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Trachypithecus popa sp. nov. Popa langur Holotype: NHMUK ZD.1914.7.19.3 (adult male, stuffed skin and skull, left zygomatic arch slightly damaged; Figures S4–S 6), collected by Guy C. Shortridge on 11 September 1913. Head-body length (HBL): 600 mm, tail length (TL): 800 mm, hindfoot length (HFL): 174 mm, ear length (EL): 33 mm, body mass (BM): 7.9 kg. Mitogenome GenBank accession No.: MT 806047. Type locality: Mount Popa, Myingyan District, Myanmar (N20°55’, E95°15’, 4 961 feet =1 512 m a.s.l.) (location 6 in Figures 1, 5). Paratypes: NHMUK ZD.1914.7.19.4 (adult male, stuffed skin and skull) collected at the type locality by Guy C. Shortridge on 27 September 1913. HBL: 580 mm, TL: 795 mm, HFL: 161 mm, EL: 32 mm, BM: 8.2 kg. NHMUK ZD.1914.7.19.5 (adult female, stuffed skin) collected at the type locality by Guy C. Shortridge on 3 September 1913. HBL: 540 mm, TL: 780 mm, HFL: 152 mm, EL: 30 mm, BM: 7.0 kg. NHMUK ZD.1917.4.24.1 (adult male, stuffed skin and skull) collected at South Zamayi Reserve, 60 miles north of Pegu by J.M.D. Mackenzie on 10 March 1916. HBL: 498 mm, TL: 795 mm, HFL: 168 mm, EL: 33.5 mm, BM: 7.7 kg. NHMUK ZD.1937.9.10.4 (subadult male, stuffed skin and skull) collected 30 miles northwest of Toungoo by J.M.D. Mackenzie on 8 January 1928. HBL: 508 mm, TL: 785 mm, HFL: 165 mm, EL: 31 mm. NHMUK ZD.1937.9.10.5 (subadult male, stuffed skin and skull) collected 30 miles northwest of Toungoo by J.M.D. Mackenzie on 8 January 1928. HBL: 509 mm, TL: 795 mm, HFL: 165 mm, EL: 31 mm. AMNH M-54 770 (juvenile male, skull) collected at Camp Pinmezali, Pegu Yoma by John C. Faunthorpe on 27 April 1924. RMNH MAM.59807 (adult male, stuffed skin with skull in situ) collected at Yado, Mount Cariani, Tounghoo (= Taungoo) District, Myanmar (800–1 000 m) by Leonardo Fea in December 1887 (field number: 40). HBL: 555 mm, TL: 750 mm. Etymology: The English name for Trachypithecus popa is Popa langur. Mount Popa is a major landmark of the Myingyan District in Myanmar, and the place where the designated holotype was originally collected. The specific name “popa” is used as a noun in apposition. Description: The species is dark brown or gray-brown on the dorsum, with a sharply contrasting gray or whitish venter. Hands and feet are black. From above the elbow, the arms on the dorsal side gradually darken to black hands. The pale underside extends onto the chin and down to the inner side of the arms and thighs. The tail is paler than the back, notably at the base and underside. The face is black with a wide fleshywhite muzzle and broad white rings fully encircling the eyes. The hairs on the head are raised to a crest or are at least long and irregularly structured, but with no parting or whorl behind the brows present. This crest of hair and the forward-facing whiskers give the head a rhomb-like shape (Figure 6, Supplementary Figures S4–S 6). Body measurements (median and range) are: males (n =5) HBL: 562 (498–600) mm, TL: 795 (775–858) mm, HFL: 168 (144–178) mm, EL: 32 (30.0–33.5) mm, BM: 7.9 (7.7–8.2) kg; females (n =3) HBL: 585 (540–589) mm, TL: 780 (720–784) mm, HFL: 156 (152–160) mm, EL: 30 (20–32) mm, BM (n =1): 7.0 kg (Supplementary Table S3). Diagnosis: Overall, Trachypithecus popa sp. nov. is externally more similar to T. phayrei than to T. melamera. Body coloration in all three species is variable, but generally more fawn in T. melamera and more brownish to gray in Trachypithecus popa sp. nov. and T. phayrei. In Trachypithecus popa sp. nov. and T. phayrei, but not in T. melamera, the pale venter sharply contrasts with the back. The hands and feet are black in all three species. In Trachypithecus popa sp. nov., the arms (dorsal side) gradually darken to the hands from above the elbow, while in T. phayrei, they gradually darken from below the elbow. In T. melamera, the lower arms are not darker than the upper arms. In Trachypithecus popa sp. nov. and T. phayrei, the hairs on the head are raised to a crest or are at least long and irregularly structured, while T. melamera has a whorl or a parting behind the brows. Whiskers are laterally directed in T. phayrei, but forward directed in Trachypithecus popa sp. nov. and T. melamera. The direction of the whiskers in combination with the hairs on the head gives the head of T. phayrei a triangular shape, versus a rhomb-like shape for Trachypithecus popa sp. nov. and a round shape for T. melamera. All three species have a fleshy-white muzzle, which is wider in Trachypithecus popa sp. nov. and T. melamera. In T. melamera, the white around the eyes is restricted to the inner side, while in T. phayrei, the white normally encircles the eyes fully, although it is sometimes restricted to the inner side. In Trachypithecus popa sp. nov., the eyes are always fully encircled with broad white eye-rings. Males of T. phayrei have significantly shorter tails than males of the other two species (Figure 3, Supplementary Tables S5–S6). Cranially, Trachypithecus popa sp. nov. has a slightly longer skull, especially relative to its width, than in T. phayrei and T. melamera; this is achieved by a slight anterior elongation of the facial region of the skull relative to these taxa, rendering Trachypithecus popa sp. nov. slightly more prognathic in lateral and dorsal views and creating a more rectangular shape of the bony palate in ventral view (vs. a more square palate in T. phayrei and T. melamera). The teeth are, on average, larger in Trachypithecus popa sp. nov. than in T. phayrei and T. melamera, and molar measurements are the clearest means for separating the skulls of this new taxon from its closest relatives (Supplementary Tables S3, S7; Figure 4, Supplementary Figures S2–S 3); in particular, the third molar (M3/m3) appears larger overall in Trachypithecus popa sp. nov. when skulls are directly compared. PCAs using molar measurements and combined craniodental measurements separated T. phayrei, T. melamera, and Trachypithecus popa sp. nov., but cranial measurements alone did not separate them (Figure 4, Supplementary Figures S2, S 3). Distribution: Between the Ayeyarwaddy and Thanlwin rivers in the central dry zone of Myanmar and into the western foothills of the Kayah-Karen Mountains (Figure 5). The northeastern limit is undefined (see Discussion), but the species may occur throughout the Kayah-Karen Mountains. This species is endemic to Myanmar. Conservation status: As evident from historical records (museum specimens and travel notes), the species was once widespread in the central dry zone of Myanmar. Only two of these populations are known to have survived (location 6: Mount Popa, location 8: Bago Yoma), while all others are considered possibly extirpated. However, during recent fieldwork, three new populations (locations 10–12) were discovered. At location 10, Myogyi Monastery, the langur population is estimated at 75–100 individuals (Quyet et al., 2019), but these langurs are probably hybrids between Trachypithecus popa sp. nov. and T. melamera. The populations at location 11, Panlaung-Pyadalin Cave Wildlife Sanctuary, and location 12, Mount Yathae Pyan, consist of 46–96 individuals (Quyet et al., 2019) and 20–30 individuals (A.K.L. and A.L. pers. observation), respectively. The population at Bago Yoma (location 8) contains about 22 individuals (A.K.L. pers. observation) and at Mount Popa (location 6), field surveys conducted in 2019 revealed a population size of 111 individuals (Thaung Win pers. communication). Mount Popa was declared a national park (Popa Mountain Park) in 1989 and has an area of 128.54 km 2, including 26.97 km 2 classified as suitable to highly suitable for langurs (Thant, 2013; Thant et al., 2013). Throughout its range, Trachypithecus popa sp. nov. is threatened by hunting, habitat loss, degradation, and fragmentation caused by agricultural encroachment, illegal/unsustainable timber extraction, and disturbances caused by collection of non-timber products and free cattle grazing (Quyet et al., 2019; Thant et al., 2013). Considering a total population size of 199–259 individuals (excluding the possible hybrid population at Myogyi Monastery) in the four disjunct populations and the dramatic habitat loss over the last century, we propose to classify Trachypithecus popa sp. nov. as Critically Endangered (CR) as it meets the IUCN Red List criteria B1a and B1b (i-v) (IUCN, 2001). Furthermore, Trachypithecus popa sp. nov. needs to be added to the national and international lists of threatened species (IUCN, CITES). Improved protected area management, in particular improved law enforcement, in Popa Mountain Park and Panlaung-Pyadalin Cave Wildlife Sanctuary is essential to stabilize the two largest known populations. Mount Yathae Pyan is an isolated karst hill. This population could be protected through the designation of a community-protected area (CPA). The population status of the species in Bago Yoma is poorly understood and additional surveys are urgently required. The forests in Bago Yoma are severely degraded and fragmented, but could still provide the largest, contiguous habitat if deforestation and forest degradation are reversed through improved forest protection and restoration. Comments: Except for species of the T. pileatus group, the natal coat of Trachypithecus spp. is generally yellowish, orange, or light brown (Anandam et al., 2013; Rowe & Myers, 2016). Trachypithecus popa sp. nov. may be an exception as photos show an infant with creamy white fur coloration (Supplementary Figure S7).

Trachypithecus phayrei (Blyth, 1847) English name: Phayre’s langur. Synonyms: Presbytis barbei Blyth, 1863; Semnopithecus holotephreus Anderson, 1878. Distribution: East Bangladesh, Northeast India (Assam, Mizoram, and Tripura), and West Myanmar, west of the Chindwin and Ayeyarwaddy rivers (Figure 5). Conservation status: Currently listed as Endangered (Bleisch et al., 2008a), but reassessment required., Published as part of Roos, Christian, M. Helgen, Kristofer, Portela Miguez, Roberto, May Lay Thant, Naw, Lwin, Ngwe, Ko Lin, Aung, Lin, Aung, Mar Yi, Khin, Soe, Paing, Mar Hein, Zin, Nyein Nyein Myint, Margaret, Ahmed, Tanvir, Chetry, Dilip, Urh, Melina, Grace Veatch, E., Duncan, Neil, Kamminga, Pepijn, A. H. Chua, Marcus, Yao, Lu, Matauschek, Christian, Meyer, Dirk, Liu, Zhi-Jin, Li, Ming, Nadler, Tilo, Fan, Peng-Fei, Khac Quyet, Le, Hofreiter, Michael, Zinner, Dietmar & Momberg, Frank, 2020, Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei (Blyth, 1847) and description of a new species, pp. 656-669 in Zoological Research 41 (6) on page 664, DOI: 10.24272/j.issn.2095-8137.2020.254, http://zenodo.org/record/4395899, {"references":["Blyth E. 1847. Supplementary report of the curator of the Zoological Department. Journal of the Asiatic Society of Bengal, 16 (2): 728 - 732.","Blyth E. 1863. Catalogue of the Mammalia in the Museum Asiatic Society. Calcutta: Savielle and Cranenburgh.","Anderson J. 1878. Anatomical and Zoological Researches: Comprising an Account of the Zoological Results of the Two Expeditions to Western Yunnan in 1868 and 1875, and a Monograph of the Two Cetacean Genera, Platanista and Orcella. Volume 1. London: B. Quaritch.","Bleisch B, Brockelman W, Timmins RJ, Nadler T, Thun S, Das J, et al. 2008 a [2020 - 11 - 03]. Trachypithecus phayrei ssp. phayrei. The IUCN red list of threatened species 2008: e. T 136928 A 4350467. https: // dx. doi. org / 10. 2305 / IUCN. UK. 2008. RLTS. T 136928 A 4350467. en."]}

[Abstract] Domestic cattle were brought to Spain by early settlers and agricultural societies. Due to missing Neolithic sites in the Spanish region of Galicia, very little is known about this process in this region. We sampled 18 cattle subfossils from different ages and different mountain caves in Galicia, of which 11 were subject to sequencing of the mitochondrial genome and phylogenetic analysis, to provide insight into the introduction of cattle to this region. We detected high similarity between samples from different time periods and were able to compare the time frame of the first domesticated cattle in Galicia to data from the connecting region of Cantabria to show a plausible connection between the Neolithization of these two regions. Our data shows a close relationship of the early domesticated cattle of Galicia and modern cow breeds and gives a general insight into cattle phylogeny. We conclude that settlers migrated to this region of Spain from Europe and introduced common European breeds to Galicia. Ministerio de Ciencia e Innovación; CGL2014–57209-P Xunta de Galicia; CGL2014–57209-P

Objective Plant carnivory is distributed across the tree of life and has evolved at least six times independently, but sequenced and annotated nuclear genomes of carnivorous plants are currently lacking. We have sequenced and structurally annotated the nuclear genome of the carnivorous Roridula gorgonias and that of a non-carnivorous relative, Madeira’s lily-of-the-valley-tree, Clethra arborea, both within the Ericales. This data adds an important resource to study the evolutionary genetics of plant carnivory across angiosperm lineages and also for functional and systematic aspects of plants within the Ericales. Results Our assemblies have total lengths of 284 Mbp (R. gorgonias) and 511 Mbp (C. arborea) and show high BUSCO scores of 84.2% and 89.5%, respectively. We used their predicted genes together with publicly available data from other Ericales’ genomes and transcriptomes to assemble a phylogenomic data set for the inference of a species tree. However, groups of orthologs showed a marked absence of species represented by a transcriptome. We discuss possible reasons and caution against combining predicted genes from genome- and transriptome-based assemblies., Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe; 1141

Obtaining information about functional details of proteins of extinct species is of critical importance for a better understanding of the real-life appearance, behavior and ecology of these lost entries in the book of life. In this chapter, we discuss the possibilities to retrieve the necessary DNA sequence information from paleogenomic data obtained from fossil specimens, which can then be used to express and subsequently analyze the protein of interest. We discuss the problems specific to ancient DNA, including mis-coding lesions, short read length and incomplete paleogenome assemblies. Finally, we discuss an alternative, but currently rarely used approach, direct PCR amplification, which is especially useful for comparatively short proteins.

Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.

Rana guttulata Boulenger, 1881 Lectotype. BMNH 1947.2.25.51, designated lectotype by Blommers-Schlösser and Blanc (1991), from the region of Betsileo (S.E. Betsileo), collected by Bartlett. Paralectotypes. Four specimens, BMNH 1947.2. 25.48–50, BMNH 1947.2. 25.52, with same collection locality and data as lectotype. Junior synonym. Rana pigra Mocquard, 1900. Holotype: MNHN 1899.410, from 'forêt d' Ikongo'. Referred material. For field numbers of additional specimens referred to M. guttulat us genetically, see Figure 1. For morphological measurements of types and five additional specimens in the ZSM collection, see Table 1. Remarks. Mantidactylus (M.) guttulatus is a large nocturnal stream-dwelling frog, distributed at elevations from 810 m a.s.l. (Vohidrazana) to ca. 1500 m a.s.l. (Antoetra). It is typically found in slow-moving parts of small streams in rainforest, and almost, nothing is known about its natural history. Based on genetic data herein, confirmed localities are (from north to south) Fierenana, Andasibe, Maromizaha, Mangabe region, An' Ala and Vohidrazana in the Northern Central East, and Antoetra, Vohiparara, Ranomafana and Ivohibe in the Southern Central East of Madagascar (map in Figure 1). If Rana pigra is correctly assigned as a junior synonym to M. guttulatus, then a further locality would be Ikongo Forest. The definition of this species has had a very convoluted history, and many populations and specimens have intermittently been named M. guttulatus. A complete revision of all these uses in the literature is beyond the scope of this paper. Glaw and Vences (2007) defined populations from Tsaratanana as M. guttulatus, and calls and tadpoles of the lineage occurring at Tsaratanana were also described under this name (Vences et al. 2004; Schulze et al. 2016). However, this population corresponds to the new species M. radaka sp. nov. described below. The tadpole described by Altig and McDiarmid (2006) as M. guttulatus actually belongs to M. majori, a representative of the subgenus Hylobatrachus (Randrianiaina et al. 2011)., Published as part of Rancilhac, Loïs, Bruy, Teddy, Scherz, Mark D., Pereira, Elvis Almeida, Preick, Michaela, Straube, Nicolas, Lyra, Mariana L., Ohler, Annemarie, Streicher, Jeffrey W., Andreone, Franco, Crottini, Angelica, Hutter, Carl R., Randrianantoandro, J. Christian, Rakotoarison, Andolalao, Glaw, Frank, Hofreiter, Michael & Vences, Miguel, 2020, Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus), pp. 87-118 in Journal of Natural History (J. Nat. Hist.) (J. Nat. Hist.) 54 (1 - 4) on page 106, DOI: 10.1080/00222933.2020.1748243, http://zenodo.org/record/5020653, {"references":["Boulenger GA. 1881. Description of a new species of frog from Madagascar. Ann Mag Nat Hist. 5: 360 - 361. doi: 10.1080 / 00222938109459533.","Blommers-Schlosser RMA, Blanc CP. 1991. Amphibiens (premiere partie). Faune de Madagascar. 75: 1 - 379.","Mocquard F. 1900. Nouvelle contribution a la faune herpetologique de Madagascar. Bulletin de la Societe Philomathique de Paris Series 9. 2: 111.","Glaw F, Vences M. 2007. A field guide to the amphibians and reptiles of Madagascar. 3 rd ed. Cologne: Vences & Glaw Verlag; p. 496.","Schulze A, Randrianiaina RD, Perl B, Glaw F, Vences M. 2016. The unexpectedly dull tadpole of Madagascar' s largest frog Mantidactylus guttulatus. Acta Herpetologica. 11: 119 - 125.","Altig R, McDiarmid RW. 2006. Descriptions and biological notes on three unusual mantellid tadpoles (Amphibia: Anura: Mantellidae) from southeastern Madagascar. Proc Biol Soc Washington. 119: 418 - 426.","Randrianiaina R-D, Strauss A, Glos J, Glaw F, Vences M, Arntzen JW. 2011. Diversity, external morphology and ' reverse taxonomy' in the specialized tadpoles of Malagasy river bank frogs of the subgenus Ochthomantis (genus Mantidactylus). Contrib Zoo. 80 (1): 17 - 65. doi: 10.1163 / 18759866 - 08001002."]}

Mantidactylus (Mantidactylus) grandidieri Mocquard, 1895 Syntypes. Two specimens, MNHN 1883.580 and MNHN 1895.255 collected by Humblot and Grandidier, from ' Madagascar... côte Est'. Referred material. For field numbers of additional specimens referred to M. grandidieri genetically, see Figure 1. For morphological measurements of types and additional six specimens in the ZSM collection, see Table 1. Remarks. Mantidactylus (M.) grandidieri is a large nocturnal stream-dwelling frog, distributed at elevations from near sea level (Nosy Mangabe) to ca. 1500 m a.s.l. (Ambohitantely), but appears to be more common at low elevations M. guttulatus, the definition of this species has changed multiple times in the past. A complete revision of all these uses in the literature is beyond the scope of this paper. Glaw and Vences (2007) partially following Blommers-Schlösser and Blanc (1991) used the name M. grandidieri primarily to refer to highland populations in the Northern Central East and Southern Central East, which, according to the present revision, are to be referred to as M. guttulatus. Instead, populations of M. grandidieri were named Mantidactylus sp. aff. grandidieri 'North' by Glaw and Vences (2007), Mantidactylus sp. 57 by Vieites et al. (2009) and Mantidactylus sp. Ca57 by Perl et al. (2014)., Published as part of Rancilhac, Loïs, Bruy, Teddy, Scherz, Mark D., Pereira, Elvis Almeida, Preick, Michaela, Straube, Nicolas, Lyra, Mariana L., Ohler, Annemarie, Streicher, Jeffrey W., Andreone, Franco, Crottini, Angelica, Hutter, Carl R., Randrianantoandro, J. Christian, Rakotoarison, Andolalao, Glaw, Frank, Hofreiter, Michael & Vences, Miguel, 2020, Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus), pp. 87-118 in Journal of Natural History (J. Nat. Hist.) (J. Nat. Hist.) 54 (1 - 4) on page 107, DOI: 10.1080/00222933.2020.1748243, http://zenodo.org/record/5020653, {"references":["Mocquard F. 1895. Sur les reptiles recueillis a Madagascar de 1867 a 1885 par M. Grandidier. Bulletin de la Societe philomathique de Paris. 7: 93 - 111.","Glaw F, Vences M. 2007. A field guide to the amphibians and reptiles of Madagascar. 3 rd ed. Cologne: Vences & Glaw Verlag; p. 496.","Blommers-Schlosser RMA, Blanc CP. 1991. Amphibiens (premiere partie). Faune de Madagascar. 75: 1 - 379.","Vieites DR, Wollenberg KC, Andreone F, Kohler J, Glaw F, Vences M. 2009. Vast underestimation of Madagascar' s biodiversity evidenced by an integrative amphibian inventory. Proc Nat Acad Sci USA. 106 (20): 8267 - 8272. doi: 10.1073 / pnas. 0810821106.","Perl RGB, Nagy ZT, Sonet G, Glaw F, Wollenberg KC, Vences M. 2014. DNA barcoding Madagascar' s amphibian fauna. Amphibia-Reptilia. 35 (2): 197 - 206. doi: 10.1163 / 15685381 - 00002942."]}

Additional file 2: Figure S1. Identification of scaffolds linked to chromosome X using sequencing coverage and scaffold length. Green dots correspond to scaffolds assigned as linked to chromosome X. The red lines indicate the median coverage for all scaffolds. The blue lines represent half the median coverage which corresponds to the coverage of scaffolds linked to chromosome X. Figure S2. Past demography for moose (Alces alces) using PSMC. Thin lines represent 100 bootstrap runs. The x-axis corresponds to time before present in years on a log scale, assuming an estimated substitution rate of 0.7 × 10− 8 substitutions/site/generation [30] and a generation time of 7 years [31]. The y-axis corresponds to the effective population size Ne. Figure S3. Past demography for moose (Alces alces) using a Bayesian Skyline Plot (BSP). Demographic reconstruction was inferred in BEAST using 14 European 16,693 bp mitogenomes. Timing of events was estimated assuming a mean rate of 9 × 10− 9 substitutions/site/year based on Zurano et al. [93] and a standard deviation of 0.01. The x axis is in calendar years before present and y axis represents changes in effective population size (shown as the product of Nef and generation time T). The black line corresponds to the median estimate and the blue lines show the 95% highest posterior density intervals. Figure S4. Distribution of runs of homozygosity (ROH) in moose (Alces alces). ROH ≥500 kb are shown.

Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics., Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe, 908

The straight-tusked elephants Palaeoloxodon spp. were widespread across Eurasia during the Pleistocene. Phylogenetic reconstructions using morphological traits have grouped them with Asian elephants (Elephas maximus), and many paleontologists place Palaeoloxodon within Elephas. Here, we report the recovery of full mitochondrial genomes from four and partial nuclear genomes from two P. antiquus fossils. These fossils were collected at two sites in Germany, Neumark-Nord and Weimar-Ehringsdorf, and likely date to interglacial periods ~120 and ~244 thousand years ago, respectively. Unexpectedly, nuclear and mitochondrial DNA analyses suggest that P. antiquus was a close relative of extant African forest elephants (Loxodonta cyclotis). Species previously referred to Palaeoloxodon are thus most parsimoniously explained as having diverged from the lineage of Loxodonta, indicating that Loxodonta has not been constrained to Africa. Our results demonstrate that the current picture of elephant evolution is in need of substantial revision. DOI: http://dx.doi.org/10.7554/eLife.25413.001, eLife digest Understanding how extinct species are related to each other or to their living relatives is often a difficult task. Many extinct species have been identified only from incomplete fragments of some of their bones. However, even if complete skeletons have been found, determining the relationships between species can be tricky because researchers often have to rely solely on the shapes of the bones. It is sometimes possible to retrieve DNA sequences from fossil bones. This is easier with younger fossils and those that have been recovered from cold environments. Ancient DNA sequences have been retrieved from only a few fossils older than 100,000 years, but such DNA sequences can be tremendously useful in determining how different species are related to each other. Today there are three living elephant species: the African forest elephant, the African savanna elephant and the Asian elephant. However, there are many extinct elephant species. For example, the European straight-tusked elephant went extinct at least 30,000 years ago, although most of the fossils that have been discovered are at least 100,000 years old. Straight-tusked elephants are generally assumed to be closely related to the Asian elephant, but this conclusion had been based solely on reconstructing skeletons. Meyer et al. have now obtained DNA sequences from fossils of four straight-tusked elephants ranging from around 120,000 to 240,000 years in age. These sequences were analysed to determine how straight-tusked elephants are related to the three living elephant species and the extinct mammoth, the DNA sequences for which can be found in public databases. The analyses revealed that straight-tusked elephants are in fact most closely related to the African forest elephant, not the Asian elephant as previously thought. This result completely changes our picture of elephant evolution and suggests that it is extremely difficult to determine elephant relationships based on the shape of their skeleton alone. It also shows that the African elephant lineage was not restricted to the African continent (the place where all elephant lineages originated), but that it also left Africa. Overall, the results presented by Meyer et al. confirm that DNA sequences are of critical importance for understanding the evolution of animals. Future research should include obtaining DNA sequences from additional extinct elephant species as well as careful re-evaluation of skeletal measurements for reconstructing elephant evolution. DOI: http://dx.doi.org/10.7554/eLife.25413.002