Karen D. Crow

Sympatric speciation in a genus of marine reef fishes

Sympatric speciation has been contentious since its inception, yet is increasingly recognized as important based on accumulating theoretical and empirical support. Here, we present a compelling case of sympatric speciation in a taxon of marine reef fishes using a comparative and mechanistic approach. Hexagrammos otakii and H. agrammus occur in sympatry throughout their ranges. Molecular sequence data from six loci, with complete sampling of the genus, support monophyly of these sister species. Although hybridization occurrs frequently with an allopatric congener in an area of slight distributional overlap, we found no F1 hybrids between the focal sympatric taxa throughout their coextensive ranges. We present genetic evidence for complete reproductive isolation based on SNP analysis of 382 individuals indicating fixed polymorphisms, with no shared haplotypes or genotypes, between sympatric species. To address questions of speciation, we take a mechanistic approach and directly compare aspects of reproductive isolation between allopatric and sympatric taxa both in nature and in the laboratory. We conclude that the buildup of reproductive isolation is strikingly different in sympatric vs. allopatric taxa, consistent with theoretical predictions. Lab reared hybrids from allopatric species crosses exhibit severe fitness effects in the F1 or backcross generation. No intrinsic fitness effects are observed in F1 hybrids from sympatric species pairs, however these treatments exhibited reduced fertilization success and complete pre‐mating isolation is implied in nature because F1 hybrid adults do not occur. Our study addresses limitations of previous studies and supports new criteria for inferring sympatric speciation.

Expression of Hoxa-11 and Hoxa-13 in the pectoral fin of a basal ray-finned fish, Polyodon spathula : implications for the origin of tetrapod limbs

Summary Paleontological and anatomical evidence suggests that the autopodium (hand or foot) is a novel feature that distinguishes limbs from fins, while the upper and lower limb (stylopod and zeugopod) are homologous to parts of the sarcopterygian paired fins. In tetrapod limb development Hoxa‐11 plays a key role in differentiating the lower limb and Hoxa‐13 plays a key role in differentiating the autopodium. It is thus important to determine the ancestral functions of these genes in order to understand the developmental genetic changes that led to the origin of the tetrapod autopodium. In particular it is important to understand which features of gene expression are derived in tetrapods and which are ancestral in bony fishes. To address these questions we cloned and sequenced the Hoxa‐11 and Hoxa‐13 genes from the North American paddlefish, Polyodon spathula, a basal ray‐finned fish that has a pectoral fin morphology resembling that of primitive bony fishes ancestral to the tetrapod lineage. Sequence analysis of these genes shows that they are not orthologous to the duplicated zebrafish and fugu genes. This implies that the paddlefish has not duplicated its HoxA cluster, unlike zebrafish and fugu. The expression of Hoxa‐11 and Hoxa‐13 in the pectoral fins shows two main phases: an early phase in which Hoxa‐11 is expressed proximally and Hoxa‐13 is expressed distally, and a later phase in which Hoxa‐11 and Hoxa‐13 broadly overlap in the distal mesenchyme of the fin bud but are absent in the proximal fin bud. Hence the distal polarity of Hoxa‐13 expression seen in tetrapods is likely to be an ancestral feature of paired appendage development. The main difference in HoxA gene expression between fin and limb development is that in tetrapods (with the exception of newts) Hoxa‐11 expression is suppressed by Hoxa‐13 in the distal limb bud mesenchyme. There is, however, a short period of limb bud development where Hoxa‐11 and Hoxa‐13 overlap similarly to the late expression seen in zebrafish and paddlefish. We conclude that the early expression pattern in tetrapods is similar to that seen in late fin development and that the local exclusion by Hoxa‐13 of Hoxa‐11 from the distal limb bud is a derived feature of limb developmental regulation.

An independent genome duplication inferred from Hox paralogs in the American paddlefish--a representative basal ray-finned fish and important comparative reference.

Vertebrates have experienced two rounds of whole-genome duplication (WGD) in the stem lineages of deep nodes within the group and a subsequent duplication event in the stem lineage of the teleosts—a highly diverse group of ray-finned fishes. Here, we present the first full Hox gene sequences for any member of the Acipenseriformes, the American paddlefish, and confirm that an independent WGD occurred in the paddlefish lineage, approximately 42 Ma based on sequences spanning the entire HoxA cluster and eight genes on the HoxD gene cluster. These clusters comprise different HOX loci and maintain conserved synteny relative to bichir, zebrafish, stickleback, and pufferfish, as well as human, mouse, and chick. We also provide a gene genealogy for the duplicated fzd8 gene in paddlefish and present evidence for the first Hox14 gene in any ray-finned fish. Taken together, these data demonstrate that the American paddlefish has an independently duplicated genome. Substitution patterns of the “alpha” paralogs on both the HoxA and HoxD gene clusters suggest transcriptional inactivation consistent with functional diploidization. Further, there are similarities in the pattern of sequence divergence among duplicated Hox genes in paddlefish and teleost lineages, even though they occurred independently approximately 200 Myr apart. We highlight implications on comparative analyses in the study of the “fin-limb transition” as well as gene and genome duplication in bony fishes, which includes all ray-finned fishes as well as the lobe-finned fishes and tetrapod vertebrates.

Microsatellite diversity and conservation of a relic trout population: McCloud River redband trout.

Rainbow trout native to the McCloud River, California, USA (Oncorhynchus mykiss stonei) are thought to represent a relic, nonanadromous trout adapted to harsh, fragmented environments. These fish, commonly named McCloud River ‘redband’ trout, survive in their most primitive form in a small, spring‐fed stream, Sheepheaven Creek, in the upper McCloud River drainage. Turn‐of‐the‐century fisheries records document both coastal anadromous steelhead and freshwater resident trout within the McCloud River drainage. The phylogenetic position of the McCloud River redband trout within O. mykiss has been debated for over 50 years. Based on phenotypic evidence, these fish were first reported as ‘southern Sierra golden trout’ by Wales in 1939. Behnke (1970) considered them a relic subspecies of nonanadromous, fine‐scaled trout. Allozyme and mitochondrial DNA evidence suggested a coastal lineage. In this study, we examined within‐ and among‐basin genetic associations for Sheepheaven Creek redband trout using 11 microsatellite loci. Within‐basin analyses supported unique genetic characteristics in Sheepheaven Creek’s trout in comparisons with other McCloud River rainbow trout. Microsatellite data supported significant independence between Sheepheaven Creek fish and hatchery rainbow trout. Inter‐basin genetic distance analyses positioned Sheepheaven Creek fish with samples collected from Lassen Creek, a geographically proximate stream containing inland redband trout. California’s redband trout shared a close genetic association with Little Kern River golden trout (O.m. whitei) and isolated rainbow trout from Rio Santo Domingo, Baja, Mexico (O.m. nelsoni), suggesting a vicariant distribution of microsatellite diversity throughout the southern range of this species.

Hypermutability of HoxA13A and functional divergence from its paralog are associated with the origin of a novel developmental feature in zebrafish and related taxa (Cypriniformes).

Gene duplication is widely regarded as the predominant mechanism by which genes with new functions and associated phenotypic novelties arise. A whole genome duplication occurred shortly before the most recent common ancestor of teleosts, the most diverse chordate group, resulting in duplication and retention of many Hox cluster genes. Because they play a key role in determination of body plan morphology, it has been widely assumed that Hox genes play a key role in the evolution of diverse metazoan body plans. However, it is not clear whether certain aspects of molecular evolution, such as asymmetric divergence and neofunctionalization, contribute to the initial retention of paralogs. We investigate the molecular evolution and functional divergence of the duplicated HoxA13 paralogs in zebrafish to determine when asymmetric divergence and functional divergence occurred after the duplication event. Our findings demonstrate the contribution of gene duplication to the evolution of novel features through evolutionary mechanisms other than those traditionally investigated, such as positive selection occurring immediately after gene duplication. Rather, we find a latent build up of molecular changes in a gene associated with the development of a novel feature in a very diverse group of fishes.

Evidence for Multiple Maternal Contributors in Nests of Kelp Greenling (Hexagrammos decagrammus, Hexagrammidae)

Twenty-three nests of kelp greenling (Hexagrammos decagrammus) were examined from British Columbia and central California. The average nest had four clutches of eggs that were associated with rock or rock and a biological substrate, encompassed an area of 1.7 m2, and was guarded by a male averaging 31 cm in length. Frequency distributions of egg-size classes were examined for 13 gravid females. Females were batch spawners capable of producing at least three clutches of eggs per spawning season. Variation in mitochondrial DNA among 107 individuals from 83 clutches representing 20 nests sampled from British Columbia and central California was analyzed. Different maternal contributors were found among clutches in 27% of nests from British Columbia and 55% of nests from California. ARENTAL care in fishes requires an expen

Extreme gender flexibility: Using a phylogenetic framework to infer the evolution of variation in sex allocation, phylogeography, and speciation in a genus of bidirectional sex changing fishes (Lythrypnus, Gobiidae)

The genus Lythrypnus is a group of marine gobies that exhibit extreme gender flexibility as bidirectional sex changers. The genus consists of 20 described species and several undescribed species that are distributed in the Americas. Five species have been characterized with respect to sex allocation and gonad morphology. The hormonal, morphological, and behavioral aspects of sex change have been studied extensively for one species, L. dalli. These data, however, have not been interpreted in an evolutionary context because a phylogenetic hypothesis has not previously been proposed for the genus Lythrypnus. We propose the first phylogenetic hypothesis for the genus based on molecular data from three mitochondrial genes (12s, ND2, and Cytb), one nuclear gene (Rag1) and one nuclear intron (S7). We also include three previously undescribed Lythrypnus species. Our results support the monophyly of the genus with L. heterochroma, an Atlantic species, as the basal taxon. After the divergence of L. heterochroma, there are two main clades, one comprised of species distributed in the Atlantic, the other comprised of species distributed in the Pacific. These data indicate an Atlantic origin for the genus, followed by divergence after the closure of the Isthmus of Panama. Our data also support the monophyly of three previously described species complexes, the L. rhizophora complex and L. dalli complex in the Pacific, and the L. mowbrayi complex in the Atlantic. We mapped patterns of sex allocation within this genus onto the fully resolved and supported topology, and found that sexual plasticity and gender flexibility is likely a synapomorphy for the genus. Overall our results create a well-supported framework to understand the phylogeography of the genus, and to interpret the evolution of sex allocation in Lythrypnus gobies.

The secret of the mermaid's purse: phylogenetic affinities within the Rajidae and the evolution of a novel reproductive strategy in skates.

The systematics of the skates in the family Rajidae have been contentious for over 250years, with most studies inferring relationships among geographically clustered species, and non-overlapping taxa and data sets. Rajid skates are oviparous, and lay egg capsules with a single embryo. However, two species exhibit a derived form of egg laying, with multiple embryos per egg capsule. We provide a molecular assessment of the phylogenetic relationships of skates in the family Rajidae based on three mitochondrial genes. The resulting topology supports monophyly the family. However the genusRajais polyphyletic, and several species assemblages need to be revised. We propose a new assemblage, the Rostrajini, which organizesrajid species into three well-supported tribal lineages for the first time. Further, these data provide an independent assessment of monophyly for the two species exhibiting multiple embryos per egg capsule, supporting their status as the unique genusBeringraja. In addition, we find that among the different size classes of egg capsules, ranging from 1 to 8 embryos per capsule in this genus, there is variation in frequency and survivorship. InBeringraja binoculata, the strategy of having two embryos per egg capsule occurs most frequently and with the highest fitness.

HoxA and HoxD expression in a variety of vertebrate body plan features reveals an ancient origin for the distal Hox program

BackgroundHox genes are master regulatory genes that specify positional identities during axial development in animals. Discoveries regarding their concerted expression patterns have commanded intense interest due to their complex regulation and specification of body plan features in jawed vertebrates. For example, the posterior HoxD genes switch to an inverted collinear expression pattern in the mouse autopod where HoxD13 switches from a more restricted to a less restricted domain relative to its neighboring gene on the cluster. We refer to this program as the ‘distal phase’ (DP) expression pattern because it occurs in distal regions of paired fins and limbs, and is regulated independently by elements in the 5′ region upstream of the HoxD cluster. However, few taxa have been evaluated with respect to this pattern, and most studies have focused on pectoral fin morphogenesis, which occurs relatively early in development.ResultsHere, we demonstrate for the first time that the DP expression pattern occurs with the posterior HoxA genes, and is therefore not solely associated with the HoxD gene cluster. Further, DP Hox expression is not confined to paired fins and limbs, but occurs in a variety of body plan features, including paddlefish barbels - sensory adornments that develop from the first mandibular arch (the former ‘Hox-free zone), and the vent (a medial structure that is analogous to a urethra). We found DP expression of HoxD13 and HoxD12 in the paddlefish barbel; and we present the first evidence for DP expression of the HoxA genes in the hindgut and vent of three ray-finned fishes. The HoxA DP expression pattern is predicted by the recent finding of a shared 5′ regulatory architecture in both the HoxA and HoxD clusters, but has not been previously observed in any body plan feature.ConclusionsThe Hox DP expression pattern appears to be an ancient module that has been co-opted in a variety of structures adorning the vertebrate bauplan. This module provides a shared genetic program that implies deep homology of a variety of distally elongated structures that has played a significant role in the evolution of morphological diversity in vertebrates

Multiple paternity is a shared reproductive strategy in the live-bearing surfperches (Embiotocidae) that may be associated with female fitness

According to Batemans principle, female fecundity is limited relative to males, setting the expectation that males should be promiscuous, while females should be choosy and select fewer mates. However, several surfperches (Embiotocidae) exhibit multiple paternity within broods indicating that females mate with multiple males throughout the mating season. Previous studies found no correlation between mating success and reproductive success (i.e., a Bateman gradient). However, by including samples from a broader range of reproductive size classes, we found evidence of a Bateman gradient in two surfperch species from distinct embiotocid clades. Using microsatellite analyses, we found that 100% of the spotfin surfperch families sampled exhibit multiple paternity (Hyperprosopon anale, the basal taxon from the only clade that has not previously been investigated) indicating that this tactic is a shared reproductive strategy among surfperches. Further, we detected evidence for a Bateman gradient in H. anale; however, this result was not significant after correction for biases. Similarly, we found evidence for multiple paternity in 83% of the shiner surfperch families (Cymatogaster aggregata) sampled. When we combine these data with a previous study on the same species, representing a larger range of reproductive size classes and associated brood sizes, we detect a Bateman gradient in shiner surfperch for the first time that remains significant after several conservative tests for bias correction. These results indicate that sexual selection is likely complex in this system, with the potential for conflicting optima between sexes, and imply a positive shift in fertility (i.e., increasing number) and reproductive tactic with respect to the mating system and number of sires throughout the reproductive life history of females. We argue that the complex reproductive natural history of surfperches is characterized by several traits that may be associated with cryptic female choice, including protracted oogenesis, uterine sac complexity, and sperm storage.