High-level phylogeny of early Tertiary rodents: dental evidence

Major crown‐groups of rodents were well established in the early Tertiary, and fossils provide an invaluable window into their evolutionary history. The main focus of this project was to perform a cladistic assessment of the dental evidence for early Tertiary rodent cladogenesis – the masticatory apparatus and teeth are the most frequently preserved anatomical features in the fossil record. We focused on groups that existed in a period corresponding to their early history, combining fossils belonging to extinct lineages and to stem‐groups leading to modern lineages. While the monophyly of some groups is not systematically explored, our results have important implications for high‐level rodent relationships and systematics. These results are consistent with those of recent molecular phylogenies and reliably congruent with the stratigraphic record, thus enhancing the pertinence of dental characters for phylogenetic inference. Our approach provides evidence of a fundamental dichotomy in early rodent history. Two major clades have been identified: (1) the earliest ‘ctenodactyloid’ (Ctenodactylidae, Chapattimyidae, Yuomyidae, Diatomyidae) and hystricognathous (Tsaganomyidae, Baluchimyinae, ‘phiomorphs’, ‘caviomorphs’) rodents, and (2) the earliest ‘ischyromyoid’ rodents with their closest relatives (Muroidea + Dipodoidea + Geomyoidea + Anomaluroidea + Castoroidea + Sciuravidae + Gliroidea, and Sciuroidea + Aplodontoidea + Theridomorpha). This topology has led us to endorse Ctenohystrica as the first clade and propose a new taxon, Ischyromyiformes, for the second. Although minimized in our working hypothesis, the homoplasy in dental characters remains significant. However, a number of homoplasic characters reveal structuring in their internal distribution, allowing us to discern evolutionary morphological patterns, notably the pentalophodonty of molars, zygomasseteric complex and incisor enamel microstructure. © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society, 2004, 142 , 105–134.     

Craniodental morphology and systematics of a new family of hystricognathous rodents (Gaudeamuridae) from the late eocene and early oligocene of Egypt

Background

Gaudeamus is an enigmatic hystricognathous rodent that was, until recently, known solely from fragmentary material from early Oligocene sites in Egypt, Oman, and Libya. Gaudeamus'' molars are similar to those of the extant cane rat Thryonomys, and multiple authorities have aligned Gaudeamus with Thryonomys to the exclusion of other living and extinct African hystricognaths; recent phylogenetic analyses have, however, also suggested affinities with South American caviomorphs or Old World porcupines (Hystricidae).

Methodology/Principal Findings

Here we describe the oldest known remains of Gaudeamus, including largely complete but crushed crania and complete upper and lower dentitions. Unlike younger Gaudeamus species, the primitive species described here have relatively complex occlusal patterns, and retain a number of plesiomorphic features. Unconstrained parsimony analysis nests Gaudeamus and Hystrix within the South American caviomorph radiation, implying what we consider to be an implausible back-dispersal across the Atlantic Ocean to account for Gaudeamus'' presence in the late Eocene of Africa. An analysis that was constrained to recover the biogeographically more plausible hypothesis of caviomorph monophyly does not place Gaudeamus as a stem caviomorph, but rather as a sister taxon of hystricids.

Conclusions/Significance

We place Gaudeamus species in a new family, Gaudeamuridae, and consider it likely that the group originated, diversified, and then went extinct over a geologically brief period of time during the latest Eocene and early Oligocene in Afro-Arabia. Gaudeamurids are the only known crown hystricognaths from Afro-Arabia that are likely to be aligned with non-phiomorph members of that clade, and as such provide additional support for an Afro-Arabian origin of advanced stem and basal crown members of Hystricognathi.     

Early evolutionary differentiation of morphological variation in the mandible of South American caviomorph rodents (Rodentia, Caviomorpha)

Caviomorphs are a clade of South American rodents recorded at least since the early Oligocene (> 31.5 Ma) that exhibit ample eco-morphological variation. It has been proposed that phylogenetic structure is more important than ecological factors for understanding mandibular shape variation in this clade. This was interpreted as a result of the long-standing evolutionary history of caviomorphs and the early divergence of major lineages. In this work, we test this hypothesis through the analysis of morphological variation in the mandible of living and extinct species and compare this information with that obtained through comparative phylogenetic analyses. Our results support the hypothesis of early origin of mandibular variation; moreover, they suggest the conservation of early differentiated morphologies, which could indicate the existence of constrained evolutionary diversification.     

亚洲土著类群硅藻鼠科的演化

硅藻鼠科是仅分布于亚洲的啮齿类类群,头骨具豪猪型咬肌结构,下颌则为松鼠型。该类群代表了一个从梳趾鼠类分化出的区域性支系,虽与豪猪次目相近,但并不是它的成员。最早的硅藻鼠化石记录发现于Baluchistan渐新世陆相地层中,稍晚的记录发现于南业晚渐新世。印度次大陆连续的地层为该科的演化历史提供了主要的化石依据。早中新世晚期至中中新世,硅藻科化石也发现了泰国、中国以及日本。其后的硅藻鼠种类少且鲜有化石记录。晚中新世早期在巴基斯坦有一个种,中国南部晚中新世也可能有一个种。尽管在最早的化石地点发现的标本较多,但其后的时段内除泰国李盆地外化石并不丰富,这指示了其特殊的生活习性或其生活区域化石保存的偏差。已知的化石记录并没有指示出该类群的多样性,也可能是缺少石化作用的结果。硅藻鼠类在水系外围区域延续生存与最近在老挝中部多岩石地带发现的现生Laonastes也是一个硅藻鼠的假设相一致。     

A newly recognized family from the Horn of Africa,the Heterocephalidae (Rodentia: Ctenohystrica)

The Ctenohystrica is one of the three major lineages of rodents and contains diverse forms related to gundis, porcupines, and guinea pigs. Phylogenetic analyses of this group using mitochondrial and nuclear gene sequences confirm the monophyly of the infraorder Hystricognathi and most of its recognized subclades, including both the Neotropical caviomorphs and the African phiomorphs, which are recovered as sister groups. Molecular timetrees calibrated with 22 securely placed fossils indicate that hystricognath superfamilies originated in the Eocene and Oligocene and most families had appeared by the end of the Oligocene, ～23 Mya. Divergences leading to hystricognath genera took place in the Miocene and Pliocene, with a single exception. The naked mole‐rat (Heterocephalus) diverged from other African mole‐rats (Bathyergidae) in the early Oligocene (～31.2 Mya), when the four caviomorph superfamilies (Erethizonoidea and Cavioidea at 32.4 Mya, Chinchilloidea and Octodontoidea at 32.8 Mya) were first appearing in South America. The extended independent evolution of Heterocephalus suggested by this analysis prompted a closer examination of mole‐rat characters. Heterocephalus indeed shares many characters with bathyergids, befitting their joint membership in the parvorder Bathyergomorphi and superfamily Bathyergoidea as well as their shared exploitation of subterranean lifestyles. However, a diverse array of cranial, dental, postcranial, external, and ecological characters distinguishes Heterocephalus from other African mole‐rats. These differences equal or exceed those used to diagnose caviomorph families and justify recognizing the naked mole‐rat in its own family, Heterocephalidae Landry, 1957. This taxonomic arrangement poses questions for the inter‐relationships of fossil and extant mole‐rats and brings time equivalence to the ranks assigned to the major clades of hystricognaths. © 2014 The Linnean Society of London     

Molecular evolution of the nuclear von Willebrand factor gene in mammals and the phylogeny of rodents.

Nucleotide sequences of exon 28 of the von Willebrand Factor (vWF) were analyzed for a representative sampling of rodent families and eutherian orders, with one marsupial sequence as outgroup. The aim of this study was to test if inclusion of an increased taxonomic diversity in molecular analyses would shed light on three uncertainties concerning rodent phylogeny: (1) relationships between rodent families, (2) Rodentia monophyly, and (3) the sister group relationship of rodents and lagomorphs. The results did not give evidence of any particular rodent pattern of molecular evolution relative to a general eutherian pattern. Base compositions and rates of evolution of vWF sequences of rodents were in the range of placental variation. The 10 rodent families studied here cluster in five clades: Hystricognathi, Sciuridae and Aplodontidae (Sciuroidea), Muridae, Dipodidae, and Gliridae. Among hystricognaths, the following conclusions are drawn: a single colonization event in South America by Caviomorpha, a paraphyly of Old World and New World porcupines, and an African origin for Old World porcupines. Despite a broader taxonomic sampling diversity, we did not obtain a robust answer to the question of Rodentia monophyly, but in the absence of any other alternative, we cannot reject the hypothesis of a single origin of rodents. Moreover, the phylogenetic position of Lagomorpha remains totally unsettled.     

Enamel microstructure defines a major Paleogene hippopotamoid clade: the Merycopotamini (Cetartiodactyla,Hippopotamoidea)

We present new material of the selenodont anthracothere Hemimeryx blanfordi from the Oligocene deposits of the Bugti Hills (Balochistan, Pakistan), collected between 1999 and 2002. This is the first undisputed Oligocene occurrence of the species, previously known from the early Miocene of Pakistan. Investigation of the molar enamel microstructure reveals a surprising mono-zonal Schmelzmuster, already detected in some middle to Late miocene selenedont anthracotheres. We include this observation combined with a morphological revision of H. blanfordi and a cladistic assessment of the dental evidence, to propose a new phylogenetic hypothesis regarding Hemimeryx and its close relatives. We confirm the clade including advanced bothriodontines, which we erect to a tribe rank and name Merycopotamini. The South Asian origin of Merycopotamini is consistent with hypothesized subsequent dispersal events of Merycopotamini from Asia to Africa.     

Phylogeny of the order rodentia inferred from structural analysis of short retroposon B1

A large-scale study of short retroposon (SINE) B1 has been conducted in the genome of rodents from most of the known families of this mammalian order. The B1 nucleotide sequences of rodents from different families exhibited a number of characteristic features including substitutions, deletions, and tandem duplications. Comparing the distribution of these features among the rodent families, the currently discussed phylogenetic relationships were tested. The results of analysis indicated (1) an early divergence of Sciuridae and related families (Aplodontidae and Gliridae) from the other rodents; (2) a possible subsequent divergence of beavers (Castoridae); (3) a monophyletic origin of the group Hystricognathi, which includes several families, such as porcupines (Hystricidae) and guinea pigs (Caviidae); (4) a possible monophyletic origin of the group formed by the remaining families, including six families of mouselike rodents (Myodonta). Various approaches to the use of short retroposons for phylogenetic studies are discussed.     

Phylogeny of the order Rodentia inferred from structural analysis of short retrotransposon B1

A large-scale study of short retroposon (SINE) B1 has been conducted in the genome of rodents from most of the known families of this mammalian order. The B1 nucleotide sequences of rodents from different families exhibited a number of characteristic features including substitutions, deletions, and tandem duplications. Comparing the distribution of these features among the rodent families, the currently discussed phylogenetic relationships were tested. The results of analysis indicated (1) an early divergence of Sciuridae and related families (Aplodontidae and Gliridae) from the other rodents; (2) a possible subsequent divergence of beavers (Castoridae); (3) a monophyletic origin of the group Hystricognathi, which includes several families, such as porcupines (Hystricidae) and guinea pigs (Caviidae); (4) a possible monophyletic origin of the group formed by the remaining families, including six families of mouselike rodents (Myodonta). Various approaches to the use of short retroposons for phylogenetic studies are discussed.     

Systematics and phylogeny of Vasseuromys (Mammalia,Rodentia, Gliridae) with a description of a new species from the late Miocene of eastern Europe

Vasseuromys is a species‐rich genus of small‐ to medium‐sized glirids spanning the latest Oligocene to late Miocene of Europe and western Asia. Despite extensive discoveries over the past 50 years, little phylogenetic work has been done on Vasseuromys. This study presents the first phylogenetic analysis of the genus that includes all the described species and a new taxon Vasseuromys tectus sp. nov. from the late Miocene of eastern Europe, providing the first insights into the evolutionary relationships within the clade. Results suggest that the genus is clearly paraphyletic. Two strongly supported genus‐level clades are recognized within ‘Vasseuromys’: a restricted Vasseuromys clade (containing the three species, V. pannonicus, V. rugosus and V. tectus) and the Glirulus clade that includes ‘Vasseuromys’ duplex. The remaining ‘Vasseuromys’ species are found to constitute a set of paraphyletic taxa, with the polyphyletic ‘Ramys’ nested within it. The genus Gliruloides is synonymized with Glirulus. Vasseuromys tectus sp. nov. is the most derived member of the genus in having a greater number of cheek teeth ridges including constantly present anterotrope, centrotrope, second prototrope on M1–2, third metatrope on M2, two to three posterotropids on p4 and strong ectolophids on lower molars. The results of the study confirm a European origin for Vasseuromys while suggesting that the late Miocene species of the genus dispersed from the east in the early Turolian.     

Phylogenetic structure and biogeography of the Pacific Rim clade of Sphagnum subgen. Subsecunda: haploid and allodiploid taxa

Although it is an uncommon distribution in seed plants, many bryophytes occur around the Pacific Rim of north‐western North America and eastern Asia. This work focuses on a clade of peatmosses (Sphagnum) that is distributed around the Pacific Rim region, with some individual species found across the total range. The goals were to infer divergent phylogenetic relationships among haploid species in the clade, assess parentage of allopolyploid taxa, and evaluate alternative hypotheses about inter‐ and intraspecific geographical range evolution. Multiple data sets and analyses resolved an ‘Alaska’ clade, distributed across western North America, eastern China and Japan, and an ‘Asia’ clade that includes western Chinese, Thai, Korean, eastern Chinese and Japanese lineages. Allopolyploids have arisen at least four times in the Pacific Rim clade of Sphagnum subgen. Subsecunda; it appears that all allopolyploid origins involved closely related haploid parental taxa. Biogeographical inferences were impacted by topological uncertainty and especially by the biogeographical model utilized to reconstruct ancestral areas. Most analyses converge on the conclusion that the ancestor to this clade of Pacific Rim Sphagnum species was widespread from Alaska south to eastern Asia, but a northern origin for the Alaska subclade was supported by one of the two biogeographical models we employed, under which it was robust to phylogenetic uncertainty.     

Middle Eocene rodents from Peruvian Amazonia reveal the pattern and timing of caviomorph origins and biogeography

The long-term isolation of South America during most of the Cenozoic produced a highly peculiar terrestrial vertebrate biota, with a wide array of mammal groups, among which caviomorph rodents and platyrrhine primates are Mid-Cenozoic immigrants. In the absence of indisputable pre-Oligocene South American rodents or primates, the mode, timing and biogeography of these extraordinary dispersals remained debated. Here, we describe South America's oldest known rodents, based on a new diverse caviomorph assemblage from the late Middle Eocene (approx. 41 Ma) of Peru, including five small rodents with three stem caviomorphs. Instead of being tied to the Eocene/Oligocene global cooling and drying episode (approx. 34 Ma), as previously considered, the arrival of caviomorphs and their initial radiation in South America probably occurred under much warmer and wetter conditions, around the Mid-Eocene Climatic Optimum. Our phylogenetic results reaffirm the African origin of South American rodents and support a trans-Atlantic dispersal of these mammals during Middle Eocene times. This discovery further extends the gap (approx. 15 Myr) between first appearances of rodents and primates in South America.     

Eocene ctenodactyloid rodent assemblages and diversification from Erden Obo,Nei Mongol,China

New ctenodactyloid occurrences (Yuomys magnus sp. nov., Gobiomys neimongolensis and Gobiomys exiguus) from the ‘Lower Red’ to the ‘Upper Red’ beds of the Erden Obo section in Nei Mongol, China are reported. Here, we present an updated review of the ctenodactyloid rodents from the Erden Obo section. We have recognised eight species and one indeterminate species belonging to six genera: Advenimus, Chenomys, Gobiomys, Tamquammys, Simplicimys, and Yuomys. The ctenodactyloids show an initial burst in diversification in the upper part of the ‘Basal Red’ of the early Eocene. A maximum richness peak is present at the lower part of the ‘Basal White’ which falls near the boundary of early and middle Eocene. Gobiomys, the only surviving genus from the ‘Middle Red’ to the ‘Upper Red’ beds, shows that the diversity of ctenodactyloids declined rapidly after late middle Eocene. Based on the study of the abundant ctenodactyloid rodents, we recognise some evolutionary tendencies among Eocene ctenodactyloids.

http://www.zoobank.org/urn:lsid:zoobank.org:act:33D2442E-DA27-494A-80CB-2DB9DA9E4E1A     

Lygosomine phylogeny and the origins of Australian scincid lizards

Aim Australian scincid lizards represent three distinct groups within the cosmopolitan clade Lygosominae, the Egernia, Eugongylus and Sphenomorphus groups. This paper presents a time‐calibrated phylogeny for Lygosominae that provides the necessary temporal framework for assessing the contributions of immigration from Asia and of Gondwanan inheritance in the derivation of the Australian scincid fauna. Location Australasia, Asia, Africa. Methods Phylogenetic relationships and divergence times were inferred from novel BDNF, c‐mos and PTPN12 sequences (2408 aligned sites). Results Lygosomine monophyly is well supported, and there is strong support for monophyly of the Egernia, Eugongylus and Sphenomorphus groups. A sister‐group relationship of Tribolonotus (distributed in Melanesia and the Papuan Region) and the Egernia group is strongly supported in both Bayesian and maximum likelihood analyses. Australian representatives of the Sphenomorphus group compose a significantly supported clade estimated to have originated c. 25 Ma. An age of c. 18 Ma is inferred for a strongly supported clade comprising Australian representatives of the Egernia group; this clade diverged from Corucia zebrata (confined to the Solomon Islands) c. 25 Ma and from Tribolonotus c. 54 Ma. A well‐supported clade including all Australian Eugongylus group taxa sampled is estimated to have arisen c. 20 Ma. Main conclusions The Australian Sphenomorphus group is nested within the more inclusive Sphenomorphus group (distributed primarily in Asia and Australasia), suggesting comparatively recent descent from a colonizing Asian ancestor; the divergence times inferred here indicate that colonization occurred during the mid Cenozoic, subsequent to the rifting of Australia from Antarctica. An Oligocene origin of the extant Eugongylus group fauna of Australasia (the basal members of which are distributed in the Southwest Pacific) indicates that Eugongylus group lygosomines also dispersed to Australia relatively recently. The Egernia group diverged from Tribolonotus in the Early Eocene; however, extant Egernia group lygosomines originated only during the Late Oligocene, implying extensive pruning of stem taxa (i.e. extinction). As a result, inferences of the timing of dispersal into Australia are associated with substantial uncertainty, although independent palaeontological evidence suggests that the Egernia group entered Australia prior to the Oligocene, immediately after (or perhaps before) the separation of Australia and Antarctica.     

狭义蛇葡萄属东亚支系的系统发生与生物地理演化

狭义蛇葡萄属(Ampelopsis s. str.)是葡萄科的落叶木质藤本植物,主要分布在北半球温带地区,特别是东亚为其重要的分布和演化中心。该研究选取了狭义蛇葡萄属15个种的37个样本,对其5个叶绿体基因片段(trnL-F、rps16、psbA-trnH、atpB-rbcL和trnK-petN)和2个核基因标记(ITS和GAI1)进行了分子测序;利用测序获得的分子数据探讨属内的系统发生关系,叶的性状演化以及生物地理起源演化。结果表明：(1)狭义蛇葡萄属是一个单系类群,属内东亚地区的物种聚成一支。(2)叶绿体基因数据分析结果表明,狭义蛇葡萄属东亚支系分为两支系,这两支系的分布范围大致与东亚植物区系的中国-日本森林和中国-喜马拉雅森林亚区范围相一致。(3)形态演化分析表明,掌状复叶为祖征,叶形态性状存在多次的独立起源和演化,其变化与系统进化没有明显的关系。(4)生物地理分析结果表明,狭义蛇葡萄属起源于北美,渐新世晚期至中新世早期迁移扩散至欧洲,中新世中期随着全球气温回暖迁移至东亚,并进一步在东亚地区快速分化形成多样化中心,这可能与中新世时期的气候温暖、受第四纪冰川影响较少以及东亚地区复杂...     

Main radiation events in Pan‐Octodontoidea (Rodentia,Caviomorpha)

Caviomorphs (South American hystricognaths) are recorded in the continent since the middle Eocene. The middle Eocene–early Oligocene is considered a key moment for their evolutionary history because by the early Oligocene they were differentiated into four superfamilies: Octodontoidea, Cavioidea, Chinchilloidea and Erethizontoidea. Due to their generalized dental patterns and abundance in the fossil record, Octodontoidea are interesting for analysing the origin and early history of caviomorphs. The phylogenetic relationships of the earliest octodontoids are studied herein. Results confirmed a basal caviomorph diversification in the middle Eocene (c. 45 Mya), with one lineage leading to Pan‐Octodontoidea, and another leading to Erethizontoidea, Cavioidea and Chinchilloidea, which is not in accordance with analyses based on molecular data. Three major radiations were identified: the first one (late Eocene?/early Oligocene?) occurred in low latitudes with the differentiation of Pan‐Octodontoidea and the earliest crown‐Octodontoidea. The second radiation (late Oligocene) was a large‐scale South American event; in the southernmost part of the continent it is recognized as the first Patagonian octodontoid radiation, which provided the characteristic high morphological disparity of the superfamily. The third radiation (late Miocene) is characterized by the replacement of ‘old’ by ‘modern’ octodontoids; the nature of this third event needs to be study in a broader taxonomic context. © 2015 The Linnean Society of London     

Evolutionary history of Spalacidae inferred from fossil occurrences and molecular phylogeny

1. The Spalacidae is a family of strictly subterranean rodents with a long evolutionary history. It is unclear how ecological changes have influenced the evolutionary history of these mammals, and the phylogenetic relationship of the subfamilies within Spalacidae is controversial.
2. Through compiling fossil records, reconstructing molecular phylogeny from molecular data, determining the date of divergence, and analysing their geographical evolution based on molecular data and fossil taxa, we explore the origin and evolutionary process of Spalacidae in detail. Diversification within Spalacidae dates to the Late Oligocene, approximately 25 million years ago, based on molecular data.
3. This family originated in South and East Asia in the Late Oligocene, and then split into four clades. The first clade includes Rhizomyinae, which was highly diversified in South Asia in the Early-to-Middle Miocene. Then Rhizomyinae from Asia migrated to northern Africa in multiple waves through the Afro-Eurasian land bridge. Its range largely contracted in the Late Miocene, notably in Central Asia. The second clade includes the extinct Tachyoryctoidinae, which was confined to East and Central Asia, and survived from the Late Oligocene to the Late Miocene. The third clade includes Spalacinae, which have remained around the Mediterranean region since the Late Oligocene with slight trend of northward expansion. The fourth clade is Myospalacinae. Ancient genera of this subfamily in East Asia dispersed eastward during the Late Miocene and reached northern China and south-east Russia.
4. The general distribution pattern of Spalacidae has persisted since the Late Miocene. Extinction of Tachyoryctoidinae and clear range contraction of Rhizomyinae in Central and East Asia are likely to have resulted from increased aridification, while the slight northward expansion of Myospalacinae and Spalacinae since the Quaternary was probably a response to a similar northward expansion of suitable vegetation for these animals.

     

硅藻鼠科(哺乳纲,啮齿目)与亚洲中始新世啮齿类的双脊齿(英文)

亚洲特有的啮齿类硅藻鼠科自渐新世以来分布于东亚和南亚。现生硅藻鼠类的分布只限于老挝的喀斯特地区。就目前所知,这些具有豪猪型头骨-松鼠型下颌的啮齿类的颊齿都是不同程度的横向双脊齿。时代最早的硅藻鼠类产于巴基斯坦渐新世地层中,其颊齿的双脊齿构造上仍保留齿尖残迹,基本符合双脊齿型牙齿结构。至渐新世末期,硅藻鼠科的牙齿出现分化。中新世及以后硅藻鼠类的化石记录相对较少。分子生物学证据将硅藻鼠类归入Ctenohystrica,这种归属也从始新世梳趾鼠类的臼齿形态上得到一定的支持。除此之外,有关硅藻鼠类的起源问题几乎一无所知。亚洲中始新世的Hydentomys臼齿表现出轻微的双脊型,然而其他方面却与硅藻鼠类不同。另一个具双脊齿的啮齿类Dolosimus(新属)产于江苏中始新世,其具有更为发育的双脊齿,特别是臼齿型下牙。新属的不完整记录及其形态不能解决如下问题:它是否与后来出现的像硅藻鼠类和跃兔类这些具有明显双脊齿型颊齿的啮齿类有亲缘关系,或者只是这种形态发育中没有留下后继者的早期试验品。