Arc Mountains, SRM = 756 Southern Rift Mountains. 

Q11. what is the phylogeography of a savanna-woodl?

651 McDonough, M.M., Šumbera, R., Mazoch, V., Ferguson, A.W., Phillips, C.D. & Bryja, J. 652 (2015) Multilocus phylogeography of a widespread savanna-woodland-adapted rodent 653 reveals the influence of Pleistocene geomorphology and climate change in Africa’s 654 Zambezi region.