Phylogeography of sand‐burrowing amphipods (Haustoriidae) supports an ancient suture zone in the Gulf of Mexico

Abstract

Aim To evaluate the impact of a proposed ancient suture zone in the Gulf of Mexico on the distribution and molecular diversity of dispersal‐limited, sand‐burrowing amphipods of the genera Haustorius and Lepidactylus (Haustoriidae: Amphipoda). Location Gulf of Mexico, USA and Mexico. Methods Phylogenetic and population genetic analyses were performed using mitochondrial (COI and 16S) and nuclear (18S and 28S) data from 93 amphipod individuals from 16 sites across the Gulf of Mexico. Bayesian and ML phylogenies were constructed for all genes, divergence times were estimated using a molecular clock for COI (0.007–0.013 subs./site per Myr), and four species delimitation methods were used to identify operational taxonomic units (OTUs) within each amphipod species. The mitochondrial COI gene was used to construct haplotype networks and estimate population genetic parameters to evaluate historical changes in effective population sizes. Results Deep divergences (most estimated to be >4 Ma) were uncovered between sister clades of both amphipod genera on either side of the Mississippi River as well as within Lepidactylus triarticulatus where each sample site was found to harbour a unique genetic lineage. Two cryptic OTUs of L. triarticulatus were identified living sympatrically at Pass Christian, Mississippi. Two distinct OTUs representing western and eastern Haustorius galvezi clades were identified along the Texas and Mexico coastlines with abutting ranges. Population genetic results show some support for recent population expansions for western Gulf OTUs, while eastern Gulf OTUs may have suffered population bottlenecks in the past. Main conclusions Divergences between sister species of sand‐burrowing amphipods exceeds the timing of previous vicariant hypotheses. The split appears to be consistent with Miocene sedimentation levels from the Mississippi River acting as an east–west barrier to gene flow in the Gulf of Mexico. Given their strong population structure and cryptic diversity, haustoriid amphipods are ideal model organisms for studying open coast biogeography.

Rapid genomic expansion and purging associated with habitat transitions in a clade of beach crustaceans (Haustoriidae: Amphipoda)

“…Previous work on this family has found strong population structure and widespread cryptic diversity (Hancock et al 2019). In the GoM there are at least 6 species of haustoriids:…”

“…We specified a GTR model of substitution for COI and an HKY model for 28S, as these were the indicated best models in PartitionFinder2 (Lanfear et al 2017). We applied a molecular clock to COI as an exponential prior with a mean of 0.01 substitutions per site per Myr (Hancock et al 2019;Takada et al 2018;Knowlton & Weigt 1998). We applied a relaxed lognormal clock to 28S following Hancock et al (2019).…”

“…We applied a molecular clock to COI as an exponential prior with a mean of 0.01 substitutions per site per Myr (Hancock et al 2019;Takada et al 2018;Knowlton & Weigt 1998). We applied a relaxed lognormal clock to 28S following Hancock et al (2019). We then applied two calibration points based on known vicariant events: 1) the closure of the Okefenokee Trough ~1.75 Myr separating Atlantic and Gulf taxa (Bert 1986;McClure & Greenbaum 1999); and 2) the proposed interglacial Pleistocene colonization of H. arenarius to Europe (Bousfield 1970).…”

“…Whole genomic DNA was extracted from either the whole specimen or pereopods 6-7 depending on the size of the amphipod using an EZNA Tissue DNA kit (Omega Bio-tek Inc.) following manufacturer's protocols. Mitochondrial cytochrome oxidase I (COI) was amplified using forward and reverse primers from Folmer et al (1994), and nuclear 28S ribosomal RNA (28S) was amplified using primers from Hancock et al (2019). Polymerase chain reaction (PCR) conditions followed Hancock et al (2019) for both mitochondrial and nuclear loci.…”

“…Mitochondrial cytochrome oxidase I (COI) was amplified using forward and reverse primers from Folmer et al (1994), and nuclear 28S ribosomal RNA (28S) was amplified using primers from Hancock et al (2019). Polymerase chain reaction (PCR) conditions followed Hancock et al (2019) for both mitochondrial and nuclear loci. Amplicons were verified using gel electrophoresis and purified with ExoSAP-IT (Affymetrix Inc.).…”