Morphological diversity and ecological niche divergence in goitered and sand gazelles.

The phylogeny and species boundaries of Gazella subgutturosa and G. marica have been long debated. The achievements of past conservation efforts have been compromised by a lack of knowledge about the phylogeny and taxonomic status of different populations. We integrated the recent genetic findings by previous studies with morphometric analyses and ecological niche modeling (ENM) to assess discreteness among populations of these gazelle species in Asia. Taxonomic diversity of gazelles was investigated by using principal components analysis (PCA) based on 14 cranial measures of male skulls. Ecological niche divergence was examined based on a PCA on climatic factors and a species distribution modeling (SDM) with environmental variables. Morphometric results indicated substantial differentiation in size between skulls of the western Zagros Mountains including west and south-western Iran and Arabian Peninsula from all other samples east of the Zagros Mountains from Iran to China. ENM also revealed that gazelles in the east and west of Zagros Mountains occupy distinct niches and that there are apparent areas of disconnection across the goitered gazelle suitable range. A complete divergent niche occupation was also observed between goitered gazelles of northern Mongolia and other populations of the species, except those in China. Taking the inferences from ENM and morphology together with previous genetics results, we conclude that gazelles in the west and south-west of Iran may represent G. marica. Also, our combined analyses revealed divergence among gazelles of Iran, Central Asia, and Mongolia/China. These results may pave the way for future studies and have conservation implications particularly for reintroduction/supplementation programs.

Mandibular corpus shape is a taxonomic indicator in extant hominids.

OBJECTIVES: The aim of this study is to understand whether the shape of three sub-regions of the mandibular corpus (the alveolar arch, corpus at M1 and posterior symphysis) are useful for making taxonomic assessments at the genus and species levels in extant hominids. MATERIALS AND METHODS: We use data taken from 3D surface scans of the mandibular corpus of seven extant hominid taxa: Gorilla gorilla gorilla, Gorilla beringei graueri, Homo sapiens, Pan paniscus, Pan troglodytes schweinfurthii, Pongo abelii, and Pongo pygmaeus pygmaeus to generate four shape variables: alveolar arch shape (AAS), corpus shape at M1 (CSM1 ), posterior symphysis shape at the midline (PSSM), and posterior symphysis shape (PSS). To ascertain how reliable each mandibular shape variable is for assessing taxonomy, we ran canonical discriminant and discriminant function analysis, reporting cross-validated results. RESULTS: Using a combination of three mandibular corpus shape variables, 99% of specimens were classified correctly for genus-level analyses. A maximum of 100% of Pan specimens, 94% of Gorilla specimens and 96% of Pongo specimens were classified correctly at the species level when up to three mandibular shape variables were included in the analyses. When mandibular corpus variables were considered in isolation, posterior symphysis shape yielded the highest overall correct classification results. DISCUSSION: The high taxonomic classification rates at both the genus and species level, using 3D surface data and advanced quantification techniques, show that the shape of the alveolar arch, corpus at M1 and symphysis can distinguish extant hominid taxa. These findings have implications for assessing the taxonomy of extinct hominid specimens which preserve these mandibular sub-regions.

First insights into the feeding habits of the Critically Endangered black snub-nosed monkey, Rhinopithecus strykeri (Colobinae, Primates).

Since its initial discovery in 2010 in the Gaoligong Mountains on the Sino-Myanmar border, there remains no direct information on the feeding habits of the black snub-nosed monkey (Rhinopithecus strykeri). This species is on the verge of extinction, with an estimated remaining population of < 400 individuals. Due to difficulties in following these monkeys across steep mountainous terrain, during 203 observation days (September 2015-January 2017) we recorded 80 h of behavioral records of a wild population (Luoma group). Our preliminary results identified 14 plant species and four lichen species consumed by the monkeys. In addition, we provided the only two captive individuals of this species with a cafeteria diet composed of > 600 wild-collected plant species that were gathered from known R. strykeri habitats to determine which plant species and food items were considered palatable. Our results indicate that the captive monkeys freely consumed young and mature leaves, fruits/seeds, buds, flowers, twigs, and bark from 170 different species of trees, bushes, and herbs representing 76 genera and 41 plant families, as well as 15 species of lichen. All foods consumed by the wild monkeys were also consumed by the captive individuals. Food plants consumed by R. strykeri were found principally in intact subtropical evergreen broadleaf forests and hemlock-broadleaf mixed forests at an altitude of 2200-3000 m. Strict enforcement of habitat protection and access to resources across this elevation zone appear to be essential for the conservation and survivorship of this critically endangered primate.

Overlooked mammal diversity and conservation priorities in Italy: Impacts of taxonomic neglect on a Biodiversity Hotspot in Europe.

For more than half a century, little taxonomic revisionary work has been directed towards extant European mammals so that the limits of most geographically widespread polytypic species remained scientifically untested. Occasionally, taxonomic changes have been proposed and several new species have been resurrected / discovered in the last decades mainly on the basis of genetic studies, often considered the only tool to establish objective species boundaries. Nevertheless, the precise details of species boundaries, subspecific variation and phylogenetic relationships remain unknown for several European mammal taxa. The inadequacies of outdated, incomplete taxonomic knowledge reach an extreme in southern Europe, and notably Italy, where cryptic species abound and specimen-based research is scanty. The state of mammalian taxonomic knowledge in Italy shows that Linnaean and Wallacean shortfalls are no means restricted to hyperdiverse, understudied tropics. They undermine our knowledge of temperate regions, with severe consequences for biodiversity conservation policies in Europe, where conservation assessments overlook significant endemic biodiversity. European mammalogy stands to benefit from an infusion of the tree-thinking philosophy that undergirds evolutionary theory and particularly phylogenetic methods systematics. Furthermore, it is important that taxonomic research be seen as a normal part of scientific advancement and of critical importance as the basis of a sound biodiversity conservation policy.

Impacts of taxonomic inertia for the conservation of African ungulate diversity: an overview.

We review the state of African ungulate taxonomy over the last 120 years, with an emphasis on the introduction of the polytypic species concept and the discipline's general neglect since the middle of the 20th century. We single out negative consequences of 'orthodox' taxonomy, highlighting numerous cases of neglect of threatened lineages, unsound translocations that led to lineage introgression, and cases of maladaptation to local conditions including parasitic infections. Additionally, several captive breeding programmes have been hampered by chromosome rearrangements caused by involuntary lineage mixing. We advocate that specimen-based taxonomy should regain its keystone role in mammal research and conservation biology, with its scientific values augmented with genomic evidence. While integration with molecular biology, ecology and behaviour is needed for a full understanding of ungulate alpha diversity, we stress that morphological diversity has been neglected despite its tremendous practical importance for some groups of 'utilizers' such as trophy hunters, wildlife tourists and conservationists. We conclude that there is no evidence that purported 'taxonomic inflation' has adverse effects on ungulate conservation: rather, it is taxonomic inertia that has such adverse effects. We stress that sound science, founded on robust taxonomy, should underpin effective sustainable management (hunting, ranching, captive breeding and reintroduction programmes) of this unique African natural resource.

Morphometric, Behavioral, and Genomic Evidence for a New Orangutan Species.

Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularly true for orangutans (genus: Pongo), the only Asian great apes and phylogenetically our most distant relatives among extant hominids [1]. Designation of Bornean and Sumatran orangutans, P. pygmaeus (Linnaeus 1760) and P. abelii (Lesson 1827), as distinct species occurred in 2001 [1, 2]. Here, we show that an isolated population from Batang Toru, at the southernmost range limit of extant Sumatran orangutans south of Lake Toba, is distinct from other northern Sumatran and Bornean populations. By comparing cranio-mandibular and dental characters of an orangutan killed in a human-animal conflict to those of 33 adult male orangutans of a similar developmental stage, we found consistent differences between the Batang Toru individual and other extant Ponginae. Our analyses of 37 orangutan genomes provided a second line of evidence. Model-based approaches revealed that the deepest split in the evolutionary history of extant orangutans occurred ∼3.38 mya between the Batang Toru population and those to the north of Lake Toba, whereas both currently recognized species separated much later, about 674 kya. Our combined analyses support a new classification of orangutans into three extant species. The new species, Pongo tapanuliensis, encompasses the Batang Toru population, of which fewer than 800 individuals survive. VIDEO ABSTRACT.

Global biogeography since Pangaea.

The break-up of the supercontinent Pangaea around 180 Ma has left its imprint on the global distribution of species and resulted in vicariance-driven speciation. Here, we test the idea that the molecular clock dates, for the divergences of species whose geographical ranges were divided, should agree with the palaeomagnetic dates for the continental separations. Our analysis of recently available phylogenetic divergence dates of 42 pairs of vertebrate taxa, selected for their reduced ability to disperse, demonstrates that the divergence dates in phylogenetic trees of continent-bound terrestrial and freshwater vertebrates are consistent with the palaeomagnetic dates of continental separation.

The affinities of Homo floresiensis based on phylogenetic analyses of cranial, dental, and postcranial characters.

Although the diminutive Homo floresiensis has been known for a decade, its phylogenetic status remains highly contentious. A broad range of potential explanations for the evolution of this species has been explored. One view is that H. floresiensis is derived from Asian Homo erectus that arrived on Flores and subsequently evolved a smaller body size, perhaps to survive the constrained resources they faced in a new island environment. Fossil remains of H. erectus, well known from Java, have not yet been discovered on Flores. The second hypothesis is that H. floresiensis is directly descended from an early Homo lineage with roots in Africa, such as Homo habilis; the third is that it is Homo sapiens with pathology. We use parsimony and Bayesian phylogenetic methods to test these hypotheses. Our phylogenetic data build upon those characters previously presented in support of these hypotheses by broadening the range of traits to include the crania, mandibles, dentition, and postcrania of Homo and Australopithecus. The new data and analyses support the hypothesis that H. floresiensis is an early Homo lineage: H. floresiensis is sister either to H. habilis alone or to a clade consisting of at least H. habilis, H. erectus, Homo ergaster, and H. sapiens. A close phylogenetic relationship between H. floresiensis and H. erectus or H. sapiens can be rejected; furthermore, most of the traits separating H. floresiensis from H. sapiens are not readily attributable to pathology (e.g., Down syndrome). The results suggest H. floresiensis is a long-surviving relict of an early (>1.75 Ma) hominin lineage and a hitherto unknown migration out of Africa, and not a recent derivative of either H. erectus or H. sapiens.

Phylogenomic Reconstruction of Sportive Lemurs (genus Lepilemur) Recovered from Mitogenomes with Inferences for Madagascar Biogeography.

The family Lepilemuridae includes 26 species of sportive lemurs, most of which were recently described. The cryptic morphological differences confounded taxonomy until recent molecular studies; however, some species' boundaries remain uncertain. To better understand the genus Lepilemur, we analyzed 35 complete mitochondrial genomes representing all recognized 26 sportive lemur taxa and estimated divergence dates. With our dataset we recovered 25 reciprocally monophyletic lineages, as well as an admixed clade containing Lepilemur mittermeieri and Lepilemur dorsalis. Using modern distribution data, an ancestral area reconstruction and an ecological vicariance analysis were performed to trace the history of diversification and to test biogeographic hypotheses. We estimated the initial split between the eastern and western Lepilemur clades to have occurred in the Miocene. Divergence of most species occurred from the Pliocene to the Pleistocene. The biogeographic patterns recovered in this study were better addressed with a combinatorial approach including climate, watersheds, and rivers. Generally, current climate and watershed hypotheses performed better for western and eastern clades, while speciation of northern clades was not adequately supported using the ecological factors incorporated in this study. Thus, multiple mechanisms likely contributed to the speciation and distribution patterns in Lepilemur.

Description of a new species of Hoolock gibbon (Primates: Hylobatidae) based on integrative taxonomy.

We describe a species of Hoolock gibbon (Primates: Hylobatidae) that is new to science from eastern Myanmar and southwestern China. The genus of hoolock gibbons comprises two previously described living species, the western (Hoolock hoolock) and eastern hoolock (H. leuconedys) gibbons, geographically isolated by the Chindwin River. We assessed the morphological and genetic characteristics of wild animals and museum specimens, and conducted multi-disciplinary analyses using mitochondrial genomic sequences, external morphology, and craniodental characters to evaluate the taxonomic status of the hoolock population in China. The results suggest that hoolocks distributed to the east of the Irrawaddy-Nmai Hka Rivers, which were previously assigned to H. leuconedys, are morphologically and genetically distinct from those to the west of the river, and should be recognized as a new species, the Gaoligong hoolock gibbon or skywalker hoolock gibbon (H. tianxing sp. nov.). We consider that the new species should be categorized as Endangered under IUCN criteria. The discovery of the new species focuses attention on the need for improved conservation of small apes, many of which are in danger of extinction in southern China and Southeast Asia.

Early cave art and ancient DNA record the origin of European bison.

The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus) before the Holocene (<11.7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison (Bison priscus) and ancestors of modern cattle (aurochs, Bos primigenius) before 120 kya, and contains up to 10% aurochs genomic ancestry. Although undetected within the fossil record, ancestors of the wisent have alternated ecological dominance with steppe bison in association with major environmental shifts since at least 55 kya. Early cave artists recorded distinct morphological forms consistent with these replacement events, around the Last Glacial Maximum (LGM, ∼21-18 kya).

Systematics of the Artiodactyla of China in the 21(st) century.

In this paper, I have introduced the concept of the Evolutionary Species, and shown how it affects the taxonomy of the Artiodactyla of China. The "traditional" taxonomy of the Artiodactyla, which has remained almost unchanged for 100 years, relies on ill-formulated notions of species and subspecies, only slightly modified by the population-thinking of the 1930s. Species are populations (or metapopulations) differentiated by the possession of fixed heritable differences from other such populations (or metapopulations). In the Artiodactyla, there are many more species than "traditionally" recognised; this is by no means a drawback, as it enables the units of biodiversity to be identified in a testable fashion, and brings the taxonomy of large mammals into line with that long practised for small mammals. Species are likely to differentiate where there are natural gaps in the distribution of a genus, such as mountain blocks (for example in the genus Budorcas) or otherwise dissected habitat (for example in the genus Cervus). Natural hybridisation between distinct species is not an uncommon phenomenon, again illustrated well in the genus Cervus, where hybridisation between the elaphus and nippon groups occurs today and evidently occurred in the past, as shown by the distribution of mtDNA.

Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence.

BACKGROUND: Titi monkeys, Callicebus, comprise the most species-rich primate genus-34 species are currently recognised, five of them described since 2005. The lack of molecular data for titi monkeys has meant that little is known of their phylogenetic relationships and divergence times. To clarify their evolutionary history, we assembled a large molecular dataset by sequencing 20 nuclear and two mitochondrial loci for 15 species, including representatives from all recognised species groups. Phylogenetic relationships were inferred using concatenated maximum likelihood and Bayesian analyses, allowing us to evaluate the current taxonomic hypothesis for the genus. RESULTS: Our results show four distinct Callicebus clades, for the most part concordant with the currently recognised morphological species-groups-the torquatus group, the personatus group, the donacophilus group, and the moloch group. The cupreus and moloch groups are not monophyletic, and all species of the formerly recognized cupreus group are reassigned to the moloch group. Two of the major divergence events are dated to the Miocene. The torquatus group, the oldest radiation, diverged c. 11 Ma; and the Atlantic forest personatus group split from the ancestor of all donacophilus and moloch species at 9-8 Ma. There is little molecular evidence for the separation of Callicebus caligatus and C. dubius, and we suggest that C. dubius should be considered a junior synonym of a polymorphic C. caligatus. CONCLUSIONS: Considering molecular, morphological and biogeographic evidence, we propose a new genus level taxonomy for titi monkeys: Cheracebus n. gen. in the Orinoco, Negro and upper Amazon basins (torquatus group), Callicebus Thomas, 1903, in the Atlantic Forest (personatus group), and Plecturocebus n. gen. in the Amazon basin and Chaco region (donacophilus and moloch groups).

The evolutionary origin and population history of the grauer gorilla.

Gorillas living in western central Africa (Gorilla gorilla) are morphologically and genetically distinguishable from those living in eastern central Africa (Gorilla beringei). Genomic analyses show eastern gorillas experienced a significant reduction in population size during the Pleistocene subsequent to geographical isolation from their western counterparts. However, how these results relate more specifically to the recent biogeographical and evolutionary history of eastern gorillas remains poorly understood. Here we show that two rare morphological traits are present in the hands and feet of both eastern gorilla subspecies at strikingly high frequencies (>60% in G. b. graueri; ∼28% in G. b. beringei) in comparison with western gorillas (<1%). The intrageneric distribution of these rare traits suggests that they became common among eastern gorillas after diverging from their western relatives during the early to middle Pleistocene. The extremely high frequencies observed among grauer gorillas-which currently occupy a geographic range more than ten times the size of that of mountain gorillas-imply that grauers originated relatively recently from a small founding population of eastern gorillas. Current paleoenvironmental, geological, and biogeographical evidence supports the hypothesis that a small group of eastern gorillas likely dispersed westward from the Virungas into present-day grauer range in the highlands just north of Lake Kivu, either immediately before or directly after the Younger Dryas interval. We propose that as the lowland forests of central Africa expanded rapidly during the early Holocene, they became connected with the expanding highland forests along the Albertine Rift and enabled the descendants of this small group to widely disperse. The descendant populations significantly expanded their geographic range and population numbers relative to the gorillas of the Virunga Mountains and the Bwindi-Impenetrable Forest, ultimately resulting in the grauer gorilla subspecies recognized today. This founder-effect hypothesis offers some optimism for modern conservation efforts to save critically endangered eastern gorillas from extinction.

The 'temporal effect' in hominids: Reinvestigating the nature of support for a chimp-human clade in bone morphology.

In 2004, an analysis by Lockwood and colleagues of hard-tissue morphology, using geometric morphometrics on the temporal bone, succeeded in recovering the correct phylogeny of living hominids without resorting to potentially problematic methods for transforming continuous shape variables into meristic characters. That work has increased hope that by using modern analytical methods and phylogenetically informative anatomical data we might one day be able to accurately infer the relationships of hominins, including the closest extinct relatives of modern humans. In the present study, using 3D virtually generated models of the hominid temporal bone and a larger suite of geometric morphometric and comparative techniques, we have re-examined the evidence for a Pan-Homo clade. Despite differences in samples, as well as the type of raw data, the effect of measurement error (and especially landmark digitization by a different operator), but also a broader perspective brought in by our diverse set of approaches, our reanalysis largely supports Lockwood and colleagues' original results. However, by focusing not only mainly on shape (as in the original 2004 analysis) but also on size and 'size-corrected' (non-allometric) shape, we demonstrate that the strong phylogenetic signal in the temporal bone is largely related to similarities in size. Thus, with this study, we are not suggesting the use of a single 'character', such as size, for phylogenetic inference, but we do challenge the common view that shape, with its highly complex and multivariate nature, is necessarily more phylogenetically informative than size and that actually size and size-related shape variation (i.e., allometry) confound phylogenetic inference based on morphology. This perspective may in fact be less generalizable than often believed. Thus, while we confirm the original findings by Lockwood et al., we provide a deep reinterpretation of their nature and potential implications for hominid phylogenetics and we show how crucial it is not to overlook size in geometric morphometric analyses.