Molecular Systematics of the Long-Snouted Deep Water Dogfish (Centrophoridae, Deania) With Implications for Identification, Taxonomy, and Conservation

According to the most recent taxonomical revision, the deep-sea dogfish genus Deania encompasses four species. Three of them, D. calcea, D. profundorum, and D. hystricosa, occur in the North Atlantic. Whilst D. profundorum can be identified by the presence of a subcaudal keel, the other two species are not easily visually distinguished. Uncertainties over identification raises concerns over stock units and whether management plans are adequate. In this study we compared onboard visual identification of Deania specimens, with morphological inspection of skin denticles under stereo microscope and with independent molecular taxonomical assignment using two molecular markers. Particular emphasis was paid to specimens identified as D. calcea and D. hystricosa in the NE Atlantic where these species potentially occur sympatrically and may be easily confused. In the past the species have been discriminated on the basis of the size of skin denticles (skin roughness), but our study showed that the crown length of skin denticles covaries with size (and sex), irrespective of species, and therefore this is not a reliable morphological character and should not be used to discriminate between the two species. Phylogenetic analyses did not indicate that D. hystricosa to be a distinct lineage from D. calcea. Interestingly, however four individuals (specimens from: UK, Azores Is., Madeira Is. and Seine seamount) formed a well-defined sub-clade nested within the D. calcea clade, possibly a signature of a past vicariance event or a result of coalescent stochasticity.

Molecular phylogeny and biogeography of Pabstiella (Pleurothallidinae: Orchidaceae) highlight the importance of the Atlantic Rainforest for speciation in the genus

Pabstiella consists of c. 130 epiphytic species in the Neotropics. We present a phylogenetic analysis based on nrITS, matK and trnH-psbA sequences from 59 species of the genus and 40 Pleurothallidinae and two Laeliinae and one Bletiinae as an outgroup, using maximum likelihood, Bayesian inference and maximum parsimony. We also performed molecular dating, biogeographical analyses and ancestral morphological character reconstruction. Our results confirm the monophyly of Pabstiella with strong support. Ten clades are inferred and are herein proposed as sections. Pabstiella originated in the Andes and the Atlantic Rainforest in the Late Miocene (c. 7.93 Mya) in an epoch when these biomes were probably connected. A main vicariance event divided an early-diverging lineage that inhabited the Andes from an Atlantic Rainforest lineage that diversified in this region during the Pliocene and Pleistocene, mainly in the Serra do Mar in south-eastern Brazil. Our findings also suggest that the Atlantic Rainforest may have played an important role in the origin of subtribe Pleurothallidinae. The morphological character reconstruction showed high levels of homoplasy, with few recognized synapomorphies associated with stems and petals. Other characters related to the habit and stems were identified as important in the evolutionary history of the genus.

Population Connectivity and Phylogeography of Crustaceans

Crustacea display diverse life histories and occur in all marine habitats. This makes them particularly useful when thinking about how we can predict geographical distribution from life history and ecology. As would be expected from such diversity, crustaceans exhibit various population connectivity patterns, from panmictic, well-connected populations to small and isolated populations. Here we ask first what can be learned from exploring crustacean phylogeography and connectivity around well-understood vicariance events with known ages. We find that vicariance events are generally useful in calibrating molecular rates of evolution, but that there is substantial variation between taxa. This variation can be linked, on the one hand, to habitat differences (which determine when gene flow between populations actually ceased) and, on the other hand, to population size differences (which determine how fast genetic differences accumulate). In a few instances, populations must have diverged much earlier or later than the hypothesized vicariance event, providing evidence of earlier or later dispersal or more ancient separation. Second, we ask when comparative studies of multiple taxa show consistent results, predictable from their similar life history, and when not. For example, species that disperse little, such as brooding peracarids, have smaller, more isolated populations than species with planktonic larvae, such as decapods. Less consistent are the patterns across biogeographic breaks. While gene flow is clearly limited across such breaks in some species, other species do not seem to perceive them. This to-date-unexplained variation challenges our understanding of marine phylogeography.

Continental island effect in Sichuan Basin based on the genetic structure of sparrow

Islands are ideal settings for the study of evolution, ecology and genetic diversity. The tree sparrow (Passer montanus), which is distributed both inside and outside the Sichuan Basin and is relatively easy to capture, was used as our study species to test whether any genetic differences exist between within and outside of the Sichuan Basin. We analyzed mitochondrial and nuclear gene sequence variations to illustrate the continental island effect within the Sichuan Basin. Overall, fragments from four mtDNA and one nuclear sequence (Cytb + COI + 12S rRNA + Dloop + Myo) were amplified, with the concatenated alignment comprising 3234 bp. The results of Bayesian and maximum parsimony trees indicated two major branches, one of which is composed mainly of populations within the Sichuan Basin, while the other comprised populations distributed in the surrounding mountains. The population in Sichuan Basin was more basal than that in the surrounding mountains. The genetic distance between inner and outer populations was 0.095 and genetic differentiation index (FST) between inner and outer populations was 0.342. This study shows that the overall distribution pattern of tree sparrow populations in the Sichuan Basin and its surrounding mountains is probably the result of a vicariance event due to spatial isolation.

Functional volumes, niche packing and species richness: biogeographic legacies in the Congo Basin

Understanding the determinants of species coexistence in complex and species-rich communities is a fundamental goal of ecology. Patterns of species coexistence depend on how biotic interactions and environmental filtering act over ecological and evolutionary time scales. Climatic fluctuations in lowland rainforests of the Congo Basin led to the number of vertebrate species being significantly lower in central compared with northern ecoregions of the Basin. We used null models to assess whether climatic variations affected the community assembly of shrews. A consistent limit to functional similarity of species was not related to species richness. Rather, species richness is constrained by environmental factors, and these constraints are stronger in the central lowland forests of the Congo Basin. By constraining species geographic distributions, historical effects of rainforest refugia arising from climatic fluctuations may affect contemporary species composition of local shrew communities. The Congo River represents a vicariance event that led to allopatric speciation of shrews and continues to represent a barrier to dispersal. Ultimately, the historical effects of this barrier have led to differences in the functional volume of shrew communities in northern and central ecoregions. We suggest that the analyses of community assembly can be used to identify Holocene refugia in the Congo Basin.

Phylogenetic systematics and biogeography of Coptis (Ranunculaceae), an eastern Asian and North American genus

The goldthread genus Coptis includes 15 species disjunctly distributed in eastern Asia and North America. Here, we provide a dated phylogeny for the genus with all 15 species. Our results indicate that Coptis contains two strongly supported clades (I and II). Clade I consists of subg. Coptis and sect. Japonocoptis of subg. Metacoptis; clade II composes sect. Japonocoptis of subg. Metacoptis. Central leaflet base, sepal shape, and petal blade carry a strong phylogenetic signal in Coptis, while leaf type, sepal and petal color, and petal shape exhibit relatively higher levels of evolutionary flexibility. Our dating and biogeographic analyses indicate that a vicariance event between Japan-North America occurred in the middle Miocene, resulting in the split of Coptis and its sister group. Subsequently, a colonization event occurred at 9.55 Ma from Japan to mainland China. Both vicariance and dispersal events have played important roles in shaping the current distribution and endemism of Coptis, likely resulting from eustatic sea-level changes, mountain formation processes and an increasing drier and cooler climate from the middle Miocene onwards.

Integrative taxonomy unravels the species diversity of Parachristianella (Cestoda : Trypanorhyncha) from both sides of the Panamanian isthmus

The uplift of the Panamanian isthmus in the Pliocene caused the termination of gene flow among members of many ancestral populations of marine lineages leading the diversification of geminate species confined to opposite sides of Central America. This palaeogeographical event has been evoked to explain the diversification of few lineages of batoids with trans-isthmian distribution. As such, there is the expectation that this vicariance event also affected lineages of parasites associated with them. Our study suggests that this event can explain the diversification of Parachristianella Dollfus, 1946 (Trypanorhyncha:Eutetrarhynchidae) in the Caribbean Sea and tropical eastern Pacific Ocean. We provide molecular, morphological and biogeographical evidence to recognise five lineages within this genus inhabiting the coastal waters of Panama, including P. parva Campbell & Beveridge, 2007 and four new species: P. mendozai, sp. nov., P. kuchtai, sp. nov., P. campbelli, sp. nov. and P. soldanovae, sp. nov. These species can be diagnosed by unambiguous sets of molecular characters. The morphological cohesiveness of sister species, which most likely diverged from around 3million years ago through the uplift of the Panamanian isthmus, suggests that the traditional emphasis on the tentacular armature to circumscribe species within trypanorhynchs might underestimate the diversity of recently diverged lineages.

Fossils know it best: using a new set of fossil calibrations to improve the temporal phylogenetic framework of murid rodents (Rodentia: Myomorpha: Muroidea: Muridae)

Murid rodents (Rodentia: Myomorpha: Muroidea: Muridae) represent the most diverse and abundant mammalian group. In this study, we reconstruct a dated phylogeny of the family using a multilocus dataset (six nuclear and nine mitochondrial gene fragments) encompassing 160 species representing 82 distinct murid genera from four extant subfamilies (Deomyinae, Gerbillinae, Lophiomyinae, and Murinae). In comparison with previous studies on murid or muroid rodents, our work stands out for the implementation of multiple fossil constraints within the Muridae thanks to a thorough review of the fossil record. Before being assigned to specific nodes of the phylogeny, all potential fossil constraints were carefully assessed; they were also subjected to several cross-validation analyses. The resulting phylogeny is consistent with previous phylogenetic studies on murids, and recovers the monophyly of all sampled murid subfamilies and tribes. Based on nine controlled fossil calibrations, our inferred temporal timeframe indicates that the murid family likely originated in the course of the Early Miocene, 23.0-16.0 million years ago (Ma), and that most major lineages (i.e. tribes) have started diversifyingca.10 Ma. Historical biogeography analyses support the Paleotropical origin for the family, with an initial internal split (vicariance event) followed by subsequent migrations between Afrotropical and Indomalayan lineages. During the course of their diversification, the biogeographic pattern of murids is marked by several dispersal events toward the Australasian and the Palearctic regions, mostly from the Indomalaya. The Afrotropical region was also secondarily colonized at least three times from the Indomalaya, indicating that the latter region has acted as a major centre of diversification for the family.

Latitudinal variation of genecological traits in native grasses of Patagonian rangelands

Geographical variation in genetically based traits helps to elucidate the effect of distinct ecological and evolutionary processes on widespread plants. Whereas abundant information exists on genetic patterns of woody species in western humid Andes, such information is scarce for the neighbouring dry Patagonian steppe. We examined genecological traits of two native forage species vulnerable to overgrazing (Bromus pictus and Poa ligularis) in dry Occidental Phytogeographical District. We compared within-population genetic diversity and among-population (n = 6) divergence by using isozyme electrophoresis. We also cultivated plants under common garden to compare genetically based morphology (plant height, number of tillers by plant and weight per tiller). Analysis showed that 8 and 13 loci were polymorphic of 9 and 19 resolved loci in at least one population for Bromus and Poa, respectively. In general, plant traits decreased from north to south in both species. Genetic and quantitative results (FST/QST index) showed evidence of local adaptation in populations of both species. Genetic divergence among populations was significant. We detected two different geographical groups divided at the same latitude (42–43°S) in both species, supporting the hypothesis of a past vicariance event. Sustainable management of these forage species to cope with land-use and climate change will be enriched by the inclusion of genecological knowledge.