Development and characterization of microsatellite markers in the Point Arena mountain beaver Aplodontia rufa nigra

The Point Arena mountain beaver (Aplodontia rufa nigra) is an endangered subspecies. Efforts to recover this sub‐species will be aided by advances in molecular genetics, specifically the ability to estimate population size using noninvasive genetic sampling. Here we report on the development of nine polymorphic loci for the Point Arena mountain beaver. These markers provide us sufficient power to distinguish individuals, and thus can be used for calculating population size and delineating population substructure.     

Incisal biting in the mountain beaver (Aplodontia rufa) and woodchuck (Marmota monax)

Analysis of synchronously recorded cine-radiographs and electromyograms in two rodents (Aplodontia rufa and Marmota monax) demonstrates that jaw movements and muscle activiteis during incisal functions are distinctly different from those found during mastication. Movements during incisal biting are primarily along the midline, accompanied by symmetrical activity of the jaw adductor muscles. Most biting cycles do not end in contact between upper and lower incisors. When contact does occur, the lower incisors are dragged along the lingual surfaces of the upper incisors. Cropping, or tip-to-tip occlusion of upper and lower incisors, was not observed. Sharpening of the lower incisors, a behavior which may be unique to the Rodentia, was recorded in both A. rufa and M. monax. During sharpening, the lingual surface of the lower incisor is dragged across the tip of the upper incisor producing a lingual wear facet. Like incisal biting, sharpening movements are primarily confined to the midline, although there may be lateral movements in some sharpening cycles. Sharpening cycles are among the most rapid cyclic movements recorded in mammals, as the mean frequencies of sharpening are 11 cycles/s in A. rufa and 8 cycles/s in M. monax. © 1995 Wiley-Liss, Inc.     

Development of 10 polymorphic microsatellite loci isolated from the mountain beaver, Aplodontia rufa rufa (Rafinesque)

We developed 10 microsatellite markers for the mountain beaver, Aplodontia rufa rufa. In three populations of A. r. rufa, the number of alleles for these loci ranged from monomorphic to nine. Average observed heterozygosities in these populations ranged from 0.29 to 0.60. We also tested previously published markers from the endangered subspecies A. r. nigra in A. r. rufa populations.     

Metazoan parasites of the mountain beaver, Aplodontia rufa (Rodentia: Aplodontidae), from Washington and Oregon, with a checklist of parasites.

Four species of fleas, 2 species of mites, and the cysticerci of Taenia tenuicollis were collected from mountain beavers, Aplodontia rufa, collected in Washington and Oregon. A summary of the metazoan parasites reported from A. rufa is included.     

Defensive spines are associated with large geographic range but not diversification in spiny ants (Hymenoptera: Formicidae: Polyrhachis)

Several prominent evolutionary theories propose mechanisms whereby the evolution of a defensive trait or suite of traits causes significant shifts in species diversification rate and niche evolution. We investigate the role of cuticular spines, a highly variable morphological defensive trait in the hyperdiverse ant genus Polyrhachis, on species diversification and geographic range size. Informed by key innovation theory and the escape-and-radiate hypothesis, we predicted that clades with longer spines would exhibit elevated rates of diversification and larger range sizes compared to clades with shorter spines. To address these predictions, we estimated phylogenetic relationships with a phylogenomic approach utilizing ultraconserved elements and compiled morphological and biogeographic trait databases. In contrast to the first prediction, we found no association between diversification rate and any trait (spine length, body size and range size), with the sole exception of a positive association between range size and diversification in one of three trait-based diversification analyses. However, we recovered a positive phylogenetic correlation between spine length and geographic range size, suggesting that spines promote expanded geographic range. Notably, these results were consistent across analyses using different phylogenetic inference approaches and spine trait measurement schemes. This study provides a rare investigation of the role of a defensive trait on geographic range size, and ultimately supports the hypothesis that defensive spines are a factor in increased range size in Polyrhachis ants. Furthermore, the lack of support for an association between spines and diversification, which contrasts with previous work demonstrating a positive association between spines and diversification rate, is intriguing and warrants further study.     

The population structure of the geographic range of the Caucasian suslik (Citellus pygmaeus musicus, Menetrie 1832) in the Elbrus mountain area

Population structure of Caucasian gopher has been studied using genetic and evolutionary criteria. It was shown that plague [correction of plaque] affects genetic isolation of populations and microevolutionary processes.     

Population genetic structure and connectivity in the endangered Ethiopian mountain Nyala (Tragelaphus buxtoni): recommending dispersal corridors for future conservation

Habitat fragmentation is an increasing threat to wildlife species across the globe and it has been predicted that future biodiversity will decrease rapidly without the intervention of scientifically-based management. In this study we have applied a landscape genetics approach to suggest a network design that will maintain connectivity among populations of the endangered mountain Nyala (Tragelaphus buxtoni) in the fragmented highlands of Ethiopia. DNA was obtained non-invasively from 328 individuals and genetic population structure and gene flow were estimated using 12 microsatellite markers. In addition, a 475-bp segment of the mitochondrial control region was sequenced for 132 individuals. Potential dispersal corridors were determined from least-cost path analysis based on a habitat suitability map. The genetic data indicated limited gene flow between the sampled mountain Nyala populations of the Bale Massif and the Arsi Massif. The genetic differentiation observed among five sampling areas of the Bale Massif followed a pattern of isolation by distance. We detected no impact of habitat resistance on the gene flow. In the future, however, the current expanding human population in the highlands of Ethiopia may reduce the current mountain Nyala habitat and further limit migration. Hence, maintaining habitat connectivity and facilitating survival of stepping-stone populations will be important for the future conservation of the species. The approach used here may also be useful for the study and conservation of other wildlife species inhabiting areas of increasing human encroachment.     

Genetically diverse but with surprisingly little geographical structure: the complex history of the widespread herb Carex nigra (Cyperaceae)

Aim Based on extensive range‐wide sampling, we address the phylogeographical history of one of the most widespread and taxonomically complex sedges in Europe, Carex nigra s. lat. We compare the genetic structure of the recently colonized northern areas (front edge) and the long‐standing southern areas (rear edge), and assess the potential genetic basis of suggested taxonomic divisions at the rank of species and below. Location Amphi‐Atlantic, central and northern Europe, circum‐Mediterranean mountain ranges, central Siberia, Himalayas. Methods A total of 469 individuals sampled from 83 populations, covering most of the species’ range, were analysed with amplified fragment length polymorphism (AFLP) and chloroplast DNA (cpDNA) markers. Bayesian clustering, principal coordinates analysis, and estimates of diversity and differentiation were used for the analysis of AFLP data. CpDNA data were analysed with statistical parsimony networks and maximum parsimony and Bayesian inference of phylogenetic trees. Results Overall genetic diversity was high, but differentiation among populations was limited. Major glacial refugia were inferred in the Mediterranean Basin and in western Russia; in addition, there may have been minor refugia in the North Atlantic region. In the southern part of the range, we found high levels, but geographically quite poorly structured genetic diversity, whereas the levels of genetic diversity varied among different areas in the north. North American populations were genetically very similar to the European populations. Main conclusions The data are consistent with extensive gene flow, which has obscured the recent history of the taxon. The limited differentiation in the south probably results from the mixing of lineages expanding from several local refugia. Northward post‐glacial colonization resulted in a leading‐edge pattern of low diversity in the Netherlands, Belgium, Scotland and Iceland, whereas the observed high diversity levels in Fennoscandia suggest broad‐fronted colonization from the south as well as from the east. The patterns found in the American populations are consistent with post‐glacial colonization, possibly even with anthropogenic introduction from Europe. Our data also suggest that the tussock‐forming populations of C. nigra, often referred to as a distinct species (Carex juncella), represent an ecotype that has originated repeatedly from different populations with creeping rhizomes.     

Redescription and range extension of the endangered Paiva's blenny Lupinoblennius paivai (Perciformes: Blenniidae)

The Paiva's blenny Lupinoblennius paivai is redescribed and its range redefined along the Brazilian coast. It differs from its congeners by the presence of three cephalic pores between the dorsal‐fin base and lateral line, dorsal‐fin elements XII, 12, anal‐fin elements II, 16, pectoral‐fin rays 14 and 10 + 20 vertebrae. It is here reported from Amazon estuaries (Marajó and Mosqueiro islands, Pará State), increasing its range by c. 3000 km. Lupinoblennius paivai is one of the few blenniid species able to tolerate low salinities. New data about its meristics and morphometrics are presented, as well as a new habitat type.     

Carnivora: the primary structure of hemoglobin from adult coati (Nasua nasua rufa, Procyonidae)

The complete primary structure of the hemoglobin from the adult coati (Nasua nasua rufa) is presented. The erythrocytes contain one hemoglobin component and two globin chains. The isolation of globin chains was achieved by reversed-phase HPLC on a column of Nucleosil-C4. The primary structure of globin chains and tryptic peptides was determined in liquid- and gas-phase sequenators. The sequence of the and -chains of coati compared with those of other Carnivora species. Results are discussed with respect to structural variations and the phylogenetic relationship.Deceased on May 27, 1989.     

Postglacial expansion and not human influence best explains the population structure in the endangered kea (Nestor notabilis)

Inferring past demography is a central question in evolutionary and conservation biology. It is, however, sometimes challenging to infer the processes that shaped the current patterns of genetic variation in endangered species. Population substructuring can occur as a result of survival in several isolated refugia and subsequent recolonization processes or via genetic drift following a population decline. The kea (Nestor notabilis) is an endemic parrot widely distributed in the mountains of the South Island of New Zealand that has gone through a major human‐induced population decline during the 1860s–1970s. The aims of this study were to understand the glacial and postglacial history of kea and to determine whether the recent population decline played a role in the shaping of the current genetic variation. We examined the distribution of genetic variation, differentiation and admixture in kea using 17 microsatellites and the mitochondrial control region. Mitochondrial data showed a shallow phylogeny and a genetic distinction between the North and South of the range consistent with the three genetic clusters identified with microsatellite data. Both marker types indicated an increase in genetic isolation by geographic distance. Approximate Bayesian Computation supported a scenario of postglacial divergence from a single ancestral glacial refugium, suggesting that the contemporary genetic structure has resulted from recolonization processes rather than from a recent population decline. The recent evolutionary origin of this genetic structure suggests that each genetic cluster does not need to be considered as independent conservation units.     

Life cycles,phenology and genetic structure of endangered Megacrania tsudai Shiraki (Phasmatodea: Phasmatidae): Male individuals from a geographic parthenogenesis species

Megacrania tsudai, a peripherally distributed member of Megacrania, requires conservation in Taiwan; it has limited distribution in Taiwan and its eastern offshore islands. It feeds on screw pines (Pandanus odoratissimus) in nature and has demonstrated a specific defensive mechanism involving actinidine secretion from the prothoracic gland. However, details of its distribution area, life cycle and developmental phenology remain largely unknown. In this study, a field survey and review of published works revealed M. tsudai distribution in coastal zones and along river shores near estuaries. At room temperature, the egg period was 128 days. The development of the first to sixth instars required 17, 26, 27, 26, 34 and 43 days, respectively, on average; and a generation cycle required approximately 204 days. The phenology of the mesonotal granules was recorded. Moreover, genetic analysis of the mitochondrial cytochrome oxidase I (COI), 16S ribosomal DNA (16S rDNA) and the nuclear ribosomal spacer indicated the occurrence of genetic drift. Therefore, the rearing procedures proposed in this study for the primary and last instars of M. tsudai can facilitate its conservation. Megacrania tsudai was previously recorded as parthenogenetic; however, two male individuals were fostered unexpectedly. The male body length was 91 mm, which is shorter than the female length (120 mm). During mating, the male climbs onto the female's back and protrudes its genitalia downward. Geographical parthenogenesis is likely the reproductive strategy among peripheral M. tsudai; however, the rarely found M. tsudai male could be an intermediate link of reproductive strategy in the transition from tychoparthenogenesis to parthenogenesis.     

Low genetic diversity and limited genetic structure across the range of the critically endangered Mexican howler monkey (Alouatta palliata mexicana)

Genetic diversity provides populations with the possibility to persist in ever-changing environments, where selective regimes change over time. Therefore, the long-term survival of a population may be affected by its level of genetic diversity. The Mexican howler monkey (Alouatta palliata mexicana) is a critically endangered primate restricted to southeast Mexico. Here, we evaluate the genetic diversity and population structure of this subspecies based on 83 individuals from 31 groups sampled across the distribution range of the subspecies, using 29 microsatellite loci. Our results revealed extremely low genetic diversity (H_O = 0.21, H_E = 0.29) compared to studies of other A. palliata populations and to other Alouatta species. Principal component analysis, a Bayesian clustering method, and analyses of molecular variance did not detect strong signatures of genetic differentiation among geographic populations of this subspecies. Although we detect small but significant F_ST values between populations, they can be explained by a pattern of isolation by distance. These results and the presence of unique alleles in different populations highlight the importance of implementing conservation efforts in multiple populations across the distribution range of A. p. mexicana to preserve its already low genetic diversity. This is especially important given current levels of population isolation due to the extreme habitat fragmentation across the distribution range of this primate.     

The wide but disjunct range of the European mountain plant Androsace lactea L. (Primulaceae) reflects Late Pleistocene range fragmentation and post‐glacial distributional stasis

Aim Our aim was to reconstruct the spatio‐temporal genetic diversification of Androsace lactea, a widely but disjunctly distributed European mountain plant, to test the hypothesis that its distribution is the result of vicariance, in the late Tertiary or during the Pleistocene, or alternatively of long‐distance dispersal. We also addressed the phylogeographic history of the Alps, emphasizing the role of Pleistocene refugia at their northern margin. Location The central and southern European mountain ranges. Methods We gathered amplified fragment length polymorphism (AFLP) data and plastid DNA sequences from one to four individuals of each of 26 populations spanning the entire distribution area. AFLP data were analysed with Bayesian clustering approaches, neighbour‐joining analysis and NeighbourNet. Plastid sequences were used to depict relationships among haplotypes in a statistical parsimony network, to test for population expansions, and to obtain age estimates in a Bayesian framework. Results The AFLP data suggested that many populations were genetically strongly differentiated. The internal structure, however, was weak, and only two major groups of populations, from the north‐western Alps and adjacent regions and from the easternmost Alps, were supported in the neighbour‐joining analysis. One of the Bayesian clustering approaches differentiated three groups of populations: Northern Alps, easternmost Alps and the remaining distribution area. Eleven closely related plastid haplotypes were found, separated by maximally four mutational steps, resulting in a star‐like parsimony network. None of several estimators suggested statistically significant population expansions. The diversification age was inferred to be (mean/median) 0.135/0.08 Ma (95% highest posterior density interval 0.364–0.006 Ma). Main conclusions We found no evidence that long‐distance dispersal shaped the disjunct distribution range; our data rather favoured a vicariance scenario. However, in contrast to the hypothesis that wide but disjunct distributions are old, we conclude that range fragmentation probably happened in the Late Pleistocene, perhaps during the last glaciation. In the Alps, most populations are at least close to formerly unglaciated areas. Our data support distributional stasis and suggest that important refugia were situated at the north‐eastern, but also at the northern and north‐western edges of the Alps, thereby strengthening the evidence for glacial refugia in this strongly glaciated region.     

Small but not ephemeral: newly discovered species of Aphelinidae and Trichogrammatidae (Insecta: Hymenoptera: Chalcidoidea) from Eocene amber

New species of fossil Aphelinidae and Trichogrammatidae are described from middle Eocene (Lutetian) Baltic amber (41.3–47.8 Ma). A new subfamily, two new genera and three new species of Aphelinidae are described, with comments on their placement: Phtuaria fimbriae gen.n. , sp.n. in Phtuariinae subf.n. , Glaesaphytis interregni gen.n. , sp.n. and Centrodora brevispinae sp.n. These represent the first described true fossil Aphelinidae. Four new species of Trichogrammatidae are described: Mirufens illusionis sp.n. , Palaeogramma eos gen.n. , sp.n. , Pterandrophysalis plasmans sp.n. and Szelenyia terebrae sp.n. , thus expanding our knowledge of fossil Trichogrammatidae beyond the single previously described species. The presence of recognizable extant genera of Aphelinidae and Trichogrammatidae in the Eocene suggests that the morphology of these genera has been relatively invariant despite highly variable conditions during and since the Eocene. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:E9AD60B6‐3D56‐4E74‐AA54‐F7B91F4FDC79 .     

Individual variation in the booming calls of captive Horned Guans (Oreophasis derbianus): an endangered Neotropical mountain bird

The Horned Guan (Oreophasis derbianus) is a cracid restricted to cloud forests in the Sierra Madre of Chiapas in Mexico and the western-central Mountains in Guatemala. It is an endangered species and urgent conservation measures are required, such as non-invasive monitoring techniques. Here, we study individual features in the boom calls of Horned Guans. Boom calls are acoustic signals used by males during courtship and territorial displays. This call is made of seven notes, divided into two parts: an introductory section characterized by low-amplitude notes and a body section characterized by high-amplitude notes. We recorded 10 males during the breeding seasons of 2010 and 2011 in two captive populations and measured 22 acoustic variables of the calls. We used a combination of statistical analyses to test individuality in Horned Guan vocalizations. Our results showed that time-related variables – but not frequency-related traits – varied between individuals, and that individual calls showed no variation between years. Our results suggest that Horned Guan individuals can be distinguished using fine structural characteristics of their calls and that calls remain stable across years. We argue that such vocal signature could be used to track wild populations as a non-invasive technique in order to improve census data in the short and long term.     

Phylogeography of the endangered rosewood Dalbergia nigra (Fabaceae): insights into the evolutionary history and conservation of the Brazilian Atlantic Forest

The Brazilian rosewood (Dalbergia nigra) is an endangered tree endemic to the central Brazilian Atlantic Forest, one of the world''s most threatened biomes. The population diversity, phylogeographic structure and demographic history of this species were investigated using the variation in the chloroplast DNA (cpDNA) sequences of 185 individuals from 19 populations along the geographical range of the species. Fifteen haplotypes were detected in the analysis of 1297 bp from two non-coding sequences, trnV-trnM and trnL. We identified a strong genetic structure (F_ST=0.62, P<0.0001), with a latitudinal separation into three phylogeographic groups. The two northernmost groups showed evidence of having maintained historically larger populations than the southernmost group. Estimates of divergence times between these groups pointed to vicariance events in the Middle Pleistocene (ca. 350 000–780 000 years ago). The recurrence of past climatic changes in the central part of the Atlantic forest, with cycles of forest expansion and contraction, may have led to repeated vicariance events, resulting in the genetic differentiation of these groups. Based on comparisons among the populations of large reserves and small, disturbed fragments of the same phylogeographic group, we also found evidence of recent anthropogenic effects on genetic diversity. The results were also analysed with the aim of contributing to the conservation of D. nigra. We suggest that the three phylogeographic groups could be considered as three distinct management units. Based on the genetic diversity and uniqueness of the populations, we also indicate priority areas for conservation.     

Size-Dependent Female Mate Copying in the Guppy (Poecilia reticulata): Large Females are Role Models but Small Ones are not

Previous work on guppies has shown that small females copy the mate‐choice decisions of larger females, but not vice versa. We extended this work to ask, when put in a situation where they have little information available to distinguish between males, whether large females will also copy large females, and small females will copy small ones. Using Dugatkin's criteria, our study suggests that large females copy the mate‐choice decisions of large females, that small females might copy the decisions of large females, but that neither small nor large females copy small females. Our results provide support for the notion that females are more likely to copy when they perceive that there is an imbalance between their ability to assess a male's quality and the ability of another female to assess that male. However, we did not find evidence of mate copying using criteria used by other researchers.