DOI: 10.5061/dryad.m7rc3
title: Data from: Contrasting insights provided by single and multispecies data in a regional comparative phylogeographic study

description: 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.
description: TCS input
 filesThis 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
 filesThis 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
 filesThis 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.