Many single-species freshwater phylogeographic studies have been carried out in south-east Queensland; however comparative phylogeography requires multiple lines of evidence to infer deep, significant relationships between landscape and biota. The present study aimed to test conclusions resulting from single taxon studies in a multispecies comparative framework: (1) how influential are river basins in the genetic structure of freshwater species; (2) are there biogeographic frontiers between groups of basins; and (3) could deep intraspecific lineages be explained by a single event? New and existing data from 33 freshwater species (23 fishes and 10 crustaceans) were combined, and both standard single-species analyses (haplotype networks, genetic distances, ΦST) and multispecies methods (hierarchical ABC) were carried out for 1814 sequences from eight basins. More than half of the species displayed a high phylogeographic structure and contained at least two distinct lineages. Almost all of the lineage divergences displayed an element of north/south geographic breaks, with the most influential boundary being between the Mary and Brisbane rivers. Of the 11 basin-pair multispecies coalescent analyses, four implied a single divergence as being most likely. A regional analysis of deep lineages within 16 taxon-pairs resulted in a strongly supported inference of a single divergence, probably dating to the Pleistocene. Basin boundaries are a key determinant of phylogeographic patterns for most of these freshwater species, although the specific biogeographic relationship between basins often varies depending on the species. There are a number of influential biogeographic frontiers, with the Brisbane-Mary being the most important. The finding that a single event may be responsible for multiple deep lineages across the region implies that a highly influential climate change event may have been detected.
TCS input files
This is a ZIP file consisting of 33 separate input files for the program TCS version 1.21 (Clement et al. 2000), which creates haplotype networks. Each file is a separate species. All specific haplotype details can be found in Table S2 of the online Supporting information for this paper. Species codes: AA = Ambassis agassizi, AM = Ambassis marianus, AS = Australatya striolata, CA = Caridina indistincta "A", CB = Caridina indistincta "B", CC = Caridina indistincta "C", CH = Cherax dispar "C", CM = Craterocephalus marjoriae, CP = Caridina sp. "D", CS = Craterocephalus stercusmuscarum, GA = Gobiomorphus australis, GP = Glossamia aprion, HC = Hypseleotris compressa, HG = Hypseleotris galii, HK = Hypseleotris klunzingeri, HM = Hypseleotris sp. Midgleys, LU = Leiopotherapon unicolor, MA = Mogurnda adspersa, MD = Melanotaenia duboulayi, MT = Macrobrachium tolmerum, MU = Macrobrachium australiense, NE = Nematalosa erebi, NO = Nannoperca oxleyana, P4 = Paratya australiensis "4", P6 = Paratya australiensis "6", PA = Philypnodon macrostomus, PG = Philypnodon grandiceps, PM = Pseudomugil mellis, PR = Porochilus rendalhi, PS = Pseudomugil signifer, RO = Rhadinocentrus ornatus "SEQ", RS = Retropinna semoni "SEQ", TT = Tandanus tandanus.
Arlequin input files
This is a ZIP file consisting of 33 separate Arlequin input files. Arlequin version 3.5 (Excoffier et al. 2005) was used to calculate overall ΦST for each species separately (populations grouped into river basins). All specific haplotype details can be found in Table S2 of the online Supporting information for this paper. Species codes: AA = Ambassis agassizi, AM = Ambassis marianus, AS = Australatya striolata, CA = Caridina indistincta "A", CB = Caridina indistincta "B", CC = Caridina indistincta "C", CH = Cherax dispar "C", CM = Craterocephalus marjoriae, CP = Caridina sp. "D", CS = Craterocephalus stercusmuscarum, GA = Gobiomorphus australis, GP = Glossamia aprion, HC = Hypseleotris compressa, HG = Hypseleotris galii, HK = Hypseleotris klunzingeri, HM = Hypseleotris sp. Midgleys, LU = Leiopotherapon unicolor, MA = Mogurnda adspersa, MD = Melanotaenia duboulayi, MT = Macrobrachium tolmerum, MU = Macrobrachium australiense, NE = Nematalosa erebi, NO = Nannoperca oxleyana, P4 = Paratya australiensis "4", P6 = Paratya australiensis "6", PA = Philypnodon macrostomus, PG = Philypnodon grandiceps, PM = Pseudomugil mellis, PR = Porochilus rendalhi, PS = Pseudomugil signifer, RO = Rhadinocentrus ornatus "SEQ", RS = Retropinna semoni "SEQ", TT = Tandanus tandanus.
MTML-msbayes input files
This is a ZIP file consisting of 17 pairs of input files for MTML-msBayes (Huang et al. 2011), which estimates the number of divergence events. Each separate MTML-msBayes analysis requires 2 input files ("batch.masterIn.fromIM" and "obsSS.txt"). These have been labeled to differentiate the different analyses, which correspond to those listed in Table 2 of the paper. Basin Codes et al: BRI = Brisbane, GOL = Gold Coast, LOG = Logan-Albert, MCY = Maroochy, MRY = Mary, NOO = Noosa, PIN = Pine, TCB = Tin Can Bay, CR = Control Region, PS = Pseudomugil signifier.