Phylogeography of vertebrates on the Sunda Shelf: a multi‐species comparison

Abstract

26Aim Pleistocene environmental fluctuations had well-characterized impacts on the 27 patterns of within-species divergences and diversity in temperate habitats. Here we 28 examine the impact the Pleistocene had on widely distributed forest vertebrates in a 29 tropical system where the distribution of the habitat was affected by those 30 fluctuations. 31Location Sundaland, tropical Southeast Asia. 32Methods We conducted a comparative phylogeographical analysis of 28 non-33 migratory, forest-dependent vertebrates for which we constructed rooted, intraspecifc 34 phylogenies based on mitochondrial DNA sequences of individuals from at least the 35 three major landmasses in the area (Borneo, Sumatra and the Malay Peninsula) and 36 compared them to hypothetical phylogenies based on independent geological data and 37 climate models regarding connections and relationships between the major 38 landmasses of Sundaland. Java was included where possible. We dated the 39 phylogenies to determine whether patterns of differentiation were concordant across 40 species. 41Results In most species, populations on the Malay Peninsula and Sumatra were most 42 closely related, and sister to those from Borneo. The dates of these divergences, 43 however, varied extensively between species. Borneo harbours multiple deeply 44 divergent lineages of many species compared to the diversity within those species. Peninsula supports the existence of forest on the exposed shelf during the Pleistocene 51 at many different times, and suggests that proximity was more important than the 52 presence of palaeorivers for dispersal of forest taxa between landmasses. 53

Indochinese‐Sundaic faunal transition and phylogeographical divides north of the Isthmus of Kra in Southeast Asian Bulbuls (Aves: Pycnonotidae)

“…According to Leonard et al . (), within‐species divergences in 28 Southeast Asian bird and rodent species were not caused by a single event but occurred during the course of repeated climatic fluctuations and sea‐level changes. These processes included local extinctions and re‐colonizations during and after the Pleistocene.…”

“…In many terrestrial vertebrate species, populations from Sumatra, Java and the Malay Peninsula were identified as closest relatives and were sister to those from Borneo (Fig. a1; Gorog et al, ; Lim et al ., ; Leonard et al ., ) However, the geographical sampling in most studies does not allow identification of the Sundaic‐Indochinese transition zone. Knowledge about the degree of genetic divergence among populations north–south of the Isthmus of Kra is crucial for evaluating potential historical factors that may have influenced a postulated disjunction.…”

Within‐island diversification underlies parachuting frog (Rhacophorus) species accumulation on the Sunda Shelf

“…Leonard et al. () compared 28 taxonomic groups across the Sunda Shelf and found that the oldest dispersal event was 3.9 Ma (Pliocene). De Bruyn et al.…”

Human‐mediated introduction of introgressed deer across Wallace's line: Historical biogeography of Rusa unicolor and R. timorensis

“…Speciation may have resulted from the ecological adaptation of Javan deer Rusa timorensis to the prevailing vegetation type on Java, separating it from its sister species, the subtropical forest‐adapted sambar Rusa unicolor . Java and Bali, although part of Sundaland, had (and still have) different climatic conditions than Sumatra and Borneo and thus allowed differentiation between species based on evolved ecological adaptations (Leonard et al., ). The climate on Java is characterized by a West–East gradient, a transition from a slightly seasonal climate in the West to a strongly seasonal one in the East.…”

“…Two major clades were recovered and are indicated by the species names. Haplotypes are described in Table A1 H_39 Borneo and thus allowed differentiation between species based on evolved ecological adaptations (Leonard et al, 2015). The climate on Java is characterized by a West-East gradient, a transition from a slightly seasonal climate in the West to a strongly seasonal one in the East.…”