taxonID	type	format	identifier	references	title	description	created	creator	contributor	publisher	audience	source	license	rightsHolder	datasetID
C46987C9356FB13CBC65F9A398D0C285.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971751/files/figure.png	https://doi.org/10.5281/zenodo.14971751	Figure 5. Taxonomic summary of the cometes group (= selousi group of Bryja et al. 2017). A, the distribution of mtDNA lineages.The different colours of triangles correspond to different lineages (se1–se5 described by Bryja et al.2017; se6 and se7 are new discoveries in this study). B, delimitation of MOTUs based on ddRAD data. All studied populations in the cometes group (purple triangles) were grouped in the single clade no. 8 by a branch-cutting approach (indicated by a number in a coloured rectangle).Likewise, they clustered together by INFOMAP as a single MOTU IX (see also Fig.3). The proposed taxonomy is shown on the right side of the maps.Stars show type localities for the cometes group. The proposed species name for the whole group, Grammomys cometes, is shown in larger bold letters, while smaller letters correspond to synonyms.	Figure 5. Taxonomic summary of the cometes group (= selousi group of Bryja et al. 2017). A, the distribution of mtDNA lineages.The different colours of triangles correspond to different lineages (se1–se5 described by Bryja et al.2017; se6 and se7 are new discoveries in this study). B, delimitation of MOTUs based on ddRAD data. All studied populations in the cometes group (purple triangles) were grouped in the single clade no. 8 by a branch-cutting approach (indicated by a number in a coloured rectangle).Likewise, they clustered together by INFOMAP as a single MOTU IX (see also Fig.3). The proposed taxonomy is shown on the right side of the maps.Stars show type localities for the cometes group. The proposed species name for the whole group, Grammomys cometes, is shown in larger bold letters, while smaller letters correspond to synonyms.	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C9356FB13CBC65F9A398D0C285.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971745/files/figure.png	https://doi.org/10.5281/zenodo.14971745	Figure 2. Mitochondrial phylogeny (Bayesian inference) based on CYTB sequences.Black dots show node support with posterior probability> 0.95. Four major groups of Grammomys (sensu Bryja et al. 2017), split into numbered lineages, are shown by different colours: cometes (previously selousi; se1–se7) group in purple; dolichurus (d) group in orange, macmillani (m1–m11) group in blue; and surdaster (su1–su13) group in red. A summary of available karyotypic data for particular mitochondrial lineages is shown on the right side (see more details in the ‘Taxonomic revision of Grammomys’ section).	Figure 2. Mitochondrial phylogeny (Bayesian inference) based on CYTB sequences.Black dots show node support with posterior probability> 0.95. Four major groups of Grammomys (sensu Bryja et al. 2017), split into numbered lineages, are shown by different colours: cometes (previously selousi; se1–se7) group in purple; dolichurus (d) group in orange, macmillani (m1–m11) group in blue; and surdaster (su1–su13) group in red. A summary of available karyotypic data for particular mitochondrial lineages is shown on the right side (see more details in the ‘Taxonomic revision of Grammomys’ section).	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C93568B13CBC21FF1B9FCDC13E.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971751/files/figure.png	https://doi.org/10.5281/zenodo.14971751	Figure 5. Taxonomic summary of the cometes group (= selousi group of Bryja et al. 2017). A, the distribution of mtDNA lineages.The different colours of triangles correspond to different lineages (se1–se5 described by Bryja et al.2017; se6 and se7 are new discoveries in this study). B, delimitation of MOTUs based on ddRAD data. All studied populations in the cometes group (purple triangles) were grouped in the single clade no. 8 by a branch-cutting approach (indicated by a number in a coloured rectangle).Likewise, they clustered together by INFOMAP as a single MOTU IX (see also Fig.3). The proposed taxonomy is shown on the right side of the maps.Stars show type localities for the cometes group. The proposed species name for the whole group, Grammomys cometes, is shown in larger bold letters, while smaller letters correspond to synonyms.	Figure 5. Taxonomic summary of the cometes group (= selousi group of Bryja et al. 2017). A, the distribution of mtDNA lineages.The different colours of triangles correspond to different lineages (se1–se5 described by Bryja et al.2017; se6 and se7 are new discoveries in this study). B, delimitation of MOTUs based on ddRAD data. All studied populations in the cometes group (purple triangles) were grouped in the single clade no. 8 by a branch-cutting approach (indicated by a number in a coloured rectangle).Likewise, they clustered together by INFOMAP as a single MOTU IX (see also Fig.3). The proposed taxonomy is shown on the right side of the maps.Stars show type localities for the cometes group. The proposed species name for the whole group, Grammomys cometes, is shown in larger bold letters, while smaller letters correspond to synonyms.	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C93568B13CBC21FF1B9FCDC13E.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971749/files/figure.png	https://doi.org/10.5281/zenodo.14971749	Figure 4. The scatter plot of the first three between-group principal component scores. The large, filled points mark group mean shapes, and small open points are projections of individual shapes onto the axes. Four major groups of Grammomys (sensu Bryja et al. 2017) are shown by different colours. The projections of type skull shapes are indicated by grey triangles labelled by the respective names (‘_p’ means paratypes).	Figure 4. The scatter plot of the first three between-group principal component scores. The large, filled points mark group mean shapes, and small open points are projections of individual shapes onto the axes. Four major groups of Grammomys (sensu Bryja et al. 2017) are shown by different colours. The projections of type skull shapes are indicated by grey triangles labelled by the respective names (‘_p’ means paratypes).	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C93568B13CBC21FF1B9FCDC13E.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971753/files/figure.png	https://doi.org/10.5281/zenodo.14971753	Figure 6. Taxonomic summary of the dolichurus and surdaster groups (sensu Bryja et al. 2017). A, the distribution of mtDNA lineages for the dolichurus (grey circles) and surdaster (triangles) groups.The different colours of triangles correspond to different lineages (su1–su10 described by Bryja et al. 2017; su11 and su12 discovered in this study). The short sequences from the type series of G. caniceps (su13) cluster unequivocally with the surdaster group as a sister to su11 (see Fig.2). We show the only two known localities of this taxon by green rhombuses (arrow ‘su13’ shows the type locality Malindi in Kenya; arrow ‘Roche et al.(1984)’ indicates the second known locality, close to Mogadisho in Somalia).B, delimitation of MOTUs based on ddRAD data. The numbers in coloured rectangles show one MOTU in the dolichurus group and three MOTUs in the surdaster group, delimited by a branch-cutting approach (numbers correspond to Fig. 3), with circles (dolichurus) and triangles (surdaster) in the same colours indicating localities of ddRAD-genotyped specimens. The proposed taxonomy is shown below the maps, with Roman numerals showing MOTUs from the INFOMAP clustering (VIII for the dolichurus group, and I and II for the surdaster group).Note that we failed to genotype G. caniceps (i.e. su13 mtDNA lineage) by ddRAD.Stars show type localities for the dolichurus (red) and surdaster (green) groups. The proposed species names for the two groups (i.e. Grammomys dolichurus and Grammomys surdaster), are shown in larger bold letters, while smaller letters correspond to synonyms.	Figure 6. Taxonomic summary of the dolichurus and surdaster groups (sensu Bryja et al. 2017). A, the distribution of mtDNA lineages for the dolichurus (grey circles) and surdaster (triangles) groups.The different colours of triangles correspond to different lineages (su1–su10 described by Bryja et al. 2017; su11 and su12 discovered in this study). The short sequences from the type series of G. caniceps (su13) cluster unequivocally with the surdaster group as a sister to su11 (see Fig.2). We show the only two known localities of this taxon by green rhombuses (arrow ‘su13’ shows the type locality Malindi in Kenya; arrow ‘Roche et al.(1984)’ indicates the second known locality, close to Mogadisho in Somalia).B, delimitation of MOTUs based on ddRAD data. The numbers in coloured rectangles show one MOTU in the dolichurus group and three MOTUs in the surdaster group, delimited by a branch-cutting approach (numbers correspond to Fig. 3), with circles (dolichurus) and triangles (surdaster) in the same colours indicating localities of ddRAD-genotyped specimens. The proposed taxonomy is shown below the maps, with Roman numerals showing MOTUs from the INFOMAP clustering (VIII for the dolichurus group, and I and II for the surdaster group).Note that we failed to genotype G. caniceps (i.e. su13 mtDNA lineage) by ddRAD.Stars show type localities for the dolichurus (red) and surdaster (green) groups. The proposed species names for the two groups (i.e. Grammomys dolichurus and Grammomys surdaster), are shown in larger bold letters, while smaller letters correspond to synonyms.	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C9356BB13FBFD9FD8A9FF2C4F3.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971753/files/figure.png	https://doi.org/10.5281/zenodo.14971753	Figure 6. Taxonomic summary of the dolichurus and surdaster groups (sensu Bryja et al. 2017). A, the distribution of mtDNA lineages for the dolichurus (grey circles) and surdaster (triangles) groups.The different colours of triangles correspond to different lineages (su1–su10 described by Bryja et al. 2017; su11 and su12 discovered in this study). The short sequences from the type series of G. caniceps (su13) cluster unequivocally with the surdaster group as a sister to su11 (see Fig.2). We show the only two known localities of this taxon by green rhombuses (arrow ‘su13’ shows the type locality Malindi in Kenya; arrow ‘Roche et al.(1984)’ indicates the second known locality, close to Mogadisho in Somalia).B, delimitation of MOTUs based on ddRAD data. The numbers in coloured rectangles show one MOTU in the dolichurus group and three MOTUs in the surdaster group, delimited by a branch-cutting approach (numbers correspond to Fig. 3), with circles (dolichurus) and triangles (surdaster) in the same colours indicating localities of ddRAD-genotyped specimens. The proposed taxonomy is shown below the maps, with Roman numerals showing MOTUs from the INFOMAP clustering (VIII for the dolichurus group, and I and II for the surdaster group).Note that we failed to genotype G. caniceps (i.e. su13 mtDNA lineage) by ddRAD.Stars show type localities for the dolichurus (red) and surdaster (green) groups. The proposed species names for the two groups (i.e. Grammomys dolichurus and Grammomys surdaster), are shown in larger bold letters, while smaller letters correspond to synonyms.	Figure 6. Taxonomic summary of the dolichurus and surdaster groups (sensu Bryja et al. 2017). A, the distribution of mtDNA lineages for the dolichurus (grey circles) and surdaster (triangles) groups.The different colours of triangles correspond to different lineages (su1–su10 described by Bryja et al. 2017; su11 and su12 discovered in this study). The short sequences from the type series of G. caniceps (su13) cluster unequivocally with the surdaster group as a sister to su11 (see Fig.2). We show the only two known localities of this taxon by green rhombuses (arrow ‘su13’ shows the type locality Malindi in Kenya; arrow ‘Roche et al.(1984)’ indicates the second known locality, close to Mogadisho in Somalia).B, delimitation of MOTUs based on ddRAD data. The numbers in coloured rectangles show one MOTU in the dolichurus group and three MOTUs in the surdaster group, delimited by a branch-cutting approach (numbers correspond to Fig. 3), with circles (dolichurus) and triangles (surdaster) in the same colours indicating localities of ddRAD-genotyped specimens. The proposed taxonomy is shown below the maps, with Roman numerals showing MOTUs from the INFOMAP clustering (VIII for the dolichurus group, and I and II for the surdaster group).Note that we failed to genotype G. caniceps (i.e. su13 mtDNA lineage) by ddRAD.Stars show type localities for the dolichurus (red) and surdaster (green) groups. The proposed species names for the two groups (i.e. Grammomys dolichurus and Grammomys surdaster), are shown in larger bold letters, while smaller letters correspond to synonyms.	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C9356BB13FBFD9FD8A9FF2C4F3.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971755/files/figure.png	https://doi.org/10.5281/zenodo.14971755	Figure 7. Taxonomic summary of the macmillani group. A and C, the distribution of mtDNA lineages.The different colours correspond to different lineages (m1–m8 described by Bryja et al. 2017; m9–m11 discovered in this study). B and D, delimitation of MOTUs based on ddRAD data. The Roman numerals III–VII in coloured rectangles show MOTUs delimited by INFOMAP clustering, with symbols in the same colours indicating localities of ddRAD-genotyped specimens.The Arabic numerals 4–6 show the MOTUs identified by branch-cutting of the ML tree.The proposed taxonomy is shown below the maps; MOTUs IV–VI from INFOMAP were grouped together by branch-cutting as MOTU 5 (see Fig. 3), but we propose to split them into two ecologically different species, Grammomys ibeanus (IV and V) and Grammomys macmillani (VI); see main text for more details. Stars show type localities for the macmillani group.The proposed species names are shown by larger bold letters next to their type localities, while smaller letters correspond to synonyms.	Figure 7. Taxonomic summary of the macmillani group. A and C, the distribution of mtDNA lineages.The different colours correspond to different lineages (m1–m8 described by Bryja et al. 2017; m9–m11 discovered in this study). B and D, delimitation of MOTUs based on ddRAD data. The Roman numerals III–VII in coloured rectangles show MOTUs delimited by INFOMAP clustering, with symbols in the same colours indicating localities of ddRAD-genotyped specimens.The Arabic numerals 4–6 show the MOTUs identified by branch-cutting of the ML tree.The proposed taxonomy is shown below the maps; MOTUs IV–VI from INFOMAP were grouped together by branch-cutting as MOTU 5 (see Fig. 3), but we propose to split them into two ecologically different species, Grammomys ibeanus (IV and V) and Grammomys macmillani (VI); see main text for more details. Stars show type localities for the macmillani group.The proposed species names are shown by larger bold letters next to their type localities, while smaller letters correspond to synonyms.	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C9356BB13EBCC2FA029B0EC57B.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971755/files/figure.png	https://doi.org/10.5281/zenodo.14971755	Figure 7. Taxonomic summary of the macmillani group. A and C, the distribution of mtDNA lineages.The different colours correspond to different lineages (m1–m8 described by Bryja et al. 2017; m9–m11 discovered in this study). B and D, delimitation of MOTUs based on ddRAD data. The Roman numerals III–VII in coloured rectangles show MOTUs delimited by INFOMAP clustering, with symbols in the same colours indicating localities of ddRAD-genotyped specimens.The Arabic numerals 4–6 show the MOTUs identified by branch-cutting of the ML tree.The proposed taxonomy is shown below the maps; MOTUs IV–VI from INFOMAP were grouped together by branch-cutting as MOTU 5 (see Fig. 3), but we propose to split them into two ecologically different species, Grammomys ibeanus (IV and V) and Grammomys macmillani (VI); see main text for more details. Stars show type localities for the macmillani group.The proposed species names are shown by larger bold letters next to their type localities, while smaller letters correspond to synonyms.	Figure 7. Taxonomic summary of the macmillani group. A and C, the distribution of mtDNA lineages.The different colours correspond to different lineages (m1–m8 described by Bryja et al. 2017; m9–m11 discovered in this study). B and D, delimitation of MOTUs based on ddRAD data. The Roman numerals III–VII in coloured rectangles show MOTUs delimited by INFOMAP clustering, with symbols in the same colours indicating localities of ddRAD-genotyped specimens.The Arabic numerals 4–6 show the MOTUs identified by branch-cutting of the ML tree.The proposed taxonomy is shown below the maps; MOTUs IV–VI from INFOMAP were grouped together by branch-cutting as MOTU 5 (see Fig. 3), but we propose to split them into two ecologically different species, Grammomys ibeanus (IV and V) and Grammomys macmillani (VI); see main text for more details. Stars show type localities for the macmillani group.The proposed species names are shown by larger bold letters next to their type localities, while smaller letters correspond to synonyms.	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C9356BB13EBCC2FA029B0EC57B.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971747/files/figure.png	https://doi.org/10.5281/zenodo.14971747	Figure 3. Maximum likelihood phylogenetic tree (IQ-TREE) inferred from the concatenated dataset of 3066 loci (92 687 single nucleotide polymorphisms) genotyped by the ddRAD approach. Black dots show node support with ultrafast bootstrap (1000 replicates)> 95, lower support at two nodes is shown by numbers. Four major groups of Grammomys (sensu Bryja et al. 2017, i.e. based mostly on mtDNA) are shown by different colours. Bars on the right side show delimitations by mtDNA lineages (see Fig. 2), MOTUs from the branch-cutting of the ML tree and from the INFOMAP clustering based on the co-ancestry matrix, and the proposed taxonomy (for more details, see the ‘Taxonomic revision of Grammomys’ section).	Figure 3. Maximum likelihood phylogenetic tree (IQ-TREE) inferred from the concatenated dataset of 3066 loci (92 687 single nucleotide polymorphisms) genotyped by the ddRAD approach. Black dots show node support with ultrafast bootstrap (1000 replicates)> 95, lower support at two nodes is shown by numbers. Four major groups of Grammomys (sensu Bryja et al. 2017, i.e. based mostly on mtDNA) are shown by different colours. Bars on the right side show delimitations by mtDNA lineages (see Fig. 2), MOTUs from the branch-cutting of the ML tree and from the INFOMAP clustering based on the co-ancestry matrix, and the proposed taxonomy (for more details, see the ‘Taxonomic revision of Grammomys’ section).	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C9356AB121BFC4FDFE9BCBC490.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971755/files/figure.png	https://doi.org/10.5281/zenodo.14971755	Figure 7. Taxonomic summary of the macmillani group. A and C, the distribution of mtDNA lineages.The different colours correspond to different lineages (m1–m8 described by Bryja et al. 2017; m9–m11 discovered in this study). B and D, delimitation of MOTUs based on ddRAD data. The Roman numerals III–VII in coloured rectangles show MOTUs delimited by INFOMAP clustering, with symbols in the same colours indicating localities of ddRAD-genotyped specimens.The Arabic numerals 4–6 show the MOTUs identified by branch-cutting of the ML tree.The proposed taxonomy is shown below the maps; MOTUs IV–VI from INFOMAP were grouped together by branch-cutting as MOTU 5 (see Fig. 3), but we propose to split them into two ecologically different species, Grammomys ibeanus (IV and V) and Grammomys macmillani (VI); see main text for more details. Stars show type localities for the macmillani group.The proposed species names are shown by larger bold letters next to their type localities, while smaller letters correspond to synonyms.	Figure 7. Taxonomic summary of the macmillani group. A and C, the distribution of mtDNA lineages.The different colours correspond to different lineages (m1–m8 described by Bryja et al. 2017; m9–m11 discovered in this study). B and D, delimitation of MOTUs based on ddRAD data. The Roman numerals III–VII in coloured rectangles show MOTUs delimited by INFOMAP clustering, with symbols in the same colours indicating localities of ddRAD-genotyped specimens.The Arabic numerals 4–6 show the MOTUs identified by branch-cutting of the ML tree.The proposed taxonomy is shown below the maps; MOTUs IV–VI from INFOMAP were grouped together by branch-cutting as MOTU 5 (see Fig. 3), but we propose to split them into two ecologically different species, Grammomys ibeanus (IV and V) and Grammomys macmillani (VI); see main text for more details. Stars show type localities for the macmillani group.The proposed species names are shown by larger bold letters next to their type localities, while smaller letters correspond to synonyms.	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C9356AB121BFC4FDFE9BCBC490.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971747/files/figure.png	https://doi.org/10.5281/zenodo.14971747	Figure 3. Maximum likelihood phylogenetic tree (IQ-TREE) inferred from the concatenated dataset of 3066 loci (92 687 single nucleotide polymorphisms) genotyped by the ddRAD approach. Black dots show node support with ultrafast bootstrap (1000 replicates)> 95, lower support at two nodes is shown by numbers. Four major groups of Grammomys (sensu Bryja et al. 2017, i.e. based mostly on mtDNA) are shown by different colours. Bars on the right side show delimitations by mtDNA lineages (see Fig. 2), MOTUs from the branch-cutting of the ML tree and from the INFOMAP clustering based on the co-ancestry matrix, and the proposed taxonomy (for more details, see the ‘Taxonomic revision of Grammomys’ section).	Figure 3. Maximum likelihood phylogenetic tree (IQ-TREE) inferred from the concatenated dataset of 3066 loci (92 687 single nucleotide polymorphisms) genotyped by the ddRAD approach. Black dots show node support with ultrafast bootstrap (1000 replicates)> 95, lower support at two nodes is shown by numbers. Four major groups of Grammomys (sensu Bryja et al. 2017, i.e. based mostly on mtDNA) are shown by different colours. Bars on the right side show delimitations by mtDNA lineages (see Fig. 2), MOTUs from the branch-cutting of the ML tree and from the INFOMAP clustering based on the co-ancestry matrix, and the proposed taxonomy (for more details, see the ‘Taxonomic revision of Grammomys’ section).	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C9356AB121BFC4FDFE9BCBC490.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971749/files/figure.png	https://doi.org/10.5281/zenodo.14971749	Figure 4. The scatter plot of the first three between-group principal component scores. The large, filled points mark group mean shapes, and small open points are projections of individual shapes onto the axes. Four major groups of Grammomys (sensu Bryja et al. 2017) are shown by different colours. The projections of type skull shapes are indicated by grey triangles labelled by the respective names (‘_p’ means paratypes).	Figure 4. The scatter plot of the first three between-group principal component scores. The large, filled points mark group mean shapes, and small open points are projections of individual shapes onto the axes. Four major groups of Grammomys (sensu Bryja et al. 2017) are shown by different colours. The projections of type skull shapes are indicated by grey triangles labelled by the respective names (‘_p’ means paratypes).	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C9356AB121BFC4FDFE9BCBC490.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971745/files/figure.png	https://doi.org/10.5281/zenodo.14971745	Figure 2. Mitochondrial phylogeny (Bayesian inference) based on CYTB sequences.Black dots show node support with posterior probability> 0.95. Four major groups of Grammomys (sensu Bryja et al. 2017), split into numbered lineages, are shown by different colours: cometes (previously selousi; se1–se7) group in purple; dolichurus (d) group in orange, macmillani (m1–m11) group in blue; and surdaster (su1–su13) group in red. A summary of available karyotypic data for particular mitochondrial lineages is shown on the right side (see more details in the ‘Taxonomic revision of Grammomys’ section).	Figure 2. Mitochondrial phylogeny (Bayesian inference) based on CYTB sequences.Black dots show node support with posterior probability> 0.95. Four major groups of Grammomys (sensu Bryja et al. 2017), split into numbered lineages, are shown by different colours: cometes (previously selousi; se1–se7) group in purple; dolichurus (d) group in orange, macmillani (m1–m11) group in blue; and surdaster (su1–su13) group in red. A summary of available karyotypic data for particular mitochondrial lineages is shown on the right side (see more details in the ‘Taxonomic revision of Grammomys’ section).	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C93575B121BF8DFC599E76C4B1.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971745/files/figure.png	https://doi.org/10.5281/zenodo.14971745	Figure 2. Mitochondrial phylogeny (Bayesian inference) based on CYTB sequences.Black dots show node support with posterior probability> 0.95. Four major groups of Grammomys (sensu Bryja et al. 2017), split into numbered lineages, are shown by different colours: cometes (previously selousi; se1–se7) group in purple; dolichurus (d) group in orange, macmillani (m1–m11) group in blue; and surdaster (su1–su13) group in red. A summary of available karyotypic data for particular mitochondrial lineages is shown on the right side (see more details in the ‘Taxonomic revision of Grammomys’ section).	Figure 2. Mitochondrial phylogeny (Bayesian inference) based on CYTB sequences.Black dots show node support with posterior probability> 0.95. Four major groups of Grammomys (sensu Bryja et al. 2017), split into numbered lineages, are shown by different colours: cometes (previously selousi; se1–se7) group in purple; dolichurus (d) group in orange, macmillani (m1–m11) group in blue; and surdaster (su1–su13) group in red. A summary of available karyotypic data for particular mitochondrial lineages is shown on the right side (see more details in the ‘Taxonomic revision of Grammomys’ section).	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C93575B121BF8DFC599E76C4B1.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971755/files/figure.png	https://doi.org/10.5281/zenodo.14971755	Figure 7. Taxonomic summary of the macmillani group. A and C, the distribution of mtDNA lineages.The different colours correspond to different lineages (m1–m8 described by Bryja et al. 2017; m9–m11 discovered in this study). B and D, delimitation of MOTUs based on ddRAD data. The Roman numerals III–VII in coloured rectangles show MOTUs delimited by INFOMAP clustering, with symbols in the same colours indicating localities of ddRAD-genotyped specimens.The Arabic numerals 4–6 show the MOTUs identified by branch-cutting of the ML tree.The proposed taxonomy is shown below the maps; MOTUs IV–VI from INFOMAP were grouped together by branch-cutting as MOTU 5 (see Fig. 3), but we propose to split them into two ecologically different species, Grammomys ibeanus (IV and V) and Grammomys macmillani (VI); see main text for more details. Stars show type localities for the macmillani group.The proposed species names are shown by larger bold letters next to their type localities, while smaller letters correspond to synonyms.	Figure 7. Taxonomic summary of the macmillani group. A and C, the distribution of mtDNA lineages.The different colours correspond to different lineages (m1–m8 described by Bryja et al. 2017; m9–m11 discovered in this study). B and D, delimitation of MOTUs based on ddRAD data. The Roman numerals III–VII in coloured rectangles show MOTUs delimited by INFOMAP clustering, with symbols in the same colours indicating localities of ddRAD-genotyped specimens.The Arabic numerals 4–6 show the MOTUs identified by branch-cutting of the ML tree.The proposed taxonomy is shown below the maps; MOTUs IV–VI from INFOMAP were grouped together by branch-cutting as MOTU 5 (see Fig. 3), but we propose to split them into two ecologically different species, Grammomys ibeanus (IV and V) and Grammomys macmillani (VI); see main text for more details. Stars show type localities for the macmillani group.The proposed species names are shown by larger bold letters next to their type localities, while smaller letters correspond to synonyms.	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C93575B121BF8DFC599E76C4B1.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971747/files/figure.png	https://doi.org/10.5281/zenodo.14971747	Figure 3. Maximum likelihood phylogenetic tree (IQ-TREE) inferred from the concatenated dataset of 3066 loci (92 687 single nucleotide polymorphisms) genotyped by the ddRAD approach. Black dots show node support with ultrafast bootstrap (1000 replicates)> 95, lower support at two nodes is shown by numbers. Four major groups of Grammomys (sensu Bryja et al. 2017, i.e. based mostly on mtDNA) are shown by different colours. Bars on the right side show delimitations by mtDNA lineages (see Fig. 2), MOTUs from the branch-cutting of the ML tree and from the INFOMAP clustering based on the co-ancestry matrix, and the proposed taxonomy (for more details, see the ‘Taxonomic revision of Grammomys’ section).	Figure 3. Maximum likelihood phylogenetic tree (IQ-TREE) inferred from the concatenated dataset of 3066 loci (92 687 single nucleotide polymorphisms) genotyped by the ddRAD approach. Black dots show node support with ultrafast bootstrap (1000 replicates)> 95, lower support at two nodes is shown by numbers. Four major groups of Grammomys (sensu Bryja et al. 2017, i.e. based mostly on mtDNA) are shown by different colours. Bars on the right side show delimitations by mtDNA lineages (see Fig. 2), MOTUs from the branch-cutting of the ML tree and from the INFOMAP clustering based on the co-ancestry matrix, and the proposed taxonomy (for more details, see the ‘Taxonomic revision of Grammomys’ section).	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C93575B120BCDFFC389BDCC4B1.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971747/files/figure.png	https://doi.org/10.5281/zenodo.14971747	Figure 3. Maximum likelihood phylogenetic tree (IQ-TREE) inferred from the concatenated dataset of 3066 loci (92 687 single nucleotide polymorphisms) genotyped by the ddRAD approach. Black dots show node support with ultrafast bootstrap (1000 replicates)> 95, lower support at two nodes is shown by numbers. Four major groups of Grammomys (sensu Bryja et al. 2017, i.e. based mostly on mtDNA) are shown by different colours. Bars on the right side show delimitations by mtDNA lineages (see Fig. 2), MOTUs from the branch-cutting of the ML tree and from the INFOMAP clustering based on the co-ancestry matrix, and the proposed taxonomy (for more details, see the ‘Taxonomic revision of Grammomys’ section).	Figure 3. Maximum likelihood phylogenetic tree (IQ-TREE) inferred from the concatenated dataset of 3066 loci (92 687 single nucleotide polymorphisms) genotyped by the ddRAD approach. Black dots show node support with ultrafast bootstrap (1000 replicates)> 95, lower support at two nodes is shown by numbers. Four major groups of Grammomys (sensu Bryja et al. 2017, i.e. based mostly on mtDNA) are shown by different colours. Bars on the right side show delimitations by mtDNA lineages (see Fig. 2), MOTUs from the branch-cutting of the ML tree and from the INFOMAP clustering based on the co-ancestry matrix, and the proposed taxonomy (for more details, see the ‘Taxonomic revision of Grammomys’ section).	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C93575B120BCDFFC389BDCC4B1.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971755/files/figure.png	https://doi.org/10.5281/zenodo.14971755	Figure 7. Taxonomic summary of the macmillani group. A and C, the distribution of mtDNA lineages.The different colours correspond to different lineages (m1–m8 described by Bryja et al. 2017; m9–m11 discovered in this study). B and D, delimitation of MOTUs based on ddRAD data. The Roman numerals III–VII in coloured rectangles show MOTUs delimited by INFOMAP clustering, with symbols in the same colours indicating localities of ddRAD-genotyped specimens.The Arabic numerals 4–6 show the MOTUs identified by branch-cutting of the ML tree.The proposed taxonomy is shown below the maps; MOTUs IV–VI from INFOMAP were grouped together by branch-cutting as MOTU 5 (see Fig. 3), but we propose to split them into two ecologically different species, Grammomys ibeanus (IV and V) and Grammomys macmillani (VI); see main text for more details. Stars show type localities for the macmillani group.The proposed species names are shown by larger bold letters next to their type localities, while smaller letters correspond to synonyms.	Figure 7. Taxonomic summary of the macmillani group. A and C, the distribution of mtDNA lineages.The different colours correspond to different lineages (m1–m8 described by Bryja et al. 2017; m9–m11 discovered in this study). B and D, delimitation of MOTUs based on ddRAD data. The Roman numerals III–VII in coloured rectangles show MOTUs delimited by INFOMAP clustering, with symbols in the same colours indicating localities of ddRAD-genotyped specimens.The Arabic numerals 4–6 show the MOTUs identified by branch-cutting of the ML tree.The proposed taxonomy is shown below the maps; MOTUs IV–VI from INFOMAP were grouped together by branch-cutting as MOTU 5 (see Fig. 3), but we propose to split them into two ecologically different species, Grammomys ibeanus (IV and V) and Grammomys macmillani (VI); see main text for more details. Stars show type localities for the macmillani group.The proposed species names are shown by larger bold letters next to their type localities, while smaller letters correspond to synonyms.	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
C46987C93575B120BCDFFC389BDCC4B1.taxon	http://purl.org/dc/dcmitype/StillImage	image/png	https://zenodo.org/record/14971745/files/figure.png	https://doi.org/10.5281/zenodo.14971745	Figure 2. Mitochondrial phylogeny (Bayesian inference) based on CYTB sequences.Black dots show node support with posterior probability> 0.95. Four major groups of Grammomys (sensu Bryja et al. 2017), split into numbered lineages, are shown by different colours: cometes (previously selousi; se1–se7) group in purple; dolichurus (d) group in orange, macmillani (m1–m11) group in blue; and surdaster (su1–su13) group in red. A summary of available karyotypic data for particular mitochondrial lineages is shown on the right side (see more details in the ‘Taxonomic revision of Grammomys’ section).	Figure 2. Mitochondrial phylogeny (Bayesian inference) based on CYTB sequences.Black dots show node support with posterior probability> 0.95. Four major groups of Grammomys (sensu Bryja et al. 2017), split into numbered lineages, are shown by different colours: cometes (previously selousi; se1–se7) group in purple; dolichurus (d) group in orange, macmillani (m1–m11) group in blue; and surdaster (su1–su13) group in red. A summary of available karyotypic data for particular mitochondrial lineages is shown on the right side (see more details in the ‘Taxonomic revision of Grammomys’ section).	2024-05-25	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej		Zenodo	biologists	Bryja, Josef;Kerbis Peterhans, Julian C.;Lavrenchenko, Leonid A.;Nicolas, Violaine;Denys, Christiane;Bryjová, Anna;Šumbera, Radim;Mikula, Ondřej			
