Global species delimitation and phylogeography of the circumtropical ‘sexy shrimp’ Thor amboinensis reveals a cryptic species complex and secondary contact in the Indo‐West Pacific

Abstract

Aim:The "sexy shrimp" Thor amboinensis is currently considered a single circumtropical species. However, the tropical oceans are partitioned by hard and soft barriers to dispersal, providing ample opportunity for allopatric speciation. Herein, we test the null hypothesis that T. amboinensis is a single global species, reconstruct its global biogeographical history, and comment on population-level patterns throughout the Tropical Western Atlantic.Location: Coral reefs in all tropical oceans.Methods: Specimens of Thor amboinensis were obtained through field collection and museum holdings. We used one mitochondrial (COI) and two nuclear (NaK, enolase) gene fragments for global species delimitation and phylogenetic analyses (n = 83 individuals, 30 sample localities), while phylogeographical reconstruction in the TWA was based on COI only (n = 303 individuals, 10 sample localities).Results: We found evidence for at least five cryptic lineages (9%-22% COI pairwise sequence divergence): four in the Indo-West Pacific and one in the Tropical Western Atlantic. Phylogenetic reconstruction revealed that endemic lineages from Japan and the South Central Pacific are more closely related to the Tropical Western Atlantic lineage than to a co-occurring lineage that is widespread throughout the Indo-West Pacific. Concatenated and species tree phylogenetic analyses differ in the placement of an endemic Red Sea lineage and suggest alternate dispersal pathways into the Atlantic. Phylogeographical reconstruction throughout the Tropical Western Atlantic reveals little genetic structure over more than 3,000 km.Main conclusions: Thor amboinensis is a species complex that has undergone a series of allopatric speciation events and whose members are in secondary contact in the Indo-West Pacific. Nuclear-and mitochondrial-gene phylogenies show evidence of introgression between lineages inferred to have been separated more than 20 Ma. Phylogenetic discordance between multi-locus analyses suggest that T. amboinensis originated in the Tethys sea and dispersed into the Atlantic and Indo-West Pacific through the Tethys seaway or, alternatively, originated in the Indo-

Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan (Hexacorallia: Actiniaria)

“…Anemone samples were collected by hand using SCUBA at 14 localities spanning the geographic range of B. annulata , including localities separated by known phylogeographic barriers (Figure ; Table ; DeBiasse, Richards, Shivji, & Hellberg, ; Titus, Daly, Hamilton, Berumen, & Baeza, ). Samples were collected between 5 and 20 m depth, preserved on shore, and transferred back to The Ohio State University for DNA extraction and sequencing.…”

“…Much of the species-level diversity could be cryptic, a point highlighted by a global study of the genus Anthothoe in the southern hemisphere (Spano et al, 2018). Many molecular studies routinely recover evidence of cryptic lineages when conducting biogeographic surveys in marine habitats (Meyer-Wachsmuth, Galletti, & Jondelius, 2014;Postaire, Magalon, Bourmaud, & Bruggemann, 2016;Titus et al, 2018). Metabarcoding studies further underscore the extent to which marine biodiversity is probably underdescribed (Al-Rshaidat et al, 2016;Leray & Knowlton, 2016).…”

Molecular phylogeny and historical biogeography of marine palaemonid shrimps (Palaemonidae: Palaemonella–Cuapetes group)

“…The eastern Pacific Cuapetes canariensis closely related to IWP Cuapetes spp., has been recently described by Fransen et al 41 , from the Canary Islands. This could indicate alternative dispersal pathways into the Atlantic, as suggested by recent studies 17,42 . The Tethys seaway allowed natural dispersion between the Atlantic and Indian Oceans across the region of the Mediterranean Sea.…”

Population structure and reproductive performance in the sea anemone associated shrimp Ancylocaris brevicarpalis (Caridea: Palaemonidae)

“…Many studies have considered caridean shrimps as a suitable model organism to study different habitat/hosts (Bauer, 2004), host use patterns (Fautin et al ., 1995; Levitt-Barmats & Shenkar, 2018), sexual biology (Baeza & Bauer, 2004; Prakash et al ., 2017 a ; Dickson et al ., 2020), mating behaviour (Baeza & Thiel, 2007; Zhang et al ., 2007; Prakash et al ., 2016), phylogenetic relationships (Baeza, 2010, 2013; De Grave et al ., 2015 b ; Horka et al ., 2016), cryptic species complexes (Titus et al ., 2018; Baeza & Prakash, 2019) and eusociality (Duffy, 1996). Apart from being a potential model for various studies, caridean shrimps from coral reef areas are also commercially exploited to meet the demand of the global marine aquarium trade (Calado et al ., 2003; Rhyne et al ., 2009; Baeza & Behringer, 2017; Prakash et al ., 2017 b ).…”