Phylogenomics, Lineage Diversification Rates, and the Evolution of Diadromy in Clupeiformes (Anchovies, Herrings, Sardines, and Relatives).

Migration independently evolved numerous times in animals, with a myriad of ecological and evolutionary implications. In fishes, perhaps the most extreme form of migration is diadromy, the migration between marine and freshwater environments. Key and longstanding questions are: how many times has diadromy evolved in fishes, how frequently do diadromous clades give rise to non-diadromous species, and does diadromy influence lineage diversification rates? Many diadromous fishes have large geographic ranges with constituent populations that use isolated freshwater habitats. This may limit gene flow among some populations, increasing the likelihood of speciation in diadromous lineages relative to non-diadromous lineages. Alternatively, diadromy may reduce lineage diversification rates if migration is associated with enhanced dispersal capacity that facilitates gene flow within and between populations. Clupeiformes (herrings, sardines, shads and anchovies) is a model clade for testing hypotheses about the evolution of diadromy because it includes an exceptionally high proportion of diadromous species and several independent evolutionary origins of diadromy. However, relationships among major clupeiform lineages remain unresolved and existing phylogenies sparsely sampled diadromous species, limiting the resolution of phylogenetically-informed statistical analyses. We assembled a phylogenomic dataset and used multi-species coalescent and concatenation-based approaches to generate the most comprehensive, highly-resolved clupeiform phylogeny to date, clarifying associations among several major clades and identifying recalcitrant relationships needing further examination. We determined that variation in rates of sequence evolution (heterotachy) and base-composition (non-stationarity) had little impact on our results. Using this phylogeny, we characterized evolutionary patterns of diadromy and tested for differences in lineage diversification rates between diadromous, marine, and freshwater lineages. We identified thirteen transitions to diadromy, all during the Cenozoic Era (ten origins of anadromy, two origins of catadromy, and one origin of amphidromy), and seven losses of diadromy. Two diadromous lineages rapidly generated non-diadromous species, demonstrating that diadromy is not an evolutionary dead-end. We discovered considerably faster transition rates out of diadromy than to diadromy. The largest lineage diversification rate increase in Clupeiformes was associated with a transition to diadromy, but we uncovered little statistical support for categorically faster lineage diversification rates in diadromous versus non-diadromous fishes. We propose that diadromy may increase the potential for accelerated lineage diversification, particularly in species that migrate long distances. However, this potential may only be realized in certain biogeographic contexts, such as when diadromy allows access to ecosystems in which there is limited competition from incumbent species.

Sourcing aliphatic and polycyclic aromatic hydrocarbons (PAHs) in Jinga shrimp (Metapenaeus affinis) muscle tissues and surface sediments (study case: Northwest Persian Gulf).

This study addresses the sources of aliphatic hydrocarbons (AHs) and polycyclic aromatic hydrocarbons (PAHs) in the surface sediments of the northwestern Persian Gulf and the muscle tissues of Jinga shrimp (Metapenaeus affinis), a commercially important aquatic species. In November 2018, 28 Jinga shrimp samples were systematically collected from four key fishing areas in Behrgan and Khormusi: Imam Khomeini Port (S1), Mahshahr Port (S2), Sejafi (S3), and Behrgan Wharf (S4). Additionally, sediment samples were collected from these locations, and AHs and PAHs concentrations were analyzed using gas chromatography-mass spectrometry (GC-MS). The average aliphatic concentration in Jinga shrimp was 4800.32 (µg g-1 DW), exceeding the sediment samples' 2496.69 (µg g-1 DW) estimate. Hydrocarbon component analysis revealed EPA priority list (PAH-16) and measured PAHs (PAH-29) concentrations in Jinga shrimp ranging from 1095.8 to 2698.3 (ng g-1 DW) and in sediments from 653.6 to 1019.5 (ng g-1 DW). Elevated AHs and PAHs in Jinga shrimp, compared to sediments, suggest a petrogenic source, notably at station S4 near Behrgansar and Nowruz oil fields. Low molecular weight (LMW) compounds dominated in both shrimp and sediment PAHs. Aliphatic composition profiles in shrimps closely mirrored sediment profiles, illustrating an even-to-odd carbon dominance gradient. Diagnostic ratio examinations of hydrocarbons indicated pervasive petroleum derivatives in the environment. This study establishes a direct correlation between hydrocarbon concentrations in shrimp and sediment samples and the corresponding aliphatic groups, PAH-16, and PAH-29. The findings underscore the potential of Jinga shrimp as a reliable indicator of hydrocarbon pollution in the northwestern Persian Gulf.

Metals bioaccumulation, possible sources and consumption risk assessment in five Sillaginid species, a case study: Bandar Abbas (Persian Gulf) and Chabahar Bay (Oman Sea), Iran.

In this study, the concentrations of 10 metals (As, Al, Cd, Cr, Cu, Fe, Hg, Ni, Pb and Zn) in different tissues (gill, muscle and otolith) of five sillaginid species (Sillago arabica, S. attenuata and S. sihama from the Persian Gulf and S. indica, S. sihama and Sillaginopodys chondropus from the Oman Sea) were analyzed using ICP-MS, and the potential human health risk assessment for local consumers was also conducted using standard indices. The concentration of trace metals (µg g-1 dw) in fish ranged from 0.24 to 16.09 (As), 7.88 to 167.51 (Al), 0.005 > -0.866 (Cd), 0.006 > -7.95 (Cr), 1.02-5.58 (Cu), 24.86 to 390.85 (Fe), 0.005 > -1.93 (Hg), 0.021 > -7.80 (Ni), 0.33-4.41 (Pb) and 4.78-170.43 (Zn). The levels of trace metals varied significantly among sampling sites, fish species and their tissues. Gill tissues accumulate higher concentrations of the analyzed elements, except for As and Hg, whose higher concentrations were found in muscle tissues. Among the species, S. sihama in the Persian Gulf showed the highest levels of toxic metals compared to the other species. The dendrogram of metal association in fish muscle tissues revealed that Ni, Cr, Cd, Pb and Hg in muscles mainly originated from anthropogenic sources, especially petroleum activities. A second dendrogram based on the association of these five metals in the muscle tissue separated the sillaginid species of the Persian Gulf from the Oman Sea. The mean concentrations of the analyzed metals in the edible tissues were lower than international standards of maximum permissible limits (MPL), except for inorganic As (iAs) and Pb. The index of estimated daily intake (EDI) for Cr and Hg in all sillaginid species, and iAs, Pb and Ni only in the Persian Gulf's sillaginid species was higher than the recommended values. The value of the target hazard quotient (THQ) indicated that the intake of individual heavy metals due to the consumption of sillaginid species was safe for human health (except Hg in S. arabica) whereas combined heavy metals' intake revealed potential health problems in the case of increased consumption for all three sillaginids in the Persian Gulf. Target cancer risk (TR) for iAs in all species and Cd, Cr and Ni in Persian Gulf species was higher than the acceptable range. The results indicated the health issues associated with high consumption, especially for sillaginids in the Persian Gulf, which should be considered in food safety monitoring for local people in the area.

Taillessness and skeletal deformity in striped piggy Pomadasys stridens (Osteichthyes: Haemulidae) from the Persian Gulf.

Taillessness (absence of the caudal fin and some of the caudal peduncle) and skeletal deformity is described in 2 striped piggy Pomadasys stridens (Haemulidae) specimens collected from the Persian Gulf along the coast of Hormuz Island, Iran. Deformed specimens were entirely missing caudal fins along with at least 1 caudal vertebra, caudal portions of vertebral columns were bent dorsoventrally, posterior sections of swim bladders were reduced in size, and caudal vertebral centra were compacted anteroposteriorly in 1 individual. Environmental conditions in the Persian Gulf may be responsible for these deformities, but genetic causes cannot be entirely ruled out.

Taxonomic validity and phylogenetic relationships of a newly-described tooth-carp, Aphanius mesopotamicus Coad, 2009 (Teleostei: Cyprinodontidae).

Variation among complete cytb sequences (1140 bp) of Aphanius mesopotamicus Coad, 2009 was compared with closely related species, to investigate the validity of this taxon as a newly-described tooth-carp based on morphological characteristics. Maximum likelihood and Bayesian likelihood trees supported the monophyly of A. mesopotamicus and its sister group relationship to A. sophiae. Some 10-16 differences were found when compared to four different population samples of A. sophiae, whereas, intraspecific differences were only up to 6 bp. These distances suggest divergence from a common ancestor with A. sophiae at roughly 1 million years ago. These results are congruent with morphology-based hypotheses, indicating a recent speciation event.