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Damselflies and dragonflies (Order: Odonata) play important roles in both aquatic and terrestrial food webs and can serve as sentinels of ecosystem health and predictors of population trends in other taxa. The habitat requirements and limited dispersal of lotic damselflies make them especially sensitive to habitat loss and fragmentation. As such, landscape genomic studies of these taxa can help focus conservation efforts on watersheds with high levels of genetic diversity, local adaptation, and even cryptic endemism. Here, as part of the California Conservation Genomics Project (CCGP), we report the first reference genome for the American rubyspot damselfly, Hetaerina americana, a species associated with springs, streams and rivers throughout California. Following the CCGP assembly pipeline, we produced two de novo genome assemblies. The primary assembly includes 1,630,044,487 base pairs, with a contig N50 of 5.4 Mb, a scaffold N50 of 86.2 Mb, and a BUSCO completeness score of 97.6%. This is the seventh Odonata genome to be made publicly available and the first for the subfamily Hetaerininae. This reference genome fills an important phylogenetic gap in our understanding of Odonata genome evolution, and provides a genomic resource for a host of interesting ecological, evolutionary, and conservation questions for which the rubyspot damselfly genus Hetaerina is an important model system.

Background: Digital transcriptomics is rapidly emerging as a powerful new technology for modelling the environmental dynamics of the adaptive landscape in diverse lineages. This is particularly valuable in taxa such as turtles and tortoises (order Testudines) which contain a large fraction of endangered species at risk due to anthropogenic impacts on the environment, including pollution, overharvest, habitat degradation, and climate change. Sea turtles (family Cheloniidae) in particular invite a genomics-enabled approach to investigating their remarkable portfolio of adaptive evolution. The sex of the endangered loggerhead sea turtle (Caretta caretta) is subject to temperature-dependent sex determination (TSD), a mechanism by which exposure to temperatures during embryonic development irreversibly determines sex. Higher temperatures produce mainly female turtles and lower temperatures produce mainly male turtles. Incubation temperature can have long term effects on the immunity, migratory ability, and ultimately longevity of hatchlings. We perform RNA-seq differential expression analysis to investigate tissue- and temperature-specific gene expression within brain (n = 7) and gonadal (n = 4) tissue of male and female loggerhead hatchlings. Results: We assemble tissue- and temperature-specific transcriptomes and identify differentially expressed genes relevant to sexual development and life history traits of broad adaptive interest to turtles and other amniotic species. We summarize interactions among differentially expressed genes by producing network visualizations, and highlight shared biological pathways related to migration, immunity, and longevity reported in the avian and reptile literature. Conclusions: The measurement of tissue- and temperature-specific global gene expression of an endangered, flagship species such as the loggerhead sea turtle (Caretta caretta) reveals the genomic basis for potential resiliency and is crucial to future management and conservation strategies with attention to changing climates. Brain and gonadal tissue collected from experimentally reared loggerhead male and female hatchlings comprise an exceedingly rare dataset that permits the identification of genes enriched in functions related to sexual development, immunity, longevity, and migratory behavior and will serve as a large, new genomic resource for the investigation of genotype–phenotype relationships in amniotes.

In the era of genomics, single-nucleotide polymorphisms (SNPs) have become a preferred molecular marker to study signatures of selection and population structure and to enable improved population monitoring and conservation of vulnerable populations. We apply a SNP calling pipeline to assess population differentiation, visualize linkage disequilibrium, and identify loci with sex-specific genotypes of 45 loggerhead sea turtles (Caretta caretta) sampled from the southeastern coast of the United States, including 42 individuals experimentally confirmed for gonadal sex. By performing reference-based SNP calling in independent runs of Stacks, 3,901–6,998 SNPs and up to 30 potentially sex-specific genotypes were identified. Up to 68 pairs of loci were found to be in complete linkage disequilibrium, potentially indicating regions of natural selection and adaptive evolution. This study provides a valuable SNP diagnostic workflow and a large body of new biomarkers for guiding targeted studies of sea turtle genome evolution and for managing legally protected nonmodel iconic species that have high economic and ecological importance but limited genomic resources.

Biomphalaria snails are instrumental in transmission of the human blood fluke Schistosoma mansoni. With the World Health Organization's goal to eliminate schistosomiasis as a global health problem by 2025, there is now renewed emphasis on snail control. Here, we characterize the genome of Biomphalaria glabrata, a lophotrochozoan protostome, and provide timely and important information on snail biology. We describe aspects of phero-perception, stress responses, immune function and regulation of gene expression that support the persistence of B. glabrata in the field and may define this species as a suitable snail host for S. mansoni. We identify several potential targets for developing novel control measures aimed at reducing snail-mediated transmission of schistosomiasis., Biomphalaria glabrata is a fresh water snail that acts as a host for trematode Schistosoma mansoni that causes intestinal infection in human. This work describes the genome and transcriptome analyses from 12 different tissues of B glabrata, and identify genes for snail behavior and evolution.

The Spotted Eagle Ray, Aetobatus narinari, is a semi-pelagic myliobatoid recognized as near threatened by the World Conservation Union. A decreasing population trend, K-selected life history, and primarily inshore, coastal habitat renders this species susceptible to over-exploitation by targeted fisheries, drift netting, and capture as bycatch. Recent molecular investigations and subsequent taxonomic recognition as a species complex have left a large deficiency in current knowledge of A. narinari and a complete absence of data concerning population structure and genetic health for the northwestern Atlantic Ocean. Our study is the first to examine fine-scale structure on a regional basis in the Gulf of Mexico and coastal Atlantic waters off the United States. Individuals sampled non-invasively from four sites, Sarasota, FL (n = 143), the Everglades, FL (n = 36), Ft. Pierce, FL (n = 8), and the southeastern U.S. Atlantic coast (n = 24), were genotyped across eight microsatellite loci. Standard tests...

Observations of elasmobranchs in groups suggest sociality in sharks and rays. However we currently lack a strong understanding of social structure and the role kinship has in structuring group organization in cartilaginous fishes. The spotted eagle ray, Aetobatus narinari (Euphrasen, 1790) frequents the shallow waters near Sarasota, FL, often in pairs or groups suggesting a social component to their behavior. In the present study, eight eagle ray-specific microsatellite markers were used to investigate relatedness in A. narinari groups, and used to determine if kin structure contributed to group organization. Using regression-based and maximum-likelihood approaches, relatedness was quantified and compared within and among groups of juveniles, and adults in mixed sex and same sex groups. Results showed a lack of kin-structured sociality in A. narinari, suggesting factors apart from relatedness shape social interactions among spotted eagle rays in the near-shore waters of Sarasota, FL. Our results add to the limited amount of published literature on elasmobranch kinship, which are important for understanding implications of anthropogenic disturbance on genetic variability for coastal populations.

The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse—more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations., National Science Foundation (U.S.) (NSF grant DEB-0920892), National Science Foundation (U.S.) (NSF grant DEB-0844624), National Human Genome Research Institute (U.S.)

We present a strategy for phylogenetic marker development in non-model systems. Rather than using the traditional approach of comparing distantly related taxa to develop conserved primers for unknown species, we explore an alternative strategy that builds primers directly from a single, relatively well characterized species and applies those primers to increasingly distantly related taxa. We develop and test our protocol with turtles. Using a single BAC end-sequence library consisting of 3461 sequences totaling 2.43 million base pairs of data, we outline a procedure to flag repeat elements, followed by a BLAST approach to categorize sequences into high, low, and no similarity compartments compared to GenBank sequences. We developed and tested a panel of 96 primer pairs with a set of turtle tissues that forms a series of increasingly distantly related taxa with respect to the BAC reference species. Finally, we sequenced 11 of these newly discovered markers across a diverse set of 18 turtle species that spans the 210 million years of chelonian crown-group history and that includes representatives of most of the major clades of extant turtles. Our results indicate that large numbers of new, phylogenetically informative markers can be developed quickly and inexpensively from a single BAC, EST, or similar genomic resource, and that those markers provide reliable phylogenetic information across both shallow and deep levels of phylogenetic history. Our results also highlight the importance of screening for and managing repetitive elements found in randomly sequenced DNA fragments. We presume that our strategy should work well across any similarly divergent clade, suggesting that many-marker datasets can be developed quickly and efficiently for phylogenetic analysis.

The two living groups of flying vertebrates, birds and bats, both have constricted genome sizes compared with their close relatives. But nothing is known about the genomic characteristics of pterosaurs, which took to the air over 70 Myr before birds and were the first group of vertebrates to evolve powered flight. Here, we estimate genome size for four species of pterosaurs and seven species of basal archosauromorphs using a Bayesian comparative approach. Our results suggest that small genomes commonly associated with flight in bats and birds also evolved in pterosaurs, and that the rate of genome-size evolution is proportional to genome size within amniotes, with the fastest rates occurring in lineages with the largest genomes. We examine the role that drift may have played in the evolution of genome size within tetrapods by testing for correlated evolution between genome size and body size, but find no support for this hypothesis. By contrast, we find evidence suggesting that a combination of adaptation and phylogenetic inertia best explains the correlated evolution of flight and genome-size contraction. These results suggest that small genome/cell size evolved prior to or concurrently with flight in pterosaurs. We predict that, similar to the pattern seen in theropod dinosaurs, genome-size contraction preceded flight in pterosaurs and bats.

Poaching and habitat encroachment for human settlement are the two major factors that caused contraction of elephant populations in Africa. While the effects of poaching on many aspects of elephant social systems have been studied, the impacts on mating patterns are not yet understood and such information is still lacking in most African countries. In this study, we used elephant specific-microsatellite DNA to generate genotypes from 86 elephant samples (84 fresh faeces and two tissue samples) from Tarangire National Park (TNP), Tanzania to assess the mating success of individual males. We also tested whether the oldest bulls are more likely to sire most of the offspring in a severely poached population. Genetic paternity analysis was compared to behavioural observations of matings collected over a 3-year period (1998–2001) to determine the success of bull mating strategy. The genotypes of 26 infants, their known mothers and 10 out of 43 potential breeding bulls in TNP were used to assign 31% of the offspring at 80% confidence level to their potential fathers with simulation assuming that 23% (10/43) of the breeding males were sampled. Mating success of individual bull based on both behavioural and genetic data showed that the oldest remaining bulls performed most of the matings and fathered the majority of infants. We speculate that the lifetime fitness of bulls that have survived poaching may be elevated because their period of dominance increases.

One of the less well known factors associated with flight in vertebrates is a reduction of the size of the genome. Birds have remarkably small genomes compared with other vertebrates, and bats tend to have smaller genomes than do non-flying mammals. But does flight cause genome loss, or does genome loss predispose animals to take flight? The latter seems to be the case, to judge from an extensive analysis of bone cell volume and genome size in dinosaurs. Genome reduction can be traced deep into the lineage of saurischian dinosaurs — the dinosaur group of which the birds are the only surviving members — but not in ornithischian dinosaurs. A correlate of flight in vertebrates is a reduction of the genome. But does flight cause genome loss, or does genome loss predispose animals to take flight? Histology and statistical techniques shows that genome reduction can be traced deep into the lineage of saurischian dinosaurs. Genome reduction thus joins the morphological features we now associate with birds that can be traced far back into the dinosaurian ancestry. Avian genomes are small and streamlined compared with those of other amniotes by virtue of having fewer repetitive elements and less non-coding DNA1,2. This condition has been suggested to represent a key adaptation for flight in birds, by reducing the metabolic costs associated with having large genome and cell sizes3,4. However, the evolution of genome architecture in birds, or any other lineage, is difficult to study because genomic information is often absent for long-extinct relatives. Here we use a novel bayesian comparative method to show that bone-cell size correlates well with genome size in extant vertebrates, and hence use this relationship to estimate the genome sizes of 31 species of extinct dinosaur, including several species of extinct birds. Our results indicate that the small genomes typically associated with avian flight evolved in the saurischian dinosaur lineage between 230 and 250 million years ago, long before this lineage gave rise to the first birds. By comparison, ornithischian dinosaurs are inferred to have had much larger genomes, which were probably typical for ancestral Dinosauria. Using comparative genomic data, we estimate that genome-wide interspersed mobile elements, a class of repetitive DNA, comprised 5–12% of the total genome size in the saurischian dinosaur lineage, but was 7–19% of total genome size in ornithischian dinosaurs, suggesting that repetitive elements became less active in the saurischian lineage. These genomic characteristics should be added to the list of attributes previously considered avian but now thought to have arisen in non-avian dinosaurs, such as feathers5, pulmonary innovations6, and parental care and nesting7.

Building accurate predictive models for biological data sets from next-generation high-throughput data sources is essential to bioinformatics. However, confounding variables such as sex, age, and habitat can skew the results of such models, leading to biased and inaccurate results. While Li et. al have developed a confounder-correcting framework for Support Vector Machines (SVMs) [1], there is no such method available for machine learning algorithms suited for high-dimensional data sets with small sample sizes (d≫n). We have extended Li et. al's confounder-correcting (cc) algorithm (ccSVM) to allow Kernel Orthogonal Projections to Latent Structures (KOPLS) to explicitly account for confounding factors. We demonstrate that our novel method complements and improves the accuracy of a non-cc KOPLS with implicit orthogonal signal correction. Finally, we show that ccKOPLS is better suited to high-dimensionality data sets than ccSVM.

The family Geoemydidae is one of three in the superfamily Testudinoidea and is the most diversified family of extant turtle species. The phylogenetic relationships in this family and among related families have been vigorously investigated from both morphological and molecular viewpoints. The evolutionary history of Geoemydidae, however, remains controversial. Therefore, to elucidate the phylogenetic relationships of Geoemydidae and related species, we applied the SINE insertion method to investigate 49 informative SINE loci in 28 species. We detected four major evolutionary lineages (Testudinidae, Batagur group, Siebenrockiella group, and Geoemyda group) in the clade Testuguria (a clade of Geoemydidae + Testudinidae). All five specimens of Testudinidae form a monophyletic clade. The Batagur group comprises five batagurines. The Siebenrockiella group has one species, Siebenrockiella crassicollis. The Geoemyda group comprises 15 geoemydines (including three former batagurines, Mauremys reevesii, Mauremys sinensis, and Heosemys annandalii). Among these four groups, the SINE insertion patterns were inconsistent at four loci, suggesting that an ancestral species of Testuguria radiated and rapidly diverged into the four lineages during the initial stage of its evolution. Furthermore, within the Geoemyda group we identified three evolutionary lineages, namely Mauremys, Cuora, and Heosemys. The Heosemys lineage comprises Heosemys, Sacalia, Notochelys, and Melanochelys species, and its monophyly is a novel assemblage in Geoemydidae. Our SINE phylogenetic tree demonstrates extensive convergent morphological evolution between the Batagur group and the three species of the Geoemyda group, M. reevesii, M. sinensis, and H. annandalii.

It is unlikely that taxonomically diverse phylogenetic studies will be completed rapidly in the near future for nonmodel organisms on a whole-genome basis. However, one approach to advancing the field of "phylogenomics" is to estimate the structure of poorly known genomes by mining libraries of clones from suites of taxa, rather than from single species. The present analysis adopts this approach by taking advantage of megabase-scale end-sequence scanning of reptilian genomic clones to characterize diversity of CR1-like LINEs, the dominant family of transposable elements (TEs) in the sister group of mammals. As such, it helps close an important gap in the literature on the molecular systematics and evolution of retroelements in nonavian reptiles. Results from aligning more than 14 Mb of sequence from the American alligator (Alligator mississippiensis), painted turtle (Chrysemys picta), Bahamian green anole (Anolis smaragdinus), Tuatara (Sphenodon punctatus), Emu (Dromaius novaehollandiae), and Zebra Finch (Taeniopygia guttata) against a comprehensive library approximately 3000 TE-encoding peptides reflect an increasing abundance of LINE and non-long-terminal-repeat (non-LTR) retrotransposon repeat types with the age of common ancestry among exemplar reptilian clades. The hypothesis that repeat diversity is correlated with basal metabolic rate was tested using comparative methods and a significant nonlinear relationship was indicated. This analysis suggests that the age of divergence between an exemplary clade and its sister group as well as metabolic correlates should be considered in addition to genome size in explaining patterns of retroelement diversity. The first phylogenetic analysis of the largely unexplored chicken repeat 1 (CR1) 3' reverse transcriptase (RT) conserved domains 8 and 9 in nonavian reptiles reveals a pattern of multiple lineages with variable branch lengths, suggesting presence of both old and young elements and the existence of several distinct well-supported clades not apparent from previous characterization of CR1 subfamily structure in birds and the turtle. This mode of CR1 evolution contrasts with historical patterns of LINE 1 diversification in mammals and hints toward the existence of a rich but still largely unexplored diversity of nonavian retroelements of importance to advancing both comparative vertebrate genomics and amniote systematics.

Resurgence of illicit trade in African elephant ivory is placing the elephant at renewed risk. Regulation of this trade could be vastly improved by the ability to verify the geographic origin of tusks. We address this need by developing a combined genetic and statistical method to determine the origin of poached ivory. Our statistical approach exploits a smoothing method to estimate geographic-specific allele frequencies over the entire African elephants' range for 16 microsatellite loci, using 315 tissue and 84 scat samples from forest ( Loxodonta africana cyclotis ) and savannah ( Loxodonta africana africana ) elephants at 28 locations. These geographic-specific allele frequency estimates are used to infer the geographic origin of DNA samples, such as could be obtained from tusks of unknown origin. We demonstrate that our method alleviates several problems associated with standard assignment methods in this context, and the absolute accuracy of our method is high. Continent-wide, 50% of samples were located within 500 km, and 80% within 932 km of their actual place of origin. Accuracy varied by region (median accuracies: West Africa, 135 km; Central Savannah, 286 km; Central Forest, 411 km; South, 535 km; and East, 697 km). In some cases, allele frequencies vary considerably over small geographic regions, making much finer discriminations possible and suggesting that resolution could be further improved by collection of samples from locations not represented in our study.

Nature Communications 8: Article number: 15451 (2017); Published 16 May 2017; Updated 23 August 2017 The original version of this Article contained an error in the spelling of the author Leon Di Stefano, which was incorrectly given as Leon di Stephano. This has now been corrected in both the PDF andHTML versions of the Article.

ANDREW M. SHEDLOCK,1,2 MICHELC. MILINKOVITCH,3 AND NORIHIRO OKADA1,4 Tokyo Institute of Technology, Molecular Evolution Laboratory, Graduate School of Bioscience and Biotechnology, Yokohama, Japan The Institute of Statistical Mathematics, Molecular Systematics Group, Tokyo, Japan Free University of Brussels, cp300, Unit of Evolutionary Genetics, Institute of Molecular Biology and Medicine, 6041 Gosselies, Belgium

Short interspersed repetitive elements, or SINEs, are tRNA-derived retroposons that are dispersed throughout eukaryotic genomes and can be present in well over 10(4) total copies. The enormous volume of SINE amplifications per organism makes them important evolutionary agents for shaping the diversity of genomes, and the irreversible, independent nature of their insertion allows them to be used for diagnosing common ancestry among host taxa with extreme confidence. As such, they represent a powerful new tool for systematic biology that can be strategically integrated with other conventional phylogenetic characters, most notably morphology and DNA sequences. This review covers the basic aspects of SINE evolution that are especially relevant to their use as systematic characters and describes the practical methods of characterizing SINEs for cladogram construction. It also discusses the limits of their systematic utility, clarifies some recently published misunderstandings, and illustrates the effective application of SINEs for vertebrate phylogenetics with results from selected case studies. BioEssays 22:148-160, 2000.

The schizothoracine fishes, also known as “mountain carps” are widely distributed in the Qinghai-Tibetan Plateau and its peripheral regions. Although they provide a prime example of high altitude adaptation, the phylogenetic relationships and the divergence times among these carp lineages are still controversial. Moreover, the genetic basis for high altitude adaptation is also poorly understood. In this study, we determined the mitochondrial genomes from two species of the schizothoracine fishes, representing a “morphologically primitive” clade and “morphologically specialized” clade, respectively. The phylogenetic tree and the divergence times were estimated within the evolutionary framework of the entire order Cypriniformes. Our results indicate a polyphylyetic relationship of the schizothoracine fishes and suggest two independent migration events into the Qinghai-Tibetan Plateau: one by the “morphologically primitive” clade in the Late Miocene and another by the “morphologically specialized” clade in the Eocene. Rapid speciation events of each clade from the Late Miocene to the Pliocene correspond to the timing of the geologic acceleration of the Qinghai-Tibetan Plateau. Interestingly, we found evidence for positive selection acting on the protein coding genes in the mitochondrial genomes of the “morphologically specialized” clade, implying a possible genetic basis for high altitude adaptation in this derived lineage of cypriniform fishes.

The genomes of birds and nonavian reptiles (Reptilia) are critical for understanding genome evolution in mammals and amniotes generally. Despite decades of study at the chromosomal and single-gene levels, and the evidence for great diversity in genome size, karyotype, and sex chromosome diversity, reptile genomes are virtually unknown in the comparative genomics era. The recent sequencing of the chicken and zebra finch genomes, in conjunction with genome scans and the online publication of the Anolis lizard genome, has begun to clarify the events leading from an ancestral amniote genome—predicted to be large and to possess a diverse repeat landscape on par with mammals and a birdlike sex chromosome system—to the small and highly streamlined genomes of birds. Reptilia exhibit a wide range of evolutionary rates of different subgenomes and, from isochores to mitochondrial DNA, provide a critical contrast to the genomic paradigms established in mammals.

Phylogenomics research integrating established principles of systematic biology and taking advantage of the wealth of DNA sequences being generated by genome science holds promise for answering long-standing evolutionary questions with orders of magnitude more primary data than in the past. Although it is unrealistic to expect whole-genome initiatives to proceed rapidly for commercially unimportant species such as reptiles, practical approaches utilizing genomic libraries of large-insert clones pave the way for a phylogenomics of species that are nevertheless essential for testing evolutionary hypotheses within a phylogenetic framework. This chapter reviews the case for adopting genome-enabled approaches to evolutionary studies and outlines a program for using bacterial artificial chromosome (BAC) libraries or plasmid libraries as a basis for completing "genome scans" of reptiles. We have used BACs to close a critical gap in the genome database for Reptilia, the sister group of mammals, and present the methodological approaches taken to achieve this as a guideline for designing similar comparative studies. In addition, we provide a detailed step-by-step protocol for BAC-library screening and shotgun sequencing of specific clones containing target genes of evolutionary interest. Taken together, the genome scanning and shotgun sequencing techniques offer complementary diagnostic potential and can substantially increase the scale and power of analyses aimed at testing evolutionary hypotheses for nonmodel species.

Phylogenomics research integrating established principles of systematic biology and taking advantage of the wealth of DNA sequences being generated by genome science holds promise for answering long-standing evolutionary questions with orders of magnitude more primary data than in the past. Although it is unrealistic to expect whole-genome initiatives to proceed rapidly for commercially unimportant species such as reptiles, practical approaches utilizing genomic libraries of large-insert clones pave the way for a phylogenomics of species that are nevertheless essential for testing evolutionary hypotheses within a phylogenetic framework. This chapter reviews the case for adopting genome-enabled approaches to evolutionary studies and outlines a program for using bacterial artificial chromosome (BAC) libraries or plasmid libraries as a basis for completing "genome scans" of reptiles. We have used BACs to close a critical gap in the genome database for Reptilia, the sister group of mammals, and present the methodological approaches taken to achieve this as a guideline for designing similar comparative studies. In addition, we provide a detailed step-by-step protocol for BAC-library screening and shotgun sequencing of specific clones containing target genes of evolutionary interest. Taken together, the genome scanning and shotgun sequencing techniques offer complementary diagnostic potential and can substantially increase the scale and power of analyses aimed at testing evolutionary hypotheses for nonmodel species.

The emerging field of phylogenomics is influencing both the amount and type of characters being brought to bear on long-standing problems in systematic biology. Moreover, the proliferation of sequence information from genome projects in concert with the development of new informatics tools is widening access to comparative data on retroelements to a broad cross section of investigators. Motivated by this, the Society of Systematic Biologists sponsored a symposium entitled "Genome Analysis and the Molecular Systematics of Retroelements," and the resulting papers illustrate this theme of new discoveries and cover three basic areas of research: (i) the taxonomic distribution and phylogenetic structure of families of retroelements; (II) the use of SINE and LINE insertions for phylogenetic inference; and (III) the informatics and classification of repetitive elements. Contributions of each article are briefly discussed in this context and particularly fruitful directions for future research illuminated by results of this symposium are reviewed.

We report results of a megabase-scale phylogenomic analysis of the Reptilia, the sister group of mammals. Large-scale end-sequence scanning of genomic clones of a turtle, alligator, and lizard reveals diverse, mammal-like landscapes of retroelements and simple sequence repeats (SSRs) not found in the chicken. Several global genomic traits, including distinctive phylogenetic lineages of CR1-like long interspersed elements (LINEs) and a paucity of A-T rich SSRs, characterize turtles and archosaur genomes, whereas higher frequencies of tandem repeats and a lower global GC content reveal mammal-like features in Anolis. Nonavian reptile genomes also possess a high frequency of diverse and novel 50-bp unit tandem duplications not found in chicken or mammals. The frequency distributions of approximately 65,000 8-mer oligonucleotides suggest that rates of DNA-word frequency change are an order of magnitude slower in reptiles than in mammals. These results suggest a diverse array of interspersed and SSRs in the common ancestor of amniotes and a genomic conservatism and gradual loss of retroelements in reptiles that culminated in the minimalist chicken genome. The sequences reported in this paper have been deposited in the GenBank database (accession nos. CZ 250707-CZ 257443 and DX 390731-DX 389174).

The value of short interspersed elements (SINEs) for diagnosing common ancestry is being expanded to examine the differential sorting of lineages through the course of speciation events. Because most SINEs are neutral markers of identical descent, are not precisely excised from the genome and have a known ancestral condition, they are advantageous for reconciling gene trees and species trees with minimal phylogenetic error. A population perspective on SINE evolution combined with coalescence theory provides a context for investigating the phenomenon of ancestral polymorphism and its role in producing incongruent SINE insertion patterns among multiple loci. Studies of human Alu repeats demonstrate the value of young polymorphic SINEs for assessing human genomic diversity and tracking ancient demographics of human populations, whereas incongruent insertion patterns revealed by older fixed SINE loci, such as those in African cichlid fishes, contain information that might help identify ancient radiations that are otherwise obscured by accumulated mutations in sequence data. Here, we review the utility of retroposons for inferring common ancestry, discuss limits to the method, and clarify confusion by providing examples from the literature that illustrate how discordant multi-locus insertion patterns of retroelements can indicate lineage-sorting events that should not be misinterpreted as phylogenetic noise.

In the 14 years since the first higher-level bird phylogenies based on DNA sequence data, avian phylogenetics has witnessed the advent and maturation of the genomics era, the completion of the chicken genome and a suite of technologies that promise to add considerably to the agenda of avian phylogenetics. In this review, we summarize current approaches and data characteristics of recent higher-level bird studies and suggest a number of as yet untested molecular and analytical approaches for the unfolding tree of life for birds. A variety of comparative genomics strategies, including adoption of objective quality scores for sequence data, analysis of contiguous DNA sequences provided by large-insert genomic libraries, and the systematic use of retroposon insertions and other rare genomic changes all promise an integrated phylogenetics that is solidly grounded in genome evolution. The avian genome is an excellent testing ground for such approaches because of the more balanced representation of single-copy and repetitive DNA regions than in mammals. Although comparative genomics has a number of obvious uses in avian phylogenetics, its application to large numbers of taxa poses a number of methodological and infrastructural challenges, and can be greatly facilitated by a ‘community genomics’ approach in which the modest sequencing throughputs of single PI laboratories are pooled to produce larger, complementary datasets. Although the polymerase chain reaction era of avian phylogenetics is far from complete, the comparative genomics era—with its ability to vastly increase the number and type of molecular characters and to provide a genomic context for these characters—will usher in a host of new perspectives and opportunities for integrating genome evolution and avian phylogenetics.

Advances in genome sciences are demonstrating the dynamic nature of noncoding DNA regions, which are comprised largely of repetitive elements with no apparent function. Retroposons are one class of mobile genetic elements that amplify and move about the genome via a copy-and-paste mechanism that employs an RNA intermediate. Short and long interspersed elements (SINEs and LINEs, respectively) are types of retroposons of particular interest because of their active role in shaping the architecture of genomes and their diagnostic value as evolutionary markers for studies of phylogeny and population biology. Although the use of SINEs and LINEs for molecular systematic studies is proliferating, a comprehensive laboratory protocol that explicitly outlines how to isolate and characterize retroposons for systematic studies in a detailed, step-by-step fashion has been lacking. The present chapter addresses this gap in the literature by focusing on the strategy for isolating new SINEs from a genomic library, the screening process, the sequencing and characterization of clones into subfamilies, quantification of copy number in host taxa, and the critical diagnosis of phylogenetically informative SINE and LINE insertion patterns. Practical limits to the method are discussed in relation to sampling design, systematic character theory, and the empirical distribution of elements observed in eukaryotic lineages. Major steps in the experimental process are illustrated with case examples from a diversity of taxonomic groups and by published results in the molecular biology and systematics literature.

Advances in genome sciences are demonstrating the dynamic nature of noncoding DNA regions, which are comprised largely of repetitive elements with no apparent function. Retroposons are one class of mobile genetic elements that amplify and move about the genome via a copy-and-paste mechanism that employs an RNA intermediate. Short and long interspersed elements (SINEs and LINEs, respectively) are types of retroposons of particular interest because of their active role in shaping the architecture of genomes and their diagnostic value as evolutionary markers for studies of phylogeny and population biology. Although the use of SINEs and LINEs for molecular systematic studies is proliferating, a comprehensive laboratory protocol that explicitly outlines how to isolate and characterize retroposons for systematic studies in a detailed, step-by-step fashion has been lacking. The present chapter addresses this gap in the literature by focusing on the strategy for isolating new SINEs from a genomic library, the screening process, the sequencing and characterization of clones into subfamilies, quantification of copy number in host taxa, and the critical diagnosis of phylogenetically informative SINE and LINE insertion patterns. Practical limits to the method are discussed in relation to sampling design, systematic character theory, and the empirical distribution of elements observed in eukaryotic lineages. Major steps in the experimental process are illustrated with case examples from a diversity of taxonomic groups and by published results in the molecular biology and systematics literature.

Goats (Capra hircus) are one of the oldest domesticated species, and they are kept all over the world as an essential resource for meat, milk, and fiber. Although recent archeological and molecular biological studies suggested that they originated in West Asia, their domestication processes such as the timing of population expansion and the dynamics of their selection pressures are little known. With the aim of addressing these issues, the nearly complete mitochondrial protein-encoding genes were determined from East, Southeast, and South Asian populations. Our coalescent time estimations suggest that the timing of their major population expansions was in the Late Pleistocene and significantly predates the beginning of their domestication in the Neolithic era (≈10,000 years ago). The ω (ratio of non-synonymous rate/synonymous substitution rate) for each lineage was also estimated. We found that the ω of the globally distributed haplogroup A which is inherited by more than 90% of goats examined, turned out to be extremely low, suggesting that they are under severe selection pressure probably due to their large population size. Conversely, the ω of the Asian-specific haplogroup B inherited by about 5% of goats was relatively high. Although recent molecular studies suggest that domestication of animals may tend to relax selective constraints, the opposite pattern observed in our goat mitochondrial genome data indicates the process of domestication is more complex than may be presently appreciated and cannot be explained only by a simple relaxation model.

Background The teleost order Lophiiformes, commonly known as the anglerfishes, contains a diverse array of marine fishes, ranging from benthic shallow-water dwellers to highly modified deep-sea midwater species. They comprise 321 living species placed in 68 genera, 18 families and 5 suborders, but approximately half of the species diversity is occupied by deep-sea ceratioids distributed among 11 families. The evolutionary origins of such remarkable habitat and species diversity, however, remain elusive because of the lack of fresh material for a majority of the deep-sea ceratioids and incompleteness of the fossil record across all of the Lophiiformes. To obtain a comprehensive picture of the phylogeny and evolutionary history of the anglerfishes, we assembled whole mitochondrial genome (mitogenome) sequences from 39 lophiiforms (33 newly determined during this study) representing all five suborders and 17 of the 18 families. Sequences of 77 higher teleosts including the 39 lophiiform sequences were unambiguously aligned and subjected to phylogenetic analysis and divergence time estimation. Results Partitioned maximum likelihood analysis confidently recovered monophyly for all of the higher taxa (including the order itself) with the exception of the Thaumatichthyidae (Lasiognathus was deeply nested within the Oneirodidae). The mitogenomic trees strongly support the most basal and an apical position of the Lophioidei and a clade comprising Chaunacoidei + Ceratioidei, respectively, although alternative phylogenetic positions of the remaining two suborders (Antennarioidei and Ogcocephaloidei) with respect to the above two lineages are statistically indistinguishable. While morphology-based intra-subordinal relationships for relatively shallow, benthic dwellers (Lophioidei, Antennarioidei, Ogcocephaloidei, Chaunacoidei) are either congruent with or statistically indistinguishable from the present mitogenomic tree, those of the principally deep-sea midwater dwellers (Ceratioidei) cannot be reconciled with the molecular phylogeny. A relaxed molecular-clock Bayesian analysis of the divergence times suggests that all of the subordinal diversifications have occurred during a relatively short time period between 100 and 130 Myr ago (early to mid Cretaceous). Conclusions The mitogenomic analyses revealed previously unappreciated phylogenetic relationships among the lophiiform suborders and ceratioid familes. Although the latter relationships cannot be reconciled with the earlier hypotheses based on morphology, we found that simple exclusion of the reductive or simplified characters can alleviate some of the conflict. The acquisition of novel features, such as male dwarfism, bioluminescent lures, and unique reproductive modes allowed the deep-sea ceratioids to diversify rapidly in a largely unexploited, food-poor bathypelagic zone (200-2000 m depth) relative to the other lophiiforms occurring in shallow coastal areas.

To explore the evolutionary nature of the salmonid mitochondrial DNA (mtDNA) control region (D-loop) and its utility for inferring phylogenies, the entire region was sequenced from all eight species of anadromous Pacific salmon, genus Oncorhynchus , the Atlantic salmon, Salmo salar , and the Arctic grayling, Thymallus arcticus . A comparison of aligned sequences demonstrates that the generally conserved sequence elements that have been previously reported for other vertebrates are maintained in these primitive teleost fishes. Results reveal a significantly nonrandom distribution of nucleotide substitutions, insertions, and deletions that suggests that portions of the salmonid D-loop may be under differential selective constraints and that most of the control region of these fishes may evolve at a rate similar to that of the remainder of their mtDNA genomes. Maximum likelihood and Fitch parsimony analyses of 9 kb of aligned salmonid sequence data give evolutionary trees of identical topology. These results are consistent with previous molecular studies of a limited number of salmonid taxa and with more comprehensive, classical analyses of salmonid evolution. Predictions from these data, based on a molecular clock assumption for the mtDNA control region, are also consistent with fossil evidence that suggests that species of Oncorhynchus could be as old as the Middle Pliocene and would have thus given rise to the extant Pacific salmon prior to about 5 or 6 million years ago.