New molecular data for tardigrade phylogeny, with the erection of Paramacrobiotus gen. nov.

Up to few years ago, the phylogenies of tardigrade taxa have been investigated using morphological data, but relationships within and between many taxa are still unresolved. Our aim has been to verify those relationships adding molecular analysis to morphological analysis, using nearly complete 18S ribosomal DNA gene sequences (five new) of 19 species, as well as cytochrome oxidase subunit 1 (COI) mitochondrial DNA gene sequences (15 new) from 20 species, from a total of seven families. The 18S rDNA tree was calculated by minimum evolution, maximum parsimony (MP) and maximum likelihood (ML) analyses. DNA sequences coding for COI were translated to amino acid sequences and a tree was also calculated by neighbour-joining, MP and ML analyses. For both trees (18S rDNA and COI) posterior probabilities were calculated by MrBayes. Prominent findings are as follows: the molecular data on Echiniscidae (Heterotardigrada) are in line with the phylogenetic relationships identifiable by morphological analysis. Among Eutardigrada, orders Apochela and Parachela are confirmed as sister groups. Ramazzottius (Hypsibiidae) results more related to Macrobiotidae than to the genera here considered of Hypsibiidae. Macrobiotidae and Macrobiotus result not monophyletic and confirm morphological data on the presence of at least two large groups within Macrobiotus. Using 18S rDNA and COI mtDNA genes, a new phylogenetic line has been identified within Macrobiotus , corresponding to the ' richtersi-areolatus group'. Moreover, cryptic species have been identified within the Macrobiotus ' richtersi group' and within Richtersius . Some evolutionary lines of tardigrades are confirmed, but others suggest taxonomic revision. In particular, the new genus Paramacrobiotus gen. n. has been identified, corresponding to the phylogenetic line represented by the ' richtersi-areolatus group'.     

Analysis of mitochondrial COI sequences of the Diachasmimorpha longicaudata (Hymenoptera: Braconidae) species complex in Thailand

Diachasmimorpha longicaudata is an Opiinae parasitoid used to control tephritid fruit flies, which cause tremendous economic losses of fruits worldwide. In Thailand, D. longicaudata is classified as three sibling species, DLA, DLB and DLBB, based on the morphological and biological species concepts but their genetic variation has not been studied. Therefore, we investigated the genetic differentiation of the mitochondrial COI gene to clarify the ambiguous taxonomy of this species complex. The 603‐bp COI region was sequenced from laboratory‐bred colonies and field‐collected specimens from seven locations representing five geographical regions in Thailand. DLA was associated with the host Bactrocera correcta while DLB and DLBB were associated with Bactrocera dorsalis. The interspecific nucleotide differences of COI sequences among the three groups ranged from 6.70% to 7.62% (Kimura 2‐parameter distance), which adequately separates species complexes within the order Hymenoptera and supports the current sibling species classification. The neighbor joining, maximum likelihood and consensus Bayesian phylogenetic trees constructed from COI sequences revealed that the three sibling species of laboratory and field‐collected D. longicaudata are monophyletic with 100% support. The high genetic variation and molecular phylogeny of the COI sequences were shown to discriminate between the D. longicaudata species examined in this study.     

贵州四个山羊品种mtDNA多态性及起源分化

采用１５种限制性内切酶,研究贵州省４个山羊品种共９３只个体的线粒体ＤＮＡ多态性。其中ＢｏｍＨＩ、ＨｉｎｄⅢ和ＳａｌⅠ３种酶的酶切类型存在多态。共检测到１８种限制性态型,归结为３种ｍｔＤＮＡ单倍型。单倍型Ⅰ、Ⅱ在贵州山羊４个品种分布频率较高,分别为７７．４２％和２１．５０％,单倍型Ⅲ分布频率较低（１．０８％）;品种间亲缘关系聚类分析表明白山羊和黑山羊亲缘关系最近,其次为黔林羊,而与小香羊的亲缘关系最     

Unraveling the complex maternal history of Southern African Khoisan populations

The Khoisan populations of southern Africa are known to harbor some of the deepest‐rooting lineages of human mtDNA; however, their relationships are as yet poorly understood. Here, we report the results of analyses of complete mtDNA genome sequences from nearly 700 individuals representing 26 populations of southern Africa who speak diverse Khoisan and Bantu languages. Our data reveal a multilayered history of the indigenous populations of southern Africa, who are likely to be the result of admixture of different genetic substrates, such as resident forager populations and pre‐Bantu pastoralists from East Africa. We find high levels of genetic differentiation of the Khoisan populations, which can be explained by the effect of drift together with a partial uxorilocal/multilocal residence pattern. Furthermore, there is evidence of extensive contact, not only between geographically proximate groups, but also across wider areas. The results of this contact, which may have played a role in the diffusion of common cultural and linguistic features, are especially evident in the Khoisan populations of the central Kalahari. Am J Phys Anthropol 153:435–448, 2014. © 2013 Wiley Periodicals, Inc.     

Phylogenetic identification and population differentiation of bottlenose dolphins (Tursiops spp.) in Melanesia,as revealed by mitochondrial DNA

The taxonomic status of many dolphin populations remains uncertain in poorly studied regions of the world's ocean. Here we attempt to clarify the phylogenetic identity of two distinct forms of bottlenose dolphins (Tursiops spp.) described in the Melanesian region of the Pacific Ocean. Mitochondrial DNA control region sequences from samples collected in New Caledonia (n = 88) and the Solomon Islands (n = 19) were compared to previously published sequences of Tursiops spp., representing four phylogenetic units currently recognized within the genus. Phylogenetic reconstructions confirm that the smaller coastal form in Melanesia belongs to the same phylogenetic unit as T. aduncus populations in the Pacific, but differs from T. aduncus in Africa, and that the larger more oceanic form belongs to the species T. truncatus. Analyses of population diversity reveal high levels of regional population structuring among the two forms, with contrasting levels of diversity. From a conservation perspective, genetic isolation of T. aduncus in the Solomon Islands raises further concern about recent impacts of the commercial, live‐capture export industry. Furthermore, the low level of mtDNA diversity in T. aduncus of New Caledonia suggests a recent population bottleneck or founder effect and isolation. This raises concerns for the conservation status of these local populations.     

A re-evaluation of management units based on gene flow of a rare waterbird in the Americas

The maintenance of gene flow in species that have experienced population contractions and are geographically fragmented is important to the maintenance of genetic variation and evolutionary potential; thus, gene flow is also important to conservation and management of these species. For example, the Reddish Egret (Egretta rufescens) has recovered after severe population reductions during the 19th and 20th centuries, but population numbers remain below historical levels. In this study, we characterized gene flow among management units of the Reddish Egret by using ten nuclear microsatellite markers and part of the mitochondrial (mtDNA) control region from 176 nestlings captured at eight localities in Mexico (Baja California, Chiapas, Tamaulipas, and Yucatan), the USA (Texas, Louisiana, and Florida), and the Bahamas. We found evidence of population structure and that males disperse more often and across longer distances compared with females, which is congruent with previous banding and telemetry data. The maternally inherited mtDNA and biparentally inherited microsatellite data supported slightly different MU models; however, when interpreted together, a four MU model that considered population structure and geographic proximity was most optimal. Namely, MU 1 (Baja California); MU 2 (Chiapas); MU 3 (Yucatan, Tamaulipas, Texas, and Louisiana); and MU 4 (Florida and the Bahamas). Regions outside our sampled localities (e.g., the Greater Antilles and South America) require additional sampling to fully understand gene flow and movement of individuals across the species’ entire range. However, the four MUs we have defined group nesting localities into genetically similar subpopulations, which can guide future management plans.     

Population genetic structure, phylogeography and spawning philopatry in walleye (Stizostedion vitreum) from mitochondrial DNA control region sequences

Mitochondrial (mt) DNA control region sequences were used to test the genetic and phylogeographic structure of walleye Stizostedion vitreum populations at different geographical scales: among spawning sites, lake basins, lakes, and putative glacial refugia in the Great Lakes region. Sequencing 199 walleye revealed nucleotide substitutions and tandemly repeated sequences that varied in copy number, as well as in sequence composition, in 1200 bp of the mtDNA control region. Variable numbers of copies of an 11-bp tandem repeat showed no geographical patterning and were not used in further analyses. Substitutions in the other areas of the control region yielded 19 haplotypes, revealing phylogeographic structure and significant differences among glacial refugia, lakes, basins and some spawning sites. Differences among spawning populations were consistent with reduced gene flow, philopatry and possible natal homing. Analysis of spawning populations showed consistency of genotypic frequencies among years and between males and females, supporting philopatry in both sexes. The unglaciated plateau in southern Ohio, USA housed a very different haplotype that diverged prior to the Missouri, Mississippi and Atlantic glacial refugia types. Haplotypes from the three refugia colonized the Great Lakes after retreat of the Wisconsin glaciers, and their present distribution reflects the geography of their prior isolation and differential colonization. Populations that became associated with spawning localities appear to have diverged further due to philopatry, resulting in fine-scale phylogeographic structuring.     

ASK1 physically interacts with COI1 and is required for male fertility inArabidopsis

Jasmonates are a new class of plant hormones that play important roles in plant development and plant defense. TheCOI1 gene was previously shown to be required for jasmonate-regulated plant fertility and defense. We demonstrated for the first time that COI1 interacts with theArabidopsis SKP1-LIKE1 (ASK1) to form a complex that is required for jasmonate action inplanta. Functional analysis by antisense strategy showed thatASK1 is involved in male fertility.     

Complete mitochondrial genome of Tubulipora flabellaris (Bryozoa: Stenolaemata): the first representative from the class Stenolaemata with unique gene order

Mitochondrial genomes play a significant role in the reconstruction of phylogenetic relationships within metazoans. There are still many controversies concerning the phylogenetic position of the phylum Bryozoa. In this research, we have finished the complete mitochondrial genome of one bryozoan (Tubulipora flabellaris), which is the first representative from the class Stenolaemata. The complete mitochondrial genome of T. flabellaris is 13,763 bp in length and contains 36 genes, which lacks the atp8 gene in contrast to the typical metazoan mitochondrial genomes. Gene arrangement comparisons indicate that the mitochondrial genome of T. flabellaris has unique gene order when compared with other metazoans. The four known bryozoans complete mitochondrial genomes also have very different gene arrangements, indicates that bryozoan mitochondrial genomes have experienced drastic rearrangements. To investigate the phylogenetic relationship of Bryozoa, phylogenetic analyses based on amino acid sequences of 11 protein coding genes (excluding atp6 and atp8) from 26 metazoan complete mitochondrial genomes were made utilizing Maximum Likelihood (ML) and Bayesian methods, respectively. The results indicate the monopoly of Lophotrochozoa and a close relationship between Chaetognatha and Bryozoa. However, more evidences are needed to clarify the relationship between two groups. Lophophorate appeared to be polyphyletic according to our analyses. Meanwhile, neither analysis supports close relationship between Branchiopod and Phoronida. Four bryozoans form a clade and the relationship among them is T. flabellaris + (F. hispida + (B. neritina + W. subtorquata)), which is in coincidence with traditional classification system.