Microsatellite evidence for monogamy and sex-biased recombination in the Western Australian seahorse Hippocampus angustus

Nocturnal surveys of lined seahorses reveal increased densities and seasonal recruitment patterns

Although the nighttime ecology of organisms remains understudied, nocturnal surveys play an integral part in assessing fish assemblages and the selective forces shaping them. Eleuthera (Bahamas) contains an unusual population of lined seahorses (Hippocampus erectus) in an anchialine lake, possessing morphological characteristics distinct from those found in the ocean. Population surveys for seahorses and their potential predators were conducted at midnight and midday during wet and dry seasons, with belt transects perpendicular to the shoreline that increased in depth away from shore. Nocturnal surveys uncovered seahorse densities 259% higher than daytime transects on average. Sex ratios were consistently male-biased, and the frequency of animals from different reproductive categories varied significantly by time of day, with gravid males observed around the clock but females and nongravid males observed more often at night. Spatial and seasonal recruitment was detected for the first time in this species, with an increase in juveniles detected in the shallow ends of transects during dry season surveys. Juvenile recruitment is poorly understood across syngnathid fishes, so the detection of early recruits at night has broad implications for this fish family. Seahorses from all reproductive categories were perched significantly higher in the water column during the night regardless of their depth or season. Predator densities followed a similar pattern with higher densities observed at night, indicating that elevated nocturnal perch height may be a response to predator presence. However, the selective agents driving these nocturnal behaviors have yet to be identified. Considering H. erectus is listed on the IUCN Red List as "Vulnerable," the increase in nocturnal population size and the detection of juveniles has crucial implications for understanding their ecology, recruitment, and conservation.

Independent Evolution of Sex Chromosomes and Male Pregnancy-Related Genes in Two Seahorse Species

Unlike birds and mammals, many teleosts have homomorphic sex chromosomes, and changes in the chromosome carrying the sex-determining locus, termed "turnovers", are common. Recent turnovers allow studies of several interesting questions. One question is whether the new sex-determining regions evolve to become completely non-recombining, and if so, how and why. Another is whether (as predicted) evolutionary changes that benefit one sex accumulate in the newly sex-linked region. To study these questions, we analyzed the genome sequences of two seahorse species of the Syngnathidae, a fish group in which many species evolved a unique structure, the male brood pouch. We find that both seahorse species have XY sex chromosome systems, but their sex chromosome pairs are not homologs, implying that at least one turnover event has occurred. The Y-linked regions occupy 63.9% and 95.1% of the entire sex chromosome of the two species and do not exhibit extensive sequence divergence with their X-linked homologs. We find evidence for occasional recombination between the extant sex chromosomes that may account for their homomorphism. We argue that these Y-linked regions did not evolve by recombination suppression after the turnover, but by the ancestral nature of the low crossover rates in these chromosome regions. With such an ancestral crossover landscape, a turnover can instantly create an extensive Y-linked region. Finally, we test for adaptive evolution of male pouch-related genes after they became Y-linked in the seahorse.

Does the female seahorse still prefer her mating partner after a period of separation?

For species showing sexual monogamy, once one male and one female form a mating pair bond, they will be faithful to each other in subsequent breeding events. However, if their pair bond is broken for some reason, do they continue to prefer their partner when they come together again for mating? In other words, can the broken pair bond of sexually monogamous species be repaired? This is an interesting question but not yet well answered. To address this question, in the present study we used the lined seahorse (Hippocampus erectus), a typical sexually monogamous species, to study the partner preference of a female individual who experienced a complete separation followed by a reunion with her partner. Our main findings are as follows: (i) The female seahorse no longer prefers her partner after a separation, whether it is a former partner or a recent partner. No preference for partner-males may indicate that the broken pair bond cannot be repaired. (ii) The female seahorse maintains sexual fidelity to her partner in the absence of separation. However, once the health of her partner decreases, the female will switch mate, and her courtship with the new partner can take place during the pregnancy of her original partner. The first finding may provide insight into whether monogamous species still have an opportunity to reselect a new partner in the future to correct their poor choice once they have mated with a low-quality partner. The answer is that they can still gain an opportunity as long as the pair bonds with their current partners are broken. The second finding may reveal the conditions and timing at which a female seahorse switches her mate. These findings help us better understand the mating system of the seahorse H. erectus.

Female lined seahorses (Hippocampus erectus) recognize their mates based on olfactory cues

Recognition of mates from others is crucial for monogamous species to maintain their long-term pair bonds. The seahorse is widely recognized as a monogamous species, and its mate recognition cue is still not well understood. In the present study, we used the lined seahorse (Hippocampus erectus) as an experimental animal and investigated the effect of blocking olfactory, visual or behavioral (i.e., greeting) cues on mate recognition. Our results show that as long as the female seahorse can smell her mate, she will remain faithful to her mate and persistently select her mate as her next mating partner, regardless of whether the visual and/or behavioral cues between her and her mate are blocked. This finding implies that olfaction is a critical cue for a female seahorse to recognize her mate.

Diversity of Seahorse Species (Hippocampus spp.) in the International Aquarium Trade

Seahorses (Hippocampus spp.) are threatened as a result of habitat degradation and overfishing. They have commercial value as traditional medicine, curio objects, and pets in the aquarium industry. There are 48 valid species, 27 of which are represented in the international aquarium trade. Most species in the aquarium industry are relatively large and were described early in the history of seahorse taxonomy. In 2002, seahorses became the first marine fishes for which the international trade became regulated by CITES (Convention for the International Trade in Endangered Species of Wild Fauna and Flora), with implementation in 2004. Since then, aquaculture has been developed to improve the sustainability of the seahorse trade. This review provides analyses of the roles of wild-caught and cultured individuals in the international aquarium trade of various Hippocampus species for the period 1997–2018. For all species, trade numbers declined after 2011. The proportion of cultured seahorses in the aquarium trade increased rapidly after their listing in CITES, although the industry is still struggling to produce large numbers of young in a cost-effective way, and its economic viability is technically challenging in terms of diet and disease. Whether seahorse aquaculture can benefit wild populations will largely depend on its capacity to provide an alternative livelihood for subsistence fishers in the source countries. For most species, CITES trade records of live animals in the aquarium industry started a few years earlier than those of dead bodies in the traditional medicine trade, despite the latter being 15 times higher in number. The use of DNA analysis in the species identification of seahorses has predominantly been applied to animals in the traditional medicine market, but not to the aquarium trade. Genetic tools have already been used in the description of new species and will also help to discover new species and in various other kinds of applications.

Home range use in the West Australian seahorse Hippocampus subelongatus is influenced by sex and partner’s home range but not by body size or paired status

Genetic monogamy is the rule for many species of seahorse, including the West Australian seahorse Hippocampus subelongatus. In this paper, we revisit mark-recapture and genetic data of H. subelongatus, allowing a detailed characterization of movement distances, home range sizes and home range overlaps for each individual of known sex, paired status (paired or unpaired) and body size. As predicted, we find that females have larger home ranges and move greater distances compared to males. We also confirm our prediction that the home ranges of pair-bonded individuals (members of a pair known to reproduce together) overlap more on average than home ranges of randomly chosen individuals of the opposite or same sex. Both sexes, regardless of paired status, had home ranges that overlapped with, on average, 6–10 opposite-sex individuals. The average overlap area among female home ranges was significantly larger than the overlap among male home ranges, probably reflecting females having larger home ranges combined with a female biased adult sex ratio. Despite a prediction that unpaired individuals would need to move around to find a mate, we find no evidence that unpaired members of either sex moved more than paired individuals of the same sex. We also find no effect of body size on home range size, distance moved or number of other individuals with which a home range overlapped. These patterns of movement and overlap in home ranges among individuals of both sexes suggest that low mate availability is not a likely explanation for the maintenance of monogamy in the West Australian seahorse.

When more is not merrier: Using wild population dynamics to understand the effect of density on ex situ seahorse mating behaviors

Seahorses are considered one of the most iconic examples of a monogamous species in the animal kingdom. This study investigates the relationship between stocking density and mating and competitive behavior from the context of the field biology of the dwarf seahorse, Hippocampus zosterae (Jordan & Gilbert). Animals were housed in 38 liter tanks at a range of densities and sex ratios (from 2-8 animals per tank), and their reproductive and other social behaviors were monitored from tank introduction through copulation. At low tank densities and even sex ratios but comparatively high field densities, frequency of both mating and competitive behaviors was low in trials. A higher level of males in tanks across all densities increased competition, activity levels, and aggression leading to egg transfer errors and brood expulsion, resulting in lower reproductive success. Across seahorse species, mean and maximum wild densities were consistently lower than those used in ex situ breeding, with adult sex ratios that were significantly female biased. However, significant variation exists in wild seahorse densities across species, with higher densities detected in focal/mark recapture studies and on artificial habitat structures than reported with belt transect sampling techniques. Interchange of knowledge gained in both aquarium and wild contexts will allow us to better understand the biology of this genus, and improve reproduction in captivity. Interpreting ex situ reproductive behaviors of seahorses within various densities reported from natural populations will help us predict the impact of conservation efforts and increase the likelihood of long-term persistence of populations for this threatened genus.

A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data

The development of high-throughput sequencing technologies is dramatically increasing the use of single nucleotide polymorphisms (SNPs) across the field of genetics, but most parentage studies of wild populations still rely on microsatellites. We developed a bioinformatic pipeline for identifying SNP panels that are informative for parentage analysis from restriction site-associated DNA sequencing (RADseq) data. This pipeline includes options for analysis with or without a reference genome, and provides methods to maximize genotyping accuracy and select sets of unlinked loci that have high statistical power. We test this pipeline on small populations of Mexican gray wolf and bighorn sheep, for which parentage analyses are expected to be challenging due to low genetic diversity and the presence of many closely related individuals. We compare the results of parentage analysis across SNP panels generated with or without the use of a reference genome, and between SNPs and microsatellites. For Mexican gray wolf, we conducted parentage analyses for 30 pups from a single cohort where samples were available from 64% of possible mothers and 53% of possible fathers, and the accuracy of parentage assignments could be estimated because true identities of parents were known a priori based on field data. For bighorn sheep, we conducted maternity analyses for 39 lambs from five cohorts where 77% of possible mothers were sampled, but true identities of parents were unknown. Analyses with and without a reference genome produced SNP panels with ≥95% parentage assignment accuracy for Mexican gray wolf, outperforming microsatellites at 78% accuracy. Maternity assignments were completely consistent across all SNP panels for the bighorn sheep, and were 74.4% consistent with assignments from microsatellites. Accuracy and consistency of parentage analysis were not reduced when using as few as 284 SNPs for Mexican gray wolf and 142 SNPs for bighorn sheep, indicating our pipeline can be used to develop SNP genotyping assays for parentage analysis with relatively small numbers of loci.

Phylogenetic analysis and genetic structure of the seahorse, Hippocampus fuscus from the Arabian and Red Sea based on mitochondrial DNA sequences

The unique body morphology and specialized life history traits make seahorses excellent flagship species for many issues in marine conservation and biological evolution. In this study, the complete mitochondrial genome of Hippocampus fuscus was determined. Phylogenetic analyses showed that H. fuscus had a close genetic relationship to Hippocampus reidi, which give us a new insight into the speciation and dispersal among seahorse genus. A total of 843 base pairs of cytochrome b (Cytb) gene and a 646 base pairs of cytochrome oxidase I (COI) gene were obtained from 36 H. fuscus and 26 H. reidi from three populations. Population genetic analysis revealed a relatively high genetic diversity across the populations of H. fuscus compared with H. reidi. Neighbour-joining (NJ) tree of COI and Cytb gene sequences showed that H. fuscus haplotypes formed one cluster. The result of median-joining network of haplotypes based on COI and Cytb indicated a lack of structure in populations of H. fuscus. This study addressed the information about the evolution history and genetic structure of an Arabian seahorse H. fuscus, which provides insight into the genetic conservation and sustainable management for this species.

Why do some animals mate with one partner rather than many? A review of causes and consequences of monogamy

Why do some animals mate with one partner rather than many? Here, I investigate factors related to (i) spatial constraints (habitat limitation, mate availability), (ii) time constraints (breeding synchrony, length of breeding season), (iii) need for parental care, and (iv) genetic compatibility, to see what support can be found in different taxa regarding the importance of these factors in explaining the occurrence of monogamy, whether shown by one sex (monogyny or monandry) or by both sexes (mutual monogamy). Focusing on reproductive rather than social monogamy whenever possible, I review the empirical literature for birds, mammals and fishes, with occasional examples from other taxa. Each of these factors can explain mating patterns in some taxa, but not in all. In general, there is mixed support for how well the factors listed above predict monogamy. The factor that shows greatest support across taxa is habitat limitation. By contrast, while a need for parental care might explain monogamy in freshwater fishes and birds, there is clear evidence that this is not the case in marine fishes and mammals. Hence, reproductive monogamy does not appear to have a single overriding explanation, but is more taxon specific. Genetic compatibility is a promising avenue for future work likely to improve our understanding of monogamy and other mating patterns. I also discuss eight important consequences of reproductive monogamy: (i) parentage, (ii) parental care, (iii) eusociality and altruism, (iv) infanticide, (v) effective population size, (vi) mate choice before mating, (vii) sexual selection, and (viii) sexual conflict. Of these, eusociality and infanticide have been subject to debate, briefly summarised herein. A common expectation is that monogamy leads to little sexual conflict and no or little sexual selection. However, as reviewed here, sexual selection can be substantial under mutual monogamy, and both sexes can be subject to such selection. Under long-term mutual monogamy, mate quality is obviously more important than mate numbers, which in turn affects the need for pre-mating mate choice. Overall, I conclude that, despite much research on genetic mating patterns, reproductive monogamy is still surprisingly poorly understood and further experimental and comparative work is needed. This review identifies several areas in need of more data and also proposes new hypotheses to test.

De Novo Transcriptome Analysis of Two Seahorse Species (Hippocampus erectus and H. mohnikei) and the Development of Molecular Markers for Population Genetics

Seahorse conservation has been performed utilizing various strategies for many decades, and the deeper understanding of genomic information is necessary to more efficiently protect the germplasm resources of seahorse species. However, little genetic information about seahorses currently exists in the public databases. In this study, high-throughput RNA sequencing for two seahorse species, Hippocampus erectus and H. mohnikei, was carried out, and de novo assembly generated 37,506 unigenes for H. erectus and 36,113 unigenes for H. mohnikei. Among them, 17,338 (46.23%) unigenes for H. erectus and 17,900 (49.57%) for H. mohnikei were successfully annotated based on the information available from the public databases. Through comparing the unigenes of two seahorse species, 7,802 candidate orthologous genes were identified and 5,268 genes among them could be annotated. In addition, gene ontology analysis of two species was similarly performed on biological processes, cellular components, and molecular functions. Twenty-four and twenty-one unigenes in H. erectus and H. mohnikei were annotated in the biosynthesis of unsaturated fatty acids pathways, and both seahorses lacked the Δ12 and Δ15 desaturases. Total of 8,992 and 9,116 SSR loci were obtained from H. erectus and H. mohnikei unigenes, respectively. Dozens of SSR were developed and then applied to assess the population genetic diversity, as well as cross-amplified in a related species, H. trimaculatus. The HO and HE values of the tested populations for H. erectus, H. mohnikei, and H. trimaculatus were medium. These resources would facilitate the conservation of the species through a better understanding of the genomics and comparative genome analysis within the Hippocampus genus.

Discovery and characterization of single nucleotide polymorphisms in coho salmon, Oncorhynchus kisutch

Molecular population genetic analyses have become an integral part of ecological investigation and population monitoring for conservation and management. Microsatellites have been the molecular marker of choice for such applications over the last several decades, but single nucleotide polymorphism (SNP) markers are rapidly expanding beyond model organisms. Coho salmon (Oncorhynchus kisutch) is native to the north Pacific Ocean and its tributaries, where it is the focus of intensive fishery and conservation activities. As it is an anadromous species, coho salmon typically migrate across multiple jurisdictional boundaries, complicating management and requiring shared data collection methods. Here, we describe the discovery and validation of a suite of novel SNPs and associated genotyping assays which can be used in the genetic analyses of this species. These assays include 91 that are polymorphic in the species and one that discriminates it from a sister species, Chinook salmon. We demonstrate the utility of these SNPs for population assignment and phylogeographic analyses, and map them against the draft trout genome. The markers constitute a large majority of all SNP markers described for coho salmon and will enable both population- and pedigree-based analyses across the southern part of the species native range.

Conservation genetics of threatened Hippocampus guttulatus in vulnerable habitats in NW Spain: temporal and spatial stability of wild populations with flexible polygamous mating system in captivity

This study was focused on conservation genetics of threatened Hippocampus guttulatus on the Atlantic coast of NW Iberian Peninsula. Information about spatial structure and temporal stability of wild populations was obtained based on microsatellite markers, and used for monitoring a captive breeding program firstly initiated in this zone at the facilities of the Institute of Marine Research (Vigo, Spain). No significant major genetic structure was observed regarding the biogeographical barrier of Cape Finisterre. However, two management units under continuous gene flow are proposed based on the allelic differentiation between South-Atlantic and Cantabrian subpopulations, with small to moderate contemporary effective size based on single-sample methods. Temporal stability was observed in South-Atlantic population samples of H. guttulatus for the six-year period studied, suggesting large enough effective population size to buffer the effects of genetic drift within the time frame of three generations. Genetic analysis of wild breeders and offspring in captivity since 2009 allowed us to monitor the breeding program founded in 2006 in NW Spain for this species. Similar genetic diversity in the renewed and founder broodstock, regarding the wild population of origin, supports suitable renewal and rearing processes to maintain genetic variation in captivity. Genetic parentage proved single-brood monogamy in the wild and in captivity, but flexible short- and long-term mating system under captive conditions, from strict monogamy to polygamy within and/or among breeding seasons. Family analysis showed high reproductive success in captivity under genetic management assisted by molecular relatedness estimates to avoid inbreeding. This study provides genetic information about H. guttulatus in the wild and captivity within an uncovered geographical range for this data deficient species, to be taken into account for management and conservation purposes.

Mitochondrial DNA variability of the pipefish Syngnathus abaster

This study provides data on the genetic structuring of the pipefish Syngnathus abaster in the western Mediterranean and Adriatic Seas. A total of 109 specimens were collected in brackish-water biotopes. The control region and three other regions of the mitochondrial genome were analysed. The most relevant result was the high genetic structuring found by Bayesian inference (BI), maximum likelihood (ML) and network analyses, which were consistent in showing three well-separated clusters of S. abaster populations. Furthermore, BI and ML did not support the monophyly of the taxon S. abaster. These results suggest the occurrence of a species complex in the study area, whose differentiation may have occurred since the Pleistocene. The results also show a very high genetic variability at the inter-population level, with no shared haplotypes among sites. Evolutionary forces due to the fragmented nature of the brackish-water habitats may account for the high genetic divergence found among the groups and populations. Finally, although dispersal by rafting over long distances may occasionally occur, this study suggests linear stepping-stone model of colonization to be most likely. The complexity of the results obtained suggests that further studies are needed to elucidate the phylogeny of S. abaster.

Sexual signals and mating patterns in Syngnathidae

Male pregnancy in the family Syngnathidae (pipefishes, seahorses and seadragons) predisposes males to limit female reproductive success; sexual selection may then operate more strongly on females and female sexual signals may evolve (sex-role reversal). A bewildering array of female signals has evolved in Syngnathids, e.g. skin folds, large body size, colouration, markings on the body and elaborate courtship. These female sexual signals do not seem quantitatively or qualitatively different from those that evolve in males in species with conventional sex roles where males provide females or offspring with direct benefits. In several syngnathid species, males also evolve ornaments, females are choosy in addition to being competitive and males compete as well as choosing partners. Thus, sex roles form a continuum, spanning from conventional to reversed within this group of fishes. Cases are presented here suggesting that stronger sexual selection on females may be most extreme in species showing classical polyandry (one male mates with several females, such as many species where males brood their eggs on the trunk), intermediate in polygynandrous species (males and females both mate with more than one partner, as in many species where males brood their eggs on the tail) and least extreme, even exhibiting conventional sex roles, in monogamous species (one male mates solely with one female, as in many seahorses and tropical pipefishes). At the same time caution is needed before unanimously establishing this pattern: first, the connection between mating patterns, strength of sexual selection, sex roles and ornament expression is far from simple and straightforward, and second, knowledge of the actual morphology, ecology and behaviour of most syngnathid species is scanty. Basically only a few Nerophis, Syngnathus and Hippocampus species have been studied in any detail. It is known, however, that this group of fishes exhibits a remarkable variation in sex roles and ornamentation, making them an ideal group for the study of mating patterns, sexual selection and sexually selected signals.

The genetics and genomics of Syngnathidae: pipefishes, seahorses and seadragons

The goal of this review was to provide a historical overview of how molecular techniques have increased the understanding of the ecology and evolution of the family Syngnathidae (pipefishes, seahorses and seadragons). Molecular studies based primarily on mitochondrial DNA markers have proved their worth by elucidating complex phylogenetic relationships within the family. Phylogeographic studies, which have revealed how life-history traits and past climatic events shape geographic distributions and patterns of genetic variation within syngnathid species, also provide interesting case studies for the conservation and management of threatened species. The application of microsatellite DNA markers has opened a floodgate of studies concerned with the breeding biology of these fishes, which are interesting due to their unique reproductive mode of male pregnancy. Research in this area has contributed significantly to the understanding of mating patterns and sexual selection. Molecular markers may also be employed in studies of demography, migration and local breeding population sizes. Genomic studies have identified genes that are probably involved in male pregnancy and promise additional insights into various aspects of syngnathid biology at the level of the gene. Despite these advances, much more remains to be explored. Goals for future research should include: (1) a more inclusive phylogeny to resolve outstanding issues concerning the relationships within the family and higher order taxa, (2) a broader use of molecular studies to aid management and conservation efforts, (3) the inclusion of more genera in comparative behavioural studies and (4) the continued development of genomic resources for syngnathids to facilitate comparative genomic work.

Multiple mating and its relationship to brood size in pregnant fishes versus pregnant mammals and other viviparous vertebrates

We summarize the literature on rates of multiple paternity and sire numbers per clutch in viviparous fishes vs. mammals, two vertebrate groups in which pregnancy is common but entails very different numbers of embryos (for species surveyed, piscine broods averaged >10-fold larger than mammalian litters). As deduced from genetic parentage analyses, multiple mating by the pregnant sex proved to be common in assayed species but averaged significantly higher in fish than mammals. However, within either of these groups we found no significant correlations between brood size and genetically deduced incidence of multiple mating by females. Overall, these findings offer little support for the hypothesis that clutch size in pregnant species predicts the outcome of selection for multiple mating by brooders. Instead, whatever factors promote multiple mating by members of the gestating sex seem to do so in surprisingly similar ways in live-bearing vertebrates otherwise as different as fish and mammals. Similar conclusions emerged when we extended the survey to viviparous amphibians and reptiles. One notion consistent with these empirical observations is that although several fitness benefits probably accrue from multiple mating, logistical constraints on mate-encounter rates routinely truncate multiple mating far below levels that otherwise could be accommodated, especially in species with larger broods. We develop this concept into a "logistical constraint hypothesis" that may help to explain these mating outcomes in viviparous vertebrates. Under the logistical constraint hypothesis, propensities for multiple mating in each species register a balance between near-universal fitness benefits from multiple mating and species-idiosyncratic logistical limits on polygamy.

Multiple mating and its relationship to alternative modes of gestation in male-pregnant versus female-pregnant fish species

We construct a verbal and graphical theory (the "fecundity-limitation hypothesis") about how constraints on the brooding space for embryos probably truncate individual fecundity in male-pregnant and female-pregnant species in ways that should differentially influence selection pressures for multiple mating by males or by females. We then review the empirical literature on genetically deduced rates of multiple mating by the embryo-brooding parent in various fish species with three alternative categories of pregnancy: internal gestation by males, internal gestation by females, and external gestation (in nests) by males. Multiple mating by the brooding gender was common in all three forms of pregnancy. However, rates of multiple mating as well as mate numbers for the pregnant parent averaged higher in species with external as compared with internal male pregnancy, and also for dams in female-pregnant species versus sires in male-pregnant species. These outcomes are all consistent with the theory that different types of pregnancy have predictable consequences for a parent's brood space, its effective fecundity, its opportunities and rewards for producing half-sib clutches, and thereby its exposure to selection pressures for seeking multiple mates. Overall, we try to fit these fecundity-limitation phenomena into a broader conceptual framework for mating-system evolution that also includes anisogamy, sexual-selection gradients, parental investment, and other selective factors that can influence the relative proclivities of males versus females to seek multiple sexual partners.

A genetic linkage map for the saltwater crocodile (Crocodylus porosus)

Background

Genome elucidation is now in high gear for many organisms, and whilst genetic maps have been developed for a broad array of species, surprisingly, no such maps exist for a crocodilian, or indeed any other non-avian member of the Class Reptilia. Genetic linkage maps are essential tools for the mapping and dissection of complex quantitative trait loci (QTL), and in order to permit systematic genome scans for the identification of genes affecting economically important traits in farmed crocodilians, a comprehensive genetic linage map will be necessary.

Results

A first-generation genetic linkage map for the saltwater crocodile (Crocodylus porosus) was constructed using 203 microsatellite markers amplified across a two-generation pedigree comprising ten full-sib families from a commercial population at Darwin Crocodile Farm, Northern Territory, Australia. Linkage analyses identified fourteen linkage groups comprising a total of 180 loci, with 23 loci remaining unlinked. Markers were ordered within linkage groups employing a heuristic approach using CRIMAP v3.0 software. The estimated female and male recombination map lengths were 1824.1 and 319.0 centimorgans (cM) respectively, revealing an uncommonly large disparity in recombination map lengths between sexes (ratio of 5.7:1).

Conclusion

We have generated the first genetic linkage map for a crocodilian, or indeed any other non-avian reptile. The uncommonly large disparity in recombination map lengths confirms previous preliminary evidence of major differences in sex-specific recombination rates in a species that exhibits temperature-dependent sex determination (TSD). However, at this point the reason for this disparity in saltwater crocodiles remains unclear.

This map will be a valuable resource for crocodilian researchers, facilitating the systematic genome scans necessary for identifying genes affecting complex traits of economic importance in the crocodile industry. In addition, since many of the markers placed on this genetic map have been evaluated in up to 18 other extant species of crocodilian, this map will be of intrinsic value to comparative mapping efforts aimed at understanding genome content and organization among crocodilians, as well as the molecular evolution of reptilian and other amniote genomes. As researchers continue to work towards elucidation of the crocodilian genome, this first generation map lays the groundwork for more detailed mapping investigations, as well as providing a valuable scaffold for future genome sequence assembly.

Sexually selected females in the monogamous Western Australian seahorse

Studies of sexual selection in monogamous species have hitherto focused on sexual selection among males. Here, we provide empirical documentation that sexual selection can also act strongly on females in a natural population with a monogamous mating system. In our field-based genetic study of the monogamous Western Australian seahorse, Hippocampus subelongatus, sexual selection differentials and gradients show that females are under stronger sexual selection than males: mated females are larger than unmated ones, whereas mated and unmated males do not differ in size. In addition, the opportunity for sexual selection (variance in mating success divided by its mean squared) for females is almost three times that for males. These results, which seem to be generated by a combination of a male preference for larger females and a female-biased adult sex ratio, indicate that substantial sexual selection on females is a potentially important but under-appreciated evolutionary phenomenon in monogamous species.

Genetic monogamy despite social promiscuity in the pot-bellied seahorse (Hippocampus abdominalis)

Sexual selection theory predicts a positive correlation between relative parental investment and mate choice. In syngnathid fishes (seahorses and pipefish), males brood offspring in specialized brooding structures. While female-female mating competition has been demonstrated in some pipefishes, all seahorses (genus Hippocampus) studied to date have been found to have conventional sex roles with greater male-male competition for access to mates despite possessing the most complex brood structures in the family. Although multiple mating is common in pipefish, seahorses are again exceptional, exhibiting strict genetic monogamy. Both demographic and behavioural explanations have been offered to explain the lack of multiple mating in seahorse species, but these hypotheses have not yet been explicitly addressed. We investigated mating systems and brood parentage of the pot-bellied seahorse, Hippocampus abdominalis, a temperate-water species that is socially promiscuous with conventional sex roles in laboratory populations. We observed promiscuous courtship behaviour and sex-role reversal in high density, female-biased field populations of H. abdominalis. We hypothesize that sex roles are plastic in H. abdominalis, depending on local population density and sex ratio. Despite promiscuous courtship behaviour, all assayed male seahorses were genetically monogamous in both laboratory and wild populations. Physiological limitations associated with embryo incubation may explain the absence of multiple mating in seahorses and may have played an important role in the development of the unique reproductive behaviour typical in these species.

Monogamy in marine fishes

The formation of long-term pair bonds in marine fish has elicited much empirical study. However, the evolutionary mechanisms involved remain contested and previous theoretical frameworks developed to explain monogamy in birds and mammals are not applicable to many cases of monogamy in marine fish. In this review, we summarise all reported occurrences of social monogamy in marine fish, which has so far been observed in 18 fish families. We test quantitatively the role of ecological and behavioural traits previously suggested to be important for the evolution of monogamy and show that monogamous species occur primarily in the tropics and are associated with coral reef environments in which territory defence and site attachment is facilitated. However, there is little evidence that obligately monogamous species are smaller in body size than species that can adopt a polygynous mating system. We review the evidence pertaining to six hypotheses suggested for the evolution of monogamous pair bonds: (1) biparental care, (2) habitat limitation, (3) low population density/low mate availability/low mobility, (4) increased reproductive efficiency, (5) territory defence, and (6) net benefit of single mate sequestration. We outline predictions and associated empirical tests that can distinguish between these hypotheses, and assess how generally each hypothesis explains monogamy within and between breeding periods for species with different types of territories (i.e. feeding only or feeding and breeding). Hypotheses (1) and (2) have limited applicability to marine fishes, while hypotheses (3)-(5) have little empirical support beyond the species for which they were designed. However, the role of paternal care in promoting monogamous pair bonds is not explicit in these hypotheses, yet paternal care has been reported in more than 70 monogamous marine fish. We show that paternal care may act to increase the likelihood of monogamy in combination with each of the proposed hypotheses through decreased benefits to males from searching for additional mates or increased advantages to females from sequestering a single high-quality mate. Among species defending breeding and feeding territories, the benefits, both within and between reproductive periods, of sequestering a single high-quality mate (hypothesis 6) appear to be the best explanation for socially monogamous pairs. For species without parental care (i.e. holding only feeding territories), territory defence (hypothesis 5) in combination with the benefits of guarding a large mate (hypothesis 6) could potentially explain most instances of monogamy. Empirical studies of marine fishes over the past two decades are therefore slowly changing the view of monogamy from a mating system imposed upon species by environmental constraints to one with direct benefits to both sexes.

Hippocampus queenslandicus Horne, 2001 - a new seahorse species or yet another synonym?

During the past six years, 15 new seahorse species (Syngnathidae: Hippocampus) have been described on the basis of morphological characters. This approach is known to be problematic, and most species names in Hippocampus are now considered to be synonyms. Genetic methods have great potential to resolve the confused taxonomy of the genus, but none have yet been incorporated into species descriptions. In the present study, mitochondrial control region and cytochrome b DNA sequences, as well as morphological data from the recently described Queensland seahorse, Hippocampus queenslandicus Horne, 2001, were compared with corresponding data from closely related seahorse species to determine whether there is strong support for distinction of this taxon. The haplotypes of H. queenslandicus were nested among haplotypes belonging to two of the three major Southeast Asian lineages of H. spinosissimus Weber, 1913. Although incomplete lineage sorting characteristic of very recently diverged species cannot be ruled out, the genetic results suggest that H. queenslandicus is paraphyletic. Morphometric analysis further fails to provide strong support for the species status of H. queenslandicus. We conclude that support for the distinctness of H. queenslandicus is weak, and indicate that it is a synonym of H. spinosissimus. The taxonomic validity of other recently described seahorse species should be similarly scrutinised using combined genetic and detailed morphological methods.

Multiple paternity in a salamander with socially monogamous behaviour

In the majority of birds and mammals, social monogamy is not congruent with genetic monogamy. No research to date has compared social and genetic monogamy in amphibians. We analysed paternity in clutches of red-backed salamanders (Plethodon cinereus), a species in which social monogamy has been demonstrated in the laboratory, and 28% of individuals in the forest are found in male-female pairs in the noncourtship season. We collected 16 clutches of eggs of P. cinereus in the southern Appalachian Mountains of Virginia and collected tail clippings from attending mothers. We genotyped embryos and adults at five microsatellite loci in order to analyse paternity of clutches. Most clutches (84.6%) had multiple sires, with two to three sires per clutch. In this study, 25% of clutches had males in addition to females attending eggs. None of the mothers of these clutches were genetically monogamous. All attending males sired some of the offspring in the clutch that they attended (between 9% and 50%) but never sired a majority in that clutch. We conclude that, at least in this population, social monogamy in P. cinereus is not concomitant with genetic monogamy.

Differential parental nutrient allocation in two congeneric pipefish species (Syngnathidae:Syngnathusspp.)

Male seahorses and pipefishes of the family Syngnathidae are heralded for their unique brood pouch structures for incubating embryos. There are three general types of brood pouch with increasing complexity: simple ventral gluing, two pouch flaps and a completely sealed sac. The diversity of functional roles within a type in providing nutrition, aeration and protection to offspring is unknown. Here we reveal significant differences in parental nutrient allocation to embryos for two closely related, sympatric pipefishes with similar brood pouch structure. We document differences in embryo attachment, depletion of pouch fluid nutrients over development and egg nutrient partitioning between Syngnathus floridae and Syngnathus fuscus. In S. fuscus, females produce nutritionally poor eggs and the males implant developing embryos in the brood pouch adjacent to blood vessels. A female-biased breeding population was observed, supporting the hypothesis that the cost of male parental care is high in this species. The loose connection between eggs and brood pouch tissues and the appearance of undeveloped eggs and lipid droplets in the pouch of S. floridae males suggest this species utilizes nutrient-rich eggs produced by females as nurse eggs to supplement embryonic development. A balanced sex-ratio for S. floridae further supports more equal parental contribution. This comparison provides evidence of a decline in female gametic investment and reveals the rapid diversification of syngnathid brood pouch function. Our results indicate gross classification of brooding structures into one of the three general pouch types does not predict the energetic investment of males in parental care. But rather, physiological characterization of the relative investment by each sex to offspring is essential to understanding the functional significance of the brood pouch.

Interspecies mating in sympatric species of Syngnathus pipefish

Hybridization is thought to be an important source of novel genetic variation, and interspecific hybridization may increase the adaptive potential of wild populations. While hybridization has not been previously reported in syngnathid fishes (seahorses and pipefish), the sympatric occurrence of closely related species at high densities increases the probability of interspecies mating in this group. Southern California is home to five species of Syngnathus pipefish, and these species frequently co-occur in near-shore eelgrass beds along the California coast. Recent work has identified exceptionally high levels of genetic diversity in southern populations of Syngnathus leptorhynchus, a widespread species which ranges from Mexico to Alaska. Microsatellite genotyping and mitochondrial sequence data are used here to study the population genetics of S. leptorhynchus and S. auliscus at a site in San Diego Bay where they are found to co-occur at high densities. While no adult hybrids were detected in the study population, analysis of male broods indicates that interspecies mating is occurring between the two species. The lack of premating isolating mechanisms between these two relatives suggests that hybridization may be common in sympatric species of Syngnathus.

Sex-linked Markers Facilitate Genetic Parentage Analyses in Knobbed Whelk Broods

To explore the potential of sex-linked polymorphisms for genetic parentage analyses in natural populations, we have employed a recently discovered "X-linked" microsatellite marker (in conjunction with polymorphic autosomal loci) to deduce biological paternity and maternity for large numbers of encapsulated embryos within individual broods of the knobbed whelk (Busycon carica). Empirical findings illustrate how such sex-linked genetic tags can in special instances find at least three novel utilities in genetic dissections of large-clutch species: clarification of paternity assignments that had remained ambiguous from di-locus autosomal data alone; elucidation of linkage relationships among pairs of autosomal loci; and illumination of maternity (and thereby paternity also) in broods for which neither biological parent was known from independent evidence.

Evidence for genetic monogamy and female-biased dispersal in the biparental mouthbrooding cichlid Eretmodus cyanostictus from Lake Tanganyika

In this study, we investigate whether apparent social monogamy (where a species forms a pair bond but may participate in copulations outside the pair bond) corresponds with genetic monogamy (where individuals participate only in copulations within a pair bond) in a biparental mouthbrooding cichlid fish, Eretmodus cyanostictus, from Lake Tanganyika, Africa. Our findings suggest that E. cyanostictus is both socially and genetically monogamous and that monogamy may result from limited opportunities for polygyny, rather than from reproductive benefits of monogamy. Mating systems are believed to influence the relative rate of dispersal of the sexes, and our results suggest that E. cyanostictus displays female-biased dispersal, providing some support for the 'resource competition' hypothesis driving sex-biased dispersal.

Methods of parentage analysis in natural populations

The recent proliferation of hypervariable molecular markers has ushered in a surge of techniques for the analysis of parentage in natural and experimental populations. Consequently, the potential for meaningful studies of paternity and maternity is at an all-time high. However, the details and implementation of the multifarious techniques often differ in subtle ways that can influence the results of parentage analyses. Now is a good time to reflect on the available techniques and to consider their strengths and weaknesses. Here, we review the leading techniques in parentage analysis, with a particular emphasis on those that have been implemented in readily useable software packages. Our survey leads to some important insights with respect to the utility of the different approaches. This review should serve as a useful guide to anyone who wishes to embark on the study of parentage.

Breeding success of male brook trout (Salvelinus fontinalis) in the wild

Competition for females generally results in some males adopting alternative reproductive tactics to acquire matings. For fish, the ecological and evolutionary consequences of these tactics are not well understood because of an inability to link directly the interactions of individuals on the breeding grounds with genetic data. This study combines behavioural observations with genetic estimates of male reproductive success within an intensively studied wild population of lacustrine brook trout (Salvelinus fontinalis). Male brook trout exhibit a conditional reproductive strategy with small males adopting a peripheral position to that of larger dominant males in their proximity to spawning females. Parentage analysis of eggs collected from wild redds confirmed the reproductive success of individual males. Males relegated to peripheral positions during spawning participated frequently in spawning events, but in most cases the first male to spawn was the sole contributor, and no more than two males contributed successfully to a single brood. While behavioural observations of salmonines suggests that reproduction is partitioned among males in a manner dependent upon body size and proximity to spawning females, the genetic evidence from this study suggests a more limited distribution of reproductive success in the field. The genetic contributions of male brook trout are highly skewed towards larger males for this population. A review of the salmonine literature suggests little difference in individual reproductive success for males exhibiting size-related tactics within a conditional mating strategy vs. precocial maturation. Collectively, these genetic studies provide new insights on the evolution of alternative life histories among salmonines.

Genetic mating systems and reproductive natural histories of fishes: lessons for ecology and evolution

Fish species have diverse breeding behaviors that make them valuable for testing theories on genetic mating systems and reproductive tactics. Here we review genetic appraisals of paternity and maternity in wild fish populations. Behavioral phenomena quantified by genetic markers in various species include patterns of multiple mating by both sexes; frequent cuckoldry by males and rare cuckoldry by females in nest-tending species; additional routes to surrogate parentage via nest piracy and egg-thievery; egg mimicry by nest-tending males; brood parasitism by helper males in cooperative breeders; clutch mixing in oral brooders; kinship in schooling fry of broadcast spawners; sperm storage by dams in female-pregnant species; and sex-role reversal, polyandry, and strong sexual selection on females in some male-pregnant species. Additional phenomena addressed by genetic parentage analyses in fishes include clustered mutations, filial cannibalism, and local population size. All results are discussed in the context of relevant behavioral and evolutionary theory.

The dynamics of male brooding, mating patterns, and sex roles in pipefishes and seahorses (family Syngnathidae)

Modern theory predicts that relative parental investment of the sexes in their young is a key factor responsible for sexual selection. Seahorses and pipefishes (family Syngnathidae) are extraordinary among fishes in their remarkable adaptations for paternal care and frequent occurrences of sex-role reversals (i.e., female-female competition for mates), offering exceptional opportunities to test predictions of sexual selection theory. During mating, the female transfers eggs into or onto specialized egg-brooding structures that are located on either the male's abdomen or its tail, where they are osmoregulated, aerated, and nourished by specially adapted structures. All syngnathid males exhibit this form of parental care but the brooding structures vary, ranging from the simple ventral gluing areas of some pipefishes to the completely enclosed pouches found in seahorses. We present a molecular phylogeny that indicates that the diversification of pouch types is positively correlated with the major evolutionary radiation of the group, suggesting that this extreme development and diversification of paternal care may have been an important evolutionary innovation of the Syngnathidae. Based on recent studies that show that the complexity of brooding structures reflects the degree of paternal investment in several syngnathid species, we predicted sex-role reversals to be more common among species with more complex brooding structures. In contrast to this prediction, however, both parsimony- and likelihood-based reconstructions of the evolution of sex-role reversal in pipefishes and seahorses suggest multiple shifts in sex roles in the group, independent from the degree of brood pouch development. At the same time, our data demonstrate that sex-role reversal is positively associated with polygamous mating patterns, whereas most nonreversed species mate monogamously, suggesting that selection for polygamy or monogamy in pipefishes and seahorses may strongly influence sex roles in the wild.

Sympatric speciation as a consequence of male pregnancy in seahorses

The phenomenon of male pregnancy in the family Syngnathidae (seahorses, pipefishes, and sea dragons) undeniably has sculpted the course of behavioral evolution in these fishes. Here we explore another potentially important but previously unrecognized consequence of male pregnancy: a predisposition for sympatric speciation. We present microsatellite data on genetic parentage that show that seahorses mate size-assortatively in nature. We then develop a quantitative genetic model based on these empirical findings to demonstrate that sympatric speciation indeed can occur under this mating regime in response to weak disruptive selection on body size. We also evaluate phylogenetic evidence bearing on sympatric speciation by asking whether tiny seahorse species are sister taxa to large sympatric relatives. Overall, our results indicate that sympatric speciation is a plausible mechanism for the diversification of seahorses, and that assortative mating (in this case as a result of male parental care) may warrant broader attention in the speciation process for some other taxonomic groups as well.

Lizards in 'nuclear families': a novel reptilian social system in Egernia saxatilis (Scincidae)

Recent research has revealed unsuspected complexity in social organization among squamate reptiles. In particular, large Australian scincid lizards of the genus Egernia have been reported to occur in large aggregations of closely related individuals. However, the 'nuclear family' structure found in many other 'social' organisms (especially birds) has not been reported from reptiles. Our field studies on black rock skinks (Egernia saxatilis) in southeastern Australia document exactly this pattern. We quantified group composition using behavioural observations at regular intervals over three field seasons, and took tissue samples for parentage analysis. On the focal rock outcrop 72% of lizards were typically found as part of a stable social grouping, with individuals physically associated with other group members in a third of observations. Eighty-five per cent of juveniles lived in social groups, 65% in family groups with at least one of their parents (including 39% with both parents as revealed by parentage analysis of five microsatellite loci). Broader sampling in surrounding areas revealed similar patterns of group size, composition and relatedness. Overall, of the groups that contained more than one adult, 83% contained a single adult pair. Long-term monogamy and group stability were evident from our genetic data, with up to three annual cohorts of full-sib offspring living with their biological parents. Our data expand the range of social systems known for reptiles, and reveal strong convergence towards 'nuclear family' systems in distantly related vertebrates.

Genetic evidence for extreme polyandry and extraordinary sex-role reversal in a pipefish

Due to the phenomenon of male pregnancy, the fish family Syngnathidae (seahorses and pipefishes) has historically been considered an archetypal example of a group in which sexual selection should act more strongly on females than on males. However, more recent work has called into question the idea that all species with male pregnancy are sex-role reversed with respect to the intensity of sexual selection. Furthermore, no studies have formally quantified the opportunity for sexual selection in any natural breeding assemblage of pipefishes or seahorses in order to demonstrate conclusively that sexual selection acts most strongly on females. Here, we use a DNA-based study of parentage in the Gulf pipefish Syngnathus scovelli in order to show that sexual selection indeed acts more strongly on females than on males in this species. Moreover, the Gulf pipefish exhibits classical polyandry with the greatest asymmetry in reproductive roles (as quantified by variances in mating success) between males and females yet documented in any system. Thus, the intensity of sexual selection on females in pipefish rivals that of any other taxon yet studied.