Variants in Deleted in AZoospermia-Like (DAZL) are correlated with reproductive parameters in men and women

Qualitative and quantitative defects in human germ cell production that result in infertility are common and determined at least in part by genetic factors [Matzuk and Lamb, Nat Cell Biol 4(Suppl):s41–s49, 2002]. Yet, very few genes that are associated with germ cell defects in humans have been identified. In this study, we examined whether variants of the Deleted in AZoospermia-Like (DAZL) gene are associated with measures of germ cell production in three distinct populations of men and women. We identified 95 sequence variants in DAZL and further analyzed twelve single nucleotide polymorphisms (SNPs) that were present across ethnicities. We found that seven of the twelve SNPs were associated with at least one of the parameters studied (age at premature ovarian failure or menopause, total sperm count, or total motile sperm count). Surprisingly, many alleles exhibited opposing effects in men and women, which may be a result of different genetic requirements in male and female germ cells. Single SNP and haplotype analysis suggested that SNPs in the DAZL gene may act jointly to affect common reproductive characteristics in the human population. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users. Joyce Y. Tung and Mitchell P. Rosen have contributed equally     

New Species of Closely Related Endosymbiotic Dinoflagellates in the Greater Caribbean have Niches Corresponding to Host Coral Phylogeny

Symbiotic dinoflagellates in the genus Breviolum (formerly Symbiodinium Clade B) dominate coral communities in shallow waters across the Greater Caribbean. While some formally described species exist, mounting genetic, and ecological evidence indicate that numerous more comprise this genus, many of which are closely related. To test this, colonies of common reef‐building corals were sampled across a large geographical range. Phylogenetic and population genetic markers then used to examine evolutionary divergence and delineate boundaries of genetic recombination. Three new candidate species were distinguished by fixed differences in nucleotide sequences from nuclear and chloroplast DNA. Population connectivity was evident within each lineage over thousands of kilometers, however, substantial genetic structure persisted between lineages co‐occurring within sampling locations, signifying reproductive isolation. While geographically widespread with overlapping distributions, each species is ecologically distinct, exhibiting specific mutualisms with phylogenetically distinct coral hosts. Moreover, significant differences in mean cell sizes provide some morphological evidence substantiating formal species distinctions. In providing evidence that satisfies the biological, phylogenetic, ecological, and morphological species concepts, we classify and formally name Breviolum faviinorum n. sp., primarily associated with Caribbean corals belonging to the Caribbean subfamily Faviinae; B. meandrinium n. sp., associated with corals belonging to the family Meandrinidae; and B. dendrogyrum n. sp., a symbiont harbored exclusively by the threatened coral Dendrogyra cylindrus. These findings support the primary importance of niche diversification (i.e. host habitat) in the speciation of symbiotic dinoflagellates.     

ALLOPATRIC DIVERGENCE AND SPECIATION IN CORAL REEF FISH: THE THREE‐SPOT DASCYLLUS,DASCYLLUS TRIMACULATUS,SPECIES COMPLEX

Long pelagic larval phases and the absence of physical barriers impede rapid speciation and contrast the high diversity observed in marine ecosystems such as coral reefs. In this study, we used the three‐spot dascyllus (Dascyllus trimaculatus) species complex to evaluate speciation modes at the spatial scale of the Indo‐Pacific. The complex includes four recognized species and four main color morphs that differ in distribution. Previous studies of the group using mitochondrial DNA revealed a noncongruence between color morphs and genetic groupings; with two of the color morphs grouped together and one color morph separated into three clades. Using extensive geographic sampling of 563 individuals and a combination of mitochondrial DNA sequences and 13 nuclear microsatellites, we defined population/species boundaries and inferred different speciation modes. The complex is composed of seven genetically distinct entities, some of which are distinct morphologically. Despite extensive dispersal abilities and an apparent lack of barriers, observed genetic partitions are consistent with allopatric speciation. However, ecological pressure, assortative mating, and sexual selection, were likely important during periods of geographical isolation. This study therefore suggests that primarily historical factors later followed by ecological factors caused divergence and speciation in this group of coral reef fish.     

Genetic Analysis of Bemisia (Hemiptera: Aleyrodidae) Populations by Isoelectric Focusing Electrophoresis

Twenty-one whitefly populations in the genus Bemisia were evaluated for genetic variation at 3 allozyme loci. Nine of the 22 populations that exhibited polymorphic loci were subjected to allozyme analysis using a minimum of 10 enzymes, representing 10 to 14 distinct loci. Among those nine variants examined, calculated genetic distances ranged between 0.03 and 0.52, with three main groups emerging from the analysis. One group comprised two closely related Western Hemisphere variants of B. tabaci: type A from California, United States and a geographically proximal population from Culiacan, Mexico. A second cluster contained five collections previously identified as B. tabaci type B and Bemisia argentifolii, while a third group contained a single population from Benin, Africa. The latter two groups were grouped separately from New World populations and are thought to have a recent origin in the Eastern Hemisphere.     

Many corals host thermally resistant symbionts in high-temperature habitat

Physiologically distinct lines of dinoflagellate symbionts, Symbiodinium spp., may confer distinct thermal tolerance thresholds on their host corals. Therefore, if a coral can alternately host distinct symbionts, changes in their Symbiodinium communities might allow corals to better tolerate increasing environmental temperatures. However, researchers are currently debating how commonly coral species can host different symbiont types. We sequenced chloroplast 23 s rDNA from the Symbiodinium communities of nine reef-building coral species across two thermally distinct lagoon pools separated by ~500 m. The hotter of these pools reaches 35°C in the summer months, while the other pool’s maximum temperature is 1.5°C cooler. Across 217 samples from nine species, we found a single haplotype in both Symbiodinium clades A and D, but four haplotypes in Symbiodinium clade C. Eight of nine species hosted a putatively thermally resistant member of clade D Symbiodinium at least once, one of which hosted this clade D symbiont exclusively. Of the remaining seven that hosted multiple Symbiodinium types, six species showed higher proportions of the clade D symbiont in the hotter pool. Average percentage rise in the frequency of the clade D symbiont from the hotter to cooler pool was 52% across these six species. Even though corals hosted members of both the genetically divergent clades D and C Symbiodinium, some showed patterns of host–symbiont specificity within clade C. Both Acropora species that hosted clade C exclusively hosted a member of sub-clade C2, while all three Pocillopora species hosted a member of sub-clade C1 (sensu van Oppen et al. 2001). Our results suggest that coral–algal symbioses often conform to particular temperature environments through changes in the identity of the algal symbiont.     

A genomic assessment of species boundaries and hybridization in a group of highly polymorphic anoles (distichus species complex)

Delimiting young species is one of the great challenges of systematic biology, particularly when the species in question exhibit little morphological divergence. Anolis distichus, a trunk anole with more than a dozen subspecies that are defined primarily by dewlap color, may actually represent several independent evolutionary lineages. To test this, we utilized amplified fragment length polymorphisms (AFLP) genome scans and genetic clustering analyses in conjunction with a coalescent‐based species delimitation method. We examined a geographically widespread set of samples and two heavily sampled hybrid zones. We find that genetic divergence is associated with a major biogeographic barrier, the Hispaniolan paleo‐island boundary, but not with dewlap color. Additionally, we find support for hypotheses regarding colonization of two Hispaniolan satellite islands and the Bahamas from mainland Hispaniola. Our results show that A. distichus is composed of seven distinct evolutionary lineages still experiencing a limited degree of gene flow. We suggest that A. distichus merits taxonomic revision, but that dewlap color cannot be relied upon as the primary diagnostic character.     

Photobiology of Symbiodinium revisited: bio-physical and bio-optical signatures

Light is often the most abundant resource within the nutrient-poor waters surrounding coral reefs. Consequently, zooxanthellae (Symbiodinium spp.) must continually photoacclimate to optimise productivity and ensure coral success. In situ coral photobiology is becoming dominated by routine assessments using state-of-the-art non-invasive bio-optical or chlorophyll a fluorescence (bio-physical) techniques. Multiple genetic types of Symbiodinium are now known to exist; however, little focus has been given as to how these types differ in terms of characteristics that are observable using these techniques. Therefore, this investigation aimed to revisit and expand upon a pivotal study by Iglesias-Prieto and Trench (1994) by comparing the photoacclimation characteristics of different Symbiodinium types based on their bio-physical (chlorophyll a fluorescence, reaction centre counts) and bio-optical (optical absorption, pigment concentrations) ‘signatures’. Signatures described here are unique to Symbiodinium type and describe phenotypic responses to set conditions, and hence are not suitable to describe taxonomic structure of in hospite Symbiodinium communities. In this study, eight Symbiodinium types from clades and sub-clades (A–B, F) were grown under two PFDs (Photon Flux Density) and examined. The photoacclimation response by Symbiodinium was highly variable between algal types for all bio-physical and for many bio-optical measurements; however, a general preference to modifying reaction centre content over effective antennae-absorption was observed. Certain bio-optically derived patterns, such as light absorption, were independent of algal type and, when considered per photosystem, were matched by reaction centre stoichiometry. Only by better understanding genotypic and phenotypic variability between Symbiodinium types can future studies account for the relative taxonomic and physiological contribution by Symbiodinium to coral acclimation.     

Microsatellite Analysis of Japanese Sea Cucumber, Stichopus (Apostichopus) japonicus, Supports Reproductive Isolation in Color Variants

The genetic relationship among the three color variants (Red, Green, and Black) of the Japanese sea cucumber, S. japonicus, was investigated using 11 microsatellite markers. Genetic differentiation testing among the three sympatric color types showed the strong heterogeneity of Red (p < 0.001), while no significant difference was observed between Green and Black (p = 0.301 to 0.961). UPGMA trees constructed from 10 sample lots from 5 localities showed two distinct clusters, one from the Red types and the other from the Green and Black types. In addition, the sympatric Green and Black formed one subcluster with strong bootstrap support at each locality. These results indicate the separate species status of Red and the other color types, and also support the population identity of sympatric Green and Black.     

Asexual reproduction in bad times? The case of Cladocora caespitosa in the eastern Mediterranean Sea

We analysed the patterns of genetic variability of eastern Mediterranean populations of the scleractinian coral Cladocora caespitosa, from the Aegean and Levantine seas, using 19 polymorphic microsatellite loci, 11 of which were newly characterized. The observed genetic pattern reflects a scenario of isolation by environment: F_ST comparisons showed a higher degree of genetic differentiation between the two Cypriot populations that are separated by only 11 km than between these two Levantine populations and the Aegean population in Greece, which are separated by 1300 km. We hypothesize that local-scale oceanographic factors influenced the dispersal of planulae between the geographically close populations, playing a crucial role in the genetic structure of this coastal coral. Yet, despite being characterized as a species with limited dispersal and high self-recruitment, large-scale migration does eventually occur as first-generation migrants were identified between the most distant populations. In line with previous findings of reproductive plasticity in C. caespitosa, we also found localized differences in reproduction mode (sexual vs. asexual) within a geographically limited context. Several individuals were identified as clones, indicating the predominance of asexual reproduction in one of the Cypriot populations. We interpret this predominance either as a direct response to or as an indirect consequence of perturbations suffered by this C. caespitosa population. These perturbations are caused by unfavourable environmental conditions that threatened local survival, in particular water temperature changes and windstorm swells. Asexual reproduction may be a mechanism used by C. caespitosa to counteract mortality events and recolonize devastated areas, and likely accounts for the occasional high levels of clonality and low levels of genetic diversity. Local adaptations such as these should therefore be considered in conservation and management strategies to maintain and preserve the gene pool of this endangered species.

     

Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia

Sponges are among the most species‐rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model‐based approach. Based on sequence data from one mitochondrial (COI), one ribosomal (28S), and two single‐copy nuclear protein‐coding genes, we found evolutionarily distinct lineages were not concordant with current species designations in Callyspongia. While C. fallax, C. tenerrima, and C. plicifera were reciprocally monophyletic, four taxa with different morphologies (C. armigera, C. longissima, C. eschrichtii, and C. vaginalis) formed a monophyletic group and genetic distances among these taxa overlapped distances within them. A model‐based method of species delimitation supported collapsing these four into a single evolutionary lineage. Variation in spicule size among these four taxa was partitioned geographically, not by current species designations, indicating that in Callyspongia, these key taxonomic characters are poor indicators of genetic differentiation. Taken together, our results suggest a complex relationship between morphology and species boundaries in sponges.     

Positive genetic associations among fitness traits support evolvability of a reef‐building coral under multiple stressors

Climate change threatens organisms in a variety of interactive ways that requires simultaneous adaptation of multiple traits. Predicting evolutionary responses requires an understanding of the potential for interactions among stressors and the genetic variance and covariance among fitness‐related traits that may reinforce or constrain an adaptive response. Here we investigate the capacity of Acropora millepora, a reef‐building coral, to adapt to multiple environmental stressors: rising sea surface temperature, ocean acidification, and increased prevalence of infectious diseases. We measured growth rates (weight gain), coral color (a proxy for Symbiodiniaceae density), and survival, in addition to nine physiological indicators of coral and algal health in 40 coral genets exposed to each of these three stressors singly and combined. Individual stressors resulted in predicted responses (e.g., corals developed lesions after bacterial challenge and bleached under thermal stress). However, corals did not suffer substantially more when all three stressors were combined. Nor were trade‐offs observed between tolerances to different stressors; instead, individuals performing well under one stressor also tended to perform well under every other stressor. An analysis of genetic correlations between traits revealed positive covariances, suggesting that selection to multiple stressors will reinforce rather than constrain the simultaneous evolution of traits related to holobiont health (e.g., weight gain and algal density). These findings support the potential for rapid coral adaptation under climate change and emphasize the importance of accounting for corals’ adaptive capacity when predicting the future of coral reefs.     

Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants

Detailed information about the geographic distribution of genetic and genomic variation is necessary to better understand the organization and structure of biological diversity. In particular, spatial isolation within species and hybridization between them can blur species boundaries and create evolutionary relationships that are inconsistent with a strictly bifurcating tree model. Here, we analyse genome‐wide DNA sequence and genetic ancestry variation in Lycaeides butterflies to quantify the effects of admixture and spatial isolation on how biological diversity is organized in this group. We document geographically widespread and pervasive historical admixture, with more restricted recent hybridization. This includes evidence supporting previously known and unknown instances of admixture. The genome composition of admixed individuals varies much more among than within populations, and tree‐ and genetic ancestry‐based analyses indicate that multiple distinct admixed lineages or populations exist. We find that most genetic variants in Lycaeides are rare (minor allele frequency <0.5%). Because the spatial and taxonomic distributions of alleles reflect demographic and selective processes since mutation, rare alleles, which are presumably younger than common alleles, were spatially and taxonomically restricted compared with common variants. Thus, we show patterns of genetic variation in this group are multifaceted, and we argue that this complexity challenges simplistic notions concerning the organization of biological diversity into discrete, easily delineated and hierarchically structured entities.     

Phylogenetic relationship of two <Emphasis Type="Italic">Mola</Emphasis> sunfishes (Tetraodontiformes: Molidae) occurring around the coast of Japan,with notes on their geographical distribution and morphological characteristics

Phylogenetic analyses were conducted using complete nucleotide sequences of the D-loop in the mitochondrial genome of Mola specimens, collected mainly in Japanese waters, to clarify the genetic features and distribution patterns of Mola sunfishes. Two significantly distinct groups (designated A and B) were present in the genus, with a considerable net nucleotide sequence divergence between the two (8.4%). The two groups occurred sympatrically around the Japanese coast, as previously suggested by Sagara et al. (2005). Group A occurred mostly on the Pacific coast of eastern Japan, while group B was widely distributed along the Kuroshio Current, strongly suggesting different migration routes for each group. The morphological characteristics of the two group specimens were differentiated via the head bump, body proportions and shape of the clavus. Through the addition of Mola sequence data taken from outside Japan to our phylogenetic analyses, three independent groups, including groups A and B, were found, each with a wide geographical distribution, which suggests the presence of at least three independent species within the genus Mola.     

Male and female contributions to behavioral isolation in darters as a function of genetic distance and color distance

Determining which reproductive isolating barriers arise first between geographically isolated lineages is critical to understanding allopatric speciation. We examined behavioral isolation among four recently diverged allopatric species in the orangethroat darter clade (Etheostoma: Ceasia). We also examined behavioral isolation between each Ceasia species and the sympatric rainbow darter Etheostoma caeruleum. We asked (1) is behavioral isolation present between allopatric Ceasia species, and how does this compare to behavioral isolation with E. caeruleum, (2) does male color distance and/or genetic distance predict behavioral isolation between species, and (3) what are the relative contributions of female choice, male choice, and male competition to behavioral isolation? We found that behavioral isolation, genetic differentiation, and male color pattern differentiation were present between allopatric Ceasia species. Males, but not females, discerned between conspecific and heterospecific mates. Males also directed more aggression toward conspecific rival males. The high levels of behavioral isolation among Ceasia species showed no obvious pattern with genetic distance or male color distance. However, when the E. caeruleum was included in the analysis, an association between male aggression and male color distance was apparent. We discuss the possibility that reinforcement between Ceasia and E. caeruleum is driving behavioral isolation among allopatric Ceasia species.     

<Emphasis Type="Italic">Tarsius wallacei</Emphasis>: A New Tarsier Species from Central Sulawesi Occupies a Discontinuous Range

On the basis of distinguishing characteristics of various genetic markers, pelage color, tail tuft, and vocalizations, we describe a new species of the genus Tarsius Storr 1780. The new taxon Tarsius wallacei sp. nov. occupies a disjunct range in Central Sulawesi, Indonesia. The two isolated populations differ significantly in body size, but are alike in color, tail tuft dimensions, vocalizations, and genetic composition. Morphologically, the new species is similar to other Sulawesi lowland tarsiers. In the field, it can be distinguished from its congeners via a characteristic duet song and its yellow-brown pelage coloration and a copper-colored throat. Genetic analyses prove Y-chromosomal and mitochondrial DNA sequences and also microsatellite allele frequencies to be absolutely diagnostic.     

Ethnic variation in vitamin D-binding protein (GC): a review of isoelectric focusing studies in human populations

Summary Since the discovery in 1977 that the GC1 gene could be resolved into two common subcomponents on an isoelectric focusing (IEF) gel, a large number of ethnic groups have been screened to analyze the extent of genetic variation in human populations. Using the IEF technique, approximately 50,000 individuals from 160 different populations have been tested for the GC polymorphism. A marked variation in common GC suballele frequencies in different geographic areas seems to correlate with skin pigmentation and intensity of sun light. Pigmented (black) and keratinized (yellowish) skin type populations have a relatively high frequency of the GC ^*IF allele as compared to white skin populations. By comparison non-pigmented and non-keratinized white skin populations are generally characterized by having the maximum values of the GC ^*IS allele. The anthropologic significance of the GC locus has been enhanced further by detecting additional unique GC variants which provide useful information about evolutionary links between different populations. However, the presence of some electrophoretically identical unique variants in genetically and geographically distinct populations demand further investigation of these allelic variants to shed more light on their origins.     

Intracolonial genetic variation in the scleractinian coral Seriatopora hystrix

In recent years, increasing numbers of studies revealed intraorganismal genetic variation, primarily in modular organisms like plants or colonial marine invertebrates. Two underlying mechanisms are distinguished: Mosaicism is caused by somatic mutation, whereas chimerism originates from allogeneic fusion. We investigated the occurrence of intracolonial genetic variation at microsatellite loci in five natural populations of the scleractinian coral Seriatopora hystrix on the Great Barrier Reef. This coral is a widely distributed, brooding species that is at present a target of intensive population genetic research on reproduction and dispersal patterns. From each of 155 S. hystrix colonies, either two or three samples were genotyped at five or six loci. Twenty-seven (~17%) genetically heterogeneous colonies were found. Statistical analyses indicated the occurrence of both mosaicism and chimerism. In most cases, intracolonial variation was found only at a single allele. Our analyses suggest that somatic mutations present a major source of genetic heterogeneity within a single colony. Moreover, we observed large, apparently stable chimeric colonies that harbored clearly distinct genotypes and contrast these findings with the patterns typically observed in laboratory-based experiments. We discuss the error that mosaicism and chimerism introduce into population genetic analyses.     

W14/15 esterase gene haplotype can be a genetic landmark of cultivars and species of the genus <Emphasis Type="Italic">Gentiana</Emphasis> L

We have identified multiple alleles for a single gene termed W14/15. This gene encodes closely related but not identical proteins W14 and W15 that accumulate in overwinter buds of Gentiana triflora (Takahashi et al. in Breed Sci 56:39–46, 2006; Hikage et al. in Mol Genet Genomics 278:95–104, 2007). In this study, structural analysis of the W14/15 gene was carried out for 21 different gentian lines/cultivars consisting of 5 different species, to survey species- or line/cultivar-specific haplotypes. Within the samples examined, multiple variant forms were found. Those were categorized into seven major types (type I–VII) and ten subtypes based on the presence of three short insertion/deletion sites, three RFLP sites, and several SNP sites. Each line/cultivar had a distinct set of W14/15 gene variants for an allelic pair. Phylogenetic analysis showed that the W14/15 alleles cluster into groups that are characteristic of gentian species, i.e., G. triflora, G. scabra, G. pneumonanthe, G. septemfida and an unknown species other than the former four. In addition, within the same gentian species, different sets of haplotypes were found. Thus, the W14/15 alleles provide useful landmarks to resolve phylogenies of the genus or section Gentiana, as well as to analyze pedigree and breeding history of the cultivars derived from those Gentiana sp.