Speciation Events Research Articles

Comparative Mitogenomic Analysis Indicates Possible Cryptic Species in Lambis lambis (Gastropoda: Strombidae)

The spider-like strombid Lambis lambis is widely distributed in the Indo-Pacific region and possesses morphological diversity. In the present study, the complete mitochondrial genomes of two morphologically different specimens of L. lambis that were collected in Sanya (SY) and Zhaoshu (ZS) islands of the South China Sea (namely L. lambis-SY and L. lambis-ZS) were sequenced. They were also compared with that of L. lambis previously published and sampled from coastal waters of Quanfu (QF) Island of the South China Sea (namely L. lambis-QF). The newly sequenced mitochondrial genomes L. lambis-SY and L. lambis-ZS contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and several noncoding regions, indicating a similar pattern with respect to genome size, gene order, and nucleotide composition compared with that of L. lambis-QF. Although L. lambis-SY and L. lambis-ZS differed in shell morphology, the genetic distance between them was small. On the other hand, considerable genetic distance values were detected between L. lambis-QF and L. lambis-SY/L. lambis-ZS, suggesting that the former might be a possible cryptic species within L. lambis. The divergence of the cryptic lineage L. lambis-QF was dated to 4.6 Mya, falling in the lower Pliocene that corresponded to a paleoclimatic transition from cool to warm conditions. This study, therefore, suggests a correlation between paleoclimate change and speciation event.

Patterns of hybridization in a secondary contact zone between two passerine species, the common nightingale Luscinia megarhynchos and the thrush nightingale Luscinia luscinia

Understanding how reproductive isolation arises and accumulates between incipient species is an important goal of evolutionary biology. Patterns of interspecific hybridization in naturally occurring hybrid zones can provide an important insight into this process since they reflect the strength, symmetry and nature of reproductive barriers separating the species. Here we studied patterns of hybridization in two closely related passerine species, the common nightingale Luscinia megarhynchos and the thrush nightingale L. luscinia, that diverged ~1.8 Mya and co‐occur in a secondary contact zone spanning across Europe. Genome‐wide genotyping of more than three hundred individuals from the sympatric population and adjacent allopatric populations revealed that the vast majority of sympatric individuals were pure parental species. Only 6.5% of sympatric individuals were hybrids, from which 3.4% were F1 hybrids and 3.1% backcross hybrids from the first to the fifth backcross generation. Most F1 hybrids arose from the cross of a thrush nightingale female and a common nightingale male. F1 hybrids showed intermediate morphology and could be distinguished with high confidence from the parental species based on several diagnostic traits. However, backcrosses were morphologically difficult to distinguish from the parental species from which they inherited most of the genome. Our results suggest strong, yet incomplete, reproductive isolation between the two nightingale species both at a prezygotic and postzygotic level. Nightingales thus represent a useful model system for exploring the late stages of speciation with ongoing gene flow after secondary contact.

Integrative taxonomy of the stalk‐eyed bug genus Chauliops (Heteroptera: Malcidae: Chauliopinae) reveals orogeny‐driven speciation

AbstractEconomically significant bean pests of the genus Chauliops are species rich in the areas surrounding the Qinghai–Tibet Plateau and provide an excellent system for speciation studies. Here, an integrative taxonomic approach, employing morphological analyses, population genetic methods, and multiple molecular species delimitation methods, was used to clarify the taxonomy of Chauliops in East and Southeast Asia. Four new species (Chauliops parahorizontalis Li & Bu, sp. nov., Chauliops albida Li & Bu, sp. nov., Chauliops bicoloripes Li & Bu, sp. nov., and Chauliops paraconica Li & Bu, sp. nov.) were described, which increases the number of Chauliops species in this area from six to 10; a key for Chauliops species is also provided. Phylogenetic analysis and divergence time estimation revealed that Chauliops was divided into four clades: Clade A (Chauliops bisontula + [Chauliops horizontalis + C. parahorizontalis sp. nov.]), Clade B (C. albida sp. nov. and C. bicoloripes sp. nov.), Clade C (Chauliops quaternaria and Chauliops zhengi), and Clade D (Chauliops fallax + [Chauliops conica + C. paraconica sp. nov.]). Two species diversification events of Chauliops estimated to have occurred 7–1 million years ago (Ma) and 25–13 Ma were detected. These speciation events were consistent with the two historical uplift events of the Qinghai–Tibet Plateau, suggesting that orogeny might have provided opportunities for the diversification of Chauliops species on the southeastern margin of the Qinghai–Tibet Plateau. Our findings show that population genetic analyses can be used to delimit related species and that orogeny is a key driver of species diversification on the southeastern margin of the Qinghai–Tibet Plateau.

Multiple introgressions shape mitochondrial evolutionary history in Drosophila paulistorum and the Drosophila willistoni group

Hybridization and the consequent introgression of genomic elements is an important source of genetic diversity for biological lineages. This is particularly evident in young clades in which hybrid incompatibilities are still incomplete and mixing between species is more likely to occur. Drosophila paulistorum, a representative of the Neotropical Drosophila willistoni subgroup, is a classic model of incipient speciation. The species is divided into six semispecies that show varying degrees of pre- and post-mating incompatibility with each other. In the present study, we investigate the mitochondrial evolutionary history of D. paulistorum and the willistoni subgroup. For that, we perform phylogenetic and comparative analyses of the complete mitochondrial genomes and draft nuclear assemblies of 25 Drosophila lines of the willistoni and saltans species groups. Our results show that the mitochondria of D. paulistorum are polyphyletic and form two non-sister clades that we name α and β. Identification and analyses of nuclear mitochondrial insertions further reveal that the willistoni subgroup has an α-like mitochondrial ancestor and strongly suggest that both the α and β mitochondria of D. paulistorum were acquired through introgression from unknown fly lineages of the willistoni subgroup. We also uncover multiple mitochondrial introgressions across D. paulistorum semispecies and generate novel insight into the evolution of the species.

Testing hypotheses of hybrid taxon formation in the shrubby beardtongues (Penstemon subgenus Dasanthera).

Hybridization is increasingly being identified in the genomes of species across the tree of life. This has led to a general recognition that hybridization plays an important role in the generation of species diversity. While hybridization may increase species diversity directly via the formation of new taxa through hybrid speciation, it may also act indirectly via the exchange of phenotypic and genetic variance between species, which may in turn stimulate future speciation events. Using high-throughput sequence data, we resolve phylogenetic relationships and investigate the role of hybridization as a diversification mechanism in the shrubby beardtongues (Penstemon subgenus Dasanthera), a group of North American wildflowers that has undergone a recent and rapid adaptive radiation. Specifically, we test four hypotheses of hybrid taxon formation resulting from hybridization between P. davidsonii and P. fruticosus. Species tree inference supports the monophyly of subgenus Dasanthera and elucidates relationships between taxa distributed in the Cascades and Sierra Nevada Mountains. Results also provide evidence of gene flow between P. davidsonii and P. fruticosus and support at least one hybrid origin hypothesis (P. davidsonii var. menziesii) in a region of contemporary distributional overlap. Hybridization may have also been facilitated by historical overlap in geographic distribution caused by species' responses to climatic changes during the Pleistocene. Our results support a history of hybridization between focal taxa in a rapidly radiating clade of plants and more broadly contribute to our growing understanding of the role of hybridization as a diversification mechanism in plants. This article is protected by copyright. All rights reserved.

Discovery of a New Genus and Species of Allocreadiidae (Trematoda) in Mexico: Mesoamericatrema Magnisacculus n. Gen. n. Sp.

The trematodes of Allocreadiidae are mainly parasites of freshwater fish and the family contains 18 valid genera. Since 2004, 4 genera have been described in the Americas: Paracreptotrema, Paracreptotrematoides, Pseudoparacreptotrema and Auriculostoma, of which the latter was recently synonymized with Creptotrema by Franceschini et al., (2021). During a study in 2018 on fish parasites of Lacantún River, Chiapas, Mexico, allocreadiids were collected from the intestine of Atherinella alvarezi and morphological differences with other genera of the family were immediately noted. These differences were corroborated with molecular data and phylogenetic analyses, which indicated that it was a new genus and species. The objective of this study is to describe the new taxon, which we name Mesoamericatrema magnisacculus n. gen., n. sp. as well as to clarify its phylogenetic relationships, host specificity, and geographical distribution. For this, we carried out a meticulous study of the morphology and compared the new taxon with its congeners. We also obtained sequences of the 28S and ITS from the ribosomal RNA region that were used in generating molecular phylogenies and in calculating genetic distances with sequences of other species of Allocreadiidae available in the Genbank. The new genus is mainly characterized by having a very large cirrus sac in relation to the length of its body and nests in a clade that groups Creptotrema, Creptotrematina, Paracreptotrema, Paracreptotrematoides, Pseudoparacreptotrema and Wallinia, all of which have a Neotropical affinity in terms of their geographic and host distribution. Mesoamericatrema n. gen. is the fifth genus of Allocreadiidae to be described in the Americas since 2004, the third discovered in Mexico since 2016, and the first to be described as parasitizing Atheriniformes, which indicates that Middle America is a region where important speciation events have occurred in freshwater fish parasites.

The role of divergent ecological adaptation during allopatric speciation in vertebrates

After decades of debate, biologists today largely agree that most speciation events require an allopatric phase (that is, geographic separation), but the role of adaptive ecological divergence during this critical period is still unknown. Here, we show that relatively few allopatric pairs of birds, mammals, or amphibians exhibit trait differences consistent with models of divergent adaptation in each of many ecologically relevant traits. By fitting new evolutionary models to numerous sets of sister-pair trait differences, we find that speciating and recently speciated allopatric taxa seem to overwhelmingly evolve under similar rather than divergent macro-selective pressures. This contradicts the classical view of divergent adaptation as a prominent driver of the early stages of speciation and helps synthesize two historical controversies regarding the ecology and geography of species formation.

Diversification of Amazonian spiny tree rats in genus Makalata (Rodentia, Echimyidae): Cryptic diversity, geographic structure and drivers of speciation.

Amazonian mammal diversity is exceptionally high, yet new taxonomic discoveries continue to be made and many questions remain for understanding its diversification through time and space. Here we investigate the diversification of spiny rats in the genus Makalata, whose species are strongly associated with seasonally flooded forests, watercourses and flooded islands. We use a biogeographical approach based on a mitochondrial cytochrome b gene through divergence time estimation and reconstruction of ancestral areas and events. Our findings indicate an ancient origin of Makalata for the Guiana Shield and Eastern Amazonia as ancestral area. A first cladogenetic event led to a phylogeographic break into two broader clades of Makalata through dispersal, implying a pattern of western/Eastern Amazonian clades coinciding with the Purus Arch (middle Miocene). Most of subclades we infer originated between the late Pliocene to the early Pleistocene, with few recent exceptions in the early Pliocene through dispersal and vicariant events. The hypothesis of rivers as dispersal barriers is not corroborated for Makalata, as expected for mammalian species associated with seasonally flooded environments. We identify two key events for the expansion and diversification of Makalata species: the presence of geologically stable areas in the Guiana and Brazilian shields and the transition from lacustrine conditions in western Amazonia (Acre system) to a river system, with the establishment of the Amazon River transcontinental system and its tributaries. Our results are congruent with older geological scenarios for the Amazon basin formation (Miocene), but we do not discard the influence of recent dynamics on some speciation events and, mainly, on phylogeographic structuring processes.

Female preferences between incipient species of Drosophila athabasca reveal divergent closed functions, epistasis, and segregation of veiled preference alleles.

Theoretical models typically assume that speciation is driven by divergence in female preference functions for secondary sexual traits. However, little is known about how these functions diverge between incipient species. This study used song playback experiments and mate choice tests to characterize female preference functions for divergent male courtship songs between two incipient species of Drosophila athabasca complex; D. athabasca (WN) and Drosophila mahican (EA). The study focused on two male song parameters: pulses per burst (PPB) and inter-pulse interval (IPI). Preference functions for PPB were open-ended and lacked species-specificity. In contrast, preference functions for IPI revealed a closed shape, with peak preferences highly divergent between species. Thus, females imposed divergent and ongoing sexual selection on male IPI. Further work demonstrated variation in peak preferences and choosiness for IPI across genetic lines, while F1 hybrid females varied extensively in their mating preferences across different heterospecific line crosses. Finally, F2 female genotypes with foreign single-copy chromosome substitutions showed little to no change in preferences until three or four chromosomes were combined: indicating strong dominance epistasis. These results suggest "veiled" or hidden segregating female preference alleles for male speciation phenotypes. This may explain the rapid speciation observed in this species complex.

Power of Bayesian and Heuristic Tests to Detect Cross-Species Introgression with Reference to Gene Flow in the Tamias quadrivittatus Group of North American Chipmunks.

In the past two decades, genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used the heuristic method HYDE to detect gene flow, which may suffer from low power. Here we use the Bayesian method implemented in the program BPP to re-analyze these data. We develop a Bayesian test of introgression, calculating the Bayes factor via the Savage-Dickey density ratio using the Markov chain Monte Carlo (MCMC) sample under the model of introgression. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 63%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. We examine the assumptions and performance of HYDE and demonstrate that it lacks power if gene flow occurs between sister lineages or if the mode of gene flow does not match the assumed hybrid-speciation model with symmetrical population sizes. Our analyses highlight the power of likelihood-based inference of cross-species gene flow using genomic sequence data. [Bayesian test; BPP; chipmunks; introgression; MSci; multispecies coalescent; Savage-Dickey density ratio.].

Rapid Speciation of the London Underground Mosquito (Culex pipiens molestus)

In evolutionary biology, speciation is often perceived as a gradual evolutionary process spanning thousands of generations. However, the emergence of the London Underground mosquito (Culex pipiens molestus) from the common house mosquito (Culex pipiens) illustrates a recent, observable speciation event. Via allopatric speciation, the mosquito population in London’s underground railway system evolved distinct behavioural and physiological characteristics, becoming isolated and successful in its unique underground environment. The two mosquito species are significantly genetically distinct, and various reproductive barriers exist between them. The London Underground mosquito demonstrates a rapid speciation event that occurred over only a couple generations and is a strong model of evolution.

The road less travelled? Exploring the nuanced evolutionary consequences of duplicated genes

Duplicated genes have long been appreciated as both substrates and catalysts of evolutionary processes. From even the simplest cell to complex multicellular animals and plants, duplicated genes have made immeasurable contributions to the phenotypic evolution of all life on Earth. Not merely drivers of morphological innovation and speciation events, however, gene duplications sculpt the evolution of genetic architecture in ways we are only just coming to understand now we have the experimental tools to do so. As such, the present article revisits our understanding of the ways in which duplicated genes evolve, examining closely the various fates they can adopt in light of recent work that yields insights from studies of paralogues from across the tree of life that challenge the classical framework.

Generation of raptor diversity in Europe: linking speciation with climate changes and the ability to migrate.

Europe holds a rich community of diurnal birds of prey, and the highest proportion of transcontinental migratory raptorial species of any landmass. This study will test the hypotheses that the high diversification of the raptor assemblage in Europe is a recent event, that closely related species sharing the same trophic niches can only coexist in sympatry during the breeding period, when food availability is higher, and finally that migration is a function of size, with the smaller species in every trophic group moving further. A consensus molecular phylogeny for the 38 regular breeding species of raptors in Europe was obtained from BirdTree (www.birdtree.org). For the same species, a trophic niche cluster dendrogram was constructed. Size and migratory strategy were introduced in the resulting phylogeny, where trophic groups were also identified. Multispecific trophic groups tended to be composed of reciprocal sister species of different sizes, while monospecific groups (n = 3) were composed of highly specialized species. Many speciation events took place recently, during the glacial cycles of the Quaternary, and size divergence among competing species may be due to character displacement. Nowadays, the smaller species in every trophic group migrate to sub-Saharan Africa. This investigation illustrates how the rich assemblage of diurnal birds of prey in Europe, more diverse and more migratory than, for instance, the North American assemblage at equivalent latitudes, has emerged recently due to the multiplication of look-alike species with similar trophic ecologies, possibly in climate refugia during cold periods.

Eco-Geography and Phenology Are the Major Drivers of Reproductive Isolation in the Royal Irises, a Species Complex in the Course of Speciation

The continuous nature of speciation implies that different species are found at different stages of divergence, from no- to complete reproductive isolation. This process and its underlying mechanisms are best viewed in incipient species. Moreover, the species complex can offer unique insight into how reproductive isolation (RI) has evolved. The royal irises (Iris section Oncocyclus) are a young group of species in the course of speciation, providing an ideal system for speciation study. We quantified pre- and post-zygotic reproductive barriers between the eight Israeli species of this complex and estimated the total RI among them. We tested for both pre-pollination and post-pollination reproductive barriers. Pre-pollination barriers, i.e., eco-geographic divergence and phenological differentiation were the major contributors to RI among the Iris species. On the other hand, post-pollination barriers, namely pollen-stigma interactions, fruit set, and seed viability had negligible contributions to total RI. The strength of RI was not uniform across the species complex, suggesting that species may have diverged at different rates. Overall, this study in a young, recently diverged group of species provides insight into the first steps of speciation, suggesting a crucial role of the pre-zygotic barriers.

Mammalian diversification bursts and biotic turnovers are synchronous with Cenozoic geoclimatic events in Asia

Asia's rich species diversity has been linked to its Cenozoic geodiversity, including active mountain building and dramatic climatic changes. However, prior studies on the diversification and assembly of Asian faunas have been derived mainly from analyses at taxonomic or geographic scales too limited to offer a comprehensive view of this complex region's biotic evolution. Here, using the class Mammalia, we built historical biogeographic models drawn on phylogenies of 1,543 species occurring across Asia to investigate how and when the mammal diversity in Asian regions and mountain hotspots was assembled. We explore the roles of in situ speciation, colonization, and vicariance and geoclimatic events to explain the buildup of Asia's regional mammal diversity through time. We found that southern Asia has served as the main cradle of Asia's mammal diversity. Present-day species richness in other regions is mainly derived from colonization, but by the Miocene, in situ speciation increased in importance. The high biodiversity present in the mountain hotspots (Himalayas and Hengduan) that flank the Qinghai-Tibetan plateau is a product of high colonization instead of in situ speciation, making them important centers of lineage accumulation. Overall, Neogene was marked by great diversification and migrations across Asia and surrounding continents but Paleogene environments already hosted rich mammal assemblages. Our study revealed that synchronous diversification bursts and biotic turnovers are temporally associated with tectonic events (mountain building, continental collisions) and drastic reorganization of climate (aridification of Asian interior, intensification of Asian monsoons, sea retreat) that took place throughout the Cenozoic in Asia.

Initiation of speciation across multiple dimensions in a rock-restricted, tropical lizard.

Population isolation and concomitant genetic divergence, resulting in strong phylogeographical structure, is a core aspect of speciation initiation. If and how speciation then proceeds and ultimately completes depends on multiple factors that mediate reproductive isolation, including divergence in genomes, ecology and mating traits. Here we explored these multiple dimensions in two young (Plio-Pleistocene) species complexes of gekkonid lizards (Heteronotia) from the Kimberley-Victoria River regions of tropical Australia. Using mitochondrial DNA screening and exon capture phylogenomics, we show that the rock-restricted Heteronotia planiceps exhibits exceptional fine-scale phylogeographical structure compared to the codistributed habitat generalist Heteronotia binoei. This indicates pervasive population isolation and persistence in the rock-specialist, and thus a high rate of speciation initiation across this geographically complex region, with levels of genomic divergence spanning the "grey zone" of speciation. Proximal lineages of H.planiceps were often separated by different rock substrates, suggesting a potential role for ecological isolation; however, phylogenetic incongruence and historical introgression were inferred between one such pair. Ecomorphological divergence among lineages within both H.planiceps and H.binoei was limited, except that limestone-restricted lineages of H.planiceps tended to be larger than rock-generalists. By contrast, among-lineage divergence in the chemical composition of epidermal pore secretions (putative mating trait) exceeded ecomorphology in both complexes, but with less trait overlap among lineages in H.planiceps. This system-particularly the rock-specialist H.planiceps-highlights the role of multidimensional divergence during incipient speciation, with divergence in genomes, ecomorphology and chemical signals all at play at very fine spatial scales.

Modeling-informed Engineered Genetic Incompatibility strategies to overcome resistance in the invasive Drosophila suzukii.

Engineered Genetic Incompatibility (EGI) is an engineered extreme underdominance genetic system wherein hybrid animals are not viable, functioning as a synthetic speciation event. There are several strategies in which EGI could be leveraged for genetic biocontrol of pest populations. We used an agent-based model of Drosophila suzukii (Spotted Wing Drosophila) to determine how EGI would fare with high rates of endemic genetic resistance alleles. We discovered a surprising failure mode wherein field-generated females convert an incompatible male release program into a population replacement gene drive. Local suppression could still be attained in two seasons by tailoring the release strategy to take advantage of this effect, or alternatively in one season by altering the genetic design of release agents. We show in this work that data from modeling can be utilized to recognize unexpected emergent phenomena and a priori inform genetic biocontrol treatment design to increase efficacy.

Rock island melody remastered: two new species in the Afroedura bogerti Loveridge, 1944 group from Angola and Namibia

Newly collected material from northern Namibia’s Otjihipa Mountains and west-central Angola allowed us to revisit the Afroedura bogerti Loveridge, 1944 group. The employment of additional gene markers, including nuclear markers, allowed us to identify two new species in the group and infer species boundaries and potential speciation events in Afroedura from southwestern Africa. The new Namibian material is recovered as a sister species to A. donveae, from which it differs mostly by the colour of the iris (copper versus black) and dorsal colouration. Material from the first elevational gradient of the escarpment in Benguela Province, Angola was found to be more closely related to A. bogerti than A. wulfhaackei. The differences between these two species are more subtle, although the new species exhibits higher mid-body scale rows (79.5 versus 74.8), different dorsal colouration and supranasal scales always in contact (versus 57% in contact).

EggNOG 6.0: enabling comparative genomics across 12535 organisms.

The eggNOG (evolutionary gene genealogy Non-supervised Orthologous Groups) database is a bioinformatics resource providing orthology data and comprehensive functional information for organisms from all domains of life. Here, we present a major update of the database and website (version 6.0), which increases the number of covered organisms to 12 535 reference species, expands functional annotations, and implements new functionality. In total, eggNOG 6.0 provides a hierarchy of over 17M orthologous groups (OGs) computed at 1601 taxonomic levels, spanning 10 756 bacterial, 457 archaeal and 1322 eukaryotic organisms. OGs have been thoroughly annotated using recent knowledge from functional databases, including KEGG, Gene Ontology, UniProtKB, BiGG, CAZy, CARD, PFAM and SMART. eggNOG also offers phylogenetic trees for all OGs, maximising utility and versatility for end users while allowing researchers to investigate the evolutionary history of speciation and duplication events as well as the phylogenetic distribution of functional terms within each OG. Furthermore, the eggNOG 6.0 website contains new functionality to mine orthology and functional data with ease, including the possibility of generating phylogenetic profiles for multiple OGs across species or identifying single-copy OGs at custom taxonomic levels. eggNOG 6.0 is available at http://eggnog6.embl.de.

Environmental features drive lineage diversification in the Aricidea assimilis species complex (Annelida, Paraonidae) in the Mediterranean Sea

Individuals identified as Aricidea assimilis Tebble, 1959 were collected from ten localities across the Mediterranean Sea from 0.5 to 225 m depth in order to have a wide coverage of the species habitats and geographic range and to assess the effects of environmental factors and biogeographical barriers on molecular and morphological diversity. Two mitochondrial and one nuclear markers were used to reconstruct phylogenetic relationships and test the occurrence of cryptic species. We observed two highly divergent lineages, one including all individuals from shallow, sandy environments (<10 m depth) and the other with the individuals from deeper muddy bottoms (30–225 m depth). Less pronounced divergence was detected between morphologically distinct brackish-water individuals and the remaining shallow-water individuals. The divergence observed between deep-water and shallow-water lineages is consistent with the hypothesis of distinct species. The ambiguous results of species delimitation tests applied to the two shallow-water sub-lineages might instead suggest a process of incipient speciation, even if this hypothesis needs additional evidence. These results suggest that sediment represents the main factor driving genetic divergence and ultimately cryptic speciation in A. assimilis, while other depth-associated factors and geographical barriers do not seem to significantly contribute to the genetic architecture of this species, suggesting the occurrence of wide-range larval dispersal.