The steroid metabolome of pregnancy, insights into the maintenance of pregnancy and evolution of reproductive traits.

Modes of mammalian reproduction are diverse and not always conserved among related species. Progesterone is universally required to supports pregnancy but sites of synthesis and metabolic pathways vary widely. The steroid metabolome of mid-to late gestation was characterized, focusing on 5α-reduced pregnanes in species representing the Perissodactyla, Cetartiodactyla and Carnivora using mass spectrometry. Metabolomes and steroidogenic enzyme ortholog sequences were used in heirarchial analyses. Steroid metabolite profiles were similar within orders, whales within cetartiodactyls for instance, but with notable exceptions such as rhinoceros clustering with goats, and tapirs with pigs. Steroidogenic enzyme sequence clustering reflected expected evolutionary relationships but once again with exceptions. Human sequences (expected outgroups) clustered with perissodactyl CYP11A1, CYP17A1 and SRD5A1 gene orthologues, forming outgroups only for HSD17B1 and SRD5A2. Spotted hyena CYP19A1 clustered within the Perissodactyla, between rhinoceros and equid orthologues, whereas CYP17A1 clustered within the Carnivora. This variability highlights the random adoption of divergent physiological strategies as pregnancy evolved among genetically similar species.

Mammalian Orthoreovirus (MRV) Is Widespread in Wild Ungulates of Northern Italy.

Mammalian orthoreoviruses (MRVs) are emerging infectious agents that may affect wild animals. MRVs are usually associated with asymptomatic or mild respiratory and enteric infections. However, severe clinical manifestations have been occasionally reported in human and animal hosts. An insight into their circulation is essential to minimize the risk of diffusion to farmed animals and possibly to humans. The aim of this study was to investigate the presence of likely zoonotic MRVs in wild ungulates. Liver samples were collected from wild boar, red deer, roe deer, and chamois. Samples originated from two areas (Sondrio and Parma provinces) in Northern Italy with different environmental characteristics. MRV detection was carried out by PCR; confirmation by sequencing and typing for MRV type 3, which has been frequently associated with disease in pigs, were carried out for positive samples. MRV prevalence was as high as 45.3% in wild boars and 40.6% in red deer in the Sondrio area, with lower prevalence in the Parma area (15.4% in wild boars). Our findings shed light on MRV occurrence and distribution in some wild species and posed the issue of their possible role as reservoir.

Multi-aged social behaviour based on artiodactyl tracks in an early Miocene palustrine wetland (Ebro Basin, Spain).

We present a new locality with at least 880 vertebrate tracks found at the top of a limestone bed from the lower Miocene Tudela Formation (Spain). The trampled surface was formed by artiodactyls that crossed a muddy carbonate accumulated under the influence of water level variations in a palustrine environment. The tracks reflect different types of morphological preservation. The well-preserved tracks have tetradactyl digit impressions caused by both manus and pes, and are the type series of a new artiodactyl ichnotaxon, Fustinianapodus arriazui ichnogen. nov. and ichnosp. nov. The rest of the tracks, which are not as well preserved, are didactyl and were classified as undetermined artiodactyl tracks. According to their preservation, morphology, size, arrangement and orientation, we propose that this tracksite is the product of a social behaviour, particularly gregariousness, of a multi-age group of artiodactyls ~19 Ma ago. The morphologic and palaeoecologic data presented here suggest that the trackmakers were a group of anthracotheres with a livelihood similar to current hippos. They crossed, periodically, a fresh water palustrine area along some preferential pathways (trails).

Hippopotamidae (Cetartiodactyla, Hippopotamoidea) from Kanapoi, Kenya, and the taxonomic status of the late early Pliocene hippopotamids from the Turkana Basin.

New hippopotamid specimens recently collected at Kanapoi (ca. 4 Ma) are similar to the taxon previously recognized in this site and referred to aff. Hippopotamus protamphibius. Their examination provided the opportunity to reassess the taxonomic status of this taxon. It appears different from the late Miocene hippopotamids from the Turkana Basin (prominently Archaeopotamus harvardi), but also differs from the late Pliocene-early Pleistocene aff. Hip. protamphibius, which is smaller and displays more advanced features (notably canine expansion and orbit elevation). In contrast, the Kanapoi material appears very similar to the material from the Hadar Formation (3.4 Ma-2.9 Ma). However, the current confusion surrounding the taxonomic status of the Hadar specimens, previously attributed to various taxa that may be identical, does not allow attribution of a specific name to the Kanapoi material for now and, while waiting for the revision of Hadar hippopotamid diversity, it is referred here to aff. Hippopotamus cf. sp. Hadar. This contribution allows recognizing that a large hippopotamid, possibly a transitional form between the late Miocene species and Plio-Pleistocene species, was distributed from Afar to Turkana between 4.2 Ma and 2.95 Ma. The marked endemism of hippopotamids in the Pleistocene rift basins therefore initiated after 2.9 Ma.

Sequencing and characterization of the complete mitochondrial genome of Mishmi takin (Budorcas taxicolor taxicolor) and comparison with the other Caprinae species.

Mishmi takin (Budorcas taxicolor taxicolor) is an endangered and least studies species. We sequenced and annotated a 16,584 bp long complete mitogenome of Mishmi takin (B. t. taxicolor). It was encoded by 37 genes: 13 Protein-Coding Genes (PCGs), two ribosomal RNA genes, 22 transfer RNA, and non-coding control region. All tRNA genes show a typical secondary cloverleaf structure, except tRNAser(AGY) in which dihydrouridine arm did not form a stable structure. We observed 82 bp nucleotide deletions in the control region of Mishmi takin. The overall analysis of 13 PCGs, two rRNA and 22 tRNA of Mishmi takin indicates its close relationship with the B. t. tibetana than the B. t. bedfordi. The overall genetic similarity indicated that all takin species is closely related to the P. nayaur than the C. ibex and Ovibos moschatus. This study provides a useful resource for further studies on conservation and population genetics of Budorcas.

The complete mitochondrial genome of Budorcas taxicolor tibetana (Artiodactyla: Bovidae) and comparison with other Caprinae species: Insight into the phylogeny of the genus Budorcas.

Takin (Budorcas taxicolor) is one of the most endangered species. However, the taxonomy of takin is still in dispute. Here, the complete mitochondrial genome of Budorcas taxicolor tibetana was reported for the first time, which featured a typical circular molecule of 16,665 bp in length, including 13 PCGs, 22 tRNAs, two rRNAs, and one control region. A + T content was higher than G + C content. All of the genes were encoded on the heavy strand, except for eight tRNAs and ND6 gene. The OL region was 49 bp in length and highly conserved in the synthesis and stem-loop regions, and all of the substitutions and indels were found only in the loop structure. Three types of tandem repeat units, six pairs of hairpin loop structure (TACAT, ATGTA) and six CSBs were predicted in the control region. Our results clearly revealed the systematic status of Budorcas species, and the phylogenetic analyses indicated that Budorcas was closer to Capra and Pseudois, rather than to Ovis, which should be merged into the subfamily of Caprinae.

Migratory behaviour predicts greater parasite diversity in ungulates.

Long-distance animal movements can increase exposure to diverse parasites, but can also reduce infection risk through escape from contaminated habitats or culling of infected individuals. These mechanisms have been demonstrated within and between populations in single-host/single-parasite interactions, but how long-distance movement behaviours shape parasite diversity and prevalence across host taxa is largely unknown. Using a comparative approach, we analyse the parasite communities of 93 migratory, nomadic and resident ungulate species. We find that migrants have higher parasite species richness than residents or nomads, even after considering other factors known to influence parasite diversity, such as body size and host geographical range area. Further analyses support a novel 'environmental tracking' hypothesis, whereby migration allows parasites to experience environments favourable to transmission year-round. In addition, the social aggregation and large group sizes that facilitate migration might increase infection risk for migrants. By contrast, we find little support for previously proposed hypotheses, including migratory escape and culling, in explaining the relationship between host movement and parasitism in mammals at this cross-species scale. Our findings, which support mechanistic links between long-distance movement and increased parasite richness at the species level, could help predict the effects of future environmental change on parasitism in migratory animals.

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.

Milk composition of free-ranging red hartebeest, giraffe, Southern reedbuck and warthog and a phylogenetic comparison of the milk of African Artiodactyla.

The composition of major nutrients and fatty acids of the milk of three species, red hartebeest, Southern reedbuck and warthog, and milk fatty acids of giraffe, that have not been published before, are reported, and together with the same parameters of 11 species previously published, were incorporated in a phylogenetic comparison. Unique properties of milk composition have been observed. Southern reedbuck milk seems to have a complex casein composition, similar to that of sheep. Milk composition varies between species. Although some differences may be ascribed to biological condition, such as stage of lactation, or ecological factors, such as availability of certain nutrients, the contribution by evolutionary history is not well documented and the emphasis is usually on the composition of the macro nutrients. Phylogenetic comparisons often lack representatives of multiple species of taxonomic groups and sub-groups. To date phylogenetic comparisons of milk composition have been carried out by using data from different publications. The problem with this approach is that the ecological factors cannot be completely ruled out. A statistical phylogenetic comparison by PCA between 15 species representing 7 different suborders, families or subfamilies of African Artiodactyla was carried out. The phylogenetic properties showed that the milk composition of the Bovinae, represented here by the subfamilies Bovini and Tragelaphini, differs from the other taxonomic groups, in that the Alcelaphinae had a high milk fat content of the medium chain length fatty acids C8-C12 (>17% of total fatty acids) and the Hippotraginae high amounts of oligosaccharides (>0.4%).

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.

Defaunation affects Astrocaryum gratum (Arecales: Arecaceae) seed survivorship in a sub-montane tropical forest.

Animal-plant interactions in Neotropical forests are complex processes. Within these processes, mid- to large-sized mammals consume fruits and seeds from several species; however, because of their size these mammals are overhunted, resulting in defaunated forests. Our objective was to evaluate and compare seed removal and survivorship in a forest with no hunting, a forest with moderate or reduced hunting, and a forest with higher hunting pressure. We examined the interaction between Astrocaryum gratum and white lipped peccary (Tayassu pecari) to tease apart the defaunation process. To isolate and evaluate mammal seed removal rates and to identify the causes of mortality on Agratum, under the three different hunting pressures forests, we used exclosures in each one. In four different forest-patches for each forest, we positioned a block-treatment consisting of three exclosures (total exclusion, peccary exclusion, and control), randomly distributed 5m apart and the block-treatments spaced 50-75 m apart from one another. We established 15 treatments in total for each patch (5 blocks per patch). There were 20 blocks within each forest type. For total exclusion, all vertebrates were excluded using galvanized wire mesh exclosures. The second, the peccary exclusion, was designed to stop peccaries from entering treatment units, providing access only to small vertebrates; larger mammals were able to access the treatment unit by reaching over the sides and the open top; finally, the Control allowed full access for all mammals. Fresh A. gratum fruits were collected from the forest floor under different adult trees throughout the study area. In each exclosure treatment, twenty Agratum seeds were placed, and their removal was recorded. In total, 3 600 seeds were analyzed. Seed survival was lower in unhunted forest compared to areas with moderate hunting and forest with a higher hunt pressure, supporting the hypothesis of the importance of mammals in seed removal. From the initial 400 seeds left for each control exclosure in each type of forest, there was a significant difference between the seed removal; 1.75% seeds in the unhunted forest remained; 43.5% in the moderately hunted forest, and 48.5% in hunted forest. The main cause of seed mortality was white lipped peccaries; while in the forests without them, the main removal was caused by rodents and a higher insect infection was observed in the heavily hunted forest. Our results indicated that defaunation affects seed survivorship.

Defaunation affects Astrocaryum gratum (Arecales: Arecaceae) seed survivorship in a sub-montane tropical forest / La defaunación afecta la supervivencia de semillas Astrocaryum Gratum (Arecales: Arecaceae) en un bosque tropical sub-montano

Animal-plant interactions in Neotropical forests are complex processes. Within these processes, mid-to large-sized mammals consume fruits and seeds from several species; however, because of their size these mammals are overhunted, resulting in defaunated forests. Our objective was to evaluate and compare seed removal and survivorship in a forest with no hunting, a forest with moderate or reduced hunting, and a forest with higher hunting pressure. We examined the interaction between Astrocaryum gratum and white lipped peccary (Tayassu pecari) to tease apart the defaunation process. To isolate and evaluate mammal seed removal rates and to identify the causes of mortality on A.gratum, under the three different hunting pressures forests, we used exclosures in each one. In four different forest-patches for each forest, we positioned a block-treatment consisting of three exclosures (total exclusion, peccary exclusion, and control), randomly distributed 5m apart and the block-treatments spaced 50-75m apart from one another. We established 15 treatments in total for each patch (5 blocks per patch). There were 20 blocks within each forest type. For total exclusion, all vertebrates were excluded using galvanized wire mesh exclosures. The second, the peccary exclusion, was designed to stop peccaries from entering treatment units, providing access only to small vertebrates; larger mammals were able to access the treatment unit by reaching over the sides and the open top; finally, the Control allowed full access for all mammals. Fresh A. gratum fruits were collected from the forest floor under different adult trees throughout the study area. In each exclosure treatment, twenty A.gratum seeds were placed, and their removal was recorded. In total, 3 600 seeds were analyzed. Seed survival was lower in unhunted forest compared to areas with moderate hunting and forest with a higher hunt pressure, supporting the hypothesis of the importance of mammals in seed removal. From the initial 400 seeds left for each control exclosure in each type of forest, there was a significant difference between the seed removal; 1.75% seeds in the unhunted forest remained; 43.5% in the moderately hunted forest, and 48.5% in hunted forest. The main cause of seed mortality was white lipped peccaries; while in the forests without them, the main removal was caused by rodents and a higher insect infection was observed in the heavily hunted forest. Our results indicated that defaunation affects seed survivorship. Rev. Biol. Trop. 63 (1): 57-67. Epub 2015 March 01.

Las relaciones planta-animal en bosques neotropicales son procesos complejos; los mamíferos medianos y grandes consumen frutos y semillas de varias especies, sin embargo, por su tamaño, la caza excesiva de estas especies puede resultar en bosques defaunados. Nuestro objetivo fue evaluar y comparar la remoción y sobrevivencia de semillas en un bosque sin caza, un bosque con caza moderada, y un bosque con mayor presión de caza. Para estudiar el proceso de defaunación, se examinó la interacción entre la palmera Astrocaryum gratum y el pecarí de labios blancos (Tayassu pecari). Para aislar y evaluar las tasas de remoción de semillas de A. gratum por mamíferos y para identificar las causas su mortalidad, bajo diferentes presiones de caza, se utilizó tratamientos de exclusiones para cada bosque; en cuatro parches de bosque distintos, colocamos tratamientos en bloques, compuesto por tres tipos de exclusiones (exclusión total, exclusión de pecarís y control). Distribuidos a 5m de distancia entre ellos y los bloques separados por 50-75m. Establecimos 15 tratamientos en total para cada parche de bosque (5 bloques por parche), con 20 bloques dentro de cada tipo de bosque. Utilizando malla de alambre galvanizado, todos los vertebrados fueron excluidos (exclusión total). El segundo tratamiento fue la exclusión de pecarí. Estas fueron diseñadas para excluir pecarís, permitiendo el acceso sólo a pequeños vertebrados; los mamíferos grandes eran capaces de acceder a estas exclusiones por la parte superior abierta. Por último, el control permite el pleno acceso de todos los mamíferos. De forma oportunista, debajo de diferentes árboles adultos de A. gratum se recogieron frutas frescas. En cada tratamiento de exclusión, se colocaron veinte semillas de A. gratum, y su remoción fue registrada. En total, se analizaron 3 600 semillas. La supervivencia de semillas fue menor en el bosque sin caza comparado con las áreas con caza moderada y bosques con una presión de caza mayor, que apoya la hipótesis de la importancia de los mamíferos en la remoción de semillas. De las 400 semillas iniciales en el "control" de cada uno de los tipos de bosques, hubo una diferencia significativa entre la remoción de semillas; con 1.75% de supervivencia en el bosque sin caza; 43.5% en bosque de caza moderada, y 48.5% en bosque con caza. La causa principal de la mortalidad de semillas fue pecaríes de labio blanco, mientras que en los bosques sin ellos, la eliminación principal fue causada por roedores y en el bosque de alta caza, se registró una la mayor infección de insectos. Los resultados indican que la defaunación afecta a supervivencia de semillas.

A new species of Euprox (Cervidae, Artiodactyla) from the upper Miocene of the Linxia Basin, Gansu Province, China, with interpretation of its paleoenvironment.

The Linxia Basin, Gansu Province, China, is known for its abundant and well preserved fossils. Here a new species, Euprox grandis sp. nov., is established based on a skull and antlers collected from the upper Miocene Liushu Formation of the Linxia Basin. The new species is distinguishable from other Euprox species by its large body size, notably long pedicle and weak burr. The main beam and the brow tine are slightly curved both medially and backwards, and the apex of the main beam turns, curving slightly laterally. The upper cheek teeth are brachydont, with a clear central fold on the premolars and internal postprotocrista and metaconule fold on M1-M2. The cingulum is almost absent, only occasionally weakly developed at the anterior and lingual surface of the teeth. Cladistic analysis was carried out using the TNT software, and two most parsimonious trees were retained. As the strict consensus tree shows E. grandis appears to be an advanced muntiacine form, which may have a close relationship with the genus Muntiacus. The presence of E. grandis in the Linxia Basin adds new evidence to support a warm and humid environment during the late Miocene in the basin. 

A new species of Eostyloceros (Cervidae, Artiodactyla) from the Late Miocene of the Linxia Basin in Gansu, China.

A new species, Eostyloceros hezhengensis sp. nov., is established based on a skull with its cranial appendages collected from the Late Miocene Liushu Formation of the Linxia Basin in Gansu Province, northwestern China. It is a large-sized muntjak with a distinct longitudinal ridge along the lateral margin of the frontal bone that joins the antler pedicle. The pedicle is short, cylindrical, robust, and extends posteriorly from the rear of the orbit. The anterior and posterior branches arise from the burr and diverge at an angle of 30°. The posterior branch is relatively long, and its tip is strongly curved posteriorly. The anterior branch is straight and situated anteromedially from the posterior branch. The posterior branch is lateromedially compressed, and the anterior branch has a circular cross section. The morphological observation together with a cladistic and a principal component analysis indicate that E. hezhengensis is more basal than any known species of the genus Eostyloceros in having shorter pedicles, a lower position of the fork above the burr, more slender anterior branches, and a small angle between the anterior and posterior branches. Its age is the middle Late Miocene, corresponding to the late Bahean.

Systematic revision of the family Hoplitomerycidae Leinders, 1984 (Artiodactyla: Cervoidea), with the description of a new genus and four new species.

Six species of the cervoid genus Hoplitomeryx are currently recognized from the Late Miocene sites of Gargano and Scontrone, in Italy: H. matthei Leinders, 1984, H. apruthiensis Mazza & Rustioni, 2011, H. apulicus Mazza & Rustioni, 2011, H. falcidens Mazza & Rustioni, 2011, H. magnus Mazza & Rustioni, 2011, and H. minutus Mazza & Rustioni, 2011. These species are interpreted as members of an anagenetic series in these two localities, which are considered as part of the same bioprovince but with different geological ages. Comparative analysis of postcranial, dental, and cranial material from Hoplitomerycidae resulted in the reinterpretation of this current taxonomic arrangement. Two distinct genera can be distinguished. The new genus Scontromeryx is restricted to Scontrone (Early Tortonian) and is characterised by the presence of second upper and lower premolars and the absence of a nasal (median) horn. Hoplitomeryx is restricted to Gargano (Middle and/or Late Tortonian), and is characterized by the loss of the second premolar and presence of a nasal horn. Both genera are characterized by orbital appendages in some species, but the morphology of these appendages differs between the genera. Six species can be recognized for Scontromeryx gen. n.: S. minutus (type species), S. falcidens, S. apulicus, S. apruthiensis, S. magnus (new combinations) and the newly described S. mazzai sp. n.. Hoplitomeryx is represented by the H. matthei (type species) and 3 newly described species H. devosi sp. n., H. macpheei sp. n. and H. kriegsmani sp. n.. These two multispecies assemblages are best explained as independent adaptive radiations with the two genera as sister taxa. There is no evidence that the two localities were connected during the Late Miocene.

Reliable discrimination of 10 ungulate species using high resolution melting analysis of faecal DNA.

Identifying species occupying an area is essential for many ecological and conservation studies. Faecal DNA is a potentially powerful method for identifying cryptic mammalian species. In New Zealand, 10 species of ungulate (Order: Artiodactyla) have established wild populations and are managed as pests because of their impacts on native ecosystems. However, identifying the ungulate species present within a management area based on pellet morphology is unreliable. We present a method that enables reliable identification of 10 ungulate species (red deer, sika deer, rusa deer, fallow deer, sambar deer, white-tailed deer, Himalayan tahr, Alpine chamois, feral sheep, and feral goat) from swabs of faecal pellets. A high resolution melting (HRM) assay, targeting a fragment of the 12S rRNA gene, was developed. Species-specific primers were designed and combined in a multiplex PCR resulting in fragments of different length and therefore different melting behaviour for each species. The method was developed using tissue from each of the 10 species, and was validated in blind trials. Our protocol enabled species to be determined for 94% of faecal pellet swabs collected during routine monitoring by the New Zealand Department of Conservation. Our HRM method enables high-throughput and cost-effective species identification from low DNA template samples, and could readily be adapted to discriminate other mammalian species from faecal DNA.

Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders.

Conserved noncoding sequences (CNSs) of vertebrates are considered to be closely linked with protein-coding gene regulatory functions. We examined the abundance and genomic distribution of CNSs in four mammalian orders: primates, rodents, carnivores, and cetartiodactyls. We defined the two thresholds for CNS using conservation level of coding genes; using all the three coding positions and using only first and second codon positions. The abundance of CNSs varied among lineages, with primates and rodents having highest and lowest number of CNSs, respectively, whereas carnivores and cetartiodactyls had intermediate values. These CNSs cover 1.3-5.5% of the mammalian genomes and have signatures of selective constraints that are stronger in more ancestral than the recent ones. Evolution of new CNSs as well as retention of ancestral CNSs contribute to the differences in abundance. The genomic distribution of CNSs is dynamic with higher proportions of rodent and primate CNSs located in the introns compared with carnivores and cetartiodactyls. In fact, 19% of orthologous single-copy CNSs between human and dog are located in different genomic regions. If CNSs can be considered as candidates of gene expression regulatory sequences, heterogeneity of CNSs among the four mammalian orders may have played an important role in creating the order-specific phenotypes. Fewer CNSs in rodents suggest that rodent diversity is related to lower regulatory conservation. With CNSs shown to cluster around genes involved in nervous systems and the higher number of primate CNSs, our result suggests that CNSs may be involved in the higher complexity of the primate nervous system.

A revised phylogeny of Antilopini (Bovidae, Artiodactyla) using combined mitochondrial and nuclear genes.

Antilopini (gazelles and their allies) are one of the most diverse but phylogenetically controversial groups of bovids. Here we provide a molecular phylogeny of this poorly understood taxon using combined analyses of mitochondrial (CYTB, COIII, 12S, 16S) and nuclear (KCAS, SPTBN1, PRKCI, MC1R, THYR) genes. We explore the influence of data partitioning and different analytical methods, including Bayesian inference, maximum likelihood and maximum parsimony, on the inferred relationships within Antilopini. We achieve increased resolution and support compared to previous analyses especially in the two most problematic parts of their tree. First, taxa commonly referred to as "gazelles" are recovered as paraphyletic, as the genus Gazella appears more closely related to the Indian blackbuck (Antilope cervicapra) than to the other two gazelle genera (Nanger and Eudorcas). Second, we recovered a strongly supported sister relationship between one of the dwarf antelopes (Ourebia) and the Antilopini subgroup Antilopina (Saiga, Gerenuk, Springbok, Blackbuck and gazelles). The assessment of the influence of taxon sampling, outgroup rooting, and data partitioning in Bayesian analyses helps explain the contradictory results of previous studies.

Pan-biogeografia dos ungulados viventes (Mammalia: Eutheria) da região Neotropical, da Zona de Transição Sul-americana e região Andina: aspectos históricos e conservacionistas / Panbiogeography of living ungulates (Mammalia: Perissodactyla and Cetartiodactyla) of the Neotropical region, the South American Transition Zone and Andean region: historical and conservationist aspects

Os ungulados viventes (Cetartiodactyla e Perissodactyla), nas regiões estudadas, são representados por 11 gêneros e 24 espécies. O presente estudo propõe reconhecer os padrões de distribuição destas espécies, a partir da aplicação do método pan-biogeográfico de análise de traços. Este método auxilia no entendimento a priori dos padrões congruentes de distribuição e numa compreensão de padrões e processos de diferenciação geográfica no tempo e no espaço, reconstruindo a biogeografia de táxons. Em relação a aspectos conservacionistas, o método foi aplicado na identificação de áreas prioritárias para conservação. A aplicação do método consiste basicamente na marcação das localidades de ocorrência dos diferentes táxons em mapas, sendo estas localidades conectadas por intermédio de linhas seguindo um critério de mínima distância, resultando nos chamados traços individuais que foram plotados nos mapas de biomas da América Central e do Sul do programa ArcView GIS 3.2. A superposição destes traços individuais define um traço generalizado, sugerindo uma história comum, ou seja, a preexistência de uma biota ancestral subsequentemente fragmentada por eventos vicariantes. A interseção de dois ou mais traços generalizados corresponde a um nó biogeográfico, que representa áreas compostas e complexas, nas quais se agrupam distintas histórias biogeográficas. Para a análise pan-biogeográfica foi utilizado o software ArcView GIS 3.2 e a extensão Trazos 2004. A partir da superposição dos 24 traços individuais, foram reconhecidos cinco traços generalizados (TGs): TG1, Mesoamericano/Chocó, composto por Mazama pandora, M. temama e Tapirus bairdii; TG2, Andes do Norte (Mazama rufina, Pudu mephistophiles e Tapirus pinchaque); TG 3, Andes Centrais (Hippocamelus antisensis, Lama guanicoe, Mazama chunyi e Vicugna vicugna) ; TG4, Patagônia chilena (Hippocamelus bisulcus e Pudu puda).; TG5, Chaco/Centro oeste do Brasil (Blastocerus dichotomus, Catagonus wagneri e Ozotocerus bezoarticus ...

The living ungulates (Cetartiodactyla and Perissodactyla) are represented in the studied regions by 11 genera and 24 species. This study proposes to recognize the distribution patterns of these species, using the panbiogeographical method of track analysis. This method is a useful tool in a priori understanding of the congruent distribution patterns and in the knowledge of patterns and processes of geographical differentiation in time and space, reconstructing the biogeography of taxa. Regarding conservationist approaches, it was applied in order to identify priority conservation areas. The panbiogeographical method consists basically of plotting locality records of different taxa on maps and connecting them using lines following a criterion of minimum distance, resulting in the so-called individual tracks, which were plotted on maps of biomes of Central America and South America from the ArcView GIS 3.2. The individual tracks are superimposed and the coincidence of them corresponds to generalized tracks, indicating a common history, that is, the existence of an ancestral biota widespread in the past and later fragmented by vicariant events. The intersection of two or more generalized tracks corresponds to a biogeographic node, which represents composite and complex areas, implying that different ancestral biotas interrelated, possibly in different geologic times. The analysis was carried out with the aid of the software ArcView v3.2 and the Trazos2004 extension. From the overlapping of the 24 individual tracks, five generalized tracks (GTs) were recognized: GT1, Mesoamerican/Chocó, composed by Mazama pandora, M. temama and Tapirus bairdii; GT2, Northern Andes (Mazama rufina, Pudu mephistophiles and Tapirus pinchaque); GT 3, Central Andes (Hippocamelus antisensis, Lama guanicoe, Mazama chunyi and Vicugna vicugna); GT4, Chilean Patagonia (Hippocamelus bisulcus and Pudu puda); GT5, Chaco/Center-West Brazil (Blastocerus dichotomus, Catagonus wagneri ...

Phylogenetic analysis of genome rearrangements among five mammalian orders.

Evolutionary relationships among placental mammalian orders have been controversial. Whole genome sequencing and new computational methods offer opportunities to resolve the relationships among 10 genomes belonging to the mammalian orders Primates, Rodentia, Carnivora, Perissodactyla and Artiodactyla. By application of the double cut and join distance metric, where gene order is the phylogenetic character, we computed genomic distances among the sampled mammalian genomes. With a marsupial outgroup, the gene order tree supported a topology in which Rodentia fell outside the cluster of Primates, Carnivora, Perissodactyla, and Artiodactyla. Results of breakpoint reuse rate and synteny block length analyses were consistent with the prediction of random breakage model, which provided a diagnostic test to support use of gene order as an appropriate phylogenetic character in this study. We discussed the influence of rate differences among lineages and other factors that may contribute to different resolutions of mammalian ordinal relationships by different methods of phylogenetic reconstruction.