East African cichlids display extensive variation in sex determination systems. The species Astatotilapia calliptera is one of the few cichlids that reside both in Lake Malawi and in surrounding waterways. A. calliptera is of interest in evolutionary studies as a putative immediate outgroup species for the Lake Malawi species flock and possibly as a prototype ancestor-like species for the radiation. Here, we use linkage mapping to test association of sex in A. calliptera with loci that have been previously associated with genetic sex determination in East African cichlid species. We identify a male heterogametic XY system segregating at linkage group (LG) 7 in an A. calliptera line that originated from Lake Malawi, at a locus previously shown to act as an XY sex determination system in multiple species of Lake Malawi cichlids. Significant association of genetic markers and sex produce a broad genetic interval of approximately 26 megabases (Mb) using the Nile tilapia genome to orient markers; however, we note that the marker with the strongest association with sex is near a gene that acts as a master sex determiner in other fish species. We demonstrate that alleles of the marker are perfectly associated with sex in Metriaclima mbenjii, a species from the rock-dwelling clade of Lake Malawi. While we do not rule out the possibility of other sex determination loci in A. calliptera, this study provides a foundation for fine mapping of the cichlid sex determination gene on LG7 and evolutionary context regarding the origin and persistence of the LG7 XY across diverse, rapidly evolving lineages.

Movement, delays, and survival of hatchery Atlantic Salmon Salmo salar smolts were evaluated through the Piscataquis River, a tributary of the Penobscot River in Maine, USA. We explored the effects of the river's four dams (Guilford, Dover, Browns Mill, and Howland dams) from 2005 to 2019. During this period, the downstream-most dam (Howland Dam) transitioned from full hydropower generation to seasonal turbine shutdowns and later was decommissioned with the construction of a nature-like fish bypass in 2016. We estimated survival through open-river reaches and at each dam using acoustic telemetry (n = 1,611). Dams decreased survival, with per-river-kilometer (rkm) apparent survival averages of 0.972, 0.951, and 0.990 for Guilford, Dover, and Browns Mill dams compared to a per-rkm survival of 0.999 for open-river reaches. Turbine shutdowns increased survival at Howland Dam (to around 0.95), which was further increased by the nature-like fish bypass (0.99). We used radiotelemetry in 2019 (n = 75) and demonstrated that approximately one-third of the fish used the bypass, while the remaining fish used alternative routes. Smolts successfully passing the three upstream dams had lower apparent survival through Howland Dam than smolts that were released upstream of Howland Dam. Although smolts passing Browns Mill Dam had high survival, the dam caused extended delays, with median delay times surpassing 48 h in most years. Most of the delays caused by Browns Mill Dam occurred after fish had passed the dam and may indicate a sublethal effect of passage. Overall, while survival through Howland Dam has improved, passage and delays at the three upstream dams in aggregate represent a critical impediment to the effective use of the high-quality spawning habitat found upstream.

Significance Sex differences in traits can occur when those traits are modified by genetic factors inherited on sex chromosomes. We investigated how sex differences emerge in a species with more than one set of sex chromosomes, measuring a variety of morphological, physiological, and behavioral traits. Rather than exhibiting sexual dimorphism associated with primary sex, the species has higher-order sexual polymorphism in secondary sexual characteristics or more than two phenotypic sexes. Variation in secondary sexual characteristics is modular, involving the interplay of sex-linked and sex-limited traits. Our findings provide implications for how sex determination systems and whole-organism fitness traits coevolve, including that significant creation or loss of variation in diverse traits can occur during transitions among sex chromosome systems.

Since Darwin, biologists have sought to understand the evolution and origins of phenotypic adaptations. The skull is particularly diverse due to intense natural selection on feeding biomechanics. We investigated the genetic and molecular origins of trophic adaptation using Lake Malawi cichlids, which have undergone an exemplary evolutionary radiation. We analyzed morphological differences in the lateral and ventral head shape among an insectivore that eats by suction feeding, an obligate biting herbivore, and their F2 hybrids. We identified variation in a series of morphological traits—including mandible width, mandible length, and buccal length—that directly affect feeding kinematics and function. Using quantitative trait loci (QTL) mapping, we found that many genes of small effects influence these craniofacial adaptations. Intervals for some traits were enriched in genes related to potassium transport and sensory systems, the latter suggesting co-evolution of feeding structures and sensory adaptations for foraging. Despite these indications of co-evolution of structures, morphological traits did not show covariation. Furthermore, phenotypes largely mapped to distinct genetic intervals, suggesting that a common genetic basis does not generate coordinated changes in shape. Together, these suggest that craniofacial traits are mostly inherited as separate modules, which confers a high potential for the evolution of morphological diversity. Though these traits are not restricted by genetic pleiotropy, functional demands of feeding and sensory structures likely introduce constraints on variation. In all, we provide insights into the quantitative genetic basis of trophic adaptation, identify mechanisms that influence the direction of morphological evolution, and provide molecular inroads to craniofacial variation.

Atlantic salmon return to rivers in spring for an energetically costly upstream migration for spawning. These fish are often delayed in the lower river below dams, subjecting them to warmer waters than occur in upstream sections of river, that may increase metabolic costs. We sought to quantify the energetic cost of dam-mediated delays in migrating adults in the Penobscot and Kennebec Rivers, ME. We radio tagged fish at the lower most dams, released them downstream (18 and 14 km), and tracked their movements back upstream. We used a Distell Fish Fatmeter as a noninvasive measurement of full-body energy at tagging and then again after re-ascending the fish-way at the dams. We found that adults (n=99) experienced average delays of 16-23 days at dams, losing 11 to 22% of initial fat reserves. Using linear regressions, we showed thermal experience as a strong predictor of fat loss. Delay time was also a contributing factor. Extensive delays at dams expose migrating Atlantic salmon to warmer temperatures and increase the depletion rate of energy reserves required for spawning and post-spawn survival.