Preliminary estimates of cetacean abundance in the northern Gulf of Mexico, and of selected cetacean species in the U.S. Atlantic Exclusive Economic Zone from vessel surveys

The Southeast Fisheries Science Center (SEFSC) initiated annual, vessel-based visual sampling surveys of northern Gulf of Mexico marine mammals in 1990 and conducted a similar survey in U.S. Atlantic Exclusive Economic Zone (EEZ) waters from Miami, Florida, to Cape Hatteras, North Carolina, in 1992. The primary goal of these surveys was to meet Marine Mammal Protection Act requirements for estimating abundance and monitoring trends of marine mammal stocks in United States waters. The surveys were designed to collect: 1) marine mammal sighting data to estimate abundance and to determine distribution and diversity; and 2) environmental data to evaluate factors which may affect the distribution, abundance and diversity of marine mammals. The preliminary analyses for abundance estimation from the 1990-1993 surveys are presented in this report.

Estimates of cetacean abundance in the northern Gulf of Mexico from vessel surveys

The Southeast Fisheries Science Center (SEFSC) initiated annual, vessel-based visual sampling surveys of northern Gulf of Mexico marine mammals in 1990. The primary goal of these surveys was to meet Marine Mammal Protection Act requirements for estimating abundance and monitoring trends of marine mammal stocks in United States waters. The surveys were designed to collect: 1) marine mammal sighting data to estimate abundance and to determine distribution and diversity; and 2) environmental data to evaluate factors which may affect the distribution, abundance and diversity of marine mammals. The analyses for abundance estimation from the 1991-1994 surveys are presented in this report.

Marine Vertebrates and Low Frequency Sound: Technical Report for LFA EIS

Over the past 50 years, economic and technological developments have dramatically increased the human contribution to ambient noise in the ocean. The dominant frequencies of most human-made noise in the ocean is in the low-frequency range (defined as sound energy below 1000Hz), and low-frequency sound (LFS) may travel great distances in the ocean due to the unique propagation characteristics of the deep ocean (Munk et al. 1989). For example, in the Northern Hemisphere oceans low-frequency ambient noise levels have increased by as much as 10 dB during the period from 1950 to 1975 (Urick 1986; review by NRC 1994). Shipping is the overwhelmingly dominant source of low-frequency manmade noise in the ocean, but other sources of manmade LFS including sounds from oil and gas industrial development and production activities (seismic exploration, construction work, drilling, production platforms), and scientific research (e.g., acoustic tomography and thermography, underwater communication). The SURTASS LFA system is an additional source of human-produced LFS in the ocean, contributing sound energy in the 100-500 Hz band. When considering a document that addresses the potential effects of a low-frequency sound source on the marine environment, it is important to focus upon those species that are the most likely to be affected. Important criteria are: 1) the physics of sound as it relates to biological organisms; 2) the nature of the exposure (i.e. duration, frequency, and intensity); and 3) the geographic region in which the sound source will be operated (which, when considered with the distribution of the organisms will determine which species will be exposed). The goal in this section of the LFA/EIS is to examine the status, distribution, abundance, reproduction, foraging behavior, vocal behavior, and known impacts of human activity of those species may be impacted by LFA operations. To focus our efforts, we have examined species that may be physically affected and are found in the region where the LFA source will be operated. The large-scale geographic location of species in relation to the sound source can be determined from the distribution of each species. However, the physical ability for the organism to be impacted depends upon the nature of the sound source (i.e. explosive, impulsive, or non-impulsive); and the acoustic properties of the medium (i.e. seawater) and the organism. Non-impulsive sound is comprised of the movement of particles in a medium. Motion is imparted by a vibrating object (diaphragm of a speaker, vocal chords, etc.). Due to the proximity of the particles in the medium, this motion is transmitted from particle to particle in waves away from the sound source. Because the particle motion is along the same axis as the propagating wave, the waves are longitudinal. Particles move away from then back towards the vibrating source, creating areas of compression (high pressure) and areas of rarefaction (low pressure). As the motion is transferred from one particle to the next, the sound propagates away from the sound source. Wavelength is the distance from one pressure peak to the next. Frequency is the number of waves passing per unit time (Hz). Sound velocity (not to be confused with particle velocity) is the impedance is loosely equivalent to the resistance of a medium to the passage of sound waves (technically it is the ratio of acoustic pressure to particle velocity). A high impedance means that acoustic particle velocity is small for a given pressure (low impedance the opposite). When a sound strikes a boundary between media of different impedances, both reflection and refraction, and a transfer of energy can occur. The intensity of the reflection is a function of the intensity of the sound wave and the impedances of the two media. Two key factors in determining the potential for damage due to a sound source are the intensity of the sound wave and the impedance difference between the two media (impedance mis-match). The bodies of the vast majority of organisms in the ocean (particularly phytoplankton and zooplankton) have similar sound impedence values to that of seawater. As a result, the potential for sound damage is low; organisms are effectively transparent to the sound – it passes through them without transferring damage-causing energy. Due to the considerations above, we have undertaken a detailed analysis of species which met the following criteria: 1) Is the species capable of being physically affected by LFS? Are acoustic impedence mis-matches large enough to enable LFS to have a physical affect or allow the species to sense LFS? 2) Does the proposed SURTASS LFA geographical sphere of acoustic influence overlap the distribution of the species? Species that did not meet the above criteria were excluded from consideration. For example, phytoplankton and zooplankton species lack acoustic impedance mis-matches at low frequencies to expect them to be physically affected SURTASS LFA. Vertebrates are the organisms that fit these criteria and we have accordingly focused our analysis of the affected environment on these vertebrate groups in the world’s oceans: fishes, reptiles, seabirds, pinnipeds, cetaceans, pinnipeds, mustelids, sirenians (Table 1).

中国鸟类的DNA分类及系统发育研究概述

鸟类分类是鸟类学其他研究领域的基础,近年来分子技术的发展,以及计算机技术的应用为鸟类分类学和鸟类系统演化研究提供了新的研究手段,给传统的系统分类研究带来了新的机遇.Tautz等于2002年首先提出运用DNA序列作为生物分类系统的主要平台,即DNA分类学(DNA Taxonomy).而Hebert等于2003年则首次提出了DNA条形码(DNA Barcoding)的概念,并对其物种分类和鉴定意义予以肯定,建议利用线粒体细胞色素C氧化酶亚单位Ⅰ(COI)的特定区段来做DNA条形编码的基础.在鸟类DNA分类方面,国内学者应用线粒体基因Cut b,COI,c-mos,c-myc,12s rRNA,16s rRNA,ND2,ND3,CR,RAG-1以及核基因myoglobin introⅡ等不同片段对很多类群进行了分类探讨和系统发育研究.但是主要集中在鸡形目及雀形目鸟类.中国是鸟类多样性极其丰富的国家,近年来很多亚种、种及以上分类阶元依然存在问题,因此,中国鸟类物种的分类地位、系统发育与演化关系等依然有很多问题等待深入研究.目前国内基于COI的鸟类分类及系统发育研究有了一些报道,但是真正的DNA条形码工作尚需继续、深入地开展.

High Altitude Adaptation and Phylogenetic Analysis of Tibetan Horse Based on the Mitochondrial Genome

研究测定了西藏那曲(4,500 m)、云南中甸(3,300 m)、云南德钦(3,300 m)地区3匹藏马线粒体全基因组序列.3个地区的藏马线粒体基因组全长以及结构均与韩国济州岛的马类似,但比瑞典马线粒体基因组短.藏马基因组在DNA序列上的两两相似性达99.3%.通过对线粒体蛋白编码区的分析发现,NADH6基因的蛋白序列在三匹藏马中均表现快速进化的现象.这表明NADH6基因在藏马高原适应进化过程中扮演着重要角色.此外,利用7匹藏马的D-loop区域序列以及与其亲缘关系较近的马的序列首次构建的藏马的系统发育树显示,那曲藏马与中甸、德钦藏马属于不同的分支,且存在较大的遗传多样性,表明藏马可能为多地区起源.

鲤科的科下类群及其宗系发生关系

<正> 鲤科为鲤形目中最大的科,拥有275属1600种(Pattern 1975)。早在100多年前Bleeker(1863)已对该科进行了较细的类群划分,嗣后,其他作者也先后做过这方面的工作。Regan(1911)发现某些骨骼性状在宗系发生(phylogeny)上具有一定的重要性,而另一些性状则对划分类群没有意义。Berg(1912,1940)依据较特别的外部形态来规定

Comparative phylogeography of the Yellow River schizothoracine fishes (Cyprinidae): Vicariance, expansion, and recent coalescence in response to the Quaternary environmental upheaval in the Tibetan Plateau

National Natural Science Foundation of China (NSFC) [30225008, 30300036, 30530120]; Key Innovation Plan [KSCX2-SW-106]; National Basic Research Project in China [2005cb422005]; National Natural Science Foundation of China [30600062]

Morphological and molecular phylogenetic analysis of two Saprolegnia sp (Oomycetes) isolated from silver crucian carp and zebra fish

Two Saprolegnia isolates, JY isolated from silver crucian carp (Carassius auratus gibelio Bloch) and BMY isolated from zebra fish (Brachydanio rerio Hamilton) came from infections occurring concurrently in different locations in China. To confirm whether the two isolates were from the same Saprolegnia clone, comparative studies have been carried out based on their morphological, physiological and molecular characteristics. Observations showed that morphologically (both asexual and sexual organs) the two isolates were broadly similar and both isolates under-went repeated zoospore emergence. Comparing 704 base pairs of internal transcribed spacer (ITS) region and the 5.8S rDNA, we found isolates JY and BMY shared an identical ITS sequence with a minor variation (99.6 % similarity). Forty available sequences for representatives Saprolegnia spp. belonged to four phylogenetically separate clades. The two studied isolates fell within clade I that comprised a group of isolates which showed almost an identical ITS sequence but had been identified as a number of different morphological species. our findings suggest that isolates JY and BMY appear to belong to the S. ferax clade and this clade (1) contains a number of closely related phylogenetic species. This is distinct from the more common fish pathogenic isolates, which belong to the S. parasitica clade (III) and are characterized by having cysts decorated by bundles of long hooked hairs and two further clades (II and IV) containing largely saprotrophic or soil born species. (C) 2009 Published by Elsevier Ltd on behalf of The British Mycological Society.

Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

Background: Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results: A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 x 10(5) and 1.7 x 10(5) per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion: The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened the hypotheses containing the slippage model for initiation of reverse transcription, retropositional parasitism of SINEs on LINEs, the formation of the stem loop structure in 3'tail region of some SINEs and LINEs and the mechanism of template switching in generating new SINE family.

An Evaluation of Four Phylogenetic Markers in Nostoc: Implications for Cyanobacterial Phylogenetic Studies at the Intrageneric Level

The success of some phylogenetic markers in cyanobacteria owes to the design of cyanobacteria-specific primers, but a few studies have directly investigated the evolution "behavior" of the loci. In this study, we performed a case study in Nostoc to evaluate rpoC1, hetR, rbcLX, and 16S rRNA-tRNA(Ile)-tRNA(Ala)-23S rRNA internal transcribed spacer (ITS) as phylogenetic markers. The results indicated that the gene trees of these loci are not congruent with the phylogeny based on 16S rRNA gene. The mechanisms contributing to the incongruence include randomized variation and recombination. As the results suggested, one should be careful to choose the molecular markers for phylogenetic reconstruction at the intrageneric level in cyanobacteria.

Phylogeography of the freshwater catfish Hemibagrus guttatus (Siluriformes, Bagridae): Implications for South China biogeography and influence of sea-level changes

National Natural Science Foundation of China (NSFC) ; [2007CB411600]; [30530120]

Bayesian mixed models and divergence time estimation of Chinese cavefishes (Cyprinidae : Sinocyclocheilus)

The genus Sinocyclocheilus is distributed in Yun-Gui Plateau and its surrounding region only, within more than 10 cave species showing different degrees of degeneration of eyes and pigmentation with wonderful adaptations. To present, published morphological and molecular phylogenetic hypotheses of Sinocyclocheilus from prior works are very different and the relationships within the genus are still far from clear. We obtained the sequences of cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) of 34 species within Sinocyclocheilus, which represent the most dense taxon sampling to date. We performed Bayesian mixed models analyses with this data set. Under this phylogenetic framework, we estimated the divergence times of recovered clades using different methods under relaxed molecular clock. Our phyloegentic results supported the monophyly of Sinocyclocheilus and showed that this genus could be subdivided into 6 major clades. In addition, an earlier finding demonstrating the polyphyletic of cave species and the most basal position of S. jii was corroborated. Relaxed divergence-time estimation suggested that Sinocyclocheilus originated at the late Miocene, about 11 million years ago (Ma), which is older than what have been assumed.

Molecular characteristics of Camallanus spp. (Spirurida : Camallanidae) in fishes from China based on its rDNA sequences

In the,paper, we explored the intra- and interspecific evolutionary variation among species of Camallanus collected from different fish species in various regions of China. We determined the internal transcribed spacers of ribosomal DNA (ITS rDNA) sequences of these nematodes. The divergence (uncorrected p-distance) of ITS 1, ITS2, and ITS rDNA data sets confirmed 2 valid species of Camallanus in China, i.e., C. cotti and C. hypophthalmichthys. The 2 species were distinguished not only by their different morphologies and host ranges but also by a letranucleotide microsatellite (TTGC)n present in the ITS I region of C cotti. Phylogenetic analyses of the nematodes disclosed 2 main clades, corresponding to different individuals of C cotti and C. hypophthalmichthys from different fish species in various geographical locations, although the interior nodes of each clade received poor support.