A three-dimensional analysis of tooth-root morphology in living bears and implications for feeding behaviour in the extinct cave bear

ABSTRACT

The morphology of both crowns and tooth-roots reflects dietary specialisation in mammalian carnivores. In this article, we analyse the tooth-root morphology of maxillary teeth from CT scans of living bears (Ursus arctos, Ursus americanus, Ursus maritimus, Ursus thibetanus, Melursus ursinus, Helarctos malayanus, Tremarctos ornatus and Ailuropoda melanoleuca) in order to make inferences about the diet and feeding behaviour of the extinct cave bear (Ursus spelaeus sensu lato). Specifically, we investigate two major mitochondrial clades of extinct cave bears recognized by previous authors: Ursus ingressus and Ursus spelaeus (U. spelaeus spelaeus, U. spelaeus ladinicus, U. spelaeus eremus). Our results indicate a close association between tooth-root surface area and feeding behaviour in all living bear species. Tooth-root surface area values of cave bears suggest that they relied more on vegetative matter than living brown bears (Ursus arctos) but subtle differences between these species/subspecies could also indicate different feeding strategies among the members of cave bear complex.     

Multi‐locus phylogeny of African pipits and longclaws (Aves: Motacillidae) highlights taxonomic inconsistencies

The globally distributed avian family Motacillidae consists of five to seven genera (Anthus, Dendronanthus, Tmetothylacus, Macronyx and Motacilla, and depending on the taxonomy followed, Amaurocichla and Madanga) and 66–68 recognized species, of which 32 species in four genera occur in sub‐Saharan Africa. The taxonomy of the Motacillidae has been contentious, with variable numbers of genera, species and subspecies proposed and some studies suggesting greater taxonomic diversity than currently recognized (five genera and 67 species). Using one nuclear (Mb) and two mitochondrial (cyt b and CO1) gene regions amplified from DNA extracted from contemporary and museum specimens, we investigated the taxonomic status of 56 of the currently recognized motacillid species and present the most taxonomically complete and expanded phylogeny of this family to date. Our results suggest that the family comprises six clades broadly reflecting continental distributions: sub‐Saharan Africa (two clades), the New World (one clade), Palaearctic (one clade), a widespread large‐bodied Anthus clade, and a sixth widespread genus, Motacilla. Within the Afrotropical region, our phylogeny further supports recognition of Wood Pipit Anthus nyassae as a valid species, and the treatment of Long‐tailed Pipit Anthus longicaudatus and Kimberley Pipit Anthus pseudosimilis as junior subjective synonyms of Buffy Pipit Anthus vaalensis and African Pipit Anthus cinnamomeus, respectively. As the disjunct populations of Long‐billed Pipit Anthus similis in southern and East Africa are genetically distinct and geographically separated, we propose a specific status for the southern African population under the earliest available name, Nicholson's Pipit Anthus nicholsoni. Further, as our analyses indicate that Yellow‐breasted Pipit Anthus chloris and Golden Pipit Tmetothylacus tenellus are both nested within the Macronyx longclaws, we propose transferring these species to the latter genus.     

Geographic and genetic boundaries of brown bear (Ursus arctos) population in the Caucasus

The taxonomic status of brown bears in the Caucasus remains unclear. Several morphs or subspecies have been identified from the morphological (craniological) data, but the status of each of these subspecies has never been verified by molecular genetic methods. We analysed mitochondrial DNA sequences (control region) to reveal phylogenetic relationships and infer divergence time between brown bear subpopulations in the Caucasus. We estimated migration and gene flow from both mitochondrial DNA and microsatellite allele frequencies, and identified possible barriers to gene flow among the subpopulations. Our suggestion is that all Caucasian bears belong to the nominal subspecies of Ursus arctos. Our results revealed two genetically and geographically distinct maternal haplogroups: one from the Lesser Caucasus and the other one from the Greater Caucasus. The genetic divergence between these haplogroups dates as far back as the beginning of human colonization of the Caucasus. Our analysis of the least‐cost distances between the subpopulations suggests humans as a major barrier to gene flow. The low genetic differentiation inferred from microsatellite allele frequencies indicates that gene flow between the two populations in the Caucasus is maintained through the movements of male brown bears. The Likhi Ridge that connects the Greater and Lesser Caucasus mountains is the most likely corridor for this migration.     

Diet reconstruction in cave bears from craniodental morphology: past evidences,new results and future directions

ABSTRACT

The diet of the cave bear (Ursus spelaeus) is a controversial topic, as different paleobiological approaches (e.g. dental wear, isotopic biochemistry, skull morphometrics) result in different dietary inferences for the cave bear, ranging from carnivory to pure herbivory. Here, we review the main results obtained from these approaches, with special emphasis on those obtained from the morphometric analyses of the cave bear craniodental skeleton. Then, we compute a between-group Principal Components Analysis from a set of 3D-landmarks digitized on 103 mandibles of living bears and extinct cave bears and using a phylomorphospace approach. Moreover, we also reconstructed the evolutionary trajectory of the cave bear mandible from the hypothetical shape of its inferred ancestor. Our results indicate that the mandible of the cave bear possess specific traits indicative of a highly-herbivorous diet or, at least, more herbivorous than their closest living relative, the brown bear (Ursus arctos). Moreover, we also propose new directions for future research to obtain more detailed inferences on the potential food resources consumed by the cave bear being crucial to understand the ‘life and death’ of this vanished animal.     

Cranial and mandibular morphology of Middle Pleistocene cave bears (Ursus deningeri): implications for diet and evolution

ABSTRACT

Deninger’s bears (Ursus deningeri) have been studied less frequently than Ursus spelaeus s.l. Our objective is to present, for the first time, an analysis of the skull shape of U. deningeri.

Bear crania and mandibles were digitised with a Microscribe or CT-scanned and the surface models subsequently landmarked. The landmarks were chosen based on a compromise between functional morphology and sample size.

Results show that U. deningeri and U. spelaeus mandibles display very similar morphologies and allometric trajectories, both to each other and to Ailuropoda melanoleuca. It is inferred that masticatory adaptations to a herbivorous diet were already present in the Middle Pleistocene. U. deningeri displays a cranial morphology that is similar to that of U. spelaeus when comparing all species, but U. deningeri has a relatively narrower and dorsoventrally lower zygomatic arch than U. spelaeus, although the masticatory signal is less strong in the skull.

We observe intraspecific differences between different populations of U. deningeri, which could parallel the genetic diversity found in U. spelaeus. The intraspecific differences found within U. deningeri may be temporal and/or geographical in nature and could be related to the evolution of the Late Pleistocene cave bear, but this hypothesis remains to be tested.     

Alaskan brown bears (Ursus arctos) aggregate and display fidelity to foraging neighborhoods while preying on Pacific salmon along small streams

The interaction between brown bears (Ursus arctos) and Pacific salmon (Oncorhynchus spp.) is important to the population dynamics of both species and a celebrated example of consumer‐mediated nutrient transport. Yet, much of the site‐specific information we have about the bears in this relationship comes from observations at a few highly visible but unrepresentative locations and a small number of radio‐telemetry studies. Consequently, our understanding of brown bear abundance and behavior at more cryptic locations where they commonly feed on salmon, including small spawning streams, remains limited. We employed a noninvasive genetic approach (barbed wire hair snares) over four summers (2012–2015) to document patterns of brown bear abundance and movement among six spawning streams for sockeye salmon, O. nerka, in southwestern Alaska. The streams were grouped into two trios on opposite sides of Lake Aleknagik. Thus, we predicted that most bears would forage within only one trio during the spawning season because of the energetic costs associated with swimming between them or traveling around the lake and show fidelity to particular trios across years because of the benefits of familiarity with local salmon dynamics and stream characteristics. Huggins closed‐capture models based on encounter histories from genotyped hair samples revealed that as many as 41 individuals visited single streams during the annual 6‐week sampling season. Bears also moved freely among trios of streams but rarely moved between these putative foraging neighborhoods, either during or between years. By implication, even small salmon spawning streams can serve as important resources for brown bears, and consistent use of stream neighborhoods by certain bears may play an important role in spatially structuring coastal bear populations. Our findings also underscore the efficacy of noninvasive hair snagging and genetic analysis for examining bear abundance and movements at relatively fine spatial and temporal scales.     

A genomic assessment of species boundaries and hybridization in a group of highly polymorphic anoles (distichus species complex)

Delimiting young species is one of the great challenges of systematic biology, particularly when the species in question exhibit little morphological divergence. Anolis distichus, a trunk anole with more than a dozen subspecies that are defined primarily by dewlap color, may actually represent several independent evolutionary lineages. To test this, we utilized amplified fragment length polymorphisms (AFLP) genome scans and genetic clustering analyses in conjunction with a coalescent‐based species delimitation method. We examined a geographically widespread set of samples and two heavily sampled hybrid zones. We find that genetic divergence is associated with a major biogeographic barrier, the Hispaniolan paleo‐island boundary, but not with dewlap color. Additionally, we find support for hypotheses regarding colonization of two Hispaniolan satellite islands and the Bahamas from mainland Hispaniola. Our results show that A. distichus is composed of seven distinct evolutionary lineages still experiencing a limited degree of gene flow. We suggest that A. distichus merits taxonomic revision, but that dewlap color cannot be relied upon as the primary diagnostic character.     

Correlation between morphological and genetic differentiation in Cuban Hutia (<Emphasis Type="Italic">Rodentia,Capromyinae</Emphasis>): Species fragmentation on the area and the problem of excessive taxonomic status problem

The work attempts to explain the previously discovered phenomenon of excessive taxonomic status of the species and subspecies of Cuban hutias relative to their protein genetic divergence. The reasons underlying the fragmentary distribution of the species belonging to the family Capromyidae over the Antilles and Bahamas is also considered. Samples of four geographically distant hutia (genera Capromys and Mysateles) populations inhabiting different biotypes were assessed according to 32 allozyme loci. It has been demonstrated that the interpopulation and subspecies differentiation in the gene frequencies in these genera is very low. As for the pattern of polymorphism (Shannon’s measure), the populations and subspecies within these genera are well differentiated and adequate to their morphological differentiation. This suggests that the genetic divergence pattern of hutias in post-Pleistoce ne was predominantly determined by selection on the background of a relatively rapid formation of multiple morphotypes. It is assumed that the evolution within the family Capromyidae in the earlier and the later periods was associated with the geomorphological and climatic events in the history of the Earth. This standpoint provides for explaining the phenomena of both the excessive taxonomic status of the Cuban Capromyinae and the fragmentary distribution of these species over the Antilles and Bahamas, amazing at a first glance.     

Molecular taxonomy of Brazilian tyrant-flycatchers (Passeriformes: Tyrannidae)

The tyrannids are one of the most diverse groups of birds in the world, and the most numerous suboscine family in the Neotropics. Reflecting such diversity, many taxonomic issues arise in this group, mainly due to morphological similarities, even among phylogenetically distant species. Other issues appear at higher taxonomic levels, mostly brought up by genetic studies, making systematics a rather inconclusive issue. This study looks into the use of DNA barcodes method to discriminate and identify Tyrannidae species occurring in the Atlantic Forest and Cerrado biomes of Brazil. We analysed 266 individuals of 71 tyrant‐flycatcher species from different geographical locations by sequencing 542 bp of the mtDNA COI gene. The great majority of the analysed species showed exclusive haplotypes, usually displaying low intraspecific diversity and high interspecific divergence. Only Casiornis fuscus and Casiornis rufus, suggested in some studies to belong to a single species, could not be phylogenetically separated. High intraspecific diversity was observed among Elaenia obscura individuals, which can suggest the existence of cryptic species in this taxon. The same was also observed for Suiriri suiriri, considered by some authors to comprise at least two species, and by others to be divided into three subspecies. Additionally, the use of sequences from voucher specimens allowed us to correct four misidentifications that had happened in the field. Our findings suggest a great power of the COI barcodes to discriminate species of the Tyrannidae family that are found in Brazil.     

Environmental enrichment for zoo bears

The high incidence of stereotypic behaviors in zoo bears (van Keulen-Kromhout: International Zoo Yearbook 18:177–186, 1978) suggests that the environment of these animals lacks essential stimuli for guiding normal behavior. Three experiments investigated ways in which bear husbandry procedures can be altered to promote normal behavior. In experiments 1 and 2, honey-filled logs were given to a sloth (Melursus ursinus), American black (Ursus americanus), and brown bear (Ursus arctos) to determine 1) the role of food in stimulating investigatory behavior, 2) the rate of habituation to manipulable objects introduced into the exhibit, and 3) effects on locomotory behaviors. Results show specific and general habituation to the introduced objects that can be counteracted by refilling the logs with honey and by providing multiple logs in the exhibit. Investigatory activity directed toward honey-logs replaces pacing and walking in the sloth bear and is most effective in doing so when the log is novel. Experiment 3 examined the behavioral effects of feeding an American black bear in three different ways: 1) once daily in the den, 2) once daily with supplemental food from a mechanical feeder, and 3) once daily with food hidden in the exhibit in manipulatable objects. The latter method reduced stereotypic pacing from a median of 150 min/day to 20 min/day; the mechanical feeder method had no such effect. The results of a survey of 67 zoos concerning the diet and manner of feeding these three species of bears, as well as Asian black bears (Ursus thibetanus) are presented. Results are discussed with respect to the ways in which husbandry procedures can be improved to stimulate functional foraging and feeding behavior in confined bears.     

Carnivores from Los Rincones,a leopard den in the highest mountain of the Iberian range (Moncayo,Zaragoza, Spain)

Carnivores are a common element in Pleistocene fossil assemblages. However, they are not so abundant in terms of the numbers of remains. Here, we present a palaeontological study of the carnivores from the Late Pleistocene (MIS 3) of Los Rincones (Spain), one of the few deposits accumulated by leopards. One hundred and ten leopard remains have been recovered. This carnivore is not the only inhabitant of the cave, and 175 remains belonging to Ursus arctos have also been recovered, making it one of the sites with the greatest number of brown bear remains in the Iberian Peninsula. The large number of leopard remains has allowed us to make a detailed morphological and biometrical study that has enabled us to classify the remains within the subspecies Panthera pardus spelaea. The European Ice Age leopard inhabited Europe during Upper Pleistocene and it presents some similarities with Panthera uncia. A study of the scarce remains of Canis lupus indicates that this was similar in size to Canis lupus maximus; the scarcity of the remains prevents us from assigning our remains to this subspecies. A study of the brown bear remains indicates that it is similar to other populations in the north of the Iberian Peninsula with this chronology.     

Taxonomic revision of the dolphin genus Lagenorhynchus

Evolutionary relationships among cetaceans within the family Delphinidae have been difficult to resolve due to the high number of species and their relatively rapid radiation. This is the case for the dolphin species currently placed in the genus Lagenorhynchus, and their relations to Cephalorhynchus and Lissodelphis species. Phylogenetic relationships among these species have been investigated using multiple lines of evidence, and that evidence consistently suggests that the six species currently assigned to Lagenorhynchus do not form a monophyletic group. Here, we summarize findings from studies of morphology, genetics, historical biogeography, and acoustics that offer insight into the phylogenetics of these taxa. We present the taxonomic basis for revision of Lagenorhynchus, propose retention of Lagenorhynchus albirostris and reassignment of the remaining five species into other existing generic names, namely Leucopleurus acutus, Sagmatias australis, Sagmatias cruciger, Sagmatias obliquidens, and Sagmatias obscurus. Making these revisions now so that the taxonomy better reflects evolutionary relationships among these species will ensure that future studies include the most appropriate taxa for investigating the complex phylogenetic and systematic relationships among cetaceans. However, comprehensive analyses using multiple lines of evidence are still needed to clarify the phylogenetic relationships within and among the Lissodelphininae genera Cephalorhynchus, Lissodelphis, and Sagmatias.     

Efficacy of firearms for bear deterrence in Alaska

We compiled, summarized, and reviewed 269 incidents of bear–human conflict involving firearms that occurred in Alaska during 1883–2009. Encounters involving brown bears (Ursus arctos; 218 incidents, 81%), black bears (Ursus americanus; 30 incidents, 11%), polar bears (Ursus maritimus; 6 incidents, 2%), and 15 (6%) unidentified species provided insight into firearms success and failure. A total of 444 people and at least 367 bears were involved in these incidents. We found no significant difference in success rates (i.e., success being when the bear was stopped in its aggressive behavior) associated with long guns (76%) and handguns (84%). Moreover, firearm bearers suffered the same injury rates in close encounters with bears whether they used their firearms or not. Bears were killed in 61% (n = 162) of bear–firearms incidents. Additionally, we identified multiple reasons for firearms failing to stop an aggressive bear. Using logistic regression, the best model for predicting a successful outcome for firearm users included species and cohort of bear, human activity at time of encounter, whether or not the bear charged, and if fish or game meat was present. Firearm variables (e.g., type of gun, number of shots) were not useful in predicting outcomes in bear–firearms incidents. Although firearms have failed to protect some users, they are the only deterrent that can lethally stop an aggressive bear. Where firearms have failed to protect people, we identified contributing causes. Our findings suggest that only those proficient in firearms use should rely on them for protection in bear country. © 2012 The Wildlife Society.     

How many species of Paradoxurus civets are there? New insights from India and Sri Lanka

Using molecular data and morphological features, we investigated the species limits and genetic diversity among populations of the Asian palm civets of the genus Paradoxurus. Our main objectives were to determine the number of species within Paradoxurus hermaphroditus and to test the validity of the newly proposed species within Paradoxurus zeylonensis. Fragments of two mitochondrial (Cytochrome b, Control Region) and one nuclear (intron 7 of the beta fibrinogen) markers were sequenced from 128 individuals of P. hermaphroditus, P. zeylonensis and Paradoxurus jerdoni. DNA sequences were analysed using phylogenetic and haplotype network methods. Our analyses confirmed that P. hermaphroditus comprises three major clades, which should be recognized as separate species: P. hermaphroditus (Indian and Indochinese regions), Paradoxurus musangus (mainland Southeast Asia, Sumatra, Java and other small Indonesian islands) and Paradoxurus philippinensis (Mentawai Islands, Borneo and the Philippines). Furthermore, we have proposed that there are two subspecies within both P. musangus and P. philippinensis, and there might be at least two or three subspecies within P. hermaphroditus. We found a very low genetic diversity and no geographical structure within P. zeylonensis and did not find any support for splitting P. zeylonensis into several species nor subspecies. Finally, we confirmed that P. jerdoni and P. zeylonensis are sister species.     

Delimitation of sympatric Palaemon (Decapoda,Palaemonidae) species of the Laguna Madre,Mexico

Grass shrimps Palaemon mundusnovus, P. pugio and P. vulgaris sympatrically inhabit in the Laguna Madre, Mexico. They exhibit very close morphological similarity and overlap in their diagnostic characteristics, which has hindered certainty in their identification and has raised doubt regarding their taxonomic validity. In this work, we analyse intra‐ and interspecific morphometric and meristic variability through a multivariate analysis, and we determine the molecular variation using mitochondrial sequences of the 12S, 16S and COX1 genes to confirm the validity of the three taxa as having distinct lineages or to recognize a smaller number of species with phenotypic plasticity. Our results corroborate the taxonomic validity of the three species; however, there is intraspecific plasticity, interspecific overlap of characteristics and greater morphological and molecular similarity between the species P. mundusnovus and P. pugio, whereas P. vulgaris was better delimited. These species form a monophyletic group but the phylogenetic relationship obtained is discussed. Telson length was the primary variable in the principal components analysis, whereas the length of the propodus of the second pereiopod was the best discriminant. The range of variation reported in the characteristics linked to the rostrum is extended, and its influence on the separation of these species is recognized. The joint application of multivariate analysis from morphological variables and molecular tools is recommended to clarify the taxonomic status of species featuring close morphological similarity and sympatric distribution.     

Assessment of the degree of restriction fragment length polymorphism in Brassica

Summary The feasibility of creating a restriction fragment length polymorphism (RFLP) linkage map in Brassica species was assessed by screening EcoRI-, HindIII-, or EcoRV-digested total genomic DNA from several accessions of B. campestris, B. oleracea, and B. napus using random genomic DNA clones from three Brassica libraries as hybridization probes. Differences in restriction fragment hybridization patterns occurred at frequencies of 95% for comparisons of accessions among species, 79% for comparisons of accessions among subspecies within species, and 70% for comparisons among accessions within subspecies. In addition, species differences in the level of hybridization were noted for some clones. The high degree of polymorphism found even among closely related Brassica accessions indicates that RFLP analysis will be a very useful tool in genetic, taxonomic, and evolutionary studies of the Brassica genus. Development of RFLP linkage maps is now in progress.     

Cranometric Variability in Brown Bears of the Russian Far East

Morphometric analysis of 282 skulls of the brown bear Ursus arctos from the Far Eastern part of the range was carried out. The presence of two morphological clusters for both males and females is shown. Samples from two clusters were compared with their geographical location and subspecies. It was found that one cluster or another had no specific reference to the particular region or subspecies of a particular cluster, only the superiority of one over the other in a cluster of different subspecies and regions was changed. A comparison with the spread of brown bear genetic lines in the Far East of Russia is made. It was noted that the precise distribution of a particular cluster to a specific genetic line of haplotypes was not found.     

Karyotype diversity and genome size variation in Neotropical Maxillariinae orchids

• Orchidaceae is a widely distributed plant family with very diverse vegetative and floral morphology, and such variability is also reflected in their karyotypes. However, since only a low proportion of Orchidaceae has been analysed for chromosome data, greater diversity may await to be unveiled. Here we analyse both genome size (GS) and karyotype in two subtribes recently included in the broadened Maxillariinea to detect how much chromosome and GS variation there is in these groups and to evaluate which genome rearrangements are involved in the species evolution.
• To do so, the GS (14 species), the karyotype – based on chromosome number, heterochromatic banding and 5S and 45S rDNA localisation (18 species) – was characterised and analysed along with published data using phylogenetic approaches.
• The GS presented a high phylogenetic correlation and it was related to morphological groups in Bifrenaria (larger plants – higher GS). The two largest GS found among genera were caused by different mechanisms: polyploidy in Bifrenaria tyrianthina and accumulation of repetitive DNA in Scuticaria hadwenii. The chromosome number variability was caused mainly through descending dysploidy, and x=20 was estimated as the base chromosome number.
• Combining GS and karyotype data with molecular phylogeny, our data provide a more complete scenario of the karyotype evolution in Maxillariinae orchids, allowing us to suggest, besides dysploidy, that inversions and transposable elements as two mechanisms involved in the karyotype evolution. Such karyotype modifications could be associated with niche changes that occurred during species evolution.

     

Molecular survey of morphological subspecies reveals new mitochondrial lineages in Podarcis muralis (Squamata: Lacertidae) from the Tuscan Archipelago (Italy)

Recent analyses of molecular markers have significantly revised the traditional taxonomy of Podarcis species (Squamata: Lacertidae), leading to critically reconsider the taxonomic value of several subspecies described only on morphological bases. In fact, lizards often exhibit high morphological plasticity both at the intra‐specific and the intra‐population level, especially on islands, where phenotypic divergences are mainly due to local adaptation, rather than to evolutionary differentiation. The Common wall lizard Podarcis muralis exhibits high morphological variability in biometry, pholidosis values and colour pattern. Molecular analyses have confirmed the key role played by the Italian Peninsula as a multi‐glacial refuge for P. muralis, pointing out the lack of congruence between mitochondrial lineages and the four peninsular subspecies currently recognized. Here, we analyse a portion of the protein‐encoding cytochrome b gene in the seven subspecies described for the Tuscan Archipelago (Italy), in order to test whether the mitochondrial haplotypes match the morphologically based taxonomy proposed for Common wall lizard. We also compare our haplotypes with all the others from the Italian Peninsula to investigate the presence of unique genetic lineages in insular populations. Our results do not agree completely with the subspecific division based on morphology. In particular, the phylogenetic analyses show that at least four subspecies are characterized by very similar haplotypes and fall into the same monophyletic clade, whereas the other three subspecies are closer to peninsular populations from central Italy. From these results, we conclude that at least some subspecies could be better regarded as simple eco‐phenotypes; in addition, we provide an explanation for the distinctiveness of exclusive lineages found in the archipelago, which constituted a refuge for this species during last glacial periods.